Phylogenetic and phylogeographic mapping of the avian coronavirus spike protein-encoding gene in wild and synanthropic birds

Durães-Carvalho, Ricardo; Caserta, Leonardo Cardia; Barnabé, A. C. S; Martini, Matheus Cavalheiro; Simas, Paulo Vitor Marques; Santos, Márcia M.B.; Salemi, Marco; Arns, Clarice Weis

doi:10.1016/j.virusres.2015.03.002

Cited by 17 publications

(17 citation statements)

References 34 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The 5′ UTR detected 66/912 or 7.2% (95% CI: 5.6-8.9%) of samples positive for coronavirus, the nested PCR 100/916 samples or 10.9% (95% CI: 8.9-13.0%) and the modified pancoronavirus PCR 109/915 samples or 11.9% (95% CI: 9.8-14%). By combining the results from the three PCRs, 141/918 or 15.3% (95% CI: [13][14][15][16][17].7%) of all samples tested positive for coronaviruses in at least one PCR assay. Nine hundred and eight samples were tested with all three PCRs.…”

Section: Resultsmentioning

confidence: 99%

“…A real-time TaqMan PCR, originally developed to detect IBV in commercial poultry 35 , and later used to screen wild birds for the presence of coronaviruses 17 , was adapted into a real-time SYBR Green PCR assay using the Power SYBR Green RNA-to-C T 1 step kit (Applied Biosystems, California, USA). The PCR amplified a 142 bp product from the 5′ UTR of gammacoronaviruses using primers IBV5′GU391 (5′-GCT TTT GAG CCT AGC GTT-3′) and IBV5′GL533 (5′-GCC ATG TTG TCA CTG TCT ATT G-3′).…”

Section: ′ Untranslated Region (Utr) Coronavirus Real-time Pcrmentioning

confidence: 99%

“…Wild birds have been implicated in the spread of highly pathogenic H5Nx avian influenza viruses 14 and bird migration patterns describe phylogenetic patterns in the matrix gene of low pathogenic influenza virus 15 . Coronaviruses have been detected in a range of species of wild birds on all continents except for Australia and Antarctica [16][17][18][19][20][21] . It is likely that CoV's are present in wild birds on all continents.…”

mentioning

confidence: 99%

See 2 more Smart Citations

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

Chamings

Nelson

Vibin

et al. 2018

Sci Rep

View full text Add to dashboard Cite

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.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: ′ Untranslated Region (Utr) Coronavirus Real-time Pcrmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

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

Chamings

Nelson

Vibin

et al. 2018

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Due to the advance of the bioinformatics programs for recombination screening, several studies have been performed in order to evaluate if the recombinant events could be the source of these variant isolates described worldwide (Kiss et al, 2016;Naguib et al, 2016;Quinteros et al, 2016). Moreover, the high prevalence of avian coronaviruses circulating in birds other than chicken suggests that wild and synanthropic birds are potential disseminators and could play a role in the emergence of recombinant strains and the dissemination of IBV among distant regions (Durães-Carvalho et al, 2015). Therefore, it might be possible that wild birds are the source of the unclassified sequence fragments observed in the recombinant strains identified in the current study.…”

Section: Discussionmentioning

confidence: 99%

Phylodynamic analysis and molecular diversity of the avian infectious bronchitis virus of chickens in Brazil

Fraga

Gräf

Pereira

et al. 2018

Infection, Genetics and Evolution

View full text Add to dashboard Cite

Avian infectious bronchitis virus (IBV) is the etiological agent of a highly contagious disease, which results in severe economic losses to the poultry industry. The spike protein (S1 subunit) is responsible for the molecular diversity of the virus and many sero/genotypes are described around the world. Recently a new standardized classification of the IBV molecular diversity was conducted, based on phylogenetic analysis of the S1 gene sequences sampled worldwide. Brazil is one of the biggest poultry producers in the world and the present study aimed to review the molecular diversity and reconstruct the evolutionary history of IBV in the country. All IBV S1 gene sequences, with local and year of collection information available on GenBank, were retrieved. Phylogenetic analyses were carried out based on a maximum likelihood method for the classification of genotypes occurring in Brazil, according to the new classification. Bayesian phylogenetic analyses were performed with the Brazilian clade and related international sequences to determine the evolutionary history of IBV in Brazil. A total of 143 Brazilian sequences were classified as GI-11 and 46 as GI-1 (Mass). Within the GI-11 clade, we have identified a potential recombinant strain circulating in Brazil. Phylodynamic analysis demonstrated that IBV GI-11 lineage was introduced in Brazil in the 1950s (1951, 1917-1975 95% HPD) and population dynamics was mostly constant throughout the time. Despite the national vaccination protocols, our results show the widespread dissemination and maintenance of the IBV GI-11 lineage in Brazil and highlight the importance of continuous surveillance to evaluate the impact of currently used vaccine strains on the observed viral diversity of the country.

show abstract

“…Host distributions were based on the species' geographic range defined by the International Union for Conservation of Nature (IUCN) (Cosiaux et al, 2016). To assess the most likely geographic origin of the available WPV, we employed Bayesian Binary Markov Chain Monte Carlo (BBM) method analysis to reconstruct the ancestral regions occupied by PV, as previously used in other studies (Durães-Carvalho et al, 2015;Lauron et al, 2015;Forni et al, 2018). BBM was implemented using the software Reconstruction of Ancestral States in Phylogenies, RASP v3.2 (Yu et al, 2015).…”

Section: Phylogenetic Analysesmentioning

confidence: 99%

Papillomavirus in Wildlife

2019

View full text Add to dashboard Cite

Papillomaviruses (PV) are associated with epithelial malignancies in animals, including cancer in humans. Limited knowledge exists regarding the evolutionary history of non-human PV. We assessed the phylogeography of PV with emphasis in wildlife hosts. We explored the phylogenetic, geographic, and environmental relationships of PV and hosts applying Bayesian inference and spatial analyses of virus and hosts. We found that the available wildlife PV data support previous reports on the higher incidence of fibropapillomatosis over carcinoma in humans and wildlife, being mammals the most common host. We also found geographic bias on the available wildlife papillomavirus (WPV) information toward the Northern Hemisphere, which may have influenced our results to show Europe as the most likely origin of the available WPV lineages. Therefore, we highlight the need for detailed studies on the presence of WPV in regions and species not included in this study (e.g., reptiles from the tropics) to better inform sites of WPV origin, susceptible species, and spillover potential. Future studies of the clinical and subclinical occurrence, distribution, and phylogenetic signatures of WPV may help to understand the spread, virulence, and epidemiology of PV in general. From an evolutionary perspective, our overview suggests that WPV are a promising host-pathogen system to untangle questions regarding co-evolution due to its large geographic distribution and occurrence in a wide variety of aquatic and terrestrial wildlife species.

show abstract

Phylogenetic and phylogeographic mapping of the avian coronavirus spike protein-encoding gene in wild and synanthropic birds

Cited by 17 publications

References 34 publications

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

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

Phylodynamic analysis and molecular diversity of the avian infectious bronchitis virus of chickens in Brazil

Papillomavirus in Wildlife

Contact Info

Product

Resources

About