WO1992016543A1 - NORWALK VIRUS HUMAN GASTROENTERITIS AGENT AND MOLECULAR CLONING OF CORRESPONDING cDNAs - Google Patents

NORWALK VIRUS HUMAN GASTROENTERITIS AGENT AND MOLECULAR CLONING OF CORRESPONDING cDNAs Download PDF

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WO1992016543A1
WO1992016543A1 PCT/US1992/002457 US9202457W WO9216543A1 WO 1992016543 A1 WO1992016543 A1 WO 1992016543A1 US 9202457 W US9202457 W US 9202457W WO 9216543 A1 WO9216543 A1 WO 9216543A1
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seq
polypeptide
norwalk virus
group
sequence
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PCT/US1992/002457
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French (fr)
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Jungsuh P. Kim
Suzanne M. Matsui
Harry B. Greenberg
Gregory R. Reyes
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Genelabs Incorporated
The Board Of Trustees Of The Leland Stanford Junior University
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Publication of WO1992016543A1 publication Critical patent/WO1992016543A1/en

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    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/005—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from viruses
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/08—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses
    • C07K16/10—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from viruses from RNA viruses
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N2770/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssRNA viruses positive-sense
    • C12N2770/00011—Details
    • C12N2770/16011—Caliciviridae
    • C12N2770/16022—New viral proteins or individual genes, new structural or functional aspects of known viral proteins or genes

Definitions

  • Norwalk virus genomic nucleic acid sequences to specific polypeptide viral antigens which are immunoreactive with sera from human volunteers infected with Norwalk virus, to polynucleotide sequences which encode these polypep- tide antigens, to an expression system capable of produ ⁇ cing the polypeptide antigens, to methods of using the polypeptide antigens for detecting Norwalk virus anti ⁇ bodies in human sera, and to antibodies directed against these polypeptide antigens.
  • Greenberg, H.B. et al. J. Virol. 37.:994 (1981). Greenberg, H.B., et al. , in Viral Diarrheas of Man and Animals. Eds.: Saif, L.J., et al., CRC, Boca Raton (1989) , pp. 137-159.
  • a group of serologically diverse viruses have been implicated in common source outbreaks of gastroenteritis (Kapikian et al.; Greenberg et al. (1989); Dolin et al.). These viruses included pestiviruses, caliciviruses, astroviruses, parvoviruses , coronaviruses, toroviruses, and the Norwalk-like viruses (also called small round- structured viruses (SRSVs)) . It has been estimated that up to 65% of all cases of acute, non-bacterial gastroen ⁇ teritis in the United States are attributable to viral agents (Blacklow et al. (1982)).
  • SRSVs small round- structured viruses
  • Norwalk virus alone appears to cause at least one-third of all cases of gastroenteritis in U.S. epide ⁇ mics (Kaplan et al.; Greenberg et al. (1979)).
  • Norwalk virus named after a 1968 outbreak of gastroenteritis at a school in Norwalk, Ohio (Adler et al.), was the first of the heterogeneous group of SRSVs to be identified by (IEM) (Kapikian et al.).
  • the viral protein structure of Norwalk virus Greenberg et al. (1981)
  • Norwalk-like viruses such as the Snow Mountain (Madore et al.
  • Another object of the present invention is to pro ⁇ vide a recombinantly produced Norwalk virus polynucleo- tide which encodes a Norwalk virus polypeptide which is immunoreactive with sera from humans infected with Nor ⁇ walk virus 8FIIa infectious inoculum.
  • Specific embodi ⁇ ments of these polynucleotides are those which encode an immunoreactive portion of any one of the following se- quences: SEQ ID NO:2, SEQ ID NO: , SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10.
  • Specific polynucleotides which encode such poiypeptides include: SEQ ID NO:l, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, and SEQ ID NO:9.
  • the present invention also includes Norwalk-virus specific poiypeptides produced by bacterial cells con ⁇ taining a vector selected from the group consisting of lambda-Nl, lambda-N4, and lambda-N8 (these are lambda gtll vectors containing the designated inserts, see Example 3) .
  • the present invention also provides a recombinant Norwalk virus polypeptide which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infec ⁇ tious inoculum.
  • Such recombinant poiypeptides include those having matching and substantially the same sequence as one of the following poiypeptides: SEQ ID NO:2, SEQ ID NO:4, SEQ ID N0:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID N0:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, and SEQ ID NO:20.
  • the recombinant polypeptide may also include portions of other proteins, such as in-frame fusions to the la.cZ encoded / S-galactosidase protein.
  • Such recom ⁇ binant poiypeptides can be obtained from bacterial cells transformed with one of the following vectors: lambda- Nl, lambda-N4, and lambda-N8.
  • the invention includes, in one aspect, a method for the detection of Norwalk virus in human stool samples.
  • the method includes the partial purification of poly ⁇ nucleotides present in the stool sample, followed by hybridization to negative-sense oligonucleotide probes specific for the Norwalk virus polynucleotide.
  • the method also includes means for detecting the binding of the negative sense probes to polynucleotides present in the stool sample.
  • detection means include the standard detection methods of labelling the probe by biotinylation or radioactive isotopes.
  • the method may include generation of cDNA molecules from RNA templates present in the partially purified sample and sequence independent amplification of the resulting cDNA mole ⁇ cules.
  • Negative-sense oligonucleotide probes and oligo- nucleotide primers specific for the Norwalk virus poly- nucleotide are also defined by the present invention. Both the probes and primers can be derived from the above-described Norwalk virus coding sequences.
  • kits contains a recombinant Norwalk virus polypeptide antigen which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum, and means for detecting the binding of said antibodies to the antigen.
  • Polypeptide antigens include ⁇ ding an immunoreactive portion of any of the above de ⁇ scribed Norwalk virus epitopes may be used in this re ⁇ gard.
  • the kit may include a solid support to which the polypeptide antigen is attached and a reporter-labeled anti-human antibody.
  • Yet another aspect of the present invention includes an expression system and a method of producing a Norwalk virus polypeptide which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum.
  • the method includes introducing into a suit- able host a recombinant expression system containing an open reading frame (ORF) , where the ORF has a polynucleo- tide sequence which encodes a Norwalk virus polypeptide immunoreactive with sera from humans infected with Nor ⁇ walk virus 8FIIa infectious inoculum.
  • ORF open reading frame
  • the vector is designed to express the ORF in the selected host.
  • the host is then cultured under conditions resul ⁇ ting in the expression of the ORF sequence.
  • a number of expression systems can be used in this regard including the lambda gtll expression system in an Escherichia coli host.
  • Other expression systems include expression vec ⁇ tors for use in yeast, bacterial, insect, and mammalian cells.
  • the vaccine includes a recombinant Norwalk virus polype ⁇ ptide antigen which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum.
  • Such polypeptide antigens may include an immunoreactive portion of the above described Norwalk virus coding sequences.
  • the polypeptide antigen is typically prepared in a pharmacologically acceptable adjuvant.
  • the invention further includes antibodies specific against a polypeptide having a sequence selected from the following group: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10.
  • Antibodies can also be generated against the Norwalk-virus-specific antigen produced by bacterial cells transformed with one of the following vectors: lambda-Nl, lambda-N4, or lambda-N8. These antibodies may be polyclonal or monoclonal.
  • the antibodies can be used in a method of producing passive immunity in an individual against Norwalk virus, which includes administering the antibodies parenterally to the individual.
  • Figure 1 shows that radiolabeled N49-insert specific probes hybridize to only amplified nucleic acid extracted from a partially purified Norwalk virus-infected stool sample LT1-8 and not to amplified nucleic acid derived from the pre-infection stool.
  • Figure 2 shows the alignment of the following se ⁇ quences using the N35 insert sequence as a reference se ⁇ quence: N35, SEQ ID NO:l; N28, SEQ ID NO:3; N40, SEQ ID N0:5; N48, SEQ ID NO:7; N49 and N51, SEQ ID NO:9.
  • Figure 3 further demonstrates that radiolabeled N49- insert specific probes hybridize to only nucleic acid extracted from partially purified Norwalk virus-infected stool samples.
  • Figure 4 shows the results of hybridization of an internal, N49-insert specific, radiolabeled probe to RNA extracted from serial, Norwalk volunteer, fecal speci ⁇ mens.
  • Figure 5 shows the effect of RNaseA treatment on the hybridization of a N49-insert specific probe to Norwalk virus nucleic acid.
  • Figure 6 shows the differential hybridization of positive and negative strand N49-insert specific probe to Norwalk virus nucleic acid.
  • Figure 7 shows the correspondence of clone-specific probe hybridization peak and Norwalk viral antigen peak in a cesium chloride gradient fraction of buoyant density 1.37 g/ml.
  • Figure 8 shows how new Norwalk virus sequences can be identified by an epitope spanning method.
  • Figure 9 shows the sequence of the N2 insert (indi ⁇ cated by arrows, SEQ ID NO:18) with regions of homology to N35 (solid overline) and N3 (double overline) indicat ⁇ ed.
  • the KCL-2 probe is indicated by a box.
  • the SISPA primers are indicated by a single underline.
  • Figure 10 shows the sequence of the N3 insert (indi ⁇ cated by arrows; SEQ ID NO:19) with regions of homology to N35 (solid overline) and N2 (double overline) indicat ⁇ ed.
  • the KCL-2 probe is indicated by a box.
  • the SISPA primers are indicated by a single underline.
  • Figure 11 graphically illustrates the alignment of the following sequences using the N35 insert sequence as a reference sequence: N35, SEQ ID N0:1; N2, SEQ ID NO:12; and N3, SEQ ID NO:14.
  • the Norwalk virus polynucleotide refers to variations of the disclosed sequences, such as degenerate codons, or variations in sequence which may be present in isolates or strains of Norwalk virus which are immuno- logically cross reactive with the 8FIIa isolate.
  • Two nucleic acid fragments are "homologous" if they are capable of hybridizing to one another under hybridization conditions described in Maniatis et al. , op. cit.. pp. 320-323, using the following wash condi ⁇ tions: 2 x SCC, 0.1% SDS, room temperature twice, 30 minutes each; then 2 x SCC, 0.1% SDS, 50 ⁇ C once, 30 minutes; then 2 x SCC, room temperature twice, 10 minutes each, homologous sequences can be identified that contain at most about 25-30% basepair mismatches. More prefer- ably, homologous nucleic acid strands contain 15-25% basepair mismatches, even more preferably 5-15% basepair mismatches. These degrees of homology can be selected by using more stringent wash or hybridization conditions for identification of clones from gene libraries (or other sources of genetic material) , as is well known in the art.
  • a protein is a Norwalk virus polypeptide or derived from a Norwalk virus polypeptide if it is encoded by an open reading frame of a cDNA or RNA fragment repre ⁇ senting the Norwalk viral agent.
  • a protein having substantially the same sequence as one of the sequences determined for the disclosed Norwalk virus epitopes is defined as a protein having amino-acid substitutions in the protein coding sequence which do not eliminate the antigenic properties of the protein (ie. neutral substitutions) .
  • Neutral substitu ⁇ tions not adversely affecting overall antigenic function are reasonably predictable by one of ordinary skill in the art by utilizing currently available primary and secondary structure analysis (Needleman et al; Doolittle; Taylor et al, 1989; Hopp et al.) coupled with a matrix defining the relatedness between different amino acids (Taylor et al, 1989; Dayhoff; Schulz et al) . Proteins having sequence substitutions can be tested for immunore- activity with sera (e.g.. Examples 3 and 6), polyclonal, or specific monoclonal antibodies as described in the present disclosure.
  • Example 1 The partial purification of the Norwalk virus is described in Example 1.
  • a volunteer was orally inocu ⁇ lated with bacteria-free fecal filtrates containing Norwalk virus 8FIIa inoculum. This approach has the advantage that pre- and post-infection sera are available for a known Norwalk virus isolate.
  • the presence of the Norwalk virus was verified by IEM (Kapikian et al.) in the stool samples which were used as polynucleotide source material.
  • the virus particles were isolated by centrifugation and the presence of the viral antigen monitored at each step using the ELISA assay (Example 1) .
  • RNA was extracted from the partially purified viral preparation by a one-step guanidinium/phenol extraction.
  • cDNA molecules were generated from the partially purified nucleic acid mixture (Example 2A) .
  • the resul ⁇ ting mixture of cDNA molecules was amplified using the Sequence-Independent Single-Primer Amplification (SISPA) method which allows the amplification of a mixture of DNA regardless of the specific sequences of the DNA molecules (Example 2B) .
  • SISPA Sequence-Independent Single-Primer Amplification
  • this sequence independent ampli ⁇ fication is accomplished by attaching linkers of known sequence to the ends of the double-strand DNA molecules present in a mixture, typically using blunt-end ligation. These linkers then provide the common end sequences for primer-initiated amplification, using primers complemen ⁇ tary to the linker sequences.
  • the SISPA method (Reyes et al.) is carried out for 20-30 cycles of amplification, using thermal cycling to achieve successive ⁇ sive denaturation and primer-initiated polymerization of second strand DNA (Mullis; Mullis et al.).
  • the SISPA amplification provides the advantage of amplifying all Norwalk virus genomic polynucleotides present in the starting sample to ensure their final recovery.
  • the amplified cDNA molecules from above were then cloned into the lambda gtll vector (Example 2C) which al ⁇ lows expression of proteins encoded by the newly intro ⁇ quizd cDNA sequences produced as in-frame fusions to ⁇ - galactosidase (Young et al.).
  • the plaques generated by plating the recombinant phage were then screened for pro- duction of polypeptide antigens reactive with post-infec ⁇ tion serum that were not reactive with pre-infection se ⁇ rum (Example 3) . Candidates identified by the initial immunoscreening were re-screened twice.
  • Example 4C Further hybridization studies (Example 4C) showed that six of the nine clones (N35, N49, N51, N48, N28, and N40) cross-hybridized with each other, suggesting that common sequences existed between the six clones. Three of the clones (NI, N4, and N8) demonstrated no cross-hybridization and, further, showed no hybridization to either N49 or N35.
  • the N49 insert was isolated and used as a hybridiza- tion probe (Example 4B) against SISPA cDNAs from LTl-8 infected stool (Figure 1, lane 1) and SISPA cDNAs from the LTO pre-infection stool ( Figure 1, lane 2) .
  • the N49 insert-probe only hybri ⁇ dized with the cDNA derived from the post-infection stool sample suggesting that the N49 sequence is derived from the Norwalk virus 8FIIa agent and hence a unique cDNA species in the post-infection sample.
  • the nine cDNA inserts of lambda gtll were subcloned and six of the clones (N35, N28, N40, N48, N49, and N51) were sequenced (Example 5) .
  • the nucleic acid sequences for clones N35, N28, N40, N48, and N49 are presented in the Sequence Listing: the sequences for clones N49 and N51 were identical.
  • the Norwalk virus sequences present ⁇ ed in the sequence listing include the SISPA linker se- quence, used to amplify the cDNA molecules (Example 2) , at their 5' ends.
  • SEQ ID NO:5 and SEQ ID NO:6 are presented with the SISPA linker sequences at their 2 ' ends.
  • the sequence of the linker is shown in Example 2B.
  • the sequences of each strand of the linker are presented as SEQ ID NO:20 and
  • SEQ ID NO:21 The sequences were compared with "GENBANK” sequence entries and the results indicated that the clone sequences were unique in both nucleic acid and amino acid sequences.
  • the N35 sequence (SEQ ID NO:l) was used as a reference sequence to which the remaining 5 sequences were aligned ( Figure 2).
  • the heterogeneity at the 3' ends of the cDNA sequences (five different start sites; Example 5) suggested that the clones were not derived from a 3'-polyA + end of the viral genome. Two regions of disparity between the N35 reference sequence and the other clone sequences were found.
  • cDNA inserts can be used to pro ⁇ prise their corresponding Norwalk virus poiypeptides by insertion into a variety of expression vectors known to those of ordinary skill in the art.
  • Expression vectors are commercially available for a variety of organisms including the following: yeast (Clontech, Palo Alto, CA) ; bacterial (Clontech) ; mammalian (Clontech) ; and insect (Invitrogen, San Diego, CA) systems.
  • N49 probe hybridization identified a peak of viral shedding in these serial post-infection stools that were shown to contain viral antigen by RIA or ELISA assay.
  • Hybridization of the N49 probe was not detected in the post-infection specimens of two volunteers, II and V: these volunteers each had only one antigen positive stool specimen.
  • the negative-hybridization result may be attributable to either extremely low levels of viral shedding in these individuals or shedding of antigenic fragments alone, without intact viral particles in the stool. Hybridization could not be demonstrated with nucleic acid isolated from any of the pre-infection stools.
  • a 224-bp N49 specific probe was isolated by PCR (Example 7A) and labeled. Partially purified nucleic acid from the above- described LT1-8, LT1-3, and LTO stool samples was pre ⁇ pared for hybridization analysis. The LTl-8 and LTl-3 stool samples were known to be positive for the presence of the Norwalk virus as determined by IEM.
  • Figure 4 shows the results of the hybridization of the N49-speci- fic probe to these nucleic acid samples.
  • the probe hybridized to the LT1-8 sample ( Figure 4, spot 2) and LT1-3 sample ( Figure 4, spot 3), but hybridized to nei ⁇ ther LTO ( Figure 4, spot 4), the pre-infection stool sample, nor NCDV rotavirus mRNA ( Figure 4, spot 1).
  • the immunoreactive clones identified above can be used to obtain a complete set of overlapping genomic cDNA clones.
  • the lambda gtll clone N49 insert can be isolated and employed as a probe against cDNA libraries established in lambda gtlO.
  • the lambda gtlO libraries are generated essentially as was described in Example 2C for libraries in lambda gtll which were used for immunoscreening.
  • the inserts from clones identified in this fashion can then be isolated by EcoRI digestion of the lambda gtlO clone, electrophoretic fractionation of the digest products, and electroelution of the band corresponding to the insert DNA (Maniatis et al. ; Ausubel et al.) .
  • the isolated insert can then be treated with DNase I to generate random fragments (Maniatis et al.), and the resulting digest fragments inserted into lambda gtll phage vectors for immunoscreen- ing.
  • oligonucleotide primers may be used to isolate specific overlapping segments for in-phase insertion into any selected expres ⁇ sion vector.
  • Inserts from the immunoreactive clones identified above can be used in a similar manner to probe the origi ⁇ nal cDNA library generated in lambda gtlO.
  • Specific subfragments of the inserts may also be isolated by polymerase chain reaction or after cleavage with restric ⁇ tion endonucleases. These subfragments can be radioac- tively labeled and used as probes against the cDNA libra ⁇ ries generated in lambda gtlO.
  • the 5' and 3' terminal sequences of the inserts are useful as probes to identify clones which overlap this region.
  • the inserts of the cDNA library generated in lambda gtlO can also be screened using Norwalk virus sequence- specific hybridization probes.
  • Example 10 illustrates the use of an N35 specific probe, KCL-2 (SEQ ID NO:11; enclosed in a block in Figures 9 and 10) to identify further Norwalk virus coding sequences.
  • the sequences of two cDNA molecules identified by this method are present ⁇ ed in Figures 9 (SEQ ID N0:18) and 10 (SEQ ID NO:19) . These two sequences represent an extension of the Norwalk virus coding sequences by at least 356 base pairs (SEQ ID NO:16).
  • the relationship of the N2 and N3 clones to each other and to the N35 sequence is graphically presented in Figure 11.
  • sequences provided by the end- terminal sequences of the clone inserts are useful as specific sequence primers in first-strand DNA synthesis reactions (Maniatis et al.; Scharf et al.) using, for example, partially purified stool-sample-generated RNA as substrate ( Figure 8, N49) .
  • Synthesis of the second- strand of the cDNA is randomly primed (Boehringer Mannheim, Indianapolis IN) ( Figure 8, El). The above procedures identify or produce cDNA molecules correspon ⁇ ding to nucleic acid regions that are adjacent to the known clone N49 insert sequences.
  • the polymerase chain reaction can be used to clone gaps between known epi- topes.
  • the terminal sequences from any of the six related clones can be used as one primer in the polymerase chain reac ⁇ tion (e.g.. Figure 8, N49) and terminal sequences from unrelated clones (NI, N4, or N8) can be used as the second primer ( Figure 8, El) . Since the genomic rela ⁇ tionship between these two sets of epitope coding sequen- ces are unknown the following approaches may be used to generate an epitope spanning polymerase chain reaction amplification product (Figure 8) :
  • Figure 8 illustrates a productive polymerase chain reaction generating an epitope spanning region using, for example, N49 and El.
  • Norwalk virus genomic sequence will be helpful (i) in studying and establishing Norwalk virus relatedness to other viruses, and (ii) in the isolation of sequences from viruses related to Norwalk but which are as yet uncloned.
  • the invention includes antibodies specific against the recombinant antigens of the present invention.
  • a host animal such as a rabbit
  • the purified antigen or fused protein antigen may be generated using a variety of coding sequence derived from other proteins, such as 0-galac- tosidase or glutathione-S-transferase.
  • the host serum or plasma is collected following an appropriate time inter- val, and this serum is tested for antibodies specific against the antigen.
  • Example 9 describes the production of rabbit serum antibodies which are specific against the N49 antigens in the SJ26/N49 hybrid protein. These techniques are equally applicable to the other antigens of the present invention.
  • the gamma globulin fraction or the IgG antibodies of immunized animals can be obtained, for example, by use of saturated ammonium sulfate or DEAE Sephadex, or other techniques known to those skilled in the art for produ ⁇ cing polyclonal antibodies.
