Coronaviruses Detected in Brazilian Wild Birds Reveal Close Evolutionary Relationships with Beta- and Deltacoronaviruses Isolated From Mammals

Durães-Carvalho, Ricardo; Caserta, Leonardo Cardia; Barnabé, Ana Caroline de Souza; Martini, Matheus Cavalheiro; Ferreira, Helena Lage; Felippe, Paulo Anselmo Nunes; Santos, Márcia B. dos; Arns, Clarice Weis

doi:10.1007/s00239-015-9693-9

Cited by 22 publications

(25 citation statements)

References 9 publications

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“…This assay has been used for the identification and differentiation of CoV in the four genera d e s c r i b e d t o d a t e ( a l p h a -, b e t a -, g a m m a -, a n d deltacoronavirus) [17,19,20]. Similarly to our report, most of avian CoV diversity studies detected the same coronavirus genera [2,17,21,22], with the exception of a report of betacoronavirus detection in distinct birds species from a rehabilitation center in Brazil [8]. Further studies are needed to understand the circulation of betacoronavirus in birds.…”

Section: Discussionsupporting

confidence: 84%

“…The overall prevalence of CoV found in this study was 0.8% (6/746 birds), with 3.7% (3/81) from Ibirapuera Park and 1.6% (3/192) from migratory birds captured in Lagoa do Peixe National Park. Other studies report an overall prevalence of CoV in aquatic and migratory birds between 0.33 and 18.5% [8,17,21,30,31]. This data reinforces that CoVs are circulating across major migratory routes worldwide.…”

Section: Discussionsupporting

confidence: 73%

“…Moreover, many novel CoVs genetically distinct from IBV have been recently identified in different families of wild and domestic birds and mammals but their potential economic losses remain unknown. Recently, Durães-Carvalho et al (2015), described the detection of delta-and betacoronaviruses in captive wild birds, from a rehabilitation center, originally captured in São Paulo and Mato Grosso do Sul state with close evolutionary relationships with CoVs isolated from mammals [8].…”

Section: Responsible Editor: Fernando Spilkimentioning

confidence: 99%

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

et al. 2019

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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.

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Section: Discussionsupporting

confidence: 84%

Section: Discussionsupporting

confidence: 73%

Section: Responsible Editor: Fernando Spilkimentioning

confidence: 99%

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

et al. 2019

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“…Phylogenetic analyses of the spike gene of PDCoV showed that PDCoV were closely related to CoVs isolated from the Asian leopard cats and Chinese ferret badgers (nt similarity ≥ 99.8%) and also wild birds (sparrow, magpie robin), implying the potential interspecies transmission of a δ-CoV between these wild mammals, birds, and pigs (Dong et al, 2007;Jung et al, 2016). CoVs are frequently detected in the feces of wild birds, which may act as reservoirs for avian γand δ-CoVs analyse (Duraes-Carvalho et al, 2015;Torres et al, 2017). Phylogenetic analysis revealed that two isolates clustered in the δ-CoVs genus and had the closest relationship with wild avian CoV strains, indicating the existence of δ-CoV in avian fecal samples from the US.…”

Section: Discussionmentioning

confidence: 96%

Development of a one-step RT-PCR assay for detection of pancoronaviruses (α-, β-, γ-, and δ-coronaviruses) using newly designed degenerate primers for porcine and avian `fecal samples

Jung

Wang

et al. 2018

Journal of Virological Methods

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Coronaviruses (CoVs) are critical human and animal pathogens because of their potential to cause severe epidemics of respiratory or enteric diseases. In pigs, the newly emerged porcine deltacoronavirus (PDCoV) and re-emerged porcine epidemic diarrhea virus (PEDV) reported in the US and Asia, as well as the discovery of novel CoVs in wild bats or birds, has necessitated development of improved detection and control measures for these CoVs. Because the previous pancoronavirus (panCoV) RT-PCR established in our laboratory in 2007-2011 did not detect deltacoronaviruses (δ-CoVs) in swine fecal and serum samples, our goal was to develop a new panCoV RT-PCR assay to detect known human and animal CoVs, including δ-CoVs. In this study, we designed a new primer set to amplify a 668 bp-region within the RNA-dependent RNA polymerase (RdRP) gene that encodes the most conserved protein domain of α-, β-, γ-, and δ-CoVs. We established a one-step panCoV RT-PCR assay and standardized the assay conditions. The newly established panCoV RT-PCR assay was demonstrated to have a high sensitivity and specificity. Using a panel of 60 swine biological samples (feces, intestinal contents, and sera) characterized by PEDV, PDCoV and transmissible gastroenteritis virus-specific RT-PCR assays, we demonstrated that sensitivity and specificity of the newly established panCoV RT-PCR assay were 100%. 400 avian fecal (RNA) samples were further tested simultaneously for CoV by the new panCoV RT-PCR and a one-step RT-PCR assay with the δ-CoV nucleocapsid-specific universal primers. Four of 400 avian samples were positive for CoV, three of which were positive for δ-CoV by the conventional RT-PCR. PanCoV RT-PCR fragments for 3 of the 4 CoVs were sequenced. Phylogenetic analysis revealed the presence of one γ-CoV and two δ-CoV in the sequenced samples. The newly designed panCoV RT-PCR assay should be useful for the detection of currently known CoVs in animal biological samples.

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“…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.…”

Section: Discussionmentioning

confidence: 99%

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

Chamings

Nelson

Vibin

et al. 2018

Sci Rep

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We evaluated the presence of coronaviruses by PCR in 918 Australian wild bird samples collected during 2016–17. Coronaviruses were detected in 141 samples (15.3%) from species of ducks, shorebirds and herons and from multiple sampling locations. Sequencing of selected positive samples found mainly gammacoronaviruses, but also some deltacoronaviruses. The detection rate of coronaviruses was improved by using multiple PCR assays, as no single assay could detect all coronavirus positive samples. Sequencing of the relatively conserved Orf1 PCR amplicons found that Australian duck gammacoronaviruses were similar to duck gammacoronaviruses around the world. Some sequenced shorebird gammacoronaviruses belonged to Charadriiformes lineages, but others were more closely related to duck gammacoronaviruses. Australian duck and heron deltacoronaviruses belonged to lineages with other duck and heron deltacoronaviruses, but were almost 20% different in nucleotide sequence to other deltacoronavirus sequences available. Deltacoronavirus sequences from shorebirds formed a lineage with a deltacoronavirus from a ruddy turnstone detected in the United States. Given that Australian duck gammacoronaviruses are highly similar to those found in other regions, and Australian ducks rarely come into contact with migratory Palearctic duck species, we hypothesise that migratory shorebirds are the important vector for moving wild bird coronaviruses into and out of Australia.

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Coronaviruses Detected in Brazilian Wild Birds Reveal Close Evolutionary Relationships with Beta- and Deltacoronaviruses Isolated From Mammals

Cited by 22 publications

References 9 publications

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

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

Development of a one-step RT-PCR assay for detection of pancoronaviruses (α-, β-, γ-, and δ-coronaviruses) using newly designed degenerate primers for porcine and avian `fecal samples

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

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