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niman

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  1. niman
    Sequence analysisUpon direct sequencing of the RT-PCR amplicons, the two strains, PR668/2015/ITA and BA603–6/2015/ITA, were found to be identical in the short diagnostic regions A and C. We determined the sequence of a large portion (3.2 kb) of the genome at the 3’ end for strain PR668/2015/ITA. Viral RNA was extracted from 140 µl of stool suspension using the QIAmp viral RNA kit (Qiagen, GmbH, Hilden, Germany). A 3’-rapid amplification of cDNA ends (RACE)-PCR) protocol was used to generate the 3.2-kb amplicon encompassing the 3’ end of ORF1, the full-length ORF2 and ORF3, and the 3’ untranslated region (UTR) until the poly(A) tail, using the reverse primer VN3T20 [9] and the forward primer JV12Y [10]. The RACE product was cloned and the sequence was determined. Phylogenetic analysis was performed using MEGA v. 6.0 [11]. The 3.2-kb sequence of the Italian NoV GII.P17-GII.17 strain has been deposited in GenBank under accession number KT346356. The partial sequence of ORF1 (807 nt), and the full-length sequences of ORF2 (1,621 nt) and ORF3 (849 nt) of strain PR668/2015/ITA were analysed with NoV GII.P17-GII.17 sequences available in the GenBank database (Figure 1). Figure 1Phylogenetic analysis based on partial ORF1, full ORF2 and full ORF3 sequences of GII.17 norovirus, Italy, February 2015 The Italian GII.P17-GII.17 strain is indicated in bold. Trees were built with the maximum-likelihood method, and bootstrapped with 1,000 repetitions. Bootstrap values > 80% are indicated. The scale bar indicates the number of nucleotide substitutions per site. The topology of the trees in the multi-target phylogenetic analysis was conserved, with the GII.P17-GII.17 Kawasaki 2014 NoV forming a monophyletic branch and further segregating into two genetic subclades. The first subclade containing the Italian PR668/2015/ITA strain clustered with GII.P17-GII.17 NoVs detected in China and Hong Kong during 2014 and 2015, and was genetically related (99.9%) to a GII.P17-GII.17 strain detected in the United States (US) in November 2014. The second subclade included GII.P17-GII.17 NoV detected in Japan and Taiwan during 2013 and 2014. The viruses of the two subclades showed a moderate degree of nucleotide and amino acid divergence in the ORF2 and ORF3 sequences (1–1.9% nucleotide and 0–0.4% amino acid differences in ORF1, 0.4–4.1% nucleotides and 0.9–6.2% amino acids in ORF2, and 0.5–3.3% nucleotides and 1–4.9% amino acids in ORF3). Interestingly, the GII.17 capsid sequences of the two genetic subclades differed markedly from the oldest GII.17 capsid sequence available in GenBank database, dating back to 1978 (23.3–24.8% nucleotide and 14.2–16.6% amino acid differences in ORF2, and 19.4–27% nucleotide and 22.1–22.9% amino acid differences in ORF3). Several changes in the VP1 sequence were observed between the two Kawasaki 2014 subclades, mostly, but not exclusively, affecting the antibody blockade sites, i.e. the putative epitopes (A-E) located in the capsid protruding hypervariable P2 domain (Figure 2). In the 543 amino acid VP1 protein, 17 amino acid changes (3.1% divergence) and four insertions separate the two Kawasaki 2014 subclades, while 38 amino acid changes (7% divergence) and several insertions/deletions separate the Kawasaki 2014 GII.17 NoV and the former GII.17 recombinant forms. Figure 2Amino acid substitutions in the VP1 sequence of norovirus GII.17 strains, 1978 to 2015 The putative blockade epitopes A–E are indicated. The Italian GII.P17-GII.17 strain is indicated in bold. Dots indicate sequence conservation. Dashes indicate deletions/insertions of the amino acid residues. Amino acid numbering is based on the sequence of the C142 strain (JN699043).
  2. niman
    Surveillance of noroviruses in ItalyThe Italian Study Group for Enteric Viruses (ISGEV; http://isgev.net) monitors the epidemiology of enteric viruses in children through hospital-based surveillance. A subset of about half of the NoV-positive samples is systematically genotyped in both region A (ORF1, RdRp) and region C (ORF2, capsid). From September 2014 to March 2015, NoV prevalence was 12% (137/1,144) and NoVs were typed in 81 cases (59%). GII.P17-GII.17 NoV strains were detected in two sporadic cases of acute severe gastroenteritis in young children hospitalised in February 2015 in two distinct Italian regions.
  3. niman
    GenotypingThe NoV genome contains three open reading frames (ORFs). ORF1 encodes non-structural proteins including the RNA-dependent RNA polymerase (RdRp), while ORF2 and ORF3 encode the major capsid protein VP1 and a minor structural protein VP2, respectively [6]. NoVs are classified in at least six genogroups, GI to GVI [6]. NoV genogroups are further divided in various genotypes based on differences in the RdRp region (polymerase genotype, or pol type) and in the VP1 (capsid genotype, or cap type) [7]. NoV genotyping was performed using standardised sequence analysis web-based tools developed and maintained by the NoroNet [8].
  4. niman
    During the winter season 2014/15, a novel GII.P17-GII.17 norovirus (NoV) strain emerged in Asian countries [1-4]. Since its emergence, this novel NoV strain, named Kawasaki 2014, has replaced the previously dominant GII.4 genotype Sydney 2012 variant in Asia, and it has been detected in a limited number of cases on other continents [1-5]. This epidemiological trend is also reflected in the GenBank database, with the vast majority of the Kawasaki 2014 GII.17 NoV sequences generated in studies from the Asian continent. Here we report the detection of the Kawasaki 2014 GII.17 strain during the 2014/15 winter season in Italy. As sequence information on Kawasaki 2014 GII.17 NoVs detected outside the Asian continent is limited [5], we determined the sequence of a large portion of the genome, including the full-length capsid gene of the GII.17 Kawasaki NoV strain circulating in Italy, and analysed the virus sequence with similar GII.17 NoV sequences available in the GenBank database.
  5. niman
    Surveillance of noroviruses in Italy identified the novel GII.17 human norovirus strain, Kawasaki 2014, in February 2015. This novel strain emerged as a major cause of gastroenteritis in Asia during 2014/15, replacing the pandemic GII.4 norovirus strain Sydney 2012, but being reported only sporadically elsewhere. This novel strain is undergoing fast diversification and continuous monitoring is important to understand the evolution of noroviruses and to implement the future strategies on norovirus vaccines.
  6. niman
    Eurosurveillance, Volume 20, Issue 35, 03 September 2015Rapid communication IDENTIFICATION OF THE NOVEL KAWASAKI 2014 GII.17 HUMAN NOROVIRUS STRAIN IN ITALY, 2015 MC Medici 1 , F Tummolo 1 , A Calderaro 1 , M Chironna 2 , GM Giammanco 3 , S De Grazia 3 , MC Arcangeletti 1 , F De Conto 1 , C Chezzi 1 , V Martella 4+ Author affiliations 1. Unit of Microbiology and Virology, Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy 2. Department of Biomedical Science and Human Oncology, University of Bari Aldo Moro-Policlinico, Bari, Italy 3. Department of Health Promotion Sciences and Mother and Child Care ‘G. D'Alessandro’, University of Palermo, Palermo, Italy 4. Department of Veterinary Medicine, University of Bari Aldo Moro, Bari, Italy Correspondence: Maria Cristina Medici ([email protected]) Citation style for this article: Medici MC, Tummolo F, Calderaro A, Chironna M, Giammanco GM, De Grazia S, Arcangeletti MC, De Conto F, Chezzi C, Martella V. Identification of the novel Kawasaki 2014 GII.17 human norovirus strain in Italy, 2015. Euro Surveill. 2015;20(35):pii=30010. DOI: http://dx.doi.org/10.2807/1560-7917.ES.2015.20.35.30010 Received:24 August 2015; Accepted:03 September 2015
  7. niman
    Novel Kawasaki GII-17 Norovirus In Italy - Eurosurveillance http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=21222
  8. niman
    REFERENCES1.↵ Zumla A, Hui DS, Perlman S. 3 June 2015. Middle East respiratory syndrome. Lancet. 10.1016/S0140-6736(15)60454-8. CrossRef2.↵ Guery B, Poissy J, el Mansouf L, Séjourné C, Ettahar N, Lemaire X,Vuotto F, Goffard A, Behillil S, Enouf V, Caro V, Mailles A, Che D,Manuguerra JC, Mathieu D, Fontanet A, van der Werf S, MERS-CoV Study Group. 2013. Clinical features and viral diagnosis of two cases of infection with Middle East respiratory syndrome coronavirus: a report of nosocomial transmission. Lancet 381:2265–2272. 10.1016/S0140-6736(13)60982-4.CrossRefMedline3.↵ De Groot RJ, Baker SC, Baric RS, Brown CS, Drosten C, Enjuanes L,Fouchier RA, Galiano M, Gorbalenya AE, Memish ZA, Perlman S, Poon LL,Snijder EJ, Stephens GM, Woo PC, Zaki AM, Zambon M, Ziebuhr J. 2013.Middle East respiratory syndrome coronavirus (MERS-CoV): announcement of the Coronavirus Study Group. J Virol 87:7790–7792. 10.1128/JVI.01244-13.FREE Full Text4.↵ Zaki AM, Van Boheemen S, Bestebroer TM, Osterhaus AD, Fouchier RA.2012. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J Med 367:1814–1820. 10.1056/NEJMoa1211721. CrossRefMedline5.↵ Memish ZA, Mishra N, Olival KJ, Fagbo SF, Kapoor V, Epstein JH,AlHakeem R, Durosinloun A, Al Asmari M, Islam A, Kapoor A, Briese T,Daszak P, Al Rabeeah AA, Lipkin WI. 2013. Middle East respiratory syndrome coronavirus in bats, Saudi Arabia. Emerg Infect Dis 19:1819–1823.10.3201/eid1911.131172. CrossRefMedline6.↵ Alagaili AN, Briese T, Mishra N, Kapoor V, Sameroff SC, de Wit E,Munster VJ, Hensley LE, Zalmout IS, Kapoor A, Epstein JH, Karesh WB,Daszak P, Mohammed OB, Lipkin WI. 2014. Middle East respiratory syndrome coronavirus infection in dromedary camels in Saudi Arabia. mBio 5(2):e00884-00814. 10.1128/mBio.00884-14. Abstract/FREE Full Text7.↵ Cotten M, Watson SJ, Zumla AI, Makhdoom HQ, Palser AL, Ong SH,Al Rabeeah AA, Alhakeem RF, Assiri A, Al-Tawfiq JA, Albarrak A, Barry M,Shibl A, Alrabiah FA, Hajjar S, Balkhy HH, Flemban H, Rambaut A,Kellam P, Memish ZA. 2014. Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus. mBio 5(1):e01062-13.10.1128/mBio.01062-13. Abstract/FREE Full Text8.↵ Haagmans BL, Al Dhahiry SH, Reusken CB, Raj VS, Galiano M,Myers R, Godeke G-J, Jonges M, Farag E, Diab A, Ghobashy H, Alhajri F,Al-Thani M, Al-Marri SA, Al Romaihi HE, Al Khal A, Bermingham A,Osterhaus AD, AlHajri MM, Koopmans MP. 2014. Middle East respiratory syndrome coronavirus in dromedary camels: an outbreak investigation. Lancet Infect Dis 14:140–145. 10.1016/S1473-3099(13)70690-X. CrossRefMedline9.