Prevalence and genetic diversity of coronaviruses in wild birds, Finland

Abstract

Introduction: Migratory birds act as hosts for a number of zoonotic viruses, and have the ability to disperse these viruses to distant geographic locations. Coronaviruses (CoVs) represent a family of zoonotic viruses with wide variety of animal hosts, including birds and humans. The infections caused by coronaviruses vary from mild to severe, depending on the viral species and the host. Since the coronaviruses exhibit extraordinary large RNA genome, also the rate of homologous recombination is high, which in turn contributes to the genetic diversity and interspecies host-switches of CoVs. The emergence of novel CoVs has been rich during the last decades, and wild birds seem to serve as reservoirs for a variety of CoV strains. We examined the CoVs circulating among wild birds in Finland. Materials and methods: Samples (cloacal swab, tracheal swab, oropharyngeal swab, or tissue) representing 61 bird species were collected during 2010-2013, and examined by RT-PCR targeting the RdRp gene for the presence of CoV RNA. Results: Altogether 51/939 (5.4%) of the examined birds were found positive by RT-PCR. Diverse gamma- and deltacoronavirus sequences were detected. Discussion: Gamma- and deltacoronaviruses circulate among wild birds in Finland. The number of CoV-positive birds detected each year varies greatly.

Keywords: Deltacoronavirus; gammacoronavirus; wild birds; zoonoses.

Figure 1.

A map illustrating the sampling locations. The sampling locations (sub-regional units, year 2013) are indicated in the Table 2, and are here illustrated by numbers on a map of Finland.

Figure 2.

Maximum likelihood phylogeny of avian coronaviruses detected in Finland in wild birds. A 464 nucleotide long sequence region of the RdRp gene within Orf1ab was sequenced and aligned with reference sequences: the analysis includes alignments of 46 viruses detected in this study and a diverse set of reference strains obtained through BLAST search. Maximum-likelihood analysis using 1000 bootstrap replicates was used to infer tree topology. The evolutionary model GTR+G + I was used after evaluation of the best-fit model according to Bayesian Information Criterion. Bootstrap support values exceeding 70 are shown next to the nodes. Strains described in this study are marked by dots. Branches have been collapsed where our viruses share high sequence identity, and the branch wideness is relative to the number of viruses included.