Metadata beyond the sequence enables the phylodynamic inference of bovine viral diarrhea virus type 1a isolates from Western Canada

Chernick, Adam; Godson, Dale L.; Meer, Frank van der

doi:10.1016/j.meegid.2014.01.003

Cited by 20 publications

(20 citation statements)

References 43 publications

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“…It is interesting to note that the identity of the Aosta Valley sequences from different farms clustering closely were confirmed by transmission chain analysis using other BVDV genome regions (Chernick et al, 2014), given that the 5′UTR genetic resolution is not as high as that obtained with other more variable regions (Toplak et al, 2004). This could be a further evidence of the recent entry of the subtype 1f in the region.…”

Section: Discussionmentioning

confidence: 79%

Phylogeography, phylodynamics and transmission chains of bovine viral diarrhea virus subtype 1f in Northern Italy

Cerutti

Luzzago

Lauzi

et al. 2016

Infection, Genetics and Evolution

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Section: Discussionmentioning

confidence: 79%

Phylogeography, phylodynamics and transmission chains of bovine viral diarrhea virus subtype 1f in Northern Italy

Cerutti

Luzzago

Lauzi

et al. 2016

Infection, Genetics and Evolution

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“…Analysis of 5′UTR sequences of BVDV revealed a mean evolutionary rate of 9.3 × 10 −3 substitutions/site/year for the investigated sequences [27]. Moreover, evolutionary rates of 5.9 × 10 −4 and 1.26 × 10 −3 substitutions/site/year have been reported for the 5′UTR and E1–E2 regions, respectively [28]. In addition, non-homologous RNA recombination can lead to the generation of cytopathogenic (cp) BVDV variants and a large variety of different genomic alterations have been described for cp pestiviruses ([23] and references therein).…”

Section: Mechanisms Of Genetic Changes In Bvdv Genomesmentioning

confidence: 99%

“…Analyses of complete N pro and E2 coding sequences provide high confidence levels for the allocation of BVDV isolates into established and newly-identified subgenotypes. While the analysis of short partial 5′UTR sequences usually allows correct allocation of virus isolates to the established pestivirus species (e.g., BVDV-1 ) and, in many cases, also to defined subgenotypes, some of the observed BVDV-1 subgenotypes are supported by only low statistical values; consequently, several publications have indicated limitations of inferring BVDV phylogenies using the 5′UTR alone [17,28,30,46]. The main disadvantages of the 5′UTR with regard to its use for phylogenetic analyses are the restricted sequence length and lack of diversity.…”

Section: Bvdv Variabilitymentioning

confidence: 99%

“…Consequently, the lack of information does not allow to clearly infer relationships within the major clades, and some branches and BVDV-1 subgenotypes are poorly supported by statistical values. The limited resolution and statistical support observed for phylogenetic analyses of 5′UTR sequences can be significantly improved by analyses of longer sequences and, therefore, it has been recommended to use, e.g., the complete N pro and E2 coding regions, or even the complete polyprotein coding region, for inferring phylogenies and genotyping of pestivirus isolates [17,28]. …”

Section: Bvdv Variabilitymentioning

confidence: 99%

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Variability and Global Distribution of Subgenotypes of Bovine Viral Diarrhea Virus

Yeşilbağ

Alpay

Becher

2017

Viruses

204

250

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Bovine viral diarrhea virus (BVDV) is a globally-distributed agent responsible for numerous clinical syndromes that lead to major economic losses. Two species, BVDV-1 and BVDV-2, discriminated on the basis of genetic and antigenic differences, are classified in the genus Pestivirus within the Flaviviridae family and distributed on all of the continents. BVDV-1 can be segregated into at least twenty-one subgenotypes (1a–1u), while four subgenotypes have been described for BVDV-2 (2a–2d). With respect to published sequences, the number of virus isolates described for BVDV-1 (88.2%) is considerably higher than for BVDV-2 (11.8%). The most frequently-reported BVDV-1 subgenotype are 1b, followed by 1a and 1c. The highest number of various BVDV subgenotypes has been documented in European countries, indicating greater genetic diversity of the virus on this continent. Current segregation of BVDV field isolates and the designation of subgenotypes are not harmonized. While the species BVDV-1 and BVDV-2 can be clearly differentiated independently from the portion of the genome being compared, analysis of different genomic regions can result in inconsistent assignment of some BVDV isolates to defined subgenotypes. To avoid non-conformities the authors recommend the development of a harmonized system for subdivision of BVDV isolates into defined subgenotypes.

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“…Phylogeographic analysis built on the 5' UTR sequence are informative (Luzzago et al, 2012) especially over long time scales, such as decades, while regions with higher variability (e.g., Npro and E2 genes) allow resolution of phylogeny over shorter time scales (Chernick et al, 2014).…”

Section: Introductionmentioning

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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Metadata beyond the sequence enables the phylodynamic inference of bovine viral diarrhea virus type 1a isolates from Western Canada

Cited by 20 publications

References 43 publications

Phylogeography, phylodynamics and transmission chains of bovine viral diarrhea virus subtype 1f in Northern Italy

Phylogeography, phylodynamics and transmission chains of bovine viral diarrhea virus subtype 1f in Northern Italy

Variability and Global Distribution of Subgenotypes of Bovine Viral Diarrhea Virus

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

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