Rhiza Labs FluTracker Forum

The USDA has released another series of swine sequences, including H3N2v sequences from late 2011 and 2012. Several of the isolates have H3 and MP matches with the human cases in 2011 and 2012.

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N2 matches (A/swine/Illinois/A00857304a/2012, A/swine/Illinois/A00857304b/2012, A/swine/Illinois/A00857138a/2011, A/swine/Illinois/A00857138b/2011, A/swine/Illinois/A00857300/2011), are with 2011 human H3N2v cases (not West Virginia or Utah).

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All five PB2 sequences match.

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LOCUS JQ738153 2274 bp cRNA linear VRL 24-APR-2012
DEFINITION Influenza A virus (A/swine/Illinois/A00857138a/2011(H3N2)) segment
2 polymerase PB1 (PB1) and PB1-F2 (PB1-F2) genes, complete cds.
ACCESSION JQ738153
VERSION JQ738153.1 GI:383513190
KEYWORDS .
SOURCE Influenza A virus (A/swine/Illinois/A00857138a/2011(H3N2))
ORGANISM Influenza A virus (A/swine/Illinois/A00857138a/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2274)
CONSRTM USDA Swine Surveillance
TITLE Direct Submission
JOURNAL Submitted (02-MAR-2012) USDA, Ames, IA 50010, USA
COMMENT GenBank Accession Numbers JQ738152-JQ738159 represent sequences
from the 8 segments of Influenza A virus
(A/swine/Illinois/A00857138a/2011(H3N2)).
FEATURES Location/Qualifiers
source 1..2274
/organism="Influenza A virus
(A/swine/Illinois/A00857138a/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Illinois/A00857138a/2011"
/serotype="H3N2"
/isolation_source="lung tissue"
/host="swine"
/db_xref="taxon:1158258"
/segment="2"
/country="USA: Illinois"
/collection_date="20-Oct-2011"
gene 1..2274
/gene="PB1"
CDS 1..2274
/gene="PB1"
/codon_start=1
/product="polymerase PB1"
/protein_id="AFH41279.1"
/db_xref="GI:383513191"
/translation="MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVN
RTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGI
FENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANES
GRLIDFLKDVMESMDKEEIEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRVNKRSYL
IRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGN
EKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFR
NILSMAPIMFSNKMARLGKGYMFESKRMKLRTQIPAEMLSSIDLKYFNESTRKKIEKI
RPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTRTTYWWDGLQSSDDFALI
VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYGFVANFSME
LPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDT
QIQTRRSFELKKLWDQTQSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYRGRL
CNPLNPFVSHKEIDSVNSAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGI
LEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEF
SEIMKICSTIEELRRQK"
gene 95..367
/gene="PB1-F2"
CDS 95..367
/gene="PB1-F2"
/codon_start=1
/product="PB1-F2"
/protein_id="AFH41280.1"
