Complete Genome Sequences of Lineage IV Peste des Petits Ruminants Viruses from the Indian Subcontinent

Masdooq, Aliyu Abdullahi; Pawar, Rahul Mohanchandra; Parthiban, Aravindh Babu R.; Ragavendhar, K.; Sundarapandian, G.; Thangavelu, A.; Raj, G. Dhinakar

doi:10.1128/genomea.01009-15

Cited by 3 publications

(2 citation statements)

References 8 publications

(7 reference statements)

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“…The six-nucleotide deletion in the later isolate was confirmed by RT-PCR, followed by Sanger sequencing. This deletion was also reported previously in another Indian isolate [18].…”

Section: Pprv Genome Sequences Of New Indian Isolatessupporting

confidence: 89%

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Ongoing Assessment of the Molecular Evolution of Peste Des Petits Ruminants Virus Continues to Question Viral Origins

Mahapatra

Pachauri

Subramaniam

et al. 2021

Viruses

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Understanding the evolution of viral pathogens is critical to being able to define how viruses emerge within different landscapes. Host susceptibility, which is spread between different species and is a contributing factor to the subsequent epidemiology of a disease, is defined by virus detection and subsequent characterization. Peste des petits ruminants virus is a plague of small ruminant species that is a considerable burden to the development of sustainable agriculture across Africa and much of Asia. The virus has also had a significant impact on populations of endangered species in recent years, highlighting its significance as a pathogen of high concern across different regions of the globe. Here, we have re-evaluated the molecular evolution of this virus using novel genetic data to try and further resolve the molecular epidemiology of this disease. Viral isolates are genetically characterized into four lineages (I−IV), and the historic origin of these lineages is of considerable interest to the molecular evolution of the virus. Our re-evaluation of viral emergence using novel genome sequences has demonstrated that lineages I, II and IV likely originated in West Africa, in Senegal (I) and Nigeria (II and IV). Lineage III sequences predicted emergence in either East Africa (Ethiopia) or in the Arabian Peninsula (Oman and/or the United Arab Emirates), with a paucity of data precluding a more refined interpretation. Continual refinements of evolutionary emergence, following the generation of new data, is key to both understanding viral evolution from a historic perspective and informing on the ongoing genetic emergence of this virus.

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“…The six-nucleotide deletion in the later isolate was confirmed by RT-PCR, followed by Sanger sequencing. This deletion was also reported previously in another Indian isolate [18].…”

Section: Pprv Genome Sequences Of New Indian Isolatessupporting

confidence: 89%

“…One outbreak occurred during 1999 in Chirgaon village of Shimla District (PPRV/IND/HP/Chirgaon/99) and the other in 2016 in Palampur (PPRV/IND/HP/Palampur/16). The whole genome sequencing was carried out by commercial NGS following the method as described by Masdooq and colleagues [18].…”

Section: Sample Collection and Whole Genome Ngsmentioning

confidence: 99%

Ongoing Assessment of the Molecular Evolution of Peste Des Petits Ruminants Virus Continues to Question Viral Origins

Mahapatra

Pachauri

Subramaniam

et al. 2021

Viruses

View full text Add to dashboard Cite

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Genome sequencing of an Indian peste des petits ruminants virus isolate, Izatnagar/94, and its implications for virus diversity, divergence and phylogeography

et al. 2017

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Peste des petits ruminants is an important transboundary disease infecting small ruminants. Genome or gene sequence analysis enriches our knowledge about the evolution and transboundary nature of the causative agent of this disease, peste des petits ruminants virus (PPRV). Although analysis using whole genome sequences of pathogens leads to more precise phylogenetic relationships, when compared to individual genes or partial sequences, there is still a need to identify specific genes/genomic regions that can provide evolutionary assessments consistent with those predicted with full-length genome sequences. Here the virulent Izatnagar/94 PPRV isolate was assembled and compared to all available complete genome sequences (currently in the NCBI database) to estimate nucleotide diversity and to deduce evolutionary relationships between genes/genomic regions and the full length genomes. Our aim was to identify the preferred candidate gene for use as a phylogenetic marker, as well as to predict divergence time and explore PPRV phylogeography. Among all the PPRV genes, the H gene was identified to be the most diverse with the highest evolutionary relationship with the full genome sequences. Hence it is considered as the most preferred candidate gene for phylogenetic study with 93% identity set as a nucleotide cutoff. A whole genome nucleotide sequence cutoff value of 94% permitted specific differentiation of PPRV lineages. All the isolates examined in the study were found to have a most recent common ancestor in the late 19th or in the early 20th century with high posterior probability values. The Bayesian skyline plot revealed a decrease in genetic diversity among lineage IV isolates since the start of the vaccination program and the network analysis localized the ancestry of PPRV to Africa.

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Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014

Bao

Wang

et al. 2017

Virology

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Peste des petits ruminants virus (PPRV) causes a highly contagious disease, peste des petits ruminants (PPR), in sheep and goats which has been considered as a serious threat to the local economy in Africa and Asia. However, the in-depth evolutionary dynamics of PPRV during an epidemic is not well understood. We conducted phylogenetic analysis on genomic sequences of 25 PPRV strains from China 2013-2014 outbreaks. All these strains clustered into a novel clade in lineage 4. An evolutionary rate of 2.61 × 10 nucleotide substitutions per site per day was estimated, dating the most recent common ancestor of PPRV China 2013-2014 strains to early August 2013. Transmission network analysis revealed that all the virus sequences could be grouped into five clusters of infection, suggesting long-distance animal transmission play an important role in the spread of PPRV in China. These results expanded our knowledge for PPRV evolution to achieve effective control measures.

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Complete Genome Sequences of Lineage IV Peste des Petits Ruminants Viruses from the Indian Subcontinent

Cited by 3 publications

References 8 publications

Ongoing Assessment of the Molecular Evolution of Peste Des Petits Ruminants Virus Continues to Question Viral Origins

Ongoing Assessment of the Molecular Evolution of Peste Des Petits Ruminants Virus Continues to Question Viral Origins

Genome sequencing of an Indian peste des petits ruminants virus isolate, Izatnagar/94, and its implications for virus diversity, divergence and phylogeography

Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013–2014

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