Detection of a Reassortant H9N2 Avian Influenza Virus with Intercontinental Gene Segments in a Resident Australian Chestnut Teal

Soren Alexandersen,Anthony Chamings,Marcel Klaassen,Jessy Vibin,Tarka Raj Bhatta

doi:10.3390/v12010088

Abstract

The present study reports the genetic characterization of a low-pathogenicity H9N2 avian influenza virus, initially from a pool and subsequently from individual faecal samples collected from Chestnut teals (Anas castanea) in southeastern Australia. Phylogenetic analyses of six full gene segments and two partial gene segments obtained from next-generation sequencing showed that this avian influenza virus, A/Chestnut teal/Australia/CT08.18/12952/2018 (H9N2), was a typical, low-pathogenicity, Eurasian aquatic bird lineage H9N2 virus, albeit containing the North American lineage nucleoprotein (NP) gene segment detected previously in Australian wild birds. This is the first report of a H9N2 avian influenza virus in resident wild birds in Australia, and although not in itself a cause of concern, is a clear indication of spillover and likely reassortment of influenza viruses between migratory and resident birds, and an indication that any lineage could potentially be introduced in this way.

Highlights

Avian influenza virus (AIV) has major direct and indirect impacts on public and veterinary health, as well as wildlife conservation
Rerunning the same Next Generation Sequencing (NGS) libraries using a 540 chip generated another 31 million reads, of which 129 reads (0.0004% of total reads) mapped to AIV, resulting in a total of 169 reads and covering partial sequences of all eight gene segments of AIV from the pooled sample CT08.18 (Table S1)
low-pathogenicity avian influenza (LPAI) virus from faecal samples collected from two resident Chestnut teals in southeastern Australia

Summary

Introduction

Avian influenza virus (AIV) has major direct and indirect impacts on public and veterinary health, as well as wildlife conservation. AIV is a single-stranded, eight-segmented, negative-sense RNA virus in the family Orthomyxoviridae [1]. Each of the gene segments codes for one or more proteins. The virus surface proteins, hemagglutinin (HA) and neuraminidase (NA), are encoded by two separate gene segments. The internal proteins, which include the polymerase basic proteins 1 and 2 (PB1 and PB2, respectively), polymerase acidic protein (PA), matrix proteins (M1 and M2), nucleoprotein (NP), and nuclear export protein and non-structural protein 1 (NEP-NS1), are encoded by the other six gene segments, respectively [2,3]. AIVs are designated as a low-pathogenicity avian influenza (LPAI)

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Results

Conclusion