Divergent Human-Origin Influenza Viruses Detected in Australian Swine Populations
Frank Wong(Commonwealth Scientific and Industrial Research Organisation), Celeste M. Donato(Australian Regenerative Medicine Institute), Yi‐Mo Deng(Peter Doherty Institute), Don Teng(Australian Regenerative Medicine Institute), Naomi Komadina(Peter Doherty Institute), Chantal Baas(Peter Doherty Institute), Joyanta K. Modak(Australian Regenerative Medicine Institute), Mark O’Dea(Murdoch University), David W. Smith(The University of Western Australia), Paul V. Effler(The University of Western Australia), Julie Cooke(Commonwealth Scientific and Industrial Research Organisation), Kelly R. Davies(Commonwealth Scientific and Industrial Research Organisation), Aeron C. Hurt(Peter Doherty Institute), Nina Kung, Avram Levy(The University of Western Australia), Richmond Loh(Department of Primary Industries and Regional Development), Songhua Shan(Commonwealth Scientific and Industrial Research Organisation), Mustaghfira Wafa Shinwari, Vittoria Stevens(Commonwealth Scientific and Industrial Research Organisation), Joanne Taylor(Commonwealth Scientific and Industrial Research Organisation), David T. Williams(Commonwealth Scientific and Industrial Research Organisation), James Watson(Commonwealth Scientific and Industrial Research Organisation), Debbie Eagles(Commonwealth Scientific and Industrial Research Organisation), Sam McCullough(Commonwealth Scientific and Industrial Research Organisation), Ian Barr(Peter Doherty Institute), Dhanasekaran Vijaykrishna(Australian Regenerative Medicine Institute)
We describe the evolutionary origins and antigenic properties of influenza A viruses isolated from two separate Australian swine populations from 2012 to 2016, showing that these viruses are distinct from each other and from those isolated from swine globally. Whole-genome sequencing of virus isolates revealed a high genotypic diversity that had been generated exclusively through the introduction and establishment of human influenza viruses that circulated in past seasons. We detected six reassortants with gene segments derived from human H1N1/H1N1pdm09 and various human H3N2 viruses that circulated during various periods since 1968. We also found that these swine viruses were not related to swine viruses collected elsewhere, indicating independent circulation. The detection of unique lineages and genotypes in Australia suggests that isolated swine populations that are sufficiently large can sustain influenza virus for extensive periods; we show direct evidence of a sustained transmission for at least 4 years between 2012 and 2016.