WO2014153168A4 - Porcine astrovirus sequences and uses thereof - Google Patents

Porcine astrovirus sequences and uses thereof Download PDF

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Publication number
WO2014153168A4
WO2014153168A4 PCT/US2014/029394 US2014029394W WO2014153168A4 WO 2014153168 A4 WO2014153168 A4 WO 2014153168A4 US 2014029394 W US2014029394 W US 2014029394W WO 2014153168 A4 WO2014153168 A4 WO 2014153168A4
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WIPO (PCT)
Prior art keywords
amino acid
acid sequence
seq
isolated polypeptide
sequence
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PCT/US2014/029394
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French (fr)
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WO2014153168A3 (en
WO2014153168A2 (en
Inventor
W. Ian Lipkin
Cadhla FIRTH
Richard A. Hesse
John Morgan Hardham
Sudhir Keesara REDDY
Tanja I. OPRIESSNIG
Patrick G. Halbur
Jacqueline Gayle Marx
Original Assignee
The Trustees Of Columbia University In The City Of New York
Iowa State University Research Foundation, Inc.
Kansas State University Research Foundation
Zoetis Llc
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Application filed by The Trustees Of Columbia University In The City Of New York, Iowa State University Research Foundation, Inc., Kansas State University Research Foundation, Zoetis Llc filed Critical The Trustees Of Columbia University In The City Of New York
Publication of WO2014153168A2 publication Critical patent/WO2014153168A2/en
Publication of WO2014153168A3 publication Critical patent/WO2014153168A3/en
Publication of WO2014153168A4 publication Critical patent/WO2014153168A4/en

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    • 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
    • A61K39/12—Viral antigens
    • 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
    • A61K2039/51—Medicinal preparations containing antigens or antibodies comprising whole cells, viruses or DNA/RNA
    • A61K2039/525—Virus
    • A61K2039/5252—Virus inactivated (killed)
    • 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
    • A61K2039/55—Medicinal preparations containing antigens or antibodies characterised by the host/recipient, e.g. newborn with maternal antibodies
    • A61K2039/552—Veterinary vaccine
    • 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
    • C12N2770/12011—Astroviridae
    • 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
    • C12N2770/12011—Astroviridae
    • C12N2770/12034—Use of virus or viral component as vaccine, e.g. live-attenuated or inactivated virus, VLP, viral protein

Abstract

The invention is directed to isolated porcine astroviruses associated with porcine periweaning failure to thrive syndrome, high morbidity and mortality syndrome in growing pigs, mulberry heart disease, porcine respiratory disease, porcine gastrointestinal disease, or reproductive failure. The invention also relates to isolated nucleic acids sequences and polypeptides derived from porcine astroviruses. Additionally, the invention relates to antibodies against antigens from porcine astroviruses. The invention also relates to iRNAs which target nucleic acid sequences of the porcine astrovirus. The invention is further related to methods for detecting the presence or absence of porcine astroviruses in an animal. The invention is also related to immunogenic compositions for inducing an immune response against porcine astroviruses in an animal.

