EP1799830A4

EP1799830A4 - Caev-based vector systems

Info

Publication number: EP1799830A4
Application number: EP04774533A
Authority: EP
Inventors: Yeon-Soo Kim; Jong-Pil Kim; Sukyung Lee
Original assignee: MACROGEN CO Ltd
Current assignee: MACROGEN CO Ltd
Priority date: 2004-09-07
Filing date: 2004-09-07
Publication date: 2009-05-13
Also published as: WO2006028302A1; JP2008512110A; EP1799830A1; CN101014710A

Abstract

This invention relates to caprine arthritis encephalitis virus-based vectors and vector systems that are useful in the delivery of nucleic acids to both non-dividing and dividing cells. Methods for delivering nucleic acids to both non-dividing and dividing cells using the vector systems are also disclosed.

Description

CAEV-BASED VECTOR SYSTEMS

BACKGROUND OF THE INVENTION

Field of the Invention

This invention relates to lentiviral vectors useful in polynucleotide delivery, and more specifically to caprine arthritis encephalitis virus-based vectors useful in polynucleotide delivery to non-dividing and dividing cells.

Related Art

Lenti viruses a re a s ubgroup o f r etroviruses t hat are c apable o f i nfecting n on- dividing, as well as dividing cells. Vectors derived from lentiviruses are ideal tools for delivering exogenous genes to target cells because of their ability to stably integrate into the genome of dividing and non-dividing cells and to mediate long- term gene expression (Gilbert and Wong-Staal, 2001; Mitrophanous et al., 1999; Naldini et al., 1996; Sauter and Gasmi, 2001). Lentiviruses have been isolated from many vertebrate species including primates, e.g., human and simian immunodeficiency viruses (HIV-I, HIV-2, SIV), as well as non-primates, e.g., feline immunodeficiency virus (FIV), bovine immunodeficiency virus (BIV), equine infectious virus (EIAV), caprine arthritis encephalitis virus (CAEV) and the visna virus. Of these, HIV and SIV are presently best understood. However, use of such systems in humans raises serious safety concerns, due to the possibility of recombination by the vector into a virulent and disease-causing form. Accordingly, non-primate lentiviruses are preferred for use in gene therapy.

Among n on-primate 1 entiviral v ectors, v ectors d erived from FFV (Curran and Nolan, 2002) and EIAV [US 2001/0044149] are best characterized, and little progress has been made for other non-primate lentiviral vectors. CAEV, like all lentiviruses, can infect and replicate in dividing cells as well as in terminally differentiated and non-dividing cells. Several features of CAEV biology make this virus an attractive candidate to develop into a gene transfer/therapy vector. First, the normal host of CAEV is goats, and there are no reported cases of human infection by CAEV. Second, the CAEV genome is phylogenetically most distant from HIV-I among lentiviruses. Third, the genome organization of the CAEV is relatively simple compared with other lentiviruses. The CAEV genome contains three structural g enes (gag, pol, env) and three regulatory/accessory g enes (vif, tat and rev). Despite these advantages, however, efforts to develop CAEV-based delivery systems have not been successful, resulting only in unsafe and inefficient recombinant viral vector production systems, rendering the use of CAEV-based gene delivery systems impractical.

In 1998, L . Mselli-Lakhal et al. reported on the first generation CAEV-based vector system, but the viral titers of the system (i.e., 10-187 TU/ml) were below useful levels. The authors attributed the inefficiency to a lack of accumulation of genomic RNA into the cytoplasm, and the low packaging efficiency of the vector RNA. Another shortcoming of the study was the use of an infectious wild-type virus ("helper virus") as its packaging system, which is of little practical value in human applications.

Accordingly, a need remains for a safe and efficient CAEV-based lentiviral vector system capable of mediating gene transfer into a broad range of dividing and non-dividing cells.

SUMMARY OF THE INVENTION

The present invention is broadly directed to the production of CAEV-based lentiviral vector particles useful for delivering exogenous polynucleotides into target cells. These vector particles find use in anti-viral, anti-tumor and/or gene therapies.

The present invention provides in one aspect a transfer vector for use in a CAEV-based vector production system described herein, the transfer vector comprises (a) a CAEV packaging sequence consisting essentially of (i) the untranslated region between the CAEV 5' LTR and the CAEV gαg-encoding sequence, and (ii) nucleotides 1 to X of the CAEV gαg-encoding sequence linked to the 3' end of said untranslated region, wherein X is less than 613, and (b) cz^'s-acting elements required for polyadenylation, RNA transport, reverse transcription, and integration, in operable association with said packaging sequence.

In one embodiment of the invention, X is selected from the group consisting of: 60, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575 and 600. hi another embodiment of the invention, X is selected from the group consisting of:

(a) X is greater than 25 and less than 600,

(b) X is greater than 25 and less than 500,

(c) X is greater than 25 and less than 400,

(d) X is greater than 25 and less than 300, (e) X is greater than 25 and less than 200,

(f) X is greater than 50 and less than 600,

(g) X is greater than 50 and less than 500, (h) X is greater than 50 and less than 400, (i) X is greater than 50 and less than 300, (j) ^{x is} greater than 50 and less than 200,

(k) X is greater than 75 and less than 600,

(1) X is greater than 75 and less than 500,

(m) X is greater than 75 and less than 400,

(n) X is greater than 75 and less than 300, (o) X is greater than 75 and less than 200,

(p) X is greater than 100 and less than 600,

(q) X is greater than 100 and less than 500,

(r) X is greater than 100 and less than 400,

(s) X is greater than 100 and less than 300, (t) X is greater than 100 and less than 200,

(u) X is greater than 125 and less than 600,

(v) X is greater than 125 and less than 500, (w) X is greater than 125 and less than 400, (x) X is greater than 125 and less than 300, (y) X is greater than 125 and less than 200, (z) X is greater than 150 and less than 600, (aa) X is greater than 150 and less than 500,

(bb) X is greater than 150 and less than 400, (cc) X is greater than 150 and less than 300, (dd) X is greater than 150 and less than 200, (ee) X is greater than 200 and less than 600, (ff) X is greater than 200 and less than 500,

(gg) X is greater than 200 and less than 400, (hh) X is greater than 200 and less than 300, (ii) X is greater than 200 and less than 200, (jj) X is greater than 250 and less than 600, (kk) X is greater than 250 and less than 500,

(11) X is greater than 250 and less than 400, and (mm) X is greater than 250 and less than 300. In another embodiment, X is greater than 40 and less than 613. In another embodiment, X is greater than 57 and less than 613. In yet another embodiment, X is about 327.

In one embodiment of the invention, the start codon of the gag-encoding sequence is mutated to prevent translation of gag protein. In a further embodiment, the start codon is mutated to TAG.

In another embodiment of the transfer vector of the invention, the ATG codon of the gαg-encoding sequence is located X base pairs downstream of the start codon ATG, wherein start codon is mutated to prevent translation of gag protein, and wherein X is less than 30. In a further embodiment X is about 21.

The transfer vector of the invention may further comprise an RRE region. In another embodiment of the invention, the transfer vector comprises the CAEV 3 ' LTR wherein the U3 region is deleted.

The transfer vector of the present invention may further comprise a heterologous promoter. In one embodiment of the invention, the heterologous promoter is the human cytomegalovirus major immediate early promoter (HCMV MIEP). In a further embodiment, the transfer vector is pCAH/SINdl (SEQ ID NO: 68).

The transfer vector of the present invention may further comprise a transcription cassette comprising a heterologous polynucleotide of interest operably linked to a heterologous promoter (e.g., human cytomegalovirus major immediate-early promoter HCMV MIEP, or murine cytomegalovirus major immediate-early promoter

MCMV MIEP). Such a transfer vector permits the incorporation of the polynucleotide of interest into virus particles, thereby providing a means for amplifying the number of infected host cells containing the polynucleotide therein.

The present invention also provides a CAEV-based lentiviral vector system for producing CAEV-based, replication-defective vector particles useful in delivering exogenous polynucleotides into mammalian cells. The vector particles are capable of infecting and transducing mammalian cells. The vector system comprises the transfer vector described above, and a packaging vector system, wherein said packaging vector system comprises: a first polynucleotide comprising a CAEV gag- po/-encoding sequence and an RRE, and a second polynucleotide comprising a viral envelope encoding sequence.

In one embodiment, the second polynucleotide comprises a non-CAEV env- encoding sequence. In one embodiment the second polynucleotide comprises a VSV-G- or GaLV-encoding sequence.

In another embodiment, the CAEV vector system comprises a third polynucleotide sequence comprising a rev-encoding sequence.

In another embodiment, the CAEV vector system comprises a fourth polynucleotide sequence comprising a vz/-encoding sequence.

In a further embodiment, the first polynucleotide of each of the CAEV vector systems described above further comprises a heterologous regulatory sequence operably linked to the CAEV gag-pol-encoding sequence.

In a further embodiment, the second polynucleotide of the above- described CAEV vector systems further comprises a heterologous regulatory sequence operable linked to said viral envelope-encoding sequence. In a further embodiment, the third polynucleotide further comprises a heterologous regulatory sequence operably linked to the rev-encoding sequence.

In a further embodiment, the fourth polynucleotide further comprises a heterologous regulatory sequence operably linked to the vz/-encoding sequence. In one embodiment of the invention, the CAEV vector system comprises a packaging vector system which is devoid of a competent CAEV packaging sequence. In a further embodiment, the packaging vector system is devoid of the 5 ' end of the CAEV genome between the splice donor site and the gag start codon.

In one embodiment, the CAEV vector system comprises a first vector comprising the first polynucleotide and a second vector comprising the second polynucleotide. In another embodiment, the vector system comprises a first vector comprising the first polynucleotide, a second vector comprising the second polynucleotide, and a third vector comprising the third polynucleotide. In another embodiment, the vector system comprises a first vector comprising the first polynucleotide, a second vector comprising the second polynucleotide, a third vector comprising the third polynucleotide, and a fourth vector comprising the fourth polynucleotide. The third vector may be pHYK/rev (SEQ ID NO: 75), and the fourth vector may be pHYK/vif (SEQ ID NO: 76).

In yet another embodiment, the vector system comprises a first vector comprising the first polynucleotide, the third polynucleotide and the fourth polynucleotide, and a second vector comprising the second polynucleotide.

In o ne e mbodiment, t he first v ector o f t he C AEV v ector s ystem comprises a CAEV gαg-encoding sequence and an RRE operable linked to a heterologous promoter. The promoter may be an MCMV MIEP. In a further embodiment, the CAEV vector system comprises the first vector pMGP/RRE (SEQ ID NO: 77).

In one embodiment, the second vector of the CAEV vector system is a VSV-G- encoding sequence operably linked to a heterologous promoter. The promoter may be an HCMV MIEP. The second vector may further comprise a beta globin intron.

In a further embodiment, the CAEV vector system comprises the second vector pHGVSV-G (SEQ ID NO: 74).

In one embodiment, the second vector of the CAEV vector system is a GaLV ewv-encoding sequence operably linked to a heterologous promoter. The promoter may be an M CMV M IEP. T he s econd v ector may further c omprise a eukaryotic elongation factor- 1 alpha intron. In a further embodiment, the CAEV vector system comprises the second vector pMYKEF-1/env (SEQ ID NO: 72).

Another aspect of the invention is a method of producing a CAEV-based - lentiviral vector particle useful for infecting mammalian cells. The method comprises (a) transfecting a cell with the vector system described supra, under conditions suitable for production of CAEV-based particles, where the vector particle is infection- and transduction- competent, and replication-defective, and (b) recovering the vector particle. The present invention also provides a composition comprising a CAEV-based lentiviral vector particle and optionally a carrier, where the vector particle is produced by the methods described supra.

The present invention also provides a kit comprising the transfer vector or the

CAEV-based lentiviral vector system described supra. The present invention also provides a packaging cell comprising a CAEV gag- po/-encoding sequence and RRE, and optionally a viral env-encoding sequence. The packaging cell may further comprise a rev-encoding and/or a vz/-encoding sequence.

The cell is useful for packaging the RNA form of the transfer vector into an infection- and transduction-competent vector particle, which is replication-defective. In one embodiment, the vector system comprises a cell comprising the first polynucleotide described supra. The vector system may further comprise the third and/or the fourth polynucleotide described supra.

In another embodiment, the vector system comprises a cell comprising the first polynucleotide and second polynucleotides described supra. The vector system may further comprise the third and/or the fourth polynucleotide described supra.

In another embodiment, the vector system comprises a cell comprising a first vector that comprises a CAEV gαg-po/-encoding sequence and an RRE. The first vector may further comprise a rev-encoding and/or a vz/-encoding sequence.

Alternatively, the cell may comprise a first vector comprising a CAEV gag-pol- encoding sequence and an RRE, a second vector comprising a rev-encoding sequence and/or a third vector comprising a vz/-encoding sequence. In some embodiments, the vector system comprises a cell comprising a first vector that comprises a CAEV gαg-/?o/-encoding sequence and an RRE, and a second vector that comprises a viral e«v-encoding sequence. The first vector may further comprise a rev-encoding and/or a vj/-encoding sequence. Alternatively, the cell may comprise a first vector comprising the CAEV gαg-;?o/-encoding sequence and an RRE, a second vector comprising a viral e nv-encoding sequence, and optionally a third vector comprising a rev-encoding sequence and/or a fourth vector comprising a vz/-encoding sequence.

Another aspect of the present invention is a method of delivering a polynucleotide or polypeptide into a mammalian cell or replicating a polynucleotide molecule encoding said polypeptide, comprising contacting a mammalian cell with the vector particle described supra under conditions which may allow for integration of said polynucleotide into the genome of said cell and optionally under conditions allowing expansion of said polypeptide encoded by said polynucleotide. The mammalian cell may be a dividing cell, a non-dividing cell or a CD34+ stem cell. The method of delivering a polynucleotide or a polypeptide into a mammalian cell or replicating a polynucleotide molecule encoding said polypeptide, may further comprise isolating the cell from a mammal prior to contacting the cell with the vector particle. The method may further comprise expanding said cell in culture after contacting it with the vector particle. The method may further comprise reintroducing the cell into a mammal before or after expanding the contacted cell.

The p resent i nvention further p rovides a m ethod for d elivering a p olypeptide into a vertebrate, comprising administering to the vertebrate a CAEV -based lentiviral vector particle comprising a heterologous polynucleotide of interest, where the vector particle is produced by the method described supra, such that the polypeptide encoded by the delivered polynucleotide is expressed in the vertebrate, in an amount sufficient to be detectable or to elicit a biological response in the vertebrate.

The present invention further provides a vector comprising a CAEV packaging sequence consisting essentially of (a) the untranslated region between the CAEV 5' LTR and the CAEV gαg-encoding sequence, and (b) nucleotides 1 to X of the CAEV gαg-encoding sequence linked to the 3' end of the untranslated region, wherein X is less than 613. The inventors have discovered that the production of the CAEV-based lentiviral vector particles, as described herein, results in enhanced efficiency and safety in the lentiviral vector design over the existing CAEV-based vector particles. The enhanced efficiency is achieved through the discovery of the optimal length of the untranslated region between the 5'LTR and the gag start codon and the gαg-encoding region, which serves as an efficient packaging sequence by allowing efficient encapsidation, which then results in increased viral titers. Viral titer is also improved by using a strong heterologous promoter in the d esign of the packaging plasmids.

The enhanced safety is achieved through the construction of a tot-independent transfer vector and a plasmid-based packaging system.

BRIEF DESCRIPTION OF THE DRAWINGS/FIGURES

FIGURE 1 is a schematic illustration of the CAEV proviral genomic organization.

FIGURE 2A is a schematic illustration of the plasmid pMGP/RRE (SEQ ID NO: 77). pMGP/RRE (SEQ ID NO: 77) is a 9,446 bp plasmid which contains an MCMV MIEP region (located at bp 1-660) located upstream of the CAEV gag-pol coding region (bp 709-5,243), the RRE region (5,426-5,627 or bp 5,368-5,669), and the bovine growth hormone (BGH) polyadenylation signal (bp 5,751-5,984). The vector also contains a neomycin resistance gene coding region (bp 8,151-7,155), a SV40 origin of replication (bp 8,509-8,152), a Col El origin of replication (bp 6,115- 6,698), and an ampicillin resistance gene region (bp 9,362-8,528).

FIGURE 2B is a schematic illustration of the plasmid pMGP/REV/RRE. pMGP/REV/RRE is a 9,924 bp plasmid which contains an MCMV MIEP region (located at bp 1-660) and the major splicing donor of CAEV (bp 688-704) located upstream of the CAEV gag-pol coding region (bp 726-5,258), the first exon rev coding region (bp 5,383-5,494), the RRE region (bp 5,540-5,841), the second exon rev coding region(bp 5,888-6,177), and the bovine growth hormone (BGH) polyadenylation signal (bp 6,229-6,462). The vector also contains a neomycin resistance gene coding region (bp 7,633-8,629), a SV40 origin of replication (bp 8,987-8,630), a Col El origin of replication (bp 6,593-7,176), and an ampicillin resistance gene region (bp 9,840-9,006).

FIGURE 3A is a schematic illustration of the plasmid pCAH/SINd (SEQ ID NO: 73). pCAH/SINd (SEQ ID NO: 73) is a 3,566 bp plasmid which contains the HCMV MIEP (bp 1-588), the R-U5 sequence regions in the CAEV 5'LTR (bp 611- 772), the RRE region (bp 796-1,154), and the U3-deleted CAEV 3'LTR region (bp 1,275-1,458). The vector also contains a Col El origin of replication (bp 1,863- 2,466), and a kanamycin resistance gene coding region (bp 2,698-3,510).

FIGURE 3B is a schematic illustration of the plasmid pCAH/SINdO (SEQ ED NO: 67). pCAH/SINdO (SEQ ID NO: 67) is a 3,911 bp plasmid which contains the HCMV MIEP (bp 1-588), the R-U5 sequence regions in CAEV 5'LTR (bp 611-772), the residual untranslated sequences containing the primer binding site (PBS) (bp 773- 789), the RRE region (bp 1,141-1,499), and the U3-deleted CAEV 3'LTR region (bp 1,620-1,803). The vector also contains a Col El origin of replication (bp 2,208- 2,791) and a kanamycin resistance gene coding region (bp 3,043-3,855).

FIGURE 3 C is a schematic illustration of the plasmid pCAH/SINdl (SEQ ID NO: 68). pCAH/SINdl (SEQ ID NO: 68) is a 4,238 bp plasmid which contains the HCMV MIEP (bp 1-588) promoter, the R-U5 sequence regions in the CAEV 5'LTR (bp 610-772), the residual untranslated sequences containing the PBS site (bp 773- 789), the 327 bp fragment of the gag gene (bp 1 , 121 - 1 ,448) with ATG to TAG point mutations at the start ATG codon (bpl 121-1123) and the ATG codon (bpl 142-1144) located downstream of the start ATG codon, the RRE region (bp 1,468-1,826) and the U 3 -deleted C AEV 3 'LTR region (bp 1 ,947-2,130). The vector also contains a Col El origin of replication (bp 2,535-3,118) and a kanamycin resistance gene region (bp 3,370-4,182).

FIGURE 3D is a schematic illustration of the plasmid pCAH/SINd2 (SEQ ID NO: 69). Plasmid pCAH/SINd2 (SEQ ID NO: 69) is a 4,523 bp plasmid which contains the HCMV MIEP (bp 1-588), the R-U5 sequence regions in the CAEV 5'LTR (bp 610-772), the residual untranslated sequences containing the PBS site (bp 773-789), the 612 bp fragment of the gag gene (bp 1,121-1,733), with point mutations at the start ATG codon (bp 1121-1123) and the ATG codon (bp 1142-

1144) located downstream of the start ATG codon, the RRE region (bp 1,753-2,111) and the U3 -deleted CAEV 3'LTR region (bp 2,232-2,415). The vector also contains a Col El origin of replication (bp 2,820-3,403) and a kanamycin resistance gene ^" coding region (bp 3,655-4,467).

FIGURE 3E is a schematic illustration of the plasmid pCAH/SINd3 (SEQ ID NO: 70). pCAH/SINd3 (SEQ ID NO: 70) is a 4,819 bp plasmid which contains the HCMV MEEP (bp 1-588), the R-U5 sequence regions in CAEV 5'LTR (bp 610-772), the residual untranslated sequences containing PBS site (bp 773-789), the 908bp fragment of the gag gene (bpl, 121 -2,029) with point mutations at the start ATG codon (bp 1121-1123) and the ATG codon (bp 1142-1144) located downstream of the start ATG codon, the RRE region (bp 2,049-2,407) and the U3-deleted CAEV 3'LTR region (bp 2,549-2,711). The vector also contains a Col El origin of replication (bp 3,116-3,699) and a kanamycin resistance gene coding region (bp 3,951-4,763).

FIGURE 3F is a schematic illustration of the plasmid pCAH/SINd4 (SEQ ID NO: 71). pCAH/SINd4 (SEQ ID NO: 71) is a 5,112 bp plasmid which contains the HCMV MIEP (bp 1-588), the R-U5 sequence regions in the CAEV 5'LTR (bp 610- 772), the residual untranslated sequences containing the PBS site (bp 773-1,120), the 1198 bp fragment of the gag gene (bp 1,121-2,319) with point mutations at the start ATG codon (bp 1121-1123) and the ATG codon (bp 1142-1144) located downstream of the start ATG codon, the RRE region (bp 2,342-2,700) and the US- deleted CAEV 3'LTR region (bp 2,842-3,004). The vector also contains a Col El origin of replication (bp 3,409-3,992), and a kanamycin resistance gene coding region (bp 4,244-5,056).

FIGURE 3 G is a schematic illustration of the plasmid pCAH/SINdl/hlacZ (SEQ ID NO: 79). pCAH/SINdl/hlacZ (SEQ ID NO: 79) is an 8,127 bp plasmid derived from the p CAH/SINdl ( SEQ ID NO: 68) that expresses the 1 acZ reporter gene. The vector contains two HCMV MIEP promoter regions (located at bp 1-588 and bp 1,866-2,460, respectively), the R-U5 sequence regions in the CAEV 5'LTR (bp 610-772), the residual untranslated sequences containing the PBS site (bp 773- 789), the 325 bp fragment of gag gene (bp 1,121-1,446) with point mutations at the start ATG codon (bp 1121-1123) and the ATG codon (bp 1142-1144) located downstream of the start ATG codon, the RRE region (bp 1,466-1,836), the lacZ gene coding sequence (bp 2,541-5,711), and the U3-deleted CAEV 3'LTR region (bp 5,782-6,019). The vector also contains a Col El origin of replication (bp 6,424- 7,007), and a kanamycin resistance gene coding region (bp 7,259-8,071).

FIGURE 3H is a schematic illustration of the plasmid pCAH/SINd60/hlacZ (SEQ ID N O: 78). P lasmid p CAH/SlNdόO/hlacZ ( SEQ ID N O: 78) i s a 7 ,856 b p which contains two promoter regions, HCMV MIEP (located at bp 1-588 and bp 1,595-2,189, respectively), the R-U5 sequence regions in the CAEV 5'LTR (bp 610- 772), the residual untranslated sequences containing the PBS site (bp773- 789 bp), the 60 bp fragment of gag gene (bp 1,121-1,181) with point mutations at the start ATG codon (bp 1121 - 1123) and the ATG codon (bp 1142- 1144) located downstream of the start ATG codon, the RRE region (bp 1,195-1,565), the lacZ gene coding sequence (bp 2,270-5,440), and the IB-deleted CAEV 3'LTR region (bp 5,511- 5,748). The vector also contains a Col El origin of replication (bp 6,153-6,736), and a kanamycin resistance gene coding region (bp 6,988-7,800). FIGURE 4 is a schematic illustration of the plasmid pHYK/vif (SEQ ID NO:

76). pHYK/vif (SEQ ID NO: 76) is a 5,729 bp plasmid which contains the HCMV MIEP (bp 1-596), the vif gene coding region (bp 691-1,380), the BGH polyadenylation signal (bp 1,467-1,695), a Col El origin of replication (bp 1,826- 2,409), a neomycin resistance gene coding region (bp 3,862-2,866), and an ampicillin resistance gene coding region (bp 5,270-4,239).

FIGURE 5 is a schematic illustration of the plasmid pHYK/rev (SEQ ID NO: 75). pHYK/rev (SEQ ID NO: 75) is a 5,419 bp plasmid which contains the HCMV MIEP (bp 1-596), the rev gene coding region (bp 672-1,073), the BGH polyadenylation signal (bp 1,157-1,385), a Col El origin of replication (bp 1,516- 2,099), a neomycin resistance gene coding region (bp 3,552-2,556), and an ampicillin resistance gene coding region (bp 4,960-3,929).

FIGURE 6A is a schematic illustration of the plasmid pHGVSV-G (SEQ ID NO: 74). pHGVSV-G (SEQ ID NO: 74) is a 7,623bp plasmid which contains the HCMV MIEP (bp 1-596), the β-globin intron region (bp 714-1,599), the VSV-G coding region (bp 1,632-3,312), the BGH polyadenylation signal (bp 3,361-3,589), a Col El origin of replication (bp 3,720-4,303), a neomycin resistance gene coding region (bp 5,756-4,760), an ampicillin resistance gene coding region (bp 7,164- 6,133), and a Fl origin of replication (bp 7,165-7,621).

FIGURE 6B is a schematic illustration of the plasmid pMYKEFl/env (SEQ ID NO: 72). pMYKEFl/env (SEQ ID NO: 72) is a 7,579 bp plasmid which contains the MCMV MIEP (bp 1-665), a human EFl-α intron region (bp 668-1,618), the GaLV env coding region (bp 1,699-3701), the BGH polyadenylation signal (bp 3,885- 4,118), a Col El origin of replication (bp 4,349-4,832), a neomycin resistance gene coding region (bp 6,290-5,284), and an ampicillin resistance gene coding region (bp 7,496-6,666). FIGURE 7 shows a photograph illustrating the relative amount of transfer vector RNA transcribed from gene transfer vectors transfected into human 293T target cells.

FIGURE 8 shows two photographs illustrating gene transfer into human 293T target cells by CAEV (A) and MuLV (B) vectors. FIGURE 9 shows a photographic illustration of the relative amount of transfer vector RNA expressed in the transfected 293T cells (lanes 1, 2 and 3), and encapsidated in and released from the 293T packaging cells (lanes 4, 5 and 6).

FIGURE 10 shows a photograph illustrating the relative amount of transfer vector RNA encapsidated in and released from human 293T packaging cells. FIGURE l l s hows a p hotograph i llustrating t he r elative a mount o f integrated retroviral cDNA after infection and reverse transcription of lentiviral vectors pseudotyped by VSV-G or GaLV envelope protein.

FIGURE 12 shows a photograph illustrating the relative amount of viral vector cDNA integrated into the infected host cell chromosome. FIGURE 13 shows two graphs illustrating the FACS analysis of (A) the control cells, and (B) the Gl- arrested cells.

FIGURE 14 shows two graphs illustrating (A) the number of transduced cells and (B) the relative transduction efficiencies of HIV-I-, CAEV-, and MuLV-derived viral vectors on dividing and non-dividing cells. DETAILED DESCRIPTION OF THE INVENTION

The invention relates to, inter alia, CAEV-based lentiviral vector systems and methods employing said vectors to deliver polypeptides of interest into dividing and non-dividing cells.

The CAEV genome

The wild-type CAEV virus has a dimeric RNA genome (single-stranded, positive polarity) that is replicated through a double-stranded DNA intermediates and is packaged into a spherical enveloped virion containing a nucleoprotein core. The genome contains three genes that encode the structural and enzymatic proteins Gag, Pol, a nd E nv, a nd 1 ong terminal r epeats ( LTR) at e ach e nd o f t he i ntegrated v iral genome. In addition, the genome encodes three regulatory proteins, vif, tat, and rev.

The gag gene encodes the internal structural proteins, the pol gene encodes viral replication enzymes, and the env gene encodes an envelope glycoprotein that mediates attachment of virus to the cell surface. The Vif protein is associated with viral infectivity, and the Tat protein with transactivation of the 5' LTR. The Rev protein and its target sequence RRE (Rev responsive element) are associated with the stability of viral RNA, regulation of viral RNA splicing, and transport of large RNA (unspliced and singly-spliced) from the nucleus to the cytoplasm. The proviral LTR sequences c ontain t he U 3 ( unique s equence e lement 1 ocated d ownstream from t he structural proteins), R (short repeat at each end of the genome), and U5 (unique sequence element immediately after the R sequence) regions. The U3 region of 5'LTR contains the viral promoter and enhancers. The 3' end of the genome contains polyadenylation signal in the 3'LTR.

The wild-type genome of CAEV also contains several cw-acting elements, including atts (attachment site) at the end of LTRs for provirus integration); promoter elements that control transcriptional initiation of the integrated provirus at the 5'LTR; a PBS (primer binding site) located downstream of the 5'LTR; a 5'-splice donor site; a packaging sequence (herein referred to interchangeably as a packaging site or a packaging signal); a ppt (polypurine tract) site located near the 3'LTR; and polyadenylation signals at the 3'LTR.

As used herein, the term "cis" is used in reference to the presence of genes on the same chromosome or linear portion of a nucleic acid. Therefore, the term "cis- defect" refers to a defect found on a linear sequence of a nucleic acid. The term "ex¬ acting" is used in reference to the controlling effect of a regulatory gene on a gene present on the same chromosome or linear portion of a nucleic acid. For example, promoters, which affect the synthesis of downstream mRNA are cis-acting control elements. The complete genomic sequence for two isolates of CAEV are known and the sequences are deposited in the National Center for Biotechnology Information (NCBI) database as NC_001463 (SEQ ID NO: 1) and AF322109 (SEQ ID NO: 2)(Saltarelli et al., 1990, and Gjerset, BJ. et al. unpublished, respectively). The nucleic acids of the claimed invention are not limited to a particular isolate of CAEV, but rather to a sequence that retains the known function of that genomic sequence. For example, it is known in the art that natural variations in a gene sequence may occur during viral replication, resulting in a similar nucleic acid sequence that encodes proteins having a similar function.

A sequence alignment of the NC_001463 (SEQ ID NO: 1) and AF322109 (SEQ ID NO: 2) genomic sequences is shown in TABLE 1. As is visible in TABLE 1, there is considerable nucleic acid identity between the sequences, however differences at the nucleic acid level are apparent. O f p articular importance i s the variability of the CAEV gag region denoted in TABLE 2 (SEQ ID NOs: 3-6). Sequence alignments of NC_001463 5'LTR, pol, rev, and vif genes and the corresponding genes from AF322109 can be found in TABLES 3-6 (SEQ ID NOs: 7- 14), respectively. Many partial sequences of the CAEV genome are also known and have been deposited. For example, accession numbers AY081139, AY101347, AY101348, AY047362, AF402668, AF402667, AF402666, AF402665, AF402664, AJ305042, AJ305041, and AJ305040 all provide for sequences of the gag gene from Brazilian isolates of CAEV. Accession numbers AF015181, L78453, L78451, L78450, L78447, and L78446 also contain the sequences of gag genes from a variety of CAEV isolates. Accession numbers X64828 and M63106 contain the sequences of rev genes from a variety of CAEV isolates. Accession numbers AFOl 5182, AJ305053, K03327, L78448, L78452 and U35814 contain pol genes from a variety of CAEV isolates. A sequence alignment between the NC_001463 gag gene (SEQ ID NOs: 1 5, 1 7) and the AF015181 gag gene ( SEQ ID NOs: 1 6, 1 8) i s found in TABLE 7. A sequence alignment between the NCJ)Ol 463 gag gene (SEQ ID NOs: 19, 25) and the gag genes from AF402664 (SEQ ID NOs: 20, 26), AF402665 (SEQ ID NOs: 21, 27), AF402666 (SEQ ID NOs: 22, 28), AF402667 (SEQ ID NOs: 23, 29), AF402668 (SEQ ID NOs: 24, 30) is found in TABLE 8. A sequence alignment between the NC_001463 gag gene (SEQ ID NOs: 31, 35) and the gag genes from AJ305040 (SEQ ID NOs: 32, 36), AJ305041 (SEQ BD NOs: 33, 37), AJ305042 (SEQ ID NOs: 34, 38) is found in TABLE 9. A sequence alignment between the NC 001463 gag gene (SEQ ID NOs: 39, 41) and the gag gene from AY047362 (SEQ ID NOs: 40, 42) is found in TABLE 10. A sequence alignment between the NC_001463 (SEQ ID NOs: 43, 45) gag gene and the gag gene from AY081139 (SEQ ID NOs: 44, 46) is found in TABLE 11. A sequence alignment between the NC_001463 (SEQ ID NOs: 47, 5 O) gag gene and thegαg genes from AY101347 (SEQ ID NOs: 48, 51) and AY101348 (SEQ ED NOs: 49, 52) is found in TABLE 12. A sequence alignment between the NC_001463 gag gene (SEQ ID NOs: 53, 59) and the gag genes from L78446 (SEQ ID NOs: 54, 60), L78447 (SEQ ID NOs: 55, 61), L78450 (SEQ ID NOs: 56, 62), L78451 (SEQ ID NOs: 57, 63), and L78453 (SEQ ID NOs: 58, 64) is found in TABLE 13.

The a lignments w ere p erformed u sing V ectorNTI ( Informax, U SA) u sing t he following parameters:

For pairwise alignment : gap opening penalty : 15

Gap extension penalty : 6.6

For multiple alignment : gap opening penalty : 15 Gap extension penalty : 6.6

Gap separation penalty range : 8

TABLE 14 is a summary of the percent identity values for the sequence alignments of gag gene sequences listed above. TABLE 15 is a summary of the percent identity of the full genomic alignment, and alignments of the gag, 5' LTR, pol, rev, and vif regions of NC_001463 (SEQ ID NO: 1) and AF322109 (SEQ ID NO: 2). Given that the genomic sequence of two CAEV isolates, in addition to a large number of partial sequences from a variety of CAEV isolates are known and consensus sequences can be easily discerned, it would not require undue experimentation to practice the claimed invention using a variety of CAEV sequences.

CAEV vectors of the invention

The vectors of the present invention provide a means for replicating and expressing polynucleotides or genes independent of the host cell nucleus in a broad phylogenetic range of host cells. This vector-mediated incorporation of heterologous nucleic acid into a host cell is referred to as transfection or infection of the host cell, wherein infection means the use of virus particles, and transfection means the use of naked molecules of nucleic acid. The term "gene" refers to a DNA sequence that comprises control and coding sequences necessary for the production of a polypeptide or precursor. The term "polynucleotide" or "nucleic acid molecule", as used interchangeably herein, refers to nucleotide polymers of any length, such as two or more, and includes both DNA and RNA. The nucleotides can be deoxyribonucleotides, ribonucleotides, nucleotide analogs (including modified phosphate moieties, bases, or sugars), or any substrate that can be incorporated into a polymer by a suitable enzyme, such as a DNA polymerase or an RNA polymerase. The polypeptide can be encoded by a full-length coding s equence o r b y any portion o f t he c oding se quence s o 1 ong a s t he d esired activity of the polypeptide is retained. The term "wild-type" refers to a gene or gene product which has the characteristics of that gene or gene product when isolated from a naturally occurring source. A wild-type gene is that which is most frequently observed in a population and is thus arbitrarily designed the "normal" or "wild-type" form of the gene. In contrast, the term "modified" or "mutant" refers to a gene or gene product which displays modifications in sequence and or functional properties (i.e., altered characteristics) when compared to the wild-type gene or gene product. Naturally- occurring mutants can be isolated, and are identified by the fact that they have altered characteristics when compared to the wild-type gene or gene product.

It must be noted that as used in this specification and the appended claims, the singular forms "a", "an", "the", and the like, include plural references unless the context clearly dictates otherwise. Thus, for example, reference to "a polynucleotide" includes polynucleotides and "a stem cell" includes a plurality of cells.

As used herein, the term "retrovirus" is used in reference to RNA viruses that utilize reverse transcriptase during their replication cycle. The retroviral genomic RNA is converted into double-stranded DNA by reverse transcriptase. This double- stranded DNA form of the virus is capable of being integrated into the chromosome of the infected cell; once integrated, it is referred to as a "provirus." The provirus serves as a template for RNA polymerase II and directs the expression of RNA molecules which encode the structural proteins and enzymes needed to produce new viral particles.