  • purified antigen or fused antigen protein may be used for producing monoclonal antibodies.
  • the spleen or lymphocytes from an immunized animal are removed and immortalized or used to prepare hybrido- mas by methods known to those skilled in the art.
  • a human lymphocyte donor is selected.
  • a donor known to be infected with a Norwalk virus may serve as a suitable lymphocyte donor.
  • Lym ⁇ phocytes can be isolated from a peripheral blood sample.
  • Epstein-Barr virus (EBV) can be used to immortalize human lymphocytes or a human fusion partner can be used to produce human-human hybridomas.
  • Antibodies secreted by the immortalized cells are screened to determine the clones that secrete antibodies of the desired specificity, for example, by using the ELISA or Western blot method (Ausubel et al.).
  • the antigens obtained by the methods of the present invention are advantageous for use as diagnostic agents for Norwalk virus antibodies present in Norwalk virus- infected sera; particularly, the antigens represented by Clones N35, N49, N51, N48, N28, N40, NI, N4, and N8.
  • test serum is reacted with a solid phase reagent having a surface-bound Norwalk virus antigen obtained by the methods of the present invention, e.g., the N49 insert encoded antigen.
  • the reagent After binding anti-Norwalk virus anti- body to the reagent and removing unbound serum components by washing, the reagent is reacted with reporter-labeled anti-human antibody to bind reporter to the reagent in proportion to the amount of bound anti-Norwalk virus antibody on the solid support. The reagent is again washed to remove unbound labeled antibody, and the amount of reporter associated with the reagent is determined.
  • the reporter is an enzyme which is detected by incubating the solid phase in the presence of a suitable fluorometric or colorimetric substrate.
  • the solid surface reagent in the above assay is prepared by known techniques for attaching protein mate ⁇ rial to solid support material, such as polymeric beads, dip sticks, 96-well plate or filter material.
  • attachment methods generally include non-specific adsorp- tion of the protein to the support or covalent attachment of the protein, typically through a free amine group, to a chemically reactive group on the solid support, such as an activated carboxyl, hydroxyl, or aldehyde group.
  • homogeneous assay In a second diagnostic configuration, known as a homogeneous assay, antibody binding to a solid support produces some change in the reaction medium which can be directly detected in the medium.
  • Known general types of homogeneous assays proposed heretofore include (a) spin- labeled reporters, where antibody binding to the antigen is detected by a change in reported mobility (broadening of the spin splitting peaks), (b) fluorescent reporters, where binding is detected by a change in fluorescence efficiency, (c) enzyme reporters, where antibody binding effects enzyme/substrate interactions, and (d) liposome- bound reporters, where binding leads to liposome lysis and release of encapsulated reporter.
  • the assay method involves reacting the serum from a test individual with the protein antigen and examining the antigen for the presence of bound antibody.
  • the examining may in ⁇ volve attaching a labeled anti-human antibody to the antibody being examined, either IgM (acute phase/primary response) or IgG (convalescent or chronic phase/secondary response) , and measuring the amount of reporter bound to the solid support, as in the first method, or may involve observing the effect of antibody binding on a homogeneous assay reagent, as in the second method.
  • kits for carrying out the assay method just de ⁇ scribed.
  • the kit generally includes a support with surface-bound recombinant Norwalk virus antigen (e.g., the N49 insert encoded antigen) , and a reporter-labeled anti-human antibody for detecting surface-bound anti- Norwalk virus-antigen antibody.
  • surface-bound recombinant Norwalk virus antigen e.g., the N49 insert encoded antigen
  • reporter-labeled anti-human antibody for detecting surface-bound anti- Norwalk virus-antigen antibody.
  • polypeptide antigens derived from Norwalk-virus cDNA clone libraries are immunoreactive with Norwalk virus-infected sera from human patients, indicating that the poiypeptides would be useful for detecting Norwalk virus infection in human serum.
  • one or more polypeptide antigens produced by clones N35, N49, N51, N48, N28, N40, NI, N4, and N8 can be combined in kits with any number of antigens from other gastroente ⁇ ritis-causing viruses including rotaviruses, pestiviru- ses, caliciviruses, astroviruses, parvoviruses, coronavi- ruses, toroviruses, adenoviruses, and the Norwalk-like viruses (LeBaron et al.) .
  • Other members of the Norwalk- like virus family include the following variants: Hawaii, Snow Mountain, Montgomery County, Taunton, Amulree, Sapporo, and Otofuke. Kits such as these pro ⁇ vide a diagnostic composition capable of immunoreacting with a broad spectrum of human viral gastroenteritis serum samples.
  • a third diagnostic configuration involves use of the anti-Norwalk virus antibodies, described in Section IV above, capable of detecting Norwalk virus specific anti ⁇ genes.
  • the Norwalk virus antigens may be detected, for example, using an antigen capture assay where Norwalk virus antigens present in candidate fecal material or environmentally derived samples (e.g. sewage effluents) are reacted with a Norwalk virus specific monoclonal antibody.
  • the anti-Norwalk virus monoclonal antibody is bound to a solid substrate and the antigen is then detec ⁇ ted by a second, different labeled anti-Norwalk virus antibody: the monoclonal antibodies of the present invention which are directed against Norwalk virus speci ⁇ fic antigens are particularly suited to this diagnostic method.
  • This diagnostic configuration can also be ex- panded to include antibodies directed against other gastroenteritis virus families or variants of the Nor ⁇ walk-virus, as described above.
  • the Norwalk virus antigens and antibodies of the present invention provide a renewable source for these reagents.
  • these reagents can be used in solid phase radioimmunoassays for Norwalk virus antigen and a radioimmunoassay for antibody to the Norwalk virus (Greenberg et al. (1989)).
  • the monoclonal and polyclonal anti-Norwalk virus antibodies of the present invention might also be used in the immune elec ⁇ tron microscopy technique (Kapikian et al.).
  • the Norwalk virus nucleic acid sequences identified by the method of the present invention provide sequences which can be used as hybridization probes for detecting the presence of Norwalk virus coding sequences in a sample.
  • Primers useful for the Polymerase Chain Reaction (PCR) can be derived from any of the nucleic acid sequences listed in the Sequence Listing or obtained from the inserts of clones NI, N4, and N8. Further, any Norwalk virus sequence, identified as des ⁇ cribed above in Section III, can be used in this capa ⁇ city.
  • PCR Polymerase Chain Reaction
  • any Norwalk virus sequence, identified as des ⁇ cribed above in Section III can be used in this capa ⁇ city.
  • these primers are two oligonucleotide sequences — generally 15-20 bases — where the two sequences are separated by a defined distance, e.g. 500 bases, and are homologous to opposite strands.
  • Norwalk virus specific nucleic acid sequences can also be used as hybridization probes to detect the pre ⁇ sence of the Norwalk virus in a sample as was done, for instance, in Example 7. Kits containing such PCR primers and hybridization probes can also contain similar primers useful for the identification of other gastroenteritis viruses.
  • Kits based on any of the above diagnostic methods are useful tools to aid in the rapid determination of whether gastroenteritis viruses are the agents respon ⁇ sible for outbreaks of human gastroenteritis. Further ⁇ more, although person-to-person transmission is an impor ⁇ tant aspect of viral gastroenteritis, the initiating event for most outbreaks of viral gastroenteritis is contamination of a common source (Lebaron et al.). Since enteric viruses cannot multiply outside their host, in contrast to bacterial pathogens, the original inoculum present in the common source determines infectivity of the source. Accordingly, the above-described kits are also useful for identification and verification of con ⁇ taminated sources (e.g., shellfish or water-source).
  • con ⁇ taminated sources e.g., shellfish or water-source.
  • the Norwalk virus antigens identified by the methods of the present invention can be formulated for use in a Norwalk virus vaccine.
  • the vaccine can be formulated by standard methods, for example, in a suitable diluent such as water, saline, buffered salines, complete or incomplete adjuvants, and the like.
  • the im unogen is administered using standard techniques for antibody induction, such as by subcutane ⁇ ous administration of physiologically compatible, sterile solutions containing inactivated or attenuated virus particles or antigens.
  • An immune response producing amount of virus particles is typically administered per vaccinizing injection, typically in a volume of one milliliter or less.
  • a specific example of a vaccine composition in- eludes, in a pharmacologically acceptable adjuvant, a recombinantly produced N49 polypeptide.
  • the vaccine is administered at periodic intervals until a significant titer of anti-Norwalk virus antibody is detected in the serum.
  • Such a vaccine may be useful to generate short term immunity in uninfected community members against Norwalk virus infection when outbreaks of gastroenteritis have been identified as Norwalk virus induced.
  • the effect of viral gastroenteritis agents on people with immunodeficiencies is of particular interest (Lebaron et al.). Interventions, such as the administra ⁇ tion of anti-Norwalk virus immunoglobulins, that might prove successful in halting chronic Norwalk virus infec ⁇ tion of immunocompromised patients might also prove useful in other situations, such as the chronic diarrhea associated with malnourishment or in protecting unexposed community members (Lebaron et al.).
  • the anti-Norwalk virus antibodies of the invention can be used as a means of enhancing an anti-Norwalk viru ⁇ immune response since antibody-virus complexes are recog ⁇ nized by macrophages and other effector cells.
  • the anti ⁇ bodies can be administered in amounts similar to those used for other therapeutic administrations of antibody.
  • pooled gamma globulin is administered at 0.02-0.1 ml/lb body weight during the early incubation of other viral diseases such as rabies, measles and hepati ⁇ tis B to interfere with viral entry into cells.
  • antibodies reactive with, for example, the N49 antigen can be passively administered alone, in a "cocktail" with other anti-viral antibodies, or in conjunction with ano ⁇ ther anti-viral agent to a patient infected with Norwalk virus to enhance the immune response and/or the effec- tiveness of an antiviral drug.
  • the following examples illustrate various aspects of the invention, but are in no way intended to limit the scope thereof.
  • E. coli DNA polymerase I (Klenow fragment) was obtained from Boehringer Mannheim Biochemicals (Indiana ⁇ polis, IN) .
  • T4 DNA ligase and T4 DNA polymerase were obtained from New England Biolabs (Beverly, MA) ; Nitro ⁇ cellulose filters were obtained from Schleicher and Schuell (Keene, NH) .
  • Synthetic oligonucleotide linkers and primers were prepared using commercially available automated oligonu ⁇ cleotide synthesizers. Alternatively, custom designed synthetic oligonucleotides may be purchased, for example, from Synthetic Genetics (San Diego, CA) . cDNA synthesis kit and random priming labeling kits were obtained from Boehringer-Mannhei Biochemicals (BMB, Indianapolis, IN) .
  • a human volunteer, LT was orally administered the 8FIIa infectious inoculum (Dolin et al. (1971) ; Dolin et al. (1972); Levy et al.; Wyatt et al.; Blacklow et al. (1979); Parrino et al.; Johnson et al.).
  • Clinical stool specimens were obtained from this patient. Occasional Norwalk virus particles were demonstrated by immune electron microscopy (IEM) (Kapikian et al.) in LT1-8, the eighth diarrheal post-infection stool, and in LT1-3, the third post-infection stool.
  • LT1-8 was selected as the post-infection stool used in the following examples unless otherwise specified.
  • a pre-infection stool from this volunteer (LTO) served as the negative control in the following procedures.
  • specimen LT1-8 was mixed with sufficient TNMC buffer (50 mM Tris-HCl, pH 8.0, 100 mM NaCI, 25 mM MgCl 2 , 25 mM CaCl 2 ) to make a 10% (w/v) fecal suspension.
  • the suspension was shaken vigorously and pelleted at 3,000 X g for 30 minutes at 4°C.
  • the resulting pellet was placed on ice while the supernatant was pelleted at 100,000 X g for 2 hours at 4°C.
  • the low- speed and high-speed pellets were combined and resuspen ⁇ ded in 20 ml TNMC buffer.
  • the pellet suspension was extracted extensively with Blaco-TronTF* (trichlorotrifluoroethane; Baron-Blakeslee, Inc. , San Francisco, CA) and the aqueous phase saved from each extraction.
  • the extracted aqueous phase was pelle ⁇ ted at 100,000 X g for 2 hours at 4°C.
  • the resulting pellet was resuspended in 2 ml TNMC.
  • This suspension was layered on top of a 20% sucrose cushion overlaying a CsCl cushion (1.5 g/ml) and spun at 80,000 X g for 3 hours at 4°C using a Beckman SW28 rotor.
  • the band at the inter ⁇ face was collected by side puncture.
  • Half of this par ⁇ tially purified material was used for RNA extraction and half was purified further in a CsCl gradient. Viral an- tigen was monitored at each step by ELISA using antibody obtained from infected-volunteer studies.
  • Example 2 Approximately 10 ⁇ g of the nucleic acid prepared in Example 1 was transcribed into cDNA, according to the method of Gubler et al. using an oligo-(dT) or random nucleotide hexamer primers. To ensure that the resulting cDNA molecules had blunt ends, they were treated with T4 DNA polymerase (cDNA Synthesis Kit, BMB, Indianapolis, IN) in the presence of all four nucleotides (Maniatis et al.).
  • T4 DNA polymerase cDNA Synthesis Kit, BMB, Indianapolis, IN
  • the resulting cDNA molecules were amplified using the Sequence-Independent Single Primer Amplification
  • SISPA SISPA
  • the SISPA technique is detailed in co- owned U.S. Patent application for "RNA and DNA Amplifica ⁇ tion Techniques," Serial No. 224,961, filed July 26, 1988 (herein incorporated by reference) .
  • the blunt end cDNA molecules from above were ligated (Maniatis et al.) to linkers having the following se ⁇ quence (SEQ ID NO:20 and SEQ ID NO:21, respectively) :
  • the cDNA and linker were mixed at a 1:100 molar ratio in the presence of 0.3 to 0.6 Weiss units of T4 DNA ligase.
  • Tag polymerase Thermus aquaticus DNA polymerase
  • the reaction mixture was heated to 94°C for 30 seconds for denaturation, allowed to cool to 50°C for 30 seconds for primer annealing, and then heated to 72°C for 0.5-3 minutes to allow for primer extension by Tag poly ⁇ merase.
  • the replication reaction involving successive heating, cooling, and polymerase reaction, was repeated an additional 25 times with the aid of a Perkin-Elmer Cetus DNA thermal cycler.
  • the amplified cDNA fragments were digested with EcoRI. Excess linkers were removed by passage through "SEPHACRYL 300" (Pharmacia, Piscataway NJ) .
  • Phosphatase-treated lambda gtll phage vector arms were obtained from Promega Biotec (Madison, WI) .
  • the lambda gtll (Huynh) vector has a unique EcoRI cloning site 53 base pairs upstream from the ⁇ -galactosidase translation termination codon.
  • the amplified cDNAs from Part B were introduced into the EcoRI site by mixing 0.5- 1.0 ⁇ g _E ⁇ oJ?I-cleaved gtll, 0.3-3 ⁇ l of the above cDNA molecules, 0.5 ⁇ l 10X ligation buffer (above), 0.5 ⁇ l DNA ligase (200 units) , and distilled water to 5 ⁇ l. The mixture was incubated overnight at 14°C, followed by in vitro packaging, according to standard methods (Maniatis et al., pp. 256-268).
  • the packaged phage were used to infect Escherichia coli strain KM392, obtained from Dr. Kevin Moore, DNAX (Palo Alto, CA) .
  • E. coli strain Y1090 available from the American Type Culture Collection (ATCC #37197), could be used.
  • Lawns of KM392 cells infected with serial dilutions of the packaged phage were used to determine the phage titer.
  • For immunoscreening about 10 3 -10 4 pfu of the recombinant phage were plated per 150 mm plate (Maniatis et al.).
  • a secondary screening with the same DD post-infection serum identi ⁇ fied 30 positive clones. Following a third screening for plaque purification, 21 clones remained reactive. From a final screen, nine clones (designated N28, N35, N40, N48, N49, N51, NI, N4, and N8) were selected for further study by virtue of their specific reactivity with DD post- infection serum and their lack of reactivity with DD pre- infection serum.
  • the sizes of the cDNA inserts (Table 1) were determined by EcoRI digestion of the lambda gtll clones followed by electrophoretic separation of the digest fragments on an agarose gel, run in parallel with DNA size-standards.
  • Genomic DNA cDNA was tested for similarity to human and E. coli genes by Southern blot hybridization (Southern; Maniatis et al.). Human lymphocyte genomic DNA and E. coli strain 1088 genomic DNA were each digested with EcoRI and Hindlll. The DNA fragments in these digests were elec ⁇ trophoretically separated on a 1% agarose gel in parallel lanes. The DNA fragments were transferred to nitrocel ⁇ lulose (Southern) .
  • Radioactively labeled probes of each lambda gtll cDNA insert were made as follows. Primers of known lambda gtll sequences which flanked the cDNA insert (5'- GGCAGACATGGCCTGCCCGG-3' and 5'-TCGACGGTTTCCATATGGGG-3') were used to amplify the cDNA insert by the polymerase chain reaction (PCR) method of Mullis.
  • PCR polymerase chain reaction
  • the typical PCR cycle involved the following steps: melting at 94°C for 30 seconds, followed by annealing at 50°C for 1 min., and extension at 72°C for 30 seconds. The reactions were repeated for 30 cycles.
  • the PCR products were digested with EcoRI and electrophoretically resolved using a pre ⁇ parative 1.5% agarose gel.
  • the clone-specific, amplified fragment was identified by size and electrophoresis con- tinued to transfer the DNA band completely onto a NA45 membrane (Schleicher & Schuell, Keene, NH) .
  • the DNA was eluted from the membrane using a high salt buffer (Schleicher & Schuell, Keene, NH) , extracted with once with phenol:chloroform (1:1), and ethanol precipitated. After ethanol precipitation, the DNA was used as the template for random-primed DNA labeling (Boehringer- Mannheim Biochemicals, Indianapolis, IN) .
  • nitrocellulose filters were hybridized with radiolabeled probes made from each of the nine clones identified in Example 3. None of the nine clones demon ⁇ strated a positive signal with either the human or E. coli genomic DNAs.
  • the insert of lambda gtll clones N49, N51, N28, N35, N40, N48, NI, N4, and N8 were isolated and radiolabeled as above.
  • the SISPA amplified cDNAs generated from stool samples LT1-8 and LTO (Example 1) were loaded onto parallel lanes of a 1% agarose gel and electrophore ⁇ tically separated.
  • the cDNAs were transferred from the gel to nitrocellulose paper by standard procedures (Mani- atis et al.).
  • the nitrocellulose filters were indivi ⁇ dually hybridized with each radiolabeled probe made from the N49, NI, N4, and N8 clones (Example 3) as described above in Example 4A.
  • Each of the probes hybridized specifically to SISPA cDNA from LT1-8 infected stool.
  • the data for the insert from clone N49 is shown in Figure 1.
  • the N49 probe hybridizes to SISPA cDNA from LT1-8 infected stool ( Figure 1, lane 1) , but not to SISPA cDNA from the LTO pre-infection stool ( Figure 1, lane 2) .
  • Example 4A which represent each of the lambda gtll clones from Example 3.
  • the result of this hybridization study showed that six clones (N35, N49, N51, N48, N28, and N40) cross-hybridized with each other suggesting that common sequences exist among these six clones.
  • Clones NI, N4, and N8 showed no cross-hybridization to each other or to either of clones N49 and N35.
  • Each of the clones had a single open reading frame, contiguous with the £-galactosidase reading frame of the lambda gtll vector.
  • NI, N4, and N8 had 5' ends contiguous with the l-galactosidase reading frame but did not have completely open reading frames throughout the length of each insert.
  • the sequence data is presented as follows: N35, SEQ ID NO:l; N28, SEQ ID NO:3; N40, SEQ ID NO:5; N48, SEQ ID NO:7; and N49, SEQ ID NO:9. Sequences were compared with "GENBANK” sequences at both nucleic acid and amino acid levels. The "GENBANK” search indi ⁇ cated that these sequences are unique as both nucleic acid and amino acid sequences.
  • EXAMPLE 6 Expanded Immunoscreening Using Clone N49 Immunological screening of the lambda gtll N49 clone was expanded to include a panel of paired sera from seven volunteers infected with the Norwalk virus (Example 1) , along with a paired negative control sample (EM) that had an undetectable anti-Norwalk ELISA titer (Table 2) . Serum reactivity toward the Norwalk virus was determined as previously described (Gary et al.; Herrmann et al.; Madore et al. (1986A) ; and, Greenberg et al. (1978)). The reactivities of the pre- and post-infection sera are given in Table 2.
  • the immunoreactivity of the lambda gtll N49 clone was assayed by mixing plague purified N49 phage with non-recombinant lambda gtll and plaque-plating at a 1:1 ratio. Reactive plaques were detected (Young et al.; Ausubel et al.) after incubation with the test sera by using an alkaline phosphatase-conjugated anti-IgG se ⁇ cond antibody (Pierce, Rockford IL) .
  • a 224-bp N49 specific probe was isolated by direct polymerase chain reaction using the N49 specific primers given in Example 6 and indicated in Figure 2 by under ⁇ lining.
  • the conditions for the polymerase chain reaction were essentially the same as described above in Example 4A except that the duration of each segment was 30 seconds.
  • the probe was radioactively labeled as des ⁇ cribed in Example 4A.
  • Example 1 Partially purified nucleic acid from the LT1-8, LT1- 3, and LTO stool samples (Example 1) was prepared for hybridization analysis as described in Example 7B: in addition to these samples, a negative-control RNA from the NCDV (Nebraska Calf Diarrhea Virus) rotavirus was also included.
