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Frozen in Time. Coming Alive. Secrets of the Dead. The Disappearing Sun. Impending Doom. On Broken Glass. Destroy and Dominate. Virus Genes 48 , 56—63 Voorhees, I. J Virol. Weese, J. Cottam, E. Transmission pathways of foot-and-mouth disease virus in the United Kingdom in PLoS Pathog. Lam, T. Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia. PLoS Pathog 4 , e Cattoli, G. Highly pathogenic avian influenza virus subtype H5N1 in Africa: a comprehensive phylogenetic analysis and molecular characterization of isolates.

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Syst Biol. Kosakovsky Pond, S. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Murrell, B. Detecting individual sites subject to episodic diversifying selection. Plos Genet. FUBAR: a fast, unconstrained bayesian approximation for inferring selection.

Delport, W. Datamonkey a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26 , — Download references. We would like to thank Dr. Andrea Kroeker for reviewing the manuscript. You can also search for this author in PubMed Google Scholar.

B designed and planned the study. All authors reviewed and approved the final manuscript. Correspondence to Yohannes Berhane. Reprints and Permissions.

Sci Rep 10, Download citation. Received : 05 November Accepted : 12 March Published : 14 April Anyone you share the following link with will be able to read this content:. Sorry, a shareable link is not currently available for this article.

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Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily. Skip to main content Thank you for visiting nature. Download PDF. Subjects Influenza virus. Figure 1. Full size image. Results Sequence analysis Strains from epidemiological clusters C1 and C2 showed complete coding lengths for all eight gene segments i. H3 numbering is used for codon positions in HA. Full size table. Table 2 The evolutionary divergence over sequence pairs between epidemiological clusters.

Percent of amino acid differences indicated in the upper triangle and percent nucleotide differences in the lower triangle. Figure 2. Figure 3. Figure 4. Table 3 Mean nucleotide substitution rates and estimation of time of the most recent common ancestor for each gene segment of H3N2 CIVs.

Table 4 Amino acid sites under putative positive selection detected using different analytical models. H3 numbering for HA is in brackets. References 1. Article Google Scholar 2. Article Google Scholar 3. PubMed Google Scholar 4. Article Google Scholar 8. Article Google Scholar 9. Article Google Scholar View author publications.

Ethics declarations Competing interests The authors declare no competing interests. Supplementary information. Figure S1, S2 and S3. Supplementary Table S1. About this article. Cite this article Xu, W. Copy to clipboard.