↵ World Health Organization. 2015. Novel coronavirus infection—update.http://www.who.int/csr/don/20-June-2015-mers-saudi-arabia/en/. 10.↵ Hui DS, Perlman S, Zumla A. 2015. Spread of MERS to South Korea and China. Lancet Respir Med 3:509–510. 10.1016/S2213-2600(15)00238-6.CrossRef11.↵ Assiri A, Al-Tawfiq JA, Al-Rabeeah AA, Al-Rabiah FA, Al-Hajjar S,Al-Barrak A, Flemban H, Al-Nassir WN, Balkhy HH, Al-Hakeem RF,Makhdoom HQ, Zumla AI, Memish ZA. 2013. Epidemiological, demographic, and clinical characteristics of 47 cases of Middle East respiratory syndrome coronavirus disease from Saudi Arabia: a descriptive study. Lancet Infect Dis13:752–761. 10.1016/S1473-3099(13)70204-4. CrossRefMedline12.↵ Corman V, Eckerle I, Bleicker T, Zaki A, Landt O,Eschbach-Bludau M, Van Boheemen S, Gopal R, Ballhause M,Bestebroer TM, Muth TD, Müller MA, Drexler JF, Zambon M,Osterhaus AD, Fouchier RM, Drosten C. 2012. Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction. Euro Surveillance 17(39):pii=20285.http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=20285. 13.↵ Banik G, Khandaker G, Rashid H. 2015. Middle East respiratory syndrome coronavirus “MERS-CoV”: current knowledge gaps. Paediatr Respir Rev16:197–202. 10.1016/j.prrv.2015.04.002. CrossRefMedline14.↵ Zumla A, Perlman S, McNabb SJ, Shaikh A, Heymann DL,McCloskey B, Hui DS. 2015. Middle East respiratory syndrome in the shadow of Ebola. Lancet Respir Med 3:100–102. 10.1016/S2213-2600(14)70316-9.CrossRefMedline15.↵ Hemida MG, Al-Naeem A, Perera RA, Chin AW, Poon LL, Peiris M.2015. Lack of Middle East respiratory syndrome coronavirus transmission from infected camels. Emerg Infect Dis 21:699–701. 10.3201/eid2104.141949.CrossRef16.↵ Edelstein M, Heymann DL. 2015. What needs to be done to control the spread of Middle East respiratory syndrome coronavirus? Future Virol10:497–505. 10.2217/fvl.15.20. CrossRef17.↵ Yount B, Roberts RS, Lindesmith L, Baric RS. 2006. Rewiring the severe acute respiratory syndrome coronavirus (SARS-CoV) transcription circuit: engineering a recombination-resistant genome. Proc Natl Acad Sci U S A103:12546–12551. 10.1073/pnas.0605438103. Abstract/FREE Full Text18.↵ Gorbalenya AE, Snijder EJ, Spaan WJ. 2004. Severe acute respiratory syndrome coronavirus phylogeny: toward consensus. J Virol 78:7863–7866.10.1128/JVI.78.15.7863-7866.2004. FREE Full Text19.↵ Dudas G, Rambaut A. 2015. MERS-CoV recombination: implications about the reservoir and potential for adaptation. bioRxiv 10.1101/020834.Abstract/FREE Full Text20.↵ Stamatakis A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313.10.1093/bioinformatics/btu033. Abstract/FREE Full Text21.↵ Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 29:1969–1973.10.1093/molbev/mss075. Abstract/FREE Full Text22.↵ Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS,Novak NG, Ingersoll R, Sheppard HW, Ray SC. 1999. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol 73:152–160.Abstract/FREE Full Text
  9. niman
    MATERIALS AND METHODSFull-length genomic sequencing.Nasopharyngeal swabs from the South Korean patient diagnosed with MERS-CoV infection were collected and used for viral RNA extraction with the QIAamp viral RNA minikit. Forty-four sets of specific primer pairs were designed and used to amplify the complete genome, followed by Sanger sequencing; meanwhile, the extracted viral RNA was also used for next-generation sequencing with the Ion Torrent PGM after random amplification. Phylogenetic analysis.We downloaded all (n = 92) available full-length genome sequences of MERS-CoV from GenBank and used RAxML (20) for phylogenetic analyses of the complete genome, the ORF1ab gene, and the S gene, respectively. One thousand bootstrap replicates were run. Furthermore, the Bayesian Markov chain Monte Carlo method, implemented in BEAST (21), was used to estimate the time to the most recent common ancestor. Twelve different model combinations were applied. For all the analyses, we used the general time-reversible nucleotide substitution model with gamma-distributed rate heterogeneity. Bayesian Markov chain Monte Carlo analysis was run for 50 million steps. Trees and parameters were sampled every 5,000 steps, with the first 10% removed as burn-in. Genetic recombinant analysis.Similarity plots and bootscanning analysis were generated by SimPlot (22); a sliding window of 200 nucleotides was used, moving in 20-nucleotide steps. Single-nucleotide-difference analysis was used to confirm the recombination event. Nucleotide sequence accession number.The full-length virus genome (30,144 bp) of ChinaGD01 was deposited in GenBank under accession no. KT006149. Previous SectionNext SectionSUPPLEMENTAL MATERIALFIGURE S1 Substitutions in the ORF1ab genes from all available MERS-CoV genomes. Different groups are separated by lines; only positions with substitutions are shown. Different types of substitutions are indicated using different colors, as follows: blue for synonymous, claret red for nonsynonymous, and green for untranslated region. Download Figure S1, PDF file, 0.5 MB. FIGURE S2 Substitutions in the indicated genes from all available MERS-CoV genomes. Different groups are separated by lines; only positions with substitutions are shown. Different types of substitutions are indicated using different colors, as follows: blue for synonymous, claret red for nonsynonymous, and green for untranslated region. Download Figure S2, PDF file, 0.4 MB. Previous SectionNext SectionACKNOWLEDGMENTSThis work was supported by funds from the Ministry of Science and Technology of China (2011CB504704), the National Health and Family Planning Commission of China (grants 2014ZX10004-001 and 2013ZX10004601), and National Natural Science Foundation of China (NSFC; grants 81100062 and 81321063). G.F.G. is a leading principal investigator of the NSFC Innovative Research Group (81321063). We thank the clinical staff in Huizhou Central Hospital in Guangdong Province for providing the information and nasopharyngeal swab samples from this imported case.
  10. niman
    DISCUSSIONOver the past 3 years, MERS-CoV infections have continued to increase, posing a serious threat to global public health. Previous studies have revealed that MERS-CoV infections are likely due to repeated introductions of MERS-CoV from dromedary camels to humans (13–15), resulting in only limited human-to-human transmission (16). However, the large number of second- and third-generation cases in South Korea raised concerns that MERS-CoV may have evolved to become more adapted to human-to-human transmission. Our results indicate that at the whole-genome level, ChinaGD01 is >99% similar to the previously identified MERS-CoV strains. Phylogenetic analysis based on the whole-genome sequence revealed that it belongs to group 3 of clade B MERS-CoV strains and forms a separate small branch with viruses from South Korea and Saudi Arabia from 2015. Different phylogenies were observed in the trees constructed using the full-length genome and the S gene, indicating the possibility of a recombination event. Further evidence of a recombination event was obtained through bootscanning and SNP analyses. BEAST analysis revealed that it might have occurred recently, in the second half of 2014, in the Middle East. Genetic recombination has been well established in severe acute respiratory syndrome coronavirus (SARS-CoV) (17, 18); however, there is only one report of genetic recombination in MERS-CoV (19). Dudas and Rambaut point to frequent recombination in MERS-CoV and partition the genome into two parts in which nucleotides 1 to 23,722 and nucleotides 23,723 to 30,126 have independent molecular clock rates. Based on the latest genome sequences from South Korea and the Kingdom of Saudi Arabia, our research indicated that a novel type of genetic recombination has occurred in the MERS-CoV strains prevalent in South Korea. We note that six MERS-CoV isolates from 2015 (ChinaGD01, the first MERS-CoV strain from South Korea, and the four latest strains from Saudi Arabia) had high levels of nucleotide identity (99.90% to 99.96%) and showed the same recombination signal in our analyses. We speculate that they arose from a common recombination event. However, more studies are needed to understand the relationship between genetic recombination of MERS-CoV, the biological properties it conveys, and its relevance to the recent high rate of transmission.
  11. niman
    RESULTSPatient and sample history.The current outbreak in South Korea and China was initiated when a 68-year-old Korean man flew back to Seoul on 4 May 2015 after a visit to four Middle East countries (Bahrain, United Arab Emirates, Saudi Arabia, and Qatar). On 26 May 2015, a 44-year-old South Korean man presented with fever to a hospital in Guangdong. He was in close contact with the index patient in South Korea on 16 May 2015 (Fig. 1), as well as a suspected second-generation patient. The timeline of the travel history, potential virus exposure, onset of disease, and diagnosis of the first imported MERS-CoV case in China are presented in Fig. 1. View larger version:In this page In a new windowDownload as PowerPoint SlideFIG 1 Timeline of the travel history, potential virus exposure, onset of disease, and diagnosis of the first imported MERS-CoV case in China. UAE, United Arab Emirates; KSA, Kingdom of Saudi Arabia. Characterization of genome.With informed consent and the approval of the ethical committee of the National Institute of Viral Disease Control and Prevention, China Center for Disease Control and Prevention (CDC), nasopharyngeal swabs were collected and used for RNA extraction, followed by reverse transcription PCR and genome sequencing. Through both Sanger and Ion Torrent sequencing, the full-length virus genome (30,144 bp) of ChinaGD01 was obtained and deposited in GenBank (accession no. KT006149). Over 2,000,000 paired-end reads were quality trimmed and processed to remove human genome sequences. Nonhuman reads were assembled into contigs by CLC Genomic Workbench and aligned against representative sequences of MERS-CoV. No nucleotide insertions or deletions were observed in the genome. The genome sequence of this virus, referred to as ChinaGD01, had high levels of nucleotide identity (99.33% to 99.79%) to previously published MERS-CoV genomes (Fig. 2), with 99.31% to 99.78% sequence identity in the open reading frame 1a and -b (ORF1ab) gene segment and 98.91% to 99.60% identity in the S gene. The E, M, and N genes had 98.93% to 100% identity with previously described MERS-CoV strains. In total, ChinaGD01 