  • NCDV Nebraska Calf Diarrhea Virus
  • the post ⁇ infection stool specimens chosen for RNA hybridization analysis were shown to test positive for Norwalk virus viral antigen using radioimmunassays (RIA) and/or ELISA: all pre-infection controls tested negative by the same standard.
  • RIA radioimmunassays
  • ELISA all pre-infection controls tested negative by the same standard.
  • Nucleic acids were isolated from the fecal samples as follows: 500 ⁇ l of a 10% fecal suspension (in PBS) of each specimen was combined with 125 ⁇ l of 40% polyethylene glycol (PEG, molecular weight 8000) and allowed to precipitate overnight at 4°C. The suspension was pelleted at 10,000 X g for 20 min.
  • PEG polyethylene glycol
  • Nucleic acid was extracted from the pellet using a one-step guanidinium/phenol extraction procedure (Chomczynski et al.) and prepared for dot blot hybridiza- tion analysis according to the recommendations of the manufacturer of the "MINIFOLD I" apparatus (Schleicher and Schuell, Keene, NH) .
  • Hybridization was carried out in 50% formamide and IX hybridization buffer (5X Denhardts solution (Maniatis et al.), 5X SSC (Maniatis et al.), 50 mM NaH 2 P0 4 , 1 mM sodium pyrophosphate/Na 2 HP0 4 , 50 mg denatured salmon sperm DNA/500 ml, 50 mg ATP/500 ml) .
  • the hybridization probe used was the radiolabeled N49 insert (Example 3) .
  • Fol- lowing hybridization, filters were washed in (i) 2X SSC at room temperature for 15 minutes, and (ii) 0.1X SSC with 0.1% SDS at 65°C for 1 hr. Filters were dried and then exposed to X-ray film.
  • Partially purified LT1-3 virus (Example 1) was further purified by overnight centrifugation on a 40-55% CsCl gradient, at 100,000 X g maintained at 4°C. Frac- tions (0.25 ml each) were collected by bottom puncture. Six fractions spanning the density range of 1.31 to 1.41 g/ml were examined further ( Figure 7) .
  • the Norwalk virus antigen peak determined by ELISA, was centered around the fraction with density 1.37 g/ml ( Figure 7). The six fractions were tested for the presence of N49-specific sequences by RNA dot blot hybridization (Example 7B) using the N49-specific radiolabeled probe described in Example 4A.
  • the Norwalk virus antigen peak corresponded to the peak hybridization seen on the RNA blot ( Figure 7) probed with the N49-specific probe.
  • EXAMPLE 8 The Nature of the Norwalk Virus Genomic Nucleic Acid A.
  • the Norwalk virus genome is an RNA molecule
  • the nucleic acid extracted from Norwalk-infected stool samples LT1-3 and LT1-8 (Example 1) were treated with RNaseA and DNasel as per the manufacturer's sugges ⁇ tions (both enzymes were obtained from Boehringer Mannheim, Indianapolis IN) .
  • the samples were then pre ⁇ pared for hybridization as described in Example 7B.
  • the probe was the N49 specific probe used in Example 7B.
  • the Norwalk virus genome is of positive polarity.
  • Single-stranded oligonucleotide probes corresponding to both the positive strand of N49 residues 71 to 91 (i.e., coding) and negative strand of N49 residues 208 to 227 ( Figure 2) were synthesized by standard procedures.
  • the oligonucleotides were radiolabeled by phosphorylating the synthetic oligonucleotide primers with -[ 32 P]ATP (Richardson) .
  • the nucleic acid from stool sample LT1-8 was pre ⁇ pared for hybridization as described in Example 7B. Hybridization was carried out in 30% formamide and IX hybridization buffer (see above) at 42 * C. The filters were washed in 2X SSC (Maniatis et al.) at room tempera ⁇ ture for 30 minutes.
  • the N49 insert digest fragments from lambda gtll is released by EcoRI digestion of the phage, and the insert region purified by gel electrophoresis. The purified fragment is introduced into the pGEX expression vector (Smith) in-frame with the glutathione S-transferase protein. Expression of glutathione S-transferase fused protein (Sj26 fused protein) containing the N49 encoded polypeptide antigen can be achieved in E. coli strain KM392.
  • the fusion protein is isolated from lysed bac ⁇ teria by affinity chromatography on a column packed with glutathione-conjugated beads, according to published methods (Smith) .
  • the purified SJ26/N49 fused protein can be injected subcutaneously in Freund's adjuvant in a rabbit. Typi ⁇ cally, approximately 1 mg of fused protein is injected at days 0 and 21, and rabbit serum collected on days 42 and 56.
  • the above procedure can also be used to generate antibodies against the ,9-galactosidase/N49 polypeptide antigen fusion protein where the fusion protein is iso- lated by immuno-affinity chromatography using, for ex ⁇ ample, monospecific or monoclonal anti-,9-galactosidase antibodies.
  • the specificity of the antibodies can be evaluated by Western blot screening (Ausubel et al.) .
  • Lysates are prepared from bacterial strains of KM392 cells transformed with (a) pGEX, and (b) pGEX containing the N49 insert.
  • minilysates are prepared from the transformed bacteria as follows. The infected bacte ⁇ ria are streaked on solid medium containing ampicillin and grown at 37°C overnight or until colonies are appa ⁇ rent. Individual bacterial colonies are used to inocu- late 1 ml of rich bacterial medium containing ampicillin, e.g., LB broth containing 50 ⁇ g/ml ampicillin (Maniatis). This saturated overnight bacterial culture is used to inoculate a 10 ml culture of the same medium, which is incubated.with aeration to an O.D.
  • the cells are pelleted by centrifugation, and 1 ml of the pelleted material resuspended in 100 ⁇ l of lysis buffer (62 mM Tris, pH 7.5 containing 5% mercaptoethanol, 2.4 % SDS and 10% glycerol) .
  • lysis buffer 62 mM Tris, pH 7.5 containing 5% mercaptoethanol, 2.4 % SDS and 10% glycerol
  • the filters are blocked with AIB (10 mM Tris, pH 8.0, 150 mM NaCl,with 1% gelatin), and reacted with serum samples from the rabbits immunized as de- scribed above.
  • AIB 10 mM Tris, pH 8.0, 150 mM NaCl,with 1% gelatin
  • the presence of specific antibody binding to the nitrocellulose filters can also be assayed by immunobinding of alkaline-phosphatase labeled anti-rabbit IgG.
  • the results of the Western blot analysis are ex ⁇ pected to show positive anti-Norwalk virus antibody reac- tions with lysates from pGEX-N49, but not with lysates from the pGEX control strain.
  • Anti-N49 antibody present in the sera from the ani ⁇ mal immunized with the SJ26/N49 can be purified by af- finity chromatography as described above.
  • Human anti-N49 antibodies from human sera can also be obtained by af ⁇ finity chromotography by derivatizing the N49 antigen- peptide to the support beads.
  • lambda gtlO vector (Huynh, et al . j Murray, et al . ) has a unique EcoRI cloning site in the cl phage repressor gene.
  • the lambda gtlO vector is useful for screening insert molecules using nucleic acid probes. Briefly, lambda gtlO was obtained from Promega Biotec (Madison, WI) .
  • the vector was digested with EcoRI (New England Biolabs) and phosphatase-treated (Calf-Intestinal Alkaline Phosphatase (CIP) , Promega) as per the manufacturer's instructions.
  • the amplified cDNAs from Example 2, Part B were introduced into the EcoRI site by mixing 0.5-1.0 ⁇ g _5coRI-cleaved gtlO, 0.3-3 ⁇ l of the above cDNA molecules, 0.5 ⁇ l 10X ligation buffer (above), 0.5 ⁇ l DNA ligase (200 units) , and distilled water to 5 ⁇ l.
  • the mixture was incubated overnight at 14 ⁇ C, followed by in vitro packag ⁇ ing, according to standard methods (Maniatis et al., pp. 256-268) .
  • the packaged phage were used to infect Escherichia coli strain C600Hf1 (Promega) . Lawns of C600Hf1 cells infected with serial dilutions of the packaged phage were used to determine the phage titer.
  • For hybridization screening about 10 3 -10 4 pfu of the recombinant phage were plated per 150 mm plate (Maniatis et al.).
  • Plaques were transferred to nitrocellulose paper as previously described (Ausubel, et al . ; Maniatis, et al . ) .
  • a probe (KCL-2, derived from clone N35; SEQ ID N0:1) was end-labeled using ⁇ - 32 ATP and polynucleotide kinase (Boeh- ringer-Mannheim Biochemicals) .
  • the plaque transfers were screened with the radiolabeled probe using standard buffers and hybridization conditions (Maniatis, et al . ) .
  • Approximately 60,000 plaques were screened and 20 posi ⁇ tive plaques were detected. Of the 20 positives, 2 of the plaques were had very strong signals.
  • the "BLUESCRIPT" (PBS SK, Stratagene, La Jolle CA) vector was digested with Smal (New England Biolabs, as per manufacturer's directions) and treated with CIP.
  • Smal New England Biolabs, as per manufacturer's directions
  • CIP CIP-linked polymerase
  • the blunt-ended amplification fragments obtained from dT-llAS and dT-18AS were each ligated (Maniatis, et al . ) into the Smal site of the "BLUESCRIPT” vector.
  • These plasmids were then transformed into DH5 ⁇ (Bethesda Research Labo ⁇ ratories) .
  • Insert bearing plasmids were identified by hybridization with the KCL-2 probe.
  • the inserts were isolated from two plasmids designated PNW11-9 (N2) and PNW 18-12 (N3) , corresponding to isolates dT-llAS and dT- 18AS, respectively.
  • the insert of the two plasmids were sequenced as per the manufacturer's instructions for use of the "BLUE ⁇ SCRIPT" plasmid.
  • the sequences of the inserts from these two plasmids are shown in Figure 9 (PNW11-9 (N2) ; SEQ ID NO:18) and Figure 10 (PNW 18-12 (N3) : SEQ ID NO:19).
  • Clones N2 and N3 contain, respectively, 284 and 87 bases pairs of homology to N35 and 356 basepairs of homology to each other (SEQ ID NO:16).
  • ATC CAG GCT GTA GCC TTG ACG ATG GAG AGA CAG GAT GAG TTC CAA CTC 1 lie Gin Ala Val Ala Leu Thr Met Glu Arg Gin Asp Glu Phe Gin Leu 35 40 45 CAG GGG CCT ACG TAT GAC TTT GAT ACT GAC AGA GTA GCT GCG TTC ACG 19 Gin Gly Pro Thr Tyr Asp Phe Asp Thr Asp Arg Val Ala Ala Phe Thr 50 55 60
  • GGC AAA AAG CTA CGC AGT GTC ACC ACT ATT GAA GGA TTA AAG AAT GCT 288 Gly Lys Lys Leu Arg Ser Val Thr Thr lie Glu Gly Leu Lys Asn Ala 85 90 95
  • GCT GTA GCC TTG ACG ATG GAG AGA CAG GAT GAG TTC CAA CTC CAG GGG 96 Ala Val Ala Leu Thr Met Glu Arg Gin Asp Glu Phe Gin Leu Gin Gly 20 25 30
  • GGC AAA AAG CTA CGC AGT GTC ACC ACT ATT GAA GGA TTA AAG AAT GCT 288 Gly Lye Lye Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lye A ⁇ n Ala 85 90 95
  • GCC ATC ACT CGA CTC AAA GCA GCT AGG GCT GTG GCA TAC GCT TCA TGT 480 Ala Ile Thr Arg Leu Lys Ala Ala Arg Ala Val Ala Tyr Ala Ser Cys 145 150 155 160
  • GGC AAA AAG CTA CGC AGT GTC ACC ACT ATT GAA GGA TTA AAG AAT GCT 288 Gly Lye Lys Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lys Asn Ala
  • GCC ATC ACT CGA CTC AAA GCA GCT AGG GCT GTG GCA TAC GCT TCA TGT 480 Ala Ile Thr Arg Leu Lye Ala Ala Arg Ala Val Ala Tyr Ala Ser Cye 145 150 155 160
  • MOLECULE TYPE protein
  • AAATGCAGTA TACAATGGCA GTCAAGGGTG TACATTATAG AATCAGATGG TGCCAGTGTA 240
  • AAATGCAGTA TACAATGGCA GTCAAGGGTG TACATTATAG AATCAGATGG TGCCAGTGTA 6
  • MOLECULE TYPE DNA (genomic)
  • MOLECULE TYPE DNA (genomic)

Abstract

Polypeptide antigens which are immunoreactive with sera from individuals infected with Norwalk virus are disclosed. The antigens are useful in diagnostic methods for detecting Norwalk virus infection in humans. Also disclosed are corresponding genomic-fragment clones containing polynucleotides encoding the open reading frame sequences for the antigenic polypeptides.

Description

NORWALK VIRUS HUMAN GASTROENTERITIS AGENT AND MOLECULAR CLONING OF CORRESPONDING cDNAs
This work was supported in part by NIH Grants DK01811, DK38707, and Merit Review, Veterans Administra¬ tion. Accordingly, the United States Government has certain rights in this invention.
Field of the Invention This invention relates to the identification of
Norwalk virus genomic nucleic acid sequences, to specific polypeptide viral antigens which are immunoreactive with sera from human volunteers infected with Norwalk virus, to polynucleotide sequences which encode these polypep- tide antigens, to an expression system capable of produ¬ cing the polypeptide antigens, to methods of using the polypeptide antigens for detecting Norwalk virus anti¬ bodies in human sera, and to antibodies directed against these polypeptide antigens.
References
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Background of the Invention
A group of serologically diverse viruses have been implicated in common source outbreaks of gastroenteritis (Kapikian et al.; Greenberg et al. (1989); Dolin et al.). These viruses included pestiviruses, caliciviruses, astroviruses, parvoviruses , coronaviruses, toroviruses, and the Norwalk-like viruses (also called small round- structured viruses (SRSVs)) . It has been estimated that up to 65% of all cases of acute, non-bacterial gastroen¬ teritis in the United States are attributable to viral agents (Blacklow et al. (1982)). While viral induced gastroenteritis typically lasts only 1 to 2 days, its overall effect on days lost from work or school may be substantial (National Center for Health Statistics, series 10, No. 85, (1972); DHEW Publication (HRA) 74- 1512, Washington DC, Government Printing Office (1973)). Progress in the study of these viruses has been significantly restricted by the inability to- cultivate these agents in cells and by the lack of an identifiable animal model. Much of what is known about the immune response to these viruses has come from human volunteer studies (Dolin et al. (1971); Dolin et al. (1972); Levy et al.; Wyatt et al.; Blacklow et al. (1979); Parrino et al.) or epidemiologic surveys (Kaplan et al.; Greenberg et al. (1979)). Positive identification of these viruses continues to rely heavily on Immune Electron Microscopy (IEM) , a technique not well-suited for large-scale screening. Seroconversion and detection of viral anti- gens in fecal specimens by solid phase immunoassays have also been used to establish the association of these viruses with episodes of acute gastroenteritis (Gary et al.; Herrmann et al.; Madore et al. (1986A) ; Greenberg et al. (1978)). A major shortcoming of these tests is that unequivocal diagnosis requires the use of paired human sera (pre- and post-infection) which are not standardized and are in very short supply.
The Norwalk virus alone appears to cause at least one-third of all cases of gastroenteritis in U.S. epide¬ mics (Kaplan et al.; Greenberg et al. (1979)). Norwalk virus, named after a 1968 outbreak of gastroenteritis at a school in Norwalk, Ohio (Adler et al.), was the first of the heterogeneous group of SRSVs to be identified by (IEM) (Kapikian et al.). The viral protein structure of Norwalk virus (Greenberg et al. (1981)) and Norwalk-like viruses, such as the Snow Mountain (Madore et al. (1986B)) and Hawaii agents, most closely resemble calici¬ viruses which have a single structural protein of molecu- lar mass 62 kDa (Terashi a et al.). Furthermore, a one¬ way serologic relationship between caliciviruses and Nor¬ walk virus has been demonstrated by RIA (Cubitt et al.). The present specification discloses methods effec¬ tive for the isolation of Norwalk virus genomic sequences.
Summary of the Invention
It is one general object of the present invention to provide a purified Norwalk virus polynucleotide which contains at least one sequence selected from the follow¬ ing group: SEQ ID NO:l, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, and SEQ ID NO:9.
Another object of the present invention is to pro¬ vide a recombinantly produced Norwalk virus polynucleo- tide which encodes a Norwalk virus polypeptide which is immunoreactive with sera from humans infected with Nor¬ walk virus 8FIIa infectious inoculum. Specific embodi¬ ments of these polynucleotides are those which encode an immunoreactive portion of any one of the following se- quences: SEQ ID NO:2, SEQ ID NO: , SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10. Specific polynucleotides which encode such poiypeptides include: SEQ ID NO:l, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, and SEQ ID NO:9.
The present invention also includes Norwalk-virus specific poiypeptides produced by bacterial cells con¬ taining a vector selected from the group consisting of lambda-Nl, lambda-N4, and lambda-N8 (these are lambda gtll vectors containing the designated inserts, see Example 3) . The present invention also provides a recombinant Norwalk virus polypeptide which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infec¬ tious inoculum. Such recombinant poiypeptides include those having matching and substantially the same sequence as one of the following poiypeptides: SEQ ID NO:2, SEQ ID NO:4, SEQ ID N0:6, SEQ ID NO:8, SEQ ID NO:10, SEQ ID N0:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, and SEQ ID NO:20. The recombinant polypeptide may also include portions of other proteins, such as in-frame fusions to the la.cZ encoded /S-galactosidase protein. Such recom¬ binant poiypeptides can be obtained from bacterial cells transformed with one of the following vectors: lambda- Nl, lambda-N4, and lambda-N8.
The invention includes, in one aspect, a method for the detection of Norwalk virus in human stool samples. The method includes the partial purification of poly¬ nucleotides present in the stool sample, followed by hybridization to negative-sense oligonucleotide probes specific for the Norwalk virus polynucleotide. The method also includes means for detecting the binding of the negative sense probes to polynucleotides present in the stool sample. Such detection means include the standard detection methods of labelling the probe by biotinylation or radioactive isotopes. The method may include generation of cDNA molecules from RNA templates present in the partially purified sample and sequence independent amplification of the resulting cDNA mole¬ cules. Negative-sense oligonucleotide probes and oligo- nucleotide primers specific for the Norwalk virus poly- nucleotide are also defined by the present invention. Both the probes and primers can be derived from the above-described Norwalk virus coding sequences.
Another aspect of the present invention is a diag- nostic kit and a method for use in screening human blood containing antibodies specific against Norwalk virus infection. The kit contains a recombinant Norwalk virus polypeptide antigen which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum, and means for detecting the binding of said antibodies to the antigen. Polypeptide antigens inclu¬ ding an immunoreactive portion of any of the above de¬ scribed Norwalk virus epitopes may be used in this re¬ gard. The kit may include a solid support to which the polypeptide antigen is attached and a reporter-labeled anti-human antibody. In this case the binding of anti- Norwalk virus serum antibodies to the antigen can be detected by binding of the reporter-labeled antibody to the solid surface. Yet another aspect of the present invention includes an expression system and a method of producing a Norwalk virus polypeptide which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum. The method includes introducing into a suit- able host a recombinant expression system containing an open reading frame (ORF) , where the ORF has a polynucleo- tide sequence which encodes a Norwalk virus polypeptide immunoreactive with sera from humans infected with Nor¬ walk virus 8FIIa infectious inoculum. In this approach the vector is designed to express the ORF in the selected host. The host is then cultured under conditions resul¬ ting in the expression of the ORF sequence. A number of expression systems can be used in this regard including the lambda gtll expression system in an Escherichia coli host. Other expression systems include expression vec¬ tors for use in yeast, bacterial, insect, and mammalian cells.
Also forming part of the invention is a vaccine for immunizing an individual against Norwalk virus infection. The vaccine includes a recombinant Norwalk virus polype¬ ptide antigen which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum. Such polypeptide antigens may include an immunoreactive portion of the above described Norwalk virus coding sequences. The polypeptide antigen is typically prepared in a pharmacologically acceptable adjuvant.
The invention further includes antibodies specific against a polypeptide having a sequence selected from the following group: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10. Antibodies can also be generated against the Norwalk-virus-specific antigen produced by bacterial cells transformed with one of the following vectors: lambda-Nl, lambda-N4, or lambda-N8. These antibodies may be polyclonal or monoclonal. The antibodies can be used in a method of producing passive immunity in an individual against Norwalk virus, which includes administering the antibodies parenterally to the individual. These and other objects and features of the inven¬ tion will become more fully apparent when the following detailed description is read in conjunction with the accompanying drawings.
Brief Description of the Drawings
Figure 1 shows that radiolabeled N49-insert specific probes hybridize to only amplified nucleic acid extracted from a partially purified Norwalk virus-infected stool sample LT1-8 and not to amplified nucleic acid derived from the pre-infection stool.
Figure 2 shows the alignment of the following se¬ quences using the N35 insert sequence as a reference se¬ quence: N35, SEQ ID NO:l; N28, SEQ ID NO:3; N40, SEQ ID N0:5; N48, SEQ ID NO:7; N49 and N51, SEQ ID NO:9.
Figure 3 further demonstrates that radiolabeled N49- insert specific probes hybridize to only nucleic acid extracted from partially purified Norwalk virus-infected stool samples. Figure 4 shows the results of hybridization of an internal, N49-insert specific, radiolabeled probe to RNA extracted from serial, Norwalk volunteer, fecal speci¬ mens.
