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Genome sequencing and analysis of genomic diversity in the locally transmitted SARS-CoV-2 in Pakistan.
Shakeel, Muhammad; Irfan, Muhammad; Nisa, Zaib Un; Farooq, Saba; Ain, Noor Ul; Iqbal, Waseem; Kakar, Niamatullah; Jahan, Shah; Shahzad, Mohsin; Siddiqi, Saima; Khan, Ishtiaq Ahmad.
  • Shakeel M; Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.
  • Irfan M; Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.
  • Nisa ZU; Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.
  • Farooq S; National Institute of Virology, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.
  • Ain NU; Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan.
  • Iqbal W; Pathology Unit, Mardan Medical Complex, Mardan, Pakistan.
  • Kakar N; Center for Advanced Studies in Vaccinology and Biotechnology (CASVAB), University of Balochistan, Quetta, Pakistan.
  • Jahan S; Department of Immunology, University of Health Sciences Lahore, Lahore, Pakistan.
  • Shahzad M; Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan.
  • Siddiqi S; Institute of Biomedical and Genetic Engineering (IBGE), Islamabad, Pakistan.
  • Khan IA; Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi, Pakistan.
Transbound Emerg Dis ; 69(5): e2418-e2430, 2022 Sep.
Article in English | MEDLINE | ID: covidwho-1819932
ABSTRACT
Surveillance of genetic diversity of the SARS-CoV-2 is extremely important to detect the emergence of more infectious and deadly strains of the virus. In this study, we evaluated mutational events in the SARS-CoV-2 genomes through whole genome sequencing. The samples were collected from COVID-19 patients in different major cities of Pakistan during the four waves of the pandemic (May 2020 to July 2021) and subjected to whole genome sequencing. Using in silico and machine learning tools, the viral mutational events were analyzed, and variants of concern and of interest were identified during each of the four waves. The overall mutation frequency (mutations per genome) increased during the course of the pandemic from 12.19 to 23.63, 31.03, and 41.22 in the first, second, third, and fourth waves, respectively. We determined that the viral strains rose to higher frequencies in local transmission. The first wave had three most common strains B.1.36, B.1.160, and B.1.255, the second wave comprised B.1.36 and B.1.247 strains, the third wave had B.1.1.7 (Alpha variant) and B.1.36 strains, and the fourth waves comprised B.1.617.2 (Delta). Intriguingly, the B.1.36 variants were found in all the waves of the infection indicating their survival fitness. Through phylogenetic analysis, the probable routes of transmission of various strains in the country were determined. Collectively, our study provided an insight into the evolution of SARS-CoV-2 lineages in the spatiotemporal local transmission during different waves of the pandemic, which aided the state institutions in implementing adequate preventive measures.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Animals Country/Region as subject: Asia Language: English Journal: Transbound Emerg Dis Journal subject: Veterinary Medicine Year: 2022 Document Type: Article Affiliation country: Tbed.14586

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Full text: Available Collection: International databases Database: MEDLINE Main subject: SARS-CoV-2 / COVID-19 Type of study: Experimental Studies / Observational study / Prognostic study / Randomized controlled trials Topics: Variants Limits: Animals Country/Region as subject: Asia Language: English Journal: Transbound Emerg Dis Journal subject: Veterinary Medicine Year: 2022 Document Type: Article Affiliation country: Tbed.14586