As used herein, the term "lentivirus" refers to a group (or genus) of retroviruses that give rise to slowly developing disease. Viruses included within this group include human immunodeficiency virus (HIV); visna-maedi, which causes encephalitis (visna) or pneumonia (maedi) in sheep, caprine arthritis encephalitis virus (CAEV); equine infectious anemia virus (EIAV); feline immunodeficiency virus (FIV); bovine immune deficiency virus (BIV); and simian immunodeficiency virus (SIV). Diseases caused by these viruses are characterized by a long incubation period and protracted course. Usually, the viruses latently infect monocytes and macrophages, from which they spread to other cells. As used herein, the term "vector" is used in reference to nucleic acid molecules that transfer polynucleotide (e.g. DNA) segments from one cell to another. The term "vehicle" is sometimes used interchangeably with "vector." It is intended that any form of vehicle or vector be encompassed within this definition. For example, vectors include, but are not limited to viral particles, plasmids, transposons, etc. Standard techniques for the construction of the vectors of the present invention are well-known to those of ordinary skill in the art and can be found in such references as Sambrook et al., Molecular Cloning: A Laboratory Manual 2nd Ed. (Cold Spring Harbor, N. Y., 1989). A variety of strategies are available for ligating fragments of DNA, the choice of which depends on the nature of the termini of the DNA fragments and which choices can be readily made by the skilled artisan.

Suitable polyadenylation sequences of the present invention include, but are not limited t o t he b ovine growth h ormone ( BGH) p olyadenylation s ignal ( Pfarr e t al.,

1986), the SV40 early region polyadenylation site (Hall et al., 1983) and the SV40 late region polyadenylation site (Carswell and Alwine, 1989), β-globin polyA, and herpes simplex virus thymidine kinase polyA.

A promoter of the present invention may comprise a promoter of mammalian or viral origin, and will be sufficient to direct the transcription of a distally located sequence (i.e. a sequence linked to the 5' end of the promoter sequence) in a cell. The promoter region may also include control elements for the enhancement or repression of transcription. Suitable promoters include, but are not limited to, the human or murine cytomegalovirus immediate-early promoter (HCMV MIEP or MCMV MIEP), elongation factor 1 alpha (ef-lα), and Rous Sarcoma virus long terminal repeat promoter (pRSV). Intron sequences may also be combined with a promoter. Intron sequences include, but are not limited to ef-lα intron and β-globin intron. Inducible expression systems may also be used. Examples of inducible systems include, but are not limited to ecdysone-inducible mammalian expression system (Invitrogen, CA, USA) and Tet-On and Tet-Off gene expression systems (Clontech, CA, USA). Cell or tissue specific promoters can be utilized to target expression of gene sequences in specific cell populations.

Enhancer sequences upstream from the promoter or terminator sequences and downstream of the coding region may be optionally included in the vectors of the present invention to facilitate expression. Vectors of the present invention may also contain additional nucleic acid sequences, such as an intron sequence, a localization sequence, or a signal sequence, sufficient to permit a cell to efficiently and effectively process the protein expressed by the nucleic acid of the vector. Examples of intron sequences include the β-globin intron (Kim et al., 2002) and the human EF- loc intron (Kim et al., 2002). Such additional sequences are inserted into the vector such that they are operably linked with the promoter sequence, if transcription is desired, or additionally with the initiation and processing sequence if translation and processing are desired. Alternatively, the inserted sequences may be placed at any position in the vector.

The term "operably linked" is used to describe a linkage between a gene sequence and a promoter or other regulatory or p rocessing sequence such that the transcription of the gene sequence is directed by an operably linked promoter sequence, the translation of the gene sequence is directed by an operably linked translational regulatory sequence, and the post-translational processing of the gene sequence is directed by an operably linked processing sequence. The term "SIN vector" refers to the self- inactivating vector that has a truncated

U3 region in the 3' LTR. During reverse transcription, a truncated U3 is duplicated in the 5'LTR, resulting in the loss of the transcription capacity and the interference effect on an internal promoter.

The packaging sequence of the transfer vector consists essentially of (i) the untranslated region between the CAEV 5' LTR and the CAEV gαg-encoding sequence, and (ii) nucleotides 1 to X of the CAEV gαg-encoding sequence linked to the 3' end of said untranslated region, wherein X is less than 613. In one embodiment of the invention, X is selected from the group consisting of: 60, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575 and 600.

In another embodiment of the invention, X is selected from the group consisting of:

(a) X is greater than 25 and less than 600,

(b) X is greater than 25 and less than 500, (c) X is greater than 25 and less than 400,

(d) X is greater than 25 and less than 300,

(e) X is greater than 25 and less than 200,

(f) X is greater than 50 and less than 600,

(g) X is greater than 50 and less than 500, (h) X is greater than 50 and less than 400,

(i) X is greater than 50 and less than 300,

(j) X is greater than 50 and less than 200, (k) X is greater than 75 and less than 600,

(I) X is greater than 75 and less than 500, (m) X is greater than 75 and less than 400, (n) X is greater than 75 and less than 300, (o) X is greater than 75 and less than 200,

(p) X is greater than 100 and less than 600,

(q) X is greater than 100 and less than 500,

(r) X is greater than 100 and less than 400,

(u) X is greater than 125 and less than 600,

(v) X is greater than 125 and less than 500,

(w) X is greater than 125 and less than 400,

(x) X is greater than 125 and less than 300, (y) X is greater than 125 and less than 200,

(z) X is greater than 150 and less than 600,

(aa) X is greater than 150 and less than 500,

(bb) X is greater than 150 and less than 400,

(cc) X is greater than 150 and less than 300, (dd) X is greater than 150 and less than 200,

(ee) X is greater than 200 and less than 600,

(ff) X is greater than 200 and less than 500,

(gg) X is greater than 200 and less than 400,

(hh) X is greater than 200 and less than 300, (ii) X is greater than 200 and less than 200,

(jj) X is greater than 250 and less than 600,

(kk) X is greater than 250 and less than 500,

(II) X is greater than 250 and less than 400, and (mm) X is greater than 250 and less than 300. hi another embodiment, X is greater than 40 and less than 613. In yet another embodiment, X is about 327. hi one embodiment of the transfer vector, the codon which initiates gag translation has been mutated (e.g. ATG changed to TAG, TTG, CTG, or ATT) or deleted. The term "codon" refers to a sequence of three nucleotides in a DNA or messenger RNA molecule that represents the instruction for incorporation of a specific amino acid into a growing polypeptide chain. The transfer vector further comprises a heterologous promoter and one or more cw-acting sequences.

As used herein, the term "packaging signal" or "packaging sequence" refers to sequences located adjacent to the 5' LTR of the CAEV genome which are required for encapsidation of the viral RNA into the viral capsid or particle. Several retroviral vectors use the minimal packaging signal (also referred to as the psi [ψ] sequence) needed for encapsidation of the viral genome. Thus, as used herein, the terms "packaging sequence", "packaging signal", "psi", and the symbol "ψ" are used in reference to the non-coding sequence required for encapsidation of CAEV RNA strands during viral particle formation. hi another embodiment of the invention, the transfer vector further comprises a transcription cassette. The term "transcription cassette" as used herein refers to a fragment or segment of nucleic acid containing a particular grouping of genetic elements, generally a polynucleotide which expresses a polypeptide of interest, operably linked to a heterologous promoter. The cassette can be removed and inserted into a vector or plasmid as a single unit. An illustrative example of a transfer vector of the present invention is shown in

FIGURE 3C. FIGURE 3C illustrates the plasmid pCAH/SINdl (SEQ ID NO: 68). PCAH/SINdl (SEQ ID NO: 68) is a 4,238 bp plasmid that contains the HCMV MIEP promoter, the R-U5 sequence regions in the CAEV 5'LTR, the residual untranslated sequences containing a PBS site, the 327 bp fragment of the gag gene with t he A TG→TAG d ouble p oint m utations, t he R RE r egion a nd t he U 3-deleted CAEV 3'LTR region. The vector also contains a Col El origin of replication (bp 2535-3118) and a kanamycin resistance gene region (bp 3370-4182). The other illustrative examples of transfer vectors are shown in FIGURE 3A-3H.

The invention provides a CAEV vector system comprising the above- described transfer vector and a packaging vector system. The packaging vector system comprises a first and second polynucleotide vector sequence. The first polynucleotide sequence comprises CAEV gag-pol and RRE-encoding sequence and the second polynucleotide comprises a viral envelope encoding sequence. In one embodiment, the second polynucleotide encodes a non-CAEV envelope.

The phrases "structural gene" as used herein refer to the polynucleotide sequence encode proteins which are required for encapsidation (e.g., packaging) of the viral genome, and include gag, pol and env.

An illustrative example of a first packaging vector of the present invention is shown in FIGURE 2A. FIGURE 2A illustrates the plasmid pMGP/RRE ( SEQ ID NO: 77). The plasmid contains 9,446 base pairs and includes a MCMV MIEP region, the CAEV gag-pol coding region, the RRE region, and the bovine growth hormone (BGH) polyadenylation signal. The vector also contains a neomycin resistant gene coding region, a SV40 origin of replication, a Col El origin of replication, and an ampicillin resistance gene region.

It is possible to alter the host range of cells that the viral vectors of the present invention can infect by utilizing an envelope gene from another closely related virus. In other words, it is possible to expand the host range of the CAEV vectors of the present invention by taking advantage of the capacity of the envelope proteins of certain viruses to participate in the encapsidation of other viruses. Examples of retro viral-derived env gene include, but are not limited to: the G-protein of vesicular- stomatitis virus (VSV-G), gibbon ape leukemia virus (GaLV), rous sarcoma virus (RSV), moloney murine leukemia virus (MoMuLV), mouse mammary tumor virus (MMTV), and human immunodeficiency virus (HIV). All of these viral envelope proteins efficiently form pseudotyped virions with genome and matrix components of other viruses. As used herein, the term "pseudotype" refers to a viral particle that contains nucleic acid of one virus but the envelope protein of another virus. In general, either VSV-G or GaLV pseudotyped vectors have a very broad host range, and may be pelleted to titers of high concentration by ultracentrifugation (Burns et al., 1993), while still retaining high levels of infectivity.

Other illustrative examples of second packaging vectors of the present invention are shown in FIGURES 6A and 6B. FIGURE 6A illustrates the plasmid pHGVSV-G (SEQ ID NO: 74). pHGVSV-G (SEQ ID NO: 74) is a 7,623 bp plasmid which contains the HCMV MIEP, the β-globin intron region, the VSV-G coding region, the BGH polyadenylation signal, a Col El origin of replication, a neomycin resistance gene coding region, an ampicillin resistance gene coding region, and an Fl origin of replication. FIGURE 6B illustrates the plasmid pMYKEFl/env (SEQ ID NO: 72). This plasmid contains 7,579 bp which includes the MCMV MIEP, a human EFl -α intron region, the GaLV env coding region, the BGH polyadenylation signal, a Col El origin of replication, a neomycin resistance gene coding region, and an ampicillin resistance gene coding region.

In another embodiment of the invention, the packaging vector comprises a third polynucleotide which encodes Rev. In infected cells, Rev binds to the Rev- responsive element (RRE) in viral transcripts and causes the transcription of both singly-spliced and unspliced transcripts characteristic of the viral structural proteins in the late stage of replication. Accordingly, Rev mediates temporal regulation of viral gene expression. Because mammalian cell splicing mechanisms are coupled to transport of mRNA from the site of synthesis in the nucleus to the cytoplasm, Rev also influences transport of viral transcripts containing RRE.

An illustrative example of a third packaging vector of the present invention is shown in FIGURE 5. FIGURE 5 illustrates the plasmid pHYK/rev (SEQ ID NO: 75). pHYK/rev (SEQ ID NO: 75) is a 5,419 bp plasmid which contains HCMV MIEP, the rev gene coding region, BGH polyadenylation signal, a Col El origin of replication, a neomycin resistant gene coding region, and an ampicillin resistant gene coding region.

In yet another embodiment of the invention, the packaging vector comprises a fourth polynucleotide encoding Vif. Incorporation of Vif may be necessary for infection and packaging of virions, depending on the packaging cell line chosen. An illustrative example of a fourth packaging vector of the present invention is shown in FIGURE 4. pHYK/vif (SEQ ID NO: 76) is a 5,729 bp plasmid which contains the HCMV MIEP, the vif gene coding region, the BGH polyadenylation signal, a Col El origin of replication, a neomycin resistance gene coding region, and an ampicillin resistance gene coding region. When retroviral vector DNA is transfected into the cells, it may or may not become integrated into the chromosomal DNA and becomes transcribed, thereby producing full-length retroviral vector RNA that contains a ψ sequence. Under these conditions, only the vector RNA is packaged into the viral capsid structures. These complete, yet replication-defective, virus particles can then be used to deliver the retroviral vector to target cells with relatively high efficiency. As used herein, the term "replication-defective" refers to a virus that is not capable of complete, effective replication such that infective virions are not produced (e.g. replication-defective lentiviral progeny). The term "replication-competent" refers to wild-type virus or mutant virus that is capable of replication, such that viral replication o f the virus i s c apable o f producing infective virions ( e.g., replication- competent lentiviral progeny).

It is also contemplated that packaging may be inducible, as well as non- inducible. In inducible packaging cells and packaging cell lines, CAEV particles are produced in response to at least one inducer, hi preferred embodiments with inducible cell lines, the inducer is Tat. In non-inducible packaging cell lines and packaging cells, no inducer is required in order for lentiviral particle production to occur.

CAEV vector sequences

Functionally equivalent sequences of the present invention also encompass various fragments of a CAEV genome that retain substantially the same function as the respective native sequence. Such fragments will comprise at least about 10, 15 contiguous nucleotides, at least about 20 contiguous nucleotides, at least about 24, 50, 60, 80, 100, 120, 140, 160, 180, 200, 220, 240, 260, 280, 300, 340, 360, 380, or up to the entire contiguous nucleotides of the specific genetic element of interest. Such fragments may be obtained by use of restriction enzymes to cleave the native viral genome; by synthesizing a nucleotide sequence from the native nucleotide sequence of the virus genome; or may be obtained through the use of PCR technology. See particularly (Mullis and Faloona, 1987) and (Erlich, 1989). Again, variants of the various vector components, such as those resulting from site-directed mutagenesis, are encompassed by the methods of the present invention. As described in more detail below, methods are available in the art for determining functional equivalence. By "variant" it is intended to include substantially similar sequences. Thus, for nucleotide sequences or amino acid sequences, variants include sequences that are functionally equivalent to the various components of the viral vector system. Variant nucleotide sequences also include synthetically derived nucleotide sequences that have been generated, for example, by site directed mutagenesis, but which still retain the function of the native sequence. Generally, nucleotide sequence variants or amino acid sequence variants of the invention will have at least 70%, generally 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to its respective native nucleotide sequence. Variants of the invention include polynucleotides (e.g., vectors) comprising, consisting essentially of, or consisting of, sequences at least 70%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical to the sequences of the vectors disclosed herein (SEQ ID NOs: 67-79).

One of skill will appreciate that many conservative variations of the nucleic acid constructs disclosed yield a functionally identical construct. Conservative variations of a particular nucleic acid sequence refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given polypeptide. For example, due to the degeneracy of the genetic code, "silent substitutions" (i.e., substitutions of a nucleic acid sequence which do not result in an alteration in an encoded polypeptide) are an implied feature of every nucleic acid sequence which encodes an amino acid. Similarly, "conservative amino acid substitutions," in one or a few amino acids in an amino acid sequence of a packaging or packageable construct are substituted with different amino acids with highly similar properties, are also readily identified as being highly similar to a disclosed construct. For instance, the codons CGU, CGC, CGA, CGG, AGA, and AGG all encode the amino acid arginine. Thus, at every position where an arginine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent variations," which are one species of

"conservatively modified variations." Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation. One of skill will recognize t hat e ach c odon i n a n ucleic a cid ( except A UG, w hich i s o rdinarily t he only codon for methionine) can be modified to yield a functionally identical molecule by standard techniques. Accordingly, e ach "s ilent variation" of a nucleic acid which encodes a polypeptide is implicit in any described sequence. Furthermore, one of skill will recognize that individual substitutions, deletions or additions which alter, add or delete a single amino acid or a small percentage of amino acids (typically 1 ess than 5 %, more typically less than 1 %) in an encoded sequence are "conservatively modified variations" where the alterations result in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. The following six groups each contain amino acids that are conservative substitutions for one another:

1) Alanine (A), Serine (S), Threonine (T);

2) Aspartic acid (D), Glutamic acid (E);

3) Asparagine (N), Glutamine (Q);

4) Arginine (R), Lysine (K);

5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

See also, Creighton (1984) Proteins W. H. Freeman and Company. Finally, the addition of sequences which do not alter the activity of a nucleic acid molecule, such as a non-functional sequence is a conservative modification of the basic nucleic acid.

Such conservatively substituted variations of each disclosed sequence are a feature of the present invention.

With respect to the amino acid sequences for the various full-length or mature polypeptides used in the vector system of the present invention, variants include those polypeptides that are derived from the native polypeptides by deletion (so- called truncation) or addition of one or more amino acids to the N-terminal and/or C- terminal end of the native polypeptide; deletion or addition of one or more amino acids at one or more sites in the native polypeptide; or substitution of one or more amino acids at one or more sites in the native polypeptide. Such variants may result from, for example, genetic polymorphism or from human manipulation. Methods for such manipulations are generally known in the art.

One of skill will recognize many ways of generating alterations in a given nucleic acid construct. Such well-known methods include site-directed mutagenesis, PCR amplification u sing d egenerate o ligonucleotides, e xposure o f c ells c ontaining the nucleic acid to mutagenic agents or radiation, chemical synthesis of a desired oligonucleotide ( e.g., i n c onjunction w ith 1 igation and/or c loning to g enerate 1 arge nucleic acids) and other well-known techniques. See, (Gillam and Smith, 1979), (Roberts, Cheetham, and Rees, 1987), and Sambrook, Innis, Ausbel, Berger, Needham VanDevanter and Mullis (all supra).

A variant of a native nucleotide sequence or native polypeptide has substantial identity to the native sequence or native polypeptide. A variant may differ by as few as 1 to 10 amino acid residues, such as 6-10, as few as 5, as few as 4, 3, 2, or even 1 amino acid residue. A variant of a nucleotide sequence may differ by as low as 1 to 30 nucleotides, such as 6 to 20, as low as 5, as few as 4, 3, 2, or even 1 nucleotide residue. It is intended by "s equence identity" that the same nucleotides or amino acid residues are found within the variant sequence and a reference sequence when a specified, contiguous segment of the nucleotide sequence or amino acid sequence of the variant is aligned and compared to the nucleotide sequence or amino acid sequence of the _^reference sequence. Methods for sequence alignment and for determining identity between sequences are well known in the art. With respect to optimal alignment of two nucleotide sequences, the contiguous segment of the variant nucleotide sequence may have additional nucleotides or deleted nucleotides with respect to the reference nucleotide sequence. Likewise, for purposes of optimal alignment of two amino acid sequences, the contiguous segment of the variant amino acid sequence may have additional amino acid residues or deleted amino acid residues with respect to the reference amino acid sequence. The contiguous segment used for comparison to the reference nucleotide sequence or reference amino acid sequence will comprise at least 20 contiguous nucleotides, or amino acid residues, and may be 30, 40, 50, 100, or more nucleotides or amino acid residues. Corrections for increased sequence identity associated with inclusion of gaps in the variant's nucleotide sequence or amino acid sequence can be made by assigning gap penalties. The determination of percent identity between two sequences can be accomplished using a mathematical algorithm. For example, percent identity of an amino acid sequence can be determined using the Smith- Waterman homology search algorithm using an affϊne 6 gap search with a gap open penalty of 12 and a gap extension penalty of 2, BLOSUM matrix 62. Alternatively, percent identity of a nucleotide sequence is determined using the Smith- Waterman homology search algorithm using a gap open penalty of 25 and a gap extension penalty of 5. Such a determination of sequence identity can be performed using, for example, the DeCypher Hardware Accelerator from TimeLogic Version G. The Smith- Waterman homology search algorithm is taught in Smith and Waterman , herein incorporated by reference. Alternatively, the alignment program GCG Gap (Wisconsin Genetic Computing G roup, S uite V ersion 1 0.1) u sing t he d efault p arameters m ay b e u sed. The GCG Gap program applies the Needleman and Wunch algorithm and for the alignment of nucleotide sequences with an open gap penalty of 3 and an extend gap penalty of 1 may be used. Another preferred, non-limiting example of a mathematical algorithm utilized for the comparison of two sequences is the algorithm of Karlin and Altschul (Karlin and Altschul, 1990), modified as in Karlin and Altschul (Karlin and Altschul, 1993). Such an algorithm is incorporated into the NBLAST and XBLAST programs of Altschul et al. (Altschul et al., 1990). BLAST nucleotide searches can be performed with the NBLAST program, score=100, wordlength=12, to obtain nucleotide sequences having sufficient sequence identity. BLAST protein searches can be performed with the XBLAST program, score=50, wordlength=3, to obtain amino acid sequences having sufficient sequence identity. To obtain gapped alignments for comparison purposes, Gapped BLAST can be utilized as described in Altschul et al. (Altschul et al., 1997). Alternatively, PSI-Blast can be used to perform an iterated search that detects distant relationships between molecules. See Altschul et al. (1997) supra. When utilizing BLAST, Gapped BLAST, and PSI-Blast programs, the default parameters of the respective programs (e.g., XBLAST and NBLAST) can be used. See http://www.ncbi.nlm.nih.gov. Another non-limiting example of a mathematical algorithm utilized for the comparison of sequences is the algorithm of Myers and Miller (1988) CABIOS 4:11-17. Such an algorithm is incorporated into the ALIGN program (version 2.0), which is part of the GCG sequence alignment software package. When utilizing the ALIGN program for comparing amino acid sequences, a PAM 120 weight residue table, a gap length penalty of 12, and a gap penalty of 4 can be used. Percent identity of an amino acid sequence can also be determined using the VectorNTI (Informax, USA).

One of skill can select a desired nucleic acid of the invention based upon the sequences provided and upon knowledge in the art regarding CAEV generally. The life-cycle, genomic organization, developmental regulation and associated molecular biology of lentiviruses have been the focus of over a decade of intense research. The specific effects of many mutations in many lentiviral genomes are known. In addition, the nucleic acid sequence variations of some CAEV strains are known. Moreover, general knowledge regarding the nature of proteins and nucleic acids allows one of skill to select appropriate sequences with activity similar or equivalent to the nucleic acids and polypeptides disclosed in the sequence listings herein.

Finally, most modifications to nucleic acids are evaluated by routine screening techniques in suitable assays for the desired characteristic. For instance, changes in the immunological character of encoded polypeptides can be detected by an appropriate immunological assay. Modifications of other properties such as nucleic acid hybridization to a complementary nucleic acid, redox or thermal stability of encoded proteins, hydrophobicity, susceptibility to proteolysis, or the tendency to aggregate are all assayed according to standard techniques.

Polynucleotides of Interest

As will be appreciated by one skilled in the art, the nucleotide sequence of the inserted polynucleotide of interest may be of any nucleotide sequence. For example, the polynucleotide sequence may be a reporter gene sequence or a selectable marker gene sequence. A reporter gene sequence, as used herein, is any gene sequence which, when expressed, results in the production of a protein whose presence or activity can be monitored. Examples of suitable reporter genes include the gene for galactokinase, β-galactosidase, chloramphenicol acetyltransferase, β-lactamase, green fluorescent protein, enhanced green fluorescent protein, etc. Alternatively, the reporter gene sequence may be any gene sequence whose expression produces a gene product that affects cell physiology. Polynucleotide sequences of the present invention may comprise one or more gene sequences that already possess on or more promoters, initiation sequences, or processing sequences.

A selectable marker gene sequence is any gene sequence capable of expressing a protein whose presence permits one to selectively propagate a cell which contains it. Examples of selectable marker genes include gene sequences capable of conferring host resistance to antibiotics (e.g., puromycin, hygromycin, neomycin, zeocin and the like), or of conferring host resistance to amino acid analogues, or of permitting the growth o f b acteria o n a dditional c arbon s ources o r u nder o therwise i mpermissible culture conditions. Reporter or selectable marker gene sequences are sufficient to permit the recognition or selection of the vector in normal cells. In one embodiment of the invention, the reporter gene sequence may encode an enzyme or other protein which is normally absent from mammalian cells, and whose presence can, therefore, definitively establish the presence of the vector in such a cell. The transfer vectors of the present invention additionally permit the incorporation of heterologous nucleic acid, or polynucleotides, into virus particles, thereby providing a means for amplifying the number of infected host cells containing heterologous nucleic acid therein. The incorporation of the heterologous polynucleotide facilitates the replication of the heterologous nucleic acid within the viral particle, and the subsequent production of a heterologous protein therein. A heterologous protein is herein defined as a protein or fragment thereof wherein all or a portion of the protein is not expressed by the host cell. A nucleic acid or gene sequence is said to be heterologous if it is not naturally present in the wild-type of the viral vector used to deliver the gene into a cell. The term heterologous nucleic acid sequence or polynucleotide sequence, as used herein, is intended to refer to a nucleic acid molecule (preferably DNA). The polynucleotide sequence or heterologous polynucleotide sequence may also comprise the coding sequence of a desired product such as a suitable biologically active protein or polypeptide, immunogenic or antigenic protein or polypeptide, or a therapeutically active protein or polypeptide. The polypeptide may supplement deficient or nonexistent expression of an endogenous protein in a host cell. Such gene sequences may be derived from a variety of sources including DNA, cDNA, synthetic DNA, RNA or combinations thereof. Such gene sequences may comprise genomic DNA which may or may not include naturally occurring introns. Moreover, such genomic DNA may be obtained in association with promoter sequences or polyadenylation sequences. The gene sequences of the present invention are preferably cDNA. Genomic or cDNA may be obtained in any number of ways. Genomic DNA can be extracted and purified from suitable cells by means well-known in the art. Alternatively, mRNA can be isolated from a cell and used to prepare cDNA by reverse transcription, or other means. Alternatively, the polynucleotide sequence may comprise a sequence complementary to an RNA sequence, such as an antisense RNA sequence, which antisense sequence can be administered to an individual to inhibit expression of a complementary polynucleotide in the cells of the individual.

Expression of the heterologous gene may provide an immunogenic or antigenic protein or polypeptide to achieve an antibody response. The antibodies thus raised may be collected from an animal in a body fluid such as blood, serum or ascites. The heterologous gene can also be any nucleic acid of interest that can be transcribed. Generally the foreign gene encodes a polypeptide. Preferably the polypeptide has some therapeutic benefit. The polypeptide may supplement deficient or nonexistent expression of an endogenous protein in a host cell. The polypeptide can confer new properties on the host cell, such as a chimeric signaling receptor, see U.S. Pat. No. 5,359,046. One of ordinary skill can determine the appropriateness of a foreign gene practicing techniques taught herein and known in the art. For example, the artisan would know whether a foreign gene is of a suitable size for encapsidation and whether the foreign gene product is expressed properly.

The particular heterologous protein that can be employed in the present invention is not critical thereto.

Specific examples of such heterologous proteins which can be employed in the present invention include dystrophin (Hoffman, Brown, and Kunkel, 1987), coagulation factor VIII (Wion et al., 1985), Cystic Fibrosis Transmembrane Regulator Protein (CFTR) (Anderson et al., 1991; Crawford, 1991), Ornithine Transcarbamylase (OTC) (Murakami et al., 1988), and αl -antitrypsin (Fagerhol and Cox, 1981). The genes encoding many heterologous proteins are well-known in the art, and can be cloned from genomic or cDNA libraries [Sambrook et al, supra]. Examples of such genes include the dystrophin gene(Lee et al., 1991), the Factor VIII gene (Toole et al., 1984), the CFTR gene (Rommens et al., 1989; Riordan, 1989), the OTC gene (Horwich et al., 1984), and the αl -antitrypsin gene (Lemarchand et al., 1992). In addition, genes encoding heterologous proteins such as Rb, for the treatment of vascular proliferative disorders like atherosclerosis (Chang et al., 1995), and p53 for the treatment of cancer (Wills et al., 1994; dayman, 1995), and HIV disease (Bridges and Sarver, 1995), can be employed in the present invention.

The v ector d oes n ot a lways n eed t o c ode for a functional, h eterologous gene product, i.e., it may also code for a partial gene product which acts as an inhibitor of a eukaryotic enzyme (Warne, Viciana, and Downward, 1993; Wang, 1991).

It may also be desirable to modulate the expression of a gene regulating molecule in a cell by the introduction of a molecule by the method of the invention. The term "modulate" envisions the suppression of expression of a gene when it is over-expressed or augmentation of expression when it is under-expressed. Where a cell proliferative disorder is associated with the expression of a gene, nucleic acid sequences that interfere with the expression of a gene at the translational level can be used. The approach can utilize, for example, antisense nucleic acid, ribozymes or triplex agents to block transcription or translation of a specific mRNA, either by masking that mRNA with an antisense nucleic acid or triplex agent, or by cleaving same with a ribozyme.

Antisense nucleic acids are DNA or RNA molecules which are complementary to at least a portion of a specific mRNA molecule . In the cell, the antisense nucleic acids hybridize to the corresponding mRNA forming a double-stranded molecule. The antisense nucleic acids interfere with the translation of the mRNA since the cell will not translate an mRNA that is double-stranded. Antisense oligomers of about 15 nucleotides or more are preferred since such are synthesized easily and are less likely to cause problems than larger molecules when introduced into the target cell. The use of antisense methods to inhibit the in vitro translation of genes is well known in the art (Marcus-Sekura, 1988). The antisense nucleic acid can be used to block expression of a mutant protein or a dominantly active gene product, such as amyloid precursor protein that accumulates in Alzheimer's disease. Such methods are also useful for the treatment of Huntington's disease, hereditary Parkinsonism and other diseases. Antisense nucleic acids are also useful for the inhibition of expression of proteins associated with toxicity.

Use of an oligonucleotide to stall transcription can be by the mechanism known as the triplex strategy since the oligomer winds around double-helical DNA, forming a three-strand helix. Therefore, the triplex compounds can be designed to recognize a unique site on a chosen gene (Maher, Wold, and Dervan, 1991; Helene, 1991). Ribozymes are RNA molecules possessing the ability to specifically cleave other single-stranded RNA in a manner analogous to DNA restriction endonucleases. Through the modification of nucleotide sequences which encode those RNA's, it is possible to engineer molecules that recognize and cleave specific nucleotide sequences in an RNA molecule (Cech, 1988). A major advantage of that approach is only mRNA's with particular sequences are inactivated.

It may be desirable to transfer a nucleic acid encoding a biological response modifier. Included in that category are immunopotentiating agents including nucleic acids encoding a number of the cytokines classified as "interleukins", for example, interleukins 1 through 12. Also included in that category, although not necessarily working according to the same mechanism, are interferons, and in particular gamma interferon (γ-IFN), tumor necrosis factor (TNF) and granulocyte-macrophage colony stimulating factor (GM-CSF). It m ay b e d esirable to d eliver s uch n ucleic a cids t o bone marrow cells or macrophages to treat inborn enzymatic deficiencies or immune defects. Nucleic acids encoding growth factors, toxic peptides, ligands, receptors or other physiologically important proteins also can be introduced into specific non- dividing cells. Thus, the recombinant CAEV vector system of the invention can be used to treat an HIV-infected cell (e.g., T-cell or macrophage) with an anti-HIV molecule. In addition, respiratory epithelium, for example, can be infected with a recombinant lentivirus of the invention having a gene for cystic fibrosis transmembrane conductance regulator (CFTR) for treatment of cystic fibrosis.

Thus, the recombinant CAEV vector system of the invention can be used to treat many human diseases. Specific examples of possible application of the CAEV vector system in human diseases include, but are limited to: Alzheimer's diseases, Parkinson's diseases, amyotrophic lateral sclerosis disease, Huntington's disease, beta-thalassemia, retinitis pigmentosa, mucopolysaccharide disease, leukodystrophy diseases, X-linked SCID, phenylketonuria, tryosinemia, hemophilia A and B, Wilson's diseases, LDL receptor deficiency, Human Immunodeficiency, and Duchenne's dystrophy.

CAEV Vector Particles

In a method of the invention, infectious and replication-defective CAEV vector particles may be prepared according to the methods disclosed herein in combination with techniques known to those skilled in the art. The method includes transfecting a lentivirus-permissive cell with the vector expression system of the present invention; producing the CAEV-derived particles in the transfected cell; and collecting the virus particles from the cell.

The term "transfection" as used herein refers to the introduction of foreign DNA into eukaryotic cells. Transfection may be accomplished by a variety of means known to the art including but not limited to calcium phosphate-DNA co- precipitation, DEAE-dextran-mediated transfection, polybrene-mediated transfection, electroporation, microinjection, liposome fusion, lipofection and protoplast fusion. These techniques are well known in the art.

As used herein, the term "transduction" refers to the delivery of a gene using a viral or retroviral vector particles by means of infection rather than by transfection. In some embodiments, retroviral vectors are transduced. Thus, a "transduced gene" is a g ene t hat h as b een i ntroduced i nto t he c ell v ia 1 enti viral o r v ector i nfection a nd provirus integration. In certain embodiments, the CAEV viral vector particles transduce genes into "target cells" or host cells.

The step of facilitating the production of the infectious viral particles in the cells may also be carried out using conventional techniques, such as by standard cell culture growth techniques.

The step of collecting the infectious virus particles may also be carried out using conventional techniques. For example, the infectious particles may be collected by collection of the supernatant of the cell culture, as is known in the art. Optionally, the collected virus particles may be purified if desired. Suitable purification techniques are well known to those skilled in the art.

If desired by the skilled artisan, CAEV stock solutions may be prepared using the vectors and methods of the present invention. Methods of preparing viral stock solutions are known in the art and are illustrated by, e.g., (Soneoka et al., 1995) and (Landau and Littman, 1992). In a method of producing a stock solution in the present invention, lentiviral-permissive cells are transfected with the vector system of the present i nvention. T he cells are then grown under suitable cell culture conditions, and the CAEV particles are collected from the cell culture media as described above. Suitable permissive cell lines include, but are not limited to, the human cell lines 293, 293T, and HeLa the monkey cell line Vero ,and the goat cell lines GSM and ChIEs. The vectors of the present invention are also useful in preparing stable packaging cells (i.e. cells that stably express CAEV structural proteins, which cells, by t hemselves, c annot generate i nfectious v irus particles) and v irus p roducer cells (VPC). Methods for preparing packaging cells that express retrovirus proteins are known in the art and are exemplified by the methods set forth in, for example, U.S. Pat. No. 4,650,764 to Temin et al., which disclosure is incorporated herein in its entirety. Within the scope of the present invention, a packaging cell will comprise a lentivirus-permissive host cell comprising a CAEV nucleic acid sequence from at least one CAEV packaging vector described in this invention, which nucleic acid sequence is packaging-signal defective, thus rendering the cell itself capable of producing at least one CAEV structural protein, but not capable of producing replication-competent infectious virus. A packaging cell may be made by transfecting a CAEV-permissive host cell (e.g., a human embryonic kidney 293 or 293T cells) with a suitable CAEV nucleic acid sequence as provided above according to known procedures. The resulting packaging cell is thus able to express and produce at least one CAEV structural protein. However, the packaging cell is still not able to produce recombinant CAEV virus. The packaging cell may then be transfected with other nucleic acid sequences, i.e., a transfer vector, which may contain heterologous genes of interest and an appropriate packaging signal. Once transfected with the additional sequence or sequences, the packaging cell may thus be used to provide stocks of CAEV viruses that contain heterologous genes, but which viruses are themselves replication-incompetent. The resulting virus producing cell (VPC) is thus able to produce infectious virus particles containing heterologous gene of interest.

Gene Transfer and Therapy

A number of human genetic diseases that result from an alteration in a single gene are prime candidates for gene therapy. As used herein, the terms "gene therapy" or "gene transfer" are defined as the insertion of genes into cells for the purpose of medicinal therapy. There are many applications of gene therapy, particularly via stem cell genetic insertion, and thus are well known and have been extensively reviewed. The term "target" is used to indicate that the CAEV vector is intended to transduce the cells. Target cells for therapeutic gene transfer, either ex vivo or in vivo, include, but are not limited to hematopoietic stem cell, lymphocyte, vascular endothelial cell, respiratory epithelial cell, keratinocyte, skeletal and muscle cells, liver cell, neuron cell, and cancer cell .

The gene transfer technology of the present invention may also be used in elucidating the processing of peptides and identification of the functional domains of various proteins. Cloned cDNA or genomic sequences for proteins can be introduced into different target cells ex vivo, or in vivo, in order to study cell-specific differences in processing and cellular fate. By placing the coding sequences under the control of a strong promoter, a substantial amount of the desired protein can be made. Furthermore, the specific residues involved in protein processing, intracellular sorting, or biological activity can be determined by mutational change in discrete residues of the coding sequences.

Gene transfer technology of the present invention can also be applied to provide a means to control expression of a protein and to assess its capacity to modulate cellular events. Some functions of proteins, such as their role in differentiation, may be studied in tissue culture, whereas others will require reintroduction into in vivo systems a t d ifferent t imes i n d evelopment i n o rder to rn onitor c hanges i n r elevant properties.

Gene transfer provides a means to study the nucleic acid sequences and cellular factors that regulate expression of specific genes. One approach to such a study would be to fuse the regulatory elements to be studied to reported genes and subsequently assaying the expression of the reporter gene.