Figure 5 shows the effect of RNaseA treatment on the hybridization of a N49-insert specific probe to Norwalk virus nucleic acid.
Figure 6 shows the differential hybridization of positive and negative strand N49-insert specific probe to Norwalk virus nucleic acid. Figure 7 shows the correspondence of clone-specific probe hybridization peak and Norwalk viral antigen peak in a cesium chloride gradient fraction of buoyant density 1.37 g/ml. Figure 8 shows how new Norwalk virus sequences can be identified by an epitope spanning method.
Figure 9 shows the sequence of the N2 insert (indi¬ cated by arrows, SEQ ID NO:18) with regions of homology to N35 (solid overline) and N3 (double overline) indicat¬ ed. The KCL-2 probe is indicated by a box. The SISPA primers are indicated by a single underline.
Figure 10 shows the sequence of the N3 insert (indi¬ cated by arrows; SEQ ID NO:19) with regions of homology to N35 (solid overline) and N2 (double overline) indicat¬ ed. The KCL-2 probe is indicated by a box. The SISPA primers are indicated by a single underline.
Figure 11 graphically illustrates the alignment of the following sequences using the N35 insert sequence as a reference sequence: N35, SEQ ID N0:1; N2, SEQ ID NO:12; and N3, SEQ ID NO:14.
Detailed Description of the Invention
Defini ions The terms defined below have the following meaning herein:
1. The Norwalk virus polynucleotide refers to variations of the disclosed sequences, such as degenerate codons, or variations in sequence which may be present in isolates or strains of Norwalk virus which are immuno- logically cross reactive with the 8FIIa isolate.
2. Two nucleic acid fragments are "homologous" if they are capable of hybridizing to one another under hybridization conditions described in Maniatis et al. , op. cit.. pp. 320-323, using the following wash condi¬ tions: 2 x SCC, 0.1% SDS, room temperature twice, 30 minutes each; then 2 x SCC, 0.1% SDS, 50βC once, 30 minutes; then 2 x SCC, room temperature twice, 10 minutes each, homologous sequences can be identified that contain at most about 25-30% basepair mismatches. More prefer- ably, homologous nucleic acid strands contain 15-25% basepair mismatches, even more preferably 5-15% basepair mismatches. These degrees of homology can be selected by using more stringent wash or hybridization conditions for identification of clones from gene libraries (or other sources of genetic material) , as is well known in the art.
3. A protein is a Norwalk virus polypeptide or derived from a Norwalk virus polypeptide if it is encoded by an open reading frame of a cDNA or RNA fragment repre¬ senting the Norwalk viral agent.
4. A protein having substantially the same sequence as one of the sequences determined for the disclosed Norwalk virus epitopes is defined as a protein having amino-acid substitutions in the protein coding sequence which do not eliminate the antigenic properties of the protein (ie. neutral substitutions) . Neutral substitu¬ tions not adversely affecting overall antigenic function are reasonably predictable by one of ordinary skill in the art by utilizing currently available primary and secondary structure analysis (Needleman et al; Doolittle; Taylor et al, 1989; Hopp et al.) coupled with a matrix defining the relatedness between different amino acids (Taylor et al, 1989; Dayhoff; Schulz et al) . Proteins having sequence substitutions can be tested for immunore- activity with sera (e.g.. Examples 3 and 6), polyclonal, or specific monoclonal antibodies as described in the present disclosure.
I. Molecular Clone Selection bv Immunoscreening The partial purification of the Norwalk virus is described in Example 1. A volunteer was orally inocu¬ lated with bacteria-free fecal filtrates containing Norwalk virus 8FIIa inoculum. This approach has the advantage that pre- and post-infection sera are available for a known Norwalk virus isolate. The presence of the Norwalk virus was verified by IEM (Kapikian et al.) in the stool samples which were used as polynucleotide source material. The virus particles were isolated by centrifugation and the presence of the viral antigen monitored at each step using the ELISA assay (Example 1) . RNA was extracted from the partially purified viral preparation by a one-step guanidinium/phenol extraction. cDNA molecules were generated from the partially purified nucleic acid mixture (Example 2A) . The resul¬ ting mixture of cDNA molecules was amplified using the Sequence-Independent Single-Primer Amplification (SISPA) method which allows the amplification of a mixture of DNA regardless of the specific sequences of the DNA molecules (Example 2B) . Briefly, this sequence independent ampli¬ fication is accomplished by attaching linkers of known sequence to the ends of the double-strand DNA molecules present in a mixture, typically using blunt-end ligation. These linkers then provide the common end sequences for primer-initiated amplification, using primers complemen¬ tary to the linker sequences. Typically, the SISPA method (Reyes et al.) is carried out for 20-30 cycles of amplification, using thermal cycling to achieve succes¬ sive denaturation and primer-initiated polymerization of second strand DNA (Mullis; Mullis et al.). The SISPA amplification provides the advantage of amplifying all Norwalk virus genomic polynucleotides present in the starting sample to ensure their final recovery.
The amplified cDNA molecules from above were then cloned into the lambda gtll vector (Example 2C) which al¬ lows expression of proteins encoded by the newly intro¬ duced cDNA sequences produced as in-frame fusions to β- galactosidase (Young et al.). The plaques generated by plating the recombinant phage were then screened for pro- duction of polypeptide antigens reactive with post-infec¬ tion serum that were not reactive with pre-infection se¬ rum (Example 3) . Candidates identified by the initial immunoscreening were re-screened twice. From the final screen, nine clones (designated N28, N35, N40, N48, N49, N51, NI, N4, and N8) were selected for further study. These clones were specifically reactive with DD post- infection serum and unreactive with DD pre-infection serum. Sizes of the cDNA inserts are given in Table 1. These nine clones were then characterized as fol¬ lows. First, the cDNA inserts were isolated and used as probes in hybridization reactions with human lymphocyte genomic DNA and E. coli strain 1088 genomic DNA (Example 4A) . None of the inserts hybridized with the genomic DNAs, suggesting that the clones are exogenous to these two possible sources of epitope-encoding DNA (i.e., human genomic and E. coli) . Further hybridization studies (Example 4C) showed that six of the nine clones (N35, N49, N51, N48, N28, and N40) cross-hybridized with each other, suggesting that common sequences existed between the six clones. Three of the clones (NI, N4, and N8) demonstrated no cross-hybridization and, further, showed no hybridization to either N49 or N35.
The N49 insert was isolated and used as a hybridiza- tion probe (Example 4B) against SISPA cDNAs from LTl-8 infected stool (Figure 1, lane 1) and SISPA cDNAs from the LTO pre-infection stool (Figure 1, lane 2) . As can be seen from Figure 1, the N49 insert-probe only hybri¬ dized with the cDNA derived from the post-infection stool sample suggesting that the N49 sequence is derived from the Norwalk virus 8FIIa agent and hence a unique cDNA species in the post-infection sample.
The nine cDNA inserts of lambda gtll were subcloned and six of the clones (N35, N28, N40, N48, N49, and N51) were sequenced (Example 5) . The nucleic acid sequences for clones N35, N28, N40, N48, and N49 are presented in the Sequence Listing: the sequences for clones N49 and N51 were identical. The Norwalk virus sequences present¬ ed in the sequence listing include the SISPA linker se- quence, used to amplify the cDNA molecules (Example 2) , at their 5' ends. All but SEQ ID NO:5 and SEQ ID NO:6 (both corresponding to clone N40) are presented with the SISPA linker sequences at their 2 ' ends. The sequence of the linker is shown in Example 2B. The sequences of each strand of the linker are presented as SEQ ID NO:20 and
SEQ ID NO:21. The sequences were compared with "GENBANK" sequence entries and the results indicated that the clone sequences were unique in both nucleic acid and amino acid sequences. The N35 sequence (SEQ ID NO:l) was used as a reference sequence to which the remaining 5 sequences were aligned (Figure 2). The heterogeneity at the 3' ends of the cDNA sequences (five different start sites; Example 5) suggested that the clones were not derived from a 3'-polyA+ end of the viral genome. Two regions of disparity between the N35 reference sequence and the other clone sequences were found. The most likely expla¬ nation for this finding is that these (A)-rich regions (Figure 2) served as the initiation sites for oligo (dT)-primed cDNA synthesis, resulting in the 11 to 12 bp stretches of (A) residues at the 3'-end of clones N49, N51, N48, N28, and N40. The clone N49 was selected for use in further studies.
The above described cDNA inserts can be used to pro¬ duce their corresponding Norwalk virus poiypeptides by insertion into a variety of expression vectors known to those of ordinary skill in the art. Expression vectors are commercially available for a variety of organisms including the following: yeast (Clontech, Palo Alto, CA) ; bacterial (Clontech) ; mammalian (Clontech) ; and insect (Invitrogen, San Diego, CA) systems.
II. Expanded Characterization of Clone N49 Im unological screening of the lambda gtll clone N49 using an expanded panel of paired volunteer sera provided further support that these clones expressed an immunoge¬ nic epitope of Norwalk virus (Example 6) . Seven pairs of sera with high, post-infection ELISA titer for Norwalk virus antigens were used in the extended panel along with a paired negative control sample (EM) that had an unde- tectable anti-Norwalk ELISA titer. As shown in Table 2, the antigen expressed by the N49 clone reacted with 6 of the 7 post-infection sera tested. Only pre-infection sera from AT, which had a pre-existing and detectable level of reactivity to Norwalk antigen by ELISA, also reacted with the antigen produced by the N49 clone. None of the other pre-infection sera or the negative control paired sera (EM) reacted with the antigen produced by the N49 clone product. The lack of reactivity with CS post- infection serum (ELISA titer 1:6400) may be due to the lack of antibodies in the CS specimen directed to the epitope of the Norwalk virus defined by clone N49. Screening with CS post-infection serum may provide the means to identify other immunoreactive clones which define epitopes derived from regions of the viral genome other than the region defined by the N49 clone.
Three hybridization experiments provide further sup¬ port that clone N49 represented a portion of the Norwalk virus genome. First, RNA was extracted from pre-infec¬ tion and serial post-infection stools collected from 5 additional volunteers who became ill after receiving the same Norwalk virus inoculum (8FIIa) in a separate study. As shown in Figure 3, the N49 probe hybridized to nucleic acid from test specimens 1-4 and -5, III-4, -5, -6, -7, and IV-8 and -9. These specimens cover the range of the third through eighth stools collected from the 3 volun¬ teers (I, III, and IV) after the Norwalk virus 8FIIa inoculum was administered. In each case, N49 probe hybridization identified a peak of viral shedding in these serial post-infection stools that were shown to contain viral antigen by RIA or ELISA assay.
Hybridization of the N49 probe was not detected in the post-infection specimens of two volunteers, II and V: these volunteers each had only one antigen positive stool specimen. The negative-hybridization result may be attributable to either extremely low levels of viral shedding in these individuals or shedding of antigenic fragments alone, without intact viral particles in the stool. Hybridization could not be demonstrated with nucleic acid isolated from any of the pre-infection stools.
In a second hybridization experiment a 224-bp N49 specific probe was isolated by PCR (Example 7A) and labeled. Partially purified nucleic acid from the above- described LT1-8, LT1-3, and LTO stool samples was pre¬ pared for hybridization analysis. The LTl-8 and LTl-3 stool samples were known to be positive for the presence of the Norwalk virus as determined by IEM. Figure 4 shows the results of the hybridization of the N49-speci- fic probe to these nucleic acid samples. The probe hybridized to the LT1-8 sample (Figure 4, spot 2) and LT1-3 sample (Figure 4, spot 3), but hybridized to nei¬ ther LTO (Figure 4, spot 4), the pre-infection stool sample, nor NCDV rotavirus mRNA (Figure 4, spot 1).
In a third hybridization experiment to support that clone N49 represented a portion of the Norwalk virus genome, partially purified virus derived from stool sample LT1-8 was further purified by overnight centri- fugation on a CsCl gradient (Example 7C) . Fractions were collected and analyzed by ELISA for Norwalk virus-speci¬ fic antigen. RNA was extracted from these fractions and analyzed by hybridization using an N49-specific probe. The RNA dot blot hybridization signal corresponded to the same fractions that were positive for the Norwalk-virus- antigen.
These results taken together suggest that lambda gtll clone N49 and the five related clones identified in Section I by immunoscreening correspond to Norwalk virus antigen coding sequences.
III. The Nature of the Norwalk Virus Genome. The nature of the extracted nucleic acid from which the above Norwalk virus cDNAs were obtained, was further investigated (Example 8) . As shown in Figure 5 (column 1) , RNase A treatment of LT1-8 and LT1-3 nucleic acid extracts eliminated hybridization with the N49-specific probe, while DNasel treatment had no effect (Figure 5, column 2) . Accordingly, the Norwalk virus genomic ate- rial appears to be RNA. Further, only single-stranded probes of negative polarity (as defined by open reading frame analysis) hybridized to LT1-8 nucleic acid (Figure 6, spot 1) indicating that the extracted Norwalk virus RNA was plus-stranded. These findings lend support to the speculation that Norwalk and Norwalk-like viruses may be related to the caliciviridae which is an RNA virus family.
The immunoreactive clones identified above can be used to obtain a complete set of overlapping genomic cDNA clones. For example, the lambda gtll clone N49 insert can be isolated and employed as a probe against cDNA libraries established in lambda gtlO. The lambda gtlO libraries are generated essentially as was described in Example 2C for libraries in lambda gtll which were used for immunoscreening. The inserts from clones identified in this fashion can then be isolated by EcoRI digestion of the lambda gtlO clone, electrophoretic fractionation of the digest products, and electroelution of the band corresponding to the insert DNA (Maniatis et al. ; Ausubel et al.) . To identify other viral epitopes, the isolated insert can then be treated with DNase I to generate random fragments (Maniatis et al.), and the resulting digest fragments inserted into lambda gtll phage vectors for immunoscreen- ing. Alternatively, after sequencing, oligonucleotide primers may be used to isolate specific overlapping segments for in-phase insertion into any selected expres¬ sion vector.
Inserts from the immunoreactive clones identified above can be used in a similar manner to probe the origi¬ nal cDNA library generated in lambda gtlO. Specific subfragments of the inserts may also be isolated by polymerase chain reaction or after cleavage with restric¬ tion endonucleases. These subfragments can be radioac- tively labeled and used as probes against the cDNA libra¬ ries generated in lambda gtlO. In particular, the 5' and 3' terminal sequences of the inserts are useful as probes to identify clones which overlap this region.
The inserts of the cDNA library generated in lambda gtlO can also be screened using Norwalk virus sequence- specific hybridization probes. Example 10 illustrates the use of an N35 specific probe, KCL-2 (SEQ ID NO:11; enclosed in a block in Figures 9 and 10) to identify further Norwalk virus coding sequences. The sequences of two cDNA molecules identified by this method are present¬ ed in Figures 9 (SEQ ID N0:18) and 10 (SEQ ID NO:19) . These two sequences represent an extension of the Norwalk virus coding sequences by at least 356 base pairs (SEQ ID NO:16). The relationship of the N2 and N3 clones to each other and to the N35 sequence is graphically presented in Figure 11.
Furthermore, the sequences provided by the end- terminal sequences of the clone inserts are useful as specific sequence primers in first-strand DNA synthesis reactions (Maniatis et al.; Scharf et al.) using, for example, partially purified stool-sample-generated RNA as substrate (Figure 8, N49) . Synthesis of the second- strand of the cDNA is randomly primed (Boehringer Mannheim, Indianapolis IN) (Figure 8, El). The above procedures identify or produce cDNA molecules correspon¬ ding to nucleic acid regions that are adjacent to the known clone N49 insert sequences. These newly isolated sequences can in turn be used to identify further flank- ing sequences, and so on, to identify overlapping cDNA clones from which the entire Norwalk virus genome can be determined. As described above, after new Norwalk virus genomic sequences are isolated, the polynucleotides can be cloned and i munoscreened to identify specific sequen- ces encoding Norwalk virus antigens.
Alternatively, the polymerase chain reaction (Mullis) can be used to clone gaps between known epi- topes. For example, the terminal sequences from any of the six related clones (N35, N49, N51, N48, N28, and N40) can be used as one primer in the polymerase chain reac¬ tion (e.g.. Figure 8, N49) and terminal sequences from unrelated clones (NI, N4, or N8) can be used as the second primer (Figure 8, El) . Since the genomic rela¬ tionship between these two sets of epitope coding sequen- ces are unknown the following approaches may be used to generate an epitope spanning polymerase chain reaction amplification product (Figure 8) :
(i) a mixture of primers from, for example, both strands of one terminus of N49 and both strands of one terminus of NI; (ii) individual reactions of a primer from one strand of one terminus of N49 (Figure 8, N49) and a primer from one strand of one terminus of NI, N4, or N8 (Figure 8, El), and the same primer from N49 and a primer from the opposite strand of the same terminus of NI, N4, or N8 (E2) . Figure 8 illustrates a productive polymerase chain reaction generating an epitope spanning region using, for example, N49 and El.
Knowledge of the Norwalk virus genomic sequence will be helpful (i) in studying and establishing Norwalk virus relatedness to other viruses, and (ii) in the isolation of sequences from viruses related to Norwalk but which are as yet uncloned.
IV. Anti-Norwalk Virus Antigen Antibodies
In another aspect, the invention includes antibodies specific against the recombinant antigens of the present invention. Typically, to prepare antibodies, a host animal, such as a rabbit, is immunized with the purified antigen or fused protein antigen. Hybrid, or fused, proteins may be generated using a variety of coding sequence derived from other proteins, such as 0-galac- tosidase or glutathione-S-transferase. The host serum or plasma is collected following an appropriate time inter- val, and this serum is tested for antibodies specific against the antigen. Example 9 describes the production of rabbit serum antibodies which are specific against the N49 antigens in the SJ26/N49 hybrid protein. These techniques are equally applicable to the other antigens of the present invention.
The gamma globulin fraction or the IgG antibodies of immunized animals can be obtained, for example, by use of saturated ammonium sulfate or DEAE Sephadex, or other techniques known to those skilled in the art for produ¬ cing polyclonal antibodies.
Alternatively, purified antigen or fused antigen protein may be used for producing monoclonal antibodies. Here the spleen or lymphocytes from an immunized animal are removed and immortalized or used to prepare hybrido- mas by methods known to those skilled in the art. To produce a human-human hybridoma, a human lymphocyte donor is selected. A donor known to be infected with a Norwalk virus may serve as a suitable lymphocyte donor. Lym¬ phocytes can be isolated from a peripheral blood sample. Epstein-Barr virus (EBV) can be used to immortalize human lymphocytes or a human fusion partner can be used to produce human-human hybridomas. Primary in vitro sen- sitization with viral specific poiypeptides can also be used in the generation of human monoclonal antibodies. Antibodies secreted by the immortalized cells are screened to determine the clones that secrete antibodies of the desired specificity, for example, by using the ELISA or Western blot method (Ausubel et al.).
V. utility
Routes of transmission that have been documented for Norwalk virus and other gastroenteric viruses include water, food (particularly shellfish and salads), aerosol, fo ites, and person-to-person contact. Infectivity can last for as long as 2 days after resolution of symptoms (Greenberg et al. (1989)).
In gastroenteritis outbreaks, investigators often encounter the problem of having to take action before the etiologic agent responsible for the outbreak can be iden¬ tified. Because of the difficulties associated with diagnosis of gastroenteritis caused by viruses, this problem is particularly relevant for viral outbreaks. Distinguishing viral from bacterial or protozoal gastro- enteritis is sometimes difficult due to the overlap of clinical symptoms. Adequate supplies of virus-specific antigen and antibodies are essential to any virus-testing system. Identification of specific Norwalk virus anti- gens will make possible the direct diagnosis of Norwalk virus involvement in gastroenteritis outbreaks.
A. Diagnostic Methods and Kits
(i) Immunological Approaches The antigens obtained by the methods of the present invention are advantageous for use as diagnostic agents for Norwalk virus antibodies present in Norwalk virus- infected sera; particularly, the antigens represented by Clones N35, N49, N51, N48, N28, N40, NI, N4, and N8. In one preferred diagnostic configuration, test serum is reacted with a solid phase reagent having a surface-bound Norwalk virus antigen obtained by the methods of the present invention, e.g., the N49 insert encoded antigen. After binding anti-Norwalk virus anti- body to the reagent and removing unbound serum components by washing, the reagent is reacted with reporter-labeled anti-human antibody to bind reporter to the reagent in proportion to the amount of bound anti-Norwalk virus antibody on the solid support. The reagent is again washed to remove unbound labeled antibody, and the amount of reporter associated with the reagent is determined. Typically, the reporter is an enzyme which is detected by incubating the solid phase in the presence of a suitable fluorometric or colorimetric substrate. The solid surface reagent in the above assay is prepared by known techniques for attaching protein mate¬ rial to solid support material, such as polymeric beads, dip sticks, 96-well plate or filter material. These attachment methods generally include non-specific adsorp- tion of the protein to the support or covalent attachment of the protein, typically through a free amine group, to a chemically reactive group on the solid support, such as an activated carboxyl, hydroxyl, or aldehyde group.
