High Prevalence and Putative Lineage Maintenance of Avian Coronaviruses in Scandinavian Waterfowl

Abstract

Coronaviruses (CoVs) are found in a wide variety of wild and domestic animals, and constitute a risk for zoonotic and emerging infectious disease. In poultry, the genetic diversity, evolution, distribution and taxonomy of some coronaviruses have been well described, but little is known about the features of CoVs in wild birds. In this study we screened 764 samples from 22 avian species of the orders Anseriformes and Charadriiformes in Sweden collected in 2006/2007 for CoV, with an overall CoV prevalence of 18.7%, which is higher than many other wild bird surveys. The highest prevalence was found in the diving ducks--mainly Greater Scaup (Aythya marila; 51.5%)--and the dabbling duck Mallard (Anas platyrhynchos; 19.2%). Sequences from two of the Greater Scaup CoV fell into an infrequently detected lineage, shared only with a Tufted Duck (Aythya fuligula) CoV. Coronavirus sequences from Mallards in this study were highly similar to CoV sequences from the sample species and location in 2011, suggesting long-term maintenance in this population. A single Black-headed Gull represented the only positive sample from the order Charadriiformes. Globally, Anas species represent the largest fraction of avian CoV sequences, and there seems to be no host species, geographical or temporal structure. To better understand the eitiology, epidemiology and ecology of these viruses more systematic surveillance of wild birds and subsequent sequencing of detected CoV is imperative.

Fig 1. Global phylogeny of avian gammacoronavirus partial RdRp.

(a) Radial projection of all current wild bird sequences, including only a few “IBV-like” sequences to root the tree, and (b) the clade containing most of the Mallard CoV sequences generated in this study. Tips are coloured by geographic origin of sequence, Mallard CoV sequences generated in this study are indicated with a filled circle and Scaup CoV sequences with an asterisk. Scale bar represents number of substitutions per site. Traditional projection of panel A with support values is presented in S2 Fig.