Whole-Genome-Sequence-Based Evolutionary Analyses of HoBi-like Pestiviruses Reveal Insights into Their Origin and Evolutionary History
HoBi-like pestivirus (HoBiPeV), classified under <i>Pestivirus H</i> species, is an emerging cattle pathogen of high economic impact. However, the origin and evolution of HoBiPeV are not very clear due to a lack of full genomic sequences from diverse clades. This study aimed to determine...
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MDPI AG
2023-03-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/3/733 |
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| author | Semmannan Kalaiyarasu Niranjan Mishra Saravanan Subramaniam Dashprakash Moorthy Shashi Bhusan Sudhakar Vijendra Pal Singh Aniket Sanyal |
| author_facet | Semmannan Kalaiyarasu Niranjan Mishra Saravanan Subramaniam Dashprakash Moorthy Shashi Bhusan Sudhakar Vijendra Pal Singh Aniket Sanyal |
| author_sort | Semmannan Kalaiyarasu |
| collection | DOAJ |
| description | HoBi-like pestivirus (HoBiPeV), classified under <i>Pestivirus H</i> species, is an emerging cattle pathogen of high economic impact. However, the origin and evolution of HoBiPeV are not very clear due to a lack of full genomic sequences from diverse clades. This study aimed to determine full-genome sequences of HoBiPeV strains of three novel clades (c, d and e) and perform full-genome-based genetic and evolutionary analyses. Bayesian phylogenetic analyses herein confirmed the existence and independent evolution of four main HoBiPeV clades (a, c, d and e) globally, with genetic divergence ranging from 13.0% to 18.2%. Our Bayesian molecular clock estimates revealed that HoBiPeV most likely originated in India, with a dated tMRCA of 1938 (1762–2000), evidencing a more recent origin of HoBiPeV. The evolution rate of HoBiPeV was estimated to be 2.133 × 10<sup>−3</sup> subs/site/year at full-genome level but varied widely among individual genes. Selection pressure analyses identified most of the positively selected sites in <i>E2</i>. Additionally, 21.8% of the ORF codon sites were found under strong episodic diversifying selection, providing first evidence of negative selection in HoBiPeV evolution. No recombination event was evident for HoBiPeV-c, d and e strains. These findings provide new insights into HoBiPeV origin and evolutionary history for better understanding the epidemiology and host–pathogen interactions and stimulate vaccine research. |
| first_indexed | 2024-03-11T05:46:16Z |
| format | Article |
| id | doaj.art-e72ce8df13b7493fa7e92706526ef94e |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-11T05:46:16Z |
| publishDate | 2023-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-e72ce8df13b7493fa7e92706526ef94e2023-11-17T14:23:34ZengMDPI AGViruses1999-49152023-03-0115373310.3390/v15030733Whole-Genome-Sequence-Based Evolutionary Analyses of HoBi-like Pestiviruses Reveal Insights into Their Origin and Evolutionary HistorySemmannan Kalaiyarasu0Niranjan Mishra1Saravanan Subramaniam2Dashprakash Moorthy3Shashi Bhusan Sudhakar4Vijendra Pal Singh5Aniket Sanyal6ICAR—National Institute of High Security Animal Diseases, Bhopal 462022, IndiaICAR—National Institute of High Security Animal Diseases, Bhopal 462022, IndiaICAR—National Institute on Foot-and-Mouth Disease, Bhubaneswar 752050, IndiaICAR—National Institute of High Security Animal Diseases, Bhopal 462022, IndiaICAR—National Institute of High Security Animal Diseases, Bhopal 462022, IndiaICAR—National Institute of High Security Animal Diseases, Bhopal 462022, IndiaICAR—National Institute of High Security Animal Diseases, Bhopal 462022, IndiaHoBi-like pestivirus (HoBiPeV), classified under <i>Pestivirus H</i> species, is an emerging cattle pathogen of high economic impact. However, the origin and evolution of HoBiPeV are not very clear due to a lack of full genomic sequences from diverse clades. This study aimed to determine full-genome sequences of HoBiPeV strains of three novel clades (c, d and e) and perform full-genome-based genetic and evolutionary analyses. Bayesian phylogenetic analyses herein confirmed the existence and independent evolution of four main HoBiPeV clades (a, c, d and e) globally, with genetic divergence ranging from 13.0% to 18.2%. Our Bayesian molecular clock estimates revealed that HoBiPeV most likely originated in India, with a dated tMRCA of 1938 (1762–2000), evidencing a more recent origin of HoBiPeV. The evolution rate of HoBiPeV was estimated to be 2.133 × 10<sup>−3</sup> subs/site/year at full-genome level but varied widely among individual genes. Selection pressure analyses identified most of the positively selected sites in <i>E2</i>. Additionally, 21.8% of the ORF codon sites were found under strong episodic diversifying selection, providing first evidence of negative selection in HoBiPeV evolution. No recombination event was evident for HoBiPeV-c, d and e strains. These findings provide new insights into HoBiPeV origin and evolutionary history for better understanding the epidemiology and host–pathogen interactions and stimulate vaccine research.https://www.mdpi.com/1999-4915/15/3/733HoBi-like pestivirusHoBiPeVevolutionary analysisphylogenywhole-genome sequenceselection pressure |
| spellingShingle | Semmannan Kalaiyarasu Niranjan Mishra Saravanan Subramaniam Dashprakash Moorthy Shashi Bhusan Sudhakar Vijendra Pal Singh Aniket Sanyal Whole-Genome-Sequence-Based Evolutionary Analyses of HoBi-like Pestiviruses Reveal Insights into Their Origin and Evolutionary History Viruses HoBi-like pestivirus HoBiPeV evolutionary analysis phylogeny whole-genome sequence selection pressure |
| title | Whole-Genome-Sequence-Based Evolutionary Analyses of HoBi-like Pestiviruses Reveal Insights into Their Origin and Evolutionary History |
| title_full | Whole-Genome-Sequence-Based Evolutionary Analyses of HoBi-like Pestiviruses Reveal Insights into Their Origin and Evolutionary History |
| title_fullStr | Whole-Genome-Sequence-Based Evolutionary Analyses of HoBi-like Pestiviruses Reveal Insights into Their Origin and Evolutionary History |
| title_full_unstemmed | Whole-Genome-Sequence-Based Evolutionary Analyses of HoBi-like Pestiviruses Reveal Insights into Their Origin and Evolutionary History |
| title_short | Whole-Genome-Sequence-Based Evolutionary Analyses of HoBi-like Pestiviruses Reveal Insights into Their Origin and Evolutionary History |
| title_sort | whole genome sequence based evolutionary analyses of hobi like pestiviruses reveal insights into their origin and evolutionary history |
| topic | HoBi-like pestivirus HoBiPeV evolutionary analysis phylogeny whole-genome sequence selection pressure |
| url | https://www.mdpi.com/1999-4915/15/3/733 |
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