In a second diagnostic configuration, known as a homogeneous assay, antibody binding to a solid support produces some change in the reaction medium which can be directly detected in the medium. Known general types of homogeneous assays proposed heretofore include (a) spin- labeled reporters, where antibody binding to the antigen is detected by a change in reported mobility (broadening of the spin splitting peaks), (b) fluorescent reporters, where binding is detected by a change in fluorescence efficiency, (c) enzyme reporters, where antibody binding effects enzyme/substrate interactions, and (d) liposome- bound reporters, where binding leads to liposome lysis and release of encapsulated reporter. The adaptation of these methods to the protein antigen of the present invention follows conventional methods for preparing homogeneous assay reagents. In each of the assays described above, the assay method involves reacting the serum from a test individual with the protein antigen and examining the antigen for the presence of bound antibody. The examining may in¬ volve attaching a labeled anti-human antibody to the antibody being examined, either IgM (acute phase/primary response) or IgG (convalescent or chronic phase/secondary response) , and measuring the amount of reporter bound to the solid support, as in the first method, or may involve observing the effect of antibody binding on a homogeneous assay reagent, as in the second method.
Also forming part of the invention is an assay sys¬ tem or kit for carrying out the assay method just de¬ scribed. The kit generally includes a support with surface-bound recombinant Norwalk virus antigen (e.g., the N49 insert encoded antigen) , and a reporter-labeled anti-human antibody for detecting surface-bound anti- Norwalk virus-antigen antibody. As discussed in Section II above, polypeptide antigens derived from Norwalk-virus cDNA clone libraries are immunoreactive with Norwalk virus-infected sera from human patients, indicating that the poiypeptides would be useful for detecting Norwalk virus infection in human serum. In particular, one or more polypeptide antigens produced by clones N35, N49, N51, N48, N28, N40, NI, N4, and N8 can be combined in kits with any number of antigens from other gastroente¬ ritis-causing viruses including rotaviruses, pestiviru- ses, caliciviruses, astroviruses, parvoviruses, coronavi- ruses, toroviruses, adenoviruses, and the Norwalk-like viruses (LeBaron et al.) . Other members of the Norwalk- like virus family include the following variants: Hawaii, Snow Mountain, Montgomery County, Taunton, Amulree, Sapporo, and Otofuke. Kits such as these pro¬ vide a diagnostic composition capable of immunoreacting with a broad spectrum of human viral gastroenteritis serum samples.
A third diagnostic configuration involves use of the anti-Norwalk virus antibodies, described in Section IV above, capable of detecting Norwalk virus specific anti¬ gens. The Norwalk virus antigens may be detected, for example, using an antigen capture assay where Norwalk virus antigens present in candidate fecal material or environmentally derived samples (e.g. sewage effluents) are reacted with a Norwalk virus specific monoclonal antibody. The anti-Norwalk virus monoclonal antibody is bound to a solid substrate and the antigen is then detec¬ ted by a second, different labeled anti-Norwalk virus antibody: the monoclonal antibodies of the present invention which are directed against Norwalk virus speci¬ fic antigens are particularly suited to this diagnostic method. This diagnostic configuration can also be ex- panded to include antibodies directed against other gastroenteritis virus families or variants of the Nor¬ walk-virus, as described above.
Further, since the Norwalk virus, and other viruses involved in most outbreaks of gastroenteritis, generally cannot be cultivated, the antigen and antibody reagents used in diagnosis have, to date, not been easily renew¬ able (LeBaron et al.). The Norwalk virus antigens and antibodies of the present invention provide a renewable source for these reagents. For example, these reagents can be used in solid phase radioimmunoassays for Norwalk virus antigen and a radioimmunoassay for antibody to the Norwalk virus (Greenberg et al. (1989)). The monoclonal and polyclonal anti-Norwalk virus antibodies of the present invention might also be used in the immune elec¬ tron microscopy technique (Kapikian et al.). (ii) Nucleic Acid Approaches
The Norwalk virus nucleic acid sequences identified by the method of the present invention provide sequences which can be used as hybridization probes for detecting the presence of Norwalk virus coding sequences in a sample. Primers useful for the Polymerase Chain Reaction (PCR) (Mullis; Mullis et al.) can be derived from any of the nucleic acid sequences listed in the Sequence Listing or obtained from the inserts of clones NI, N4, and N8. Further, any Norwalk virus sequence, identified as des¬ cribed above in Section III, can be used in this capa¬ city. Typically these primers are two oligonucleotide sequences — generally 15-20 bases — where the two sequences are separated by a defined distance, e.g. 500 bases, and are homologous to opposite strands.
Norwalk virus specific nucleic acid sequences can also be used as hybridization probes to detect the pre¬ sence of the Norwalk virus in a sample as was done, for instance, in Example 7. Kits containing such PCR primers and hybridization probes can also contain similar primers useful for the identification of other gastroenteritis viruses.
Kits based on any of the above diagnostic methods are useful tools to aid in the rapid determination of whether gastroenteritis viruses are the agents respon¬ sible for outbreaks of human gastroenteritis. Further¬ more, although person-to-person transmission is an impor¬ tant aspect of viral gastroenteritis, the initiating event for most outbreaks of viral gastroenteritis is contamination of a common source (Lebaron et al.). Since enteric viruses cannot multiply outside their host, in contrast to bacterial pathogens, the original inoculum present in the common source determines infectivity of the source. Accordingly, the above-described kits are also useful for identification and verification of con¬ taminated sources (e.g., shellfish or water-source).
B. Polypeptide Vaccine The Norwalk virus antigens identified by the methods of the present invention, e.g. as encoded by clone N49, can be formulated for use in a Norwalk virus vaccine. The vaccine can be formulated by standard methods, for example, in a suitable diluent such as water, saline, buffered salines, complete or incomplete adjuvants, and the like. The im unogen is administered using standard techniques for antibody induction, such as by subcutane¬ ous administration of physiologically compatible, sterile solutions containing inactivated or attenuated virus particles or antigens. An immune response producing amount of virus particles is typically administered per vaccinizing injection, typically in a volume of one milliliter or less.
A specific example of a vaccine composition in- eludes, in a pharmacologically acceptable adjuvant, a recombinantly produced N49 polypeptide. The vaccine is administered at periodic intervals until a significant titer of anti-Norwalk virus antibody is detected in the serum. Such a vaccine may be useful to generate short term immunity in uninfected community members against Norwalk virus infection when outbreaks of gastroenteritis have been identified as Norwalk virus induced.
C. Passive Immunoprophylaxis
The effect of viral gastroenteritis agents on people with immunodeficiencies is of particular interest (Lebaron et al.). Interventions, such as the administra¬ tion of anti-Norwalk virus immunoglobulins, that might prove successful in halting chronic Norwalk virus infec¬ tion of immunocompromised patients might also prove useful in other situations, such as the chronic diarrhea associated with malnourishment or in protecting unexposed community members (Lebaron et al.). The anti-Norwalk virus antibodies of the invention can be used as a means of enhancing an anti-Norwalk viruε immune response since antibody-virus complexes are recog¬ nized by macrophages and other effector cells. The anti¬ bodies can be administered in amounts similar to those used for other therapeutic administrations of antibody. For example, pooled gamma globulin is administered at 0.02-0.1 ml/lb body weight during the early incubation of other viral diseases such as rabies, measles and hepati¬ tis B to interfere with viral entry into cells. Thus, antibodies reactive with, for example, the N49 antigen can be passively administered alone, in a "cocktail" with other anti-viral antibodies, or in conjunction with ano¬ ther anti-viral agent to a patient infected with Norwalk virus to enhance the immune response and/or the effec- tiveness of an antiviral drug. The following examples illustrate various aspects of the invention, but are in no way intended to limit the scope thereof.
Materials E. coli DNA polymerase I (Klenow fragment) was obtained from Boehringer Mannheim Biochemicals (Indiana¬ polis, IN) . T4 DNA ligase and T4 DNA polymerase were obtained from New England Biolabs (Beverly, MA) ; Nitro¬ cellulose filters were obtained from Schleicher and Schuell (Keene, NH) .
Synthetic oligonucleotide linkers and primers were prepared using commercially available automated oligonu¬ cleotide synthesizers. Alternatively, custom designed synthetic oligonucleotides may be purchased, for example, from Synthetic Genetics (San Diego, CA) . cDNA synthesis kit and random priming labeling kits were obtained from Boehringer-Mannhei Biochemicals (BMB, Indianapolis, IN) .
EXAMPLE 1 Partial Purification of the Norwalk Virus
A human volunteer, LT, was orally administered the 8FIIa infectious inoculum (Dolin et al. (1971) ; Dolin et al. (1972); Levy et al.; Wyatt et al.; Blacklow et al. (1979); Parrino et al.; Johnson et al.). Clinical stool specimens were obtained from this patient. Occasional Norwalk virus particles were demonstrated by immune electron microscopy (IEM) (Kapikian et al.) in LT1-8, the eighth diarrheal post-infection stool, and in LT1-3, the third post-infection stool. LT1-8 was selected as the post-infection stool used in the following examples unless otherwise specified. A pre-infection stool from this volunteer (LTO) served as the negative control in the following procedures.
Approximately 7.5 grams of specimen LT1-8 was mixed with sufficient TNMC buffer (50 mM Tris-HCl, pH 8.0, 100 mM NaCI, 25 mM MgCl2, 25 mM CaCl2) to make a 10% (w/v) fecal suspension. The suspension was shaken vigorously and pelleted at 3,000 X g for 30 minutes at 4°C. The resulting pellet was placed on ice while the supernatant was pelleted at 100,000 X g for 2 hours at 4°C. The low- speed and high-speed pellets were combined and resuspen¬ ded in 20 ml TNMC buffer.
The pellet suspension was extracted extensively with Blaco-TronTF* (trichlorotrifluoroethane; Baron-Blakeslee, Inc. , San Francisco, CA) and the aqueous phase saved from each extraction. The extracted aqueous phase was pelle¬ ted at 100,000 X g for 2 hours at 4°C. The resulting pellet was resuspended in 2 ml TNMC. This suspension was layered on top of a 20% sucrose cushion overlaying a CsCl cushion (1.5 g/ml) and spun at 80,000 X g for 3 hours at 4°C using a Beckman SW28 rotor. The band at the inter¬ face was collected by side puncture. Half of this par¬ tially purified material was used for RNA extraction and half was purified further in a CsCl gradient. Viral an- tigen was monitored at each step by ELISA using antibody obtained from infected-volunteer studies.
The negative control stool, LTO, and a second IEM- positive infection stool from the same volunteer, LTl-3, were processed in tandem with LT1-8. Nucleic acid was extracted from partially purified stool by a one-step guanidinium/phenol extraction proce¬ dure (Chomczynski et al.).
EXAMPLE 2 Cloning cDNA Molecules Derived From the Norwalk Virus Genome A. Preparing cDNA fragments.
Approximately 10 μg of the nucleic acid prepared in Example 1 was transcribed into cDNA, according to the method of Gubler et al. using an oligo-(dT) or random nucleotide hexamer primers. To ensure that the resulting cDNA molecules had blunt ends, they were treated with T4 DNA polymerase (cDNA Synthesis Kit, BMB, Indianapolis, IN) in the presence of all four nucleotides (Maniatis et al.).
B. Amplifying the cDNA Fragments
The resulting cDNA molecules were amplified using the Sequence-Independent Single Primer Amplification
(SISPA) method. The SISPA technique is detailed in co- owned U.S. Patent application for "RNA and DNA Amplifica¬ tion Techniques," Serial No. 224,961, filed July 26, 1988 (herein incorporated by reference) . The blunt end cDNA molecules from above were ligated (Maniatis et al.) to linkers having the following se¬ quence (SEQ ID NO:20 and SEQ ID NO:21, respectively) :
5'-GGAATTCGCGGCCGCTCG-3' 3'-TTCCTTAAGCGCCGGCGAGC-5'
The cDNA and linker were mixed at a 1:100 molar ratio in the presence of 0.3 to 0.6 Weiss units of T4 DNA ligase. To 100 μl of 10 mM Tris-Cl buffer, pH 8.3, containing 1.5 M MgCl2 and 50 mM KCl (Buffer A) was added about 1 x 10"3 μg of the linker-ended cDNA, 2 μK of a primer having the sequence d(5'-GGAATTCGCGGCCGCTCG-3') , 200 //M each of dATP, dCTP, dGTP, and dTTP, and 2.5 units of Thermus aquaticus DNA polymerase (Tag polymerase) (Perkin-El er Cetus). The reaction mixture was heated to 94°C for 30 seconds for denaturation, allowed to cool to 50°C for 30 seconds for primer annealing, and then heated to 72°C for 0.5-3 minutes to allow for primer extension by Tag poly¬ merase. The replication reaction, involving successive heating, cooling, and polymerase reaction, was repeated an additional 25 times with the aid of a Perkin-Elmer Cetus DNA thermal cycler.
The amplified cDNA fragments were digested with EcoRI. Excess linkers were removed by passage through "SEPHACRYL 300" (Pharmacia, Piscataway NJ) .
C. Cloning the Amplified cDNAs into Lambda gtll.
Phosphatase-treated lambda gtll phage vector arms were obtained from Promega Biotec (Madison, WI) . The lambda gtll (Huynh) vector has a unique EcoRI cloning site 53 base pairs upstream from the ø-galactosidase translation termination codon. The amplified cDNAs from Part B were introduced into the EcoRI site by mixing 0.5- 1.0 μg _EσoJ?I-cleaved gtll, 0.3-3 μl of the above cDNA molecules, 0.5 μl 10X ligation buffer (above), 0.5 μl DNA ligase (200 units) , and distilled water to 5 μl. The mixture was incubated overnight at 14°C, followed by in vitro packaging, according to standard methods (Maniatis et al., pp. 256-268).
The packaged phage were used to infect Escherichia coli strain KM392, obtained from Dr. Kevin Moore, DNAX (Palo Alto, CA) . (Alternatively, E. coli strain Y1090, available from the American Type Culture Collection (ATCC #37197), could be used.) Lawns of KM392 cells infected with serial dilutions of the packaged phage were used to determine the phage titer. For immunoscreening, about 103-104 pfu of the recombinant phage were plated per 150 mm plate (Maniatis et al.).
EXAMPLE 3 Immunoscreening of Lambda gtll Clones
Libraries were immunoscreened using pre- and post- infection sera from a volunteer (designated DD) who deve¬ loped a high titer of antibody (ELISA titer ≥ 1:25,600) to Norwalk virus after experimental infection (as in Example 1) . The sera were pre-adsorbed with lysates of E. coli infected with the lambda gtll vector containing no cDNA inserts: each serum was used at a 1:200 dilution for immunoscreening (Young et al.; Ausubel et al.). In the first immunoscreening with DD post-infection serum, 41 putative reactive plaques were identified from a total of 1.2 x 105 recombinant phage. A secondary screening with the same DD post-infection serum identi¬ fied 30 positive clones. Following a third screening for plaque purification, 21 clones remained reactive. From a final screen, nine clones (designated N28, N35, N40, N48, N49, N51, NI, N4, and N8) were selected for further study by virtue of their specific reactivity with DD post- infection serum and their lack of reactivity with DD pre- infection serum. The sizes of the cDNA inserts (Table 1) were determined by EcoRI digestion of the lambda gtll clones followed by electrophoretic separation of the digest fragments on an agarose gel, run in parallel with DNA size-standards.
Figure imgf000034_0001
A. Hybridization Testing to Human and E. coli Genomic DNA cDNA was tested for similarity to human and E. coli genes by Southern blot hybridization (Southern; Maniatis et al.). Human lymphocyte genomic DNA and E. coli strain 1088 genomic DNA were each digested with EcoRI and Hindlll. The DNA fragments in these digests were elec¬ trophoretically separated on a 1% agarose gel in parallel lanes. The DNA fragments were transferred to nitrocel¬ lulose (Southern) .
Radioactively labeled probes of each lambda gtll cDNA insert were made as follows. Primers of known lambda gtll sequences which flanked the cDNA insert (5'- GGCAGACATGGCCTGCCCGG-3' and 5'-TCGACGGTTTCCATATGGGG-3') were used to amplify the cDNA insert by the polymerase chain reaction (PCR) method of Mullis. The typical PCR cycle involved the following steps: melting at 94°C for 30 seconds, followed by annealing at 50°C for 1 min., and extension at 72°C for 30 seconds. The reactions were repeated for 30 cycles. The PCR products were digested with EcoRI and electrophoretically resolved using a pre¬ parative 1.5% agarose gel. The clone-specific, amplified fragment was identified by size and electrophoresis con- tinued to transfer the DNA band completely onto a NA45 membrane (Schleicher & Schuell, Keene, NH) . The DNA was eluted from the membrane using a high salt buffer (Schleicher & Schuell, Keene, NH) , extracted with once with phenol:chloroform (1:1), and ethanol precipitated. After ethanol precipitation, the DNA was used as the template for random-primed DNA labeling (Boehringer- Mannheim Biochemicals, Indianapolis, IN) .
The nitrocellulose filters were hybridized with radiolabeled probes made from each of the nine clones identified in Example 3. None of the nine clones demon¬ strated a positive signal with either the human or E. coli genomic DNAs. B. Hybridization of the Lambda gtll clone Inserts to LT1-8 and LTO cDNAs.
The insert of lambda gtll clones N49, N51, N28, N35, N40, N48, NI, N4, and N8 were isolated and radiolabeled as above. The SISPA amplified cDNAs generated from stool samples LT1-8 and LTO (Example 1) were loaded onto parallel lanes of a 1% agarose gel and electrophore¬ tically separated. The cDNAs were transferred from the gel to nitrocellulose paper by standard procedures (Mani- atis et al.). The nitrocellulose filters were indivi¬ dually hybridized with each radiolabeled probe made from the N49, NI, N4, and N8 clones (Example 3) as described above in Example 4A. Each of the probes hybridized specifically to SISPA cDNA from LT1-8 infected stool. The data for the insert from clone N49 is shown in Figure 1. The N49 probe hybridizes to SISPA cDNA from LT1-8 infected stool (Figure 1, lane 1) , but not to SISPA cDNA from the LTO pre-infection stool (Figure 1, lane 2) .
C. Cross-Hybridization Testing Between the Clone In¬ serts.
The nine lambda gtll clone inserts isolated in Ex¬ ample 4A and a negative control DNA were applied to nitrocellulose filters. The filters were then separately hybridized with each of the nine probes generated in
Example 4A which represent each of the lambda gtll clones from Example 3. The result of this hybridization study showed that six clones (N35, N49, N51, N48, N28, and N40) cross-hybridized with each other suggesting that common sequences exist among these six clones. Clones NI, N4, and N8 showed no cross-hybridization to each other or to either of clones N49 and N35. EXAMPLE 5 Sequencing of the cDNA Inserts and Sequence Comparisons The cDNA inserts of lambda gtll clones N28, N35, N40, N48, N49, N51, NI, N4, and N8 were subcloned into the "BLUESCRIPT KS+" vector (Stratagene, La Jolla, CA) . The sequences for the cDNA inserts N28, N35, N40, N48, N49, and N51 were determined as per the manufacturer's instructions using the dideoxy chain termination tech- nique (Sanger, 1979) . Each of the clones had a single open reading frame, contiguous with the £-galactosidase reading frame of the lambda gtll vector. NI, N4, and N8 had 5' ends contiguous with the l-galactosidase reading frame but did not have completely open reading frames throughout the length of each insert. Two of the clones, N49 and N51, had identical DNA sequences: N49 was selec¬ ted for further study. The sequence data is presented as follows: N35, SEQ ID NO:l; N28, SEQ ID NO:3; N40, SEQ ID NO:5; N48, SEQ ID NO:7; and N49, SEQ ID NO:9. Sequences were compared with "GENBANK" sequences at both nucleic acid and amino acid levels. The "GENBANK" search indi¬ cated that these sequences are unique as both nucleic acid and amino acid sequences.
Sequences which showed some homology to N35 (SEQ ID N0:1) were aligned using N35 (SEQ ID NO:l) as a reference sequence. The nucleotide (Figure 2A) and predicted amino acid (Figure 2B) sequences of the clones are shown. Re¬ gions of overlap and identity are shown by dashed lines ( ) . Non-identical nucleotides and amino acids are specifically indicated. Five different start sites are represented among the six cloned cDNAs. EXAMPLE 6 Expanded Immunoscreening Using Clone N49 Immunological screening of the lambda gtll N49 clone was expanded to include a panel of paired sera from seven volunteers infected with the Norwalk virus (Example 1) , along with a paired negative control sample (EM) that had an undetectable anti-Norwalk ELISA titer (Table 2) . Serum reactivity toward the Norwalk virus was determined as previously described (Gary et al.; Herrmann et al.; Madore et al. (1986A) ; and, Greenberg et al. (1978)). The reactivities of the pre- and post-infection sera are given in Table 2. The immunoreactivity of the lambda gtll N49 clone was assayed by mixing plague purified N49 phage with non-recombinant lambda gtll and plaque-plating at a 1:1 ratio. Reactive plaques were detected (Young et al.; Ausubel et al.) after incubation with the test sera by using an alkaline phosphatase-conjugated anti-IgG se¬ cond antibody (Pierce, Rockford IL) . For each serum sam- pie, selected reactive plaques were confirmed to contain the N49-specific insert using the polymerase chain reac¬ tion and the following N49-specific primers: 5'- CACCACCATAAACAGGCTG-3' and 5'-AAAGAATGCTCTATCAGGCT-3' (these sequences are underlined in Figure 2) . As shown in Table 2, the protein product of clone N49 reacted with 6 of the 7 post-infection sera tested. Only pre-infection serum AT, which had high pre-existing levels of reactivity to Norwalk antigen by ELISA, also reacted with the N49 fusion protein.