possessed 11 nonsynonymous nucleotide substitutions (Table 1), which occurred in the ORF1ab (n = 8), ORF3 (n = 1), ORF4b (n = 1), and M (n = 1) genes, respectively (Table 1). Although there were five nucleotide substitutions in the S gene, no amino acid change was discovered. Of note, in comparison with previously published MERS-CoV genomes, the ChinaGD01 genome shows 11 unique amino acid substitutions, and 8 of them were shared with the newly released South Korean strains and the latest strains prevalent in Saudi Arabia (Table 1). View larger version:In this page In a new windowDownload as PowerPoint SlideFIG 2 Phylogenetic relationships based on complete genomes (A), ORF1ab genes (B), and S genes (C) of MERS-CoV strains. China’s first imported MERS-CoV strain (GenBank accession no. KT006149.2), South Korea’s first MERS-CoV strain (GenBank accession no.KT029139), and the latest MERS-CoV strains prevalent in the Middle East (GenBank accession no. KT026453 to KT026456) are indicated in red. The MERS-CoV strains derived from camels are indicated in blue. All of the complete genomes were analyzed by nucleotide sequence alignment using the maximum-likelihood method implemented in the RAxML. Numbers at the nodes indicate bootstrap support for each node (percentage of 1,000 bootstrap replicates). Scale bars indicate the expected number of nucleotide substitutions per site. View this table:In this window In a new windowTABLE 1 Comparison of sites of variation between gene sequences of ChinaGD01, the first South Korean strain, the latest Saudi Arabia strains, and other MERS-CoV strainsa Phylogenetic analysis.To further investigate the genetic relationship between ChinaGD01 and other MERS-CoV strains whose genomes are available, we performed phylogenetic analyses using the complete genome, the ORF1ab gene, and the S gene. From the whole-genome phylogeny, all available MERS-CoV strains can be clustered into two clades, the earlier clade A and the more recent clade B (Fig. 2A). ChinaGD01 fell into group 3 of clade B (Fig. 2A). Within group 3, ChinaGD01 and the South Korean and Saudi Arabian strains from 2015 were closely clustered and formed a long branch, separate from others of group 3. The nearest strain to this branch was Hafr-Al-Batin-1-2013 (GenBank accession no.KF600628), isolated in August 2013. Phylogenetic analysis of the ORF1ab gene indicated a similar topology in which ChinaGD01 and the recent MERS-CoV strains identified in South Korea were closely adjacent to Hafr-Al-Batin-1-2013 in group 3 (Fig. 2B). However, the phylogeny of the S gene differed in that the new viruses fell into group 5 and were closely related to viruses from both humans and dromedaries (Fig. 2C). These findings are consistent with recombination, a phenomenon not uncommon in coronaviruses. Genetic recombination analysis.To examine whether genetic recombination has occurred in ChinaGD01, we performed bootscanning analyses. We compared ChinaGD01 with representative viruses from group 3 (Hafr-Al-Batin-1-2013; GenBank accession no. KF600628), group 5 (KSA-CAMEL-378; GenBank accession no. KJ713296), and group 1 (Abu Dhabi_UAE_9_2013; GenBank accession no.KP209312) as controls. As shown in Fig. 3A, ChinaGD01 was more similar to the group 3 strain from position 1 to 15,000 and more similar to the group 5 strain from approximately position 18,000 to 24,000. We then compared the single-nucleotide polymorphisms (SNPs) of ChinaGD01 with consensus sequences of group 3 and group 5 (Fig. 3B; see also Fig. S1 and S2 in the supplemental material). There were 78 SNPs discovered along the ChinaGD01 genome (Fig. 3B). Whereas before position 17,206, ChinaGD01’s SNP pattern is nearly identical to that of the group 3 viruses, its SNP pattern is more similar to that of group 5 viruses between positions 17,311 and 23,804. The consistency in the results of bootscanning and SNP analyses supports the hypothesis that the gene segment from approximately position 17,300 to 24,000, representing portions of the ORF1ab and S genes, reflects a recombination event (Fig. 3B). View larger version:In this page In a new windowDownload as PowerPoint SlideFIG 3 Recombination analyses of complete MERS-CoV genomes. (A) Bootscanning analysis of MERS-CoV genome. The ChinaGD01 strain was used as a query sequence and compared with one strain from group 3 (GenBank accession no.KF600628.1), one from group 5 (GenBank accession no.KJ713296.1), and one from group 1 (GenBank accession no.KP209312.1). (B) Single-nucleotide differences between the ChinaGD01 sequence and consensus sequences of group 3 and group 5. Group 3 cons, consensus sequences of group 3 strains; group 5 cons, consensus sequences of group 5 strains; South Korea, first MERS-CoV strain (GenBank accession no. KT029139) in South Korea; KSA-2015, latest strains prevalent in Saudi Arabia (GenBank accession no. KT026453 to KT026456), Bisha-1/2012, an earlier strain used as a control. Phylogenetic analysis was further performed using BEAST with the complete genome, the nonrecombinant region (positions 1 to 17,300), and the potential recombinant region (positions 17,301 to 24,000), respectively (Fig. 4). The phylogenies revealed by the BEAST trees were consistent with those from the maximum-likelihood trees. In the trees constructed using the complete genome and the nonrecombinant region, ChinaGD01 fell within group 3; however, trees constructed using the recombinant region clustered with the group 5 sequences. View larger version:In this page In a new windowDownload as PowerPoint SlideFIG 4 Time-resolved phylogenetic analyses of complete genomes (A), nonrecombination regions (B), and recombination regions (C) of MERS-CoV strains using BEAST. The nonrecombination region is approximately bp 1 to 17,300, and the recombination region is approximately bp 17,301 to 24,000. ChinaGD01 (GenBank accession no. KT006149), South Korea’s first MERS-CoV strain (GenBank accession no. KT029139), and the latest strains prevalent in Saudi Arabia (GenBank accession no. KT026453 toKT026456) are indicated in red. To date the recombination event, we estimated the time to most recent common ancestor for the novel MERS-CoV from 2015. Although there was a slight difference among results from different models, the time to most recent common ancestor of the 2015 cluster was estimated to be between 0.5 and 0.7 years before the identification of the imported case in the latter months of 2014 (Table 2). Given the observation of similar recombination events in the newly released South Korean strains and the latest strains prevalent in Saudi Arabia, the travel histories of patients, and potential opportunities for virus exposure, we surmise that the recombination likely occurred in the Arabian Peninsula. View this table:In this window In a new windowTABLE 2 Estimated times in years to most recent common ancestor of the 2015 cluster
  12. niman
    INTRODUCTIONMiddle East respiratory syndrome coronavirus (MERS-CoV), first detected in the Kingdom of Saudi Arabia (KSA) in 2012, causes severe acute respiratory tract infection in humans, with a high case fatality rate (CFR) (1–4). Dromedary camels are believed to be important reservoir hosts or vectors for human infection; bats may also be implicated (5–8). As of 17 July 2015, 1,368 laboratory-confirmed cases of human infection with MERS-CoV had been reported to the World Health Organization (WHO), including at least 490 deaths, corresponding to a CFR as high as 35.45% (9). Recent MERS clusters in South Korea are thought to be the largest outbreak outside the Middle East countries (10). As of 25 July 2015, 186 laboratory-confirmed cases of MERS-CoV infection have been confirmed (including 36 deaths) in South Korea (9). A South Korean man who was a relative of some of the laboratory-confirmed cases traveled to Guangdong Province (10) and was diagnosed as the first imported MERS-CoV case in China by molecular detection of MERS-CoV (11, 12). The rapid spread of disease in South Korea raised concerns that the imported virus had evolved to become more transmissible. Here, we report a comprehensive phylogenetic analysis of the complete MERS-CoV genome sequence of the first Chinese imported case of MERS (ChinaGD01), and the results indicate its probable origin and show evidence of genetic recombination.
  13. niman
    IMPORTANCEThe recent outbreak of MERS-CoV in South Korea has attracted global media attention due to the speed of spread and onward transmission. Here, we present the complete genome of the first imported MERS-CoV case in China and demonstrate genetic recombination events between group 3 and group 5 of clade B that may have implications for the transmissibility of MERS-CoV.
  14. niman
    ABSTRACTThe Middle East respiratory syndrome coronavirus (MERS-CoV) causes a severe acute respiratory tract infection with a high fatality rate in humans. Coronaviruses are capable of infecting multiple species and can evolve rapidly through recombination events. Here, we report the complete genomic sequence analysis of a MERS-CoV strain imported to China from South Korea. The imported virus, provisionally named ChinaGD01, belongs to group 3 in clade B in the whole-genome phylogenetic tree and also has a similar tree topology structure in the open reading frame 1a and -b (ORF1ab) gene segment but clusters with group 5 of clade B in the tree constructed using the S gene. Genetic recombination analysis and lineage-specific single-nucleotide polymorphism (SNP) comparison suggest that the imported virus is a recombinant comprising group 3 and group 5 elements. The time-resolved phylogenetic estimation indicates that the recombination event likely occurred in the second half of 2014. Genetic recombination events between group 3 and group 5 of clade B may have implications for the transmissibility of the virus.
  15. niman