Claims

AMENDED CLAIMS received by the International Bureau on 14 January 2015 (14.01 .2015)What is claimed is:
1. An isolated antibody or antigen-binding portion thereof that specifically binds to a
polypeptide encoded by the nucleic acid of any of SEQ ID NOs: 1 -21 or 58-156, a polypeptide having the sequence of any of SEQ ID NOs: 22-57, or a polypeptide comprising a variant sequence of any of SEQ ID NOs: 22-57, wherein the variant is selected from the group consisting of:
(i) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 22;
(ii) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 23;
(iii) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 24;
(iv) an isolated polypeptide comprising an amino acid sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 25;
(v) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 26;
(vi) an isolated polypeptide comprising a sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 27;
(vii) an isolated polypeptide comprising an amino acid sequence having at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 28;
189 (viii) an isolated polypeptide comprising an amino acid sequence having at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 29;
(ix) an isolated polypeptide comprising an amino acid sequence having at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 30;
(x) an isolated polypeptide comprising an amino acid sequence having at least about 63%, at least about 64%, at least about 65%, at least about 66%, at least about 67%, at least about 68%, at least about 69%, at least about 70%, at least about 71%, at least about 72%, at least about 73%, at least about 74%, at least about 75%, at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91 %, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 31 ;
(xi) an isolated polypeptide comprising an amino acid sequence having at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 32;
(xii) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 33;
190 (xiii) an isolated polypeptide comprising an amino acid sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 34;
(xiv) an isolated polypeptide comprising an amino acid sequence having at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 35;
(xv) an isolated polypeptide comprising an amino acid sequence having at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 36;
(xvi) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 37;
(xvii) an isolated polypeptide comprising an amino acid sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 38;
(xviii) an isolated polypeptide comprising a sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to a sequence of amino acids that is at least about 95% of the length of the amino acid sequence of SEQ ID NO: 39;
(xix) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to a sequence of amino acids that is at least about 99% of the length of the amino acid sequence of SEQ ID NO: 40;
(xx) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to a sequence of nucleic acids that is at least about 98% of the length of the amino acid sequence of SEQ ID NO: 41 ;
(xxi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 42;
191 (xxii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 43;
(xxiii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 44;
(xxiv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 45;
(xxv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 46;
(xxvi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 47;
(xxvii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 48;
(xxviii) (ab) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 49;
(xxix) (ac) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 50;
(xxx) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 51 ;
192 (xxxi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 52;
(xxxii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 53;
(xxxiii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 54;
(xxxiv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 55;
(xxxv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 56; and
(xxxvi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 57.
2. A method for determining the presence or absence of porcine astrovirus in a biological sample, the method comprising: a) contacting nucleic acid from a biological sample with at least one primer which is a synthetic nucleic acid comprising at least about 10 consecutive nucleotides of any of SEQ ID NOs: 1-21 or 58-156, a synthetic nucleic acid comprising at least about 10 consecutive nucleotides complementary to any of SEQ ID NOs: 1 -21 or 58-1 6, a synthetic nucleic acid comprising at least about 10 consecutive nucleotides of any of SEQ ID NOs: 157-158, or a synthetic nucleic acid comprising at least about 10 consecutive nucleotides complementary to any of SEQ ID NOs: 1 7-158, b) subjecting the nucleic acid and the primer to amplification conditions, and
193 c) determining the presence or absence of an amplification product, wherein the presence of the amplification product indicates the presence of RNA associated with porcine astrovirus in the sample.
3. A method for determining whether or not a sample contains a porcine astrovirus, the method comprising: a) contacting a biological sample with an antibody or antigen-binding portion thereof that specifically binds to a polypeptide encoded by the nucleic acid of any of SEQ ID NOs: 1- 21 or 58-156, a polypeptide having the sequence of any of SEQ ID NOs: 22-57, or a polypeptide comprising a variant sequence of any of SEQ ID NOs: 22-57, wherein the variant is selected from the group consisting of:
(i) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 22;
(ii) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 23;
(iii) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 24;
(iv) an isolated polypeptide comprising an amino acid sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 25;
(v) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 26;
(vi) an isolated polypeptide comprising a sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 27;
194 (vii) an isolated polypeptide comprising an amino acid sequence having at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 28;
(viii) an isolated polypeptide comprising an amino acid sequence having at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 29;
(ix) an isolated polypeptide comprising an amino acid sequence having at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 30;
(x) an isolated polypeptide comprising an amino acid sequence having at least aboui: 63%, at least about 64%, at least about 65%, at least about 66%, at least about 67%, at least about 68%, at least about 69%, at least about 70%, at least about 71%, at least about 72%, at least about 73%, at least about 74%, at least about 75%, at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81 %, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at leasfabout 90%7¾t least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 31 ;
(xi) an isolated polypeptide comprising an amino acid sequence having at least abou t 99% sequence identity to the amino acid sequence of SEQ ID NO: 32; (xii) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 33;
(xiii) an isolated polypeptide comprising an amino acid sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 34;
(xiv) an isolated polypeptide comprising an amino acid sequence having at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 35;
(xv) an isolated polypeptide comprising an amino acid sequence having at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 36;
(xvi) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 37;
(xvii) an isolated polypeptide comprising an amino acid sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 38;
(xviii) an isolated polypeptide comprising a sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to a sequence of amino acids that is at least about 95% of the length of the amino acid sequence of SEQ ID NO: 39;
(xix) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to a sequence of amino acids that is at least about 99% of the length of the amino acid sequence of SEQ ID NO: 40;
(xx) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to a sequence of nucleic acids that is at least about 98% of the length of the amino acid sequence of SEQ ID NO: 41 ; (xxi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at Jeast about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 42;
(xxii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 43;
(xxiii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least Ibout 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 44;
(xxiv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 45;
(xxv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 46;
(xxvi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 47;
(xxvii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 48;
197 (xxviii) (ab) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 49;
(xxix) (ac) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 50;
(xxx) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 9¾%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 51;
(xxxi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 52;
(xxxii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 5 ;
(xxxiii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 54;
(xxxiv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 55;
198 ( xxv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 56; and
(xxxvi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 57; and b) determining whether or not the antibody binds to a porcine astrovirus antigen in the biological sample, wherein fMnding indicates that the biological sample contains porcine astrovirus.