Figure imgf000039_0001
A. RNA Hybridization using IEM-Positive Stool Samples
A 224-bp N49 specific probe was isolated by direct polymerase chain reaction using the N49 specific primers given in Example 6 and indicated in Figure 2 by under¬ lining. The conditions for the polymerase chain reaction were essentially the same as described above in Example 4A except that the duration of each segment was 30 seconds. The probe was radioactively labeled as des¬ cribed in Example 4A.
Partially purified nucleic acid from the LT1-8, LT1- 3, and LTO stool samples (Example 1) was prepared for hybridization analysis as described in Example 7B: in addition to these samples, a negative-control RNA from the NCDV (Nebraska Calf Diarrhea Virus) rotavirus was also included. The LT1-8 and LT1-3 stool samples were IEM-positive for the presence of the Norwalk virus. The radiolabeled N49-specific probe hybridized to nucleic acid extracted from partially purified Norwalk— infected stools, LT1-8 (Figure 3, spot 2) and LT1-3 (Figure 3, spot 3), but not to nucleic acid derived from the pre-infection stool, LTO (Figure 3, spot 4), or to NCDV rotavirus mRNA (Figure 3, spot 1). B. Dot-Blot Analysis
To further support that clone N49 represented a por¬ tion of the Norwalk virus genome, RNA was extracted from pre-infection and serial post-infection stools collected from 5 volunteers who became ill after infection with the Norwalk virus 8FIIa inoculum (Example l) . The post¬ infection stool specimens chosen for RNA hybridization analysis were shown to test positive for Norwalk virus viral antigen using radioimmunassays (RIA) and/or ELISA: all pre-infection controls tested negative by the same standard. Nucleic acids were isolated from the fecal samples as follows: 500 μl of a 10% fecal suspension (in PBS) of each specimen was combined with 125 μl of 40% polyethylene glycol (PEG, molecular weight 8000) and allowed to precipitate overnight at 4°C. The suspension was pelleted at 10,000 X g for 20 min.
Nucleic acid was extracted from the pellet using a one-step guanidinium/phenol extraction procedure (Chomczynski et al.) and prepared for dot blot hybridiza- tion analysis according to the recommendations of the manufacturer of the "MINIFOLD I" apparatus (Schleicher and Schuell, Keene, NH) .
Hybridization was carried out in 50% formamide and IX hybridization buffer (5X Denhardts solution (Maniatis et al.), 5X SSC (Maniatis et al.), 50 mM NaH2P04, 1 mM sodium pyrophosphate/Na2HP04, 50 mg denatured salmon sperm DNA/500 ml, 50 mg ATP/500 ml) . The hybridization probe used was the radiolabeled N49 insert (Example 3) . Fol- lowing hybridization, filters were washed in (i) 2X SSC at room temperature for 15 minutes, and (ii) 0.1X SSC with 0.1% SDS at 65°C for 1 hr. Filters were dried and then exposed to X-ray film.
As can be seen from the results of the hybridization analysis (Figure 4) the N49 probe hybridized to nucleic acid from test specimens 1-4 an -5, III-4, -5, -6, and -7, and IV-8 and -9. No hybridization could be demon¬ strated with nucleic acid isolated from any of the pre¬ infection stools. C. Comigration of Norwalk virus antigen activity with N49 specific sequences.
Partially purified LT1-3 virus (Example 1) was further purified by overnight centrifugation on a 40-55% CsCl gradient, at 100,000 X g maintained at 4°C. Frac- tions (0.25 ml each) were collected by bottom puncture. Six fractions spanning the density range of 1.31 to 1.41 g/ml were examined further (Figure 7) . The Norwalk virus antigen peak, determined by ELISA, was centered around the fraction with density 1.37 g/ml (Figure 7). The six fractions were tested for the presence of N49-specific sequences by RNA dot blot hybridization (Example 7B) using the N49-specific radiolabeled probe described in Example 4A. The Norwalk virus antigen peak corresponded to the peak hybridization seen on the RNA blot (Figure 7) probed with the N49-specific probe.
EXAMPLE 8 The Nature of the Norwalk Virus Genomic Nucleic Acid A. The Norwalk virus genome is an RNA molecule The nucleic acid extracted from Norwalk-infected stool samples LT1-3 and LT1-8 (Example 1) were treated with RNaseA and DNasel as per the manufacturer's sugges¬ tions (both enzymes were obtained from Boehringer Mannheim, Indianapolis IN) . The samples were then pre¬ pared for hybridization as described in Example 7B. The probe was the N49 specific probe used in Example 7B.
Treatment with RNaseA (Figure 5, column 1) complete¬ ly eliminated hybridization with the N49-specific, radio- labeled probe, while DNase I treatment (Figure 5, column 2) had no effect. Samples which were not treated with either RNasel or DNasel are shown in Figure 5, column 3.
B. The Norwalk virus genome is of positive polarity. Single-stranded oligonucleotide probes corresponding to both the positive strand of N49 residues 71 to 91 (i.e., coding) and negative strand of N49 residues 208 to 227 (Figure 2) were synthesized by standard procedures. The oligonucleotides were radiolabeled by phosphorylating the synthetic oligonucleotide primers with -[32P]ATP (Richardson) .
The nucleic acid from stool sample LT1-8 was pre¬ pared for hybridization as described in Example 7B. Hybridization was carried out in 30% formamide and IX hybridization buffer (see above) at 42*C. The filters were washed in 2X SSC (Maniatis et al.) at room tempera¬ ture for 30 minutes.
Only the negative sense, synthetic N49 oligonucleo¬ tide probe hybridized to the RNA extracted from infected stool LT1-8 (Figure 6, spot 1), indicating that the RNA is of positive polarity. No hybridization with LT1-8 RNA was detectable when the positive sense, synthetic N49 oligonucleotide probe was used (Figure 6, spot 2). EXAMPLE 9
Antibodies Generated Against the N49 Encoded
Peptide Antigen
A. Generation of Antibodies The N49 insert digest fragments from lambda gtll is released by EcoRI digestion of the phage, and the insert region purified by gel electrophoresis. The purified fragment is introduced into the pGEX expression vector (Smith) in-frame with the glutathione S-transferase protein. Expression of glutathione S-transferase fused protein (Sj26 fused protein) containing the N49 encoded polypeptide antigen can be achieved in E. coli strain KM392. The fusion protein is isolated from lysed bac¬ teria by affinity chromatography on a column packed with glutathione-conjugated beads, according to published methods (Smith) .
The purified SJ26/N49 fused protein can be injected subcutaneously in Freund's adjuvant in a rabbit. Typi¬ cally, approximately 1 mg of fused protein is injected at days 0 and 21, and rabbit serum collected on days 42 and 56.
The above procedure can also be used to generate antibodies against the ,9-galactosidase/N49 polypeptide antigen fusion protein where the fusion protein is iso- lated by immuno-affinity chromatography using, for ex¬ ample, monospecific or monoclonal anti-,9-galactosidase antibodies.
B. Specificity Testing The specificity of the antibodies can be evaluated by Western blot screening (Ausubel et al.) .
Lysates are prepared from bacterial strains of KM392 cells transformed with (a) pGEX, and (b) pGEX containing the N49 insert. Typically, minilysates are prepared from the transformed bacteria as follows. The infected bacte¬ ria are streaked on solid medium containing ampicillin and grown at 37°C overnight or until colonies are appa¬ rent. Individual bacterial colonies are used to inocu- late 1 ml of rich bacterial medium containing ampicillin, e.g., LB broth containing 50 μg/ml ampicillin (Maniatis). This saturated overnight bacterial culture is used to inoculate a 10 ml culture of the same medium, which is incubated.with aeration to an O.D. of about 0.2 to 0.4, typically requiring 1 hour incubation at 37°C. The cells are pelleted by centrifugation, and 1 ml of the pelleted material resuspended in 100 μl of lysis buffer (62 mM Tris, pH 7.5 containing 5% mercaptoethanol, 2.4 % SDS and 10% glycerol) . The lysates are treated with DNasel to digest bac¬ terial DNA, as evidenced by a gradual loss of viscosity in the lysate. An aliquot (typically about 15 μl) of the DNase-treated lysate is diluted with "TRITON X-100" and sodium dodecyl sulfate (SDS) to a final concentration of 2% "TRITON X-100" and 0.5% SDS. Non-solubilized material is removed by centrifugation and the supernatant frac¬ tionated by SDS polyacrylamide electrophoresis (SDS- PAGE) . A portion of the gel is stained, to identify the polypeptide antigens of interest, and a corresponding unstained portion of the gel transferred onto a nitrocel¬ lulose filter according to known methods (Ausubel et al.). Briefly, the filters are blocked with AIB (10 mM Tris, pH 8.0, 150 mM NaCl,with 1% gelatin), and reacted with serum samples from the rabbits immunized as de- scribed above. The presence of specific antibody binding to the nitrocellulose filters can also be assayed by immunobinding of alkaline-phosphatase labeled anti-rabbit IgG. The results of the Western blot analysis are ex¬ pected to show positive anti-Norwalk virus antibody reac- tions with lysates from pGEX-N49, but not with lysates from the pGEX control strain.
Anti-N49 antibody present in the sera from the ani¬ mal immunized with the SJ26/N49 can be purified by af- finity chromatography as described above. Human anti-N49 antibodies from human sera can also be obtained by af¬ finity chromotography by derivatizing the N49 antigen- peptide to the support beads.
EXAMPLE 10
Further Isolation of Norwalk Virus Sequences
A. Generation in Lambda gtlO of an LT1-8 cDNA Library. The SISPA cDNA from LT1-8 infected stool (Example
2), was cloned into the lambda gtlO vector essentially as described in Example 2 for lambda vector gtll. The lambda gtlO vector (Huynh, et al . j Murray, et al . ) has a unique EcoRI cloning site in the cl phage repressor gene. The lambda gtlO vector is useful for screening insert molecules using nucleic acid probes. Briefly, lambda gtlO was obtained from Promega Biotec (Madison, WI) . The vector was digested with EcoRI (New England Biolabs) and phosphatase-treated (Calf-Intestinal Alkaline Phosphatase (CIP) , Promega) as per the manufacturer's instructions. The amplified cDNAs from Example 2, Part B were introduced into the EcoRI site by mixing 0.5-1.0 μg _5coRI-cleaved gtlO, 0.3-3 μl of the above cDNA molecules, 0.5 μl 10X ligation buffer (above), 0.5 μl DNA ligase (200 units) , and distilled water to 5 μl. The mixture was incubated overnight at 14βC, followed by in vitro packag¬ ing, according to standard methods (Maniatis et al., pp. 256-268) . The packaged phage were used to infect Escherichia coli strain C600Hf1 (Promega) . Lawns of C600Hf1 cells infected with serial dilutions of the packaged phage were used to determine the phage titer. For hybridization screening, about 103-104 pfu of the recombinant phage were plated per 150 mm plate (Maniatis et al.).
B. Screening
Plaques were transferred to nitrocellulose paper as previously described (Ausubel, et al . ; Maniatis, et al . ) . A probe (KCL-2, derived from clone N35; SEQ ID N0:1) was end-labeled using γ-32ATP and polynucleotide kinase (Boeh- ringer-Mannheim Biochemicals) . The plaque transfers were screened with the radiolabeled probe using standard buffers and hybridization conditions (Maniatis, et al . ) . Approximately 60,000 plaques were screened and 20 posi¬ tive plaques were detected. Of the 20 positives, 2 of the plaques were had very strong signals.
The two plaques having strong positive signals, using the KCL-2 probe, were designated dT-llAS and dT- 18AS. These two isolates were plaque purified and re- screened for hybridization to KCL-2. DNA was isolated from two phage which were hybridization-positive, one each from dT-llAS and dT-18AS. This DNA was then ampli- fied by polymerase chain reaction (Mullis; Mullis, et al . ) using two gtlO specific primers which flank the inserts. The resulting fragments were blunt-ended frag¬ ments.
The "BLUESCRIPT" (PBS SK, Stratagene, La Jolle CA) vector was digested with Smal (New England Biolabs, as per manufacturer's directions) and treated with CIP. The blunt-ended amplification fragments obtained from dT-llAS and dT-18AS were each ligated (Maniatis, et al . ) into the Smal site of the "BLUESCRIPT" vector. These plasmids were then transformed into DH5α (Bethesda Research Labo¬ ratories) . Insert bearing plasmids were identified by hybridization with the KCL-2 probe. The inserts were isolated from two plasmids designated PNW11-9 (N2) and PNW 18-12 (N3) , corresponding to isolates dT-llAS and dT- 18AS, respectively.
The insert of the two plasmids were sequenced as per the manufacturer's instructions for use of the "BLUE¬ SCRIPT" plasmid. The sequences of the inserts from these two plasmids are shown in Figure 9 (PNW11-9 (N2) ; SEQ ID NO:18) and Figure 10 (PNW 18-12 (N3) : SEQ ID NO:19).
These sequences were then compared to the sequence of N35 (Figures 9 (SEQ ID NO:12), 10 (SEQ ID NO:14), and 11) . Clones N2 and N3 contain, respectively, 284 and 87 bases pairs of homology to N35 and 356 basepairs of homology to each other (SEQ ID NO:16).
Although the invention has been described with reference to particular embodiments, methods, construc¬ tion and use, it will be apparent to those skilled in the art that various changes and modifications can be made without departing from the invention.
SEQUENCE LISTING
(1) GENERAL INFORMATION:
(i) APPLICANT: Kim, Jungsuh P.
Ma sui, Suzanne M. Greenberg, Harry B. Reyes, Gregory R.
(ϋ) TITLE OF INVENTION: The Norwalk Virus Human Gastroenteritis Agent and Molecular Cloning of Corresponding cDNAs
(iii) NUMBER OF SEQUENCES: 21
(iv) CORRESPONDENCE ADDRESS:
(A) ADDRESSEE: Peter J. Dehlinger
(B) STREET: 350 Cambridge Avenue, Suite 300
(C) CITY: Palo Alto
(D) STATE: CA (E) COUNTRY: USA
(F) ZIP: 94306
(v) COMPUTER READABLE FORM:
(A) MEDIUM TYPE: Floppy disk (B) COMPUTER: IBM PC compatible
(C) OPERATING SYSTEM: PC-DOS/MS-DOS
(D) SOFTWARE: Patentin Release #1.0, Version #1.25
(vi) CURRENT APPLICATION DATA: (A) APPLICATION NUMBER:
(B) FILING DATE:
(C) CLASSIFICATION:
(viii) ATTORNEY/AGENT INFORMATION: (A) NAME: Fabian, Gary R.
(B) REGISTRATION NUMBER: 33,875
(C) REFERENCE/DOCKET NUMBER: 4600-078.41
(ix) TELECOMMUNICATION INFORMATION: (A) TELEPHONE: (415) 323-8302
(B) TELEFAX: (415) 323-8306 (2) INFORMATION FOR SEQ ID NO:l:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 414 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk virus δFIIa
(vii) IMMEDIATE SOURCE: (B) CLONE: N35
(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 1..414
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:l:
GAA TTC GCG GCC GCT CGC CAA GGG GGC TTT GAT AAC CAA GGG AAT ACC 4 Glu Phe Ala Ala Ala Arg Gin Gly Gly Phe Asp Asn Gin Gly Asn Thr 1 5 10 15
CCG TTT GGT AAG GGT GTG ATG AAG CCC ACC ACC ATA AAC AGG CTG TTA 9 Pro Phe Gly Lys Gly Val Met Lys Pro Thr Thr Ile Aβn Arg Leu Leu 20 25 30
ATC CAG GCT GTA GCC TTG ACG ATG GAG AGA CAG GAT GAG TTC CAA CTC 1 lie Gin Ala Val Ala Leu Thr Met Glu Arg Gin Asp Glu Phe Gin Leu 35 40 45 CAG GGG CCT ACG TAT GAC TTT GAT ACT GAC AGA GTA GCT GCG TTC ACG 19 Gin Gly Pro Thr Tyr Asp Phe Asp Thr Asp Arg Val Ala Ala Phe Thr 50 55 60
AGG ATG GCC CGA GCC AAC GGG TTG GGT CTC ATA TCC ATG GCC TCC CTA 240 Arg Met Ala Arg Ala Aβn Gly Leu Gly Leu Ile Ser Met Ala Ser Leu 65 70 75 80
GGC AAA AAG CTA CGC AGT GTC ACC ACT ATT GAA GGA TTA AAG AAT GCT 288 Gly Lys Lys Leu Arg Ser Val Thr Thr lie Glu Gly Leu Lys Asn Ala 85 90 95
CTA TCA GGC TAT AAA ATA TCA AAA TGC AGT ATA CAA TGG CAG TCA AGG 336 Leu Ser Gly Tyr Lys Ile Ser Lys Cys Ser Ile Gin Trp Gin Ser Arg 100 105 110
GTG TAC ATT ATA GAA TCA GAT GGT GCC AGT GTA CAA ATC AAA GAA GAC 384 Val Tyr lie Ile Glu Ser Asp Gly Ala Ser Val Gin Ile Lys Glu Asp 115 120 125
AAG CAA GCT TTG ACG AGC GGC CGC GAA TTC 414
Lys Gin Ala Leu Thr Ser Gly Arg Glu Phe 130 135
(2) INFORMATION FOR SEQ ID NO:2:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 138 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
( i) SEQUENCE DESCRIPTION: SEQ ID NO:2:
Glu Phe Ala Ala Ala Arg Gin Gly Gly Phe Asp Asn Gin Gly Asn Thr 1 5 10 15 Pro Phe Gly Lys Gly Val Met Lys Pro Thr Thr Ile Aβn Arg Leu Leu 20 25 30
Ile Gin Ala Val Ala Leu Thr Met Glu Arg Gin Asp Glu Phe Gin Leu 35 40 45
Gin Gly Pro Thr Tyr Asp Phe Aβp Thr Aβp Arg Val Ala Ala Phe Thr 50 55 60
Arg Met Ala Arg Ala Asn Gly Leu Gly Leu Ile Ser Met Ala Ser Leu 65 70 75 80
Gly Lys Lys Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lys Asn Ala 85 90 95
Leu Ser Gly Tyr Lys Ile Ser Lys Cys Ser Ile Gin Trp Gin Ser Arg 100 105 110
Val Tyr Ile Ile Glu Ser Asp Gly Ala Ser Val Gin Ile Lys Glu Asp 115 120 125
Lys Gin Ala Leu Thr Ser Gly Arg Glu Phe 130 135
(2) INFORMATION FOR SEQ ID NO:3:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 285 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk virus 8FIIa (vii) IMMEDIATE SOURCE: (B) CLONE: N28
(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 1..285
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:3:
GAA TTC GCG GCC GCT CGG TTC CAA CTC CAG GGG CCT ACG TAT GAC TTT 48 Glu Phe Ala Ala Ala Arg Phe Gin Leu Gin Gly Pro Thr Tyr Asp Phe 1 5 10 15
