Diverse gammacoronaviruses detected in wild birds from Madagascar

Abstract

To date, infectious bronchitis virus (IBV) is potentially found in wild birds of different species. This work reports the survey of coronaviruses in wild birds from Madagascar based on the targeting of a conserved genome sequence among different groups of CoVs. Phyl o g e n e t i c a n a l y s e s r e v e a l e d t h e p r e s e n c e o f gammacoronaviruses in different species of Gruiformes, Passeriformes, Ciconiiformes, Anseriformes, and Charadriiformes. Furthermore, some sequences were related to various IBV strains. Aquatic and migratory birds may play an important role in the maintenance and spread of coronaviruses in nature, highlighting their possible contribution in the emergence of new coronavirus diseases in wild and domestic birds.

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

“…Even within the Charadriiformes lineages, the degree of genetic difference to duck sequences was much less than that seen in the deltacoronavirus phylogeny. The phylogeny based on the amino acid sequence of the gammacoronaviruses separated the majority of the duck and Charadriiform gammacoronaviruses into separate branches, however both the curlew sandpiper gammacoronaviruses and a single ruddy turnstone gamma-CoV were identical in amino acid homology to duck Australian duck gamma-CoV's as well as duck gamma-CoV's identified in other investigations 16,18,20,25,27 . These results again suggest that migratory Charadriiformes may share gammacoronaviruses with other avian species 16,18 and are therefore important vectors and reservoir of coronaviruses.…”

“…The phylogeny based on the amino acid sequence of the gammacoronaviruses separated the majority of the duck and Charadriiform gammacoronaviruses into separate branches, however both the curlew sandpiper gammacoronaviruses and a single ruddy turnstone gamma-CoV were identical in amino acid homology to duck Australian duck gamma-CoV's as well as duck gamma-CoV's identified in other investigations 16,18,20,25,27 . These results again suggest that migratory Charadriiformes may share gammacoronaviruses with other avian species 16,18 and are therefore important vectors and reservoir of coronaviruses. Hughes, et al 23 and Chu, et al 16 identified similar gammacoronavirus sequences between Charadriiformes and Anseriformes, while Lima, et al 18 found similar gammacoronaviruses in Charadriiformes and Gruiformes in Madagascar.…”

“…The small fragment of the coronavirus genome sequenced in this study is one of the most conserved regions of the viral polymerase gene 24 . It is the most sequenced genomic region of coronaviruses from wild bird hosts, with many studies using PCRs targeting this region to detect avian coronaviruses 16,18,24,26 . The fragment analysed in this study represents about 1% of the coronavirus genome, and therefore any interpretation of relationships in the phylogenetic tree should be made cautiously.…”

“…Wild birds have been implicated in the spread of highly pathogenic H5Nx avian influenza viruses 14 and bird migration patterns describe phylogenetic patterns in the matrix gene of low pathogenic influenza virus 15 . Coronaviruses have been detected in a range of species of wild birds on all continents except for Australia and Antarctica [16][17][18][19][20][21] . It is likely that CoV's are present in wild birds on all continents.…”

“…Studies in which wild bird coronaviruses have been successfully detected, have commonly sampled aquatic bird species such as Anseriformes (ducks, geese and swans) and Charadriiformes (gulls, migratory shorebirds and waders) 16,18,20,23,24 . This prompted our study to look for coronaviruses in Australian birds that notably belong to these two orders.…”