Gene transfer also possesses substantial potential use in understanding and providing therapy for disease states. There are a number of inherited diseases in which defective genes are known and have been cloned. In some cases, the function of these c loned genes i s known, hi general, the above disease states fall into two classes: deficiency states, usually of enzymes, which are generally inherited in a recessive manner, and unbalanced states, at least sometimes involving regulatory or structural proteins, which are inherited in a dominant manner. For deficiency state diseases, gene transfer could be used to bring a normal gene into affected tissues for replacement therapy, as well as to create animal models for the disease using antisense m utations. F or u nbalanced d isease s tates, g ene t ransfer c ould be u sed t o create a disease state in a model system, which could then be used in efforts to counteract the disease state. Thus the methods of the present invention permit the treatment of genetic diseases. As used herein, a disease state is treated by partially or wholly remedying the deficiency or imbalance which causes the disease or makes it more severe. The use of site-specific integration of nucleic sequences to cause mutations or to correct defects is also possible.

The method of the invention may also be useful for neuronal, glial, fibroblast or mesenchymal cell transplantation, or "grafting", which involves transplantation of cells infected with the recombinant lentivirus of the invention ex vivo, or infection in vivo into the central nervous system or into the ventricular cavities or subdurally onto the surface of a host brain. Such methods for grafting will be known to those skilled in the art and are described in Neural Grafting in the Mammalian CNS, Bjorklund & Stenevi, eds. (1985).

For diseases due to deficiency of a protein product, gene transfer could introduce a normal gene into the affected tissues for replacement therapy, as well as to create animal models for the disease using antisense mutations. For example, it may be desirable to insert a Factor VIII or IX encoding nucleic acid into a CAEV particle for infection of a muscle, spleen or liver cell.

There are many applications of gene therapy, particularly via stem cell genetic insertion, and thus are well known and have been extensively reviewed. As used herein, the term "stem cells" includes but is not limited to hematopoietic stem cells, neuronal stem cells, mesenchymal (particularly muscular) stem cells, and liver stem cells. Stem cells are capable of repopulating tissues in vivo. Hematopoietic stem cells are progenitor cells derived from primitive human hematopoietic cells. Gene therapy using hematopoietic stem cells is also useful to treat a genetic abnormality in lymphoid and myeloid cells that results generally in the production of a defective protein or abnormal levels of expression of the gene.

For a number of these diseases, the introduction of a normal copy or functional homolog of the defective gene and the production of even small amounts of the missing gene product would have a beneficial effect. At the same time, overexpression of the gene product would not be expected to have deleterious effects. The following provides a non-exhaustive list of diseases for which gene transfer into hematopoietic stem cells is potentially useful. These diseases generally include bone marrow disorders, erythroid cell defects, metabolic disorders and the like. Hematopoietic stem cell gene therapy is beneficial for the treatment of genetic disorders of blood cells such as α- and β-thalassemia, sickle cell anemia and hemophilia A and B in which the globin gene or clotting factor genes (e.g., Factor IX and Factor X genes) are defective. Another good example is the treatment of severe combined immunodeficiency disease (SCIDS), in which patients lack the adenosine deaminase (ADA) enzyme which helps eliminate certain byproducts that are toxic to T and B lymphocytes and render the patients defenseless against infection. Such patients are ideal candidates to receive gene therapy by introducing the ADA gene into their hematopoietic stem cells instead of the patient's lymphocytes as done in the past. Other diseases include chronic granulomatosis where the neutrophils express a defective cytochrome b and Gaucher disease resulting from an abnormal glucocerebrosidase gene product in macrophages. Additionally, neurological degenerative disorder, e.g., Parkinson's disease, is an attractive target for gene therapy by introducing the GDNF (Glial cell line-derived neurotrophic factor) gene into the striatum and the substantia (Kordower et al., 2000).

Strategies to treat various forms of cancer are also included in gene therapy. The

CAEV vector can carry a gene that encodes, for example, a toxin or an apoptosis inducer effective to specifically kill the cancerous cells. Specific killing of tumor cells can also be accomplished by introducing a suicide gene to cancerous hematopoietic cells under conditions that only the tumor cells express the suicide gene. The suicide gene product confers lethal sensitivity to the cells by converting a normally nontoxic drug to a toxic derivative. For example, the enzyme cytosine deaminase converts the nontoxic substance 5'-fluorocytosine to a toxic derivative, 5- fluorouracil (Mullen, Kilstrup, and Blaese, 1992). Tumor-specific lymphocytes can be genetically modified for example, to locally deliver gene products with anti-tumor activity to sites of the tumor to circumvent the toxicity associated with the systemic delivery of these gene products. A gene therapy approach can also be applied to render bone marrow cells resistant to the toxic effects of chemotherapy.

Gene therapy can also be used to prevent or combat viral infections such as HIV and HTLV-I infection. For example, hematopoietic stem cells can be genetically modified to r ender t hem r esistant t o i nfection b y HIV. One approach i s t o i nhibit viral gene expression specifically by using antisense RNA or by subverting existing viral regulatory pathways. Antisense RNAs complementary to retroviral RNAs have been s hown t o i nhibit the r eplication o f a n umber o f r etro viruses ( To, B ooth, a nd Neiman, 1986) including HIV (Rhodes and James, 1991) and HTLV-I (von Ruden and Gilboa, 1989).

Another area where gene therapy in hematopoietic stem cells may find use is in alleviating autoimmune disease. The therapeutic gene can encode, e.g., a B or T cell signaling molecule capable of reconstituting the normal apoptotic signal that results in the death and elimination of autoreactive cells. Ex vivo cell transformation for diagnostics, research, or for gene therapy (e.g., via re-infusion of the transformed cells into the host organism) is well known to those of skill in the art. In one embodiment of the invention, cells are isolated from the subject organism, transfected with a vector of the invention comprising a polypeptide of interest, and re-infused back into the subject organism (e.g., patient).

Various cell types suitable for ex vivo transformation are well known to those of skill i n t he a rt. P articular p referred cells a re s tern c ells d escribed s upra ( see, e .g., Freshney (1994) Culture of Animal Cells, a Manual of Basic Technique, third edition Wiley-Liss, New York, and the references cited therein for a discussion of how to isolate and culture cells from patients). Transformed cells are cultured by means well known in the art. See, also Kuchler (1977) Biochemical Methods in Cell Culture and Virology, Kuchler, R. J., Dowden, Hutchinson and Ross, Inc., and Atlas (1993) CRC Handbook of Microbiological Media (Parks ed) CRC press, Boca Raton, Fl. Mammalian cell systems often will be in the form of monolayers of cells, although mammalian cell suspensions are also used. Alternatively, cells can be derived from those stored in a cell bank (e.g., a blood bank). Illustrative examples of mammalian cell lines include the HEC-I-B cell line, VERO and HeIa cells, Chinese hamster ovary (CHO) cell lines, Wl 38, BHK, Cos-7 or MDCK cell lines (see, e.g., Freshney, supra). T cells or B cells are also used in some ex vivo gene transfer procedures. Several techniques are known for isolating T and B cells. The expression of surface markers facilitates identification and purification of such cells.

In summary, the viral vectors of the present invention can be used to stably transduce either dividing or non-dividing cells, and stably express a heterologous gene. Using this vector system, it is now possible to introduce into dividing or non- dividing cells, genes that encode proteins that can affect the physiology of the cells. The vectors of the present invention can thus be useful in gene therapy for disease states, or for experimental modification of cell physiology. Kits

It is a further object of this invention to provide a kit or drug delivery system comprising the vectors for use in the methods described herein. All the essential materials and reagents required for administration of the targeted retroviral particle may be assembled in a kit (e.g., packaging cell construct or cell line). The components of the kit may be provided in a variety of formulations. The one or more CAEV particles may be formulated with one or more agents (e.g., a chemotherapeutic agent) into a single pharmaceutically acceptable composition or separate pharmaceutically acceptable compositions. The components of these kits or drug delivery systems may also be provided in dried o r 1 yophilized forms. W hen r eagents or e omponents a re p rovided a s a d ried form, reconstitution generally is by the addition of a suitable solvent, which may also be provided in another container means. The kits of the invention may also comprise instructions regarding the dosage and or administration information for the targeted CAEV particle. The kits or drug delivery systems of the present invention also will typically include a means for containing the vials in close confinement for commercial sale such as, e.g., injection or blow-molded plastic containers into which the desired vials are retained. Irrespective of the number or type of containers, the kits m ay a lso c omprise, o r b e p ackaged w ith, an i nstrument for a ssisting w ith t he injection/administration or placement of the ultimate complex composition within the body of a subject. Such an instrument may be an applicator, inhalant, syringe, pipette, forceps, measured spoon, eye-dropper or any such medically approved delivery vehicle.

The following examples illustrate various aspects of the invention, but in no way are intended to limit the scope thereof.

EXAMPLES

The following examples serve to illustrate certain embodiments and aspects of the present invention and are not to be construed as limiting the scope thereof. The following examples demonstrate the finding that the recombinant CAEV- based lentiviral vector system of the present invention is as effective in expression as the well-known HIV-I based lentiviral system. The examples show that the level of genomic RNA transcription, encapsidation, transduction, reverse transcription, and integration of the CAEV-based vector particle production system of the present invention is comparable to that of HIV-I -based lentiviral vector system, which has long been accepted as a highly efficient gene transfer system (Naldini et al., 1996).

This is the first report on the construction of a high titer CAEV-based vector system, which is based on a minimum of three-plasmid co-transfection method, requiring the expression of just the gag-pol and env genes, and optionally a rev gene.

Materials and Methods

Plasmid Construction

The parent plasmids. The parent plasmids from which the CAEV vectors of the present invention were derived are the plasmid pWTE-BM and the plasmid pCAEV- LTR, kindly provided by Dr. Marie Suzan (Institut National de Ia Sante et de Ia Recherche M edicale " INSERM", F ranee) T he pWTE-BM p lasmid c ontains a full- length genomic CAEV cDNA except for the 0.4kb Hind III fragment which contains parts of env, rev, and U3 regions and a 1337 base pair stuffer fragment. The plasmid pCAEV-LTR contains the 0.4kb Hind III fragment lacking in the pWTE-BM (Saltarelli et al., 1990; Saltarelli, 1993). Neither of the vectors can generate a wild- type virus.

CAEV gag-pol expression vectors (pMGP/RRE (SEQ ID NO: 77) and pMGP/REV/RRE). The pMGP/RRE (SEQ ID NO: 77) plasmid is a PWTE-BM derived gag-pol expression plasmid (shown in FIGURE 2A). The pMGP/RRE (SEQ ID NO: 77) plasmid contains a strong and heterologous MCMV major immediate- early promoter (MCMV MIEP), the gag-pol g ene, and the rev responsive element (RRE). The pMGP/RRE (SEQ ID NO: 77) plasmid also encodes the neomycin resistant gene as an antibiotic selection marker. For the construction of the plasmid, the gag-pol gene fragment (nucleotide 5 12 through nucleotide 5046 o f the C AEV genome) from p WTE-BM was subcloned into the pGL2-Basic (Promega, WI, USA) cloning vector by using standard protocols for several PCR and subcloning steps. The MCMV MIEP fragment was excised from the plasmid pMYK (Kim et al, 2002) was then inserted upstream of the gag gene, and the RJRE region (from nucleotide 7824 to nucleotide 8183 or nucleotide 7849 to nucleotide 8150 of the CAEV genome) was inserted downstream of the pol gene. The pMGP/REV/RRE is another gag-pol expressing plasmid (shown in FIGURE 2B) containing the CAEV rev gene. In addition, the major splicing donor site of the CAEV (from nucleotide 330 to nucleotide 346 of the CAEV genome) was inserted downstream of the MCMV promoter. Transfer vectors (pCAH/SINd series). The plasmids in the pCAH/SINd series

(shown in FIGURES 3A-3H) (SEQ ID NOs: 67-71, 73, 78, and 79) were constructed to identify an optimal packaging sequence for the design of the transfer vectors of the present invention. Each of the plasmids in the series were designed to contain different lengths of the 5 'untranslated region and the beginning of the gαg-encoding region to allow for the side by side comparison of the effects of the various lengths in this region. To address certain safety concerns, these plasmids were designed as SIN (self-inactivation) vectors having the U3 region of the 3'LTR deleted. To allow high level expression of vector RNA from the transfer vectors in the absence of a trans¬ acting factor, tαt, the U3 region of the 5'LTR was replaced with an HCMV MEEP. In addition, all known cw-acting sequence elements required for polyadenylation, RNA transportation, reverse transcription, and integration were included in the transfer vector series.

The plasmids of the pCAH/SINd series (SEQ ID NOs: 67-71, 73, 78, 79) were constructed as follows. pCAH/SINd (PBS-deficient negative control vector) (SEQ ID NO: 73) (FIGURE 3A) was designed to contain only the 5' untranslated sequences (R and U5 region)in the 5' LTR (from nucleotide 1 to nucleotide 163 of the CAEV genome). pCAH/SINdO (SEQ ID NO: 67) (FIGURE 3B) was designed to contain the entire 5' untranslated region (from nucleotide 1 to nucleotide 511 of the CAEV genome). pCAH/SINdl (SEQ ID NO: 68) (FIGURE 3C) was designed to contain the entire 5' untranslated region and the 327 bp fragment of the gag gene (from nucleotide 1 to nucleotide 839 of the CAEV genome) with point mutations. pCAH/SINd2 (SEQ ID NO: 69) (FIGURE 3D) was designed to contain the entire 5' untranslated region and the 612 bp fragment of the gag gene (from nucleotide 1 to nucleotide 1124 of the CAEV genome) with point mutations. Plasmid pCAH/SINd3 (SEQ ID NO: 70) (FIGURE 3E) was designed to contain the entire 5' untranslated region and the 908 b p fragment o f the gag gene ( from n ucleo tide 1 to nucleotide 1420 of the CAEV genome) with point mutations. Plasmid ρCAH/SINd4 (SEQ E) NO: 71) (FIGURE 3F) was designed to contain the entire 5' untranslated region and the 1,198 bp fragment of the gag gene (from nucleotide 1 to nucleotide 1710 of the CAEV genome) with point mutations. pCAH/SINdl/hlacZ (SEQ ID NO: 78) (FIGURE 3G) was constructed by inserting the expression cassette consisting of the HCMV MIEP and the lacZ gene into the pCAH/SINdl (SEQ ID NO: 68). The plasmid pCAH/SINd60/hlacZ (SEQ ID NO: 78) (FIGURE 3H) has the same design as the pCAH/SINdl (SEQ ID NO: 68) except for the length of the gag gene, where it contains the first 60 bp fragment of the gag gene with point mutations (from nucleotide 1 to nucleotide 569 of the CAEV genome). CAEV vif expression vector (pHYK/vij) (SEQ ID NO: 76). The vif gene (from nucleotide 5006 to nucleotide 5695 of the CAEV genome), which is known to be required for rapid and efficient virus replication, was cloned into a eukaryotic expression vector pHYK (Kim et al., 2002) (FIGURE 4).

CAEV rev expression vector (pHYK/rev) (SEQ ID NO: 75). The rev gene, which regulates viral gene expression at the post-transcriptional level by interacting with the RRE, c onsists of two exons (the first exon i s p ositioned from nucleotide 6,012 to 6,123, and the second exon is from nucleotide 8514 to 8803 of the CAEV genome). The Rev/RRE system promotes the nuclear export of unspliced RNA and is known to be essential for lentiviral replication. The full-length cDNA of rev g ene was synthesized by RT-PCR and subcloned into the pHYK vector (FIGURE 5).

Viral envelope gene expression vector. The envelope gene expression vector systems used herein are the plasmid pHGVSV-G (SEQ ID NO: 74) and the plasmid pMYKEFl/env (SEQ ID NO: 72) (FIGURES 6A and 6B). The plasmid pHGVSV-G (SEQ ID NO: 74) was designed to express the vesicular stomatitis virus G (VSV-G) glycoprotein and contains the HCMV MEEP with β-globin intron as a promoter. The pMYKEF-1/env (SEQ ID NO: 72) was designed to express the gibbon ape leukemia virus (GaLV) envelope protein and contains the MCMV MIEP with eukaryotic elongation factor- lα intron as a promoter.

MuLV- and HIV-I -based plasmids. As control vector systems, pMFG/lac/Zpuro and pHR/lacZ vectors were used in the present invention, that were lacZ-containing retrovirus vectors derived from the murine leukemia virus (MuLV) (Kim et al., 1997) and the human immunodeficiency virus type 1 (HIV-I) (Naldini et al., 1996), respectively. For the packaging plasmids of MuLV and HIV-I vector systems, pEQPAM3 (Persons et al., 1998) and pCMVΔR8-2 were used, respectively. The

HIV- 1 packaging plasmid pCMVΔR8-2 is identical with pCMVΔR9 (Naldini et al., 1996) except for encoding a functional HIV-I vpu gene and deletion of the 1.3-kb

BgIII fragment in env gene.

Vector Particle Production

Pseudotyped CAEV-based lentiviral vector particles were produced by liposome mediated transient transfection of three or more plasmids into 293T cells plated one day prior to transfection at a density of 5X10⁵ cells per 6-well culture dish. Three p lasmid c otransfections w ere p erformed at a 1 :1:1 m olar r atio o f a g ag-pol expressing plasmid, a transfer vector plasmid, and an e«v-encoding plasmid. Four plasmid cotransfections were performed at a 3:3:3:1 molar ratio of a gag-pol expressing plasmid, a transfer vector plasmid, an ewv-encoding plasmid, and a rev- expressing plasmid. Five plasmid cotransfections were performed at a 3:3:3:1:1 molar ratio of a gag-pol expressing plasmid, a transfer vector plasmid, and an env- encoding plasmid, a rev-expressing plasmid and a w/-expressing plasmid. The culture supernatant containing viral vector particles was harvested 48 hours later, clarified with a 0.45 μM membrane filter (Nalgene, NY, USA), and either used immediately or stored at -7O⁰C deep-freezer.

In vitro Transduction

Transduction was carried out by adding the viral vector particles onto 293T cells for 4 hours, in the presence of 8 μg/ml polybrene followed by the addition of fresh media. After 48 hours Beta-Gal expression was assayed after the cells were fixed in a solution consisting of 1% formaldehyde and 0.2% glutaraldehyde and stained for 12 hours at 37⁰C in a solution containing 300μg of 5-bromo-4-chloro-3- indolyly b-D-galactoside (X-GaI, Promega, WI, USA), 4mM potassium ferrocyanide, 4mM potassium ferricyanide, and 2mM Mgcl₂. Titers can be determined by counting the number of blue foci as LacZ- forming units per ml (LFU/ml).

RT-PCR Assay

Total RNA was extracted from cultured cells or culture supernatant by the method using TRIzol LS Reagent (GIBCO BRL, CA, USA). The total RNA was treated with RNase free-DNase I (lunit /μg of DNA for 20 minutes at 37⁰C) (Promega, WI, USA) to eliminate DNA contamination. The DNase I reaction was stopped by adding RQl DNase stop solution provided with DNase I, and the RNA was cleaned up by the method using RNasy mini kit (Qiagen, Germany). The purified RNA was reverse transcribed into cDNA by reverse transcription (RT) reaction (90min at 37⁰C). In particular, the RT reaction was carried out in the presence of MuLV reverse transcriptase, oligo-dT primer or C -terminal specific primer, and dNTPs mix. PCR amplification was carried out for semi-quantitative analysis o f t emplate D NA w ith s pecific p rimers. In p articular, P CR p roduct D NA was synthesized from the cDNA or chromosomal DNA in the presence of heat stable Ex Taq polymerase, sequence specific DNA primers, and dNTPs mix.

Southern Blot Analysis

Genomic DNA was prepared from cells transduced with either pseudotyped HIV-I or CAEV vector particles, and mock-transduced control cells using the DNeasy Tissue Kit(Qiagen, Germany). Ten μg of genomic DNA from the HIV-I vector transduced cells were digested with BamH I and Kpn I. Ten μg each of the genomic DNA from the CAEV vector transduced cells and the negative control cells were double digested with EcoR I and Ssp I. The digested genomic DNAs were separated by electrophoresis on 0.7% agarose gel and transferred onto positive charged nylon membrane (Roche, Germany). Dig-labeled probes were prepared by

PCR with primers specific for lacL gene (Forward primer: CTGGCGTAATAGCGAAGAGG (SEQ ID NO: 65), Reverse primer: AACTCGCCGCACATCTGAAC (SEQ ID NO: 66)), and southern hybridization was carried out according to Dig application manual (Roche, Germany).

Growth Arrest of Cells and FACS Analysis of the Growth-arrested Cells

293T cells were growth-arrested with aphidicolin(Sigma, USA) treatment(25μg/ml), then transduced with CAEV viral vector particles. As a positive or negative control, cells were transduced side-by-side with either an HIV-I vector or MuLV retrovirus vector. Two days after transduction, cells were stained with X-gal for beta-gal activity. In the aphidicolin treated culture, aphidicolin was present before and after infection.

The growth arrest of c ells was confirmed by F ACS analysis. The aphidicolin treated or untreated control cells were washed in PBS, fixed overnight in 70% ethanol at -20°C, and were followed by treatment of propidium iodide (lOOμg/ml) (Sigma, USA) and RNAse A (lOOμg/ml) (Qiagen, Germany) at RT for 1 hour. The cells were evaluated by FACS analysis, and the percent of total viable cells in Gl, S and G2/M phase of the cell cycle was calculated (Becton Dickinson, Sanjose, CA).

EXAMPLE 1

Production of C AEV-based Lentiviral Vector Particles

Replication defective lentiviral vector particles were generated by transient co- transfection of human 293T cells with a minimum of three-plasmid system of a

CAEV gag-pol expressing plasmid, a CAEV env-expressing plasmid and a transfer vector plasmid. In a four-plasmid system, a CAEV rev expressing plasmid is added, and in a five-plasmid system, a CAEV vif expressing plasmid is added. For efficient packaging, transfer vectors were designed to contain the beginning of the gag- encoding sequence, where mutations were introduced into the start ATG codon and an ATG codon located downstream (ATG to TAG)to prevent the expression of gag proteins. RRE was included to boost packaging efficiency and the rev in the four- and five-plasmid systems was expressed from the vector to support the CAEV mRNA export. The internal HCMV-MIEP promoter-driven β-galactosidase gene in the transfer vector plasmid was inserted to serve as a reporter gene. The U3 region of the 5'LTR was replaced with the strong viral promoter, HCMV-MIEP, allowing the vector genome to be tat independent. Transfer vector RNA transcription level. Transcription level of genomic RNA from a transfer vector is one of the critical factors mediating high titer production of recombinant viral vectors from packaging cells. In the present invention, HCMV enhancer/promoter element was used to construct the HCMV/CAEV hybrid LTR promoter system for safe and efficient transcription of the transfer vector RNA. To examine t he t ranscription 1 evel o f t he t ransfer v ector p lasmids o f t he p CAH/SINd (SEQ E) NOs: 67-71, 73, 78, and 79) series containing the hybrid LTR promoter, each of the transfer vector plasmids was introduced into human T cells, together with the packaging plasmids (pMGP/RRE (SEQ ID NO: 77), pHYK/rev (SEQ ID NO: 75), pHYK/vif (SEQ ID NO: 76), pHGVSV-G (SEQ ID NO: 74) or pMYKEFl/env (SEQ ID NO: 72)), by liposome-mediated transfection. After 48 hours of incubation, total RNA was purified from the transfected cells and was subjected to Reverse Transcriptase Polymerase Chain Reaction (RT-PCR) analysis for the vector RNA transcript measurement. The PCR primer set (RRE primer set) for the CAEV transfer vectors was designed for synthesizing 348-bp PCR product coding for a part of RRE region. Another PCR primer set (lacZ primer set) for the HIV-I transfer vector, pHRlacZ (Naldini et al., 1996), was designed for synthesizing the 645 bp PCR product coding for a part of the lacL gene. As shown in FIGURE 7, the CAEV transfer vectors of the present invention produced RNA transcript at a level comparable to that of the HIV-I -based lentiviral transfer vector. Formation and release of the vector particles. To examine the formation and release of mature and infectious virus vector particles, CAEV vector particles were produced following liposome-mediated co-transfection of the pMGP/RRE (SEQ ID NO: 77) gag-pol expression plasmid, the pHGVSV-G (SEQ ID NO: 74) env expression plasmid, the pHYK/rev (SEQ ID NO: 75) rev expression plasmid, pHYK/vif ( SEQ ID NO: 76) vz/expression p lasmid, and the p CAH/SINd60/hlacZ (SEQ ID NO: 78) transfer vector plasmid into human 293T cells (DuBridge et al.,

1987). Forty eight hours after transfection, the culture supernatant was harvested from the transfected cells and applied to fresh human 293T cells in the presence of 8 μg/ml polybrene for infection. The results indicated that the five plasmids system of the present invention was capable of producing comparable viral vector particle titers to that of the MuLV-based retroviral vector system (pEQPAM3, pMFG/lacZ/puro, pHGVSV-G (SEQ ID NO: 74)) (Ory, Neugeboren, and Mulligan, 1996; Persons et al., 1998) (shown in FIGURE 8).

EXAMPLE 2

Effect of Rev and ^Expression on Vector Particle Production

To determine the effect of CAEV rev and vif regulatory gene expression on vector particle production, the vector particle production system of (1) the three- plasmid system (pCAH/SDSf, pMGP/RRE (SEQ ID NO: 77), pHGVSV-G (SEQ ID NO: 74) or pMYKEFl/env (SEQ ID NO: 72)), which is devoid of rev- and vif- encoding sequences, (2) the four-plasmids system (pCAH/SIN, pMGP/RRE (SEQ ID NO: 77), pHGVSV-G (SEQ ID NO: 74) or pMYKEFl/env (SEQ ID NO: 72), pHYK/rev (SEQ ID NO: 75)), which is devoid of vz/-encoding sequence and (3) the five-plasmid system (pCAH/SIN, pMGP/RRE (SEQ ID NO: 77), pHGVSV-G (SEQ ID NO: 74) or pMYKEFl/env (SEQ ID NO: 72), pHYK/rev (SEQ ID NO: 75), pHYK/vif (SEQ ID NO: 76)), which contains both rev- and vz/-encoding sequences were tested side by side for their efficiency in vector particle production. The plasmids of each system were transfected into 293T cells. At day 2 post-transfection, the transfer vector RNA and the virion RNA were extracted from the transfected cells and the culture medium of the transfected cells, respectively, and used as RT-

PCR templates with the lacZ primer set to detect the transfer vector RNA genome.

As s hown i n FIGURE 9 , a lthough t he e xpression 1 evel o f t he t ransfer v ector RNA in the packaging cells was independent of the expression of the rev or the vif genes (Lane 1 , 2 and 3 in FIGURE 9), the amount of the encapsidated transfer vector RNA in the absence of rev (Lane 4, FIGURE 9) was much lower than that in the presence of rev (Lane 5 in FIGURE 9). Surprisingly, however, the titer of the vector particles measured by RT-PCR with the encapsidated RNA in the presence of vif (Lane 6 in FIGURE 9) was lower than the vector particles measured by the RT-PCR with the encapsidated RNA in the absence of CAEV vif (Lane 5 in FIGURE 9). These data indicate that CAEV rev and vif are not required for vector particle production, but rev is preferred for efficient vector particle production.

Of note is that the results of the present invention regarding the vif expression is inconsistent with the observations reported by Harmache et al. (Harmache et al., 1995; Harmache et al., 1 996), where the v //^"gene was reported to b e e ssential for efficient replication of CAEV in the goat synovial membrane cells and to be affecting the late steps of the virus replication cycle (e.g., RNA encapsidation, release of virus particles from host cells). One plausible explanation for the inconsistency may be in the use of the human 293T cells instead of the goat cells in the production of the recombinant CAEV vector particles. This interpretation supports the hypothesis proposed by Seroude et al. that the species-specific restrictions between vif and the virus-producing cells may modulate the vif function on viral infectivity (Seroude et al., 2002).

EXAMPLE 3

Identification of the Optimal Packaging Signal Sequence

To identify the optimal packaging signal sequence for the encapsidation of CAEV transfer vector RNA, a series of plasmids containing different portions of the CAEV gαg-coding region and the untranslated region b etween the 5 'LTR and the gag start codon were compared for their vector particle production efficiency as follows. Human 293T cells were co-transfected with the pMGP/RRE (SEQ ID NO: 77) gag-pol expression plasmid, the pHGVSV-G (SEQ ID NO: 74) env expression plasmid, the pHYK/rev (SEQ ID NO: 75) rev expression plasmid, the pHYK/vif (SEQ ID NO: 76) vif expression plasmid, and the pCAH/SINd (SEQ ID NOs: 67-71, 73, 78, and 79) transfer vector series plasmid. As a negative control, a CAEV transfer vector pCAM/lacZ(L) was transfected in the absence of packaging plasmids. On day 2 post-transfection, virion RNA was extracted from the culture medium of the transfected cells and used as an RT-PCR template with the RRE primer set to detect the CAEV transfer vector series RNA genome, or with the lacL primer set to detect the HIV-I transfer vector RNA genome. As shown in FIGURE 10, a strong PCR product signal, indicating efficient release of the virus particles containing the viral RNA, was obtained from the culture medium harvested from the virus producing 293T cells transfected with pCAH/SINdl (SEQ ID NO: 68), which contained the complete 5'LTR as well as the first 327 bp of the gag region (lane 3 in FIGURE 10). This signal was comparable to that obtained with the positive control, the HIV-I vector, indicating that the amount of the encapsidated CAEV transfer vector RNA of the present invention is comparable to that of the HIV-I -based transfer vectors (lane 8 in FIGURE 10). The packaging efficiency of the CAEV transfer vectors with gag-coding region of the first 612 bp or longer was significantly reduced (lanes 4, 5, and 6). The PCR product signals were not detectable when the transfer vectors used were devoid of the gag-coding sequences (lane 1 and 2 in FIGURE 10). Negative control was transfected with a transfer vector only, and the positive control, HIV-I vector, was transfected with pCMVΔR8-2, pHR'/lacZ and pHGVSV-G (SEQ ID NO: 74) (lanes 7 and 8 in FIGURE 10). In conclusion, the transfer vector RNAs were encapsidated efficiently in the packaging cells only when the transfer vectors included less than about 600 bp of the N-terminal gag-coding sequences as well as the entire untranslated region between the 5'LTR and the gag start codon. These results indicate that the role of the secondary structure of the RNA within the packaging signal is more important than the primary structure in RNA encapsidation.

EXAMPLE 4

Pseudo typing of the CAEV Vector Virion

To determine whether the recombinant CAEV vector virion can be pseudotyped with t he G aLV g lycoprotein a s w ell a s t he V SV-G g lycoprotein, e ither t he G aLV expression vector, pMYKEFl/env (SEQ ID NO: 72), or the VSV-G expression vector, pHGVSV-G (SEQ ID NO: 74), was cotransfected with a transfer vector plasmid and the packaging plasmids into human 293T cells. Forty eight hours after transfection, culture supernatant containing pseudotyped virion particles released from the transfected cells was harvested, clarified with a 0.45 μm membrane filter, and used for infecting 293T human target cells. One day after infection, genomic DNA was purified by using a Genomic DNA Isolation kit (Qiagen, HL, Germany) and subjected to PCR experimentation to detect the integrated pro viral cDNA. As expected, CAEV vector (Lane 1 in FIGURE 11) was pseudotyped efficiently with the VSV-G protein, comparable to the MuLV- (Lane 3 in FIGURE 11) and the HIV- 1 -based vector (Lane 4 in FIGURE 11). In addition, inconsistent to the HIV-I lentiviral vector system, the CAEV vector of the present invention was pseudotyped successfully with the GaLV e nvelope ( Lane 2 in FIGURE 11). This pseudotyping ability of the CAEV vectors with the GaLV envelope can afford a great advantage in the development of a clinical grade lentiviral vector system. MuLV (transfected with pEQPAM3, pMFG/lacZ/puro and pHGVSV-G (SEQ ID NO: 74)) and HIV-I (transfected with pCMVΔR8-2, pHR'/lacZ and pHGVSV-G (SEQ ID NO: 74)) vector controls are shown in lanes 3 and 4, respectively.

EXAMPLE 5

Generation of a CAEV Packaging Cell Line

Both the pMGP/RRE (SEQ ID NO: 77) and the pHYK/rev (SEQ ID NO: 75) vectors encode a ned gene for selection in eukaryotic cells. For efficient selection after cotransfection with a gag-pol and a rev expression vectors, another CAEV gag- pol expression vector may be constructed by replacing the ned gene with the other antibiotic resistance genes such as bacterial gpt gene. Alternatively, one packaging plasmid system encoding the gag, pol and rev g enes could be used. To determine whether s table 293T c ells e xpressing C AEV p ackaging p roteins c an b e g enerated, antibiotic resistant colonies are selected under selective medium. Production of recombinant CAEV vector from the stable 293T cells suggests the feasibility of generating stable packaging cell lines for CAEV vector production.

EXAMPLE 6

Integration of the CAEV-based Vector cDNA into the Host Chromosome

To examine the integration of the CAEV vector cDNA after transduction, the

CAEV vector particles were produced by liposome-mediated co-transfection of the pMGP/REV/RRE gag-pol expression plasmid, the pHGVSV-G (SEQ ED NO: 74) env expression plasmid, and the pCAH/SINdl/hlacZ (SEQ ED NO: 79) transfer vector plasmid into human 293T cells. As a positive control, the pCMVΔR8.2 gag- pol expression plasmid, the pHGVSV-G (SEQ ID NO: 74) env expression plasmid, and the pHR/lacZ transfer vector were co-transfected into the 293T cells to produce the HIV-I vector particles. As a negative control, only the pCAH/SINdl/hlacZ (SEQ ED NO: 79) transfer vector plasmid was transfected. Forty eight hours after transfection, the culture supernatants were harvested from each of the transfected cells and applied to fresh 293T cells in the presence of 8 μg/ml polybrene for infection. After 48 hours, genomic DNA was prepared from each of the transduced cells, followed by southern blot assay after restriction enzyme digestion. The Dig- labeled lacZ probes detected 3 .15kb B anϊΑ l-Kpn I fragment for the H IV-I -based transfer vector, and 1.35kb Hind lll-Ssp I fragment for the CAEV-based transfer vector and the negative control. For the positive controls, the 0.3 ng and 3 ng of Hind m-Ssp I DNA fragment of the pCAH/SINdl/hlacZ (SEQ ED NO: 79) transfer vector plasmid were used. As shown in FIGURE 12, the CAEV-based transfer vector of the present invention was integrated at a level comparable to that of the HIV-I- based lentiviral transfer vector.

EXAMPLE 7

Gene Transfer to Non-dividing Cells

293T cells were treated with the DNA synthesis inhibitor, aphidicolin, plated on a 6-well culture plate, and then transduced with the CAEV vector particles encoding a lacZ marker gene. As controls, cells were infected side-by-side with a lacZ expressing MuLV retroviral vector and HIV-I lentiviral vector. At 48 hours after infection, in order to examine the trasduction efficiency, expression of the transduced lacZ gene was counted by X-gal staining. As shown in FIGURE 14, the MuLV- derived vector efficiently infected cells not treated with the DNA synthesis inhibitor. However, when cells were arrested in the cell cycle by the DNA synthesis inhibitor treatment, the transduction efficiency was dropped markedly. In contrast, the CAEV- -

based vector was capable of efficiently transducing non-dividing human cells as well as dividing cells at a level comparable to that of the HIV-I -based vector.

EXAMPLE 8

In Vivo Transduction of Muscle Cells

In this example, the CAH/SINdl/hlacZ (SEQ ID NO: 79) CAEV vector is used to transduce muscle cells in vivo. The hind-legs of mice (Beige strain) are intramuscularly injected with 100 μl of the CAEV vectors in the presence of 4 μg/ml of polybrene. The mice are sacrificed two days later and the injected tissue is prepared for frozen section and for β-galactosidase analysis. The expected result is that CAH/SINdllacZ (SEQ ID NO: 79) CAEV vector transduces muscle cells efficiently in vivo.

The foregoing specification, including the specific embodiments and examples, is intended to be illustrative of the invention and is not to be taken as limiting. Numerous other variations and modifications can be effected without departing from the true spirit and scope of the invention. All publications, including sequences deposited in the NCBI database, patents and patent applications cited herein are incorporated by reference in their entirety into the disclosure.