GAT ACT GAC AGA GTA GCT GCG TTC ACG AGG ATG GCC CGA GCC AAC GGG 96 Asp Thr Asp Arg Val Ala Ala Phe Thr Arg Met Ala Arg Ala Asn Gly 20 25 30
TTG GGT CTC ATA TCC ATG GCC TCC CTA GGC AAA AAG CTA CGC AGT GTC 144 Leu Gly Leu lie Ser Met Ala Ser Leu Gly Lys Lys Leu Arg Ser Val 35 40 45
ACC ACT ATT GAA GGA TTA AAG AAT GCT CTA TCA GGC TAT AAA ATA TCA 192 Thr Thr Ile Glu Gly Leu Lys Asn Ala Leu Ser Gly Tyr Lys Ile Ser 50 55 60
AAA TGC AGT ATA CAA TGG CAG TCA AGG GTG TAC ATT ATA GAA TCA GAT 240 Lys Cys Ser lie Gin Trp Gin Ser Arg Val Tyr Ile Ile Glu Ser Asp 65 70 75 80
GGT GCC AGT GTA CAA ATC AAA AAA AAA ACG AGC GGC CGC GAA TTC 285
Gly Ala Ser Val Gin Ile Lys Lys Lys Thr Ser Gly Arg Glu Phe
85 90 95
(2) INFORMATION FOR SEQ ID NO:4:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 95 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear (ii) MOLECULE TYPE: protein
( i) SEQUENCE DESCRIPTION: SEQ ID NO:4:
Glu Phe Ala Ala Ala Arg Phe Gin Leu Gin Gly Pro Thr Tyr Asp Phe 1 5 10 15
Asp Thr Asp Arg Val Ala Ala Phe Thr Arg Met Ala Arg Ala Asn Gly 20 25 30
Leu Gly Leu Ile Ser Met Ala Ser Leu Gly Lys Lys Leu Arg Ser Val 35 40 45
Thr Thr Ile Glu Gly Leu Lys Asn Ala Leu Ser Gly Tyr Lys lie Ser 50 55 60
Lys Cys Ser Ile Gin Trp Gin Ser Arg Val Tyr Ile Ile Glu Ser Asp 65 70 75 80
Gly Ala Ser Val Gin Ile Lys Lys Lys Thr Ser Gly Arg Glu Phe
85 90 95
(2) INFORMATION FOR SEQ ID NO:5:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 206 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk virus 8FIIa
(vii) IMMEDIATE SOURCE: (B) CLONE: N40 (ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 1..206
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:5:
GAA TTC GCG GCC GCT CGA CTC CAG GGG CCT ACG TAT GAC TTT GAT ACT 48 Glu Phe Ala Ala Ala Arg Leu Gin Gly Pro Thr Tyr Asp Phe Asp Thr 1 5 10 15
GAC AGA GTA GCT GCG TTC ACG AGG ATG GCC CGA GCC AAC GGG TTG GGT 96 Asp Arg Val Ala Ala Phe Thr Arg Met Ala Arg Ala Asn Gly Leu Gly 20 25 30
CTC ATA TCC ATG GCC TCC CTA GGC AAA AAG CTA CGC AGT GTC ACC ACT 144 Leu lie Ser Met Ala Ser Leu Gly Lys Lys Leu Arg Ser Val Thr Thr 35 40 45
ATT GAA GGA TTA AAG AAT GCT CTA TCA GGC TAT AAA AAA AAA AAA CGA 192 lie Glu Gly Leu Lys Asn Ala Leu Ser Gly Tyr Lys Lys Lys Lys Arg 50 55 60
GCG GCC GCG AAT TC 206
Figure imgf000054_0001
65
(2) INFORMATION FOR SEQ ID NO:6:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 68 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:6:
Glu Phe Ala Ala Ala Arg Leu Gin Gly Pro Thr Tyr Asp Phe Asp Thr 1 5 10 15 Aβp Arg Val Ala Ala Phe Thr Arg Met Ala Arg Ala Aβn Gly Leu Gly 20 25 30
Leu Ile Ser Met Ala Ser Leu Gly Lye Lye Leu Arg Ser Val Thr Thr 35 40 45
lie Glu Gly Leu Lye Aβn Ala Leu Ser Gly Tyr Lys Lys Lys Lye Arg 50 55 60
Figure imgf000055_0001
65
(2) INFORMATION FOR SEQ ID NO:7:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 345 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk virus 8FIIa
(vii) IMMEDIATE SOURCE: (B) CLONE: N48
(ix) FEATURE:
(A) NAME/KEY: CDS (B) LOCATION: 1..345
( i) SEQUENCE DESCRIPTION: SEQ ID NO:7: GAA TTC GCG GCC GCT CGC ACC ACC ATA AAC AGG CTG TTA ATC CAG GCT 48 Glu Phe Ala Ala Ala Arg Thr Thr Ile Asn Arg Leu Leu Ile Gin Ala 1 5 10 15
GTA GCC TTG ACG ATG GAG AGA CAG GAT GAG TTC CAA CTC CAG GGG CCT 96 Val Ala Leu Thr Met Glu Arg Gin Asp Glu Phe Gin Leu Gin Gly Pro 20 25 30
ACG TAT GAC TTT GAT ACT GAC AGA GTA GCT GCG TTC ACG AGG ATG GCC 144 Thr Tyr Asp Phe Aβp Thr Aβp Arg Val Ala Ala Phe Thr Arg Met Ala 35 40 45
CGA GCC AAC GGG TTG GGT CTC ATA TCC ATG GCC TCC CTA GGC AAA AAG 192 Arg Ala Aβn Gly Leu Gly Leu lie Ser Met Ala Ser Leu Gly Lye Lye 50 55 60
CTA CGC AGT GTC ACC ACT ATT GAA GGA TTA AAG AAT GCT CTA TCA GGC 240 Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lys Asn Ala Leu Ser Gly 65 70 75 80
TAT AAA ATA TCA AAA TGC AGT ATA CAA TGG CAG TCA AGG GTG TAC ATT 288 Tyr Lys Ile Ser Lys Cys Ser Ile Gin Trp Gin Ser Arg Val Tyr Ile 85 90 95
ATA GAA TCA GAT GGT GCC AGT GTA CAA ATC AAA AAA AAA ACG AGC GGC 336 lie Glu Ser Asp Gly Ala Ser Val Gin Ile Lys Lys Lys Thr Ser Gly 100 105 110
CGC GAA TTC 345
Arg Glu Phe 115
(2) INFORMATION FOR SEQ ID NO:8:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 115 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear ( ii ) MOLECULE TYPE : protein
(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 8 :
Glu Phe Ala Ala Ala Arg Thr Thr Ile Aβn Arg Leu Leu lie Gin Ala 1 5 10 15
Val Ala Leu Thr Met Glu Arg Gin Aβp Glu Phe Gin Leu Gin Gly Pro 20 25 30
Thr Tyr Aβp Phe Asp Thr Asp Arg Val Ala Ala Phe Thr Arg Met Ala 35 40 45
Arg Ala Aβn Gly Leu Gly Leu Ile Ser Met Ala Ser Leu Gly Lye Lye 50 55 60
Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lye Aβn Ala Leu Ser Gly 65 70 75 80
Tyr Lye Ile Ser Lye Cyβ Ser lie Gin Trp Gin Ser Arg Val Tyr lie
85 90 95
Ile Glu Ser Aβp Gly Ala Ser Val Gin Ile Lye Lye Lye Thr Ser Gly 100 105 110
Arg Glu Phe 115
(2) INFORMATION FOR SEQ ID NO:9:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 348 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO (vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk virus 8FIIa
(vii) IMMEDIATE SOURCE: (B) CLONE: N49
(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 1..348
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:9:
GAA TTC GCG GCC GCT CGG CCC ACC ACC ATA AAC AGG CTG TTA ATC CAG 48 Glu Phe Ala Ala Ala Arg Pro Thr Thr Ile Asn Arg Leu Leu Ile Gin 1 5 10 15
GCT GTA GCC TTG ACG ATG GAG AGA CAG GAT GAG TTC CAA CTC CAG GGG 96 Ala Val Ala Leu Thr Met Glu Arg Gin Asp Glu Phe Gin Leu Gin Gly 20 25 30
CCT ACG TAT GAC TTT GAT ACT GAC AGA GTA GCT GCG TTC ACG AGG ATG 144 Pro Thr Tyr Asp Phe Asp Thr Aβp Arg Val Ala Ala Phe Thr Arg Met 35 40 45
GCC CGA GCC AAC GGG TTG GGT CTC ATA TCC ATG GCC TCC CTA GGC AAA 192 Ala Arg Ala Asn Gly Leu Gly Leu Ile Ser Met Ala Ser Leu Gly Lys 50 55 60
AAG CTA CGC AGT GTC ACC ACT ATT GAA GGA TTA AAG AAT GCT CTA TCA 240 Lye Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lys Asn Ala Leu Ser 65 70 75 80
GGC TAT AAA ATA TCA AAA TGC AGT ATA CAA TGG CAG TCA AGG GTG TAC 288 Gly Tyr Lys Ile Ser Lye Cys Ser Ile Gin Trp Gin Ser Arg Val Tyr
85 90 95
ATT ATA GAA TCA GAT GGT GCC AGT GTA CAA ATC AAA AAA AAA ACG AGC 336 Ile Ile Glu Ser Asp Gly Ala Ser Val Gin Ile Lys Lys Lys Thr Ser 100 105 110 GGC CGC GAA TTC 34
Gly Arg Glu Phe 115
(2) INFORMATION FOR SEQ ID NO:10:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 116 amino acids (B) TYPE: amino acid
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:10:
Glu Phe Ala Ala Ala Arg Pro Thr Thr Ile Asn Arg Leu Leu Ile Gin 1 5 10 15
Ala Val Ala Leu Thr Met Glu Arg Gin Asp Glu Phe Gin Leu Gin Gly
20 25 30
Pro Thr Tyr Aβp Phe Aβp Thr Aβp Arg Val Ala Ala Phe Thr Arg Met 35 40 45
Ala Arg Ala Asn Gly Leu Gly Leu Ile Ser Met Ala Ser Leu Gly Lys 50 55 60
Lye Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lye Aβn Ala Leu Ser 65 70 75 80
Gly Tyr Lye lie Ser Lye Cys Ser Ile Gin Trp Gin Ser Arg Val Tyr 85 90 95
lie Ile Glu Ser Aβp Gly Ala Ser Val Gin Ile Lys Lys Lye Thr Ser 100 105 110
Gly Arg Glu Phe 115 (2) INFORMATION FOR SEQ ID NO:11:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 31 base pairs
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk Virus 8FIIa
(vii) IMMEDIATE SOURCE:
(B) OLIGONUCLEOTIDE: KCL-2
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:11:
CCAGTGTACA AATCAAAGAA GACAAGCAAG C 31
(2) INFORMATION FOR SEQ ID NO:12:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 936 base pairs (B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk virus 8FIIa (vii) IMMEDIATE SOURCE:
(B) CLONE: N2, Combined N35 and N2 sequences
(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 1..936
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:12:
GAA TTC GCG GCC GCT CGC CAA GGG GGC TTT GAT AAC CAA GGG AAT ACC 4 Glu Phe Ala Ala Ala Arg Gin Gly Gly Phe Asp Aβn Gin Gly Aβn Thr 1 5 10 15
CCG TTT GGT AAG GGT GTG ATG AAG CCC ACC ACC ATA AAC AGG CTG TTA 9 Pro Phe Gly Lye Gly Val Met Lye Pro Thr Thr Ile Aβn Arg Leu Leu 20 25 30
ATC CAG GCT GTA GCC TTG ACG ATG GAG AGA CAG GAT GAG TTC CAA CTC 14 Ile Gin Ala Val Ala Leu Thr Met Glu Arg Gin Aβp Glu Phe Gin Leu 35 40 45
CAG GGG CCT ACG TAT GAC TTT GAT ACT GAC AGA GTA GCT GCG TTC ACG 192 Gin Gly Pro Thr Tyr Aβp Phe Aβp Thr Aβp Arg Val Ala Ala Phe Thr 50 55 60
AGG ATG GCC CGA GCC AAC GGG TTG GGT CTC ATA TCC ATG GCC TCC CTA 240 Arg Met Ala Arg Ala Aβn Gly Leu Gly Leu Ile Ser Met Ala Ser Leu 65 70 75 80
GGC AAA AAG CTA CGC AGT GTC ACC ACT ATT GAA GGA TTA AAG AAT GCT 288 Gly Lye Lye Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lye Aβn Ala 85 90 95
CTA TCA GGC TAT AAA ATA TCA AAA TGC AGT ATA CAA TGG CAG TCA AGG 336 Leu Ser Gly Tyr Lye Ile Ser Lye Cys Ser Ile Gin Trp Gin Ser Arg 100 105 110
GTG TAC ATT ATA GAA TCA GAT GGT GCC AGT GTA CAA ATC AAA GAA GAC 384 Val Tyr Ile Ile Glu Ser Aβp Gly Ala Ser Val Gin Ile Lye Glu Asp 115 120 125 AAG CAA GCT TTG ACC CCT CTG CAG CAG ACA ATT AAC ACG GCC TCA CTT 432 Lys Gin Ala Leu Thr Pro Leu Gin Gin Thr Ile Asn Thr Ala Ser Leu 130 135 140
GCC ATC ACT CGA CTC AAA GCA GCT AGG GCT GTG GCA TAC GCT TCA TGT 480 Ala Ile Thr Arg Leu Lys Ala Ala Arg Ala Val Ala Tyr Ala Ser Cys 145 150 155 160
TTC CAG TTC CGC CAT AAC TAC CAT ACT ACA ATG GCG GGA TCT GCG CTC 528 Phe Gin Phe Arg His Aβn Tyr His Thr Thr Met Ala Gly Ser Ala Leu
165 170 175
GTA TTA ATC GAG CGT CAG GCG TAT GTT GGT ACC CGT ACA GCA GCC ATG 576 Val Leu Ile Glu Arg Gin Ala Tyr Val Gly Thr Arg Thr Ala Ala Met 180 185 190
GCA TTA GAA GGA CCT GGG AAA GAA CAT AAT TGC AGG GTC CAT AAG GCT 624 Ala Leu Glu Gly Pro Gly Lys Glu His Aβn Cyβ Arg Val Hie Lye Ala 195 200 205
AAG GAA GCT GGA AAG GGG CCC ATA GGT CAT GAT GAC ATG GTA GAA AGG 672 Lye Glu Ala Gly Lye Gly Pro Ile Gly Hie Asp Aβp Met Val Glu Arg 210 215 220
TTT GGC CTA TGT GAA ACT GAA GAG GAG GAG AGT GAG GAC CAA ATT CAA 720 Phe Gly Leu Cys Glu Thr Glu Glu Glu Glu Ser Glu Asp Gin lie Gin 225 230 235 240
ATG GTA CCA AGT GAT GCC GTC CCA GAA GGA AAA AAA AGA CTT AAT TTC 768 Met Val Pro Ser Asp Ala Val Pro Glu Gly Lys Lys Arg Leu Aβn Phe
245 250 255
GCG GCC GAC TTA CGT TTT TTT TTT TTT TAT CTA AGA TGG CCA TAT AAG 816 Ala Ala Asp Leu Arg Phe Phe Phe Phe Tyr Leu Arg Trp Pro Tyr Lye 260 265 270
CCC GTG CAG ACT GTT TGT CCC TCA CGC CTG AGT CAC TGA TGT AGA TGA 864 Pro Val Gin Thr Val Cys Pro Ser Arg Leu Ser His TER Cys Arg TER 275 280 285 TAG TAC TTC CAT ATC TAT AAC TGC TGA CTC AAT ATC TTT TAG GGT TTT 91 TER Tyr Phe Hie Ile Tyr Aβn Cyβ TER Leu Aβn Ile Phe TER Gly Phe 290 295 300
CTC TGT TCG ACG CCG GCG GAA TTC 9 Leu Cyβ Ser Thr Pro Ala Glu Phe 305 310
(2) INFORMATION FOR SEQ ID NO:13:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 312 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:13:
Glu Phe Ala Ala Ala Arg Gin Gly Gly Phe Aβp Asn Gin Gly Aβn Thr 1 5 10 15
Pro Phe Gly Lye Gly Val Met Lye Pro Thr Thr Ile Aβn Arg Leu Leu 20 25 30
Ile Gin Ala Val Ala Leu Thr Met Glu Arg Gin Aβp Glu Phe Gin Leu 35 40 45
Gin Gly Pro Thr Tyr Asp Phe Asp Thr Aβp Arg Val Ala Ala Phe Thr 50 55 60
Arg Met Ala Arg Ala Aβn Gly Leu Gly Leu Ile Ser Met Ala Ser Leu 65 70 75 80
Gly Lye Lye Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lys Asn Ala 85 90 95 Leu Ser Gly Tyr Lys lie Ser Lys Cys Ser Ile Gin Trp Gin Ser Arg 100 105 110
Val Tyr Ile Ile Glu Ser Aβp Gly Ala Ser Val Gin Ile Lys Glu Asp 115 120 125
Lys Gin Ala Leu Thr Pro Leu Gin Gin Thr Ile Asn Thr Ala Ser Leu 130 135 140
Ala Ile Thr Arg Leu Lye Ala Ala Arg Ala Val Ala Tyr Ala Ser Cys 145 150 155 160
Phe Gin Phe Arg His Asn Tyr Hie Thr Thr Met Ala Gly Ser Ala Leu 165 170 175
Val Leu Ile Glu Arg Gin Ala Tyr Val Gly Thr Arg Thr Ala Ala Met 180 185 190
Ala Leu Glu Gly Pro Gly Lys Glu His Aβn Cys Arg Val His Lye Ala 195 200 205
Lye Glu Ala Gly Lye Gly Pro Ile Gly Hie Aβp Aβp Met Val Glu Arg 210 215 220
Phe Gly Leu Cyβ Glu Thr Glu Glu Glu Glu Ser Glu Aβp Gin Ile Gin 225 230 235 240
Met Val Pro Ser Aβp Ala Val Pro Glu Gly Lys Lys Arg Leu Asn Phe 245 250 255
Ala Ala Asp Leu Arg Phe Phe Phe Phe Tyr Leu Arg Trp Pro Tyr Lye 260 265 270
Pro Val Gin Thr Val Cye Pro Ser Arg Leu Ser His TER Cys Arg TER 275 280 285
TER Tyr Phe His lie Tyr Asn Cys TER Leu Asn Ile Phe TER Gly Phe 290 295 300 Leu Cye Ser Thr Pro Ala Glu Phe 305 310
(2) INFORMATION FOR SEQ ID NO:14:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 927 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE: (C) INDIVIDUAL ISOLATE: Norwalk virus 8FIIa
(vii) IMMEDIATE SOURCE:
(B) CLONE: N3, combined N35 and N3 sequences
(ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 1..927
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:14:
GAA TTC GCG GCC GCT CGC CAA GGG GGC TTT GAT AAC CAA GGG AAT ACC 4 Glu Phe Ala Ala Ala Arg Gin Gly Gly Phe Asp Asn Gin Gly Asn Thr 1 5 10 15
CCG TTT GGT AAG GGT GTG ATG AAG CCC ACC ACC ATA AAC AGG CTG TTA 9 Pro Phe Gly Lys Gly Val Met Lys Pro Thr Thr Ile Asn Arg Leu Leu 20 25 30 ATC CAG GCT GTA GCC TTG ACG ATG GAG AGA CAG GAT GAG TTC CAA CTC 144 Ile Gin Ala Val Ala Leu Thr Met Glu Arg Gin Asp Glu Phe Gin Leu 35 40 45
CAG GGG CCT ACG TAT GAC TTT GAT ACT GAC AGA GTA GCT GCG TTC ACG 192 Gin Gly Pro Thr Tyr Asp Phe Asp Thr Asp Arg Val Ala Ala Phe Thr 50 55 60
AGG ATG GCC CGA GCC AAC GGG TTG GGT CTC ATA TCC ATG GCC TCC CTA 240 Arg Met Ala Arg Ala Asn Gly Leu Gly Leu lie Ser Met Ala Ser Leu 65 70 75 80
GGC AAA AAG CTA CGC AGT GTC ACC ACT ATT GAA GGA TTA AAG AAT GCT 288 Gly Lye Lys Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lys Asn Ala
85 90 95
CTA TCA GGC TAT AAA ATA TCA AAA TGC AGT ATA CAA TGG CAG TCA AGG 336 Leu Ser Gly Tyr Lys Ile Ser Lys Cye Ser Ile Gin Trp Gin Ser Arg 100 105 110
GTG TAC ATT ATA GAA TCA GAT GGT GCC AGT GTA CAA ATC AAA GAA GAC 384 Val Tyr Ile Ile Glu Ser Asp Gly Ala Ser Val Gin Ile Lys Glu Asp 115 120 125
AAG CAA GCT TTG ACC CCT CTG CAG CAG ACA ATT AAC ACG GCC TCA CTT 432 Lys Gin Ala Leu Thr Pro Leu Gin Gin Thr Ile Asn Thr Ala Ser Leu 130 135 140
GCC ATC ACT CGA CTC AAA GCA GCT AGG GCT GTG GCA TAC GCT TCA TGT 480 Ala Ile Thr Arg Leu Lye Ala Ala Arg Ala Val Ala Tyr Ala Ser Cye 145 150 155 160
TTC CAG TTC CGC CAT AAC TAC CAT ACT ACA ATG GCG GGA TCT GCG CTC 528 Phe Gin Phe Arg Hie Aβn Tyr His Thr Thr Met Ala Gly Ser Ala Leu
165 170 175
GTA TTA ATC GAG CGT CAG GCG TAT GTT GGT ACC CGT ACA GCA GCC ATG 576 Val Leu Ile Glu Arg Gin Ala Tyr Val Gly Thr Arg Thr Ala Ala Met 180 185 190 GCA TTA GAA GGA CCT GGG AAA GAA CAT AAT TGC AGA GTC CAT AAG GCT 62 Ala Leu Glu Gly Pro Gly Lye Glu Hie Aβn Cyβ Arg Val Hie Lye Ala 195 200 205
AAG GAA GCT GGA AAG GGG CCC ATA GGT CAT GAT GAC ATG GTA GAA AGG 672 Lye Glu Ala Gly Lye Gly Pro Ile Gly Hie Asp Aβp Met Val Glu Arg 210 215 220
TTT GGC CTA TGT GAA ACT GAA GAG GAG GAG AGT GAG GAC CAA ATT CAA 720 Phe Gly Leu Cyβ Glu Thr Glu Glu Glu Glu Ser Glu Aβp Gin Ile Gin 225 230 235 240
ATG GTA CCA AGT GAT GCC GTC CCA GAA GGA AAG AAC AAA GGC AAG ACC 768 Met Val Pro Ser Aβp Ala Val Pro Glu Gly Lye Aβn Lye Gly Lye Thr 245 250 255
AAA AAG GGA CGT GGT CGC AAA AAT AAC TAT AAT GCA TTC TCT CGC CGT 816 Lye Lys Gly Arg Gly Arg Lye Aen Aβn Tyr Aβn Ala Phe Ser Arg Arg 260 265 270
GGT CTG AGT GAT GAA GAA TAT GAA GAG TAC AAA AAG ATC AGA GAA AAA 864 Gly Leu Ser Aβp Glu Glu Tyr Glu Glu Tyr Lye Lye Ile Arg Glu Lye 275 280 285
AAA AAA AAA CGA GCG GCC GCG ATT TCT TTT GCT TTT TAC CCT GGA AGA 912 Lye Lye Lye Arg Ala Ala Ala Ile Ser Phe Ala Phe Tyr Pro Gly Arg 290 295 300
AAT ACT GGG GGA TCC 927
Figure imgf000067_0001
305
(2) INFORMATION FOR SEQ ID NO:15:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 309 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein (xi) SEQUENCE DESCRIPTION: SEQ ID NO:15:
Glu Phe Ala Ala Ala Arg Gin Gly Gly Phe Asp Aβn Gin Gly Aβn Thr 1 5 10 15
Pro Phe Gly Lys Gly Val Met Lys Pro Thr Thr Ile Aβn Arg Leu Leu 20 25 30
Ile Gin Ala Val Ala Leu Thr Met Glu Arg Gin Aβp Glu Phe Gin Leu 35 40 45
Gin Gly Pro Thr Tyr Aβp Phe Aβp Thr Aβp Arg Val Ala Ala Phe Thr 50 55 60
Arg Met Ala Arg Ala Asn Gly Leu Gly Leu Ile Ser Met Ala Ser Leu 65 70 75 80
Gly Lys Lys Leu Arg Ser Val Thr Thr Ile Glu Gly Leu Lys Asn Ala 85 90 95
Leu Ser Gly Tyr Lys Ile Ser Lys Cys Ser Ile Gin Trp Gin Ser Arg 100 105 110
Val Tyr Ile Ile Glu Ser Asp Gly Ala Ser Val Gin Ile Lys Glu Asp 115 120 125
Lye Gin Ala Leu Thr Pro Leu Gin Gin Thr Ile Aβn Thr Ala Ser Leu 130 135 140
Ala Ile Thr Arg Leu Lye Ala Ala Arg Ala Val Ala Tyr Ala Ser Cyβ 145 150 155 160
Phe Gin Phe Arg Hie Aβn Tyr Hie Thr Thr Met Ala Gly Ser Ala Leu 165 170 175
Val Leu Ile Glu Arg Gin Ala Tyr Val Gly Thr Arg Thr Ala Ala Met 180 185 190
Ala Leu Glu Gly Pro Gly Lys Glu His Asn Cys Arg Val His Lys Ala 195 200 205 Lys Glu Ala Gly Lys Gly Pro ie Gly His Aβp Aβp Met Val Glu Arg 210 215 220
Phe Gly Leu Cyβ Glu Thr Glu Glu Glu Glu Ser Glu Aβp Gin Ile Gin 225 230 235 240
Met Val Pro Ser Aβp Ala Val Pro Glu Gly Lye Aβn Lys Gly Lys Thr 245 250 255
Lye Lye Gly Arg Gly Arg Lye Asn Aβn Tyr Aβn Ala Phe Ser Arg Arg 260 265 270
Gly Leu Ser Aβp Glu Glu Tyr Glu Glu Tyr Lye Lye Ile Arg Glu Lye 275 280 285
Lye Lye Lye Arg Ala Ala Ala Ile Ser Phe Ala Phe Tyr Pro Gly Arg 290 295 300
Figure imgf000069_0001
305
(2) INFORMATION FOR SEQ ID NO:16:
(i) SEQUENCE CHARACTERISTICS: (A) LENGTH: 356 base paire
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: CDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk viruβ 8FIIa
