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Sci Rep. 2018 Apr 13;8(1):5980. doi: 10.1038/s41598-018-24407-x.

Detection and characterisation of coronaviruses in migratory and non-migratory Australian wild birds.

Author information

1
Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria, Australia.
2
Deakin University, School of Medicine, Geelong, Victoria, Australia.
3
WHO Collaborating Centre for Reference and Research on Influenza, the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
4
Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.
5
Geelong Centre for Emerging Infectious Diseases, Geelong, Victoria, Australia. soren.alexandersen@deakin.edu.au.
6
Deakin University, School of Medicine, Geelong, Victoria, Australia. soren.alexandersen@deakin.edu.au.
7
Barwon Health, University Hospital Geelong, Geelong, Victoria, Australia. soren.alexandersen@deakin.edu.au.

Abstract

We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016-17. Coronaviruses were detected in 141 samples (15.3%) from species of ducks, shorebirds and herons and from multiple sampling locations. Sequencing of selected positive samples found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive samples. Sequencing of the relatively conserved Orf1 PCR amplicons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.

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