Computational protocol: Phylogenetic Analysis of a Swine Influenza A(H3N2) Virus Isolated in Korea in 2012

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Protocol publication

[…] For the phylogenetic study, the NCBI-registered full-length nucleotide sequences of swine H3N2 viruses were used as references (the total number of full-length sequences after collapsing the identical sequences as of release date June 29, 2013 is as follows: PB2, 341; PB1, 358; PA, 354; HA, 556; NP, 352; NA, 550; M, 400; and NS, 331). By adding various lineage defining sequences or removing redundant sequences, we analyzed the phylogenetic characteristics of the swPL01 virus. The nucleotide sequences of lineage defining human H1N1 (huH1N1; A/New York/494/2002), huH3N2 (A/New York/101/2002), pH1N1 (A/California/04/2009, A/Korea/01/2009, A/Netherlands/602/2009, A/swine/Hong Kong/2995/2009, and A/swine/Hong Kong/189/2010) , CS H1N1 (A/swine/Hong Kong/5683/1999, A/swine/Hong Kong/NS143/2000, A/swine/Hong Kong/8690/2001, and A/swine/Hong Kong/227/2002) , Eurasian avian-like (EA) H1N1 (A/swine/Hong Kong/638/2003, A/swine/Hong Kong/NS129/2003, A/swine/Hong Kong/435/2007, A/swine/Hong Kong/245/2009) , TRIG H1N2 (A/swine/Ontario/52156/2003, A/swine/Ontario/48235/2004, A/swine/Oklahoma/010226-16/2008, A/swine/Texas/008648/2008, A/swine/Hong Kong/1435/2009) , , H3N2v (A/Indiana/10/2011 and A/Maine/06/2011) , and avian H1N1 (avH1N1; A/mallard/Maryland/02-181/2002) and avH3N2 (A/blue-winged teal/Ohio/908/2002) viruses were included in the analysis, except for the HA and NA sequences. For HA gene analysis, only the nucleotide sequences of swine H3N2 and H3N2v viruses were included. For NA gene analysis, only the nucleotide sequences of swine H3N2, TRIG H1N2, and H3N2v viruses were included. Using MEGA5 , each sequence of the swPL01 virus was aligned with that of the references using MUSCLE by the unweighted pair group method with the arithmetic mean . The phylogenetic tree was inferred using the Maximum Likelihood (ML) method by obtaining the initial tree(s) for the heuristic search based on the neighbor-joining method through a matrix of pairwise distances evaluated by the maximum composite likelihood (MCL) approach. The bootstrap scores were determined from 500 replicates and are shown below the branches . The sequences that met our bootstrap score standards (>95% for PB2, PB1, PA, and NP or >60% for HA, NA, M, and NS among the sequences registered since the late 1990s) and that were located in close proximity were recalculated with the Korean swine H3N2 and lineage defining sequences for the final ML tree evaluation. Some HA sequences published previously in 2008 and 2013 were included in the final HA tree for the differentiation of HA clusters. The horizontal distances are the nucleotide differences, which were proportional for the number of changes per site. The genetic distances were determined with MEGA5 by the MCL method using bootstrap estimation (500 replicates). […]

Pipeline specifications

Software tools MEGA, MUSCLE
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Influenza A virus, Sus scrofa, Homo sapiens, Viruses, Human poliovirus 1 Mahoney
Diseases HIV Infections