(vii) IMMEDIATE SOURCE: (B) CLONE: overlap of N2 and N3 (ix) FEATURE:
(A) NAME/KEY: CDS
(B) LOCATION: 1..354
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:16:
ACC CCT CTG CAG CAG ACA ATT AAC ACG GCC TCA CTT GCC ATC ACT CGA 48 Thr Pro Leu Gin Gin Thr Ile Aβn Thr Ala Ser Leu Ala Ile Thr Arg 1 5 10 15
CTC AAA GCA GCT AGG GCT GTG GCA TAC GCT TCA TGT TTC CAG TTC CGC 96 Leu Lye Ala Ala Arg Ala Val Ala Tyr Ala Ser Cyβ Phe Gin Phe Arg 20 25 30
CAT AAC TAC CAT ACT ACA ATG GCG GGA TCT GCG CTC GTA TTA ATC GAG 144 Hie Aβn Tyr Hie Thr Thr Met Ala Gly Ser Ala Leu Val Leu Ile Glu 35 40 45
CGT CAG GCG TAT GTT GGT ACC CGT ACA GCA GCC ATG GCA TTA GAA GGA 192 Arg Gin Ala Tyr Val Gly Thr Arg Thr Ala Ala Met Ala- Leu Glu Gly 50 55 60
CCT GGG AAA GAA CAT AAT TGC AGG GTC CAT AAG GCT AAG GAA GCT GGA 240 Pro Gly Lye Glu Hie Aβn Cye Arg Val Hie Lys Ala Lys Glu Ala Gly 65 70 75 80
AAG GGG CCC ATA GGT CAT GAT GAC ATG GTA GAA AGG TTT GGC CTA TGT 288 Lys Gly Pro Ile Gly Hie Aβp Aβp Met Val Glu Arg Phe Gly Leu Cye 85 90 95
GAA ACT GAA GAG GAG GAG AGT GAG GAC CAA ATT CAA ATG GTA CCA AGT 336 Glu Thr Glu Glu Glu Glu Ser Glu Asp Gin Ile Gin Met Val Pro Ser 100 105 110
GAT GCC GTC CCA GAA GGA AA 356
Figure imgf000070_0001
115
(2) INFORMATION FOR SEQ ID NO:17: (i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 118 amino acids
(B) TYPE: amino acid (D) TOPOLOGY: linear
(ii) MOLECULE TYPE: protein
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:17:
Thr Pro Leu Gin Gin Thr Ile Asn Thr Ala Ser Leu Ala Ile Thr Arg 1 5 10 15
Leu Lys Ala Ala Arg Ala Val Ala Tyr Ala Ser Cys Phe Gin Phe Arg 20 25 30
His Aβn Tyr Hie Thr Thr Met Ala Gly Ser Ala Leu Val Leu Ile Glu 35 40 45
Arg Gin Ala Tyr Val Gly Thr Arg Thr Ala Ala Met Ala Leu Glu Gly 50 55 60
Pro Gly Lye Glu Hie Asn Cys Arg Val Hie Lys Ala Lys Glu Ala Gly 65 70 75 80
Lye Gly Pro Ile Gly Hie Aβp Aβp Met Val Glu Arg Phe Gly Leu Cyβ
85 90 95
Glu Thr Glu Glu Glu Glu Ser Glu Aβp Gin Ile Gin Met Val Pro Ser 100 105 110
Figure imgf000071_0001
115
(2) INFORMATION FOR SEQ ID NO:18:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 790 baβe paire
(B) TYPE: nucleic acid (C) STRANDEDNESS: double
(D) TOPOLOGY: linear (ii) MOLECULE TYPE: cDNA to mRNA
( iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk viruβ 8FIIa
(vii) IMMEDIATE SOURCE :
(B) CLONE: N2 insert
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:18:
GATGAGTTCC AACTCCAGGG GCCTACGTAT GACTTTGATA CTGACAGAGT AGCTGCGTTC 60
ACGAGGATGG CCCGAGCCAA CGGGTTGGGT CTCATATCCA TGGCCTCCCT AGGCAAAAAG 120
CTACGCAGTG TCACCACTAT TGAAGGATTA AAGAATGCTC TATCAGGCTA TAAAATATCA 180
AAATGCAGTA TACAATGGCA GTCAAGGGTG TACATTATAG AATCAGATGG TGCCAGTGTA 240
CAAATCAAAG AAGACAAGCA AGCTTTGACC CCTCTGCAGC AGACAATTAA CACGGCCTCA 300
CTTGCCATCA CTCGACTCAA AGCAGCTAGG GCTGTGGCAT ACGCTTCATG TTTCCAGTTC 360
CGCCATAACT ACCATACTAC AATGGCGGGA TCTGCGCTCG TATTAATCGA GCGTCAGGCG 420
TATGTTGGTA CCCGTACAGC AGCCATGGCA TTAGAAGGAC CTGGGAAAGA ACATAATTGC 480
AGGGTCCATA AGGCTAAGGA AGCTGGAAAG GGGCCCATAG GTCATGATGA CATGGTAGAA 540
AGGTTTGGCC TATGTGAAAC TGAAGAGGAG GAGAGTGAGG ACCAAATTCA AATGGTACCA 600
AGTGATGCCG TCCCAGAAGG AAAAAAAAGA CTTAATTTCG CGGCCGACTT ACGTTTTTTT 660
TTTTTTTATC TAAGATGGCC ATATAAGCCC GTGCAGACTG TTTGTCCCTC ACGCCTGAGT 720
CACTGATGTA GATGATAGTA CTTCCATATC TATAACTGCT GACTCAATAT CTTTTAGGGT 780 TTTCTCTGTT 79
(2) INFORMATION FOR SEQ ID NO:19:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 618 baβe paire
(B) TYPE: nucleic acid
(C) STRANDEDNESS: double
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: cDNA to mRNA
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: Norwalk 8FIIa
(vii) IMMEDIATE SOURCE:
(B) CLONE: N3 insert
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:19:
AAATGCAGTA TACAATGGCA GTCAAGGGTG TACATTATAG AATCAGATGG TGCCAGTGTA 6
CAAATCAAAG AAGACAAGCA AGCTTTGACC CCTCTGCAGC AGACAATTAA CACGGCCTCA 12
CTTGCCATCA CTCGACTCAA AGCAGCTAGG GCTGTGGCAT ACGCTTCATG TTTCCAGTTC 18
CGCCATAACT ACCATACTAC AATGGCGGGA TCTGCGCTCG TATTAATCGA GCGTCAGGCG 24
TATGTTGGTA CCCGTACAGC AGCCATGGCA TTAGAAGGAC CTGGGAAAGA ACATAATTGC 30
AGAGTCCATA AGGCTAAGGA AGCTGGAAAG GGGCCCATAG GTCATGATGA CATGGTAGAA 36
AGGTTTGGCC TATGTGAAAC TGAAGAGGAG GAGAGTGAGG ACCAAATTCA AATGGTACCA 42
AGTGATGCCG TCCCAGAAGG AAAGAACAAA GGCAAGACCA AAAAGGGACG TGGTCGCAAA 48 AATAACTATA ATGCATTCTC TCGCCGTGGT CTGAGTGATG AAGAATATGA AGAGTACAAA 54
AAGATCAGAG AAAAAAAAAA AAAACGAGCG GCCGCGATTT CTTTTGCTTT TTACCCTGGA 60
AGAAATACTG GGGGATCC 61
(2) INFORMATION FOR SEQ ID NO:20:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 18 baβe paire
(B) TYPE: nucleic acid
(C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iii) HYPOTHETICAL: NO
(iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: SISPA Primer, Example 2
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:20:
GGAATTCGCG GCCGCTCG 18
(2) INFORMATION FOR SEQ ID NO:21:
(i) SEQUENCE CHARACTERISTICS:
(A) LENGTH: 20 base pairs
(B) TYPE: nucleic acid (C) STRANDEDNESS: single
(D) TOPOLOGY: linear
(ii) MOLECULE TYPE: DNA (genomic)
(iϋ) HYPOTHETICAL: NO ( iv) ANTI-SENSE: NO
(vi) ORIGINAL SOURCE:
(C) INDIVIDUAL ISOLATE: SISPA Primer, Example 2
(xi) SEQUENCE DESCRIPTION: SEQ ID NO:21:
CGAGCGGCCG CGAATTCCTT 20

Claims

IT IS CLAIMED:
1. A purified Norwalk virus polynucleotide which contains a sequence selected from the group consisting of: SEQ ID N0:1, SEQ ID NO:3, SEQ ID NO:5, SEQ ID N0:7, SEQ ID NO:9 and SEQ ID NO:16.
2. A recombinantly produced Norwalk virus poly¬ nucleotide which encodes a polypeptide which is immuno- reactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum.
3. The polynucleotide of claim 2, which encodes a polypeptide selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10 and SEQ ID NO:17.
4. The polynucleotide of claim 2, which is a cDNA molecule.
5. The polynucleotide of claim 4, which has a nucleic acid sequence selected from the group consisting of: SEQ ID NO:l, SEQ ID NO:3, SEQ ID NO:5, SEQ ID NO:7, SEQ ID NO:9, and SEQ ID NO:16.
6. A recombinant Norwalk virus polypeptide which is immunoreactive with sera from humans infected with Nor¬ walk virus 8FIIa infectious inoculum.
7. The polypeptide of claim 6, wherein the poly¬ peptide has substantially the same sequence as a polypep¬ tide selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID N0:6, SEQ ID NO:8, and SEQ ID N0:10.
8. The polypeptide of claim 6, which includes an immunoreactive portion of a Norwalk virus polypeptide encoded by a sequence selected from the group consisting Of: SEQ ID N0:2, SEQ ID N0:4, SEQ ID N0:6, SEQ ID N0:8, and SEQ ID NO:10.
9. The polypeptide of claim 6, which includes the entire polypeptide sequence of a polypeptide selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID N0:6, SEQ ID NO:8, and SEQ ID N0:10.
10. The polypeptide of claim 6, which is a hybrid protein.
11. The polypeptide of claim 10, wherein the hybrid protein comprises the polypeptide sequence of ,9-galac- tosidase and a polypeptide sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10.
12. The polypeptide of claim 10, which is produced by bacterial cells containing a vector selected from the group consisting of lambda-Nl, lambda-N4, and lambda-N8.
13. A method for the detection of Norwalk virus in human stool samples comprising, partial purification of polynucleotides present in the stool sample, hybridization of negative-sense oligonucleotide probes specific for the Norwalk virus polynucleotide, and means for detecting the binding of the negative sense probes to polynucleotides present in the stool sample.
14. The method of claim 13, wherein the partial purification includes generation of cDNA molecules from RNA templates present in the sample and sequence indepen¬ dent amplification of the resulting cDNA molecules.
15. The method of claim 13, wherein the negative sense probes are derived from DNA sequences which encode the polypeptide whose sequence is selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10.
16. The method of claim 13, wherein said means for detecting binding of the probes to sample polynucleotides includes the biotinylation of said probes.
17. The method of claim 13, wherein said means for detecting binding of the probes to sample polynucleotides includes radioactively labelling said probes.
18. Negative-sense oligonucleotide probes specific for the Norwalk virus polynucleotide.
19. The probes of claim 18, wherein the negative sense probes are derived from DNA sequences which encode the polypeptide whose sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID N0:10 and SEQ ID NO:17.
20. The probes of claim 18, wherein the negative sense probes are derived from the polynucleotide sequence which selected from the group consisting of: SEQ ID N0:l, SEQ ID NO:3, SEQ ID N0:5, SEQ ID NO:7, and SEQ ID NO:9 and SEQ ID NO:16.
21. Oligonucleotide primers specific for the Nor¬ walk virus polynucleotide.
22. The primers of claim 21, wherein the oligo- nucleotide sequences are derived from DNA sequences which encode the polypeptide whose sequence is selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:10 and SEQ ID NO:17.
23. The primers of claim 22, wherein the oligo¬ nucleotide sequences are derived from DNA sequences complementary to said DNA sequence.
24. A diagnostic kit for use in screening human serum containing antibodies specific against Norwalk virus infection comprising a recombinant Norwalk virus polypeptide antigen which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum, and means for detecting the binding of said antibodies to the antigen.
25. The kit of claim 24, wherein the recombinant polypeptide antigen includes an immunoreactive portion of a Norwalk virus polypeptide encoded by a sequence selec¬ ted from the group consisting of: SEQ ID NO:2, SEQ ID N0:4, SEQ ID N0:6, SEQ ID NO:8, and SEQ ID NO:10.
26. The kit of claim 24, wherein the recombinant polypeptide antigen includes the entire polypeptide sequence of a polypeptide selected from the group con¬ sisting Of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10.
27. The kit of claim 24, wherein the recombinant polypeptide antigen includes poiypeptides produced by bacterial cells transformed with a vector selected from the group consisting of: lambda-Nl, lambda-N4, and lambda-N8.
28. The kit of claim 24, wherein said detecting means includes a solid support to which said polypeptide is attached and a reporter-labeled anti-human antibody, wherein binding of said serum antibodies to said antigen can be detected by binding of the reporter-labeled anti¬ body to said solid surface.
29. A method of detecting Norwalk virus infection in an individual comprising reacting serum from a Norwalk virus-infected test individual with a recombinant Norwalk virus polypeptide antigen which is immunoreactive with sera from humans in¬ fected with Norwalk virus 8FIIa infectious inoculum, and examining the antigen for the presence of bound antibody.
30. The method of claim 29, wherein the recombinant polypeptide antigen includes an immunoreactive portion of a Norwalk virus polypeptide encoded by a sequence selec¬ ted from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID N0:6, SEQ ID N0:8, and SEQ ID N0:10.
31. The method of claim 29, wherein the recombinant polypeptide antigen includes the entire polypeptide sequence of a polypeptide selected from the group con¬ sisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10.
32. The method of claim 29, wherein the recombinant polypeptide antigen includes poiypeptides produced by bacterial cells transformed with a vector selected from the group consisting of: lambda-Nl, lambda-N4, and lambda-N8.
33. The method of claim 29, wherein the polypeptide antigen is attached to a solid support, said reacting in¬ cludes reacting the polypeptide antigen with the support, and subsequently reacting the support with a reporter-la¬ beled anti-human antibody, and said examining includes detecting the presence of reporter-labeled antibody on the solid support.
34. A method of producing a polypeptide which is immunoreactive with sera from humans infected with Nor¬ walk virus 8FIIa infectious inoculum, comprising introducing into a suitable host cell, a recombinant expression system containing an open reading frame (ORF) having a polynucleotide sequence which encodes a Norwalk virus polypeptide which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum, where the vector is designed to express the ORF in said host, and culturing said host cell under conditions resulting in the expression of the ORF sequence.
35. The method of claim 34, wherein said polypep¬ tide includes an immunoreactive portion of a Norwalk virus polypeptide encoded by a sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10.
36. The method of claim 34, wherein said polypep- tide includes the entire polypeptide sequence of a polypeptide selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10.
37. The method of claim 34, wherein the expression vector is a lambda gtll phage vector and the host is Escherichia coli.
38. The method of claim 37, wherein the lambda gtll phage vector is selected from the group consisting of: lambda-Nl, lambda-N4, and lambda-N8.
39. An expression system for expressing a recom¬ binant Norwalk virus polypeptide antigen which is im- munoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum, comprising a host capable of supporting expression of an open reading frame in a selected expression vector, and the selected expression vector containing an open reading frame (ORF) having a polynucleotide sequence which encodes said polypeptide antigen.
40. The expression system of claim 39, wherein said recombinant polypeptide antigen includes an immunoreac- tive portion of a Norwalk virus polypeptide selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID N0:6, SEQ ID N0:8, and SEQ ID NO:10.
41. The expression system of claim 39, wherein said recombinant polypeptide antigen includes the entire polypeptide sequence of a polypeptide selected from the group consisting of: SEQ ID NO:2, SEQ ID NO: , SEQ ID N0:6, SEQ ID N0:8, and SEQ ID NO:10.
42. The expression system of claim 39, wherein the selected expression vector is a lambda gtll phage vector and the host is Escherichia coli .
43. The expression system of claim 42, wherein the lambda gtll phage vector is selected from the group consisting of: lambda-Nl, lambda-N4, and lambda-N8.
44. A vaccine for immunizing an individual against Norwalk virus infection, comprising a recombinant Norwalk virus polypeptide antigen which is immunoreactive with sera from humans infected with Norwalk virus 8FIIa infectious inoculum and which includes an immunoreactive portion of a sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10; in a pharmacologically acceptable adjuvant.
45. An antibody specific against a polypeptide having a sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID NO:8, and SEQ ID NO:10.
46. The antibody of claim 45, wherein the antibody is monoclonal.
47. The antibody of claim 45, wherein the antibody is polyclonal.
48. A method of producing passive immunity in an individual against Norwalk virus, comprising administer¬ ing the antibody of claim 45 parenterally to the indivi¬ dual.
49. An antibody against a Norwalk-virus-specific polypeptide which is produced by bacterial cells trans¬ formed with a vector which is selected from the group consisting of: lambda-Nl, lambda-N4, and lambda-N8.
50. Oligonucleotide probes which hybridize with Norwalk virus specific polynucleotides.
51. The probes of claim 50, wherein the probes are derived from DNA sequences which encode the polypeptide whose sequence selected from the group consisting of: SEQ ID NO:2, SEQ ID NO:4, SEQ ID NO:6, SEQ ID N0:8, SEQ ID NO:10 and SEQ ID NO:17.
52. The probes of claim 50, wherein the probes are derived from the polynucleotide sequence which selected from the group consisting of: SEQ ID NO:l, SEQ ID NO:3, SEQ ID N0:5, SEQ ID NO:7, SEQ ID NO:9, SEQ ID NO:ll, SEQ ID NO:12, SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:18, and SEQ ID NO:19.
53. The probes of claim 50, where the Norwalk virus specific polynucleotides are cDNA molecules.
PCT/US1992/002457 1991-03-25 1992-03-25 NORWALK VIRUS HUMAN GASTROENTERITIS AGENT AND MOLECULAR CLONING OF CORRESPONDING cDNAs WO1992016543A1 (en)

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WO1994005700A2 (en) * 1992-09-07 1994-03-17 Baylor College Of Medicine Methods and reagents to detect and characterize norwalk and related viruses
WO2008042789A1 (en) 2006-09-29 2008-04-10 Ligocyte Pharmaceuticals, Inc. Norovirus vaccine formulations
US8841120B2 (en) 2008-08-08 2014-09-23 Takeda Vaccines, Inc. Virus-like particles comprising composite capsid amino acid sequences for enhanced cross reactivity
US9801934B2 (en) 2011-07-11 2017-10-31 Takeda Vaccines, Inc. Parenteral norovirus vaccine formulations
US9821049B2 (en) 2007-09-18 2017-11-21 Takeda Vaccines, Inc. Method of conferring a protective immune response to Norovirus
US10130696B2 (en) 2007-09-18 2018-11-20 Takeda Vaccines, Inc. Method of conferring a protective immune response to norovirus

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