Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan
Foot and mouth disease (FMD) causes severe economic losses to the livestock industry of endemic countries, including Pakistan. Pakistan is part of the endemic pool 3 for foot and mouth disease viruses (FMDV), characterized by co-circulating O, A, and Asia 1 serotypes, as designated by the world refe...
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-07-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/8/1634 |
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| author | Syeda Sumera Naqvi Nazish Bostan Katsuhiko Fukai Qurban Ali Kazuki Morioka Tatsuya Nishi Muhammad Abubakar Zaheer Ahmed Sadia Sattar Sundus Javed Aamira Tariq Asma Sadiq |
| author_facet | Syeda Sumera Naqvi Nazish Bostan Katsuhiko Fukai Qurban Ali Kazuki Morioka Tatsuya Nishi Muhammad Abubakar Zaheer Ahmed Sadia Sattar Sundus Javed Aamira Tariq Asma Sadiq |
| author_sort | Syeda Sumera Naqvi |
| collection | DOAJ |
| description | Foot and mouth disease (FMD) causes severe economic losses to the livestock industry of endemic countries, including Pakistan. Pakistan is part of the endemic pool 3 for foot and mouth disease viruses (FMDV), characterized by co-circulating O, A, and Asia 1 serotypes, as designated by the world reference laboratory for FMD (WRL-FMD). FMDV serotype A lineage ASIA/Iran-05 is widespread in buffalos and cattle populations and was first reported in Pakistan in 2006. This lineage has a high turnover, with as many as 10 sub-lineages reported from Pakistan over the years. In this study, we reconstructed the evolutionary, demographic, and spatial history of serotype A and one of its sub-lineages, A/ASIA/Iran-05/SIS-13, prevalent in Pakistan. We sequenced nearly complete genomes of three isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13. We estimated recombination patterns and natural selection acting on the serotype A genomes. Source and transmission routes in Pakistan were inferred, and the clustering pattern of isolates of the SIS-13 sub-lineage were mapped on a tree. We hereby report nearly complete genome sequences of isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13, along with purported recombinant genomes, and highlight that complete coding sequences can better elucidate the endemic history and evolutionary pressures acting on long-term co-circulating FMDV strains. |
| first_indexed | 2024-03-09T03:42:08Z |
| format | Article |
| id | doaj.art-14abe6f26a054310962ccff90d4d2973 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T03:42:08Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-14abe6f26a054310962ccff90d4d29732023-12-03T14:38:40ZengMDPI AGViruses1999-49152022-07-01148163410.3390/v14081634Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in PakistanSyeda Sumera Naqvi0Nazish Bostan1Katsuhiko Fukai2Qurban Ali3Kazuki Morioka4Tatsuya Nishi5Muhammad Abubakar6Zaheer Ahmed7Sadia Sattar8Sundus Javed9Aamira Tariq10Asma Sadiq11Molecular Virology Laboratory, Department of Biosciences, Comsats University Islamabad, Islamabad 45550, PakistanMolecular Virology Laboratory, Department of Biosciences, Comsats University Islamabad, Islamabad 45550, PakistanExotic Disease Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, JapanNational Veterinary Laboratory, Ministry of National Food Security & Research, Islamabad 45710, PakistanExotic Disease Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, JapanExotic Disease Research Station, National Institute of Animal Health, National Agriculture and Food Research Organization, 6-20-1 Josui-honcho, Kodaira 187-0022, JapanNational Veterinary Laboratory, Ministry of National Food Security & Research, Islamabad 45710, PakistanReagent and Vaccine Services Section, Foreign Animal Disease Diagnostic Laboratory, Animal and Plant Health Inspection Service, National Veterinary Services Laboratories, United States Department of Agriculture, Plum Island Animal Disease Centre, Orient Point, Orient Point, Southold, NY 11957, USAMolecular Virology Laboratory, Department of Biosciences, Comsats University Islamabad, Islamabad 45550, PakistanMicrobiology and Immunology Laboratory, Department of Biosciences, Comsats University Islamabad, Islamabad 45550, PakistanMicrobiology and Immunology Laboratory, Department of Biosciences, Comsats University Islamabad, Islamabad 45550, PakistanDepartment of Microbiology, University of Jhang, Jhang 35200, PakistanFoot and mouth disease (FMD) causes severe economic losses to the livestock industry of endemic countries, including Pakistan. Pakistan is part of the endemic pool 3 for foot and mouth disease viruses (FMDV), characterized by co-circulating O, A, and Asia 1 serotypes, as designated by the world reference laboratory for FMD (WRL-FMD). FMDV serotype A lineage ASIA/Iran-05 is widespread in buffalos and cattle populations and was first reported in Pakistan in 2006. This lineage has a high turnover, with as many as 10 sub-lineages reported from Pakistan over the years. In this study, we reconstructed the evolutionary, demographic, and spatial history of serotype A and one of its sub-lineages, A/ASIA/Iran-05/SIS-13, prevalent in Pakistan. We sequenced nearly complete genomes of three isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13. We estimated recombination patterns and natural selection acting on the serotype A genomes. Source and transmission routes in Pakistan were inferred, and the clustering pattern of isolates of the SIS-13 sub-lineage were mapped on a tree. We hereby report nearly complete genome sequences of isolates belonging to sub-lineage A/ASIA/Iran-05/SIS-13, along with purported recombinant genomes, and highlight that complete coding sequences can better elucidate the endemic history and evolutionary pressures acting on long-term co-circulating FMDV strains.https://www.mdpi.com/1999-4915/14/8/1634adoptive evolutionfoot and mouth disease virusnext-generation sequencingphylogeographyPakistanrecombination |
| spellingShingle | Syeda Sumera Naqvi Nazish Bostan Katsuhiko Fukai Qurban Ali Kazuki Morioka Tatsuya Nishi Muhammad Abubakar Zaheer Ahmed Sadia Sattar Sundus Javed Aamira Tariq Asma Sadiq Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan Viruses adoptive evolution foot and mouth disease virus next-generation sequencing phylogeography Pakistan recombination |
| title | Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan |
| title_full | Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan |
| title_fullStr | Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan |
| title_full_unstemmed | Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan |
| title_short | Evolutionary Dynamics of Foot and Mouth Disease Virus Serotype A and Its Endemic Sub-Lineage A/ASIA/Iran-05/SIS-13 in Pakistan |
| title_sort | evolutionary dynamics of foot and mouth disease virus serotype a and its endemic sub lineage a asia iran 05 sis 13 in pakistan |
| topic | adoptive evolution foot and mouth disease virus next-generation sequencing phylogeography Pakistan recombination |
| url | https://www.mdpi.com/1999-4915/14/8/1634 |
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