4. The method of claim 3, wherein the determining comprises use of an antigen-antibody assay.
5. The method of claim 4, wherein the antigen-antibody assay is a lateral flow assay, an ELISA, a western blot, or a bead-based flow assay.
6. A method for determining whether or not an animal has been infected by porcine astrovirus, the method comprising determining whether or not a biological sample from the animal contains antibodies that specifically bind to a polypeptide encoded by the nucleic acid of any of SEQ ID NOs: 1-21 or 58-156, a polypeptide having the sequence of any of SEQ ID NOs: 22-57, or a polypeptide comprising a variant sequence of any of SEQ ID NOs: 22-57, wherein the variant is selected from the group consisting of:
(i) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 22;
(ii) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 23;
(iii) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 24;
199 (iv) an isolated polypeptide comprising an amino acid sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 25;
(v) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID O: 26;
(vi) an isolated polypeptide comprising a sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO:
-27;
(vii) an isolated polypeptide comprising an amino acid sequence having at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence ofSEQ ID NO: 28;
(viii) an isolated polypeptide comprising an amino acid sequence having at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 9 %, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 29;
(ix) an isolated polypeptide comprising an amino acid sequence having at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 30;
(x) an isolated polypeptide comprising an amino acid sequence having at least about 63%, at least about 64%, at least about 65%, at least about 66%, at least about 67%, at least about 68%, at least about 69%, at least about 70%, at least about 71%, at least about 72%, at least about 73%, at least about 74%, at least
200 about 75%, at least about 76%, at least about 77%, at least about 78%, at least about 79%, at least about 80%, at least about 81%, at least about 82%, at least about 83%, at least about 84%, at least about 85%, at least about 86%, at least about 87%, at least about 88%, at least about 89%, at least about 90%, at least about 91%, at least about 92%, at least about 93%, at least about 94%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 31 ;
(xi) an isolated polypeptide comprising an amino acid sequence having at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 32;
(xii) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 33;
(xiii) an isolated polypeptide comprising an amino acid sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 34;
(xiv) an isolated polypeptide comprising an amino acid sequence having at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 35;
(xv) an isolated polypeptide comprising an amino acid sequence having at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 36;
(xvi) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 37;
(xvii) an isolated polypeptide comprising an amino acid sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 38;
(xviii) an isolated polypeptide comprising a sequence having at least about 97%, at least about 98%, or at least about 99% sequence identity to a sequence of
201 amino acids that is at least about 95% of the length of the amino acid sequence of SEQ ID NO: 39;
(xix) an isolated polypeptide comprising an amino acid sequence having at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to a sequence of amino acids that is at least about 99% of the length of the amino acid sequence of SEQ ID NO: 40;
(xx) an isolated polypeptide comprising an amino acid sequence having at least about 98%, or at least about 99% sequence identity to a sequence of nucleic acids that is at least about 98% of the length of the amino acid sequence of SEQ ID NO: 41;
(xxi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 42;
(xxii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 43;
(xxiii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 44;
(xxiv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 45; an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at
202 least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 46;
(xxvi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 47;
(xxvii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 48;
(xxviii) (ab) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 49;
(xxix) (ac) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 50;
(xxx) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 51 ;
(xxxi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 52;
(xxxii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at
203 least about 99% sequence identity to the amino acid sequence of SEQ ID NO:
53;
(xxxiii) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 54;
(xxxiv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 55;
(xxxv) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 56; and
(xxxvi) an isolated polypeptide comprising an amino acid sequence having at least about 95%, at least about 96%, at least about 97%, at least about 98%, or at least about 99% sequence identity to the amino acid sequence of SEQ ID NO: 57.