/db_xref="GI:383513192"
/translation="MEQEQDTPWTQSTEHTNIQKKGNGRQIQRLGHPSSIRLMDHYLK
IMNQVDMHKQTVSWRPWLSLKNPTQGYLRIHALKQWKLSNKQGWIN"
ORIGIN
1 atggatgtca atccgactct acttttccta aaggttccag cgcaaaatgc cataagcacc
61 acattccctt atactggaga tcctccatac agccatggaa caggaacagg atacaccatg
121 gacacagtca acagaacaca ccaatattca gaaaaaggga aatggacgac aaatacagag
181 actggggcac cccagctcaa tccgattgat ggaccactac ctgaagataa tgaaccaagt
241 ggatatgcac aaacagactg tgtcctggag gccatggctt tccttgaaga atcccaccca
301 gggatatttg agaattcatg ccttgaaaca atggaaattg tccaacaaac aagggtggat
361 aaactaaccc agggtcgcca gacatatgat tggacattaa atagaaatca accggcagca
421 actgcattgg ccaacaccat agaagttttt agatcaaatg gtctaacagc taatgagtca
481 ggaaggctga tagatttctt aaaagatgta atggaatcaa tggataaaga ggaaatagag
541 ataacaacac actttcaaag aaaaaggaga gtaagggata acatgaccaa gaagatggtc
601 acacaaagaa caatagggaa gaaaaaacaa agagtgaata agaggagtta tttaataaga
661 gcactaacat tgaatacgat gaccaaagat gcagagagag gcaaattaaa aagaagggct
721 attgcaacac ctggaatgca aattagaggg ttcgtgtact ttgttgagac tctagctaga
781 agcatttgcg agaagcttga acaatccgga ctcccagtag ggggcaatga aaagaaagcc
841 aaattggcaa acgttgtgag aaagatgatg actaattcac aagacacaga gctttccttc
901 acaattactg gggacaacac taaatggaat gaaaaccaaa accctcgaat gttcctggcg
961 atgattacat acatcaccag aaaccaaccc gagtggttca gaaacatcct gagcatggca
1021 cccataatgt tctcaaacaa aatggcaaga ctaggaaaag ggtacatgtt cgagagtaaa
1081 aggatgaagc tccgaacaca gataccagca gaaatgctat caagcattga cctgaagtat
1141 ttcaatgaat caacaaggaa gaaaattgag aaaataaggc ccctcctaat agatggcaca
1201 gcatcactga gccctgggat gatgatgggc atgttcaaca tgctaagtac ggttttggga
1261 gtctcgatac tgaatcttgg acaaaagaaa tacaccagga caacatactg gtgggacgga
1321 ctccaatcct ccgacgattt tgccctcata gtaaacgcac caaatcatga gggaatccaa
1381 gcaggagtgg atagattcta caggacctgc aagttagtag gaatcaacat gagcaaaaag
1441 aagtcctata taaataagac tgggacattt gaattcacaa gcttttttta tcgctatggg
1501 tttgtagcta attttagcat ggagctgccc agttttggag tgtctggaat aaacgaatca
1561 gctgatatga gtattggggt aacagtgata aagaacaaca tgataaacaa tgatcttgga
1621 cctgcaacag ctcagatggc ccttcagttg ttcatcaaag actacagata cacctataga
1681 tgccatagag gggacacaca gattcaaacg agaagatcat tcgagctaaa gaagctgtgg
1741 gatcaaaccc aatcaaaggc aggattacta gtatctgatg gaggaccaaa tttatacaat
1801 atccggaatc ttcacattcc tgaagtctgc ttaaaatggg agctaatgga tgaggattat
1861 cggggaagac tttgcaatcc cctgaatccc tttgtcagcc ataaagagat tgattctgta
1921 aacagtgctg tggtgatgcc agcccatggt ccagccaaaa gcatggaata tgatgccgtt
1981 gcaactacac actcctggat ccccaagagg aaccgctcta ttctcaacac aagccaaagg
2041 ggaattcttg aggatgaaca gatgtaccag aagtgctgca atctgttcga gaaatttttc
2101 cctagtagtt cgtacaggag accggttgga atttctagca tggtagaggc catggtgtct
2161 agggcccgaa ttgatgccag gattgacttc gagtctggac ggattaagaa agaagagttc
2221 tctgagatca tgaagatctg ttccaccatt gaagaactca gacggcaaaa gtaa