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PileUp

MSF: 9300 Type: Ii I Check: 9398

Name: NC 001463 (SEQ ID NO: 1) Len: 9300 Check: 3957 Weight: 0 Name: AF322109 (SEQ ID NO: 2) Len: 9300 Check: 5441 Weight: 0

//

1 50

NC 001463 ....GAGTTC TAGG...AGA GTCCCTCCTA GTCTCTCCTC AF322109 GTGAGTGCTC TGAGGAGCTC GAAGGAAAGA GTCC.TC..A GCCTCTCCTC

51 100

NC 001463 TCCGAGGAGG TACCGAGACC TCAAAATAAA GGAGTGATTG CCTTACTGCC AF322109 TCCGAGGAGC TTCGG....C TCATAATAAA GGAGTGCTTG CTTCA..ACA

101 150

NC_001463 GAGTGGAGAG TGATTACTGA GCGGCCGGTG TATCGGGAGT CGTCCCTTAA AF322109 GAACTGAG CTGG TCGTGGTTAT TATCGGG... .GACCGAAGT

151 200

NC_001463 TCTGTGCAAT ACCAGAGCGG CTCTCGCAGC TGGCGCCCAA CGTGGGGCCC AF322109 CCCGTGCAAC ACCGGGGCGG TTCTCGCAGC TGGCGCCCAA CGTGGGGCTC

201 250

NC 001463 GAGGAG....

AF322109 GAGTAGCTTG AGAAGCTCGA CTGAGATCTG AATCCAAGAG CGACATCAGA

251 300

NC_001463 ....AAGAAA AGAAAGC... GGCCCTGAGA ACTCGGCTTC TG..AAAAAG AF322109 CAGCAAGAAA TGAGAGTAAT GAGACCGCGA GCTCTGCTGC TGTAAAAAAG

301 350

NC_001463 ^' AGGAAGAGGA CAAGTTGCTA TAGCAACAAG AGAGAAGAAG TAGAGCAAAG AF322109 AGGAAGTAG. CGGGTTGCCG AGGCAACTGC TCAGAAGAAC CAGGGGAAAG

351 400

NC 001463 GTCCAGTGGC T.CGGAAAAA GAGGAACTGA AACTTCGGGG ACGCCTGAAG AF322109 GGCTTCCAGC AACCTCAAAA GAGGAACCGA GACTTCGGGG ACGCCTGAA.

401 450

NC 001463 GAGTAAGGTA AGTGACTCTG CTGTACGCGG GGCGAGGCAG AGGTT.TCCT AF322109 ..GTAAGGTA AGTGACTCTG CTGTACGCGG GGCGAGGCAT AGGAGATCCT

451 500

NC_001463 TCTAAATT.G AAAGAGAAGT GTTGCTGCGA GAGGTCTTGG TGGTCGAGAA AF322109 TCTATTCTAG GAAGAGAAGC GCTGTTCTGG GAGGTCTTGG CGACCGAGAA

501 550

NC_001463 TCCTGTACAA AAAAAAGGAG GGATCTCGGT CAGGACCAGG ACCCCTGGGA AF322109 TCTTGTT... AAATAAGCCA GGATCTCGAT CAGGACCAAG ACCCCTCAGG

551 600

NC_001463 GTAATACAAC AGCAACACCG TAAGAAAATC CGCCATGGTG AGTCTAGATA AF322109 AGAGGGTATA GACAGCGTGG TAAGAAA.TC CGCCGTGGTG AGTCTAGATA

601 650

NC 001463 GAGACATGGC GAGGCAAGTC TCCGGGGGGA AAAGAGATTA TCCTGAGCTC AF322109 GAGACATGGT GAGGCAGGCC TCCGGAAGGG GAAAGGAGTA CCCCGAGCTA

651 700

NC_001463 GAAAAATGTA TCAAGCATGC ATGCAAGATA AAAGTTCGAC TCAGAGGGGA

AF322109 AAAGAATGTC TGAAAAAGGC ATGCAAAATA AAAGTAAGGG CTGGGGGGGA

701 750

NC 001463 GCACTTGACA GAAGGAAATT GTTTATGGTG CCTTAAAACA TTAGATTACA

AF322109 GCGCCTGACA GAAGGAAATT GTCTCTGGTG TATAAAAACA CTAGAGTGTA

751 800

NC_001463 TGTTTGAGGA CCATAAAGAG GAACCTTGGA CAAAAGTAAA ATTTAGGACA

AF322109 TGTATGAGGA TTGTAGGGAG GAACCTTGGA CCCCAGAAAA ATGTAAACAA

801 850

NC 001463 ATATGGCAGA AGGTGAAGAA TCTAACTCCT GAGGAGAGTA ACAAAAAAGA

AF322109 TTATGGAAAA AGTTGAAGCA GGTAGAGCCT GAGGAGAGTA GCAAAGCAGA

851 900

NC 001463 CTTTATGTCT TTGCAGGCCA CATTAGCGGG TCTAATGTGT TGCCAAATGG

AF322109 CTATAACTCG TTAAAAGCAA CCTTGGCGGG GATAGTCTGT GTGCAAATGG

901 950

NC 001463 GGATGAGACC TGAGACATTG CAAGATGCAA TGGCTACAGT AATCATGAAA

AF322109 GAATGCAGCC CGAGACACTG CAGGATGCGA TAGCAACCTT AAACATGAGA

951 1000

NC_001463 GATGGGTTAC TGGAACAAGA GGAAAAGAAG GAAGACAAAA GAGAAAAGGA

AF322109 GA TGAAGTAAAA GGAAAGGAA. .AAGCCATCA GAAGAAAAGA

1001 1050

NC_001463 AGAGAGTGTC TTCCCAATAG TAGTGCAAGC AGCAGGAGGG AGAAGCTGGA

AF322109 AGGGAATATA TCCC..ATAT TAGTGCAGGC AGGAGGAGGA AGAGCATGGA

1051 1100

NC_001463 AAGCAGTAGA TTCTGTAATG TTCCAGCAAC TGCAAACAGT AGCAATGCAG

AF322109 GAGCGGTAGA GCCTGCTACC TTTCAGCAGC TCCAAACAGT GGCAATGCAG

1101 1150

NC 001463 CATGGCCTCG TGTCTGAGGA CTTTGAAAGG CAGTTGGCAT ATTATGCTAC

AF322109 CATGGACTAG TATCAGAAGA ATTTGAAAGG CAGCTAGCAT ACTATGCCAC

1151 1200

NC_001463 TACCTGGACA AGTAAAGACA TACTAGAAGT ATTGGCCATG ATGCCTGGAA

AF322109 CACATGGACA AGCAAGGATA TCTTAGAAGT ATTAGCCATG ATGCCAGGAA

1201 1250

NC_001463 ATAGAGCTCA AAAGGAGTTA ATTCAAGGGA AATTAAATGA AGAAGCAGAA

AF322109 ATAGAGCGCA AAAAGAACTA ATACAAGGAA AGTTAAATGA GGAAGCAGAG

1251 1300

NC_001463 AGGTGGAGAA GGAATAATCC ACCACCTCCA GCAGGAGGAG GATTAACAGT

AF322109 AGATGGAGAA GGCAGAATCC ACAACCT GCGGGCG GGTTAACCGT

1301 1350

NC_001463 GGATCAAATT ATGGGGGTAG GACAAACAAA TCAAGCAGCA GCACAAGCTA

AF322109 GGATCAGATA ATGGGGGTAG GACAAACGAA TCAGGCAGCG GCACAGGCTA

1351 1400

NC 001463 ACATGGATCA GGCAAGGCAA ATATGCCTGC AATGGGTAAT AAATGCATTA AF322109 ATATGGATCA AGCAAGACAA ATATGCCTAC AATGGGTTAT AACAGCAATA

1401 1450

NC_001463 AGAGCAGTAA GACATATGGC GCACAGGCCA GGGAATCCAA TGCTAGTAAA

AF322109 AGAGGAGTTA GGCATATGGC CCATAGACCA GGAAATCCCA TGCTGGTAAG

1451 1500

NC 001463 GCAAAAAACG AATGAGCCAT ATGAAGATTT TGCAGCAAGA CTGCTAGAAG

AF322109 ACAAAAACCA AATGAGAACT ATGAAGAGTT TGCCGCAAGG TTGTTAGAAG

1501 1550

NC_001463 CAATAGATGC AGAGCCAGTT ACACAGCCTA TAAAAGATTA TCTAAAGCTA

AF322109 CAGTGGATGC AGAACCCGTT ACCCAACCTA TAAAAGAATA TTTAAAGGTA

1551 1600

NC_001463 ACACTATCTT ATACAAATGC ATCAGCAGAT TGTCAGAAGC AAATGGATAG

AF322109 ACTCTGTCTT ACACAAATGC AAATTCGGAA TGTCAAAAAC ATATGGACAG

1601 1650

NC_001463 AACACTAGGA CAAAGAGTAC AACAAGCTAG TGTAGAAGAA AAAATGCAAG

AF322109 AGTGTTGGGG CAAAGAGTAC AGCAGGCCTC AATAGAAGAA AAAATGCAGG

1651 1700

NC_001463 CATGTAGAGA TGTGGGATCA GAAGGGTTCA AAATGCAATT GTTAGCACAA

AF322109 CATGCAGGGA CATCGGGGGA ACAGCATATC AGATGCAGTT GCTTGCACAA

1701 1750

NC_001463 GCATTAAGGC CAGGAAAAGG AAAAGGGAAT GGACAGCCAC AAAGGTGTTA

AF322109 GCCCTCCGTG GCGGAAAAGA AGATGGGAAA AAATCTGTAG GGAAGTGTTA

1751 1800

NC_001463 CAACTGTGGA AAACCGGGAC ATCAAGCAAG GCAATGTAGA CAAGGAATCA

AF322109 TAACTGTGGA AGGCCCGGAC ACAGAGCAAA AGAATGCAGA CAAGGCATTA

1801 1850

NC_001463 TATGTCACAA CTGTGGAAAG AGAGGACATA TGCAAAAAGA ATGCAGAGGA

AF322109 TATGTCACAA CTGTGGAAAA AGAGGGCATA TACAGAAAAA CTGCA....A

1851 1900

NC_001463 AAGAGAGACA TAAGGGGAAA ACAGCAGGGA AACGGGAGGA GGGGGATACG

AF322109 ACAGAA... .AAGAAGAAA GGAGCAGGGA AACATGAGGA GGGGGCTACG

1901 1950

NC 001463 TGTGGTGCCG TCCGCTCCTC CTATGGAATA ACTTCAGCAC CACCTATGGT

AF322109 TGTGGTGCCG TCCGCACCCC CTATGGAGTA ACGCAAGCAC CACTAATAGT

1951 2000

NC 001463 TCAGGTCCGC ATAGGTTCCC AGCAGAGGAA CTTGTTATTT GATACCGGGG

AF322109 TAGGGTACAA ATAGGGAATC AGGAGAAACA ATTATTATTT GACACAGGGG

2001 2050

NC_001463 CGGACCGAAC TATAGTTAGA TGGCATGAGG GCTCGGGAAA CCCAGCCGGA

AF322109 CAGATAAAAC GATAGTAAGA ATGCATGATG GAACAGGGAT TCCAAACGGA

2051 2100

NC_001463 AGGATAAAAC TGCAAGGAAT AGGAGGAATA GTAGAAGGAG AAAAATGGAA

AF322109 AGAATAAAAT TACAAGGGAT AGGAGGAATA GTAGAAGGAG AAAAATGGAA

2101 2150

NC 001463 TAATGTAGAA TTAGAATATA AAGGAGAAAC AAGAAAGGGA ACAATAGTAG AF322109 TAAAGTACCC ATGACATATA AGGGAGAAAC ATCCTGCCCA AGCTTGGTTG

2151 2200

NC 001463 TGTTACCACA AAGTCCAGTA GAAGTATTAG GACGAGATAA CATGGCCCGA

AF322109 TGCTAAGAGA TAGCCCAGTA GAAGTATTGG GAAGAGATAA CATGGAAGCA

2201 2250

NC 001463 TTTGGAATAA AGATAATAAT GGCAAATTTA GAGGAAAAAA GAATCCCAAT

AF322109 TTCGGCGTAA CCCTAATAAT GGCAAATTTA GAAGATAAGA AAATTCCCAC

2251 2300

NC_001463 TACAAAAGTA AAATTGAAAG AGGGATGTAC GGGTCCACAT GTCCCACAAT

AF322109 AATACCAGTA GAATTGAAAG AAGGATGTAA AGGGCCACAT GTGCCCCAGT

2301 2350

NC_001463 GGCCATTAAC AGAAGAGAAA TTAAAAGGTC TAACAGAAAT CATAGATAAA

AF322109 GGCCATTAAC AGCAGAGAAA TTACAAGGAC TAACAGGAAT AGTAGAAAAA

2351 2400

NC_001463 TTAGTGGAAG AAGGAAAACT AGGAAAGGCA CCCCCACATT GGACATGTAA

AF322109 TTACTACAGG AAGGAAAATT GGCAGAGGCC CCAGAGGGAT GGACGTGGAA

2401 2450

NC_001463 TACTCCAATC TTTTGCATAA AAAAGAAATC AGGGAAGTGG AGAATGTTAA

AF322109 CACGCCCATC TTCTGCATAA AAAAGAAGTC AGGAAAATGG AGAATGTTAA

2451 2500

NC 001463 TAGATTTCAG AGAATTGAAC AAACAGACAG AAGATTTAAC AGAAGCGCAG

AF322109 TAGATTTTAG GGAATTAAAT AAGCAAACAG CAGATTTAGC AGAAGCGCAG

2501 2550

NC_001463 TTAGGACTCC CGCATCCGGG AGGACTACAA AAGAAAAAAC ATGTTACAAT

AF322109 CTAGGACTGC CACACCCAGG AGGGTTGCAA AGGAAAAAGA ATGTAACAAT

2551 2600

NC_001463 ATTGGACATA GGAGATGCAT ATTTTACTAT ACCCCTATAT GAACCATATC

AF322109 TCTGGACATA GGAGATGCAT ATTTCACAAT TCCCTTATAC GAGCCCTATC

2601 2650

NC 001463 GAGAGTACAC ATGTTTTACT CTATTAAGTC CTAATAATCT AGGACCATGT

AF322109 AGAAATATAC ATGCTTCACA CTCCTAAGTC CTAACAATTT GGGACCATGT

2651 2700

NC_001463 AAAAGATACT ATTGGAAAGT GCTGCCACAA GGTTGGAAAT TGAGTCCATC

AF322109 AAAAGGTATT ATTGGAAAGT ATTACCCCAG GGATGGAAAT TGAGCCCAGC

2701 2750

NC 001463 TGTATATCAA TTTACTATGC AGGAGATCTT AGAGGATTGG ATACAGCAGC

AF322109 TGTATATCAA TTCACCATGC AAAGGTTGTT AAAAGGATGG ATACAACAGC

2751 2800

NC_001463 ATCCAGAAAT TCAATTTGGC ATATATATGG ATGATATTTA CATAGGAAGT

AF322109 ATAAAAACAT ACAATTTGGA ATATATATGG ATGATATCTA TATTGGAAGT

2801 2850

NC_001463 GATTTAGAAA TTAAAAAGCA TAGAGAAATA GTGAAAGATT TAGCCAATTA

AF322109 GATCTAACGA TAGCCCAACA TAGGAAGATA ATAGAAGAAT TAGCCTCATT

2851 2900

NC 001463 TATTGCCCAA TATGGATTCA CTCTGCCAGA AGAGAAGAGA CAAAAGGGAT AF322109 TATAGAACAA TTTGGGTTTA CATTACCAGA AGATAAGAGA CAAGAGGGCT

2901 2950

NC_001463 ATCCAGCAAA ATGGCTAGGA TTTGAACTAC ACCCGCAGAC CTGGAAATTT

AF322109 ATCCAGCAAA ATGGCTAGGA TTCGAGCTAC ATCCAGAAAA ATGGAAATAT

2951 3000

NC_001463 CAGAAGCATA CATTACCTGA ATTAACAAAG GGAACAATAA CATTAAATAA

AF322109 CAAAAGCATA AATTGCCGGA ATTACAAGAG GGGGTAATAA CCCTGAACAA

3001 3050

NC_001463 ATTACAGAAA TTAGTAGGAG AATTAGTATG GAGACAATCC ATAATTGGGA

AF322109 ATTACAGAAG ATAGTAGGGG AATTAGTGTG GAGACAATCC TTGATAGGAA

3051 3100

NC 001463 AAAGCATTCC TAACATTCTG AAATTAATGG AAGGAGATAG AGAATTACAA

AF322109 AGAGCATCCC CAATATCATA AAATTAATGG AAGGAGATCG CGCATTACAA

3101 3150

NC_001463 AGTGAAAGAA AAATTGAAGA AGTACATGTG AAAGAATGGG AAGCATGTAG

AF322109 AGTGAAAGGA AAATAGAAAG AATACATGTA CAAGAATGGG AAGCATGTCA

3151 3200

NC 001463 GAAAAAATTA GAAGAAATGG AAGGAAATTA TTATAATAAA GACAAAGATG

AF322109 AAAGAAATTA GATGAAATGG TAGGAAATTA TTACAGAGAA GAAGAAGATA

3201 3250

NC_001463 TCTATGGACA ATTGGCTTGG GGAGACAAAG CTATAGAATA TATAGTGTAT

AF322109 TCTATGGACA AATAACTTGG GGGGATAAGG CAATAAAATA CATAGTATTC

3251 3300

NC 001463 CAGGAGAAAG GGAAACCATT ATGGGTAAAT GTGGTTCACA ATATAAAGAA

AF322109 CAAAGGAAAG GGGAACCCCT ATGGGTAAAT GTAGTACATG ACATAAAAAA

3301 3350

NC_001463 CCTAAGCATC CCGCAACAGG TTATTAAAGC AGCGCAAAAA TTAACCCAAG

AF322109 TTTGAGTCTC CCACAGCAAG TGATAAAAGC AGCACAGAAA TTAACCCAGG

3351 3400

NC_001463 AAGTCATCAT TAGGACAGGA AAAATACCAT GGATATTGTT GCCAGGGAAA

AF322109 AAGTAATCAT AAGAACAGGA AAAATCCCAT GGCTGCTACT ACCAGGAAGA

3401 3450

NC_001463 GAAGAAGATT GGAGACTAGA ATTGCAATTA GGGAACATCA CATGGATGCC

AF322109 GAAGAAGACT GGAGATTAGA ACTGCAGGTA GGGAACATCA CGTGGATGCC

3451 3500

NC 001463 AAAATTTTGG TCCTGTTATC GAGGA.CATA CAAGATGGAG AAAAAGAAAT

AF322109 ATCATTTTGG TCATGTTATC GAGGAGCACC CAAG.TGGAA AAGAAGGAAC

3501 3550

NC_001463 ATAATAGAAG AAGTAGTAGA AGGGCCTACA TATTATACAG ATGGAGGAAA

AF322109 ATAGTGGCAG CAGTGGTAGA TGGACCGACA TATTATACAG ATGGGGGAAA

3551 3600

NC_001463 AAAGAATAAA GTAGGAAGTC TAGGGTTCAT AGTATCAACA GGGGAAAAAT

AF322109 GAAAAACGCA CAGGGAAGCT TTGGCTTCAT CTCCCCAACA GGAGAAAAGT

3601 3650

NC 001463 TTAGAAAGCA TGAAGAGGGC ACAAACCAGC AACTAGAATT AAGAGCCATA AF322109 TCAGAAGGCA TGAAGATGGA ACTAATCAGG TATTAGAATT AAGGGCAATA

3651 3700

NC_001463 GAGGAAGCTC TAAAACAAGG GCCTCAAACA ATGAATTTAG TAACAGATAG

AF322109 GAAGATCCAT GTAAACAAGG ACCTGAAAGC ATGAACATTG TAACTGACAG

3701 3750

NC_001463 TAGATATGCA TTTGAATTTT TATTAAGAAA TTGGGATGAA GAAGTAATAA

AF322109 CAGGTATGCT TATGAATTCA TGCTCCGAAA CTGGGATGAA CAGGTCATAA

3751 3800

NC_001463 AGAATCCAAT TCAAGCAAGA ATTATGGAAA TTGCCCACAA GAAAGATAGG

AF322109 GAAACCCCAT TCAGGCAAGA ATCATGGCAG AAGTGCACAA GAAAAAGCAG

3801 3850

NC_001463 ATAGGAGTGC ATTGGGTGCC AGGACATAAA GGGATTCCCC AAAATGAAGA

AF322109 GTAGGAATAC ACTGGGTGCC AGGGCATAAA GGAATACCTC AGAATGAAGA

3851 3900

NC_001463 AATAGACAAA TATATTTCGG AAATATTTCT TGCAAAAGAA GGAGAAGGAA

AF322109 GATAGACCAG TACATATCAG AAGTATTCTT AGCACGAGAA GGAACAGGGA

3901 3950

NC_001463 TTCTCCCAAA AAGAGAAGAG GATGCAGGGT ATGATTTAAT ATGCCCAGAA

AF322109 TATGTGAAAA AAGGAAGGAA GATGCTGGAT ATGATTTATT ATGCCCGCAT

3951 4000

NC_001463 GAGGTTACCA TAGAGCCAGG ACAAGTGAAA TGCATCCCCA TAGAGCTAAG

AF322109 GAGGTAATAC TTAAACCCCA AGAAGTAAAA CGGATCCCAA TAGACCTAAA

4001 4050

NC 001463 ATTAAATTTA AAGAAATCAC AATGGGCTAT GATTGCTACA AAAAGCAGCA

AF322109 ATTAAAATTG AAAGAAAAGC AATGGGCCAT GATAAGTGGG AAAAGTAGCG

4051 4100

NC_001463 TGGCTGCCAA AGGAGTGTTC ACACAAGGAG GAATCATAGA CTCAGGATAT

AF322109 TTGCAGCAAA AGGAATATTT GTACAAGGAG GCATAATAGA TTCAGGGTAT

4101 4150

NC_001463 CAGGGACAAA TACAGGTAAT AATGTATAAT AGCAATAAAA TAGCAGTAGT

AF322109 CAGGGACAAG TACAAGTCAT CCTATATAAT AGTAATAAGA TAGAGGTCAA

4151 4200

NC_001463 CATACCCCAA GGGAGAAAAT TTGCACAATT AATATTAATG GATAAAAAGC

AF322109 AATACCACAA GGCAGGAAAT TTGCCCAATT AATATTAATG AACTTACAAC

4201 4250

NC_001463 ATGGAAAATT GGAACCCTGG GGGGAAAGCA GAAAAACAGA AAGGGGAGAA

AF322109 ATGAAGAATT AGAAGAATGG GGAAAGGAAA GAAAAACAGA AAGAGGAACA

4251 4300

NC_001463 AAAGGATTTG GGTCTACAGG AATGTATTGG ATAGAAAATA TTCCTCTGGC

AF322109 ' AAAGGATTTG GGTCTACAGG AGCATTTTGG ATAGAGAATA TTCCCCAAGC

4301 4350

NC_001463 AGAGGAAGAC CACACAAAAT GGCATCAAGA TGCCCGATCA TTGCATCTAG

AF322109 AGAGGAAGAA CATTACAAAT GGCATCAAGA TGCTAGATCT CTGCAGCTAG

4351 4400

NC 001463 AATTTGAAAT TCCAAGAACA GCAGCAGAAG ACATAGTAAA TCAATGTGAA AF322109 AATTCAAGAT ACCTAGAGCA GCAGCAGAAG ACATTATACA GCACTGTGAG

4401 4450

NC 001463 ATATGCAAAG AAGCGAGGAC ACCTGCAGTA ATTAGAGGCG GAAACAAAAG

AF322109 GTATGTCAAG AAGGCAAACC CGCAGCGATC ACGAGAGGGG GAAATAAAAG

4451 4500

NC 001463 GGGGGTAAAT CATTGGCAAG TGGATTATAC CCATTATGAA AATATCATAC

AF322109 AGGAATAGAT CATTGGCAGG TAGACTATAC ACATTACAAA GAACACATAA

4501 4550

NC_001463 TATTAGTATG GGTAGAAACA AATTCAGGAC TAATATATGC AGAAAAAGTA

AF322109 TATTAGTATG GGTAGAGACT AATTCAGGAT TAATATTTGC AGAGAAAGTA

4551 4600

NC_001463 AAAGGAGAAT CAGGGCAAGA ATTCAGAATA AAAGTGATGC ATTGGTATGC

AF322109 AAAGGAGAAT CAGGACAAGA ATTTAGGATG CAGACATTGA AATGGTATGC

4601 4650

NC_001463 ATTATTTGGT CCAGAGTCAT TGCAGTCAGA CAATGGACCT GCATTTGCAG

AF322109 TTTGTTTCAA CCAAAATCAG TGCAATCAGA TAATGGGACA GCCTTCACAG

4651 4700

NC_001463 CAGAGCCCAC ACAGCTGTTA ATGCAATACC TAGGAGTAAA ACACACAACA

AF322109 CTGAGGCTAC GCAGCATCTA ATGAAGTATT TAGGGATTCA GCACACTACG

4701 4750

NC 001463 GGCATACCTT GGAATCCACA GTCTCAGGCT ATAGTAGAAA GGGCACATCA

AF322109 GGTATTCCGT GGAACCCCCA GTCACAAAGT TTAGTAGAAA GAGCTCATCA

4751 4800

NC 001463 ACTATTGAAA AGCACTTTAA AGAAGTTCCA GCCACAATTT GTCGCTGTAG

AF322109 AACATTAAAA CACATGTTAG AAAAATTAGA ACCACAATTT GTGGCCCTAC

4801 4850

NC_001463 AATCAGCCAT AGCAGCAGCC CTAGTCGCCA TAAATATAAA AAGAAAGGGT

AF322109 AGTCTGCCAT CGCAGCCACT CTAGTTGCGC TCAATATAAA AAGAAAGGGT

4851 4900

NC_001463 GGGCTGGGGA CAAGCCCTAT GGATATTTTT ATATATAATA AAGAACAGAA

AF322109 GGACTAGGGG CAAGCCCTAT GGATATTTAC ATATATAATA AGGAGCAACA

4901 4950

NC 001463 AAGAATAAAT AATAAATATA ATAAAAATTC TCAAAAAATT CAATTCTGTT

AF322109 AAGACAACAA GATAATAGTA ATAAATTAAT TCAGAAAA.. .AATTTTGTT

4951 5000

NC_001463 ATTACAGAAT AAGGAAAAGA GGACATC.AG GAGAGTGGAA AGGACCAACC

AF322109 ATTACAGGAT CAGAAAAAGA GGCCATCCAG GAGAGTGGAA CGGCCCAACT

5001 5050

NC 001463 CAGGTACTGT GGAAAGGGGA AGGAGCCAAT TGTGGTAAAG GATATAGAAA

AF322109 GAGGTACTGT GGGAAGGGGA AGGAGCCA.T AGTAGTTAAA GACAAAGAAA

5051 5100

NC_001463 GTGAAAAGTA TTTAGTAATA CCTTACAAAG ATGCAAAATT CATCCCGCCA

AF322109 GTGATAGATA TCTAGTCATC CCATATAAAG ATGCAAAATT TATTCCGCCA

5101 5150

NC 001463 CCAACAAAAG AAAAGGAATA AAAAACCTGG ACCAGAATTA CCCTTAGCAC AF322109 CCGTCGGAAC AGAAGGGATA GAAGAATAGG TCCAGAATTG CCTTTATCTT

5151 5200

NC_001463 TATGGATACA TATAGCAGAA AGCATTAATG GGGATAGCTC ATGGTACATA

AF322109 TATGGACTTA TACAGCATAC AGCATAAATA AAGATCCCGC ATGGTATACA

5201 5250

NC 001463 ACAATGAGAC TGCAACAGAT GATGTGGGGA AAAAGAGGAA ATAAGTTACA

AF322109 ACCCTAAGAC TGCAGCAAAT GATGTGGCAT AGGAGGGGAA ATAAATTGAC

5251 5300

NC_001463 ATATAAGAAT GAAGACAGGG AATATGAAAA TTGGGAAATT ACATCATGGG

AF322109 ATATGTCAGG GAAAATGCAC AGTACGAGGA GTGGGAAATG ACCTCGTATG

5301 5350

NC_001463 GATGGAAAAT GCACCTAAGG AGAGTGAAAC AATGGATACA AGACAACAGG

AF322109 AGTGGAGGAT AAGAATGAGA AGGGACAAAA CAAAAAGTCA TC.CAAGAGG

5351 5400

NC 001463 AGAGGAAGC. CCATGGCAGT ACAAAGTAGG AGGAACATGG AAAAGTATAG

AF322109 GCATACTTCG CCATGGCAAT ATCGGAGACA GGATGGATGG AAGGATGTGG

5401 5450

NC_001463 GAGTGTGGTT CCTGCAAGCA GGAGATTACA GAAAGGTAGA CAGGCACTTC

AF322109 GAACGTGGTT CCTACAGCCA GGGGACTATA GAAAGGCGGA TCAGCAGTTC

5451 5500

NC_001463 TGGTGGGCAT GGAGGATACT GATATGTTCC TGCAGGAAAG AAAAGTTTGA

AF322109 TGGTTCGCTT GGAGAATAGT GTCGTGTTCA TGTAAAAAGG AAGGATTTAA

5501 5550

NC_001463 TATAAGAGAA TTTATGAGAG GAAGACATAG ATGGGATTTG TGCAAATCCT

AF322109 CATAAGAGAA TTTATGCTAG GTACCCATAG ATGGGATTTG TGTAAGTCGT

5551 5600

NC_001463 GTGCTCAAGG AGAAGTAGTA AAGCATACTA GAACAAAAAG TCTGGAAAGA

AF322109 GTTGCCAGGG TGAAGTAGTA AAGAGAACAC AACCCTACAC CTTGCAAAGG

5601 5650

NC_001463 CTAGTACTGC TACAGATGGT AGAACAGCAT GTGTTTCAAG TATTGCCATT

AF322109 CTCACGTGGC TTAAATTAAC AGAAGACCAT GTATTTCAAG TAATGCCCTT

5651 5700

NC_001463 GTGGAGAGCC AGGAGAAGTA GTACAACAGA TTTCCCATGG TGCAGGGACA

AF322109 GTGGAGAGCT CGCAAAGGGA TTACCATAGA CTTTCCCTGG TGCAGGGACA

5701 5750

NC_001463 CAACGGGATA CACGCATGCG TGGTCTGTCC AGGAGTGCTG GTTGATGGAA

AF322109 CAAAAGGATT CCTGGAGCCG TGGACAACGC AAGAGTGTTG GCAAATAGAG

5751 5800

NC_001463 TATCTCTTAG AGGATGAGTG AAGAACTGCC TCAAAGAAGG GAGACACATC

AF322109 TATCCCTTGG AGGATGAGTG AGGAAACCCC AGCAGGAAGA GAACCGACTG

5801 5850

NC 001463 CAGAAGAACT .TGTAAGGAA CGTACGGGAA AGAGAAAGGG ATACATGGCA

AF322109 CAGAGGAAAT ATTTGAGCAA GAA GCAGAAAGT. TGGAA

5851 5900

NC 001463 ATGGACAAGC ATCAGAGTAC CTGCGGAAAT ACTGCAAAGA TGGCTTGCTA AF322109 GAGAACAAGC GTGCGAGTCC CAAATGACAT ATTACAAAGA TGGCTAGCAA

5901 5950

NC_001463 TGCTTAGGTC AGGCAGAAAT AGAAAGAAAG TGTATAGAGA AATGCAAAAA

AF322109 TGCTTAGGCA AAGAGGAAAT AGAAAGAAAG TGCTTAGGGA AATGCAAAAA

5951 6000

NC_001463 TGGATGTGGA TACATCCCAA GGCGCCTGTG ATTAGGGCCT GTGGATGCAG

AF322109 TGGGCATGGA GGAATCCCAC GGCGCGGGTG ATTCGGCCGT GTGGATGTCG

6001 6050

NC_001463 ACTATGTAAC CCGGGGTGGG GAACATAATC AAGGGAATAA TAAATGCAAA

AF322109 GCTATGTAAC CCCGGCTGGG GGAG.TAATT AAT..CATAA TAAA.GCAAA

6051 6100

NC_001463 TAAATGTAAC TAACAAGTAG CAAAAGTGTC TGTGTTAGAT GGATGCTGGG

AF322109 T...TGTAAC ATGCTGTG

6101 6150

NC_001463 GCCAGATACA TGCGCTTAAC TGGGAAGGAA AACTGGGTTG AAGTAACCAT

AF322109 TC A GG TGTCTTG CAGGAA...T

6151 6200

NC_001463 GGACGGAGAG AAGGAAAGGA AAAGAGAAGG TTTCACTGCG GGACAGCAAG

AF322109 GG.CGGAGAT AAGAAAAG.. AA.GCAAAGG AGCCACT AATCCAGG

6201 6250

NC_001463 GTAAGTATCA ACCCCAGGTA AGTAAGCAAA TAGGGAACAG AAATACTAAC

AF322109 GTAAGTATAA AAAACAGGTA AGTA G AA....TAAC

6251 6300

NC_001463 CCATGCTTTG CCTATAAAGG GATATTCCTA TGGAGGATAT CACTAACAAT

AF322109 TATAGT TATATT A CTAACAGT

6301 6350

NC_001463 GTGGATATTG CTAGGGATAA ATATGTGTGT CAGTGCAGAG GATTACATAA

AF322109 AAGAGCAGCA CTAGG A GCAGAA ...TACATAA

6351 6400

NC_001463 CACTAATATC AGATCCCTAT GGGTTCTCAC CCATAAAAAA TGTGTCTGGG

AF322109 CCATAATATC AGACCCATAT GGGTTCTCTC CCGTGAGAAA TGTGTCAGGA

6401 6450

NC_001463 GTACCAGTGA CTTGTGTAAC AAAAGAATTC GCAAAATGGG GATGTCAACC

AF322109 GTACCTGTAA CTTGTGTGAC AAAAGAATTT AGTAAGTGGG GATGTCAGCC

6451 6500

N£_001463 ACTAGGAGCG TACCCTGATC CAGAAATAGA ATACAGAAAT GTGAGTCAGG

AF322109 AATAGGAGCC TACCCAGACC CAGACTTAGA ATACAGAAAT ATAAGTAAAG

6501 6550

NC_001463 AAGTAGTGAA AGAAGTATAT CAAGAGAATT GGCCATGGAA TACATATCAT

AF322109 AAATATTAGA GGAAGTATAT CAACAAGACT GGCCGTGGAA TACTTATCAT

6551 6600

NC_001463 TGGCCTCTCT GGCAAATGGA GAATGTTAGG TACTGGTTAA AAGAAAATAT

AF322109 TGGCCATTAT GGCAAATGGA TAATGTAGTA CAATGGGCAA GGCAAAATTT

6601 6650

NC 001463 GCAAGAAAAT CAACAGAGAA AAAATAATAC AAAAGAGGGT ATAGAGGAAT AF322109 ACAGGATAAC CGCAAG.GAA AAAAG GGAC CTGGCAGACC

6651 6700

NC 001463 TATTAGCAGG AACTATAAGG GGAAGATTCT GTGTACCATA CCCATTTGCC

AF322109 TATTAGCAGG AAAAATAAGG GGAAGATTCT GTGTACCCTA CCCATTTGCG

6701 6750

NC_001463 TTGTTAAAAT GCACAAAGTG GTGCTGGTAT ACAGCGGCCA TAAA..CAAC

AF322109 CTCCTGGAGT GCATGGAATG GTGCTGGTGG GTTAAGAACA CTAATGCAGG

6751 6800

NC_001463 GAGTCA.GGA AAAGCAGGAA AAATAAAAAT AAATTGCACA GAAGCAAGAG

AF322109 GGGGTATGGA GAAGCAG..A .CATAAGAAT AAATTGCTCA AGGGCAAGAG

6801 6850

NC_001463 CAGTCTCCTG TACAGAGGAC ATGCCATTAG CCTCAATACA AAGAGCATAT

AF322109 CAGTGAGCTG CACAAGTGAA ATGCCCTTAG CATCCCTACA GAGGGTATAT

6851 6900

NC_001463 TGGGATGAGA AAGACAGAGA GAGCATGGCC TTTATGAATA TCAAAGCATG

AF322109 TGGGAAAAGG AGGAACGAAA AAACATGGAG AAAATGACCA TCAAACCTTG

6901 6950

NC 001463 TGATAGCAAC CTAAGGTGTC AGAAAAGACC TGGAGGGTGT ATGGAAGGAT

AF322109 CAATAAAAAT TTGGAATGCA AGAACAGAA. .G.GGGATGC GCAGAAGGGT

6951 7000

NC 001463 ACCCTATCCC AGTAGGAGCA GAAATAATCC CTGAAAGTAT GAAATACCTA

AF322109 ATCCAGTACC TCCCAAGGCA GAGTTATTCC CTCCAGCGTT TCAGGATTTA

7001 7050

NC_001463 AGGGGAGCAA AGAGTCAG.. TATGGGGGAA TAAAAGATAA GAATGGAGAA

AF322109 CAGCCA..AA AGGGTACGCA TATGGGGCAC TTAGAG...G GAACAGCAAA

7051 7100

NC_001463 TTAAAATTAC CATTAACATT AAGAGTGTGG GTAAAATTAG CAAATGTGTC

AF322109 TTTCCACAAA GAGTGTCGCT AAGAACATGG GTGAAAATAG CTAACCTGAC

7101 7150

NC_001463 AGAATGGGTA AATGGGACAC CCCCGGATTG GCAAGACAGA ATTAACGGAT

AF322109 AGGATGGGAA AAAGGAAAGC CAGCAGAATG GT GG AATACCAG..