7. The method of claim 6, wherein the determining comprises determining whether the
antibodies are IgM or IgG antibodies, wherein detection of said antibodies is indicative of a infection of the animal by a porcine astrovirus.
8. A method of determining whether an animal has, or is at risk of having Porcine Periweaning Failure-to-Thrive Syndrome (PFTS), the method comprising: a) obtaining a biological sample from the animal, b) contacting nucleic acid from a biological sample with at least one nucleic acid primer comprising at least about 10 consecutive nucleotides of any of SEQ ID NOs: 1-21 or 58-156, at least about 10 consecutive nucleotides complementary to any of SEQ ID NOs: 1 -21 or 58-1 6, at least about 10 consecutive nucleotides of any of SEQ
204 ID NOs: 157-158, or at least about 10 consecutive nucleotides complementary to any of SEQ ID NOs: 157-158, c) subjecting the nucleic acid and the primer to amplification conditions, and d) determining the presence or absence of amplification product, wherein the presence of amplification product indicates that the animal has, or is at risk of having Porcine Periweaning Failure-to-Thrive Syndrome (PFTS).
9. A method of determining whether an animal has, or is at risk of having porcine
gastrointestinal disease, the method comprising: a) obtaining a biological sample from the animal, b) contacting nucleic acid from a biological sample with at least one nucleic acid primer comprising at least about 10 consecutive nucleotides of any of SEQ ID NOs: 1-21 or 58-156, at least about 10 consecutive nucleotides complementary to any of SEQ ID NOs: 1-21 or 58-156, at least about 10 consecutive nucleotides of any of SEQ ID NOs: 157-158, or at least about 10 consecutive nucleotides complementary to any of SEQ ID NOs: 157-158, c) subjecting the nucleic acid and the primer to amplification conditions, and d) determining the presence or absence of amplification product, wherein the presence of amplification product indicates that the animal has, or is at risk of having porcine gastrointestinal disease.
10. A method of determining whether an animal has, or is at risk of having Porcine Periweaning Failure-to-Thrive Syndrome (PFTS), the method comprising: a) obtaining a biological sample from the animal,
b) contacting a biological sample with an antibody that specifically binds a polypeptide encoded by the nucleic acid sequence of any of SEQ ID NOs: 1 -21 or 58- 156, and
205 c) determining whether or not the antibody binds to an antigen in the biological sample, wherein binding indicates that the animal has, or is at risk of having Porcine Periweaning Failure-to-Thrive Syndrome (PFTS).
11. A method of determining whether an animal has, or is at risk of having porcine
gastrointestinal disease, the method comprising: a) obtaining a. biological sample from the animal,
b) contacting a biological sample with an antibody that specifically binds a polypeptide encoded by the nucleic acid sequence of any of SEQ ID NOs: 1-21 or 58- 156, and
c) determining whether or not the antibody binds to an antigen in the biological sample, wherein binding indicates that the animal has, or is at risk of having porcine gastrointestinal disease.
12. A method for determining whether an animal has, or is at risk of having Porcine Periweaning Failure-to-Thrive Syndrome (PFTS), the method comprising: a) obtaining a biological sample from the animal, b) determining whether or not a biological sample contains antibody that specifically binds a polypeptide encoded by the nucleic sequence acid of any of SEQ ID NOs: 1- 21 or 58-156.
13. A method for determining whether an animal has, or is at risk of having porcine
gastrointestinal disease, the method comprising: a) obtaining a biological sample from the animal, b) determining whether or not a biological sample contains antibody that specifically binds a polypeptide encoded by the nucleic sequence acid of any of SEQ ID NOs: 1- 21 or 58-156.
14. A method of diagnosing Porcine Periweaning Failure-to-Thrive Syndrome (PFTS) in an animal, the method comprising determining the porcine astrovirus content in a sample of a body fluid or a tissue sample from the animal, wherein PFTS is diagnosed if the porcine astrovirus content in the sample is significantly elevated compared to that of an animal not having PFTS.
