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.

Coronaviruses in wild birds – A potential and suitable vector for global distribution

“…showing the capacity for spillover events between bird and mammal hosts of CoVs (Barbosa et al, 2019). Other studies also found delta-CoV from Psittaciformes (Duraes-Carvalho et al, 2015) and IBV (Mass, Conn) from Columbiformes birds in Brazil (Felippe et al, 2010).…”

“…Barbosa et al. (2019) carried out a retrospective study of the existence of CoVs in 746 wild birds whereby CoV RNA was observed and sequenced from six samples (0.8%), three of which were linked to gamma‐CoV and the other three to delta‐CoV. The research evidence indicates the finding of avian gamma‐ and delta‐CoV in birds obtained in the south‐eastern and southern regions of Brazil, more precisely in Sao Paulo and the state of Rio Grande do Sul.…”

“…One sample revealed similarity (93%) with sequences from gamma‐CoV viruses that are related only to migratory birds, whereas the other two (84%) belonged to delta‐CoV. Despite these sequences being closely similar to those of wild bird CoVs, this category also contains ferret, pig and leopard CoVs, showing the capacity for spillover events between bird and mammal hosts of CoVs (Barbosa et al., 2019). Other studies also found delta‐CoV from Psittaciformes (Duraes‐Carvalho et al., 2015) and IBV (Mass, Conn) from Columbiformes birds in Brazil (Felippe et al., 2010).…”

“…Gamma‐CoV‐positive samples were collected from one individual Calidris alba and one individual Calidris fuscicollis belonging to a restricted species of sandpiper. Delta‐CoV‐positive samples were obtained from a black skimmer ( Rynchops niger ), carrying a strain that clustered similarly to the clade of viruses found in Ibirapuera Forest in a phylogenetic study (Barbosa et al., 2019). Although it is difficult to foresee, many migratory species may have past interaction with migratory birds from Western/Central Siberia, the Balkans, the Black Sea and Central Asia using East African flyways to enter wintering areas to rest along with the river systems that cross the Arab Peninsula and the Nile (Lima et al., 2015).…”

Taking a lesson from the COVID-19 pandemic: Preventing the future outbreaks of viral zoonoses through a multi-faceted approach

“…Importantly, it is not only Asian bats that should be covered by environmental coronavirus surveillance but also strains associated with avian hosts, including synanthropic species. A number of previous studies have already indicated that birds from different geographical areas and related to terrestrial and aquatic ecosystems serve as the reservoirs for various delta- and gammacoronaviruses ( Barbosa et al, 2019 ; Chamings et al, 2018 ; Chu et al, 2011 ; Hughes et al, 2009 ; Miłek and Blicharz-Domańska, 2018 ; Paim et al, 2019 ; Wartecki and Rzymski, 2020 ). None of these are known to be pathogenic to humans, although potential cross-species transmission must be taken into account because: i) selected strains associated with avian hosts are closely related to coronaviruses identified in mammals ( Woo et al, 2009 ), and ii) a recent bird-swine transmission of deltacoronavirus is believed to have occurred ( Lau et al, 2018 ), and recombination, which is a common phenomenon in coronaviruses, has frequently concerned the spike region which is involved in receptor binding ( Lau et al, 2018 ).…”