Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan
The emergence of SARS-CoV-2 variants has posed a challenge to disease control efforts worldwide. This study explored the genomic diversity and phylogenetic relationship of SARS-CoV-2 variants reported in Pakistan. Our objective was to understand the transmission dynamics of different lineages within...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-06-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/15/7/1450 |
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| author | Muhammad Waqar Aziz Nadia Mukhtar Aftab Ahamd Anjum Muhammad Hassan Mushtaq Muhammad Adnan Ashraf Amar Nasir Muhammad Furqan Shahid Muhammad Nawaz Muhammad Zubair Shabbir Noreen Sarwar Rabia Tanvir Tahir Yaqub |
| author_facet | Muhammad Waqar Aziz Nadia Mukhtar Aftab Ahamd Anjum Muhammad Hassan Mushtaq Muhammad Adnan Ashraf Amar Nasir Muhammad Furqan Shahid Muhammad Nawaz Muhammad Zubair Shabbir Noreen Sarwar Rabia Tanvir Tahir Yaqub |
| author_sort | Muhammad Waqar Aziz |
| collection | DOAJ |
| description | The emergence of SARS-CoV-2 variants has posed a challenge to disease control efforts worldwide. This study explored the genomic diversity and phylogenetic relationship of SARS-CoV-2 variants reported in Pakistan. Our objective was to understand the transmission dynamics of different lineages within the country. We retrieved and analyzed spike protein sequences from Pakistan and compared them with reference sequences reported worldwide. Our analysis revealed the clustering of Pakistan-origin isolates in nine different clades representing different regions worldwide, suggesting the transmission of multiple lineages within the country. We found 96 PANGO lineages of SARS-CoV-2 in Pakistan, and 64 of these corresponded to 4 WHO-designated variants: Alpha, Beta, Delta, and Omicron. The most dominant variants in Pakistan were Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2, AY.108), and Omicron (BA.2.75, BA.5.2), and the N-terminal domain and receptor binding regions were the most hypervariable regions of the spike gene. Compared to the reference strain, characteristic substitutions were found in dominant variants. Our findings emphasize the importance of continuously monitoring and assessing nucleotide and residue substitutions over time to understand virus evolutionary trends better and devise effective disease control interventions. |
| first_indexed | 2024-03-11T00:34:39Z |
| format | Article |
| id | doaj.art-d8a20fe02a6d4f748d6b108c2d77c959 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-11T00:34:39Z |
| publishDate | 2023-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-d8a20fe02a6d4f748d6b108c2d77c9592023-11-18T21:43:53ZengMDPI AGViruses1999-49152023-06-01157145010.3390/v15071450Genomic Diversity and Evolution of SARS-CoV-2 Lineages in PakistanMuhammad Waqar Aziz0Nadia Mukhtar1Aftab Ahamd Anjum2Muhammad Hassan Mushtaq3Muhammad Adnan Ashraf4Amar Nasir5Muhammad Furqan Shahid6Muhammad Nawaz7Muhammad Zubair Shabbir8Noreen Sarwar9Rabia Tanvir10Tahir Yaqub11Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanInstitute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanInstitute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanDepartment of Epidemiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanInstitute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanDepartment of Clinical Sciences, Sub Campus Jhang, University of Veterinary and Animal Sciences, Lahore 54000, PakistanInstitute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanInstitute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanInstitute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanInstitute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanInstitute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanInstitute of Microbiology, University of Veterinary and Animal Sciences, Lahore 54000, PakistanThe emergence of SARS-CoV-2 variants has posed a challenge to disease control efforts worldwide. This study explored the genomic diversity and phylogenetic relationship of SARS-CoV-2 variants reported in Pakistan. Our objective was to understand the transmission dynamics of different lineages within the country. We retrieved and analyzed spike protein sequences from Pakistan and compared them with reference sequences reported worldwide. Our analysis revealed the clustering of Pakistan-origin isolates in nine different clades representing different regions worldwide, suggesting the transmission of multiple lineages within the country. We found 96 PANGO lineages of SARS-CoV-2 in Pakistan, and 64 of these corresponded to 4 WHO-designated variants: Alpha, Beta, Delta, and Omicron. The most dominant variants in Pakistan were Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1.617.2, AY.108), and Omicron (BA.2.75, BA.5.2), and the N-terminal domain and receptor binding regions were the most hypervariable regions of the spike gene. Compared to the reference strain, characteristic substitutions were found in dominant variants. Our findings emphasize the importance of continuously monitoring and assessing nucleotide and residue substitutions over time to understand virus evolutionary trends better and devise effective disease control interventions.https://www.mdpi.com/1999-4915/15/7/1450genomic diversityevolutionSARS-CoV-2lineagesvariantsphylogenetic |
| spellingShingle | Muhammad Waqar Aziz Nadia Mukhtar Aftab Ahamd Anjum Muhammad Hassan Mushtaq Muhammad Adnan Ashraf Amar Nasir Muhammad Furqan Shahid Muhammad Nawaz Muhammad Zubair Shabbir Noreen Sarwar Rabia Tanvir Tahir Yaqub Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan Viruses genomic diversity evolution SARS-CoV-2 lineages variants phylogenetic |
| title | Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan |
| title_full | Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan |
| title_fullStr | Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan |
| title_full_unstemmed | Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan |
| title_short | Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan |
| title_sort | genomic diversity and evolution of sars cov 2 lineages in pakistan |
| topic | genomic diversity evolution SARS-CoV-2 lineages variants phylogenetic |
| url | https://www.mdpi.com/1999-4915/15/7/1450 |
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