7151 7200

NC_001463 CCAAAGGAAT AAATGGGACG CTCTGGGGAG AGCTTAACAG TATGCATCAC

AF322109 CCAACAGGTT CATTGGTTTG ATACCACGCC ACAATATCAT TTAGGAT...

7201 7250

NC_001463 CTAGGATTTG CCCTTAGCCA GAACGGCAAA TGGTGTAACT ACACCGGGGA

AF322109 .ATGTATTAT CCCGAGCGCC TGAGAACAGG AGTTGTAATT TCACAGGGGA

7251 7300

NC_001463 AATAAAATTA GGGCAAGAAA CATTCCAATA TCATTACAAG CCAAACTGGA

AF322109 AATACGAATA GGGCAACATC AGTTTGAGTA TAATTACACC CTGACAAAGA

7301 7350

NC 001463 ACTGTACC.. .GGGAATTGG ACGCAATATC CGGTGTGGCA AGTGATTAGA

AF322109 ATTGCACAAA GGAGAAGTGG AAAGAGTACC CCATGTGGCA TGTCTGGAGG

7351 7400

NC 001463 AACCTGGATA TGGTGGAACA TATGACAGGA GAATGTGTGC AGAGACCACA AF322109 CATTTAGATC AAAATGAGCA CTTATCTAGC ATATGTTTCA AAAGACCGAG

7401 7450

NC 001463 AAGGCACAAT ATAACAGTAG GAAATGGAAC CATAACAGGG AATTGCAGTA

AF322109 AAGAAATGCA ACACAAATAG GGAACAGTAC ACTGCAAGGG CAATGTAATA

7451 7500

NC 001463 CAACAAACTG GGATGGATGT AATTGCTCAC GATCAGGAAA CTACCTATAT

AF322109 GAAGTAATTG GACAGGATGC CACTGCAATG AGACAGGGAT AAAC..AC..

7501 7550

NC_001463 AACAGCTCTG AGGGAGGATT GTTATTAATT CTGTGCAGAC AAAACAGCAC

AF322109 AACA TGGAGAA TAAATGGCAC

7551 7600

NC_001463 CCTAACAAGG ATCCTGGGAA CAAATACAAA TTGGACAACT ATGTGGGGAA

AF322109 ....AAAGGG AGC.TT..AT CTCTTA..AA TAGCACTAAT GGAAA

7601 7650

NC_001463 TATACAAAAA TTGTTCAGGA TGCGAGAATG CAACATTAGA CAACACAGGA

AF322109 CATCATGGTC TTGTT....A TGCTGGAACA CAACAGTGG. CAGGG

7651 7700

NC_001463 GAAGGAACCT TAGGAGGTGT AGCTAATAAG AACTGTAGCT TGCCTCATAA

AF322109 GTA TATGAGAGTC AGCTAA.... A.GTGGAATG AGAGTCTTAA

7701 7750

NC_001463 AAATGAGAGC AACAAGTGGA CTTGTGCCCC AAGACAAAGA .GATGGAAAAA

AF322109 AGACGGAGAC TATGGGCTCT GTTTTAATTC AACAAACAGG AATTGTACTA

7751 7800

NC 001463 CAGATTC.GC TATACATAGC AGGAGGAAAA AAGTTTTGGA CACGAATTAA

AF322109 GAAATGGAGC TCGGCACTAT GTAAACAAGA GAGTGATAAA AAACGAC.AC

7801 7850

NC_001463 GGCCCAATTC AGCTGTGAAA GTAACATAGG ACAATTAGAT GGAATGTTGC

AF322109 AGCAGATCAT AATTGTGATA GCAGCATATC AGCAATAGAT GGAATGGTAC

7851 7900

NC_001463 ATCAGCAAAT ACTATTGCAA AAATATCAAG TAATTAAGGT AAGAGCTTAT

AF322109 ATCAACAAAT ATTACTGCAA AGGTATCAAG TAATTAGAGT AAGAGCTTAC

7901 7950

NC_001463 ACATATGGGG TGATAGAAAT GCCAGAAAAC TATGCAAAAA CAAGAATCAT

AF322109 ACATACGGAG TGATTGATAT GCCAGACAAT TATG.AGACC CTACCAGGA.

7951 8000

NC_001463 AAACAGGAAA AAAAGAGAAC TCAGCCACAA GAGGAAGAAG AGAGGCGTTG

AF322109 ....AGGAGA AGGAGAGATC TCGCAAAGGC CAGGAAAAAG AGGGGCGTGG

8001 8050

NC_001463 GCTTGGTCAT TATGCTAGTT ATCATGGCAA TAGTAGCTGC CGCAGGGGCT

AF322109 GCCTGGTCAT CATGTTAGCT ATCATGGCCA TAGTGGCTGC TGCAGGAGCA

8051 8100

NC_001463 TCTCTGGGAG TCGCAAACGC GATTCAGCAG TCTTACACTA AGGCAGCTGT

AF322109 TCTCTGGGAG TCGCGAACGC GATTCAGCAG TCCTACACCA GGGACGCTGT

8101 8150

NC 001463 CCAGACCCTT GCTAATGCAA CTGCTGCACA GCAGGATGTG TTAGAGGCAA AF322109 CCAGACTCTT GCTAACGCGA CTGCTGTGCA ACAGCAGGTG TTAGAGGCGT

8151 8200

NC_001463 CCTATGCCAT GGTACAGCAT GTGGCTAAAG GCGTACGAAT CTTGGAAGCT

AF322109 CCTATGCCAT GATACAGCAT GTGGCTAAGG GAATACGCAT CCTTGAAGCA

8201 8250

NC 001463 CGAGTGGCTC GAGTGGAAGC TATCACAGAT AGAATAATGC TATACCAAGA

AF322109 CGCGTGGCGA GAATGGAAGT TATGATGGAT AGAATGATGT TATATCAGGA

8251 8300

NC_001463 ATTGGATTGT TGGCACTATC ATCAATACTG TATAACCTCT ACAAAAACAG

AF322109 AGTAGACTGC TGGCATTATC ACCAATATTG TGTAACCTCT ACAAGAGCAG

8301 8350

NC_001463 AAGTAGCAAA ATATATCAAT TGGACGAGGT TTAAGGATAA TTGCACATGG

AF322109 ACATAGTGAA TTACATTAAT TGGACAAGGT TTAAAGATAA TTGCACATGG

8351 8400

NC_001463 CAGCAGTGGG AGAGAGGATT ACAGGGGTAT GATACAAACT TAACAATACT

AF322109 CAAGAGTGGG AAAGGGAGAT AAGTGCGCAT GAAGGAAACA TCACTATATT

8401 8450

NC_001463 GTTAAAGGAA TCAGCAGCAA TGACACAACT AGCAGAAGAG CAAGCAAGGA

AF322109 ACTCAAAGAA TCAGCAAGGA TAACACAATT AGCACAACAA AAGGTACAAA

8451 8500

NC_001463 GGATACCAGA AGTATGGGAA AGTTTAAAAG ACGTCTTTGA TTGGTCAGGA

AF322109 GAATACCAGA TGTGTGGACA GCACTAAGGG AGTCACTAGG ATGGACACAA

8501 8550

NC_001463 TGGTTCTCAT GGCTAAAGTA TATTCCTATT ATAGTAGTAG GATTATTAGG

AF322109 TGGCTGGCTT GGATAAAATA CCTTCCCATA ATAGTAGTAG GGATATTAGG

8551 8600

NC 001463 ATGCATTCTG ATAAGAGCTG TGATATGTGT ATGTCAACCT CTTGTGCAGA

AF322109 ATGCATAATC ATAAGAATAA TGTTGTGTGT AGTACAACCA GTTCTTCAGA

8601 8650

NC_001463 TATACAGAAC TCTAAGTACC CCGACATACC AACGGGTCAC AGTCATCATG

AF322109 TTTACAGAAC CTTGACTCAG ACCAGGTATC AACAAGTCAA CTTGGTGATG

8651 8700

NC_001463 GAAACAAGAG CAGACGTCGC AGGAGAAAAT CAGGATTTTG GC...GATGG

AF322109 GAGACCCGGG TGCAACTAGA AGAAGAAGAA GAAGAAGACG GAAGGGATGG

8701 8750

NC 001463 CTTAGAGGAA TCAGACAA.. .CAGCGAAAC AAGCGAAAGA GTGACAGTAC

AF322109 TGGAGATGGC TCAGAGAGAT GCAGCGATCC CGACAACAAA GG...AATTA

8751 8800

NC 001463 AGAAAGCTTG GAGCCGTGCC TGGGAGCTTT GGCAGAACTC ACCCTGGAAG

AF322109 TGAACGCCTG GAGGAGAGCT TGGGTGACTT GGAGAAACTC ACCTTGGCAG

8801 8850

NC_001463 GAGCCATGGA AAAGGGGCCT GCTGAGGCTG CTCGTCCTTC CGCTGACGAT

AF322109 AACACATGGA AGAATGTGGT GGTGGCGCCG TTGGTGATTC CGCTGACAAT

8851 8900

NC 001463 GGGAATCTGG ATAAATGGAT GGCTTGGAGA ACACCACAAA AATAAAAAAA AF322109 CAGAATTTGG CTCCTTGGAG AGAATGGAGA GAACCCCTAA AAGAAAAATA

8901 8950

NC_001463 GAAAGGGTG. ACTGTGAGAC ATGGGCTAAA GAGGACTAAT AACAAGCTAG

AF322109 AAAAGGGTGG ACTGTGAGGA CTGTG .AGGCCTAGG AGCGAGATAG

8951 9000

NC_001463 GCCAAATTCC TGTAAATCAC TTGGGGGGTT ATAAGAAAAG CAAGTTCACT

AF322109 AAACTTA TAGGCCTCTC TTCCCGG .AAAG CTAACTCACT

9001 9050

NC 001463 ATGACAAAGC AAAATGTAAA GGCCAAATTC CTGTAAATCA CTTGGGGGGT

AF322109 GTG .AGAGGAATA G..CAAGTCA CAGTGA..CA CT GCT

9051 9100

NC_001463 TATAAGAAAA GCAAGTTCAC TATGACAAAG CAAAATGTAA CCGCAAG...

AF322109 AATTGTACCC GCAA...CCC TGAGATCATG CAAACCACAA TCCTGAGATT

9101 9150

NC 001463 .TGCTGACAG ATGTAACAGC TGACATATCA GCTGATGCTT GCTCATGCTG

AF322109 ATGCTGACAT GTGTAACAGC TGATGCCTCA GCTGATGCTT GCTCATGCTG

9151 9200

NC 001463 ACACTGTAGC TCTGAGCTGT ATATAAGGAG AAGCTTGCTG CTTGC.ACTT

AF322109 ACAATGTAAC TAGGAGCTCT ATATAAACAG AGCCCTAGAG CTTGCTACTT

9201 9250

NC 001463 CAGAGTTCTA GGAGAGTCCC .TCCT.AGTC TCTCCTCTCC

AF322109 CAGAGTGCTC TGAGGAGCTC GAAGGAAAGA GTCCTCAGCC TCTCCTCTCC

9251 9300

NC_001463 GAGGAGGTAC CGAGACCTCA AAATAAAGGA GTGATTGCCT TACTGCCGA.

AF322109 GAGGAGCTTC GG....CTCA TAATAAAGGA GTGCTTGCTT CA..ACAGAA

TABLE 2

PileUp

MSF: 759 Type: N Check: 1376

Name: NC_001463 (gag720bp) (SEQ IE ) NO: 3) Len: 759 Check: 9060 Weight: 0 Name: AF322109 (gag720bp) (SEQ IE) NO: 4) Len: 759 Check: 2316 Weight: 0

1 I1!

1 50

NC_001463 (gag720bp) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG AF322109 (gag720bp) .ATGGTGAGG CAGGCCTCCG GAAGGGGAAA

51 100

NC 001463 (gag720bp) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG AF322109(gag720bp) GGAGTACCCC GAGCTAAAAG AATGTCTGAA AAAGGCATGC AAAATAAAAG

101 150

NC 001463 (gag720bp) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT AF322109(gag720bp) TAAGGGCTGG GGGGGAGCGC CTGACAGAAG GAAATTGTCT CTGGTGTATA

151 200

NC 001463 (gag720bp) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA AF322109(gag720bp) AAAACACTAG AGTGTATGTA TGAGGATTGT AGGGAGGAAC CTTGGACCCC

201 250

NC 001463 (gag720bp) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG AF322109(gag720bp) AGAAAAATGT AAACAATTAT GGAAAAAGTT GAAGCAGGTA GAGCCTGAGG

251 300

NC_001463 (gag720bp) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA AF322109(gag720bp) AGAGTAGCAA AGCAGACTAT AACTCGTTAA AAGCAACCTT GGCGGGGATA

301 350

NC 001463 (gag720bp) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC AF322109(gag720bp) GTCTGTGTGC AAATGGGAAT GCAGCCCGAG ACACTGCAGG ATGCGATAGC

351 400

NC_001463 (gag720bp) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG AF322109(gag720bp) AACCTTAAAC ATGAGAGATG AAGT AAAAGGAA AGGAA..AAG

401 450

NC 001463 (gag720bp) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA AF322109(gag720bp) CCATCAGAAG AAAAGAAGGG AATATAT..C CCATATTAGT GCAGGCAGGA

451 500

NC 001463 (gag720bp) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA AF322109(gag720bp) GGAGGAAGAG CATGGAGAGC GGTAGAGCCT GCTACCTTTC AGCAGCTCCA

501 550

NC_0014S3 (gag720bp) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT AF322109(gag720bp) AACAGTGGCA ATGCAGCATG GACTAGTATC AGAAGAATTT GAAAGGCAGC

551 600

NC_001463 (gag720bp) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG AF322109 (gag720bp) TAGCATACTA TGCCACCACA TGGACAAGCA AGGATATCTT AGAAGTATTA

601 650

NC 001463 (gag720bp) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT AF322109(gag720bp) GCCATGATGC CAGGAAATAG AGCGCAAAAA GAACTAATAC AAGGAAAGTT

651 700

NC_001463 (gag720bp) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG AF322109(gag720bp) AAATGAGGAA GCAGAGAGAT GGAGAAGGCA GAATCCACAA CCTGCGG...

701 750

NC_001463 (gag720bp) GAGGAGGATT AACAGTGGAT AF322109(gag720bp) ...GCGGGTT AACCGTGGAT CAGATAATGG GGGTAGGACA AACGAATCAG

751 NCJ301463 (gag720bp) AF322109 (gag720bp) GCAGCGGCA

PiIeUp

MSF : 1347 Type : N Check : 2008

Name : NC_001463 (gag ) ( SEQ ID NO : 5 ) Len : 1347 Check : 6959 Weight : 0 Name : AF322109 (gag) (SEQ ID NO : 6 ) Len : 1347 Check : 5049 Weight : 0

//

1 50

NC_00i463 (gag) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG AF322109(gag) ATGGTGAGG CAGGCCTCCG GAAGGGGAAA

51 100

NC_001463 (gag) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG AF322109(gag) GGAGTACCCC GAGCTAAAAG AATGTCTGAA AAAGGCATGC AAAATAAAAG

101 150

NC_001463 (gag) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT AF322109(gag) TAAGGGCTGG GGGGGAGCGC CTGACAGAAG GAAATTGTCT CTGGTGTATA

151 200

NC_001463 (gag) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA AF322109(gag) AAAACACTAG AGTGTATGTA TGAGGATTGT AGGGAGGAAC CTTGGACCCC

201 250

NC_001463 (gag) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG AF322109 (gag) AGAAAAATGT AAACAATTAT GGAAAAAGTT GAAGCAGGTA GAGCCTGAGG

251 300

NC_001463 (gag) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA AF322109(gag) AGAGTAGCAA AGCAGACTAT AACTCGTTAA AAGCAACCTT GGCGGGGATA

301 350

NC_001463 (gag) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC AF322109 (gag) GTCTGTGTGC AAATGGGAAT GCAGCCCGAG ACACTGCAGG ATGCGATAGC

351 400

NC_001463 (gag) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG AF322109(gag) AACCTTAAAC ATGAGAGATG AA GTAAAAGGAA AGGAA..AAG

401 450

NC_00l463 (gag) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA AF322109(gag) CCATCAGAAG AAAAGAAGGG AATATATCCC ..ATATTAGT GCAGGCAGGA

451 500

NC_001463 (gag) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA AF322109(gag) GGAGGAAGAG CATGGAGAGC GGTAGAGCCT GCTACCTTTC AGCAGCTCCA

501 550

NC_001463 (gag) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT AF322109(gag) AACAGTGGCA ATGCAGCATG GACTAGTATC AGAAGAATTT GAAAGGCAGC

551 GOO

NC_OO1463 (gag) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG AF322109(gag) TAGCATACTA TGCCACCACA TGGACAAGCA AGGATATCTT AGAAGTATTA

601 650

NC_001463 (gag) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT AF3-22109(gag) GCCATGATGC CAGGAAATAG AGCGCAAAAA GAACTAATAC AAGGAAAGTT 651 700

NC_001463 (gag) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA^' CCTCCAGCAG

AF322109 (gag) AAATGAGGAA GCAGAGAGAT GGAGAAGGCA GAATCCACAA CCTGCGG...

701 750

NC_001463 (gag) GAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

AF322109 (gag) ...GCGGGTT AACCGTGGAT CAGATAATGG GGGTAGGACA AACGAATCAG

751 800

NC_001463 (gag) GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGGCAAATAT GCCTGCAATG

AF322109 (gag) GCAGCGGCAC AGGCTAATAT GGATCAAGCA AGACAAATAT GCCTACAATG

801 850

NC_001463 (gag) GGTAATAAAT GCATTAAGAG CAGTAAGACA TATGGCGCAC AGGCCAGGGA

AF322109 (gag) GGTTATAACA GCAATAAGAG GAGTTAGGCA TATGGCCCAT AGACCAGGAA

851 900

NC_001463 (gag) ATCCAATGCT AGTAAAGCAA AAAACGAATG AGCCATATGA AGATTTTGCA

AF322109 (gag) ATCCCATGCT GGTAAGACAA AAACCAAATG AGAACTATGA AGAGTTTGCC

901 950

NC_001463 (gag) GCAAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTTACAC AGCCTATAAA

AF322109 (gag) GCAAGGTTGT TAGAAGCAGT GGATGCAGAA CCCGTTACCC AACCTATAAA

951 1000

NC_001463 (gag) AGATTATCTA AAGCTAACAC TATCTTATAC AAATGCATCA GCAGATTGTC

AF322109 (gag) AGAATATTTA AAGGTAACTC TGTCTTACAC AAATGCAAAT TCGGAATGTC

1001 1050

NC_001463 (gag) AGAAGCAAAT GGATAGAACA CTAGGACAAA GAGTACAACA AGCTAGTGTA

AF322109 (gag) AAAAACATAT GGACAGAGTG TTGGGGCAAA GAGTACAGCA GGCCTCAATA

1051 1100

NC_001463 (gag) GAAGAAAAAA TGCAAGCATG TAGAGATGTG GGATCAGAAG GGTTCAAAAT

AF322109 (gag) GAAGAAAAAA TGCAGGCATG CAGGGACATC GGGGGAACAG CATATCAGAT

1101 1150

NC_001463 (gag) GCAATTGTTA GCACAAGCAT TAAGGCCAGG AAAAGGAAAA GGGAATGGAC

AF322109 (gag) GCAGTTGCTT GCACAAGCCC TCCGTGGCGG AAAAGAAGAT GGGAAAAAAT

1151 1200

NC_001463 (gag) AGCCACAAAG GTGTTACAAC TGTGGAAAAC CGGGACATCA AGCAAGGCAA

AF322109 (gag) CTGTAGGGAA GTGTTATAAC TGTGGAAGGC CCGGACACAG AGCAAAAGAA

1201 1250

NC_001463 (gag) TGTAGACAAG GAATCATATG TCACAACTGT GGAAAGAGAG GACATATGCA

AF322109 (gag) TGCAGACAAG GCATTATATG TCACAACTGT GGAAAAAGAG GGCATATACA

1251 1300

NC_001463 (gag) AAAAGAATGC AGAGGAAAGA GAGACATAAG GGGAAAACAG CAGGGAAACG

AF322109 (gag) GAAAAACTGC A AACA GAAA....AG AAGAAAGGAG CAGGGAAACA

1301 1347

NC_001463 (gag) GGAGGAGGGG GATACGTGTG GTGCCGTCCG CTCCTCCTAT GGAATAA

AF322109 (gag) TGAGGAGGGG GCTACGTGTG GTGCCGTCCG CACCCCCTAT GGAGTAA TABLE 3

PileUp

MSF: 605 Type: N Check: 9138

Name: NC 001463 (5' ) (SEQ ID NO: 7) Len 605 Check: 5398 Weight: 0

Name: AF322109(5') (SEQ ID NO: 8) Len 605 Check: 3740 Weight: 0

//

1 50

NC 001463 (5 ' ) ....GAGTTC TAGG...AGA GTCCCTCCTA GTCTCTCCTC

AF322109 (5') GTGAGTGCTC TGAGGAGCTC GAAGGAAAGA GTCCTC..A GCCTCTCCTC

51 100

NC_001463 (5¹) TCCGAGGAGG TACCGAGACC TCAAAATAAA GGAGTGATTG CCTTACTGCC

AF322109 (5') TCCGAGGAGC TTCGG....C TCATAATAAA GGAGTGCTTG CTTCA..ACA

101 150

NC_001463 (5') GAGTGGAGAG TGATTACTGA GCGGCCGGTG TATCGGGAGT CGTCCCTTAA

AF322109 (5 ' ) GAACTGAG CTGG TCGTGGTTAT TATCGGG... .GACCGAAGT

151 200

NC_001463 (5') TCTGTGCAAT ACCAGAGCGG CTCTCGCAGC TGGCGCCCAA CGTGGGGCCC

AF322109 (5') CCCGTGCAAC ACCGGGGCGG TTCTCGCAGC TGGCGCCCAA CGTGGGGCTC

201 250

NC 001463 (B' ) GAGGAG....

AF322109(5') GAGTAGCTTG AGAAGCTCGA CTGAGATCTG AATCCAAGAG CGACATCAGA

251 300

NC_001463 (5') ....AAGAAA AGAAAGC... GGCCCTGAGA ACTCGGCTTC TG..AAAAAG

AF322109 (5¹) CAGCAAGAAA TGAGAGTAAT GAGACCGCGA GCTCTGCTGC TGTAAAAAAG

301 350

NC_001463 (5') AGGAAGAGGA CAAGTTGCTA TAGCAACAAG AGAGAAGAAG TAGAGCAAAG

AF322109 (5') AGGAAGTAG. CGGGTTGCCG AGGCAACTGC TCAGAAGAAC CAGGGGAAAG

351 400

NC 001463 (5') GTCCAGTGGC T.CGGAAAAA GAGGAACTGA AACTTCGGGG ACGCCTGAAG

AF322109 (5') GGCTTCCAGC AACCTCAAAA GAGGAACCGA GACTTCGGGG ACGCCTGAA.

401 450

NC_001463 (5') GAGTAAGGTA AGTGACTCTG CTGTACGCGG GGCGAGGCAG AGGTT.TCCT

AF322109 (5') ..GTAAGGTA AGTGACTCTG CTGTACGCGG GGCGAGGCAT AGGAGATCCT

451 500

NC_001463 (5') TCTAAATT.G AAAGAGAAGT GTTGCTGCGA GAGGTCTTGG TGGTCGAGAA

AF322109 (5') TCTATTCTAG GAAGAGAAGC GCTGTTCTGG GAGGTCTTGG CGACCGAGAA

501 550

NC_001463 (5') TCCTGTACAA AAAAAAGGAG GGATCTCGGT CAGGACCAGG ACCCCTGGGA

AF322109 (5') TCTTGTT... AAATAAGCCA GGATCTCGAT CAGGACCAAG ACCCCTCAGG

551 600

NC 001463 (5¹) GTAATACAAC AGCAACACCG TAAGAAAATC CGCC

AF322109 (5') AGAGGGTATA GACAGCGTGG TAAGAAA.TC CGCCGTGGTG AGTCTAGATA

601

NC 001463 (5')

AF322109(5') GAGAC TABLE 4

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MSF: 3338 Type: N Check: 5428

Name: NC_001463 (pol) (SEQ ID NO: 9) Len: 3338 Check: 8114 Weight: 0 Name: AF322109 (pol) (SEQ ID NO: 10) Len: 3338 Check: 7314 Weight: 0

//

1 50

NC 001463 (pol) AT GTCACAACTG TGGAAAGAGA GGACATATGC AF322109(pol) ATGCAGACAA GGCATTATAT GTCACAACTG TGGAAAAAGA GGGCATATAC

51 100

NC_001463 (pol) AAAAAGAATG CAGAGGAAAG AGAGACATAA GGGGAAAACA GCAGGGAAAC AF322109 (pol) AGAAAAACTG CA AAC AGAAA....A GAAGAAAGGA GCAGGGAAAC

101 150

NC 001463 (pol) GGGAGGAGGG GGATACGTGT GGTGCCGTCC GCTCCTCCTA TGGAATAACT AF322109 (pol) ATGAGGAGGG GGCTACGTGT GGTGCCGTCC GCACCCCCTA TGGAGTAACG

151 200

NC 001463 (pol) TCAGCACCAC CTATGGTTCA GGTCCGCATA GGTTCCCAGC AGAGGAACTT AF322109 (pol) CAAGCACCAC TAATAGTTAG GGTACAAATA GGGAATCAGG AGAAACAATT

201 250

NC_001463 (pol) GTTATTTGAT ACCGGGGCGG ACCGAACTAT AGTTAGATGG CATGAGGGCT AF322109 (pol) ATTATTTGAC ACAGGGGCAG ATAAAACGAT AGTAAGAATG CATGATGGAA

251 300

NC_001463 (pol) CGGGAAACCC AGCCGGAAGG ATAAAACTGC AAGGAATAGG AGGAATAGTA AF322109 (pol) CAGGGATTCC AAACGGAAGA ATAAAATTAC AAGGGATAGG AGGAATAGTA

301 350

NC_001463 (pol) GAAGGAGAAA AATGGAATAA TGTAGAATTA GAATATAAAG GAGAAACAAG AF322109 (pol) GAAGGAGAAA AATGGAATAA AGTACCCATG ACATATAAGG GAGAAACATC

351 400

NC 001463 (pol) AAAGGGAACA ATAGTAGTGT TACCACAAAG TCCAGTAGAA GTATTAGGAC AF322109(pol) CTGCCCAAGC TTGGTTGTGC TAAGAGATAG CCCAGTAGAA GTATTGGGAA

401 450

NC 001463 (pol) GAGATAACAT GGCCCGATTT GGAATAAAGA TAATAATGGC AAATTTAGAG AF322109 (pol) GAGATAACAT GGAAGCATTC GGCGTAACCC TAATAATGGC AAATTTAGAA

451 500

NC_001463 (pol) GAAAAAAGAA TCCCAATTAC AAAAGTAAAA TTGAAAGAGG GATGTACGGG AF322109 (pol) GATAAGAAAA TTCCCACAAT ACCAGTAGAA TTGAAAGAAG GATGTAAAGG

501 550

NC_001463 (pol) TCCACATGTC CCACAATGGC CATTAACAGA AGAGAAATTA AAAGGTCTAA AF322109 (pol) GCCACATGTG CCCCAGTGGC CATTAACAGC AGAGAAATTA CAAGGACTAA

551 600

NC 001463 (pol) CAGAAATCAT AGATAAATTA GTGGAAGAAG GAAAACTAGG AAAGGCACCC AF322109 (pol) CAGGAATAGT AGAAAAATTA CTACAGGAAG GAAAATTGGC AGAGGCCCCA

601 650

NC_001463 (pol) CCACATTGGA CATGTAATAC TCCAATCTTT TGCATAAAAA AGAAATCAGG AF322109 (pol) GAGGGATGGA CGTGGAACAC GCCCATCTTC TGCATAAAAA AGAAGTCAGG 651 700