    Origin and Possible Genetic Recombination of the Middle East Respiratory Syndrome Coronavirus from the First Imported Case in China: Phylogenetics and Coalescence AnalysisYanqun Wanga, Di Liub,c, Weifeng Shid, Roujian Lua, Wenling Wanga,Yanjie Zhaoa, Yao Denga, Weimin Zhoua, Hongguang Rene, Jun Wub, Yu Wangf,Guizhen Wua, George F. Gaoa,b,f, Wenjie Tana+Author Affiliations aKey Laboratory of Medical Virology, Ministry of Health, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, ChinabCAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, ChinacNetwork Information Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, ChinadInstitute of Pathogen Biology, Taishan Medical College, Taian, ChinaeState Key Laboratory of Pathogen and Biosecurity, Beijing, ChinafOffice of Director-General, Chinese Center for Disease Control and Prevention, Beijing, ChinaAddress correspondence to George F. Gao, [email protected], or Wenjie Tan,[email protected] Wang, Di Liu, Weifeng Shi, and Roujian Lu contributed equally to this work. Editor Michael J. Buchmeier, University of California, Irvine http://mbio.asm.org/content/6/5/e01280-15 FOOTNOTESCitation Wang Y, Liu D, Shi W, Lu R, Wang W, Zhao Y, Deng Y, Zhou W, Ren H, Wu J, Wang Y, Wu G, Gao GF, Tan W. 2015. Origin and possible genetic recombination of the Middle East respiratory syndrome coronavirus from the first imported case in China: phylogenetics and coalescence analysis. mBio 6(5):e01280-15. doi:10.1128/mBio.01280-15. This article is a direct contribution from a Fellow of the American Academy of Microbiology. Received 28 July 2015 Accepted 30 July 2015 Published 8 September 2015Copyright © 2015 Wang et al.
  16. niman
    DescriptionsAlignSegment-IDNameScoreE-ValueIdentityEPI643070A/Indonesia/NIHRD/15023/2015 (A/H5N1) segment 6 (NA)2494.10.000000e+001350/1350 (100%)EPI643071A/Indonesia/NIHRD15028/2015 (A/H5N1) segment 6 (NA)2422.10.000000e+001338/1351 (99%)EPI492525A/Indonesia/NIHRD13233/2013 (A/H5N1) segment 6 (NA)2388.80.000000e+001331/1350 (98%)EPI509938A/Indonesia/NIHRD13269/2013 (A/H5N1) segment 6 (NA)2377.80.000000e+001329/1350 (98%)EPI442758A/Indonesia/NIHRD12162/2012 (A/H5N1) segment 6 (NA)2327.90.000000e+001320/1350 (97%)EPI487551A/Indonesia/NIHRD11046/2011 (A/H5N1) segment 6 (NA)2228.20.000000e+001303/1351 (96%)EPI340809A/chicken/Lampung/BPPVRIII-10-161/2010 (A/H5N1) segment 6 (NA)2222.60.000000e+001300/1348 (96%)EPI340789A/bird/Gunung Kidul/BBVW-52-I/2010 (A/H5N1) segment 6 (NA)2222.60.000000e+001299/1347 (96%)EPI487456A/Indonesia/NIHRD10728/2010 (A/H5N1) segment 6 (NA)2217.10.000000e+001301/1351 (96%)EPI487527A/Indonesia/NIHRD10459/2010 (A/H5N1) segment 6 (NA)2211.60.000000e+001300/1351 (96%)EPI356475A/Indonesia/NIHRD11949/2012 (A/H5N1) segment 6 (NA)2189.40.000000e+001295/1350 (95%)EPI356473A/Indonesia/NIHRD11931/2012 (A/H5N1) segment 6 (NA)2189.40.000000e+001295/1350 (95%)EPI486489A/Indonesia/NIHRD9340/2009 (A/H5N1) segment 6 (NA)2128.50.000000e+001284/1350 (95%)EPI463649A/Indonesia/NIHRD13157/2013 (A/H5N1) segment 6 (NA)2128.50.000000e+001285/1351 (95%)EPI340777A/chicken/Temanggung/BBVW-1203d-VIII/2009 (A/H5N1) segment 6 (NA)2128.50.000000e+001282/1347 (95%)EPI340775A/chicken/Temanggung/BBVW-1203b-VIII/2009 (A/H5N1) segment 6 (NA)2128.50.000000e+001282/1347 (95%)EPI164210A/Indonesia/8228/2008 (A/H5N1) segment 6 (NA)2126.60.000000e+001273/1334 (95%)EPI340773A/chicken/Tasikmalaya/BBVW-991-VI/2009 (A/H5N1) segment 6 (NA)2122.90.000000e+001281/1347 (95%)EPI340767A/chicken/Kuningan/BBVW-1004-VI/2009 (A/H5N1) segment 6 (NA)2111.80.000000e+001279/1347 (94%)EPI49168A/Indonesia/CDC938E/2006 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1352 (94%)EPI49149A/Indonesia/CDC938/2006 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1352 (94%)EPI531960A/Indonesia/NIHRD14122/2014 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1352 (94%)EPI55647A/Indonesia/CDC1031RE2/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1352 (94%)EPI55628A/Indonesia/CDC1031T2/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1352 (94%)EPI55609A/Indonesia/CDC1031T/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1352 (94%)EPI55590A/Indonesia/CDC1031/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1352 (94%)EPI49268A/Indonesia/CDC887/2006 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1352 (94%)EPI55704A/Indonesia/CDC1032T/2007 (A/H5N1) segment 6 (NA)2095.20.000000e+001280/1352 (94%)EPI55685A/Indonesia/CDC1032N/2007 (A/H5N1) segment 6 (NA)2095.20.000000e+001280/1352 (94%)EPI55666A/Indonesia/CDC1032/2007 (A/H5N1) segment 6 (NA)2095.20.000000e+001280/1352 (94%)EPI164765A/Indonesia/7272/2008 (A/H5N1) segment 6 (NA)2093.40.000000e+001269/1336 (94%)EPI163112A/Indonesia/7261/2008 (A/H5N1) segment 6 (NA)2087.80.000000e+001268/1336 (94%)EPI443392A/chicken/West Java Tangerang/PTB6/2008 (A/H5N1) segment 6 (NA)2084.10.000000e+001276/1349 (94%)EPI443362A/chicken/Siantar/BPPVRI-231-2/2008 (A/H5N1) segment 6 (NA)2084.10.000000e+001276/1349 (94%)EPI443361A/chicken/Siantar/BPPVRI-231-1/2008 (A/H5N1) segment 6 (NA)2084.10.000000e+001276/1349 (94%)EPI443316A/chicken/Ponorogo/BBVW-197b/2007 (A/H5N1) segment 6 (NA)2084.10.000000e+001277/1350 (94%)EPI340765A/chicken/Kudus/BBVW-1186-IX/2009 (A/H5N1) segment 6 (NA)2084.10.000000e+001274/1347 (94%)EPI41557A/Indonesia/CDC523T/2006 (A/H5N1) segment 6 (NA)2084.10.000000e+001280/1354 (94%)EPI41538A/Indonesia/CDC523E/2006 (A/H5N1) segment 6 (NA)2084.10.000000e+001280/1354 (94%)EPI41403A/Indonesia/CDC523/2006 (A/H5N1) segment 6 (NA)2084.10.000000e+001280/1354 (94%)EPI443404A/pigeon/Bukittinggi/BPPVRII-178-B/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443389A/chicken/Agam/BPPVRII-694/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443382A/chicken/Pariaman/BPPVRII-370/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443373A/chicken/Batam/BPPVRII-188/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443372A/duck/Padang/BPPVRII-151/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443371A/swan/Bukittinggi/BPPVRII-178-S/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443370A/Muscovy duck/Bukittinggi/BPPVRII-178-M/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443369A/chicken/Padang/BPPVRII-151/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443368A/chicken/Bukittinggi/BPPVRII-178-C/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443365A/chicken/Medan/BPPVRI-15/2008 (A/H5N1) segment 6 (NA)2078.60.000000e+001275/1349 (94%)EPI443357A/chicken/Taput/BPPVRI-235/2007 (A/H5N1) segment 6 (NA)2078.60.000000e+001275/1349 (94%)EPI443376A/duck/Kerinci/BPPVRII-262-D/2007 (A/H5N1) segment 6 (NA)2073.10.000000e+001275/1350 (94%)EPI443375A/chicken/Kerinci/BPPVRII-262-C/2007 (A/H5N1) segment 6 (NA)2073.10.000000e+001275/1350 (94%)EPI443374A/chicken/Solok Selatan/BPPVRII-217/2007 (A/H5N1) segment 6 (NA)2073.10.000000e+001275/1350 (94%)EPI443367A/chicken/Pesisir Selatan/BPPVRII-119/2007 (A/H5N1) segment 6 (NA)2073.10.000000e+001275/1350 (94%)EPI443352A/chicken/Tanjung Balai/BPPVRI-97/2007 (A/H5N1) segment 6 (NA)2073.10.000000e+001274/1349 (94%)EPI443351A/chicken/Simalungun/BPPVRI-391/2007 (A/H5N1) segment 6 (NA)2073.10.000000e+001274/1349 (94%)EPI340781A/chicken/Sleman/BBVW-180-III/2010 (A/H5N1) segment 6 (NA)2073.10.000000e+001275/1350 (94%)EPI41851A/Indonesia/CDC699/2006 (A/H5N1) segment 6 (NA)2073.10.000000e+001278/1354 (94%)EPI123850A/Pigeon/Indonesia/Rohkit1631-6/2006 (A/H5N1) segment 6 (NA)2069.40.000000e+001267/1339 (94%)EPI123848A/Chicken/Indonesia/Agam1631-3/2006 (A/H5N1) segment 6 (NA)2069.40.000000e+001267/1339 (94%)EPI123844A/Chicken/Indonesia/Padang1631-1/2006 (A/H5N1) segment 6 (NA)2069.40.000000e+001267/1339 (94%)EPI443378A/chicken/Sawahlunto/BPPVRII-273/2007 (A/H5N1) segment 6 (NA)2067.50.000000e+001274/1350 (94%)EPI443358A/chicken/Karo/BPPVRI-320/2007 (A/H5N1) segment 6 (NA)2067.50.000000e+001273/1349 (94%)EPI342499A/Indonesia/NIHRD11771/2011(H5N1) (A/H5N1) segment 6 (NA)2067.50.000000e+001275/1352 (94%)EPI123846A/Chicken/Indonesia/Siak1631-2/2006 (A/H5N1) segment 6 (NA)2067.50.000000e+001266/1338 (94%)EPI49244A/Indonesia/CDC836T/2006 (A/H5N1) segment 6 (NA)2067.50.000000e+001277/1354 (94%)EPI49225A/Indonesia/CDC836/2006 (A/H5N1) segment 6 (NA)2067.50.000000e+001277/1354 (94%)EPI41576A/Indonesia/CDC582/2006 (A/H5N1) segment 6 (NA)2067.50.000000e+001277/1354 (94%)EPI342500A/Indonesia/NIHRD11767/2011(H5N1) (A/H5N1) segment 6 (NA)2063.80.000000e+001274/1352 (94%)EPI123852A/Chicken/Indonesia/Pekenbaru1631-11/2006 (A/H5N1) segment 6 (NA)2063.80.000000e+001266/1339 (94%)EPI443384A/chicken/Bengkalis/BPPVRII-532/2007 (A/H5N1) segment 6 (NA)2062.00.000000e+001273/1350 (94%)EPI443379A/chicken/Payakumbuh/BPPVRII-307/2007 (A/H5N1) segment 6 (NA)2062.00.000000e+001273/1350 (94%)EPI443306A/chicken/West Java/Drd-20/2007 (A/H5N1) segment 6 (NA)2062.00.000000e+001274/1351 (94%)EPI124480A/Indonesia/567H/2006 (A/H5N1) segment 6 (NA)2062.00.000000e+001277/1355 (94%)EPI124276A/Indonesia/292H/2006 (A/H5N1) segment 6 (NA)2062.00.000000e+001276/1354 (94%)EPI55780A/Indonesia/CDC1047S/2007 (A/H5N1) segment 6 (NA)2062.00.000000e+001276/1354 (94%)EPI55761A/Indonesia/CDC1047/2007 (A/H5N1) segment 6 (NA)2062.00.000000e+001276/1354 (94%)EPI55742A/Indonesia/CDC1046T/2007 (A/H5N1) segment 6 (NA)2062.00.000000e+001276/1354 (94%)EPI55723A/Indonesia/CDC1046/2007 (A/H5N1) segment 6 (NA)2062.00.000000e+001276/1354 (94%)EPI41919A/Indonesia/CDC739/2006 (A/H5N1) segment 6 (NA)2062.00.000000e+001276/1354 (94%)EPI41883A/Indonesia/CDC644/2006 (A/H5N1) segment 6 (NA)2062.00.000000e+001277/1355 (94%)EPI41864A/Indonesia/CDC644T/2006 (A/H5N1) segment 6 (NA)2062.00.000000e+001277/1355 (94%)EPI41832A/Indonesia/CDC669P/2006 (A/H5N1) segment 6 (NA)2062.00.000000e+001276/1354 (94%)EPI41813A/Indonesia/CDC669/2006 (A/H5N1) segment 6 (NA)2062.00.000000e+001276/1354 (94%)EPI356567A/Muscovy duck/West Java/Bks3/2007 (A/H5N1) segment 6 (NA)2060.10.000000e+001255/1324 (94%)EPI443387A/chicken/Siak/BPPVRII-635/2007 (A/H5N1) segment 6 (NA)2056.40.000000e+001271/1349 (94%)EPI443385A/chicken/Kuantan Singingi/BPPVRII-620/2007 (A/H5N1) segment 6 (NA)2056.40.000000e+001271/1349 (94%)EPI443381A/chicken/Tanah Datar/BPPVRII-365/2007 (A/H5N1) segment 6 (NA)2056.40.000000e+001272/1350 (94%)EPI443377A/chicken/Padang Panjang/BPPVRII-272/2007 (A/H5N1) segment 6 (NA)2056.40.000000e+001271/1349 (94%)EPI443359A/chicken/Aceh Barat/BPPVRI-327/2007 (A/H5N1) segment 6 (NA)2056.40.000000e+001271/1349 (94%)EPI124426A/Indonesia/542H/2006 (A/H5N1) segment 6 (NA)2056.40.000000e+001275/1354 (94%)EPI124219A/Indonesia/286H/2006 (A/H5N1) segment 6 (NA)2056.40.000000e+001275/1354 (94%)EPI41952A/Indonesia/CDC759/2006 (A/H5N1) segment 6 (NA)2056.40.000000e+001276/1355 (94%)EPI41756A/Indonesia/CDC634T/2006 (A/H5N1) segment 6 (NA)2056.40.000000e+001277/1356 (94%)EPI41737A/Indonesia/CDC634P/2006 (A/H5N1) segment 6 (NA)2056.40.000000e+001277/1356 (94%)EPI41718A/Indonesia/CDC634/2006 (A/H5N1) segment 6 (NA)2056.40.000000e+001277/1356 (94%)EPI620902A/chicken/WestJava/SMI-PAT/2006 (A/H5N1) segment 6 (NA)2050.90.000000e+001274/1354 (94%)EPI443364A/chicken/Deli Serdang/BPPVRI-238-2/2008 (A/H5N1) segment 6 (NA)2050.90.000000e+001270/1349 (94%)EPI443363A/chicken/Deli Serdang/BPPVRI-238-1/2008 (A/H5N1) segment 6 (NA)2050.90.000000e+001270/1349 (94%)
