title: Phylogenetic and phylogeographic mapping of the avian coronavirus spike protein-encoding gene in wild and synanthropic birds.
abstract: The evolution and population dynamics of avian coronaviruses (AvCoVs) remain underexplored. In the present study, in-depth phylogenetic and Bayesian phylogeographic studies were conducted to investigate the evolutionary dynamics of AvCoVs detected in wild and synanthropic birds. A total of 500 samples, including tracheal and cloacal swabs collected from 312 wild birds belonging to 42 species, were analysed using molecular assays. A total of 65 samples (13%) from 22 bird species were positive for AvCoV. Molecular evolution analyses revealed that the sequences from samples collected in Brazil did not cluster with any of the AvCoV S1 gene sequences deposited in the GenBank database. Bayesian framework analysis estimated an AvCoV strain from Sweden (1999) as the most recent common ancestor of the AvCoVs detected in this study. Furthermore, the analysis inferred an increase in the AvCoV dynamic demographic population in different wild and synanthropic bird species, suggesting that birds may be potential new hosts responsible for spreading this virus.
authors.affiliation: Laboratory of Virology, Department of Genetics, Evolution and Bioagents, University of Campinas (UNICAMP), São Paulo, Brazil; Emerging Pathogens Institute & Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA. Electronic address: rdcarval@gmail.com.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Durães-Carvalho
authors.affiliation: Laboratory of Virology, Department of Genetics, Evolution and Bioagents, University of Campinas (UNICAMP), São Paulo, Brazil.
authors.forename: Leonardo C
authors.initials: LC
authors.lastname: Caserta
authors.affiliation: Laboratory of Virology, Department of Genetics, Evolution and Bioagents, University of Campinas (UNICAMP), São Paulo, Brazil.
authors.forename: Ana C S
authors.initials: AC
authors.lastname: Barnabé
authors.affiliation: Laboratory of Virology, Department of Genetics, Evolution and Bioagents, University of Campinas (UNICAMP), São Paulo, Brazil.
authors.forename: Matheus C
authors.initials: MC
authors.lastname: Martini
authors.affiliation: Laboratory of Virology, Department of Genetics, Evolution and Bioagents, University of Campinas (UNICAMP), São Paulo, Brazil.
authors.forename: Paulo V M
authors.initials: PV
authors.lastname: Simas
authors.affiliation: Department of Biological Sciences, Federal University of Juiz de Fora, Minas Gerais, Brazil.
authors.forename: Márcia M B
authors.initials: MM
authors.lastname: Santos
authors.affiliation: Emerging Pathogens Institute & Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL, USA.
authors.forename: Marco
authors.initials: M
authors.lastname: Salemi
authors.affiliation: Laboratory of Virology, Department of Genetics, Evolution and Bioagents, University of Campinas (UNICAMP), São Paulo, Brazil. Electronic address: clarns@gmail.com.
authors.forename: Clarice W
authors.initials: CW
authors.lastname: Arns
mesh_terms: D000818:Animals; D001715:Bird Diseases / Q000821:virology*; D001717:Birds; D002988:Cloaca / Q000821:virology; D016000:Cluster Analysis; D019295:Computational Biology; D017934:Coronavirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D018352:Coronavirus Infections / Q000662:veterinary* / Q000821:virology; D019143:Evolution, Molecular; D014644:Genetic Variation; D005838:Genotype; D014943:Global Health; D058974:Phylogeography; D012367:RNA, Viral / Q000235:genetics; D064370:Spike Glycoprotein, Coronavirus / Q000235:genetics*; D014132:Trachea / Q000821:virology
chemical_list: D012367:RNA, Viral; D064370:Spike Glycoprotein, Coronavirus
keywords: Avian coronaviruses; Bayesian phylogeography; Phylogeny