15. A method of diagnosing porcine gastrointestinal disease, the method comprising determining the porcine astrovirus content in a sample of a body fluid or a tissue sample from the animal, wherein porcine gastrointestinal disease is diagnosed if the porcine astrovirus content in the sample is significantly elevated compared to that of an animal not having porcine gastrointestinal disease.
16. A method of diagnosing Porcine Periweaning Failure-to-Thrive Syndrome (PFTS) in a sick animal, the method comprising determining whether or not porcine astrovirus is present in a biological sample from the sick animal, wherein PFTS is diagnosed if porcine astrovirus is present in the biological sample from the sick animal but not in a biological sample from a healthy animal.
17. A method of diagnosing porcine gastrointestinal disease, the method comprising determining whether or not porcine astrovirus is present in a biological sample from the sick animal, wherein porcine gastrointestinal disease is diagnosed if porcine astrovirus is present in the biological sample from the sick animal but not in a biological sample from a healthy animal.
18. The method of any of claims 8, 9, 10, 1 1, 12, 13, 14, 15, 16, or 17, wherein the animal is a Pig-
19. An immunogenic composition for inducing an immune response in a porcine animal, wherein the composition comprises an isolated inactivated porcine astrovirus; and a pharmaceutically acceptable vehicle or diluent.
20. The composition of claim 19, wherein the porcine astrovirus is of a subtype selected from the group consisting of subtype 2a, subtype 2b, subtype 3, subtype 4 and subtype 5.
21. The composition of claim 19, wherein the composition is for protecting swine against
periweaning failure to thrive syndrome (PFTS).
22. The composition of claim 19, wherein the composition is for protecting swine against porcine gastrointestinal disease.
23. The composition of claim 22, wherein the composition protecting swine against porcine gastrointestinal disease, delays the onset of symptoms associated with porcine gastrointestinal disease, or reduces the severity of symptoms of porcine gastrointestinal disease.
24. The composition of claim 19, wherein the porcine astrovirus encodes an ORF2 polypeptide sequence having at least 90% identity to the amino acid sequence selected from the group consisting of SEQ ID NO: 23, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, and SEQ ID NO: 57.
25. The composition of claim 19, further comprising an adjuvant.
26. An immunogenic composition for inducing an immune response in a porcine animal, wherein the composition comprises a recombinant or isolated capsid polypeptide derived from a porcine astrovirus; and a pharmaceutically acceptable vehicle or diluent.
27. The composition of claim 26, wherein the capsid polypeptide is selected from the group
consisting of VP70, VP34, VP27, VP25, Spike, and combinations thereof.
28. The composition of claim 27, wherein the capsid polypeptide is VP70.
29. The composition of claim 26, wherein the porcine astrovirus is of a subtype selected from the group consisting of subtype 2a, subtype 2b, subtype 3, subtype 4 and subtype 5.
30. The composition of claim 26, wherein the composition is for protecting swine against
periweaning failure to thrive syndrome (PFTS).
31. The composition of claim 26, wherein the composition is for protecting swine against porcine gastrointestinal disease.
32. The composition of claim 31, wherein the composition protecting swine against porcine
gastrointestinal disease, delays the onset of symptoms associated with porcine gastrointestinal disease, or reduces the severity of symptoms of porcine gastrointestinal disease.
208
33. The composition of claim 26, wherein the capsid polypeptide is derived from an ORF2 capsid polypeptide sequence having at least 90% identity to the amino acid sequence selected from the group consisting of SEQ ID NO: 23, SEQ ID NO: 27, SEQ ID NO: 29, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, and SEQ ID NO: 57.
34. The composition of claim 26, further comprising an adjuvant.
35. A method of immunizing a porcine animal against periweaning failure to thrive syndrome (PFTS), the method comprising administering to the porcine animal the immunogenic composition of claim 19.
36. A method of immunizing a porcine animal against porcine gastrointestinal disease, the
method comprising administering to the porcine animal the immunogenic composition of claim 19.
37. A method of immunizing a porcine animal against periweaning failure to thrive syndrome (PFTS), the method comprising administering to the porcine animal the immunogenic composition of claim 26.
38. A method of immunizing a porcine animal against porcine gastrointestinal disease, the
method comprising administering to the porcine animal the immunogenic composition of claim 26.
209
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