  17. niman
    AlignSegment-IDNameScoreE-ValueIdentityEPI643072A/Indonesia/NIHRD15028/2015 (A/H5N1) segment 4 (HA)3153.40.000000e+001707/1707 (100%)EPI643069A/Indonesia/NIHRD/15023/2015 (A/H5N1) segment 4 (HA)3153.40.000000e+001707/1707 (100%)EPI492524A/Indonesia/NIHRD13233/2013 (A/H5N1) segment 4 (HA)3053.60.000000e+001689/1707 (98%)EPI547699A/Indonesia/NIHRD14157/2014 (A/H5N1) segment 4 (HA)3037.00.000000e+001686/1707 (98%)EPI509937A/Indonesia/NIHRD13269/2013 (A/H5N1) segment 4 (HA)3025.90.000000e+001684/1707 (98%)EPI537677A/Environment/West Java/Bksi34/2013 (A/H5N1) segment 4 (HA)2953.90.000000e+001671/1707 (97%)EPI442757A/Indonesia/NIHRD12162/2012 (A/H5N1) segment 4 (HA)2915.10.000000e+001664/1707 (97%)EPI340810A/chicken/Lampung/BPPVRIII-10-161/2010 (A/H5N1) segment 4 (HA)2887.40.000000e+001659/1707 (97%)EPI324340A/chicken/Indonesia/D10014/2010 (A/H5N1) segment 4 (HA)2881.90.000000e+001658/1707 (97%)EPI487549A/Indonesia/NIHRD11046/2011 (A/H5N1) segment 4 (HA)2865.30.000000e+001655/1707 (96%)EPI356474A/Indonesia/NIHRD11949/2012 (A/H5N1) segment 4 (HA)2865.30.000000e+001655/1707 (96%)EPI356472A/Indonesia/NIHRD11931/2012 (A/H5N1) segment 4 (HA)2865.30.000000e+001655/1707 (96%)EPI340790A/bird/Gunung Kidul/BBVW-52-I/2010 (A/H5N1) segment 4 (HA)2865.30.000000e+001655/1707 (96%)EPI487467A/Indonesia/NIHRD10623/2010 (A/H5N1) segment 4 (HA)2854.20.000000e+001653/1707 (96%)EPI487454A/Indonesia/NIHRD10728/2010 (A/H5N1) segment 4 (HA)2854.20.000000e+001654/1708 (96%)EPI487461A/Indonesia/NIHRD10364/2010 (A/H5N1) segment 4 (HA)2843.10.000000e+001651/1707 (96%)EPI487525A/Indonesia/NIHRD10459/2010 (A/H5N1) segment 4 (HA)2837.60.000000e+001651/1708 (96%)EPI341332A/Indonesia/NIHRD11073/2011(H5N1) (A/H5N1) segment 4 (HA)2832.00.000000e+001650/1708 (96%)EPI340778A/chicken/Temanggung/BBVW-1203d-VIII/2009 (A/H5N1) segment 4 (HA)2815.40.000000e+001646/1707 (96%)EPI340776A/chicken/Temanggung/BBVW-1203b-VIII/2009 (A/H5N1) segment 4 (HA)2815.40.000000e+001646/1707 (96%)EPI164208A/Indonesia/8228/2008 (A/H5N1) segment 4 (HA)2809.90.000000e+001645/1707 (96%)EPI486487A/Indonesia/NIHRD9340/2009 (A/H5N1) segment 4 (HA)2782.20.000000e+001641/1708 (96%)EPI162940A/Indonesia/7261/2008 (A/H5N1) segment 4 (HA)2782.20.000000e+001640/1707 (96%)EPI340774A/chicken/Tasikmalaya/BBVW-991-VI/2009 (A/H5N1) segment 4 (HA)2760.00.000000e+001637/1708 (95%)EPI340768A/chicken/Kuningan/BBVW-1004-VI/2009 (A/H5N1) segment 4 (HA)2748.90.000000e+001635/1708 (95%)EPI307911A/chicken/Indonesia/SmiWN18/2009 (A/H5N1) segment 4 (HA)2747.10.000000e+001588/1638 (96%)EPI164763A/Indonesia/7272/2008 (A/H5N1) segment 4 (HA)2739.70.000000e+001627/1699 (95%)EPI55643A/Indonesia/CDC1031RE2/2007 (A/H5N1) segment 4 (HA)2737.90.000000e+001632/1707 (95%)EPI49264A/Indonesia/CDC887/2006 (A/H5N1) segment 4 (HA)2737.90.000000e+001632/1707 (95%)EPI356512A/chicken/Banten/Srg-Fadh/2008 (A/H5N1) segment 4 (HA)2732.30.000000e+001629/1704 (95%)EPI340766A/chicken/Kudus/BBVW-1186-IX/2009 (A/H5N1) segment 4 (HA)2732.30.000000e+001633/1709 (95%)EPI340782A/chicken/Sleman/BBVW-180-III/2010 (A/H5N1) segment 4 (HA)2726.80.000000e+001632/1709 (95%)EPI49164A/Indonesia/CDC938E/2006 (A/H5N1) segment 4 (HA)2726.80.000000e+001630/1707 (95%)EPI49145A/Indonesia/CDC938/2006 (A/H5N1) segment 4 (HA)2726.80.000000e+001630/1707 (95%)EPI324615A/tree sparrow/Indonesia/D10013/2010 (A/H5N1) segment 4 (HA)2721.20.000000e+001630/1708 (95%)EPI489378A/Indonesia/NIHRD11454/2011 (A/H5N1) segment 4 (HA)2715.70.000000e+001629/1708 (95%)EPI120008A/Indonesia/TLL012/2006 (A/H5N1) segment 4 (HA)2715.70.000000e+001629/1708 (95%)EPI376537A/Indonesia/5/2005 (A/H5N1) segment 4 (HA)2710.20.000000e+001627/1707 (95%)EPI181390A/Indonesia/5/2005 (A/H5N1) segment 4 (HA)2710.20.000000e+001627/1707 (95%)EPI55776A/Indonesia/CDC1047S/2007 (A/H5N1) segment 4 (HA)2710.20.000000e+001628/1708 (95%)EPI55757A/Indonesia/CDC1047/2007 (A/H5N1) segment 4 (HA)2710.20.000000e+001628/1708 (95%)EPI55738A/Indonesia/CDC1046T/2007 (A/H5N1) segment 4 (HA)2710.20.000000e+001628/1708 (95%)EPI41399A/Indonesia/CDC523/2006 (A/H5N1) segment 4 (HA)2706.50.000000e+001626/1707 (95%)EPI119998A/Indonesia/TLL007/2006 (A/H5N1) segment 4 (HA)2704.60.000000e+001626/1707 (95%)EPI116487A/Indonesia/5/2005 (A/H5N1) segment 4 (HA)2704.60.000000e+001626/1707 (95%)EPI55719A/Indonesia/CDC1046/2007 (A/H5N1) segment 4 (HA)2704.60.000000e+001627/1708 (95%)EPI120002A/Indonesia/TLL009/2006 (A/H5N1) segment 4 (HA)2702.80.000000e+001625/1707 (95%)EPI124067A/Indonesia/5/2005 (A/H5N1) segment 4 (HA)2699.10.000000e+001623/1704 (95%)EPI120006A/Indonesia/TLL011/2006 (A/H5N1) segment 4 (HA)2699.10.000000e+001625/1707 (95%)EPI120004A/Indonesia/TLL010/2006 (A/H5N1) segment 4 (HA)2699.10.000000e+001625/1707 (95%)EPI119994A/Indonesia/TLL005/2006 (A/H5N1) segment 4 (HA)2699.10.000000e+001625/1707 (95%)EPI119990A/Indonesia/TLL003/2006 (A/H5N1) segment 4 (HA)2699.10.000000e+001625/1707 (95%)EPI533457A/chicken/Jambi/184/2011 (A/H5N1) segment 4 (HA)2697.20.000000e+001526/1559 (97%)EPI533452A/chicken/Lampung/153/2011 (A/H5N1) segment 4 (HA)2697.20.000000e+001526/1559 (97%)EPI356559A/Muscovy duck/West Java/Bks3/2007 (A/H5N1) segment 4 (HA)2693.50.000000e+001623/1705 (95%)EPI224608A/Chicken/West Java/TASIKSOL/2006 (A/H5N1) segment 4 (HA)2693.50.000000e+001624/1707 (95%)EPI124421A/Indonesia/542H/2006 (A/H5N1) segment 4 (HA)2693.50.000000e+001624/1707 (95%)EPI124217A/Indonesia/286H/2006 (A/H5N1) segment 4 (HA)2693.50.000000e+001624/1707 (95%)EPI123831A/Chicken/Indonesia/Rejang Lebong1631-22/2006 (A/H5N1) segment 4 (HA)2693.50.000000e+001622/1704 (95%)EPI533456A/chicken/South Sumatra/170/2011 (A/H5N1) segment 4 (HA)2691.70.000000e+001525/1559 (97%)EPI41801A/Indonesia/CDC669/2006 (A/H5N1) segment 4 (HA)2689.80.000000e+001623/1707 (95%)EPI620916A/chicken/WestJava/TASIKO B/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI321749A/peaceful dove/Badung/BBVD-493/2007 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI321408A/chicken/Tabanan/BBVD-339/2007 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI321339A/chicken/Klungkung/BBVD-417/2007 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI321293A/chicken/Bangli/BBVD-387ab/2007 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI224706A/Muscovy Duck/Jakarta/HABWIN/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI124201A/Indonesia/283H/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI123832A/Chicken/Indonesia/Lampung1631-23/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001622/1705 (95%)EPI119996A/Indonesia/TLL006/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI41820A/Indonesia/CDC669P/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI376585A/ferret/Indonesia/5-F7/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI376578A/ferret/Indonesia/5-F6/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI376571A/ferret/Indonesia/5-F5/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI376564A/ferret/Indonesia/5-F3/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI376557A/ferret/Indonesia/5-F2/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321750A/peaceful dove/Denpasar/BBVD-480/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321364A/chicken/Magelang/BBVW-662-762A/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321341A/chicken/Klungkung/BBVD-484/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321321A/chicken/Flores Timur/BBVD-256/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321318A/chicken/Denpasar/BBVD-494/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321313A/chicken/Denpasar/BBVD-291/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321280A/chicken/Badung/BBVD-175/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI226652A/Chicken/Pakun Baru/BPPV-II/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001620/1704 (95%)EPI226651A/Chicken/Murao Jambi/BBPV-II/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI225050A/chicken/West Java/TASIKSOB/2006 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI120000A/Indonesia/TLL008/2006 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI55624A/Indonesia/CDC1031T2/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001590/1659 (95%)EPI55605A/Indonesia/CDC1031T/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001590/1659 (95%)EPI55586A/Indonesia/CDC1031/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001590/1659 (95%)EPI49202A/Indonesia/CDC835/2006 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI119992A/Indonesia/TLL004/2006 (A/H5N1) segment 4 (HA)2678.80.000000e+001621/1707 (94%)EPI41948A/Indonesia/CDC759/2006 (A/H5N1) segment 4 (HA)2678.80.000000e+001621/1707 (94%)EPI356581A/muscovy duck/Jakarta/Sum106/2006 (A/H5N1) segment 4 (HA)2676.90.000000e+001619/1704 (95%)EPI356515A/chicken/West Java/Smi-Hay/2005 (A/H5N1) segment 4 (HA)2676.90.000000e+001619/1704 (95%)EPI341633A/Indonesia/NIHRD11771/2011(H5N1) (A/H5N1) segment 4 (HA)2676.90.000000e+001622/1708 (94%)EPI341632A/Indonesia/NIHRD11767/2011(H5N1) (A/H5N1) segment 4 (HA)2676.90.000000e+001622/1708 (94%)EPI321582A/duck/Sleman/BBVW-599-33289/2007 (A/H5N1) segment 4 (HA)2676.90.000000e+001612/1693 (95%)EPI321520A/duck/Bantul/BBVW-358-24381/2007 (A/H5N1) segment 4 (HA)2676.90.000000e+001622/1708 (94%)EPI321409A/chicken/Tabanan/BBVD-461/2007 (A/H5N1) segment 4 (HA)2676.90.000000e+001621/1707 (94%)
  18. niman
    Isolate detailIsolate name: A/Indonesia/NIHRD/15023/2015 Isolate ID: EPI_ISL_195731 Passage details/history: e1 Type: A / H5N1 Lineage: Sample information Collection date: 2015-03-24 Host Human Additional host information: Zip code: Patient status: Deceased Last vaccinated: In-vivo pathogenicity test: Location: Indonesia / Banten Additional location information: Patient age: 40 Year(s) Gender: Male Outbreak: Treatment: unknown Specimen source: Oropharyngeal Institute information Originating lab: National Institute of Health Research and Development Sample ID given by the sample provider: 15023 Address: National Institute of Health Research and Development Jl. Percetakan Negara Jakarta, 10560 Indonesia Submitting lab: National Institute of Health Research and Development Sample ID given by the submitting laboratory: 15023 Authors: HA,Pawestri; AA,Nugraha; KD,Puspa; HD,Ikawati; V,Setiawaty Address: National Institute of Health Research and Development Jl. Percetakan Negara 29 Jakarta, 10560 Indonesia PublicationPublication In vivo antiviral resistance PhenotypeGenotypeUnspecifiedAntiviral resistance tested by experimental procedures Adamantanes: Unknown Oseltamivir: Unknown Zanamivir: Unknown Peramivir: Unknown Other: Unknown Additional informationAntigenic characterization: Note: Sequence segmentidentifierlengthaccession #INSDCSequence HA A/Indonesia/NIHRD/15023 1707 EPI643069 NA A/Indonesia/NIHRD/15023 1350 EPI643070 Submitter information Submitter: Pawestri, Hana Apsari Submission Date: 2015-09-09 Last modifier: Pawestri, Hana Apsari Last modified: 2015-09-09 Address: NIHRD-MOH percetakan negara 29 Jakarta, 10560 Indonesia