NC_001463 (pol) GAAGTGGAGA ATGTTAATAG ATTTCAGAGA ATTGAACAAA CAGACAGAAG

AF322109 (pol) AAAATGGAGA ATGTTAATAG ATTTTAGGGA ATTAAATAAG CAAACAGCAG

701 750

NC_001463 (pol) ATTTAACAGA AGCGCAGTTA GGACTCCCGC ATCCGGGAGG ACTACAAAAG

AF322109 (pol) ATTTAGCAGA AGCGCAGCTA GGACTGCCAC ACCCAGGAGG GTTGCAAAGG

751 800

NC_001463 (pol) AAAAAACATG TTACAATATT GGACATAGGA GATGCATATT TTACTATACC

AF322109 (pol) AAAAAGAATG TAACAATTCT GGACATAGGA GATGCATATT TCACAATTCC

801 850

NC_001463 (pol) CCTATATGAA CCATATCGAG AGTACACATG TTTTACTCTA TTAAGTCCTA

AF322109 (pol) CTTATACGAG CCCTATCAGA AATATACATG CTTCACACTC CTAAGTCCTA

851 900

NC 001463 (pol) ATAATCTAGG ACCATGTAAA AGATACTATT GGAAAGTGCT GCCACAAGGT

AF322109 (pol) ACAATTTGGG ACCATGTAAA AGGTATTATT GGAAAGTATT ACCCCAGGGA

901 950

NC 001463 (pol) TGGAAATTGA GTCCATCTGT ATATCAATTT ACTATGCAGG AGATCTTAGA

AF322109 (pol) TGGAAATTGA GCCCAGCTGT ATATCAATTC ACCATGCAAA GGTTGTTAAA

951 1000

NC 001463 (pol) GGATTGGATA CAGCAGCATC CAGAAATTCA ATTTGGCATA TATATGGATG

AF322109 (pol) AGGATGGATA CAACAGCATA AAAACATACA ATTTGGAATA TATATGGATG

1001 1050

NC 001463 (pol) ATATTTACAT AGGAAGTGAT TTAGAAATTA AAAAGCATAG AGAAATAGTG

AF322109 (pol) ATATCTATAT TGGAAGTGAT CTAACGATAG CCCAACATAG GAAGATAATA

1051 1100

NC_001463 (pol) AAAGATTTAG CCAATTATAT TGCCCAATAT GGATTCACTC TGCCAGAAGA

AF322109 (pol) GAAGAATTAG CCTCATTTAT AGAACAATTT GGGTTTACAT TACCAGAAGA

1101 1150

NC_001463 (pol) GAAGAGACAA AAGGGATATC CAGCAAAATG GCTAGGATTT GAACTACACC

AF322109 (pol) TAAGAGACAA GAGGGCTATC CAGCAAAATG GCTAGGATTC GAGCTACATC

1151 1200

NC_001463 (pol) CGCAGACCTG GAAATTTCAG AAGCATACAT TACCTGAATT AACAAAGGGA

AF322109 (pol) CAGAAAAATG GAAATATCAA AAGCATAAAT TGCCGGAATT ACAAGAGGGG

1201 1250

NC_001463 (pol) ACAATAACAT TAAATAAATT ACAGAAATTA GTAGGAGAAT TAGTATGGAG

AF322109 (pol) GTAATAACCC TGAACAAATT ACAGAAGATA GTAGGGGAAT TAGTGTGGAG

1251 1300

NC 001463 (pol) ACAATCCATA ATTGGGAAAA GCATTCCTAA CATTCTGAAA TTAATGGAAG

AF322109 (pol) ACAATCCTTG ATAGGAAAGA GCATCCCCAA TATCATAAAA TTAATGGAAG

1301 1350

NC_001463 (pol) GAGATAGAGA ATTACAAAGT GAAAGAAAAA TTGAAGAAGT ACATGTGAAA

AF322109 (pol) GAGATCGCGC ATTACAAAGT GAAAGGAAAA TAGAAAGAAT ACATGTACAA

1351 1400

NC_001463 (pol) GAATGGGAAG CATGTAGGAA AAAATTAGAA GAAATGGAAG GAAATTATTA

AF322109 (pol) GAATGGGAAG CATGTCAAAA GAAATTAGAT GAAATGGTAG GAAATTATTA

1401 1450 NC_001463 (pol) TAATAAAGAC AAAGATGTCT ATGGACAATT GGCTTGGGGA GACAAAGCTA

AF322109 (pol) CAGAGAAGAA GAAGATATCT ATGGACAAAT AACTTGGGGG GATAAGGCAA

1451 1500

NC 001463 (pol) TAGAATATAT AGTGTATCAG GAGAAAGGGA AACCATTATG GGTAAATGTG

AF322109 (pol) TAAAATACAT AGTATTCCAA AGGAAAGGGG AACCCCTATG GGTAAATGTA

1501 1550

NC_001463 (pol) GTTCACAATA TAAAGAACCT AAGCATCCCG CAACAGGTTA TTAAAGCAGC

AF322109 (pol) GTACATGACA TAAAAAATTT GAGTCTCCCA CAGCAAGTGA TAAAAGCAGC

1551 1600

NC_001463 (pol) GCAAAAATTA ACCCAAGAAG TCATCATTAG GACAGGAAAA ATACCATGGA

AF322109 (pol) ACAGAAATTA ACCCAGGAAG TAATCATAAG AACAGGAAAA ATCCCATGGC

1601 1650

NC 001463 (pol) TATTGTTGCC AGGGAAAGAA GAAGATTGGA GACTAGAATT GCAATTAGGG

AF322109 (pol) TGCTACTACC AGGAAGAGAA GAAGACTGGA GATTAGAACT GCAGGTAGGG

1651 1700

NC 001463 (pol) AACATCACAT GGATGCCAAA ATTTTGGTCC TGTTATCGAG GA.CATACAA

AF322109 (pol) AACATCACGT GGATGCCATC ATTTTGGTCA TGTTATCGAG GAGCACCCAA

1701 1750

NC 001463 (pol) GATGGAGAAA AAGAAATATA ATAGAAGAAG TAGTAGAAGG GCCTACATAT

AF322109 (pol) G.TGGAAAAG AAGGAACATA GTGGCAGCAG TGGTAGATGG ACCGACATAT

1751 1800

NC_001463 (pol) TATACAGATG GAGGAAAAAA GAATAAAGTA GGAAGTCTAG GGTTCATAGT

AF322109 (pol) TATACAGATG GGGGAAAGAA AAACGCACAG GGAAGCTTTG GCTTCATCTC

1801 1850

NC_001463 (pol) ATCAACAGGG GAAAAATTTA GAAAGCATGA AGAGGGCACA AACCAGCAAC

AF322109 (pol) CCCAACAGGA GAAAAGTTCA GAAGGCATGA AGATGGAACT AATCAGGTAT

1851 1900

NC_001463 (pol) TAGAATTAAG AGCCATAGAG GAAGCTCTAA AACAAGGGCC TCAAACAATG

AF322109 (pol) TAGAATTAAG GGCAATAGAA GATCCATGTA AACAAGGACC TGAAAGCATG

1901 1950

NC_001463 (pol) AATTTAGTAA CAGATAGTAG ATATGCATTT GAATTTTTAT TAAGAAATTG

AF322109 (pol) AACATTGTAA CTGACAGCAG GTATGCTTAT GAATTCATGC TCCGAAACTG

1951 2000

NC_001463 (pol) GGATGAAGAA GTAATAAAGA ATCCAATTCA AGCAAGAATT ATGGAAATTG

AF322109 (pol) GGATGAACAG GTCATAAGAA ACCCCATTCA GGCAAGAATC ATGGCAGAAG

2001 2050

NC 001463 (pol) CCCACAAGAA AGATAGGATA GGAGTGCATT GGGTGCCAGG ACATAAAGGG

AF322109 (pol) TGCACAAGAA AAAGCAGGTA GGAATACACT GGGTGCCAGG GCATAAAGGA

2051 2100

NC 001463 (pol) ATTCCCCAAA ATGAAGAAAT AGACAAATAT ATTTCGGAAA TATTTCTTGC

AF322109 (pol) ATACCTCAGA ATGAAGAGAT AGACCAGTAC ATATCAGAAG TATTCTTAGC

2101 2150

NC_001463 (pol) AAAAGAAGGA GAAGGAATTC TCCCAAAAAG AGAAGAGGAT GCAGGGTATG

AF322109 (pol) ACGAGAAGGA ACAGGGATAT GTGAAAAAAG GAAGGAAGAT GCTGGATATG

2151 2200

NC_001463 (pol) ATTTAATATG CCCAGAAGAG GTTACCATAG AGCCAGGACA AGTGAAATGC

AF322109 (pol) ATTTATTATG CCCGCATGAG GTAATACTTA AACCCCAAGA AGTAAAACGG

2201 2250 NC 001463 (pol) ATCCCCATAG AGCTAAGATT AAATTTAAAG AAATCACAAT GGGCTATGAT

AF322109 (pol) ATCCCAATAG ACCTAAAATT AAAATTGAAA GAAAAGCAAT GGGCCATGAT

2251 2300

NC 001463 (pol) TGCTACAAAA AGCAGCATGG CTGCCAAAGG AGTGTTCACA CAAGGAGGAA

AF322109 (pol) AAGTGGGAAA AGTAGCGTTG CAGCAAAAGG AATATTTGTA CAAGGAGGCA

2301 2350

NC_001463 (pol) TCATAGACTC AGGATATCAG GGACAAATAC AGGTAATAAT GTATAATAGC

AF322109 (pol) TAATAGATTC AGGGTATCAG GGACAAGTAC AAGTCATCCT ATATAATAGT

2351 2400

NC 001463 (pol) AATAAAATAG CAGTAGTCAT ACCCCAAGGG AGAAAATTTG CACAATTAAT

AF322109 (pol) AATAAGATAG AGGTCAAAAT ACCACAAGGC AGGAAATTTG CCCAATTAAT

2401 2450

NC 001463 (pol) ATTAATGGAT AAAAAGCATG GAAAATTGGA ACCCTGGGGG GAAAGCAGAA

AF322109 (pol) ATTAATGAAC TTACAACATG AAGAATTAGA AGAATGGGGA AAGGAAAGAA

2451 2500

NC_001463 (pol) AAACAGAAAG GGGAGAAAAA GGATTTGGGT CTACAGGAAT GTATTGGATA

AF322109 (pol) AAACAGAAAG AGGAACAAAA GGATTTGGGT CTACAGGAGC ATTTTGGATA

2501 2550

NC_001463 (pol) GAAAATATTC CTCTGGCAGA GGAAGACCAC ACAAAATGGC ATCAAGATGC

AF322109 (pol) GAGAATATTC CCCAAGCAGA GGAAGAACAT TACAAATGGC ATCAAGATGC

2551 2600

NC 001463 (pol) CCGATCATTG CATCTAGAAT TTGAAATTCC AAGAACAGCA GCAGAAGACA

AF322109 (pol) TAGATCTCTG CAGCTAGAAT TCAAGATACC TAGAGCAGCA GCAGAAGACA

2601 2650

NC_001463 (pol) TAGTAAATCA ATGTGAAATA TGCAAAGAAG CGAGGACACC TGCAGTAATT

AF322109 (pol) TTATACAGCA CTGTGAGGTA TGTCAAGAAG GCAAACCCGC AGCGATCACG

2651 2700

NC_001463 (pol) AGAGGCGGAA ACAAAAGGGG GGTAAATCAT TGGCAAGTGG ATTATACCCA

AF322109 (pol) AGAGGGGGAA ATAAAAGAGG AATAGATCAT TGGCAGGTAG ACTATACACA

2701 2750

NC 001463 (pol) TTATGAAAAT ATCATACTAT TAGTATGGGT AGAAACAAAT TCAGGACTAA

AF322109 (pol) TTACAAAGAA CACATAATAT TAGTATGGGT AGAGACTAAT TCAGGATTAA

2751 2800

NC_001463 (pol) TATATGCAGA AAAAGTAAAA GGAGAATCAG GGCAAGAATT CAGAATAAAA

AF322109 (pol) TATTTGCAGA GAAAGTAAAA GGAGAATCAG GACAAGAATT TAGGATGCAG

2801 2850

NC_001463 (pol) GTGATGCATT GGTATGCATT ATTTGGTCCA GAGTCATTGC AGTCAGACAA

AF322109 (pol) ACATTGAAAT GGTATGCTTT GTTTCAACCA AAATCAGTGC AATCAGATAA

2851 2900

NC_001463 (pol) TGGACCTGCA TTTGCAGCAG AGCCCACACA GCTGTTAATG CAATACCTAG

AF322109 (pol) TGGGACAGCC TTCACAGCTG AGGCTACGCA GCATCTAATG AAGTATTTAG

2901 2950

NC_001463 (pol) GAGTAAAACA CACAACAGGC ATACCTTGGA ATCCACAGTC TCAGGCTATA

AF322109 (pol) GGATTCAGCA CACTACGGGT ATTCCGTGGA ACCCCCAGTC ACAAAGTTTA

2951 3000

NC 001463 (pol) GTAGAAAGGG CACATCAACT ATTGAAAAGC ACTTTAAAGA AGTTCCAGCC

AF322109 (pol) GTAGAAAGAG CTCATCAAAC ATTAAAACAC ATGTTAGAAA AATTAGAACC

3001 3050 NC_001463 (pol) ACAATTTGTC GCTGTAGAAT CAGCCATAGC AGCAGCCCTA GTCGCCATAA

AF322109 (pol) ACAATTTGTG GCCCTACAGT CTGCCATCGC AGCCACTCTA GTTGCGCTCA

3051 3100

NC 001463 (pol) ATATAAAAAG AAAGGGTGGG CTGGGGACAA GCCCTATGGA TATTTTTATA

AF322109 (pol) ATATAAAAAG AAAGGGTGGA CTAGGGGCAA GCCCTATGGA TATTTACATA

3101 3150

NC_001463 (pol) TATAATAAAG AACAGAAAAG AATAAATAAT AAATATAATA AAAATTCTCA

AF322109 (pol) TATAATAAGG AGCAACAAAG ACAACAAGAT AATAGTAATA AATTAATTCA

-

3151 3200

NC_001463 (pol) AAAAATTCAA TTCTGTTATT ACAGAATAAG GAAAAGAGGA CATC.AGGAG

AF322109 (pol) GAAAA...AA TTTTGTTATT ACAGGATCAG AAAAAGAGGC CATCCAGGAG

3201 3250

NC 001463 (pol) AGTGGAAAGG ACCAACCCAG GTACTGTGGA AAGGGGAAGG AGCCAATTGT

AF322109 (pol) AGTGGAACGG CCCAACTGAG GTACTGTGGG AAGGGGAAGG AGCCA.TAGT

3251 3300

NC 001463 (pol) GGTAAAGGAT ATAGAAAGTG AAAAGTATTT AGTAATACCT TACAAAGATG

AF322109 (pol) AGTTAAAGAC AAAGAAAGTG ATAGATATCT AGTCATCCCA TATAAAGATG

3301 3338

NC_001463 (pol) CAAAATTCAT CCCGCCACCA ACAAAAGAAA AGGAATAA

AF322109 (pol) CAAAATTTAT TCCGCCACCG TCGGAACAGA AGGGATAG

TABLE 5

PileUp

MSF: 408 Type: N Check: 517

Name: NC_001463 (rev) (SEQ ID NO: 11) Len: 408 Check: 7287 Weight: 0 Name: AF322109 (rev) (SEQ ID NO: 12)Len: 408 Check: 3230 Weight: 0

//

1 50

NC_001463 ( rev) ATGGATGCTG GGGCCAGATA CATGCGCTTA ACTGGGAAGG AAAACTGGGT AF322109 ( rev)

51 100

NCJD01463 ( rev) TGAAGTAACC ATGGACGGAG AGAAGGAAAG GAAAAGAGAA GGTTTCACTG AF322109 ( rev) ATGG.CGGAG ATAAGAAAAG ..A.AGCAAA GGAGCCACTA

101 150

NC_001463 (rev) CGGGACAGCA AGATATACAG AACTCTAAGT ACCCCGACAT ACCAACGGGT AF322109(rev) ATCCAGGACC AGGTATCAAC AAGTCAACTT GGTGATGGAG ACC..CGGGT

151 200

NC_001463 (rev) CACAGTCATC ATGGAAACAA GAGCAGACGT CGCAGGAGAA AATCAGGATT AF322109(rev) GCAACTAG AAGAAGAAGA AGAAGAAGAC GGAAGGGATG

201 250

NC_001463 (rev) TTGGCGATGG CTTAGAGGAA TCAGACAACA GCGAAACAAG CGAAAGAGTG AF322109(rev) GTGGAGATGG CTCAGAGAGA TG CA GCGATCCCGA CAACAAAGGA

251 300

NC_001463 (rev) ACAGTACAGA AAGCTTGGAG CCGTGCCTGG GAGCTTTGGC AGAACTCACC AF322109(rev) A...TTATGA ACGCCTGGAG GAGAGCTTGG GTGACTTGGA GAAACTCACC

301 350

NC_001463 (rev) CTGGAAGGAG CCATGGAAAA GGGGCCTGCT GAGGCTGCTC GTCCTTCCGC AF322109 (rev) TTGGCAGAAC ACATGGAAGA ATGTGGTGGT GGCGCCGTTG GTGATTCCGC

351 400

NC_001463 (rev) TGACGATGGG AATCTGGATA AATGGATGGC TTGGAGAACA CCACAAAAAT AF322109(rev) TGACAATCAG AATTTGGCTC CTTGGAGAGA ATGGAGAGAA CCCCTAAAAG

401

NC_001463 (rev) AA AF322109 (rev) AAAAATAA

TABLE 6

PileUp

MSF: 691 Type: N Check: 6528

Name: NC 001463 (vif) (SEQ ID NO: 13) Len: 691 Check: 5882 Weight: 0 Name: AF322109 (vif) (SEQ ID NO: 14) Len: 691 Check: 646 Weight : 0

/ _//_/

1 50

NC_001463 (vif) ATGCAAAATT CATCCCGCCA CCAACAAAAG AAAAGGAATA AAAAACCTGG AF322109 (vif) ATGCAAAATT TATTCCGCCA CCGTCGGAAC AGAAGGGATA GAAGAATAGG

51 100

NC_001463 (vif) ACCAGAATTA CCCTTAGCAC TATGGATACA TATAGCAGAA AGCATTAATG AF322109 (vif) TCCAGAATTG CCTTTATCTT TATGGACTTA TACAGCATAC AGCATAAATA

101 150

NC_001463 (vif) GGGATAGCTC ATGGTACATA ACAATGAGAC TGCAACAGAT GATGTGGGGA AF322109 (vif) AAGATCCCGC ATGGTATACA ACCCTAAGAC TGCAGCAAAT GATGTGGCAT

151 200

NC_001463 (vif) AAAAGAGGAA ATAAGTTACA ATATAAGAAT GAAGACAGGG AATATGAAAA AF322109 (vif) AGGAGGGGAA ATAAATTGAC ATATGTCAGG GAAAATGCAC AGTACGAGGA

201 250

NC_001463 (vif) TTGGGAAATT ACATCATGGG GATGGAAAAT GCACCTAAGG AGAGTGAAAC AF322109 (vif) GTGGGAAATG ACCTCGTATG AGTGGAGGAT AAGAATGAGA AGGGACAAAA

251 300

NC_001463 (vif) AATGGATACA AGACAACAGG AGAGGAAGC. CCATGGCAGT ACAAAGTAGG AF322109 (vif) CAAAAAGTCA TC.CAAGAGG GCATACTTCG CCATGGCAAT ATCGGAGACA

301 350

NC_001463 (vif) AGGAACATGG AAAAGTATAG GAGTGTGGTT CCTGCAAGCA GGAGATTACA AF322109 (vif) GGATGGATGG AAGGATGTGG GAACGTGGTT CCTACAGCCA GGGGACTATA

351 400

NC_001463 (vif) GAAAGGTAGA CAGGCACTTC TGGTGGGCAT GGAGGATACT GATATGTTCC AF322109 (vif) GAAAGGCGGA TCAGCAGTTC TGGTTCGCTT GGAGAATAGT GTCGTGTTCA

401 450

NC_001463(vif) TGCAGGAAAG AAAAGTTTGA TATAAGAGAA TTTATGAGAG GAAGACATAG AF322109(vif) TGTAAAAAGG AAGGATTTAA CATAAGAGAA TTTATGCTAG GTACCCATAG

451 500

NC_001463 (vif) ATGGGATTTG TGCAAATCCT GTGCTCAAGG AGAAGTAGTA AAGCATACTA AF322109 (vif) ATGGGATTTG TGTAAGTCGT GTTGCCAGGG TGAAGTAGTA AAGAGAACAC

501 550

NC_001463 (vif) GAACAAAAAG TCTGGAAAGA CTAGTACTGC TACAGATGGT AGAACAGCAT AF322109 (vif) AACCCTACAC CTTGCAAAGG CTCACGTGGC TTAAATTAAC AGAAGACCAT

551 600

NC 001463 (vif) GTGTTTCAAG TATTGCCATT GTGGAGAGCC AGGAGAAGTA GTACAACAGA AF322109 (vif) GTATTTCAAG TAATGCCCTT GTGGAGAGCT CGCAAAGGGA TTACCATAGA

601 650

NC_001463 (vif) TTTCCCATGG TGCAGGGACA CAACGGGATA CACGCATGCG TGGTCTGTCC AF322109 (vif) CTTTCCCTGG TGCAGGGACA CAAAAGGATT CCTGGAGCCG TGGACAACGC 651 691

NC_001463 (vif) AGGAGTGCTG GTTGATGGAA TATCTCTTAG AGGATGAGTG A AF322109(vif) AAGAGTGTTG GCAAATAGAG TATCCCTTGG AGGATGAGTG A

TABLE 7

PileUp

MSF: 736 Type: N Check: 513

Name: NC_001463 (gag720bp) (SEQ II ) NO: 15) Len: 736 Check: 4701 Weight: 0 Name: >AF015181 (SEQ ID NO: 16) Len: 736 Check: 5812 Weight: 0

Il

1 50 NC_ 001463 (gag720bp) .ATGGTGAGT CTAGATAGAG ACATGGCGAG GCAAGTCTCC GGGGGGAAAA >AF015181 GCTGTAGACT CTGTAATGTT CCAACAA.AT GCAAA....C AGTAGCAATG

51 100

NC 001463 (gag720bp) GAGATTATCC TGAGCTCGAA AAATGTATCA AGCATGCATG CAAGATAAAA >AF015181 CAGCATGGCC TCGTGTCCGA GGATTTTGAA AGACAGTTAG CAT.ATTATG

101 150

NC_ 001463 (gag720bp) GTTCGACTCA GAGGGG..AG CACTTGACAG AAGGAAATTG TTTATGGTGC >AF015181 CTACTACCTG GACAAGTAAA GACATACTAG AAGTA..TTG GCCATGATGC

151 200

NC_ 001463 (gag720bp) CTTAAAACA. ...TTAGATT ..ACATGTTT GAGGACCAT. .AAAGAGGAA >AF015181 CTGGGAATAG GGCTCAGAAA GAACTTATTC AAGGGAAATT GAATGAAGAA

201 250

NC_ 001463 (gag720bp) CCTTGGACAA AAGTAAAATT TAGGACAATA TGGCAGAAGG .TGAAGAATC >AF015181 GCA..GACAG GTGGAGAAG. ..GAACAATC CACCAGGAGG ATTAACAGTG

251 300

NC_ 001463 (gag720bp) TAACTCCTGA GGAGAGTAAC AAAAAAGACT TTATGTCTTT GCAGGCCACA >AF015181 GATCAAATTA TGGGGGTAGG ACAAACAAAT CAAGCA.... GCAGCACAAG

301 350

NC_ 001463 (gag720bp) TTAGCGGGTC TAATGTGTTG CCAAATGGGG ATGAGACCTG AGACATTGCA >AF015181 CTAACATGGA TCAGGCAA.G ACAAATATGC CT...ACAAT GGGTAATAAA

351 400

NC_ 001463 (gag720bp) AGATGCAATG GCTACAGTAA TCATGAAAGA TGGGTTACTG GAACAAGAGG >AF015181 CGCCTTAAGA GCAGTAAGGC ATATGGCTCA TAGGCCAGGG AATCCAATGC

401 450

NC_ _001463 (gag720bp) AAAAGAAGGA AGACAAAAGA GAAAAGGAAG AGAGTGTCTT CCCAATAGTA >AF015181 TAGTAAAGCA A...AAAACA AATGAGCCAT ATGAAGAATT TGCAGCAAGA

451 500

NC_ _001463 (gag720bp) GTGCAAGCAG CA..GGAGGG AGAAGCTGGA AAGCAGTAGA TTCTGTAATG >AF015181 CTGCTAGAAG CAATAGATGC AGAAGCGGTT ACACAGCCCA TAAAAGAGTA

501 550

NC_ _001463 (gag720bp) T.TCCAGC.A ACTGCAAACA GTAGCAATGC AGCATGGCCT CGTGTCTGAG >AF015181 TCTAAAGCTA ACATTATCCT ATACAAATGC AGC CT CA

551 600

NC_ _001463 (gag720bp) GACTTTGAAA GGCAGTTGGC ATATTATGCT ACTACCTGGA CAAGTAAAGA >AF015181 GATTGTCAAA AGCAAATGG. AGAGAGTGCT AGGACAAAGA ...GTACA.A

601 650

NC_ _001463 (gag720bp) CATACTAGAA GTATTGGCCA TGATGCCTGG AAATAGAGCT CAAAAGGAGT >AF015181 CAGGCTAGT. GTAGAAAAAA AAATGCAAGC ATGT ..

651 700

NC 001463 (gag720bp) TAATTCAAGG GAAATTAAAT GAAGAAGCAG AAAGGTGGAG AAGGAATAAT >AF015181

701 736

NC_001463 (gag720bp) CCACCACCTC CAGCAGGAGG AGGATTAACA GTGGAT •_*&Fni ςi Ri

PiIeUp

MSF: 1347 Type: N Check: 939

Name: NC_001463 (gag) (SEQ ID NO: 17)Len: 1347 Check: 6959 Weight: 0 Name: >AF015181 (SEQ ID NO: 18) Len: 1347 Check: 3980 Weight: 0

Il

1 50

NC_ 001463 (gag) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG >AF015181

51 100

NC_ 001463 (gag) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG >AF015181

101 150

NC_ _001463 (gag) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT >AF015181

151 200

NC_ _001463 (gag) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA >AF015181

201 250

NC_ _001463 (gag) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG >AF015181

251 300

NC_ 001463 (gag) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA >AF015181

301 350

NC_ 001463 (gag) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC >AF015181

351 400

NC_ _001463 (gag) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG >AF015181

401 450

NC_ _001463 (gag) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA >AF015181

451 500

NC_ _001463 (gag) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA >AF015181 GC TGTAGACTCT GTAATGTTCC AACAAATGCA

501 550

NC_ _001463 (gag) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT >AF015181 AACAGTAGCA ATGCAGCATG GCCTCGTGTC CGAGGATTTT GAAAGACAGT

551 600

NC_ _001463(gag) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG >AF015181 TAGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG 601 650

NC_ 001463 (gag) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT >AF015181 GCCATGATGC CTGGGAATAG GGCTCAGAAA GAACTTATTC AAGGGAAATT

651 700

NC_ 001463 (gag) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG >AF015181 GAATGAAGAA GCAGACAGGT GGAGAAGGAA CAATCCACCA

701 750

NC_ 001463 (gag) GAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA >AF015181 ..GGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

751 800

NC_ 001463 (gag) GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGGCAAATAT GCCTGCAATG >AF015181 GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGACAAATAT GCCTACAATG

801 850

NC_ 001463 (gag) GGTAATAAAT GCATTAAGAG CAGTAAGACA TATGGCGCAC AGGCCAGGGA >AF015181 GGTAATAAAC GCCTTAAGAG CAGTAAGGCA TATGGCTCAT AGGCCAGGGA

851 900

NC_ 001463 (gag) ATCCAATGCT AGTAAAGCAA AAAACGAATG AGCCATATGA AGATTTTGCA >AF015181 ATCCAATGCT AGTAAAGCAA AAAACAAATG AGCCATATGA AGAATTTGCA

901 950

NC_ 001463 (gag) GCAAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTTACAC AGCCTATAAA >AF015181 GCAAGACTGC TAGAAGCAAT AGATGCAGAA GCGGTTACAC AGCCCATAAA

951 1000

NC_ 001463 (gag) AGATTATCTA AAGCTAACAC TATCTTATAC AAATGCATCA GCAGATTGTC >AF015181 AGAGTATCTA AAGCTAACAT TATCCTATAC AAATGCAGCC TCAGATTGTC

1001 1050

NC_ _001463 (gag) AGAAGCAAAT GGATAGAACA CTAGGACAAA GAGTACAACA AGCTAGTGTA >AF015181 AAAAGCAAAT GGAGAGAGTG CTAGGACAAA GAGTACAACA GGCTAGTGTA

1051 1100

NC_ 001463 (gag) GAAGAAAAAA TGCAAGCATG TAGAGATGTG GGATCAGAAG GGTTCAAAAT >AF015181 GAAAAAAAAA TGCAAGCATG T

1101 1150

NC_ _001463 (gag) GCAATTGTTA GCACAAGCAT TAAGGCCAGG AAAAGGAAAA GGGAATGGAC >AF015181

1151 1200

NC_ _001463 (gag) AGCCACAAAG GTGTTACAAC TGTGGAAAAC CGGGACATCA AGCAAGGCAA >AF015181

1201 1250

NC_ _001463 (gag) TGTAGACAAG GAATCATATG TCACAACTGT GGAAAGAGAG GACATATGCA >AF015181

1251 1300

NC_ _001463 (gag) AAAAGAATGC AGAGGAAAGA GAGACATAAG GGGAAAACAG CAGGGAAACG >AF015181

1301 1347

NC_ 001463 (gag) GGAGGAGGGG GATACGTGTG GTGCCGTCCG CTCCTCCTAT GGAATAA >AF015181 TABLE 8

PileUp

MSF: 727 Type: N Check: 1231

Name: NC_001463 (gag720bp) (SEQ ID NO: 19) Len: 727 Check: 1714 Weight: 0

Name: >AF402664 (SEQ ID NO: 20) Len: 727 Check: 1659 Weight: 0

Name: >AF402665 (SEQ ID NO: 21) Len: 727 Check: 331 Weight: 0

Name: >AF402666 (SEQ ID NO: 22) Len: 727 Check: 7190 Weight: 0

Name: >AF402667 (SEQ ID NO: 23) Len: 727 Check: 9833 Weight: 0

Name: >AF402668 (SEQ ID NO: 24) Len: 727 Check: 504 Weight: 0 //

1 50

NC_001463 (gag720bp) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG

>AF402664 TC AAGCAGCAGG .AGGGAGAAG CTGGAAAGCA GTAGACTCAG

>AF402665 GC AAGCAGCAGG .AGGGAGAAG CTGGAAAGCA GTAGACTCAG

>AF402666 GC AAGCAGCAGG .AGGGAGAAG CTGGAAAGCA GTAGACTCAG

>AF402667 GC AAGCAGCAGG .AGGGAGAAG CTGGAAAGCA GTAGACTCAG

>AF402668 GC AAGCAGCAGG .AGGGAGAAG CTGGAAAGCA GTAGACTCAG

51 100

NC_001463 (gag720bp) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG

>AF402664 TGATGTTCCA GCAACTGCAA AATGTAGCAA TGCAGCATGG CCTCGTGTCC

>AF402665 TGATGTTCCA GCAACTGCAA AATGTAGCAA TGCAGCATGG CCTCGTGTCC

>AF402666 TGATGTTCCA GCAACTGCAA AATGTAGCAA TGCAGCATGG CCTCGTGTCC

>AF402667 TGATGTTCCA GCAACTGCAA AATGTAGCAA TGCAGCATGG CCTCGTGTCC

>AF402668 TGATGTTCCA GCAACTGCAA AATGTAGCAA TGCAGCATGG CCTCGTGTCC

101 150

NC_001463 (gag720bp) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT

>AF402664 GAGGATTTTG AAAGG..CAG TTAGTATATT ATGCTACTAC CTGGACAAGT

>AF402665 GAGGATTTTG AAAGG..CAG TTAGCATATT ATGCTACTAC CTGGACAAGT

>AF402666 GAGGATTTTG AAAGG..CAG TTGGCATATT ATGCTACTAC CTGGACAAGT

>AF402667 GAGGATTTTG AAAGG..CAG TTAGCATATT ATGCTACTAC CTGGACAAGT

>AF402668 GAGGATTTTG AAAGG..CAG TTAGCATATT ATGCTACTAC CTGGACAAGT

151 200

NC_001463 (gag720bp) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA

>AF402664 AAAGA..TAT ATTAGAAGTA TTGG..CCAT GATG C CTGGAAATAG

>AF402665 AAAGA..TAT ATTAGAAGTA TTGG..CCAT GATG C CTGGAAATAG

>AF402666 AAAGA..TAT ATTAGAAGTA TTGG..CCAT GATG C CTGGAAACAG

>AF402667 AAAGA..TAT ATTAGAAGTA TTGG..CCAT GATG C CTGGAAATAG

>AF402668 AAAGA..TAT ATTAGAAGTA TTGG..CCAT GATG C CTGGAAATAG

201 250

NC_001463 (gag720bp) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG

>AF402664 AGCTCAAAAA GAGTTAATTC AAGGGAAATT GAATGAGGAA GCAGAAAGGT

>AF402665 AGCTCAAAAA GAGTTAATTC AAGGGAAATT GAATGAGGAA GCAGAAAGGT

>AF402666 AGCTCAAAAA GAGTTAATTC AGGGGAAATT GAATAAGGAA GCAGAAAGGT

>AF402667 AGCTCAAAAA GAGTTAATTC AAGGGAAATT GAATGAGGAA GCAGAAAGGT

>AF402668 AGCTCAAAAA GAGTTAATTC AAGGGAAATT GAATGAGGAA GCAGAAAGGT

251 300

NC_001463 (gag720bp) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA

>AF402664 GGAG.AAGAA ATAATCCACC ACCTCAA.GC AGGCG .GAGGATTAA

>AF402665 GGAG.AAGGA ATAATCCACC ACCTCAA.GC AGGCG .GAGGATTAA

>AF402666 GGAG.AAGGA ATAATCCACC ACCTCAA.GC ACAAG .GAGGATTAA

>AF402667 GGAG.AAGGA ATAATCCACC ACCTCAA.GC AGGCG .GAGGATTAA

>AF402668 GGAG.AAGGA ATAATCCACC ACCTCAA.GC AGGCG .GAGGATTAA

301 350

NC 001463 (gag720bp) ATGTGTTGCC AA..ATGGGG ATGAGACCTG AGACATTGCA AGATGCAATG >AF402664 CAGTGGATCA AATTATGGGG GTAGGACAAA CAAATCAAGC AGCGGCACAG

>AF402665 CAGTGGATCA AATTATGGGG GTAGGACAAA CAAATCAAGC AGCGGCACAG

>AF402666 CAGTGGATCA AATTATGGGG GTAGGACAAA CAAATCAGGC AGCGGCACAG

>AF402667 CAGTGGATCA AATTATGGGG GTAGGACAAA CAAATCAAGC AGCGGCACAG

>AF402668 CAGTGGATCA AATTATGGGG GTAGGACAAA CAAATCAAGC AGCGGCACAG

351 400

NC-. 001463 (gag720bp) GCTA.CAGTA ATCATGAAAG ATGGGTT..A CTGGAACAAG .AGGAAAAGA

>AF402664 GCTAACATGG ATCAGGCAAG ACAAATATGT CTGCAATGGG TAATAACAGC

>AF402665 GCTAACATGG ATCAGGCAAG ACAAATATGC CTGCAATGGG TAATAACAGC

>AF402666 GCTAACATGG ATCAGGCAAG ACAAATATGC CTGCAATGGG TAATAACAGC

>AF402667 GCTAACATGG ATCAGGCAAG ACAAATATGC CTGCAATGGG TAATAACAGC

>AF402668 GCTAACATGG ATCAGGCAAG ACAAATATGC CTGCAATGGG TAATAACAGC

401 450

NC_ 001463 (gag720bp) AGGAAGACAA AAGAGAAAAG GAAGAGAGTG TCTTCCCAAT AGTAGTGCAA

>AF402664 ACTAAGAGCA GTGAGACATA TGGCTCACAA ACCAGGGAAT CCAA.TGCTA

>AF402665 ACTAAGAGCA GTGAGACATA TGGCTCACAA ACCAGGGAAT CCAA.TGCTA

>AF402666 ACTAAGAGCA GTGAGACATA TGGCTCACAA ACCAGGGAAT CCAA.TGCTA

>AF402667 ACTAAGAGCA GTGAGACATA TGGCTCACAA ACCAGGGAAT CCAA.TGCTA

>AF402668 ACTAAGAGCA GTGAGACATA TGGCTCACAA ACCAGGGAAT CCAA.TGCTA

451 500

NC_ 001463 (gag720bp) GCAGCAGGAG GGAGAAGCTG GAAAGCAGTA GATTCTGTAA TGTTCCAGCA

>AF402664 GTAAAGCAAA AAACAAATGA GTCATATGAA GATTTTGCCG CAAGACTGCT

>AF402665 GTAAAGCAAA AGACAAATGA GTCATATGAA GATTTTGCCG CAAGACTGCT

>AF402666 GTAAAGCAAA AGACAAATGA GTCATATGAA GATTTTGCCG CAAGACTGCT

>AF402667 GTAAAGCAAA AGACAAATGA GTCATATGAA GATTTTGCCG CAAGACTGCT

>AF402668 GTAAAGCAAA AGACAAATGA GTCATATGAA AAATTTTCAG CAAGACTCCT

501 550

NC_ 001463 (gag720bp) ACTGCAAACA GTAGCA.ATG CAGCATGGCC TCGTGTCTGA GGACTTTGAA

>AF402664 AGAAGCAATA GATGCAGAAC CAGTTACACA GCAAATAAAA GAATATTTAA

>AF402665 AGAAGCAATA GATGCAGAAC CAGTTACACA GCAAATAAAA GAATATTTAA

>AF402666 AGAAGCAATA GATGCAGAAC CAGTTACACA GCAAATAAAA GAATATTTAA

>AF402667 AGAAGCAATA GATGCAGAAC CAGTTACACA GCAAATAAA. GAATATTTAA

>AF402668 AGAAGCAATA GATGCAGAAC CAGTTACACA GCCTATAAAA GAATATTTAA

551 600

NC_ _001463 (gag720bp) AGGCAGTTGG CATATTATGC TACTACCTGG ACAAGTAAAG ACATACTAGA

>AF402664 AGTTA .ACATTATCT TAC.ACAAAT GCATCCTCAG ACTGTCAGAA

>AF402665 AGTTA .ACATTATCT TAC.ACAAAT GCATCCTCAG ACTGTCAAAA

>AF402666 AGTTA .ACATTATCT TAC.ACAAAT GCATCCTCAG ACTGTCAGAA

>AF402667

>AF402668 AGTTA .ACATTATCT TAC.ACAAAT GCATCCTCAG ACTGTCAAAA

601 650

NC_ _001463 (gag720bp) AGTATTGGCC ATGATGCCTG GAAATAGAGC TCAAAAGGAG TTAATTCAAG

>AF402664 ACAGATGGAT AGAGTACTAG GACAGAGAGT GCAACAAGCT AGTGTGGAAG

>AF402665 ACAAATGGAT AGAATACTAG GACAGAGAGT GCAACAAGCT AGTGTGGAAG

>AF402666 ACAAATGGAT AGAGTACTAG GACAGAGAGT GCAACAAGCT AGTGTGGAAG

>AF402667

>AF402668 ACAAATGGAT AGAGTACTAG GACAGAGAGT GCAACAAGCT AGTGTGGAAG

651 700

NC_ _001463 (gag720bp) GGAAATTAAA TGAAGAAGCA GAAAGGTGGA GAAGGAATAA TCCACCACCT

>AF402664 AAAAAATGCA AGCAT..GCA GAGATGTGGG ATCAGAAGGA TTCAGAATGC

>AF402665 AAAAAATGCA AGCAT..GCA GAGATGTGGG ATCAGAAGGG TTCAGAATGC

>AF402666 AAAAAATGCA AGCAT..GCA GAGATGTGGG ATCAGAAGG.

