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

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.

Metagenomic characterisation of additional and novel avian viruses from Australian wild ducks

“…Using this method, we have now conducted a surveillance study of Australian wild ducks from which faecal samples were collected at different time points from a single location. As reported earlier 1,3,4,6 and also shown in the current study, we were able to detect and characterise both DNA and RNA viruses. We were also able to characterise novel viruses from these ducks 6 .…”

“…Birds, notably wild ducks, can be reservoirs for zoonotic viruses including, but not limited to, influenza viruses 1 , 2 and coronaviruses 3 , 4 . These viruses could become potential threats to other wild animals, poultry and possibly humans under the right set of circumstances 2 .…”

SARS-CoV-2 genomic and subgenomic RNAs in diagnostic samples are not an indicator of active replication

“…In addition, two of the samples (GC-11 and GC-14) that yielded a low virus coverage by this method, were amplified separately (GC-11/38 and GC-14/37) using essentially the same method, but with the Ampliseq HiFi mix replaced with Amplitaq Gold 360 Master mix for the amplification step. Amplification was done for either 21, 27, or 35 cycles depending on the estimated virus load in the samples 26 and libraries prepared and run on Ion Torrent 530 chips on an Ion S5 XL genetic sequencer (Thermofisher Scientific) at a concentration of 50 pM as per the manufacturer's protocols 26,32,35 . Generated sequence reads were then mapped to a SARS-CoV-2 reference genome (Wuhan-Hu-1-NC_045512/MN908947.3 [https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2/ and https://www.ncbi.nlm.nih.gov/nuccore/MN908947.3]) using the TMAP software included in the Torrent Suite 5.10.1 36 , and virus genomic consensus sequences generated using additional Torrent Suite plugins supplied by Thermofisher Scientific, and visualized in Integrative Genomic Viewer 37 (IGV 2.6.3) (Broad Institute, Cambridge, MA, USA).…”

Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks

“…Following template preparation, the chips were run on an Ion Torrent S5XL System (Thermo Fisher Scientific) as per company protocols. Two individual Chestnut teal samples (CT08.18/11356 and CT08.18/12952) from August 2018 and which formed part of pool CT08.18 were also processed and sequenced as described for the pooled samples, to obtain more virus sequences of a low pathogenicity H9N2 avian influenza virus detected in that sample 4 .…”

“…Birds and other animals can be reservoirs for zoonotic viruses that may have serious implications for human health and agriculture, for example, avian influenza A virus 1 or severe acute respiratory syndrome coronavirus 2 . Among birds, notably wild ducks constitute a significant reservoir for viruses including, but not limited to, influenza viruses 3 , 4 and coronaviruses 5 , 6 . Such viruses can become potential threats by spreading to other animals and humans.…”