  19. niman
    AlignSegment-IDNameScoreE-ValueIdentityEPI643071A/Indonesia/NIHRD15028/2015 (A/H5N1) segment 6 (NA)2494.10.000000e+001350/1350 (100%)EPI643070A/Indonesia/NIHRD/15023/2015 (A/H5N1) segment 6 (NA)2422.10.000000e+001338/1351 (99%)EPI492525A/Indonesia/NIHRD13233/2013 (A/H5N1) segment 6 (NA)2416.50.000000e+001337/1351 (98%)EPI509938A/Indonesia/NIHRD13269/2013 (A/H5N1) segment 6 (NA)2405.50.000000e+001335/1351 (98%)EPI442758A/Indonesia/NIHRD12162/2012 (A/H5N1) segment 6 (NA)2355.60.000000e+001326/1351 (98%)EPI487551A/Indonesia/NIHRD11046/2011 (A/H5N1) segment 6 (NA)2255.90.000000e+001308/1351 (96%)EPI340809A/chicken/Lampung/BPPVRIII-10-161/2010 (A/H5N1) segment 6 (NA)2250.30.000000e+001305/1348 (96%)EPI340789A/bird/Gunung Kidul/BBVW-52-I/2010 (A/H5N1) segment 6 (NA)2250.30.000000e+001305/1348 (96%)EPI487527A/Indonesia/NIHRD10459/2010 (A/H5N1) segment 6 (NA)2239.30.000000e+001305/1351 (96%)EPI487456A/Indonesia/NIHRD10728/2010 (A/H5N1) segment 6 (NA)2233.70.000000e+001305/1352 (96%)EPI356475A/Indonesia/NIHRD11949/2012 (A/H5N1) segment 6 (NA)2217.10.000000e+001301/1351 (96%)EPI356473A/Indonesia/NIHRD11931/2012 (A/H5N1) segment 6 (NA)2217.10.000000e+001301/1351 (96%)EPI463649A/Indonesia/NIHRD13157/2013 (A/H5N1) segment 6 (NA)2161.70.000000e+001292/1352 (95%)EPI486489A/Indonesia/NIHRD9340/2009 (A/H5N1) segment 6 (NA)2156.20.000000e+001290/1351 (95%)EPI340777A/chicken/Temanggung/BBVW-1203d-VIII/2009 (A/H5N1) segment 6 (NA)2156.20.000000e+001288/1348 (95%)EPI340775A/chicken/Temanggung/BBVW-1203b-VIII/2009 (A/H5N1) segment 6 (NA)2156.20.000000e+001288/1348 (95%)EPI164210A/Indonesia/8228/2008 (A/H5N1) segment 6 (NA)2154.30.000000e+001279/1335 (95%)EPI340773A/chicken/Tasikmalaya/BBVW-991-VI/2009 (A/H5N1) segment 6 (NA)2150.60.000000e+001287/1348 (95%)EPI531960A/Indonesia/NIHRD14122/2014 (A/H5N1) segment 6 (NA)2145.10.000000e+001290/1353 (95%)EPI340767A/chicken/Kuningan/BBVW-1004-VI/2009 (A/H5N1) segment 6 (NA)2139.50.000000e+001285/1348 (95%)EPI55647A/Indonesia/CDC1031RE2/2007 (A/H5N1) segment 6 (NA)2128.50.000000e+001287/1353 (95%)EPI55628A/Indonesia/CDC1031T2/2007 (A/H5N1) segment 6 (NA)2128.50.000000e+001287/1353 (95%)EPI55609A/Indonesia/CDC1031T/2007 (A/H5N1) segment 6 (NA)2128.50.000000e+001287/1353 (95%)EPI55590A/Indonesia/CDC1031/2007 (A/H5N1) segment 6 (NA)2128.50.000000e+001287/1353 (95%)EPI49268A/Indonesia/CDC887/2006 (A/H5N1) segment 6 (NA)2128.50.000000e+001287/1353 (95%)EPI55704A/Indonesia/CDC1032T/2007 (A/H5N1) segment 6 (NA)2122.90.000000e+001286/1353 (95%)EPI55685A/Indonesia/CDC1032N/2007 (A/H5N1) segment 6 (NA)2122.90.000000e+001286/1353 (95%)EPI55666A/Indonesia/CDC1032/2007 (A/H5N1) segment 6 (NA)2122.90.000000e+001286/1353 (95%)EPI49168A/Indonesia/CDC938E/2006 (A/H5N1) segment 6 (NA)2122.90.000000e+001286/1353 (95%)EPI49149A/Indonesia/CDC938/2006 (A/H5N1) segment 6 (NA)2122.90.000000e+001286/1353 (95%)EPI164765A/Indonesia/7272/2008 (A/H5N1) segment 6 (NA)2121.10.000000e+001275/1337 (95%)EPI163112A/Indonesia/7261/2008 (A/H5N1) segment 6 (NA)2121.10.000000e+001275/1337 (95%)EPI443392A/chicken/West Java Tangerang/PTB6/2008 (A/H5N1) segment 6 (NA)2111.80.000000e+001282/1350 (94%)EPI443362A/chicken/Siantar/BPPVRI-231-2/2008 (A/H5N1) segment 6 (NA)2111.80.000000e+001282/1350 (94%)EPI443361A/chicken/Siantar/BPPVRI-231-1/2008 (A/H5N1) segment 6 (NA)2111.80.000000e+001282/1350 (94%)EPI443316A/chicken/Ponorogo/BBVW-197b/2007 (A/H5N1) segment 6 (NA)2111.80.000000e+001283/1351 (94%)EPI340765A/chicken/Kudus/BBVW-1186-IX/2009 (A/H5N1) segment 6 (NA)2111.80.000000e+001280/1348 (94%)EPI41557A/Indonesia/CDC523T/2006 (A/H5N1) segment 6 (NA)2111.80.000000e+001286/1355 (94%)EPI41538A/Indonesia/CDC523E/2006 (A/H5N1) segment 6 (NA)2111.80.000000e+001286/1355 (94%)EPI41403A/Indonesia/CDC523/2006 (A/H5N1) segment 6 (NA)2111.80.000000e+001286/1355 (94%)EPI443404A/pigeon/Bukittinggi/BPPVRII-178-B/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1351 (94%)EPI443389A/chicken/Agam/BPPVRII-694/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1351 (94%)EPI443382A/chicken/Pariaman/BPPVRII-370/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1351 (94%)EPI443373A/chicken/Batam/BPPVRII-188/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1351 (94%)EPI443372A/duck/Padang/BPPVRII-151/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1351 (94%)EPI443371A/swan/Bukittinggi/BPPVRII-178-S/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1351 (94%)EPI443370A/Muscovy duck/Bukittinggi/BPPVRII-178-M/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1351 (94%)EPI443369A/chicken/Padang/BPPVRII-151/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1351 (94%)EPI443368A/chicken/Bukittinggi/BPPVRII-178-C/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001282/1351 (94%)EPI443365A/chicken/Medan/BPPVRI-15/2008 (A/H5N1) segment 6 (NA)2106.30.000000e+001281/1350 (94%)EPI443357A/chicken/Taput/BPPVRI-235/2007 (A/H5N1) segment 6 (NA)2106.30.000000e+001281/1350 (94%)EPI443376A/duck/Kerinci/BPPVRII-262-D/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1351 (94%)EPI443375A/chicken/Kerinci/BPPVRII-262-C/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1351 (94%)EPI443374A/chicken/Solok Selatan/BPPVRII-217/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1351 (94%)EPI443367A/chicken/Pesisir Selatan/BPPVRII-119/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1351 (94%)EPI443352A/chicken/Tanjung Balai/BPPVRI-97/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001280/1350 (94%)EPI443351A/chicken/Simalungun/BPPVRI-391/2007 (A/H5N1) segment 6 (NA)2100.80.000000e+001280/1350 (94%)EPI340781A/chicken/Sleman/BBVW-180-III/2010 (A/H5N1) segment 6 (NA)2100.80.000000e+001281/1351 (94%)EPI41851A/Indonesia/CDC699/2006 (A/H5N1) segment 6 (NA)2100.80.000000e+001284/1355 (94%)EPI123850A/Pigeon/Indonesia/Rohkit1631-6/2006 (A/H5N1) segment 6 (NA)2097.10.000000e+001273/1340 (95%)EPI123848A/Chicken/Indonesia/Agam1631-3/2006 (A/H5N1) segment 6 (NA)2097.10.000000e+001273/1340 (95%)EPI123844A/Chicken/Indonesia/Padang1631-1/2006 (A/H5N1) segment 6 (NA)2097.10.000000e+001273/1340 (95%)EPI443378A/chicken/Sawahlunto/BPPVRII-273/2007 (A/H5N1) segment 6 (NA)2095.20.000000e+001280/1351 (94%)EPI443358A/chicken/Karo/BPPVRI-320/2007 (A/H5N1) segment 6 (NA)2095.20.000000e+001279/1350 (94%)EPI123846A/Chicken/Indonesia/Siak1631-2/2006 (A/H5N1) segment 6 (NA)2095.20.000000e+001272/1339 (94%)EPI49244A/Indonesia/CDC836T/2006 (A/H5N1) segment 6 (NA)2095.20.000000e+001283/1355 (94%)EPI49225A/Indonesia/CDC836/2006 (A/H5N1) segment 6 (NA)2095.20.000000e+001283/1355 (94%)EPI41576A/Indonesia/CDC582/2006 (A/H5N1) segment 6 (NA)2095.20.000000e+001283/1355 (94%)EPI123852A/Chicken/Indonesia/Pekenbaru1631-11/2006 (A/H5N1) segment 6 (NA)2091.50.000000e+001272/1340 (94%)EPI443384A/chicken/Bengkalis/BPPVRII-532/2007 (A/H5N1) segment 6 (NA)2089.70.000000e+001279/1351 (94%)EPI443379A/chicken/Payakumbuh/BPPVRII-307/2007 (A/H5N1) segment 6 (NA)2089.70.000000e+001279/1351 (94%)EPI443306A/chicken/West Java/Drd-20/2007 (A/H5N1) segment 6 (NA)2089.70.000000e+001280/1352 (94%)EPI342499A/Indonesia/NIHRD11771/2011(H5N1) (A/H5N1) segment 6 (NA)2089.70.000000e+001280/1353 (94%)EPI124480A/Indonesia/567H/2006 (A/H5N1) segment 6 (NA)2089.70.000000e+001283/1356 (94%)EPI124276A/Indonesia/292H/2006 (A/H5N1) segment 6 (NA)2089.70.000000e+001282/1355 (94%)EPI55780A/Indonesia/CDC1047S/2007 (A/H5N1) segment 6 (NA)2089.70.000000e+001282/1355 (94%)EPI55761A/Indonesia/CDC1047/2007 (A/H5N1) segment 6 (NA)2089.70.000000e+001282/1355 (94%)EPI55742A/Indonesia/CDC1046T/2007 (A/H5N1) segment 6 (NA)2089.70.000000e+001282/1355 (94%)EPI55723A/Indonesia/CDC1046/2007 (A/H5N1) segment 6 (NA)2089.70.000000e+001282/1355 (94%)EPI41919A/Indonesia/CDC739/2006 (A/H5N1) segment 6 (NA)2089.70.000000e+001282/1355 (94%)EPI41883A/Indonesia/CDC644/2006 (A/H5N1) segment 6 (NA)2089.70.000000e+001283/1356 (94%)EPI41864A/Indonesia/CDC644T/2006 (A/H5N1) segment 6 (NA)2089.70.000000e+001283/1356 (94%)EPI41832A/Indonesia/CDC669P/2006 (A/H5N1) segment 6 (NA)2089.70.000000e+001282/1355 (94%)EPI41813A/Indonesia/CDC669/2006 (A/H5N1) segment 6 (NA)2089.70.000000e+001282/1355 (94%)EPI356567A/Muscovy duck/West Java/Bks3/2007 (A/H5N1) segment 6 (NA)2087.80.000000e+001261/1325 (95%)EPI342500A/Indonesia/NIHRD11767/2011(H5N1) (A/H5N1) segment 6 (NA)2086.00.000000e+001279/1353 (94%)EPI443387A/chicken/Siak/BPPVRII-635/2007 (A/H5N1) segment 6 (NA)2084.10.000000e+001277/1350 (94%)EPI443385A/chicken/Kuantan Singingi/BPPVRII-620/2007 (A/H5N1) segment 6 (NA)2084.10.000000e+001277/1350 (94%)EPI443381A/chicken/Tanah Datar/BPPVRII-365/2007 (A/H5N1) segment 6 (NA)2084.10.000000e+001278/1351 (94%)EPI443377A/chicken/Padang Panjang/BPPVRII-272/2007 (A/H5N1) segment 6 (NA)2084.10.000000e+001277/1350 (94%)EPI443359A/chicken/Aceh Barat/BPPVRI-327/2007 (A/H5N1) segment 6 (NA)2084.10.000000e+001277/1350 (94%)EPI124426A/Indonesia/542H/2006 (A/H5N1) segment 6 (NA)2084.10.000000e+001281/1355 (94%)EPI124219A/Indonesia/286H/2006 (A/H5N1) segment 6 (NA)2084.10.000000e+001281/1355 (94%)EPI41952A/Indonesia/CDC759/2006 (A/H5N1) segment 6 (NA)2084.10.000000e+001282/1356 (94%)EPI41756A/Indonesia/CDC634T/2006 (A/H5N1) segment 6 (NA)2084.10.000000e+001283/1357 (94%)EPI41737A/Indonesia/CDC634P/2006 (A/H5N1) segment 6 (NA)2084.10.000000e+001283/1357 (94%)EPI41718A/Indonesia/CDC634/2006 (A/H5N1) segment 6 (NA)2084.10.000000e+001283/1357 (94%)EPI620902A/chicken/WestJava/SMI-PAT/2006 (A/H5N1) segment 6 (NA)2078.60.000000e+001280/1355 (94%)EPI443364A/chicken/Deli Serdang/BPPVRI-238-2/2008 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)EPI443363A/chicken/Deli Serdang/BPPVRI-238-1/2008 (A/H5N1) segment 6 (NA)2078.60.000000e+001276/1350 (94%)
  20. niman
