Prevalence and evolution of avian H1 subtype influenza A viruses in Southern China

Abstract

H1 subtype influenza A viruses were the causative agents for three major pandemics in the last century, and have been circulating in human and pigs for decades. However, the natural reservoirs of H1 subtype avian influenza viruses (AIVs) are aquatic birds, which could provide highly diversified candidates for avian-to-mammalian transmissions. Currently, most of the avian H1 sequences in public database are contributed by surveillance of North American wild waterfowl, with only a very small amount from Europe and Asia, implicating a surveillance gap. How H1 AIVs persist in the gene pool and interact with other lineages or subtypes of AIVs remains unclear. Based on long-term surveillance conducted in seven provinces in southern China during the 1970s and from 2001 to 2013, we identified 351 H1 AIVs out of 556,122 samples (0.06 per cent) from wild birds, domestic ducks, geese, chickens, and minor poultry. This only accounted for 0.77 per cent of the influenza positive samples. No H1 AIVs were isolated from terrestrial poultry and 83.5 per cent of the H1 AIVs were isolated from domestic ducks. About 252 avian H1 isolates were selected for NGS sequencing and 148 non-mixed H1 genomes were obtained. Preliminary phylogenetic analysis revealed that the majority of the H1 AIVs belonged to the large monophyletic Eurasian avian gene pool clade, with frequent reassortments with other subtypes of influenza viruses. Of the 148 H1 AIVs analyzed, 64 genotypes were identified. Despite the low prevalence of H1 AIVs, which may restrict their chance of interspecies transmission, we discovered a superior mammalian infectivity of H1 AIVs compared with other subtypes including H2 to H10, except H5 and H8. Taking the complicated regional poultry farming system and live poultry marketing into consideration, the H1 viruses might be able to reassort with other viruses and generate advantageous variants to cause outbreak in human and other mammals, as exemplified by the case of H7N9. Early identification of emerging H1 AIVs with inter-species transmission potential requires continuous surveillance and monitor on the gene flow and evolutionary patterns of these viruses.