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Evolutionary genomics of the pandemic 2009 H1N1 influenza viruses (pH1N 1v)

Yanhua Qu1, Ruiying Zhang13, Peng Cui1, Gang Song1, Ziyuan Duan2* and Fumin Lei1*

Author Affiliations

1 Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China

2 Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China

3 Graduate School of the Chinese Academy of Sciences, Beijing, 100039, China

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Virology Journal 2011, 8:250  doi:10.1186/1743-422X-8-250

Published: 21 May 2011

Additional files

Additional file 1:

Figure S1. Phylogenetic trees of H1N1 influenza viruses. ML phylogenies based on PB1, PB2, NP, MP and NS gene segments respectively. Human lineage is showed in red; while swine and avian are characterized in green and blue, respectively. Transmissions among swine, avian and human viruses between 1988 and 1992 are highlighted in blue. The closest related swine viruses of 2009 H1N1 viruses are highlighted in red.

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Additional file 2:

Figure S2. Possible reassortments of PB1 in the emergence of 2009 H1N1 viruses. The PB1 has undergone more complex reassortments, which occurred among North American avian, human and swine viruses.

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Additional file 3:

Table S1. Nucleotide identities (uncorrected P distance) between 2009 H1N1 viruses and their closest related swine viruses.

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Additional file 4:

Table S2. Time of recent common ancestors (TMRCA) for 2009 H1N1 viruses and their closest related swine viruses.

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Additional file 5:

Figure S3. Population dynamic estimates for classical, Eurasian and avian-to-swine reassortant swine sublineages. X-axis: time in years before present; Y-axis: estimated population size [units = Neτ, the product of effective population size and generation length in years (log-transformed)]. The median estimate and both 95% HPD limits are indicated.

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