_________________
www.twitter.com/hniman

LOCUS JQ738145 2274 bp cRNA linear VRL 24-APR-2012
DEFINITION Influenza A virus (A/swine/Illinois/A00857300/2011(H3N2)) segment 2
polymerase PB1 (PB1) and PB1-F2 (PB1-F2) genes, complete cds.
ACCESSION JQ738145
VERSION JQ738145.1 GI:383513209
KEYWORDS .
SOURCE Influenza A virus (A/swine/Illinois/A00857300/2011(H3N2))
ORGANISM Influenza A virus (A/swine/Illinois/A00857300/2011(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2274)
CONSRTM USDA Swine Surveillance
TITLE Direct Submission
JOURNAL Submitted (02-MAR-2012) USDA, Ames, IA 50010, USA
COMMENT GenBank Accession Numbers JQ738144-JQ738151 represent sequences
from the 8 segments of Influenza A virus
(A/swine/Illinois/A00857300/2011(H3N2)).
FEATURES Location/Qualifiers
source 1..2274
/organism="Influenza A virus
(A/swine/Illinois/A00857300/2011(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Illinois/A00857300/2011"
/serotype="H3N2"
/isolation_source="lung tissue"
/host="swine"
/db_xref="taxon:1158260"
/segment="2"
/country="USA: Illinois"
/collection_date="28-Nov-2011"
gene 1..2274
/gene="PB1"
CDS 1..2274
/gene="PB1"
/codon_start=1
/product="polymerase PB1"
/protein_id="AFH41290.1"
/db_xref="GI:383513210"
/translation="MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVN
RTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGI
FENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANES
GRLIDFLKDVMESMDKEEIEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRVNKRSYL
IRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGN
EKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFR
NILSMAPIMFSNKMARLGKGYMFESKRMKLRTQIPAEMLSSIDLKYFNESTRKKIEKI
RPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTRTTYWWDGLQSSDDFALI
VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYGFVANFSME
LPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDT
QIQTRRSFELKKLWDQTQSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYRGRL
CNPLNPFVSHKEIDSVNSAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGI
LEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEF
SEIMKICSTIEELRRQK"
gene 95..367
/gene="PB1-F2"
CDS 95..367
/gene="PB1-F2"
/codon_start=1
/product="PB1-F2"
/protein_id="AFH41291.1"
/db_xref="GI:383513211"
/translation="MEQEQDTPWTQSTEHTNIQKKGNGRQIQRLGHPSSIRLMDHYLK
IMNQVDMHKQTVSWRPWLSLKNPTQGYLRIHALKQWKLSNKQGWIN"
ORIGIN
1 atggatgtca atccgactct acttttccta aaggttccag cgcaaaatgc cataagcacc
61 acattccctt atactggaga tcctccatac agccatggaa caggaacagg atacaccatg
121 gacacagtca acagaacaca ccaatattca gaaaaaggga aatggacgac aaatacagag
181 actggggcac cccagctcaa tccgattgat ggaccactac ctgaagataa tgaaccaagt
241 ggatatgcac aaacagactg tgtcctggag gccatggctt tccttgaaga atcccaccca
301 gggatatttg agaattcatg ccttgaaaca atggaaattg tccaacaaac aagggtggat
361 aaactaaccc agggtcgcca gacatatgat tggacattaa atagaaatca accggcagca
421 actgcattgg ccaacaccat agaagttttt agatcaaatg gtctaacagc taatgagtca
481 ggaaggctga tagatttctt aaaagatgta atggaatcaa tggataaaga ggaaatagag
541 ataacaacac actttcaaag aaaaaggaga gtaagggata acatgaccaa gaagatggtc
601 acacaaagaa caatagggaa gaaaaaacaa agagtgaata agaggagtta tttaataaga
661 gcactaacat tgaatacgat gaccaaagat gcagagagag gcaaattaaa aagaagggct
721 attgcaacac ctggaatgca aattagaggg ttcgtgtact ttgttgagac tctagctaga
781 agcatttgcg agaagcttga acaatccgga ctcccagtag ggggcaatga aaagaaagcc
841 aaattggcaa acgttgtgag aaagatgatg actaattcac aagacacaga gctttccttc
901 acaattactg gggacaacac taaatggaat gaaaaccaaa accctcgaat gttcctggcg
961 atgattacat acatcaccag aaaccaaccc gagtggttca gaaacatcct gagcatggca
1021 cccataatgt tctcaaacaa aatggcaaga ctaggaaaag ggtacatgtt cgagagtaaa
1081 aggatgaagc tccgaacaca gataccagca gaaatgctat caagcattga cctgaagtat
1141 ttcaatgaat caacaaggaa gaaaattgag aaaataaggc ccctcctaat agatggcaca
1201 gcatcactga gccctgggat gatgatgggc atgttcaaca tgctaagtac ggttttggga
1261 gtctcgatac tgaatcttgg acaaaagaaa tacaccagga caacatactg gtgggacgga
1321 ctccaatcct ccgacgattt tgccctcata gtaaacgcac caaatcatga gggaatccaa
1381 gcaggagtgg atagattcta caggacctgc aagttagtag gaatcaacat gagcaaaaag
1441 aagtcctata taaataagac tgggacattt gaattcacaa gcttttttta tcgctatggg
1501 tttgtagcta attttagcat ggagctgccc agttttggag tgtctggaat aaacgaatca
1561 gctgatatga gtattggggt aacagtgata aagaacaaca tgataaacaa tgatcttgga
1621 cctgcaacag ctcagatggc ccttcagttg ttcatcaaag actacagata cacctataga
1681 tgccatagag gggacacaca gattcaaacg agaagatcat tcgagctaaa gaagctgtgg
1741 gatcaaaccc aatcaaaggc aggattacta gtatctgatg gaggaccaaa tttatacaat
1801 atccggaatc ttcacattcc tgaagtctgc ttaaaatggg agctaatgga tgaggattat
1861 cggggaagac tttgcaatcc cctgaatccc tttgtcagcc ataaagagat tgattctgta
1921 aacagtgctg tggtgatgcc agcccatggt ccagccaaaa gcatggaata tgatgccgtt
1981 gcaactacac actcctggat ccccaagagg aaccgctcta ttctcaacac aagccaaagg
2041 ggaattcttg aggatgaaca gatgtaccag aagtgctgca atctgttcga gaaatttttc
2101 cctagtagtt cgtacaggag accggttgga atttctagca tggtagaggc catggtgtct
2161 agggcccgaa ttgatgccag gattgacttc gagtctggac ggattaagaa agaagagttc
2221 tctgagatca tgaagatctg ttccaccatt gaagaactca gacggcaaaa gtaa