    AlignSegment-IDNameScoreE-ValueIdentityEPI643072A/Indonesia/NIHRD15028/2015 (A/H5N1) segment 4 (HA)3153.40.000000e+001707/1707 (100%)EPI643069A/Indonesia/NIHRD/15023/2015 (A/H5N1) segment 4 (HA)3153.40.000000e+001707/1707 (100%)EPI492524A/Indonesia/NIHRD13233/2013 (A/H5N1) segment 4 (HA)3053.60.000000e+001689/1707 (98%)EPI547699A/Indonesia/NIHRD14157/2014 (A/H5N1) segment 4 (HA)3037.00.000000e+001686/1707 (98%)EPI509937A/Indonesia/NIHRD13269/2013 (A/H5N1) segment 4 (HA)3025.90.000000e+001684/1707 (98%)EPI537677A/Environment/West Java/Bksi34/2013 (A/H5N1) segment 4 (HA)2953.90.000000e+001671/1707 (97%)EPI442757A/Indonesia/NIHRD12162/2012 (A/H5N1) segment 4 (HA)2915.10.000000e+001664/1707 (97%)EPI340810A/chicken/Lampung/BPPVRIII-10-161/2010 (A/H5N1) segment 4 (HA)2887.40.000000e+001659/1707 (97%)EPI324340A/chicken/Indonesia/D10014/2010 (A/H5N1) segment 4 (HA)2881.90.000000e+001658/1707 (97%)EPI487549A/Indonesia/NIHRD11046/2011 (A/H5N1) segment 4 (HA)2865.30.000000e+001655/1707 (96%)EPI356474A/Indonesia/NIHRD11949/2012 (A/H5N1) segment 4 (HA)2865.30.000000e+001655/1707 (96%)EPI356472A/Indonesia/NIHRD11931/2012 (A/H5N1) segment 4 (HA)2865.30.000000e+001655/1707 (96%)EPI340790A/bird/Gunung Kidul/BBVW-52-I/2010 (A/H5N1) segment 4 (HA)2865.30.000000e+001655/1707 (96%)EPI487467A/Indonesia/NIHRD10623/2010 (A/H5N1) segment 4 (HA)2854.20.000000e+001653/1707 (96%)EPI487454A/Indonesia/NIHRD10728/2010 (A/H5N1) segment 4 (HA)2854.20.000000e+001654/1708 (96%)EPI487461A/Indonesia/NIHRD10364/2010 (A/H5N1) segment 4 (HA)2843.10.000000e+001651/1707 (96%)EPI487525A/Indonesia/NIHRD10459/2010 (A/H5N1) segment 4 (HA)2837.60.000000e+001651/1708 (96%)EPI341332A/Indonesia/NIHRD11073/2011(H5N1) (A/H5N1) segment 4 (HA)2832.00.000000e+001650/1708 (96%)EPI340778A/chicken/Temanggung/BBVW-1203d-VIII/2009 (A/H5N1) segment 4 (HA)2815.40.000000e+001646/1707 (96%)EPI340776A/chicken/Temanggung/BBVW-1203b-VIII/2009 (A/H5N1) segment 4 (HA)2815.40.000000e+001646/1707 (96%)EPI164208A/Indonesia/8228/2008 (A/H5N1) segment 4 (HA)2809.90.000000e+001645/1707 (96%)EPI486487A/Indonesia/NIHRD9340/2009 (A/H5N1) segment 4 (HA)2782.20.000000e+001641/1708 (96%)EPI162940A/Indonesia/7261/2008 (A/H5N1) segment 4 (HA)2782.20.000000e+001640/1707 (96%)EPI340774A/chicken/Tasikmalaya/BBVW-991-VI/2009 (A/H5N1) segment 4 (HA)2760.00.000000e+001637/1708 (95%)EPI340768A/chicken/Kuningan/BBVW-1004-VI/2009 (A/H5N1) segment 4 (HA)2748.90.000000e+001635/1708 (95%)EPI307911A/chicken/Indonesia/SmiWN18/2009 (A/H5N1) segment 4 (HA)2747.10.000000e+001588/1638 (96%)EPI164763A/Indonesia/7272/2008 (A/H5N1) segment 4 (HA)2739.70.000000e+001627/1699 (95%)EPI55643A/Indonesia/CDC1031RE2/2007 (A/H5N1) segment 4 (HA)2737.90.000000e+001632/1707 (95%)EPI49264A/Indonesia/CDC887/2006 (A/H5N1) segment 4 (HA)2737.90.000000e+001632/1707 (95%)EPI356512A/chicken/Banten/Srg-Fadh/2008 (A/H5N1) segment 4 (HA)2732.30.000000e+001629/1704 (95%)EPI340766A/chicken/Kudus/BBVW-1186-IX/2009 (A/H5N1) segment 4 (HA)2732.30.000000e+001633/1709 (95%)EPI340782A/chicken/Sleman/BBVW-180-III/2010 (A/H5N1) segment 4 (HA)2726.80.000000e+001632/1709 (95%)EPI49164A/Indonesia/CDC938E/2006 (A/H5N1) segment 4 (HA)2726.80.000000e+001630/1707 (95%)EPI49145A/Indonesia/CDC938/2006 (A/H5N1) segment 4 (HA)2726.80.000000e+001630/1707 (95%)EPI324615A/tree sparrow/Indonesia/D10013/2010 (A/H5N1) segment 4 (HA)2721.20.000000e+001630/1708 (95%)EPI489378A/Indonesia/NIHRD11454/2011 (A/H5N1) segment 4 (HA)2715.70.000000e+001629/1708 (95%)EPI120008A/Indonesia/TLL012/2006 (A/H5N1) segment 4 (HA)2715.70.000000e+001629/1708 (95%)EPI376537A/Indonesia/5/2005 (A/H5N1) segment 4 (HA)2710.20.000000e+001627/1707 (95%)EPI181390A/Indonesia/5/2005 (A/H5N1) segment 4 (HA)2710.20.000000e+001627/1707 (95%)EPI55776A/Indonesia/CDC1047S/2007 (A/H5N1) segment 4 (HA)2710.20.000000e+001628/1708 (95%)EPI55757A/Indonesia/CDC1047/2007 (A/H5N1) segment 4 (HA)2710.20.000000e+001628/1708 (95%)EPI55738A/Indonesia/CDC1046T/2007 (A/H5N1) segment 4 (HA)2710.20.000000e+001628/1708 (95%)EPI41399A/Indonesia/CDC523/2006 (A/H5N1) segment 4 (HA)2706.50.000000e+001626/1707 (95%)EPI119998A/Indonesia/TLL007/2006 (A/H5N1) segment 4 (HA)2704.60.000000e+001626/1707 (95%)EPI116487A/Indonesia/5/2005 (A/H5N1) segment 4 (HA)2704.60.000000e+001626/1707 (95%)EPI55719A/Indonesia/CDC1046/2007 (A/H5N1) segment 4 (HA)2704.60.000000e+001627/1708 (95%)EPI120002A/Indonesia/TLL009/2006 (A/H5N1) segment 4 (HA)2702.80.000000e+001625/1707 (95%)EPI124067A/Indonesia/5/2005 (A/H5N1) segment 4 (HA)2699.10.000000e+001623/1704 (95%)EPI120006A/Indonesia/TLL011/2006 (A/H5N1) segment 4 (HA)2699.10.000000e+001625/1707 (95%)EPI120004A/Indonesia/TLL010/2006 (A/H5N1) segment 4 (HA)2699.10.000000e+001625/1707 (95%)EPI119994A/Indonesia/TLL005/2006 (A/H5N1) segment 4 (HA)2699.10.000000e+001625/1707 (95%)EPI119990A/Indonesia/TLL003/2006 (A/H5N1) segment 4 (HA)2699.10.000000e+001625/1707 (95%)EPI533457A/chicken/Jambi/184/2011 (A/H5N1) segment 4 (HA)2697.20.000000e+001526/1559 (97%)EPI533452A/chicken/Lampung/153/2011 (A/H5N1) segment 4 (HA)2697.20.000000e+001526/1559 (97%)EPI356559A/Muscovy duck/West Java/Bks3/2007 (A/H5N1) segment 4 (HA)2693.50.000000e+001623/1705 (95%)EPI224608A/Chicken/West Java/TASIKSOL/2006 (A/H5N1) segment 4 (HA)2693.50.000000e+001624/1707 (95%)EPI124421A/Indonesia/542H/2006 (A/H5N1) segment 4 (HA)2693.50.000000e+001624/1707 (95%)EPI124217A/Indonesia/286H/2006 (A/H5N1) segment 4 (HA)2693.50.000000e+001624/1707 (95%)EPI123831A/Chicken/Indonesia/Rejang Lebong1631-22/2006 (A/H5N1) segment 4 (HA)2693.50.000000e+001622/1704 (95%)EPI533456A/chicken/South Sumatra/170/2011 (A/H5N1) segment 4 (HA)2691.70.000000e+001525/1559 (97%)EPI41801A/Indonesia/CDC669/2006 (A/H5N1) segment 4 (HA)2689.80.000000e+001623/1707 (95%)EPI620916A/chicken/WestJava/TASIKO B/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI321749A/peaceful dove/Badung/BBVD-493/2007 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI321408A/chicken/Tabanan/BBVD-339/2007 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI321339A/chicken/Klungkung/BBVD-417/2007 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI321293A/chicken/Bangli/BBVD-387ab/2007 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI224706A/Muscovy Duck/Jakarta/HABWIN/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI124201A/Indonesia/283H/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI123832A/Chicken/Indonesia/Lampung1631-23/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001622/1705 (95%)EPI119996A/Indonesia/TLL006/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI41820A/Indonesia/CDC669P/2006 (A/H5N1) segment 4 (HA)2688.00.000000e+001623/1707 (95%)EPI376585A/ferret/Indonesia/5-F7/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI376578A/ferret/Indonesia/5-F6/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI376571A/ferret/Indonesia/5-F5/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI376564A/ferret/Indonesia/5-F3/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI376557A/ferret/Indonesia/5-F2/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321750A/peaceful dove/Denpasar/BBVD-480/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321364A/chicken/Magelang/BBVW-662-762A/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321341A/chicken/Klungkung/BBVD-484/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321321A/chicken/Flores Timur/BBVD-256/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321318A/chicken/Denpasar/BBVD-494/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321313A/chicken/Denpasar/BBVD-291/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI321280A/chicken/Badung/BBVD-175/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI226652A/Chicken/Pakun Baru/BPPV-II/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001620/1704 (95%)EPI226651A/Chicken/Murao Jambi/BBPV-II/2005 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI225050A/chicken/West Java/TASIKSOB/2006 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI120000A/Indonesia/TLL008/2006 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI55624A/Indonesia/CDC1031T2/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001590/1659 (95%)EPI55605A/Indonesia/CDC1031T/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001590/1659 (95%)EPI55586A/Indonesia/CDC1031/2007 (A/H5N1) segment 4 (HA)2682.50.000000e+001590/1659 (95%)EPI49202A/Indonesia/CDC835/2006 (A/H5N1) segment 4 (HA)2682.50.000000e+001622/1707 (95%)EPI119992A/Indonesia/TLL004/2006 (A/H5N1) segment 4 (HA)2678.80.000000e+001621/1707 (94%)EPI41948A/Indonesia/CDC759/2006 (A/H5N1) segment 4 (HA)2678.80.000000e+001621/1707 (94%)EPI356581A/muscovy duck/Jakarta/Sum106/2006 (A/H5N1) segment 4 (HA)2676.90.000000e+001619/1704 (95%)EPI356515A/chicken/West Java/Smi-Hay/2005 (A/H5N1) segment 4 (HA)2676.90.000000e+001619/1704 (95%)EPI341633A/Indonesia/NIHRD11771/2011(H5N1) (A/H5N1) segment 4 (HA)2676.90.000000e+001622/1708 (94%)EPI341632A/Indonesia/NIHRD11767/2011(H5N1) (A/H5N1) segment 4 (HA)2676.90.000000e+001622/1708 (94%)EPI321582A/duck/Sleman/BBVW-599-33289/2007 (A/H5N1) segment 4 (HA)2676.90.000000e+001612/1693 (95%)EPI321520A/duck/Bantul/BBVW-358-24381/2007 (A/H5N1) segment 4 (HA)2676.90.000000e+001622/1708 (94%)EPI321409A/chicken/Tabanan/BBVD-461/2007 (A/H5N1) segment 4 (HA)2676.90.000000e+001621/1707 (94%)
  21. niman
    Isolate detailIsolate name: A/Indonesia/NIHRD15028/2015 Isolate ID: EPI_ISL_195732 Passage details/history: e2 Type: A / H5N1 Lineage: Sample information Collection date: 2015-03-25 Host Human Additional host information: Zip code: Patient status: Last vaccinated: In-vivo pathogenicity test: Location: Indonesia / Banten Additional location information: Patient age: 2 Year(s) Gender: Male Outbreak: Treatment: Specimen source: Nasopharyngeal Institute information Originating lab: National Institute of Health Research and Development Sample ID given by the sample provider: 15028 Address: National Institute of Health Research and Development Jl. Percetakan Negara Jakarta, 10560 Indonesia Submitting lab: National Institute of Health Research and Development Sample ID given by the submitting laboratory: 15028 Authors: HA,Pawestri; KD,Puspa; HD,Ikawati; AA,Nugraha; V,Setiawaty Address: National Institute of Health Research and Development Jl. Percetakan Negara No. 29 Jakarta, 10560 Indonesia PublicationPublication In vivo antiviral resistance PhenotypeGenotypeUnspecifiedAntiviral resistance tested by experimental procedures Adamantanes: Unknown Oseltamivir: Unknown Zanamivir: Unknown Peramivir: Unknown Other: Unknown Additional informationAntigenic characterization: Note: Sequence segmentidentifierlengthaccession #INSDCSequence HA A/Indonesia/NIHRD15028/2015 1707 EPI643072 NA A/Indonesia/NIHRD15028/2015 1350 EPI643071 Submitter information Submitter: Pawestri, Hana Apsari Submission Date: 2015-09-09 Last modifier: Pawestri, Hana Apsari Last modified: 2015-09-09 Address: NIHRD-MOH percetakan negara 29 Jakarta, 10560 Indonesia
  22. niman
    Indonesia NIHRD releases H5N1 H5 & N1 sequences from 2015 cases (40M & 2M).
