Metagenomic characterisation of avian parvoviruses and picornaviruses from Australian wild ducks

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

doi:10.1038/s41598-020-69557-z

Abstract

Ducks can shed and disseminate viruses and thus play a role in cross-species transmission. In the current study, we detected and characterised various avian parvoviruses and picornaviruses from wild Pacific black ducks, Chestnut teals, Grey teals and Wood ducks sampled at multiple time points from a single location using metagenomics. We characterised 46 different avian parvoviruses belonging to three different genera Dependoparvovirus, Aveparvovirus and Chaphamaparvovirus, and 11 different avian picornaviruses tentatively belonging to four different genera Sicinivirus, Anativirus, Megrivirus and Aalivirus. Most of these viruses were genetically different from other currently known viruses from the NCBI dataset. The study showed that the abundance and number of avian picornaviruses and parvoviruses varied considerably throughout the year, with the high number of virus reads in some of the duck samples highly suggestive of an active infection at the time of sampling. The detection and characterisation of several parvoviruses and picornaviruses from the individual duck samples also suggests co-infection, which may lead to the emergence of novel viruses through possible recombination. Therefore, as new and emerging diseases evolve, it is relevant to explore and monitor potential animal reservoirs in their natural habitat.

Highlights

Ducks can shed and disseminate viruses and play a role in cross-species transmission
From the initial data analysis, it became apparent that reads mapped to parvoviruses and picornaviruses were abundant compared to other avian viruses in many of the samples included in the current study
Avian parvoviruses and picornaviruses were present in samples from each of the species of ducks captured, and all but one pooled sample contained more than one parvovirus and picornavirus

Summary

Introduction

Ducks can shed and disseminate viruses and play a role in cross-species transmission. 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. Viruses are shown to co-circulate within a community leading to co-infections[6,7,8,9] and may result in the emergence of new viruses through possible reassortment or recombination[10,11,12,13] These novel viruses could have the potential to cause new virus disease with little prophylaxis or therapy to counteract, becoming a OneHealth concern. Little is known about the diversity, host spectrum, pathogenicity, seasonal variation and factors that affect co-circulation and co-infection of avian parvo- and picornaviruses circulating in wild ducks

Methods

Results

Conclusion