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Volume 26, Number 1—January 2020
Dispatch

Locally Acquired Human Infection with Swine-Origin Influenza A(H3N2) Variant Virus, Australia, 2018

Yi-Mo DengComments to Author , Frank Y.K. Wong, Natalie Spirason, Matthew Kaye, Rebecca Beazley, Migue L.l Grau, Songhua Shan, Vittoria Stevens, Kanta Subbarao, Sheena Sullivan, Ian G. Barr, and Vijaykrishna DhanasekaranComments to Author 
Author affiliations: World Health Organization Collaborating Centre for Reference and Research on Influenza, Melbourne, Victoria, Australia (Y.-M. Deng, N. Spirason, M. Kaye, K. Subbarao, S. Sullivan, I.G. Barr, V. Dhanasekaran); CSIRO Australian Animal Health Laboratory, Geelong, Victoria, Australia (F.Y.K. Wong, S. Shan, V. Stevens); South Australian Department of Health and Wellbeing, Adelaide, South Australia, Australia (R. Beazley); Monash University, Melbourne (M.L. Grau, V. Dhanasekaran); University of Melbourne, Melbourne (S. Sullivan, I.G. Barr)

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Figure 1

Genetic origin of influenza A/South Australia/85/2018 virus isolated from a human patient in Australia (red) from swine influenza A(H3N2) and H1N1pdm09 viruses. Blue indicates influenza A viruses from swine in Australia. A, B) Maximum-likelihood phylogenies estimated by using RAxML version 8 (10) of the HA and NA genes (A) and PB2 gene (B) showing bootstrap values at branch nodes (Appendix). The origins of the remaining 5 internal proteins genes (PB1, PA, NP, MP, and NS) are provided in Appendix

Figure 1. Genetic origin of influenza A/South Australia/85/2018 virus isolated from a human patient in Australia (red) from swine influenza A(H3N2) and H1N1pdm09 viruses. Blue indicates influenza A viruses from swine in Australia. A, B) Maximum-likelihood phylogenies estimated by using RAxML version 8 (10) of the HA and NA genes (A) and PB2 gene (B) showing bootstrap values at branch nodes (Appendix). The origins of the remaining 5 internal proteins genes (PB1, PA, NP, MP, and NS) are provided in Appendix Figure 2, and the GenBank accession numbers and dates of sampling are provided in Appendix Table 4. Scale bars indicate nucleotide substitutions per site. C) Calculation of tMRCA. Red indicates means and 95% CIs of the time of origin of each of the Australia swine influenza A virus lineages from human seasonal influenza viruses. Numbers denote viruses that shared the same tMRCA and that formed a similar lineage. Green indicates the time of divergence of A/South Australia/85/2018 from A/swine/WA/2577766G/2012 (H3N2) (for the H3 HA gene) and A/swine/Victoria/18-04095-0003/2018 (H1N1) (for 5 internal protein genes: PB2, PB1, PA, NP, and MP). N2 and NS proteins of A/South Australia/85/2018 are directly derived from human viruses. Divergence times were estimated by using the uncorrelated log-normal relaxed clock model (11) in a Bayesian Markov chain Monte Carlo framework in BEAST version 1.10 (https://beast.community). A/SA, A/South Australia/85/2018 virus; HA, hemagglutinin; MP, matrix protein; NA, neuraminidase; NP, nucleoprotein; NS, nonstructural; PA, polymerase acidic; PB, polymerase basic; A(H1N1)pdm09 virus, 2009 pandemic influenza H1N1 virus; tMRCA, time to most recent common ancestor.

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