>AF402667

>AF402668 AAAAAATGCA AGCAT..GCA GAGATGTGGG ATCAGAAGGA TTCAGAATGC

701 727

NC_ _001463 (gag720bp) CCAGCAGGAG GAGGATTAAC AGTGGAT

>AF402664

>AF402665

>AF402666

>AF402667 >AF402668

PiIeUp

MSF : 1347 Type : N Check : 5320

Name: NC_001463 (gag) (SEQ ID NO: 25) Len: 1347 Check : 6959 Weight

Name: >AF402664 (SEQ ID NO: 26) Len: 1347 Check: 1590 Weight: 0

Name: >AF402665 (SEQ ID NO: 27) Len: 1347 Check: 9222 Weight: 0

Name: >AF402666 (SEQ ID NO: 28) Len: 1347 Check: 4950 Weight: 0

Name: >AF4026S7 (SEQ ID NO: 29) Len: 1347 Check: 3156 Weight: 0

Name: >AF402668 (SEQ ID NO: 30) Len: 1347 Check: 9443 Weight: 0

//

1 50

NC_001463 (gag) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

51 100

NC_001463 (gag) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

101 150

NC_001463 (gag) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

151 200

NC_001463 (gag) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

201 250

NC_001463 (gag) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

251 300

NC_001463 (gag) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA

>AF402664

>AF402665 >AF402666 >AF402667

>AF402668

301 350

NC_ 001463 (gag) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

351 400

NC_ 001463 (gag) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

401 450

NC_ 001463 (gag) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA

>AF402664 TCAAGCAGCA

>AF402665 GCAAGCAGCA

>AF402666 GCAAGCAGCA

>AF402667 GCAAGCAGCA

>AF402668 GCAAGCAGCA

451 500

NC_ 001463 (gag) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA

>AF402664 GGAGGGAGAA GCTGGAAAGC AGTAGACTCA GTGATGTTCC AGCAACTGCA

>AF402665 GGAGGGAGAA GCTGGAAAGC AGTAGACTCA GTGATGTTCC AGCAACTGCA

>AF402666 GGAGGGAGAA GCTGGAAAGC AGTAGACTCA GTGATGTTCC AGCAACTGCA

>AF402667 GGAGGGAGAA GCTGGAAAGC AGTAGACTCA GTGATGTTCC AGCAACTGCA

>AF402668 GGAGGGAGAA GCTGGAAAGC AGTAGACTCA GTGATGTTCC AGCAACTGCA

501 550

NC_ 001463 (gag) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT

>AF402664 AAATGTAGCA ATGCAGCATG GCCTCGTGTC CGAGGATTTT GAAAGGCAGT

>AF402665 AAATGTAGCA ATGCAGCATG GCCTCGTGTC CGAGGATTTT GAAAGGCAGT

>AF402666 AAATGTAGCA ATGCAGCATG GCCTCGTGTC CGAGGATTTT GAAAGGCAGT

>AF402667 AAATGTAGCA ATGCAGCATG GCCTCGTGTC CGAGGATTTT GAAAGGCAGT

>AF402668 AAATGTAGCA ATGCAGCATG GCCTCGTGTC CGAGGATTTT GAAAGGCAGT

551 600

NC_ 001463 (gag) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG

>AF402664 TAGTATATTA TGCTACTACC TGGACAAGTA AAGATATATT AGAAGTATTG

>AF402665 TAGCATATTA TGCTACTACC TGGACAAGTA AAGATATATT AGAAGTATTG

>AF402666 TGGCATATTA TGCTACTACC TGGACAAGTA AAGATATATT AGAAGTATTG

>AF402667 TAGCATATTA TGCTACTACC TGGACAAGTA AAGATATATT AGAAGTATTG

>AF402668 TAGCATATTA TGCTACTACC TGGACAAGTA AAGATATATT AGAAGTATTG

601 650

NC_ 001463 (gag) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT

>AF402664 GCCATGATGC CTGGAAATAG AGCTCAAAAA GAGTTAATTC AAGGGAAATT

>AF402665 GCCATGATGC CTGGAAATAG AGCTCAAAAA GAGTTAATTC AAGGGAAATT

>AF402666 GCCATGATGC CTGGAAACAG AGCTCAAAAA GAGTTAATTC AGGGGAAATT

>AF402667 GCCATGATGC CTGGAAATAG AGCTCAAAAA GAGTTAATTC AAGGGAAATT

>AF402668 GCCATGATGC CTGGAAATAG AGCTCAAAAA GAGTTAATTC AAGGGAAATT

651 700 NC_001463 (gag) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG

_>AF402664 GAATGAGGAA GCAGAAAGGT GGAGAAGAAA TAATCCACCA CCTCAAGCAG

>AF402665 GAATGAGGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCAAGCAG

>AF402666 GAATAAGGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCAAGCAC

>AF402667 GAATGAGGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCAAGCAG

>AF402668 GAATGAGGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCAAGCAG

701 750

NC_ 001463 (gag) GAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

>AF402664 GCGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

>AF402665 GCGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

>AF402666 AAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAG

>AF402667 GCGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

>AF402668 GCGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

751 800

NC_ 001463 (gag) GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGGCAAATAT GCCTGCAATG

>AF402664 GCAGCGGCAC AGGCTAACAT GGATCAGGCA AGACAAATAT GTCTGCAATG

>AF402665 GCAGCGGCAC AGGCTAACAT GGATCAGGCA AGACAAATAT GCCTGCAATG

>AF402666 GCAGCGGCAC AGGCTAACAT GGATCAGGCA AGACAAATAT GCCTGCAATG

>AF402667 GCAGCGGCAC AGGCTAACAT GGATCAGGCA AGACAAATAT GCCTGCAATG

>AF402668 GCAGCGGCAC AGGCTAACAT GGATCAGGCA AGACAAATAT GCCTGCAATG

801 850

NC_ 001463 (gag) GGTAATAAAT GCATTAAGAG CAGTAAGACA TATGGCGCAC AGGCCAGGGA

>AF402664 GGTAATAACA GCACTAAGAG CAGTGAGACA TATGGCTCAC AAACCAGGGA

>AF402665 GGTAATAACA GCACTAAGAG CAGTGAGACA TATGGCTCAC AAACCAGGGA

>AF402666 GGTAATAACA GCACTAAGAG CAGTGAGACA TATGGCTCAC AAACCAGGGA

>AF402667 GGTAATAACA GCACTAAGAG CAGTGAGACA TATGGCTCAC AAACCAGGGA

>AF402668 GGTAATAACA GCACTAAGAG CAGTGAGACA TATGGCTCAC AAACCAGGGA

851 900

NC_ 001463 (gag) ATCCAATGCT AGTAAAGCAA AAAACGAATG AGCCATATGA AGATTTTGCA

>AF402664 ATCCAATGCT AGTAAAGCAA AAAACAAATG AGTCATATGA AGATTTTGCC

>AF402665 ATCCAATGCT AGTAAAGCAA AAGACAAATG AGTCATATGA AGATTTTGCC

>AF402666 ATCCAATGCT AGTAAAGCAA AAGACAAATG AGTCATATGA AGATTTTGCC

>AF402667 ATCCAATGCT AGTAAAGCAA AAGACAAATG AGTCATATGA AGATTTTGCC

>AF402668 ATCCAATGCT AGTAAAGCAA AAGACAAATG AGTCATATGA AAAATTTTCA

901 950

NC_ _001463 (gag) GCAAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTTACAC AGCCTATAAA

>AF402664 GCAAGACTGC TAGAAGCAAT AGATGCAGAA CCAGTTACAC AGCAAATAAA

>AF402665 GCAAGACTGC TAGAAGCAAT AGATGCAGAA CCAGTTACAC AGCAAATAAA

>AF402666 GCAAGACTGC TAGAAGCAAT AGATGCAGAA CCAGTTACAC AGCAAATAAA

>AF402667 GCAAGACTGC TAGAAGCAAT AGATGCAGAA CCAGTTACAC AGCAAATAAA

>AF402668 GCAAGACTCC TAGAAGCAAT AGATGCAGAA CCAGTTACAC AGCCTATAAA

951 1000

NC_ _001463 (gag) AGATTATCTA AAGCTAACAC TATCTTATAC AAATGCATCA GCAGATTGTC

>AF402664 AGAATATTTA AAGTTAACAT TATCTTACAC AAATGCATCC TCAGACTGTC

>AF402665 AGAATATTTA AAGTTAACAT TATCTTACAC AAATGCATCC TCAGACTGTC

>AF402666 AGAATATTTA AAGTTAACAT TATCTTACAC AAATGCATCC TCAGACTGTC

>AF402667 .GAATATTTA A

>AF402668 AGAATATTTA AAGTTAACAT TATCTTACAC AAATGCATCC TCAGACTGTC

1001 1050

NC_ _001463 (gag) AGAAGCAAAT GGATAGAACA CTAGGACAAA GAGTACAACA AGCTAGTGTA

>AF402664 AGAAACAGAT GGATAGAGTA CTAGGACAGA GAGTGCAACA AGCTAGTGTG

>AF402665 AAAAACAAAT GGATAGAATA CTAGGACAGA GAGTGCAACA AGCTAGTGTG

>AF402666 AGAAACAAAT GGATAGAGTA CTAGGACAGA GAGTGCAACA AGCTAGTGTG >AF402667

>AF402668 AAAAACAAAT GGATAGAGTA CTAGGACAGA GAGTGCAACA AGCTAGTGTG

1051 1100

NC 001463 (gag) GAAGAAAAAA TGCAAGCATG TAGAGATGTG GGATCAGAAG GGTTCAAAAT

>AF402664 GAAGAAAAAA TGCAAGCATG CAGAGATGTG GGATCAGAAG GATTCAGAAT

>AF402665 GAAGAAAAAA TGCAAGCATG CAGAGATGTG GGATCAGAAG GGTTCAGAAT

>AF402666 GAAGAAAAAA TGCAAGCATG CAGAGATGTG GGATCAGAAG G

>AF402667

>AF402668 GAAGAAAAAA TGCAAGCATG CAGAGATGTG GGATCAGAAG GATTCAGAAT

1101 1150

NC 001463 (gag) GCAATTGTTA GCACAAGCAT TAAGGCCAGG AAAAGGAAAA GGGAATGGAC

>AF402664 GC

>AF402665 GC

>AF402666

>AF402667

>AF402668 GC...

1151 1200

NC 001463 (gag) AGCCACAAAG GTGTTACAAC TGTGGAAAAC CGGGACATCA AGCAAGGCAA

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

1201 1250

NC 001463 (gag) TGTAGACAAG GAATCATATG TCACAACTGT GGAAAGAGAG GACATATGCA

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

1251 1300

NC 001463 (gag) AAAAGAATGC AGAGGAAAGA GAGACATAAG GGGAAAACAG CAGGGAAACG

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668

1301 1347

NC 001463 (gag) GGAGGAGGGG GATACGTGTG GTGCCGTCCG CTCCTCCTAT GGAATAA

>AF402664

>AF402665

>AF402666

>AF402667

>AF402668 TABLE 9

PileUp

MSF: 742 Type: N Check: 6523

Name: NC_001463 (gag720bp) (SEQ ID NO: 31) Len: 742 Check: 3818 Weight: 0

Name: >AJ305040 (SEQ ID NO: 32) Len: 742 Check: 1263 Weight: 0

Name: >AJ305041 (SEQ ID NO: 33) Len: 742 Check: 9126 Weight: 0

Name: >AJ305042 (SEQ ID NO: 34) Len: 742 Check: 2316 Weight: 0

//

1 50

NC_001463 (gag720bp) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTC.. CGGGGGGAAA

>AJ305040 GCAG TCGATGCTGT AATGTTCCAG CAAATGCAAA CAGTAGCCAT

>AJ305041 GCAG TAGACTCAGT AATGTTCCAG CAACTGCAAA CAGTAGCAAT

>AJ305042 GCAG TCGATGCTGT AATGTTCCAG CAAATGCAAA CAGTAGCCAT

51 100

NC_001463 (gag720bp) AGAGATTATC CTGAGCTCGA AAAATGTATC AAGCATGCAT GCAAGATAAA

>AJ305040 GCAGCATGGT CTTGTGTCTG AGGACTTTGA AAGGCAGTTA GCAT.ATTGT

>AJ305041 GCAGCATGGC CTCGTGTCCG AGGATTTTGA AAGGCAGTTG GCAT.ATTAT

>AJ305042 GCAGCATGGT CTTGTGTCTG AGGACTTTGA AAGGCAGTTA GCAT.ATTAT

101 150

NC_001463 (gag720bp) AGTTCGACTC AGAGGGG..A GCACTTGACA GAAGGAAATT GTTTATGGTG >AJ305040 GCTACTACCT GGACAAGTAA AGATATATTA GAAGTA..TT GGCCATGATG >AJ305041 GCTACTACCT GGACGAGTAA AGACATACTA GAAGTA..TT GGCCATGATG >AJ305042 GCTACTACCT GGACAAGTAA AGATATATTA GAAGTA..TT GGCCATGATG

151 200

NC_001463 (gag720bp) CCTTAAAACA TTAGATTACA TGTTTGAGGA CCATAAAGAG GAACCTTGGA

>AJ305040 CCTGGAAATA G.AGCTCAAA AA...GAGTT AATTCAAG.G AAAATTAAAC

>AJ305041 CCTGGAAACA G.AGCTCAAA AG...GAGTT AATTCAAG.G GAAATTAAAT

>AJ305042 CCTGGAAATA G.AGCTCAAA AA...GAGTT AATTCAAG.G AAAATTAAAT

201 250

NC_001463 (gag720bp) CAAAAGTAAA ATTTAGGACA ATATGGCAGA AGGTGAAGAA TCTAACTCCT >AJ305040 GAGGAAGCAG AA..AGGTGG AGAAGGAATA A..TCCACCG CCTCCACAAG >AJ305041 GAAGAGGCAG AA..AGGTGG AGAAGACATA A..TCCACCC CCTCCGGCGG >AJ305042 GAGGAAGCAG AA..AGGTGG AGAAGGAATA A..TCCACCG CCTCCACAGG

251 300

NC_001463 (gag720bp) GAGGAG.AGT AACAAAAAAG .ACTTTATGT CTTTGCAGGC CACATTAGCG >AJ305040 GAGGGGGATT AACAGTGGAT CAAATTATGG GGAT..AGGA CAAACAAATC >AJ305041 GAGGAGGATT AACAGTGGAT CAAATTATGG GGGT..AGGA CAAACAAATC >AJ305042 GAGGGGGATT AACAGTGGAT CAAATTATGG GGAT..AGGA CAAACAAATC

301 350

NC_001463 (gag720bp) GGTCTAATGT GTTGCCAAAT GGGGATGAGA CCTGAGACAT TGCAA

>AJ305040 AAGCAGCAGC ACAAGCTAAC ATGGATCAGG CAAGACACAT ATGCCTGCAA

>AJ305041 AAGCAGCAGC ACAAGCTAAC ATGGATCAGG CAAGACAAAT ATGCCTGCAA

>AJ305042 AAGCAGCAGC ACAAGCTAAC ATGGATCAGG CAAGACACAT ATGCCTGCAA

351 400

NC_001463 (gag720bp) GATGCAATGG CTACAGTAAT ..CA.TGAAA GATGGGTTAC TGGAACAAGA >AJ305040 TGGGTAATAA CAGCATTAAG AGCAGTAAGA CATATGGCTC ACAGACCAGG >AJ305041 TGGGTAATAA CAGCATTAAG AGCAGTGAGG TATATGACTC ACAAACCAGG >AJ305042 TGGGTAATAA CAGCATTAAG AGCAGTAAGA CATATGGCTC ACAGACCAGG

401 450

NC_001463 (gag720bp) GGA...AAAG A.AGGAAGAC AAAAGAGAAA AGGAAGAGAG T..GTCTTCC >AJ305040 GAATCCAATG CTCGTAAAAC AAAAAACAAA TGAGCCATAT GAAGAGTTTG >AJ305041 GAATCCAATG CTAGTAAAAC AAAAAACAAA TGAAGCATAT GAAGAGTTTA >AJ305042 GAATCCAATG CTCGTAAAAC AAAAAACAAA TGAGCCATAT GAAGAGTTTG

451 500

NC_001463 (gag720bp) CAATAGTAGT GCAAGCAGCA GGAG..GGAG AAGCTGGAAA GCAGTAGATT >AJ305040 CAGCAAAACT ATTAGAAGCA ATAGATGCAG AACCAGTAAC ACAGCCCATA >AJ305041 CAGCGAGACT GCTAGAAGCA ATAGATGCAG AGCCAGTAAC ACAGCCCACA >AJ305042 CAGCAAAACT ATTAGAAGCA ATAGATGCAG AACCAGTAAC ACAGCTCATA

501 550

NC_001463 (gag720bp) CTGTAATGTT CCAGCAACTG CAAACAGTAG CAATGCAGCA TGGCCTCGTG

>AJ305040 AAAGACTAT. .CTAAAGTT. ..AACATTAT CT.TATACAA ATGCGTC...

>AJ305041 AAAGAATAT. .CTAAAACT. ..AACATTAT CT.TATACAA ATGCATC...

>AJ305042 AAAGACTAT. .CTAAAGTT. ..AACATTAT CT.TATACAA ATGCGTC...

551 600

NC_001463 (gag720bp) TCTGAGGACT TTGAAAGGCA GTTGGCATAT TATGCTACTA CCTGGACAAG >AJ305040 .CTCAG.ACT GTCAAAAGCA AATGG.ATAG AGTGCTGGGA CAAAG...AG >AJ305041 .CTCAG.ACT GTCAAAAGCA AATGG.ATAG AGTACTAGGA CAAAG...AG >AJ305042 .CTCAG.ACT GTCAAAAGCA AATGG.ATAG AGTGCTGGGA CAAAG...AG

601 650

NC_001463 (gag720bp) TAAAGACATA CTAGAAGTAT TGGCCATGAT GCCTGGAAAT AGAGCTCAAA

>AJ305040 TGCA.ACAAG CTAGT.GTAG ACGAGAAAAT GCAA

>AJ305041 TGCA.ACAAG CTAGT.GTAG AAGAAAAAAT GCAA

>AJ305042 TGCA.ACAAG CTAGT.GTAG ACGAGAAGAT GCAA

651 700

NC_001463 (gag720bp) AGGAGTTAAT TCAAGGGAAA TTAAATGAAG AAGCAGAAAG GTGGAGAAGG

>AJ305040

>AJ305041

>AJ305042

701 742

NC_001463 (gag720bp) AATAATCCAC CACCTCCAGC AGGAGGAGGA TTAACAGTGG AT

>AJ305040

>AJ305041

>AJ305042

PiIeUp

MSF: 1347 Type: N Check: 9510 Name: NC_001463 (gag) (SEQ ID NO: 35) Len: 1347 Check: 6959 Weight: 0

Name: >AJ305040 (SEQ ID NO: 36) Len: 1347 Check: 1930 Weight: 0

Name: >AJ305041 (SEQ ID NO: 37) Len: 1347 Check: 7682 Weight: 0

Name: >AJ305042 (SEQ ID NO: 38) Len: 1347 Check: 2939 Weight: 0

Il

1 50

NC_001463 (gag) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG

>AJ305040

>AJ305041

>AJ305042

51 100

NC_001463 (gag) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG

>AJ305040

>AJ305041

>AJ305042

101 150

NC_001463 (gag) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT >AJ305040 >AJ305041

>AJ305042

151 200

NC 001463 (gag) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA

>AJ305040

>AJ305041

>AJ305042

201 250

NC 001463 (gag) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG

>AJ305040

>AJ305041

>AJ305042

251 300

NC 001463 (gag) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA

>AJ305040

>AJ305041

>AJ305042

301 350

NC 001463 (gag) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC

>AJ305040

>AJ305041

>AJ305042

351 400

NC 001463 (gag) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG

>AJ305040

>AJ305041

>AJ305042

401 450

NC 001463 (gag) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA

>AJ305040

>AJ305041

>AJ305042

451 500

NC 001463 (gag) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA

>AJ305040 GC AGTCGATGCT GTAATGTTCC AGCAAATGCA

>AJ305041 GC AGTAGACTCA GTAATGTTCC AGCAACTGCA

>AJ305042 GC AGTCGATGCT GTAATGTTCC AGCAAATGCA

501 550

NC 001463 (gag) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT

>AJ305040 AACAGTAGCC ATGCAGCATG GTCTTGTGTC TGAGGACTTT GAAAGGCAGT

>AJ305041 AACAGTAGCA ATGCAGCATG GCCTCGTGTC CGAGGATTTT GAAAGGCAGT

>AJ305042 AACAGTAGCC ATGCAGCATG GTCTTGTGTC TGAGGACTTT GAAAGGCAGT

551 600

NC 001463 (gag) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG

>AJ305040 TAGCATATTG TGCTACTACC TGGACAAGTA AAGATATATT AGAAGTATTG

>AJ305041 TGGCATATTA TGCTACTACC TGGACGAGTA AAGACATACT AGAAGTATTG

>AJ305042 TAGCATATTA TGCTACTACC TGGACAAGTA AAGATATATT AGAAGTATTG

601 650

NC 001463 (gag) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT

>AJ305040 GCCATGATGC CTGGAAATAG AGCTCAAAAA GAGTTAATTC AAGGAAAATT >AJ305041 GCCATGATGC CTGGAAACAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT

>AJ305042 GCCATGATGC CTGGAAATAG AGCTCAAAAA GAGTTAATTC AAGGAAAATT

651 700

NC_ 001463 (gag) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG

>AJ305040 AAACGAGGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCG CCTCCACAAG

>AJ305041 AAATGAAGAG GCAGAAAGGT GGAGAAGACA TAATCCACCC CCTCCGGCGG

>AJ305042 AAATGAGGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCG CCTCCACAGG

701 750

NC_ 001463 (gag) GAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

>AJ305040 GAGGGGGATT AACAGTGGAT CAAATTATGG GGATAGGACA AACAAATCAA

>AJ305041 GAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

>AJ305042 GAGGGGGATT AACAGTGGAT CAAATTATGG GGATAGGACA AACAAATCAA

751 800

NC_ 001463 (gag) GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGGCAAATAT GCCTGCAATG

>AJ305040 GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGACACATAT GCCTGCAATG

>AJ305041 GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGACAAATAT GCCTGCAATG

>AJ305042 GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGACACATAT GCCTGCAATG

801 850

NC_ 001463 (gag) GGTAATAAAT GCATTAAGAG CAGTAAGACA TATGGCGCAC AGGCCAGGGA

>AJ305040 GGTAATAACA GCATTAAGAG CAGTAAGACA TATGGCTCAC AGACCAGGGA

>AJ305041 GGTAATAACA GCATTAAGAG CAGTGAGGTA TATGACTCAC AAACCAGGGA

>AJ305042 GGTAATAACA GCATTAAGAG CAGTAAGACA TATGGCTCAC AGACCAGGGA

851 900

NC_ 001463 (gag) ATCCAATGCT AGTAAAGCAA AAAACGAATG AGCCATATGA AGATTTTGCA

>AJ305040 ATCCAATGCT CGTAAAACAA AAAACAAATG AGCCATATGA AGAGTTTGCA

>AJ305041 ATCCAATGCT AGTAAAACAA AAAACAAATG AAGCATATGA AGAGTTTACA

>AJ305042 ATCCAATGCT CGTAAAACAA AAAACAAATG AGCCATATGA AGAGTTTGCA

901 950

NC_ _001463 (gag) GCAAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTTACAC AGCCTATAAA

>AJ305040 ^■GCAAAACTAT TAGAAGCAAT AGATGCAGAA CCAGTAACAC AGCCCATAAA

>AJ305041 GCGAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTAACAC AGCCCACAAA

>AJ305042 GCAAAACTAT TAGAAGCAAT AGATGCAGAA CCAGTAACAC AGCTCATAAA

951 1000

NC_ _001463 (gag) AGATTATCTA AAGCTAACAC TATCTTATAC AAATGCATCA GCAGATTGTC

>AJ305040 AGACTATCTA AAGTTAACAT TATCTTATAC AAATGCGTCC TCAGACTGTC

>AJ305041 AGAATATCTA AAACTAACAT TATCTTATAC AAATGCATCC TCAGACTGTC

>AJ305042 AGACTATCTA AAGTTAACAT TATCTTATAC AAATGCGTCC TCAGACTGTC

1001 1050

NC_ _001463 (gag) AGAAGCAAAT GGATAGAACA CTAGGACAAA GAGTACAACA AGCTAGTGTA

>AJ305040 AAAAGCAAAT GGATAGAGTG CTGGGACAAA GAGTGCAACA AGCTAGTGTA

>AJ305041 AAAAGCAAAT GGATAGAGTA CTAGGACAAA GAGTGCAACA AGCTAGTGTA

>AJ305042 AAAAGCAAAT GGATAGAGTG CTGGGACAAA GAGTGCAACA AGCTAGTGTA

1051 1100

NC _001463 (gag) GAAGAAAAAA TGCAAGCATG TAGAGATGTG GGATCAGAAG GGTTCAAAAT

>AJ305040 GACGAGAAAA TGCAA

>AJ305041 GAAGAAAAAA TGCAA

>AJ305042 GACGAGAAGA TGCAA

1101 1150

NC_ _001463 (gag) GCAATTGTTA GCACAAGCAT TAAGGCCAGG AAAAGGAAAA GGGAATGGAC

>AJ305040 >AJ305041

>AJ305042

1151 1200

NC_001463 (gag) AGCCACAAAG GTGTTACAAC TGTGGAAAAC CGGGACATCA AGCAAGGCAA

>AJ305040

>AJ305041

>AJ305042

1201 1250

NC_001463 (gag) TGTAGACAAG GAATCATATG TCACAACTGT GGAAAGAGAG GACATATGCA

>AJ305040

>AJ305041

>AJ305042

1251 1300

NC_001463 (gag) AAAAGAATGC AGAGGAAAGA GAGACATAAG GGGAAAACAG CAGGGAAACG

>AJ305040

>AJ305041

>AJ305042

1301 1347

NC_001463(gag) GGAGGAGGGG GATACGTGTG GTGCCGTCCG CTCCTCCTAT GGAATAA

>AJ305040

>AJ305041

>AJ305042

TABLE 10

Pi IeUp

MSF: 728 Type: N Check: 9403

Name: NC_001463 (gag720bp) (SEQ ID NO: 39) Len: 728 Check: 5765 Weight: 0 Name: >AY047362 (SEQ ID NO: 40) Len: 728 Check: 3638 Weight: 0

//

1 50

NC_001463 (gag720bp) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG >AY047362

51 100

NC_001463 (gag720bp) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG >AY047362 TAAA GATATATTAG AA.GTATTGG CCATG.ATGC CTGGAAATAG

101 150

NC_001463 (gag720bp) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT >AY047362 AGC...TCAA AAAGAGTTAA TTCA...AGG GAAATTGAAT GAAGAAGCAG

151 200

NC_001463 (gag720bp) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA >AY047362 AAAGGTGGAG AAGGAATAAT CCACCACCTC AAGCAGG..C GGAGGATTAA

201 250

NC_001463 (gag720bp) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAG..AATC TAACTCCTGA >AY047362 C.AG..TGG ATCAAATTAT GGGGGTAGGA CAAACAAATC AAGCAGCGGC

251 300

NC_001463 (gag720bp) GGAGAGTAAC AAAAAAGACT TTATGTCTTT GCAGGCCACA TTAGCGGGTC >AY047362 ACAGGCTAAC ATGGATCAG GCAAGACAAA TATGC..CTG

301 350

NC_001463 (gag720bp) TAATGTGTTG CCAAATGGGG ATGAGACCTG AGACATTGCA AGATGCAATG >AY047362 CAATGGGTAA TAACAGCACT AAGAGCAGTG AGACAT A TG

351 400

NC_001463 (gag720bp) GCTACAGTAA TCATGAAAGA TGGGTTACTG GAACAAGAGG AAAAGAAGGA >AY047362 GCT.CACAAA CCAGGGA..A TCCGATGCT AGT.. AAAGCAA..A

401 450

NC_001463 (gag720bp) AGACAAAAGA GAAA.AGGAA GAGAGTGTCT TCCCAATAGT AGTGCAAGCA >AY047362 AAACAAATGA GTCATATGAA GATTTTGCCG ...CAAGACT GCTAGAAGCA

451 500

NC_001463 (gag720bp) GCAGGAGGGA GAAGCTGGAA AGCAGTAGAT TCTGTAATGT TCCAGCAACT >AY047362 ATAG.ATGCA GAACCAGTTA CAAAGCAAAT AAAAGAATAT TT AAA

501 550

NC_001463 (gag720bp) GCAAACAGTA GCAATGCAGC ATGGCCTCGT GTCTGAGGAC TTTGAAAGGC >AY047362 GTTAACATTA TCT.TACACA AATGCATC.. ..CTCAG.AC TGTAAGAAAC

551 600

NC_001463 (gag720bp) AGTTGGCATA TTATGCTACT ACCTGGACAA GTA.AAGACA TACTAGAAGT >AY047362 AGATGG.ATA GAGTACTAGG ACAGAGAGTG CAACAAGCTA GTGTGGAAGA

601 650

NC_001463 (gag720bp) ATTG..GCCA TGATGCCTGG AAATAGAGCT CAAAAGGAGT TA..ATTCAA >AY047362 AAAAATGCAA GCATGCAGAG ATGT.GGGAT CAGAAGGATT CAGAATGC..

651 700

NC_001463 (gag720bp) GGGAAATTAA ATGAAGAAGC AGAAAGGTGG AGAAGGAATA ATCCACCACC >AY047362

701 728

NC_001463 (gag720bp) TCCAGCAGGA GGAGGATTAA CAGTGGAT

PiIeUp

MSF: 1347 Type: N Check: 3238

Name: NC_001463 (gag) (SEQ ID NO: 41) Len: 1347 Check: 6959 Weight: 0 Name: >AY047362 (SEQ ID NO: 42) Len: 1347 Check: 6279 Weight: 0

Il

1 50

NC_ 001463 (gag) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG >AY047362

51 100

NC_ 001463 (gag) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG >AY047362

101 150

NC_ 001463 (gag) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT >AY047362

151 200

NC_ _001463 (gag) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA >AY047362

201 250

NC_ _001463 (gag) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG >AY047362

251 300

NC_ _001463 (gag) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA >AY047362

301 350

NC_ _001463 (gag) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC >AY047362

351 400

NC_ _001463 (gag) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG >AY047362

401 450

NC_ _001463 (gag) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA >AY047362

451 500

NC_ 001463 (gag) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA >AY047362

501 550

NC_ _00i463 (gag) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT >AY047362

551 600

NC _001463 (gag) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG >AY047362 TA AAGATATATT AGAAGTATTG 601 650

NC_ 001463 (gag) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT >AY047362 GCCATGATGC CTGGAAATAG AGCTCAAAAA GAGTTAATTC AAGGGAAATT

651 700

NC_ 001463 (gag) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG >AY047362 GAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCAAGCAG

701 750

NC-. 001463 (gag) GAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA >AY047362 GCGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

751 800

NC_ 001463 (gag) GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGGCAAATAT GCCTGCAATG >AY047362 GCAGCGGCAC AGGCTAACAT GGATCAGGCA AGACAAATAT GCCTGCAATG

801 850

NC_ 001463 (gag) GGTAATAAAT GCATTAAGAG CAGTAAGACA TATGGCGCAC AGGCCAGGGA >AY047362 GGTAATAACA GCACTAAGAG CAGTGAGACA TATGGCTCAC AAACCAGGGA

851 900

NC_ 001463 (gag) ATCCAATGCT AGTAAAGCAA AAAACGAATG AGCCATATGA AGATTTTGCA >AY047362 ATCCGATGCT AGTAAAGCAA AAAACAAATG AGTCATATGA AGATTTTGCC

901 950

NC_ 001463 (gag) GCAAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTTACAC AGCCTATAAA >AY047362 GCAAGACTGC TAGAAGCAAT AGATGCAGAA CCAGTTACAA AGCAAATAAA

951 1000

NC_ _001463 (gag) AGATTATCTA AAGCTAACAC TATCTTATAC AAATGCATCA GCAGATTGTC >AY047362 AGAATATTTA AAGTTAACAT TATCTTACAC AAATGCATCC TCAGACTGTA

1001 1050

NC_ 001463 (gag) AGAAGCAAAT GGATAGAACA CTAGGACAAA GAGTACAACA AGCTAGTGTA >AY047362 AGAAACAGAT GGATAGAGTA CTAGGACAGA GAGTGCAACA AGCTAGTGTG

1051 1100

NC_ _001463(gag) GAAGAAAAAA TGCAAGCATG TAGAGATGTG GGATCAGAAG GGTTCAAAAT >AY047362 GAAGAAAAAA TGCAAGCATG CAGAGATGTG GGATCAGAAG GATTCAGAAT

1101 1150

NC_ _001463 (gag) GCAATTGTTA GCACAAGCAT TAAGGCCAGG AAAAGGAAAA GGGAATGGAC >AY047362 GC

1151 1200

NC_ 001463 (gag) AGCCACAAAG GTGTTACAAC TGTGGAAAAC CGGGACATCA AGCAAGGCAA >AY047362

1201 1250

NC_ 001463 (gag) TGTAGACAAG GAATCATATG TCACAACTGT GGAAAGAGAG GACATATGCA >AY047362

1251 1300

NC_ _001463 (gag) AAAAGAATGC AGAGGAAAGA GAGACATAAG GGGAAAACAG CAGGGAAACG >AY047362

1301 1347

NC_ _00i463 (gag) GGAGGAGGGG GATACGTGTG GTGCCGTCCG CTCCTCCTAT GGAATAA >AY047362 TABLE I l

PileUp

MSF: 733 Type: S Check: 5855

Name: NC_001463 (gag720bp) (SEQ ID NO: 43) Len: 733 Check: 9482 Weight: 0 Name: >AY081139 (SEQ ID NO: 44) Len: 733 Check: 6373 Weight: 0

/ _//_/

1 50 NC_001463 (gag720bp) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG

^AYOPH 139 TGCC GTAGACTCTG

51 100

NC_ 001463 (gag720bp) AGATTATCCT G.AGCTCGAA AAATGTATCA AGCATGCATG CAAGATAAAA >AY081139 TGATGTTCCA CCAGCT.GCA TACAGTAGCA ATGCCGCATG GCCTCGTGTC

)

101 150

NC_ 001463 (gag720bp) GTTCGACTCA GAGGGGAGCA CTTGACAGAA GGAAATTGTT TATGGTGCCT >AY081139 TGAGGACTTT GAAAGG..CA GTTGGCATAT TATGCTACTA CCTGGACAAG

151 200

NC_ 001463 (gag720bp) TAAAACATTA GATTACATGT .TTGAGGACC ATAAAGAGGA ACCTTGGACA >AY081139 TAAAGA..TA TACTGGAAGT ATTGGCCATG ATGCCTGGGA ATAGAGCTCA

201 250

NC_ 001463 (gag720bp) AAAGTAA..A ATTTAGGACA ATATGGCAGA AGGTGAAGAA TCTAACTCCT >AY081139 AAAAGAATTA ATTCAAGGAA AATTAAATGA AGAAGCAGAA

251 300

NC_ 001463 (gag720bp) GAGGAGAGTA ACAAAAAAGA CTTTATGTCT TTGCAGGCCA CATTAGCGGG >AY081139 .AGGTGGAGA AGGAATAATC CACCACCTCA A.GCAGGCG. GAGGA

301 350

NC_ 001463 (gag720bp) TCTAATGTGT TGCCAA..AT GGGGATGAGA CCTGAGACAT TGCAAGATGC >AY081139 TTAACAGTGG ATCAAATTAT GGGGGTAGGA CAAACAAATC AAGCAGCTGC

351 400

NC_ _001463 (gag720bp) AATGGCTA.C AGTAATCATG AAAGATGGGT TACTGGAACA AGAGGAAAAG >AY081139 ACAAGCTAAC ATGGATCAGG CAAGACAAAT A..TGCCTGC AATGGGTAAT

401 450

NC_ _001463 (gag720bp) AAGGAAGACA AAAGAGAAAA GGAAGAGAGT GTCTTCCCAA TAGTAGTGCA >AY081139 ATC..AGCCT TAAGAGCAGT GAGACATA.T GTCT..CATA AACCAGGG.A

451 500

NC_ 001463 (gag720bp) AGCAGCAGGA GGGAGAAGCT GGAAAGCAGT AGATTCTGTA ATGTTCCAGC >AY081139 ATCCGCTGCT AGTA.AAGCA AAAAACAAAT GAGTCATATG AAGATTTTGC

501 550

NC_ 001463 (gag720bp) AACTGCAAAC ..AGTAGCAA TGCAGCATGG CCTCGTGTCT GAGGACTTTG >AY081139 AGCTAGACTG CTAGAAGCAA TAGATCCAGC CCCAGTAGCA CATC.CTATA

551 600

NC_ _001463 (gag720bp) AAAGGCAGTT GGCATATTAT GCTAC....T ACCTGGACAA GTAAAGACAT >AY081139 AAAGATTATT TAAAGTTAAC ACTATCTTAT ACGAATGCAT CATCAGATTG

601 650

NC_ _001463 (gag720bp) ACTAGAAGTA TTGGCCATGA TGCCTGGAAA TAGAGCTCAA AAGGAGTTAA >AY081139 TCAAAAGCAA ATGGGTAGAA TGCTAGGATC GAGAGTCCAT CA..AGCCAG

651 700

NC 001463 (gag720bp) TTCAAGGGAA ATTAAATGAA GAAGCAGAAA GGTGGAGAAG GAATAATCCA _>AY081139 TGTGGGCCAA AAAA....

