Divergent coronaviruses detected in wild birds in Brazil, including a central park in São Paulo

Abstract

Coronaviruses are single-stranded positive-sense RNA viruses associated with important avian diseases. Their relatively high rates of mutation and recombination frequencies allow them to adapt to new hosts and ecological niches. Although Brazil has 18% of global avian species diversity, studies regarding the presence of avian viral diseases in wild birds in South America are scarce. In this study, we performed a retrospective analysis of the presence of CoVs in 746 wild birds. Oropharyngeal and cloacal swabs were obtained and placed together in vials containing VTM transport medium collected in different regions of Brazil between 2006 and 2013. Screening for viral nucleic acid was performed using conventional RT-PCR and pancoronavirus nested PCR. Positive samples were characterized by partial sequencing of the RNA-dependent RNA polymerase (RdRp) gene, and ensuing phylogenetic analysis was performed to investigate the association between virus epidemiology and bird migration routes. Coronavirus RNA were detected and sequenced from six samples, in which three were related to gammacoronaviruses group and the other three to deltacoronavirus group. Our study documents the presence of CoVs related to avian gamma- and deltacoronaviruses circulating in both urban- and poultry-farm regions of Brazil, implicating wild birds as potential carriers of CoVs which may represent a risk to poultry farms and public health in Brazil.

Keywords: Brazil; Deltacoronavirus; Gammacoronavirus; South America; Wild birds.

Fig. 1

Location of sampling sites with positive results for avian CoVs and their relationship with the main bird migratory routes and congregation sites in North and South America. Congregation sites include reproduction, wintering, and tagging areas of boreal migrant birds (modified from http://www.icmbio.gov.br/cemave/)

Fig. 2

Phylogenetic analysis of partial RdRp gene sequence of avian gammacoronaviruses. Phylogenetic tree of partial sequences of the RdRp-encoding region constructed using the neighbor-joining method. In green, CoVs related to gammacoronaviruses sequences detected in samples from Lagoa do Peixe National Park, state of Rio Grande do Sul, southern Brazil. In red, CoVs related to gammacoronaviruses sequences detected in samples from Ibirapuera Park, São Paulo, southeast Brazil. Bootstrap values > 55% were obtained in the analysis of 10,000 replicates and are presented at the branching points

Fig. 3

Phylogenetic analysis of partial RdRp gene sequence of avian deltacoronaviruses. Phylogenetic tree of partial sequences of the RdRp-encoding region constructed using the neighbor-joining method. In green, CoVs related to deltacoronavirus sequences detected in samples from Lagoa do Peixe National Park, state of Rio Grande do Sul, southern Brazil. In red, CoVs related to deltacoronavirus sequences detected in samples from Ibirapuera Park, São Paulo, southeast Brazil. Bootstrap values > 55% were obtained in the analysis of 10,000 replicates and are presented at the branching points