Time scale evolution of avipoxviruses

Loc’h, Guillaume Le; Bertagnoli, Stéphane; Ducatez, Mariette

doi:10.1016/j.meegid.2015.07.031

Cited by 7 publications

(5 citation statements)

References 27 publications

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“…Tajima's D test of neutrality resulted in a significant negative value (-0.14928), suggesting that this virus might be undergoing a period of evolutionary expansion. A similar pattern of θ values was obtained using partial gene sequences of recently studied avipoxviruses and ORFV, with values ranging from 0.065 to 0.200 [ 9 , 10 ]. These results were consistent with the observed dN and dS values and suggested that selection pressure had altered the rate of evolution.…”

supporting

confidence: 71%

Recombination drives the emergence of orf virus diversity: evidence from the first complete genome sequence of an Indian orf virus isolate and comparative genomic analysis

et al. 2022

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Contagious pustular dermatitis is a disease that primarily infects small ruminants and possesses zoonotic potential. It is caused by orf virus (ORFV), a member of the genus Parapoxvirus . In this study, we evaluated an ORFV outbreak in goats in Madhya Pradesh, a state in central India, during 2017. The transboundary potential of this virus was evaluated by constructing phylogenetic trees. The complete genome sequence of an ORFV isolate named Ind/MP/17 was found to be 139,807 bp in length with 63.7% GC content and 132 open reading frames (ORFs) flanked by 3,910-bp inverted terminal repeats (ITRs). An investigation into evolutionary parameters such as selection pressure (θ = dN/dS) and nucleotide diversity (π) demonstrated that ORFV has undergone purifying selection. A total of 40 recombination events were identified, 21 of which were evident in the Ind/MP/17 genome, indicating its ability to generate new variants. Supplementary Information The online version contains supplementary material available at 10.1007/s00705-022-05443-5.

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confidence: 71%

Recombination drives the emergence of orf virus diversity: evidence from the first complete genome sequence of an Indian orf virus isolate and comparative genomic analysis

et al. 2022

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“…Selection pressure analysis (θ=dN/dS) obtained the value 0.02911 suggested that ORFV under purifying selection. This result coincides with the recently reported θ value of avipoxvirus and ORFV partial genes, which range between 0.065 and 0.200 (Le Loc'h, Bertagnoli, & Ducatez, 2015;Sahu et al, 2019;Velazquez-Salinas et al, 2018). The synonymous (dN) and non-synonymous mutations (dS) drive the selection pressure to fluctuate the evolution rate.…”

Section: Discussionsupporting

confidence: 91%

Recombination may drive the emergence of Orf virus diversity: Evidence from the first complete genome of Indian Orf virus and comparative genomic analysis.

Sahu¹,

Majee²,

Singh³

et al. 2020

Preprint

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Contagious ecthyma is a zoonotic disease caused by the Parapoxvirus virus, Orf (ORFV) affecting sheep, goats, humans and is widely distributed across the world, including India. Here, we have investigated the 2017 ORFV outbreak in goats that occurred in the central Indian state of Madhya Pradesh. The outbreak was characterized by a moderate rate of morbidity (up to 20%) with no mortality. Phylogenetic analysis of four partial genes, such as ORFV011, ORFV020, ORFV059, and ORFV108, revealed the transboundary potential of the virus by showing its relationship with a distinct geographical area. We characterized the complete genome of this strain named Ind/MP and performed comparative genomic analysis. The Ind/MP whole genome consists of 139,807 bp with GC content 63.7%. The genome contains 132 potential open reading frames (ORFs) flanked by inverted terminal repeats (ITRs) of 3,910 bp at both ends having terminal BamHI sites and conserved telomere resolution sequences. Population genetic parameters such as nucleotide diversity (π), selection pressure analysis (θ=dN/dS), etc. suggest that the ORFV resides under purifying selection. The potent molecular markers, such as Simple Sequence Repeats (SSRs) and compound SSRs (cSSRs) were more prevalent within the functional protein with the value 70% and 67%, respectively. A total number of forty recombination events were identified, out of which Ind/MP strain actively participate in twenty-one events suggesting that this strain can recombine for the generation of new variants.

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“…This is supportive of earlier suggestions that some DNA viruses have a long history of co-divergence with their hosts [ 4 ], which in some cases may be a reflection of relatively long durations of infection. Indeed, long-term virus-host associations have been observed in the Herpesviridae [ 1 ], the Poxviridae [ 17 ] and the Polyomaviridae [ 18 ]. However, it is also important to note that we found these viruses contain more instances of host jumping than previously thought.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

2017

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The cross-species transmission of viruses from one host species to another is responsible for the majority of emerging infections. However, it is unclear whether some virus families have a greater propensity to jump host species than others. If related viruses have an evolutionary history of co-divergence with their hosts there should be evidence of topological similarities between the virus and host phylogenetic trees, whereas host jumping generates incongruent tree topologies. By analyzing co-phylogenetic processes in 19 virus families and their eukaryotic hosts we provide a quantitative and comparative estimate of the relative frequency of virus-host co-divergence versus cross-species transmission among virus families. Notably, our analysis reveals that cross-species transmission is a near universal feature of the viruses analyzed here, with virus-host co-divergence occurring less frequently and always on a subset of viruses. Despite the overall high topological incongruence among virus and host phylogenies, the Hepadnaviridae, Polyomaviridae, Poxviridae, Papillomaviridae and Adenoviridae, all of which possess double-stranded DNA genomes, exhibited more frequent co-divergence than the other virus families studied here. At the other extreme, the virus and host trees for all the RNA viruses studied here, particularly the Rhabdoviridae and the Picornaviridae, displayed high levels of topological incongruence, indicative of frequent host switching. Overall, we show that cross-species transmission plays a major role in virus evolution, with all the virus families studied here having the potential to jump host species, and that increased sampling will likely reveal more instances of host jumping.

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Time scale evolution of avipoxviruses

Cited by 7 publications

References 27 publications

Recombination drives the emergence of orf virus diversity: evidence from the first complete genome sequence of an Indian orf virus isolate and comparative genomic analysis

Recombination drives the emergence of orf virus diversity: evidence from the first complete genome sequence of an Indian orf virus isolate and comparative genomic analysis

Recombination may drive the emergence of Orf virus diversity: Evidence from the first complete genome of Indian Orf virus and comparative genomic analysis.

Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families

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