_________________
www.twitter.com/hniman

LOCUS JQ738169 2274 bp cRNA linear VRL 24-APR-2012
DEFINITION Influenza A virus (A/swine/Illinois/A00857304a/2012(H3N2)) segment
2 polymerase PB1 (PB1) and PB1-F2 (PB1-F2) genes, complete cds.
ACCESSION JQ738169
VERSION JQ738169.1 GI:383513152
KEYWORDS .
SOURCE Influenza A virus (A/swine/Illinois/A00857304a/2012(H3N2))
ORGANISM Influenza A virus (A/swine/Illinois/A00857304a/2012(H3N2))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 2274)
CONSRTM USDA Swine Surveillance
TITLE Direct Submission
JOURNAL Submitted (02-MAR-2012) USDA, Ames, IA 50010, USA
COMMENT GenBank Accession Numbers JQ738168-JQ738175 represent sequences
from the 8 segments of Influenza A virus
(A/swine/Illinois/A00857304a/2012(H3N2)).
FEATURES Location/Qualifiers
source 1..2274
/organism="Influenza A virus
(A/swine/Illinois/A00857304a/2012(H3N2))"
/mol_type="viral cRNA"
/strain="A/swine/Illinois/A00857304a/2012"
/serotype="H3N2"
/isolation_source="lung tissue"
/host="swine"
/db_xref="taxon:1158261"
/segment="2"
/country="USA: Illinois"
/collection_date="05-Jan-2012"
gene 1..2274
/gene="PB1"
CDS 1..2274
/gene="PB1"
/codon_start=1
/product="polymerase PB1"
/protein_id="AFH41257.1"
/db_xref="GI:383513153"
/translation="MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVN
RTHQYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGI
FENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANES
GRLIDFLKDVMESMDKEEIEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRVNKRSYL
IRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGN
EKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFR
NILSMAPIMFSNKMARLGKGYMFESKRMKLRTQIPAEMLSSIDLKYFNESTRKKIEKI
RPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTRTTYWWDGLQSSDDFALI
VNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINKTGTFEFTSFFYRYGFVANFSME
LPSFGVSGINESADMSIGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDT
QIQTRRSFELKKLWDQTQSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYRGRL
CNPLNPFVSHKEIDSVNSAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGI
LEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEF
SEIMKICSTIEELRRQK"
gene 95..367
/gene="PB1-F2"
CDS 95..367
/gene="PB1-F2"
/codon_start=1
/product="PB1-F2"
/protein_id="AFH41258.1"
/db_xref="GI:383513154"
/translation="MEQEQDTPWTQSTEHTNIQKKGNGRQIQRLGHPSSIRLMDHYLK
IMNQVDMHKQTVSWRPWLSLKNPTQGYLRIHALKQWKLSNKQGWIN"
ORIGIN
1 atggatgtca atccgactct acttttccta aaggttccag cgcaaaatgc cataagcacc
61 acattccctt atactggaga tcctccatac agccatggaa caggaacagg atacaccatg
121 gacacagtca acagaacaca ccaatattca gaaaaaggga aatggacgac aaatacagag
181 actggggcac cccagctcaa tccgattgat ggaccactac ctgaagataa tgaaccaagt
241 ggatatgcac aaacagactg tgtcctggag gccatggctt tccttgaaga atcccaccca
301 gggatatttg agaattcatg ccttgaaaca atggaaattg tccaacaaac aagggtggat
361 aaactaaccc agggtcgcca gacatatgat tggacattaa atagaaatca accggcagca
