Rhiza Labs FluTracker Forum

Morag Graham1,2*, Binhua Liang1, Gary Van Domselaar1,2,3, Nathalie Bastien1, Carole Beaudoin1,4, Shaun Tyler1, Brynn Kaplen1, Erika Landry1, the National Influenza A/H1N1pdm Genomics Study Team (NIGST)¶, Yan Li1,2

1 National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada, 2 Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada, 3 Department of Computer Science, University of Manitoba, Winnipeg, Manitoba, Canada, 4 Department of Community Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada

Abstract Top
Background
In April 2009, a novel triple-reassortant swine influenza A H1N1 virus (“A/H1N1pdm”; also known as SOIV) was detected and spread globally as the first influenza pandemic of the 21st century. Sequencing has since been conducted at an unprecedented rate globally in order to monitor the diversification of this emergent virus and to track mutations that may affect virus behavior.

Methodology/Principal Findings
By Sanger sequencing, we determined consensus whole-genome sequences for A/H1N1pdm viruses sampled nationwide in Canada over 33 weeks during the 2009 first and second pandemic waves. A total of 235 virus genomes sampled from unique subjects were analyzed, providing insight into the temporal and spatial trajectory of A/H1N1pdm lineages within Canada. Three clades (2, 3, and 7) were identifiable within the first two weeks of A/H1N1pdm appearance, with clades 5 and 6 appearing thereafter; further diversification was not apparent. Only two viral sites displayed evidence of adaptive evolution, located in hemagglutinin (HA) corresponding to D222 in the HA receptor-binding site, and to E374 at HA2-subunit position 47. Among the Canadian sampled viruses, we observed notable genetic diversity (1.47×10−3 amino acid substitutions per site) in the gene encoding PB1, particularly within the viral genomic RNA (vRNA)-binding domain (residues 493–757). This genome data set supports the conclusion that A/H1N1pdm is evolving but not excessively relative to other H1N1 influenza A viruses. Entropy analysis was used to investigate whether any mutated A/H1N1pdm protein residues were associated with infection severity; however no virus genotypes were observed to trend with infection severity. One virus that harboured heterozygote coding mutations, including PB2 D567D/G, was attributed to a severe and potentially mixed infection; yet the functional significance of this PB2 mutation remains unknown.

Conclusions/Significance
These findings contribute to enhanced understanding of Influenza A/H1N1pdm viral dynamics.

Citation: Graham M, Liang B, Van Domselaar G, Bastien N, Beaudoin C, et al. (2011) Nationwide Molecular Surveillance of Pandemic H1N1 Influenza A Virus Genomes: Canada, 2009. PLoS ONE 6(1): e16087. doi:10.1371/journal.pone.0016087

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Sequences associated with above paper are at Genbank.

A/Canada-ON/RV2904/2009 has S186P.

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LOCUS HQ239572 1671 bp cRNA linear VRL 12-JAN-2011
DEFINITION Influenza A virus (A/Canada-ON/RV2904/2009(H1N1)) segment 4
hemagglutinin (HA) gene, partial cds.
ACCESSION HQ239572
VERSION HQ239572.1 GI:307070022
DBLINK Project: 37813
KEYWORDS .
SOURCE Influenza A virus (A/Canada-ON/RV2904/2009(H1N1))
ORGANISM Influenza A virus (A/Canada-ON/RV2904/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 1671)
AUTHORS Graham,M., Liang,B., Van Domselaar,G., Bastien,N., Beaudoin,C.,
Tyler,S., Kaplen,B., Landry,E. and Li,Y.
CONSRTM National Influenza A/H1N1pdm Genomics Study Team (NIGST)
TITLE Nationwide Molecular Surveillance of Pandemic H1N1 Influenza A
Virus Genomes: Canada, 2009
JOURNAL PLoS ONE 6 (1), e16087 (2011)
REMARK Publication Status: Online-Only
REFERENCE 2 (bases 1 to 1671)
AUTHORS Graham,M., Liang,B., Van Domselaar,G., Bastien,N., Beaudoin,C.,
Tyler,S., Kaplen,B., Landry,E. and Li,Y.
CONSRTM National Influenza A/H1N1pdm Genomics Study Team (NIGST)
TITLE Direct Submission
JOURNAL Submitted (09-SEP-2010) Public Health Agency of Canada, National
Microbiology Laboratory, 1015 Arlington Street, Winnipeg, Manitoba
R3E 3R2, Canada
COMMENT GenBank Accession Numbers HQ240400, HQ240193, HQ241021, HQ239779,
HQ240814, HQ239572, HQ240607, HQ239986 represent sequences from the
8 segments of Influenza A virus (A/Canada-ON/RV2904/2009(H1N1)).

Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009-2010.
FEATURES Location/Qualifiers
source 1..1671
/organism="Influenza A virus
(A/Canada-ON/RV2904/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Canada-ON/RV2904/2009"
/serotype="H1N1"
/isolate="NML RV2904/09"
/isolation_source="TCF"
/host="Homo sapiens; gender M; age 2Y"
/db_xref="taxon:885221"
/segment="4"
/country="Canada: Ontario"
/collection_date="07-Sep-2009"
/note="lineage: swl
P1 passage(s)"
gene 1..>1671
/gene="HA"
CDS 1..>1671
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ADN24109.1"
/db_xref="GI:307070023"
/translation="MEAILVVLLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVT
HSVNLLEDKHNGKLCKLRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSS
DNGTCYPGDFIDYEELREQLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKS
FYKNLIWLVKKGNSYPKLSKSYINDKGKEVLVLWGIHHPPTSADQQSLYQNADAYVFV
GSSKYSKKFKPEIAIRPKVRDQEGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMER
NAGSGIIISDTPAHDCNTTCQTPKGAINTSLPFHNIHPITIGKCPKYVKSTKLRLATG
LRNVPSIQSRGLFGAIAGFIEGGWTGMVDGWYGYHHQNEQGSGYAADLKSTQNAIDEI
TNKVNSVIEKMNTQFTAVGKEFNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENER
TLDYHDSNVKNLYEKVRSQLKNNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSE
EAKLNREEIDGVKLESTKIYQILAIYSTVASSLVLVVSLGAISFWMCSN"
ORIGIN
1 atggaggcaa tactagtagt tctgctatat acatttgcaa ccgcaaatgc agacacatta
61 tgtataggtt atcatgcgaa caattcaaca gacactgtag acacagtact agaaaagaat
121 gtaacagtaa cacactctgt taaccttcta gaagacaagc ataacgggaa actatgcaaa
181 ctaagagggg tagccccatt gcatttgggt aaatgtaaca ttgctggctg gatcctggga
241 aatccagagt gtgaatcact ctccacagca agctcatggt cctacattgt ggaaacatct
301 agttcagaca atggaacgtg ttacccagga gatttcatcg attatgagga gctaagagag
361 caattgagct cagtgtcatc atttgaaagg tttgagatat tccccaagac aagttcatgg
421 cccaatcatg actcgaacaa aggtgtaacg gcagcatgtc ctcatgctgg agcaaaaagc
481 ttctacaaaa atttaatatg gctagttaaa aaaggaaatt catacccaaa gctcagcaaa
541 tcctacatta atgataaagg gaaagaagtc ctcgtgctat ggggcattca ccatccacct
601 actagtgctg accaacaaag tctctatcag aatgcagatg catatgtttt tgtggggtca
661 tcaaaataca gcaagaagtt caagccggaa atagcaataa gacccaaagt gagggatcaa
721 gaagggagaa tgaactatta ctggacacta gtagagccgg gagacaaaat aacattcgaa
781 gcaactggaa atctagtggt accgagatat gcattcgcaa tggaaagaaa tgctggatct
841 ggtattatca tttcagatac accagcccac gattgcaata caacttgtca gacacccaag
901 ggtgctataa acaccagcct cccatttcat aatatacatc cgatcacaat tggaaaatgt
961 ccaaaatatg taaaaagcac aaaattgaga ctggccacag gattgaggaa tgtcccgtct
1021 attcaatcta gaggcctatt tggggccatt gccggtttca ttgaaggggg gtggacaggg
1081 atggtagatg gatggtacgg ttatcaccat caaaatgagc aggggtcagg atatgcagcc
1141 gacctgaaga gcacacagaa tgccattgac gagattacta acaaagtaaa ttctgttatt
1201 gaaaagatga atacacagtt cacagcagta ggtaaagagt tcaaccacct ggaaaaaaga
1261 atagagaatt taaataaaaa agttgatgat ggtttcctgg acatttggac ttacaatgcc
1321 gaactgttgg ttctattgga aaatgaaaga actttggact accacgattc aaatgtgaag
1381 aacttatatg aaaaggtaag aagccagtta aaaaacaatg ccaaggaaat tggaaacggc
1441 tgctttgaat tttaccacaa atgcgataac acgtgcatgg aaagtgtcaa aaatgggact
1501 tatgactacc caaaatactc agaggaagca aaattaaaca gagaagaaat agatggggta
1561 aagctggaat caacaaagat ttaccagatt ttggcgatct attcaactgt cgccagttca
1621 ttggtactgg tagtctccct gggggcaatc agtttctgga tgtgctctaa t
//

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