  23. niman
    Johnny Adolphson/Shutterstock Wild duck found with avian flu near Great Salt LakeBy The Associated Press | Updated - Sep 8th, 2015 @ 4:46pmSALT LAKE CITY (AP) — Utah wildlife officials have discovered another wild duck with avian flu. Leslie McFarlane of the Utah Division of Wildlife Resources said Tuesday that her agency was notified about an infected mallard duck in late August. The duck had been tagged earlier in the summer at Farmington Bay on the Great Salt Lake. McFarlane says it is the third waterfowl found with avian flu since December. The highly pathogenic strain found in the ducks can lead to outbreaks at chicken and turkey farms. But McFarlane says poultry farms in Utah have taken precautions to prevent that from happening. McFarlane cautions people to stay away from sick animals. She says people with backyard chickens should also be careful to shield their poultry from wild waterfowl. http://www.ksl.com/?sid=36426970&nid=148&fm=most_popular&s_cid=popular-9
  24. niman
    AlignSegment-IDNameScoreE-ValueIdentityEPI642507A/Michigan/39/2015 (A/H3N2) segment 8 (NS)1548.60.000000e+00838/838 (100%)EPI502441A/swine/North Carolina/A01290378/2013 (A/H1N1) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI467760A/swine/North Carolina/A01203272/2012 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI457159A/swine/Korea/CY03-19/2012 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI457151A/swine/Korea/CY03-18/2012 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI457143A/swine/Korea/CY03-17/2012 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI457135A/swine/Korea/CY03-16/2012 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI457127A/swine/Korea/CY03-15/2012 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI457119A/swine/Korea/CY03-14/2012 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI457113A/swine/Korea/CY02-07/2012 (A/H3N1) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI453438A/swine/Korea/A18/2011 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI395846A/mink/Wisconsin/31512-7/2012 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI395323A/West Virginia/06/2011 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI384181A/swine/Indiana/A01202621/2011 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI342599A/swine/NY/A01104005/2011 (A/H3N2) segment 8 (NS)1509.80.000000e+00831/838 (99%)EPI615610A/swine/Illinois/A01047046/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI615559A/swine/Illinois/A01047045/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI615552A/swine/Illinois/A01047044/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI603619A/swine/Iowa/A01202439/2011 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI602573A/swine/Iowa/A01202438/2011 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI602541A/swine/Iowa/A01202091/2011 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593925A/swine/Illinois/A01047806/2011 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593922A/swine/Illinois/A01047805/2011 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593861A/swine/Illinois/A01047518/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593857A/swine/Illinois/A01047149/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593853A/swine/Illinois/A01047166/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593835A/swine/Illinois/A01047155/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593831A/swine/Illinois/A01047172/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593824A/swine/Illinois/A01047153/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593817A/swine/Illinois/A01047525/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593813A/swine/Illinois/A01047145/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593797A/swine/Illinois/A01047112/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593793A/swine/Illinois/A01047177/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593789A/swine/Illinois/A01047089/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593787A/swine/Illinois/A01047108/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593775A/swine/Illinois/A01047097/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593771A/swine/Illinois/A01047085/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593767A/swine/Illinois/A01047099/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593746A/swine/Illinois/A01047041/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593742A/swine/Illinois/A01047042/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI593734A/swine/Illinois/A01047024/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI589908A/swine/Iowa/A01049344/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI584479A/swine/Minnesota/A01076626/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI558827A/swine/Illinois/A01047020/2010 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI542342A/swine/Ohio/10SW130/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI530366A/swine/Indiana/A00968364/2012 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI493692A/swine/Iowa/13E045/2013 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI468745A/swine/Illinois/A01432127/2012 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI468661A/swine/Ohio/A01349305/2013 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI468630A/swine/Maryland/A01319694/2013 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI468202A/swine/Indiana/13TOSU482/2013 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI467901A/swine/Ohio/A01349485/2013 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI467757A/swine/Iowa/A01244302/2012 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI467637A/swine/Pennsylvania/A01380412/2013 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI461379A/swine/Ohio/11SW190/2011 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI459566A/swine/Ohio/11SW193/2011 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI459536A/swine/Ohio/11SW349/2011 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI459467A/swine/Ohio/11SW344/2011 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI453439A/swine/Korea/D79/2011 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI453437A/swine/Korea/KSB/2012 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI451231A/swine/Ohio/A01208181/2012 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI451225A/swine/Ohio/A01208180/2012 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI443427A/swine/Minnesota/A01134331/2010 (A/H1N1) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI441119A/swine/Indiana/A00968380/2012 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI433529A/swine/Iowa/A01267939/2012 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415969A/swine/Ohio/11SW347/2011 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415670A/swine/Ohio/11SW192/2011 (A/H1N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415533A/swine/Ohio/11SW170/2011 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415212A/swine/Ohio/10SW220/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415204A/swine/Ohio/10SW219/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415196A/swine/Ohio/10SW218/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415188A/swine/Ohio/10SW216/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415180A/swine/Ohio/10SW214/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415172A/swine/Ohio/10SW213/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415164A/swine/Ohio/10SW212/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415156A/swine/Ohio/10SW211/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415148A/swine/Ohio/10SW210/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415140A/swine/Ohio/10SW209/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415132A/swine/Ohio/10SW208/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415124A/swine/Ohio/10SW207/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415116A/swine/Ohio/10SW206/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415108A/swine/Ohio/10SW205/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415100A/swine/Ohio/10SW204/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415092A/swine/Ohio/10SW203/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415084A/swine/Ohio/10SW202/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415076A/swine/Ohio/10SW156/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415068A/swine/Ohio/10SW139/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415060A/swine/Ohio/10SW137/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415052A/swine/Ohio/10SW136/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415044A/swine/Ohio/10SW135/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415036A/swine/Ohio/10SW134/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415028A/swine/Ohio/10SW133/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415020A/swine/Ohio/10SW132/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415012A/swine/Ohio/10SW131/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI415004A/swine/Ohio/10SW128/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI414996A/swine/Ohio/10SW127/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI414988A/swine/Ohio/10SW126/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI414980A/swine/Ohio/10SW125/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI414972A/swine/Ohio/10SW122/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)EPI414964A/swine/Ohio/10SW121/2010 (A/H3N2) segment 8 (NS)1504.30.000000e+00830/838 (99%)
  25. niman
    AlignSegment-IDNameScoreE-ValueIdentityEPI642506A/Michigan/39/2015 (A/H3N2) segment 5 (NP)2765.60.000000e+001497/1497 (100%)EPI468660A/swine/Ohio/A01349305/2013 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI467900A/swine/Ohio/A01349485/2013 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI397947A/Ohio/85/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI397497A/Indiana/104/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI397397A/Indiana/99/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI397378A/Indiana/138/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI396235A/Indiana/103/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI396176A/Indiana/77/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI395719A/swine/Indiana/A01104023/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI395359A/swine/Indiana/A01104016/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI395244A/Indiana/152/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI388357A/Indiana/16/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI388353A/Indiana/21/2012 (A/H3N2) segment 5 (NP)2704.60.000000e+001486/1497 (99%)EPI393512A/Indiana/65/2012 (A/H3N2) segment 5 (NP)2700.90.000000e+001485/1497 (99%)EPI615639A/swine/Illinois/A01047044/2010 (A/H1N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI615607A/swine/Illinois/A01047046/2010 (A/H1N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI615556A/swine/Illinois/A01047045/2010 (A/H1N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI593745A/swine/Illinois/A01047041/2010 (A/H1N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI593741A/swine/Illinois/A01047042/2010 (A/H1N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI593733A/swine/Illinois/A01047024/2010 (A/H1N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI542340A/swine/Ohio/10SW130/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI542335A/swine/Ohio/10SW215/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI467759A/swine/North Carolina/A01203272/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI433541A/swine/Ohio/12TOSU374/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI433534A/swine/Ohio/12TOSU371/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415211A/swine/Ohio/10SW220/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415203A/swine/Ohio/10SW219/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415195A/swine/Ohio/10SW218/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415187A/swine/Ohio/10SW216/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415171A/swine/Ohio/10SW213/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415163A/swine/Ohio/10SW212/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415155A/swine/Ohio/10SW211/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415147A/swine/Ohio/10SW210/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415139A/swine/Ohio/10SW209/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415131A/swine/Ohio/10SW208/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415123A/swine/Ohio/10SW207/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415115A/swine/Ohio/10SW206/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415107A/swine/Ohio/10SW205/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415099A/swine/Ohio/10SW204/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415091A/swine/Ohio/10SW203/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415083A/swine/Ohio/10SW202/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415075A/swine/Ohio/10SW156/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415067A/swine/Ohio/10SW139/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415059A/swine/Ohio/10SW137/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415051A/swine/Ohio/10SW136/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415035A/swine/Ohio/10SW134/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415027A/swine/Ohio/10SW133/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415019A/swine/Ohio/10SW132/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415011A/swine/Ohio/10SW131/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI415003A/swine/Ohio/10SW128/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI414995A/swine/Ohio/10SW127/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI414987A/swine/Ohio/10SW126/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI414979A/swine/Ohio/10SW125/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI414971A/swine/Ohio/10SW122/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI414963A/swine/Ohio/10SW121/2010 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI414187A/swine/Indiana/A00968394/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI414179A/swine/Pennsylvania/A01104050/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI414171A/swine/Indiana/A00968398/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI401714A/swine/Pennsylvania/A01104049/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI401673A/swine/Ohio/A00138552/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI401658A/swine/Ohio/12TOSU527/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI401624A/swine/Ohio/12TOSU522/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI401622A/swine/Ohio/12TOSU484/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI401618A/swine/Ohio/12TOSU483/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI401614A/swine/Minnesota/A01301908/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI398543A/swine/Ohio/A00152576/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI398535A/swine/Ohio/A01208457/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI398527A/swine/Wisconsin/A00677500/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI398501A/swine/Ohio/A01133466/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397963A/Wisconsin/34/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397955A/Ohio/88/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397932A/Ohio/41/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397901A/Hawaii/03/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397556A/Wisconsin/29/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397549A/Ohio/86/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397541A/Ohio/83/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397533A/Ohio/56/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397525A/Ohio/47/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397517A/Ohio/44/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397510A/Ohio/36/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397440A/Wisconsin/31/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397433A/Wisconsin/30/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397427A/Ohio/81/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397419A/Minnesota/15/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397357A/Ohio/79/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI397205A/Ohio/34/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI396285A/Ohio/57/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI396278A/Indiana/144/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI396271A/Indiana/135/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI396247A/Indiana/126/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI396201A/Indiana/149/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI396185A/Ohio/77/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI396170A/Ohio/80/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI395949A/swine/Indiana/A00968376/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI395941A/swine/Indiana/A00968373/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI395933A/swine/Indiana/A00968370/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI395884A/swine/Ohio/12TOSU307/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI395875A/swine/Ohio/12TOSU447/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)EPI395867A/swine/Ohio/12TOSU450/2012 (A/H3N2) segment 5 (NP)2699.10.000000e+001485/1497 (99%)
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