421 actgcattgg ccaacaccat agaagttttt agatcaaatg gtctaacagc taatgagtca
481 ggaaggctga tagatttctt aaaagatgta atggaatcaa tggataaaga ggaaatagag
541 ataacaacac actttcaaag aaaaaggaga gtaagggata acatgaccaa gaagatggtc
601 acacaaagaa caatagggaa gaaaaaacaa agagtgaata agaggagtta tttaataaga
661 gcactaacat tgaatacgat gaccaaagat gcagagagag gcaaattaaa aagaagggct
721 attgcaacac ctggaatgca aattagaggg ttcgtgtact ttgttgagac tctagctaga
781 agcatttgcg agaagcttga acaatccgga ctcccagtag ggggcaatga aaagaaagcc
841 aaattggcaa acgttgtgag aaagatgatg actaattcac aagacacaga gctttccttc
901 acaattactg gagacaacac taaatggaat gaaaaccaaa atcctcgaat gttcctggcg
961 atgattacat acatcaccag aaaccaaccc gagtggttca gaaacatcct gagcatggca
1021 cccataatgt tctcaaacaa aatggcaaga ctaggaaaag ggtacatgtt cgagagtaaa
1081 aggatgaagc tccgaacaca gataccagca gaaatgctat caagcattga cctgaagtat
1141 ttcaatgaat caacaaggaa gaaaattgag aaaataaggc ccctcctaat agatggcaca
1201 gcatcactga gccctgggat gatgatgggc atgttcaaca tgctaagtac ggttttggga
1261 gtctcgatac tgaatcttgg acaaaagaaa tacaccagga caacatactg gtgggacgga
1321 ctccaatcct ccgacgattt tgccctcata gtaaacgcac caaatcatga gggaatccaa
1381 gcaggagtgg atagattcta caggacctgc aagttagtag ggatcaacat gagcaaaaag
1441 aagtcctata taaataagac tgggacattt gaattcacaa gcttttttta tcgctatggg
1501 tttgtagcta attttagcat ggaactgccc agttttggag tgtctggaat aaacgaatca
1561 gctgatatga gtattggggt aacagtgata aagaacaaca tgataaacaa tgatcttgga
1621 cctgcaacag ctcagatggc ccttcagttg ttcatcaaag actacagata cacctataga
1681 tgccatagag gggacacaca gattcaaacg agaagatcat tcgagctaaa gaagctgtgg
1741 gatcaaaccc aatcgaaggc aggattacta gtatctgatg gaggaccaaa tttatacaat
1801 atccggaatc ttcacattcc tgaagtctgc ttaaaatggg agctaatgga tgaggattat
1861 cggggaagac tttgcaatcc cctgaatccc tttgtcagcc ataaagagat tgattctgta
1921 aacagtgctg tggtgatgcc agcccatggt ccagccaaaa gcatggaata tgatgccgtt
1981 gcaactacac actcctggat ccccaagagg aaccgctcta ttctcaacac aagccaaagg
2041 ggaattcttg aggatgaaca gatgtaccag aagtgctgca atctgttcga gaaatttttc
2101 cctagtagtt cgtacaggag accggttgga atttctagca tggtagaggc catggtgtct
2161 agggcccgaa ttgatgccag gattgacttc gagtctggac ggattaagaa agaagagttc
2221 tctgagatca tgaagatctg ttccaccatt gaagaactca gacggcaaaa gtaa

_________________
www.twitter.com/hniman

All three cases (five isolates) collected after initial human cases and all from lung tissue (collections in Oct, Dec, Jan) suggesting infections are severe or fatal in swine.

_________________
www.twitter.com/hniman

or slaughterhouse ?

_________________
no patents on genes, publish the GISAID sequences !

No, these samples are sent in as part of the USDA anonymous testing program.

Other samples are nasal swabs.

All five matches with the human 2011 cases have been from lung tissue.

_________________
www.twitter.com/hniman

All five isolates match in all 8 gene segments.

_________________
www.twitter.com/hniman