Distribution of Avian Influenza Viruses According to Environmental Surveillance During 2014-2017, China

Abstract Background Avian influenza viruses persist in animal hosts and continue to cause human infections in China. It is important to analyse the geographic and seasonal distributions of avian influenza viruses and compare the subtypes and their prevalence among sample sites in environment.MethodsA total of 329,276 environmental samples were collected from locations associated with poultry and wild birds from 2014 to 2017. Viral RNA was extracted from the environmental samples. Real-time PCR assays for influenza A, and the H5, H7, and H9 subtypes were performed on all the samples. Virus isolation was performed on the influenza A-positive samples detected by real-time PCR. Whole-genome sequencing was then performed on an Illumina sequencer.ResultsThe proportions of samples that tested positive for total influenza A and the H5, H9 and H7 subtypes varied among different geographical regions and seasons. Significantly higher proportions of influenza A- and H5-, H9-, and H7-positive samples were collected from live poultry markets and poultry slaughtering locations. Influenza A positivity rates in sewage and chopping board swab samples were higher than those in other sample types. Multiple subtypes related to avian influenza viruses, including 9 HA and 7 NA subtypes, were detected in environmental samples.ConclusionsThese findings indicate that multiple subtypes of avian influenza A viruses continuously coexist in environments associated with poultry and increase the risk of reassortment and transmission, highlighting the need for environmental surveillance in China.