701 733

NC_001463 (gag720bp) CCACCTCCAG CAGGAGGAGG ATTAACAGTG GAT

>AYOSIΠQ

PiIeUp

MSF: 1347 Type: N Check: 2072

Name: NC_001463 (gag) (SEQ ID NO: 45) Len: 1347 Check: 6959 Weight: 0 Name: >AY081139 (SEQ ID NO: 46) Len: 1347 Check: 5113 Weight: 0

Il

1 50

NC_ 001463 (gag) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG >AY081139

51 100

NC_ 001463 (gag) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG >AY081139

101 150

NC_ 001463 (gag) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT >AY081139

151 200

NC_ 001463 (gag) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA >AY081139

201 250

NC_ 001463 (gag) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG >AY081139

251 300

NC_ _001463 (gag) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA >AY081139

301 350

NC_ _001463 (gag) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC >AY081139

351 400

NC_ _001463 (gag) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG >AY081139

401 450

NC_ _001463 (gag) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA >AY081139

451 500

NC_ _001463 (gag) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA >AY081139 TGC CGTAGACTCT GTGATGTTCC ACΓAGΓTWA

501 550

NC_ 001463 (gag) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT >AY081139 TACAGTAGCA ATGCCGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT

551 600

NC_ _OO1463 (gag) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG >AY081139 TGGCATATTA TGCTACTACC TGGACAAGTA AAGATATACT GGAAGTATTG

601 650 NC_001463 (gag) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT >AY081139 GCCATGATGC CTGGGAATAG AGCTCAAAAA GAATTAATTC AAGGAAAATT

651 700

NC_ 001463 (gag) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG >AY081139 AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCAAGCAG

701 750

NC_ 001463 (gag) GAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA >AY081139 GCGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

751 800

NC_ 001463 (gag) GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGGCAAATAT GCCTGCAATG >AY081139 GCAGCTGCAC AAGCTAACAT GGATCAGGCA AGACAAATAT GCCTGCAATG

801 850

NC_ 001463 (gag) GGTAATAAAT GCATTAAGAG CAGTAAGACA TATGGCGCAC AGGCCAGGGA >AY081139 GGTAATATCA GCCTTAAGAG CAGTGAGACA TATGTCTCAT AAACCAGGGA

851 900

NC_ 001463 (gag) ATCCAATGCT AGTAAAGCAA AAAACGAATG AGCCATATGA AGATTTTGCA >AY081139 ATCCGCTGCT AGTAAAGCAA AAAACAAATG AGTCATATGA AGATTTTGCA

901 950

NC_ 001463 (gag) GCAAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTTACAC AGCCTATAAA >AY081139 GCTAGACTGC TAGAAGCAAT AGATCCAGCC CCAGTAGCAC ATCCTATAAA

951 1000

NC_ 001463 (gag) AGATTATCTA AAGCTAACAC TATCTTATAC AAATGCATCA GCAGATTGTC >AY081139 AGATTATTTA AAGTTAACAC TATCTTATAC GAATGCATCA TCAGATTGTC

1001 1050

NC_ 001463 (gag) AGAAGCAAAT GGATAGAACA CTAGGACAAA GAGTACAACA AGCTAGTGTA >AY081139 AAAAGCAAAT GGGTAGAATG CTAGGATCGA GAGTCCATCA AGCCAGTGTG

1051 1100

NC_ 001463 (gag) GAAGAAAAAA TGCAAGCATG TAGAGATGTG GGATCAGAAG GGTTCAAAAT >AY081139 GGCCAAAAAA

1101 1150

NC_ 001463 (gag) GCAATTGTTA GCACAAGCAT TAAGGCCAGG AAAAGGAAAA GGGAATGGAC >AY081139

1151 1200

NC_ 001463 (gag) AGCCACAAAG GTGTTACAAC TGTGGAAAAC CGGGACATCA AGCAAGGCAA >AY081139

1201 1250

NC_ 001463 (gag) TGTAGACAAG GAATCATATG TCACAACTGT GGAAAGAGAG GACATATGCA >AY081139

1251 1300

NC_ _001463 (gag) AAAAGAATGC AGAGGAAAGA GAGACATAAG GGGAAAACAG CAGGGAAACG >AY081139

1301 1347

NC_ 001463 (gag) GGAGGAGGGG GATACGTGTG GTGCCGTCCG CTCCTCCTAT GGAATAA >AY081139 TABLE 12

PileUp

MSF: 731 Type: N Check: 9546

Name: NC_001463 (gag720bp) (SEQ ID NO: 47) Len: 731 Check: 7595 Weight: 0 Name: >AY101347 (SEQ ID NO: 48) Len: 731 Check: 7962 Weight: 0 Name: >AY101348 (SEQ ID NO: 49) Len: 731 Check: 3989 Weight: 0

/ /

//

1 50 NC-. 001463 (gag720bp) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG >AY101347 >AY101348

51 100

NC-. 001463 (gag720bp) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG >AY101347 AGCAG TAGATTCTGT AATGTTCCAG >AY101348 ... AGCCG TAGATTCTGT AATGTTCCAG

101 150

NC_ 001463 (gag720bp) TTCGACT.CA GAGGGGAGCA CTTGACAGAA GGAAATTGTT TATGGTGCCT >AY101347 ..CAACTGCA AACAGTAGCA AT..GCAGCA TGGACTCGTG TATGAAGACT >AY101348 ..CAGCTGCA AACAGTAGCA AT..GCAGCA TGGCCTCGTG TCAGAGGACT

151 200

NC-. 001463 (gag720bp) TAAAACATTA GATTACATGT TTGAGGACCA TAAAGAGGAA CCTTGGACAA >AY101347 TTGAAAGGCT GTCGGCATAT TATGCTACTA CCTGGACAA GTAAAGATAT >AY101348 TTGAAAGGCT TCCAGCATAT CATGCTACTA CCTGGGCAA GTAAAGATAT

201 250

NC_ 001463 (gag720bp) AAGTAAAATT TAGGACAATA TGGCAGAAGG TGAAGAATCT AACTCCTGAG >AY101347 ACTGGAAGTA TTGGCCATGA TGCCTG..G. ....GAATAG AGCTCAAAAA >AY101348 CTTAGAAGTA CTGGCCATGA TGCCTG..G. ....AAATAG AGCTCAAAAA

251 300

NC_ 001463 (gag720bp) GAGAGTAA.. CAAAAAAGAC TTTATGTCTT TGCAGGCCAC ATTAGCGGGT >AY101347 GA.ATTAATT CAAGGAAAAT TAAATGAAGA AGCAGAAAGG TGGAGAAGGA >AY101348 GA.GTTAATT CAAGGGAAAT TAAATGAAGA AGCAGAGAGG TGGAGAAGGA

301 350

NC_ 001463 (gag720bp) CTAATGTGTT GCCAAATGGG GATGAGACCT GAGACATTGC AAGATGCAAT >AY101347 ATAATCCACC ACCTCAAGCA GGCG.GAGGA TTAACAGTGG ATCAAATTAT >AY101348 ATAATCCACC ACCTCCAGCA GGAG.GAGGG TTAACAGTGG ATCAAATTAT

351 400

NC_ 001463 (gag720bp) GGCTACAGTA ATCATGAAAG ATGG.GTTAC TGGAACAAGA GGAAAAGAAG >AY101347 GGGGGTAGGA CAAACAAATC AAGCAGCTGC ACAAGCTAAC ATGGATCAGG >AY101348 GGGAGTAGGA CAAACAAATC AGGCAGCGGC ACAAGCAAAC ATGGATCAGG

401 450

NC_ 001463 (gag720bp) GAAGACAAAA GAGAAAAGGA AGAG.AGTGT CTTCCC.AAT AGTAGTGCAA >AY101347 CAAGACAAAT ATGCCTGCAA TGGGTAATAT CAGCCTTAAG AGCAGTGAGA >AY101348 CAAGACAAAT ATGCCTACAA TGGGTGATAT CAGCACTAAG AGCAGTAAGG

451 500

NC_ _001463 (gag720bp) GCAGCAGGAG GGAGAAGCTG GAAAGCAGTA GATTCTGTAA TGTTCCAGCA >AY101347 .CATATGTCT CATAAACCAG GGAATCCGCT GCTAGTA.AA GCAAAAAACA >AY101348 .CATATGGCT CACAAGCCAG GGAATCCAAT GTTAGTA.AA GCAAAAAGCA

501 550

NC_ 001463 (gag720bp) ACTG...CAA ACAGTAGCAA TGCAGCATGG CCTCGTGTCT GAGGACTTTG >AY101347 AATGAGTCAT ATGAAGATTT TGCAGCAAGA CTGCTAGAAG CAATAGATGC >AY101348 AATGAGCCAT ATGAAGAATT TGCAGCAAGG CTGCTGGAAG CAATAGATGC

551 600

NC_001463 (gag720bp) AAAGGCAGTT GG.CATATTA TGCTACTACC TGGACAAGTA AAGACATAC >AY101347 AGAGCCAGTA GCACATCCTA TAAAAGAATA CTTA.AAGTT AACACTATCT >AY101348 CGAGCCAGTT AATCAGCCCA TAAAAGAATA TCTA.AAACT AACGTTGTCT

GOl 650

NC_001463 (gag720bp) TAGAAGTATT GGCCATGATG CCTGGAAATA GAGCTCAAAA GGAGTTAATT >AY101347 TATACGAATG CATCATCA.G ATTGTCAAAA G....CAAAT GGATAGAATG >AY101348 TATACGAATG CATCCTCA.G ATTGTCAGAA G....CAAAT GGATAGAACA

651 700

NC_001463 (gag720bp) CAAGGGAAAT TAAATGAAGA AGCAGAAAGG TGGAGAAGGA ATAATCCACC

>AY101347 CTGG...AAT CAAGAGTACA ACAAGCTAG. TGTAGAACAA AAAA

>AY101348 CTAG...GAC AAAGAGTCAA ACAAGCTAG. TGTAGAACAA AAAA

701 731

NC_001463 (gag720bp) ACCTCCAGCA GGAGGAGGAT TAACAGTGGA T >AY101347 >AY101348

PiIeUp

MSF: 1347 Type: N Check: 2815

Name: NC_001463 (gag) (SEQ ID NO: 50) Len: 1347 Check: 6959 Weight: 0 Name: >AY101347 (SEQ ID NO: 51) Len: 1347 Check: 969 Weight: 0 Name: >AY101348 (SEQ ID NO: 52) Len: 1347 Check: 4887 Weight: 0

//

1 50

NC_001463 (gag) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG

>AY101347

>AY101348

51 100

NC_001463 (gag) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG

>AY101347

>AY101348

101 150

NC_001463 (gag) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT

>AY101347 ^'.

>AY101348

151 200

NC_001463 (gag) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA

>AY101347

>AY101348

201 250

NC_001463 (gag) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG

>AY101347

>AY101348

251 300

NC_001463 (gag) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA

>AY101347

>AY101348

301 350

NC_001463 (gag) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC >AY101347 >AY101348

351 400

NC_ 001463 (gag) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG >AY101347 >AY101348

401 450

NC_ 001463 (gag) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA >AY101347 >AY101348

451 500

NC_ 001463 (gag) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA >AY101347 AGC AGTAGATTCT GTAATGTTCC AGCAACTGCA >AY101348 AGC CGTAGATTCT GTAATGTTCC AGCAGCTGCA

501 550

NC_ _001463 (gag) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT >AY101347 AACAGTAGCA ATGCAGCATG GACTCGTGTA TGAAGACTTT GAAAGGCTGT >AY101348 AACAGTAGCA ATGCAGCATG GCCTCGTGTC AGAGGACTTT GAAAGGCTTC

551 600

NC_ 001463 (gag) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG >AY101347 CGGCATATTA TGCTACTACC TGGACAAGTA AAGATATACT GGAAGTATTG >AY101348 CAGCATATCA TGCTACTACC TGGGCAAGTA AAGATATCTT AGAAGTACTG

601 650

NC_ 001463 (gag) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT >AY101347 GCCATGATGC CTGGGAATAG AGCTCAAAAA GAATTAATTC AAGGAAAATT >AY101348 GCCATGATGC CTGGAAATAG AGCTCAAAAA GAGTTAATTC AAGGGAAATT

651 700

NC_ 001463 (gag) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG >AY101347 AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCAAGCAG >AY101348 AAATGAAGAA GCAGAGAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG

701 750

NC_ 001463 (gag) GAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA >AY101347 GCGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA >AY101348 GAGGAGGGTT AACAGTGGAT CAAATTATGG GAGTAGGACA AACAAATCAG

751 800

NC_ 001463 (gag) GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGGCAAATAT GCCTGCAATG >AY101347 GCAGCTGCAC AAGCTAACAT GGATCAGGCA AGACAAATAT GCCTGCAATG >AY101348 GCAGCGGCAC AAGCAAACAT GGATCAGGCA AGACAAATAT GCCTACAATG

801 850

NC_ 001463 (gag) GGTAATAAAT GCATTAAGAG CAGTAAGACA TATGGCGCAC AGGCCAGGGA >AY101347 GGTAATATCA GCCTTAAGAG CAGTGAGACA TATGTCTCAT AAACCAGGGA >AY101348 GGTGATATCA GCACTAAGAG CAGTAAGGCA TATGGCTCAC AAGCCAGGGA

851 900

NC_ 001463 (gag) ATCCAATGCT AGTAAAGCAA AAAACGAATG AGCCATATGA AGATTTTGCA >AY101347 ATCCGCTGCT AGTAAAGCAA AAAACAAATG AGTCATATGA AGATTTTGCA >AY101348 ATCCAATGTT AGTAAAGCAA AAAGCAAATG AGCCATATGA AGAATTTGCA

901 950

NC_ _001463 (gag) GCAAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTTACAC AGCCTATAAA >AY101347 GCAAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTAGCAC ATCCTATAAA >AY101348 GCAAGGCTGC TGGAAGCAAT AGATGCCGAG CCAGTTAATC AGCCCATAAA

951 1000 NC 001463 (gag) AGATTATCTA AAGCTAACAC TATCTTATAC AAATGCATCA GCAGATTGTC

>AY101347 AGAATACTTA AAGTTAACAC TATCTTATAC GAATGCATCA TCAGATTGTC

>AY101348 AGAATATCTA AAACTAACGT TGTCTTATAC GAATGCATCC TCAGATTGTC

1001 1050

NC 001463 (gag) AGAAGCAAAT GGATAGAACA CTAGGACAAA GAGTACAACA AGCTAGTGTA

>AY101347 AAAAGCAAAT GGATAGAATG CTGGAATCAA GAGTACAACA AGCTAGTGTA

>AY101348 AGAAGCAAAT GGATAGAACA CTAGGACAAA GAGTCAAACA AGCTAGTGTA

1051 1100

NC 001463 (gag) GAAGAAAAAA TGCAAGCATG TAGAGATGTG GGATCAGAAG GGTTCAAAAT

>AY101347 GAACAAAAAA

>AY101348 GAACAAAAAA

1101 1150

NC 001463 (gag) GCAATTGTTA GCACAAGCAT TAAGGCCAGG AAAAGGAAAA GGGAATGGAC

>AY101347

>AY101348

1151 1200

NC 001463 (gag) AGCCACAAAG GTGTTACAAC TGTGGAAAAC CGGGACATCA AGCAAGGCAA

>AY101347

>AY101348

1201 1250

NC 001463 (gag) TGTAGACAAG GAATCATATG TCACAACTGT GGAAAGAGAG GACATATGCA

>AY101347

>AY101348

1251 1300

NC 001463 (gag) AAAAGAATGC AGAGGAAAGA GAGACATAAG GGGAAAACAG CAGGGAAACG

>AY101347

>AY101348

1301 1347

NC 001463 (gag) GGAGGAGGGG GATACGTGTG GTGCCGTCCG CTCCTCCTAT GGAATAA

>AY101347

>AY101348

TABLE 13

PileUp

MSF: 720 Type: N Check: 3690

Name NC_001463 (gag720bp) (SEQ ID NO: 53) Len: 720 Check: 5792 Weight: Name >L78446 (SEQ ID NO: 54) Len: 720 Check: 272 Weight : Name >L78447 (SEQ ID NO: 55) Len: 720 Check: 1999 Weight: 0 Name >L78450 (SEQ ID NO: 56) Len: 720 Check: 9633 Weight: 0 Name >L78451 (SEQ ID NO: 57) Len: 720 Check: 5177 Weight : 0 Name >L78453 (SEQ ID NO: 58) Len: 720 Check: 817 Weight : 0

//

1 50

NC_001463 (gag720bp) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG

>L78446

>L78447

>L78450

>L78451

>L78453

51 100

NC_001463 (gag720bp) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG

>L78446

>L78447

>L78450

>L78451

>L78453

101 150

NC_001463 (gag720bp) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT

>L78446

>L78447

>L78450

>L78451

>L78453

151 200

NC_001463 (gag720bp) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA

>L78446

>L78447

>L78450

>L78451

>L78453

201 250

NC_001463 (gag720bp) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG

>L78446

>L78447

>L78450

>L78451

>L78453

251 300

NC_001463 (gag720bp) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA

>L78446

>L78447

>L78450

>L78451

>L78453

301 350

NC 001463 (gag720bp) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC >L78446

>L78447

>L78450

>L78451

>L78453

351 400

NC 001463 (gag720bp) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG

>L78446

>L78447

>L78450

>L78451

>L78453

401 450

NC 001463 (gag720bp) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA

>L78446

>L78447

>L78450

>L78451

>L78453

451 500

NC 001463 (gag720bp) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA

>L78446

>L78447

>L78450

>L78451

>L78453

501 550

NC 001463 (gag720bp) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT

>L78446 ...CAGCATG GCCTCGTGTC CGAGGACTTT GAAAGGCAGT

>L78447 CAGCATG GAATAGTATC AGAAGAGTTT GAGAGGCAAC

>L78450 CAACATG GGATAGTATC AGAGGAATTT GAGAGACAAA

>L78451 ...CAGCATG GACTAGTATC AGAAGAATTT GAAAGGCAGC

>L78453 CAGCATG GACTTGTGTC CGAAGATTTT GAGAGGCAAT

551 600

NC 001463 (gag720bp) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG

>L78446 TGGCATATTA TGCTACTACC TGGACAAGTA AGGACATATT AGAAGTATTG

>L78447 TGTCTTATTA TGCTACCACT TGGACAAGCA AGGATATCTT AGAGGTACTA

>L78450 TGTCTTATTA TGCTACCACA TGGACAAGTA AGGATATTTT AGAAGTACTA

>L78451 TAGCATACTA TGCCACAACG TGGACAAGCA AAGACATACT AGAGGTGTTA

>L78453 TGGCATATTA TGCTACAACC TGGACTAGTG AAGATATATT AGAAGTATTG

601 650

NC 001463 (gag720bp) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT

>L78446 GCCATGATGC CAGGAAATAG AGCTCAAAAG GAGCTAATTC AA

>L78447 GCCATGATGC CTGGCAATAG AGCATTAAAA GAGCTAATAC AA

>L78450 GCAATGATGC CCGGGAACAG AGCATTAAAG GAGCTGATAC AA

>L78451 GCCATGATGC CAGGGAATAG AGCACAAAAA GAACTAATAC AA

>L78453 GCTATGATGC CTGGGAATAG AGCACAGAAA GAATTAATAC AA

651 700

NC 001463 (gag720bp) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG

>L78446

>L78447

>L78450

>L78451

>L78453

701 720

NC 001463 (gag720bp) GAGGAGGATT AACAGTGGAT

>L78446

>L78447

>L78450

>L78451 >L78453

PiIeUp

MSF: 1347 Type: N Check: 6947

Name NC_001463 (gag) (SEQ ID NO: 59) Len: 1347 Check: 6959 Weight: 0 Name >L78446 (SEQ ID NO: 60) Len: 1347 Check: 6690 Weight: 0 Name >L78447 (SEQ ID NO: 61) Len: 1347 Check: 8417 Weight: 0 Name >L78450 (SEQ ID NO: 62) Len: 1347 Check: 6051 Weight: 0 Name >L78451 (SEQ ID NO: 63) Len: 1347 Check: 1595 Weight: 0 Name >L78453 (SEQ ID NO: 64) Len: 1347 Check: 7235 Weight: 0

//

1 - 50

NC_001463 (gag) ATGGTGAGTC TAGATAGAGA CATGGCGAGG CAAGTCTCCG GGGGGAAAAG

>L78446

>L78447

>L78450

>L78451

>L78453

51 100

NC_001463 (gag) AGATTATCCT GAGCTCGAAA AATGTATCAA GCATGCATGC AAGATAAAAG

>L78446

>L78447

>L78450

>L78451

>L78453

101 150

NC_001463 (gag) TTCGACTCAG AGGGGAGCAC TTGACAGAAG GAAATTGTTT ATGGTGCCTT

>L78446

>L78447

>L78450

>L78451

>L78453

151 200

NC_001463 (gag) AAAACATTAG ATTACATGTT TGAGGACCAT AAAGAGGAAC CTTGGACAAA

>L78446

>L78447

>L78450

>L78451

>L78453

201 250

NC_001463 (gag) AGTAAAATTT AGGACAATAT GGCAGAAGGT GAAGAATCTA ACTCCTGAGG

>L78446

>L78447

>L78450

>L78451

>L78453

251 300

NC_001463 (gag) AGAGTAACAA AAAAGACTTT ATGTCTTTGC AGGCCACATT AGCGGGTCTA

>L78446

>L78447

>L78450

>L78451

>L78453

301 350

NC_0.01463 (gag) ATGTGTTGCC AAATGGGGAT GAGACCTGAG ACATTGCAAG ATGCAATGGC

>L78446 >L78447 >L78450

>L78451

>L78453

351 400

NC 001463 (gag) TACAGTAATC ATGAAAGATG GGTTACTGGA ACAAGAGGAA AAGAAGGAAG

>L78446

>L78447

>L78450

>L78451

>L78453

401 450

NC 001463 (gag) ACAAAAGAGA AAAGGAAGAG AGTGTCTTCC CAATAGTAGT GCAAGCAGCA

>L78446

>L78447

>L78450

>L78451

>L78453

451 500

NC 001463 (gag) GGAGGGAGAA GCTGGAAAGC AGTAGATTCT GTAATGTTCC AGCAACTGCA

>L78446

>L78447

>L78450

>L78451

>L78453

501 550

NC 001463 (gag) AACAGTAGCA ATGCAGCATG GCCTCGTGTC TGAGGACTTT GAAAGGCAGT

>L78446 CAGCATG GCCTCGTGTC CGAGGACTTT GAAAGGCAGT

>L78447 CAGCATG GAATAGTATC AGAAGAGTTT GAGAGGCAAC

>L78450 CAACATG GGATAGTATC AGAGGAATTT GAGAGACAAA

>L78451 ...CAGCATG GACTAGTATC AGAAGAATTT GAAAGGCAGC

>L78453 ...CAGCATG GACTTGTGTC CGAAGATTTT GAGAGGCAAT

551 600

NC 001463 (gag) TGGCATATTA TGCTACTACC TGGACAAGTA AAGACATACT AGAAGTATTG

>L78446 TGGCATATTA TGCTACTACC TGGACAAGTA AGGACATATT AGAAGTATTG

>L78447 TGTCTTATTA TGCTACCACT TGGACAAGCA AGGATATCTT AGAGGTACTA

>L78450 TGTCTTATTA TGCTACCACA TGGACAAGTA AGGATATTTT AGAAGTACTA

>L78451 TAGCATACTA TGCCACAACG TGGACAAGCA AAGACATACT AGAGGTGTTA

>L78453 TGGCATATTA TGCTACAACC TGGACTAGTG AAGATATATT AGAAGTATTG

601 650

NC 001463 (gag) GCCATGATGC CTGGAAATAG AGCTCAAAAG GAGTTAATTC AAGGGAAATT

>L78446 GCCATGATGC CAGGAAATAG AGCTCAAAAG GAGCTAATTC AA

>L78447 GCCATGATGC CTGGCAATAG AGCATTAAAA GAGCTAATAC AA

>L78450 GCAATGATGC CCGGGAACAG AGCATTAAAG GAGCTGATAC AA

>L78451 GCCATGATGC CAGGGAATAG AGCACAAAAA GAACTAATAC AA

>L78453 GCTATGATGC CTGGGAATAG AGCACAGAAA GAATTAATAC AA

651 700

NC 001463 (gag) AAATGAAGAA GCAGAAAGGT GGAGAAGGAA TAATCCACCA CCTCCAGCAG

>L78446

>L78447

>L78450

>L78451

>L78453

701 750

NC 001463 (gag) GAGGAGGATT AACAGTGGAT CAAATTATGG GGGTAGGACA AACAAATCAA

>L78446

>L78447

>L78450

>L78451

>L78453 ^•751 800

NC_001463 (gag) GCAGCAGCAC AAGCTAACAT GGATCAGGCA AGGCAAATAT GCCTGCAATG

>L78446 _,

>L78447

>L78450

>L78451

>L78453

801 850

NC_001463 (gag) GGTAATAAAT GCATTAAGAG CAGTAAGACA TATGGCGCAC AGGCCAGGGA

>L78446

>L78447

>L78450

>L78451

>L78453

851 900

NC_001463 (gag) ATCCAATGCT AGTAAAGCAA AAAACGAATG AGCCATATGA AGATTTTGCA

>L78446

>L78447

>L78450

>L78451

>L78453

901 950

NC_001463 (gag) GCAAGACTGC TAGAAGCAAT AGATGCAGAG CCAGTTACAC AGCCTATAAA

>L78446

>L78447

>L78450

>L78451

>L78453

951 1000

NC_001463 (gag) AGATTATCTA AAGCTAACAC TATCTTATAC AAATGCATCA GCAGATTGTC

>L78446

>L78447

>L78450

>L78451

>L78453

1001 1050

NC_001463 (gag) AGAAGCAAAT GGATAGAACA CTAGGACAAA GAGTACAACA AGCTAGTGTA

>L78446

>L78447

>L78450

>L78451

>L78453

1051 1100

NC_001463 (gag) GAAGAAAAAA TGCAAGCATG TAGAGATGTG GGATCAGAAG GGTTCAAAAT

>L78446

>L78447

>L78450

>L78451

>L78453

1101 1150

NC_001463 (gag) GCAATTGTTA GCACAAGCAT TAAGGCCAGG AAAAGGAAAA GGGAATGGAC

>L78446

>L78447

>L78450

>L78451

>L78453

1151 1200 NC_001463 (gag) AGCCACAAAG GTGTTACAAC TGTGGAAAAC CGGGACATCA AGCAAGGCAA

>L78446

_>L78447

>L78450

>L78451

>L78453

1201 1250

NC_001463 (gag) TGTAGACAAG GAATCATATG TCACAACTGT GGAAAGAGAG GACATATGCA

>L78446

>L78447

>L78450

>L78451

>L78453

1251 1300

NC_001463 (gag) AAAAGAATGC AGAGGAAAGA GAGACATAAG GGGAAAACAG CAGGGAAACG

>L78446

>L78447

>L78450

>L78451

>L78453

1301 1347

NC_001463 (gag) GGAGGAGGGG GATACGTGTG GTGCCGTCCG CTCCTCCTAT GGAATAA

>L78446

>L78447

>L78450

>L78451

>L78453

TABLE 14

Tables for alignment of gag sequences NC_001463(gag720bp) vs. AF015181 Positives: 41.0 % Identity : 41.0 %

NCJ)Ol 463(gag) vs. AF015181 Positives: 40.6% Identity : 40.6%

NC_001463(gag 720bp) vs. AF402664-8 Positives: 91.1 % Identity : 32.2%

10

NC_001463(gag) vs. AF402664-8 Positives: 49.1% Identity :35.0%

15

NC_001463(gag720bp) vs. AJ305040-2 Positives: 80.5 % Identity : 38.1%

NC_001463(gag) vs. AJ305040-2 Positives: 44.3% Identity : 38.8%

NC_001463(gag720bp) vs. AY047362 Positives: 40.2 % Identity : 40.2 %

NCJ)01463(gag) vs. AY047362 ^• Positives: 35.7% Identity : 35.7%

NC_001463(gag720bp) vs. AY081139 Positives: 40.0% Identity : 40.0%

NC_001463(gag) vs. AY081139 Positives: 39.8% Identity : 39.8%

NC_001463(gag720bp) vs. AY101347-8 Positives: 78.1 % Identity : 35.0%

5 NC_001463(gag) vs. AY101347-8 Positives: 43.9 % Identity : 37.9%

NC_001463(gag720bp) vs. L78446, 7, 50,51,53 Positives: 17.6 % Identity : 11.9%

10

NC_001463(gag) vs. L78446,47,50,51,53 Positives: 9.4% Identity : 6.4%

15

TABLE 15

NC_001463 (full genome) vs.AF322109(full genome) Positives: 68.2% Identity: 68.2%

20

NCJ)Ol 463(gag) vs.AF322109(gag) Positives: 73.1% Identity: 73.1%

NC_001463(5'LTR region) vs.AF322109(5 'LTR region) Positives: 59.8% Identity: 59.8%

NCJ)Ol 463(ρol) vs.AF322109(ρol) Positives: 74.9% Identity: 74.9%

NCJ)01463(rev) vs.AF322109(rev) Positives: 48.3% Identity: 48.3%

NCJ)01463(vif) vs.AF322109(vif) Positives: 66.0% Identity: 66.0%

Claims

WHAT IS CLAIMED IS:

1. A transfer vector, comprising:

(a) A caprine arthritis encephalitis virus (CAEV) packaging sequence consisting essentially of (i) the untranslated region between the CAEV 5 ' LTR and the CAEV gαg-encoding sequence and (ii) nucleotides 1 to X of the CAEV gag- encoding sequence linked to the 3' end of said untranslated region, wherein X is less than 613; and

(b) cis-acύng elements required for polyadenylation, RNA transport, reverse transcription, and integration, in operable association with said packaging sequence.

2. The transfer vector of claim 1, wherein X is selected from the group consisting of: 60, 100, 125, 150, 175, 200, 225, 250, 275, 300, 325, 350, 375, 400, 425, 450, 475, 500, 525, 550, 575 and 600.

3. The transfer vector of claim 1, wherein X is selected from the group consisting of:

(a) X is greater than 25 and less than 600,

(d) X is greater than 25 and less than 300,

(e) X is greater than 25 and less than 200,

(f) X is greater than 50 and less than 600,

(i) X is greater than 50 and less than 300, (j) X is greater than 50 and less than 200, (k) X is greater than 75 and less than 600, (1) X is greater than 75 and less than 500, (m) X is greater than 75 and less than 400, (n) X is greater than 75 and less than 300,

(o) X is greater than 75 and less than 200,

(p) X is greater than 100 and less than 600,

(q) X is greater than 100 and less than 500, (r) X is greater than 100 and less than 400,

(s) X is greater than 100 and less than 300,

(t) X is greater than 100 and less than 200,

(u) X is greater than 125 and less than 600,

(v) X is greater than 125 and less than 500, (w) X is greater than 125 and less than 400,

(x) X is greater than 125 and less than 300,

(y) X is greater than 125 and less than 200,

(z) X is greater than 150 and less than 600,

(aa) X is greater than 150 and less than 500, (bb) X is greater than 150 and less than 400,

(cc) X is greater than 150 and less than 300,

(dd) X is greater than 150 and less than 200,

(ee) X is greater than 200 and less than 600,

(ff) X is greater than 200 and less than 500, (gg) X is greater than 200 and less than 400,

(hh) X is greater than 200 and less than 300,

(ii) X is greater than 200 and less than 200,

(jj) X is greater than 250 and less than 600,

(kk) X is greater than 250 and less than 500, (11) X is greater than 250 and less than 400, and

(mm) X is greater than 250 and less than 300.

4. The transfer vector of claim 1, wherein X is greater than 40 and less than 613.

5. The transfer vector of claim 1, wherein X is greater than 57 and less than 613.

6. The transfer vector of claim 1, wherein X is about 327. 7. The transfer vector of claim 1, wherein the start codon of the gαg-encoding sequence is mutated to prevent translation of gag protein.

8. The transfer vector of claim 7, wherein said start codon is mutated to TAG.

9. The transfer vector of claim 7, wherein the ATG codon of the gαg-encoding sequence located x base pairs downstream of the start codon ATG is mutated to prevent translation of gag protein, wherein x is less than 30.

10. The transfer vector of claim 9, wherein x is about 21.

11. The transfer vector of claim 1 , which further comprises an RRE region.

12. The transfer vector of claim 1, which further comprises the CAEV 3' LTR, wherein the U3 region is deleted.

13. The transfer vector of claim 1, which further comprises a heterologous promoter.

14. The transfer vector of claim 13, wherein the heterologous promoter is the human cytomegalovirus major immediate early promoter (HCMV MIEP).

15. The transfer vector of claim 1, wherein said vector has the structure of pCAH/SINdl shown in Figure 3C.

16. The transfer vector of claim 1, which further comprises a transcription cassette.

17. The transfer vector of claim 16, wherein said transcription cassette comprises a polynucleotide of interest operably linked to a heterologous promoter. 18. A vector system comprising the transfer vector of claim 1, and a packaging vector system, wherein said packaging vector system comprises: a first polynucleotide comprising a CAEV gag-pol-encoding sequence and an RRE, and a second polynucleotide comprising a viral envelope-encoding sequence.

19. The vector system of claim 18, wherein said transfer vector further comprises a transcription cassette.

20. The vector system of claim 19, wherein said transcription cassette comprises a polynucleotide of interest operably linked to a heterologous promoter.

21. The vector system of claim 18, wherein said viral envelope-encoding sequence is a non-CAEV envelope-encoding sequence.

22. The vector system of claim 21, wherein said non-CAEV envelope-encoding sequence is a VSV-G-encoding sequence or a GaLV-encoding sequence.

23. The vector system of claim 22, wherein said envelope-encoding sequence is a VSV-G-encoding sequence.

24. The vector system of claim 22, wherein said envelope-encoding sequence is a GaLV-encoding sequence.

25. The vector system of claim 18, wherein said vector system further comprises a third polynucleotide sequence comprising a rev-encoding sequence.

26. The vector system of claim 18 or 25, wherein said vector system further comprises a fourth polynucleotide sequence comprising a sequence.

27. The vector system of any of claims 18, 25 or 26, wherein said first polynucleotide further comprises a heterologous regulatory sequence operably linked to said CAEV gag-pol-encoding sequence. 28. The vector system of any of claims 18, 21 or 22, wherein said second polynucleotide further comprises a heterologous regulatory sequence operably linked to said viral envelope-encoding sequence.

29. The vector system of claim 18, wherein said first polynucleotide further comprises a heterologous regulatory sequence operably linked to said CAEV gag- pσ/-encoding sequence and said second polynucleotide further comprises a heterologous regulatory sequence operably linked to said viral envelope-encoding sequence.

30. The vector system of claim 25, wherein said third polynucleotide further comprises a heterologous regulatory sequence operably linked to said rev-encoding sequence.

31. The vector system of claim 26, wherein said fourth polynucleotide further comprises a heterologous regulatory sequence operably linked to said vz/-encoding sequence.

32. The vector system of claims 27, 28, 29, 30 or 31, wherein said heterologous regulatory sequence is a promoter.

33. The vector system of claim 18, wherein said packaging vector system is devoid of a competent CAEV packaging sequence.

34. The vector system of claim 18, wherein said packaging vector system is devoid of the 5' end of the CAEV genome between the splice donor site and the gag start codon.

35. The vector system of claim 18, which comprises a first vector comprising said first polynucleotide and a second vector comprising said second polynucleotide. 36. The vector system of claim 25, which comprises a first vector comprising said first polynucleotide, a second vector comprising said second polynucleotide, and a third vector comprising said third polynucleotide.

37. The vector system of claim 26, which comprises a first vector comprising said first polynucleotide, a second vector comprising said second polynucleotide, a third vector comprising said third polynucleotide, and a fourth vector comprising said fourth polynucleotide.

38. The vector system of claim 25, which comprises a first vector comprising said first polynucleotide and said third polynucleotide, and a second vector comprising said second polynucleotide.

39. The vector system of claim 26, which comprises a first vector comprising said first polynucleotide, and said fourth polynucleotide, and a second vector comprising said second polynucleotide.

40. The vector system of claim 32, wherein said CAEV gαg-po/-encoding sequence is operably linked to an MCMV MIEP promoter.

41. The vector system of claim 40, wherein said first vector has the structure of pMGP/RRE shown in Figure 2A.

42. The vector system of claim 35, wherein said viral envelope-encoding sequence is a VSV-G-encoding sequence operably linked to an HCMV MIEP promoter, and wherein said second vector further comprises a beta globin intron.

43. The vector system of claim 42, wherein said second vector has the structure of ρHGVSV-G shown in Figure 6 A.

44. The vector system of claim 35, wherein said viral envelope-encoding sequence is a GaLV-encoding sequence operably linked to an MCMV MIEP promoter, and wherein said second vector further comprises a eukaryotic elongation factor- 1 alpha intron.

45. The vector system of claim 44, wherein said second vector has the structure of pMYKEF- 1 /env shown in Figure 6B .

46. The vector system of claim 36, wherein said third vector has the structure of pHYK/rev shown in Figure 5.

47. The vector system of claim 37, wherein said fourth vector has the structure of pHYK/vif shown in Figure 4.

48. A method of producing a CAEV-based vector particle comprising:

(a) transfecting a cell with the vector system of claim 20; (b) incubating said cell under conditions allowing for the production of

CAEV-based lentiviral vector particles, where the vector particles are infectious and transduction competent, and replication defective; and (c) recovering said vector particle.

49. A vector particle produced by the method of claim 48.

50. A composition comprising the vector particle of claim 49 and a carrier.

51. A kit comprising the vector system of any one of claims 18-47.

52. A method for delivering a polypeptide into a mammalian cell comprising contacting said mammalian cell with the vector particle of claim 49.

53. The method of claim 52, wherein said cell is isolated from a mammal prior to contacting the cell with the vector particle.

54. The method of claim 52, wherein said mammalian cell is a dividing cell. 55. The method of claim 52, wherein said mammalian cell is a non-dividing cell.

56. The method of claim 52, wherein said mammalian cell is a CD34+ stem cell.

57. A method of delivering a polypeptide into a vertebrate comprising administering to the vertebrate the vector particle of claim 49.

58. A kit comprising the transfer vector of any one of claims 1-17.

59. The vector system of any of claims 18-47, which further comprises a cell comprising said first polynucleotide.

60. The vector system of any of claims 28, 30, 32, 36 or 38, which further comprises a cell comprising said first and third polynucleotides.

61. The vector system of any of claims 26-28, 31-32, 37, 39, 41, 43, or 45, which further comprises a cell comprising said first and fourth polynucleotides.

62. The vector system of any of claims 26-28, 31-32, 37, 39, 41, 43, or 45, which further comprises a cell comprising said first, third and fourth polynucleotides.

63. The vector system of any of claims 18-24, 26, 29, 33-35, 40, 42, 44, or 46, which further comprises a cell comprising said first and second polynucleotides.

64. The vector system of any of claims 25-28, 30, 32, 36, or 38, which further comprises a cell comprising said first, second, and third polynucleotides.

65. The vector system of any of claims 26-28, 31-32, 37, 39, 41, 43, or 45, which further comprises a cell comprising said first, second and fourth polynucleotides. 66. The vector system of any of claims 26-28, 31-32, 37, 39, 41, 43, or 45, which further comprises a cell comprising said first, second, third, and fourth polynucleotides.

67. The vector system of any of claims 35-47, which further comprises a cell comprising said first and second vectors.

68. The vector system of any of claims 36-46, which further comprises a cell comprising said first, second, and third vectors.

69. The vector system of any of claims 36-47, which further comprises a cell comprising said first, second, third, and fourth vectors.

70. The vector system of any of claims 35-47, which further comprises a cell comprising said first vector.

71. A method of producing a CAEV-based vector particle comprising:

(a) preparing a cell comprising a CAEV gαg-/?o/-encoding sequence and an RRE. (b) transfecting said cell with the transfer vector of claim 17.

(c) incubating said cell under conditions allowing for the production of CAEV-based lentiviral vector particles, where the vector particles are infectious and transduction competent, and replication defective; and

(d) recovering said vector particle.

72. A vector comprising a C AEV packaging sequence consisting essentially o f (a) the untranslated region between the CAEV 5'LTR and the CAEV gαg-encoding sequence, and (b) nucleotides 1 to X of the CAEV gαg-encoding sequence linked to the 3' end of said untranslated region, wherein X is less than 613. 73. The transfer vector of claim 15, wherein said vector is at least 70% identical to SEQ ID NO: 68. 74. The vector system of claim 41, wherein said first vector is at least 70% identical to SEQ ID NO: 77.

75. The vector system of claim 43, wherein said second vector is at least 70% identical to SEQ ID NO: 74. 76. The vector system of claim 45, wherein said second vector is at least 70% identical to SEQ ID NO: 72.

77. The vector system of claim 46, wherein said third vector is at least 70% identical to SEQ ID NO: 75.

78. The vector system of claim 47, wherein said fourth vector is at least 70% identical to SEQ ID NO: 76.