Evolution of Bovine viral diarrhea virus in Canada from 1997 to 2013

Chernick, Adam; Meer, Frank van der

doi:10.1016/j.virol.2017.06.024

Cited by 26 publications

(29 citation statements)

References 52 publications

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“…The evolution of the CSFV E2 gene was estimated between 1.73 × 10 −3 and 5.76 × 10 −4 substitutions/site/year [ 34 , 35 ], while the full genome estimation was 1.03 × 10 −4 substitutions/site/year [ 36 ]. For BVDV, evolutionary rates of 1.40 × 10 −4 substitutions/site/year for the full genome and 1.26 × 10 −3 substitutions/site/year for the E1-E2 coding region were reported [ 37 ]. A recombination analysis was done using the RDP4 software in order to find breakpoints within the multiple sequence alignment that might have undergone recombination, and to screen them for evidence of phylogenetic incongruence previous to phylogenetic tree building [ 28 ].…”

Section: Resultsmentioning

confidence: 99%

Atypical Porcine Pestivirus Circulation and Molecular Evolution within an Affected Swine Herd

Folgueiras-González

Braak

Simmelink

et al. 2020

Viruses

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Atypical porcine pestivirus (APPV) is a single-stranded RNA virus from the family Flaviviridae, which is linked to congenital tremor (CT) type A-II in newborn piglets. Here, we retrospectively investigated the molecular evolution of APPV on an affected herd between 2013 and 2019. Monitoring was done at regular intervals, and the same genotype of APPV was found during the entire study period, suggesting no introductions from outside the farm. The nucleotide substitutions over time did not show substantial amino acid variation in the structural glycoproteins. Furthermore, the evolution of the virus showed mainly purifying selection, and no positive selection. The limited pressure on the virus to change at immune-dominant regions suggested that the immune pressure at the farm might be low. In conclusion, farms can have circulation of APPV for years, and massive testing and removal of infected animals are not sufficient to clear the virus from affected farms.

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Section: Resultsmentioning

confidence: 99%

Atypical Porcine Pestivirus Circulation and Molecular Evolution within an Affected Swine Herd

Folgueiras-González

Braak

Simmelink

et al. 2020

Viruses

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“…Some previous studies had been done on the evolution of other pestiviruses. A mean substitution rate of 1.4 × 10 − 3 s/s/y was found across both BVDV1 and BVDV2 and the tMRCA was estimated to be 1498 (95% HPD: 1182-1750) years ago [38]; the estimated mean evolutionary rate of the 5' UTR BDV sequences was 2.9 × 10 − 3 s/s/y (95% HPD:…”

Section: Discussionmentioning

confidence: 99%

Evolution and genetic diversity of atypical porcine pestivirus (APPV) from piglets with congenital tremor in Guangxi province, Southern China

Shi

Xie

Zhao

et al. 2020

Preprint

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Background: Atypical porcine pestivirus (APPV) was identified and associated with congenital tremor (CT) type A-II in new born piglets and has been reported in many countries around the world since 2015. In China, the first APPV infection in swine herds was reported in Guangdong province in 2016.To investigate the genetic characteristics of APPV from Guangxi province seated in Southern China, the full-length sequences of APPV strains were amplified and analyzed.Results: Tissue samples from neonatal piglets with CT from Guangxi province were detected by reverse transcription-polymerase chain reaction (RT-PCR). APPV positive samples were amplified, cloned and sequenced, and the complete genomic sequences of five APPV strains were obtained.Sequence analysis revealed that all six APPV strains from Guangxi province, including five strains from this study and one from other researchers, shared 83.3%-97.5% nucleotide identity of complete genome and 91.7%-99.1% amino acid identity of open reading frame (ORF) with one another, and shared 77.7%-97.7% nucleotide identity of complete genome and 90.6%-99.3% amino acid identity of ORF with other reference strains available in Genbank. Phylogenetic analysis indicated that the APPV strains from Guangxi province belonged to four different subgroups in the phylogenetic tree based on the complete genomic sequences, and similar topology was observed in the phylogenetic trees based on N pro , E rns and E2 gene sequences, respectively. No sign of recombination was observed for strains from Guangxi province by using Recombination Detection Program 4 (RDP4) and Simplot analysis. Evolution analysis performed on the complete genome of 58 APPV strains available in Genbank showed that APPV strains from America, Europe and Asia during 2006-2019 evolved at a mean rate of 1.37×10 -4 substitutions/site/year, and the most recent common ancestor ( tMRCA ) of them was estimated as 1700.5 years ago.Conclusions: The findings of this study indicated that there existed a high degree of genetic diversity of APPV from Guangxi province, Southern China, which provided important information on the epidemiological features and evolutionary relationships of APPV.

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“…The ancient origin of BVDV-1b was established by the results of tree root tMRCA estimation, suggesting an origin of this subtype dating back to a time span between 1889 and 1950, with a mean estimation falling in the end of the 20s of the last century. Moreover, our tMRCAs are included within the HDP 95% range of BVDV-1b recently estimated across all genes by other Authors (Chernick & van der Meer, 2017).…”

Section: Discussionmentioning

confidence: 99%

Highlighting priority areas for bovine viral diarrhea control in Italy: A phylogeographic approach

Ebranati

Lauzi

Cerutti

et al. 2018

Infection, Genetics and Evolution

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The prevalence and genetic diversity of bovine viral diarrhea virus (BVDV) in a geographic area are largely influenced by live animal trade and management practices. Despite control and eradication programs currently underway in several European countries, the risk of BVDV spread within and among countries is still present. BVDV-1 is the predominant type circulating in European cattle population. In this study, a phylogeographic analysis was applied to the BVDV-1 highest prevalent subtypes in Italy to reconstruct the origin and spatial-temporal distribution and to trace main viral flows between different locations to highlight priority areas for BVDV control. A comprehensive dataset of BVDV-1b (n = 173) and 1e (n = 172) 5' UTR sequences was analysed, including both novel and published sequences from Italy and from European countries bordering and/or with commercial cattle flows with Italy. A common phylogeographic pattern was observed for BVDV-1b and 1e subtypes: interspersion from multiple Italian areas and European countries was widespread until the end of the last century, whereas significant local clusters were observed starting from 2000. These findings support a continuous viral flow among different areas over long time scales with no evidence of significant geographical structure, while local transmission networks are limited to more recent years. Northern Italy has been confirmed as the area of origin of the main clades of both BVDV subtypes at national level, acting both as a crucial area for introduction and a maintenance source for other areas. Piedmont, Central and Southern Italian regions contributed to limited geographical distribution and local BVDV-1b and 1e persistence. On the whole, priority control measures for BVDV-1b and 1e in Italy should be focused on: i) implementation of BVDV systematic control in all Northern Italian regions to break the viral flow from larger to smaller animal populations; and ii) breaking the dynamics of infections in regions with self-maintenance of BVDV by voluntary control programs.

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Evolution of Bovine viral diarrhea virus in Canada from 1997 to 2013

Cited by 26 publications

References 52 publications

Atypical Porcine Pestivirus Circulation and Molecular Evolution within an Affected Swine Herd

Atypical Porcine Pestivirus Circulation and Molecular Evolution within an Affected Swine Herd

Evolution and genetic diversity of atypical porcine pestivirus (APPV) from piglets with congenital tremor in Guangxi province, Southern China

Highlighting priority areas for bovine viral diarrhea control in Italy: A phylogeographic approach

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