TY - JOUR
T1 - Genome sequencing and analysis of genomic diversity in the locally transmitted SARS-CoV-2 in Pakistan
AU - Shakeel, Muhammad
AU - Irfan, Muhammad
AU - Nisa, Zaib un
AU - Farooq, Saba
AU - Ain, Noor ul
AU - Iqbal, Waseem
AU - Kakar, Niamatullah
AU - Jahan, Shah
AU - Shahzad, Mohsin
AU - Siddiqi, Saima
AU - Khan, Ishtiaq Ahmad
N1 - Publisher Copyright:
© 2022 Wiley-VCH GmbH.
PY - 2022/9
Y1 - 2022/9
N2 - 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.
AB - 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.
KW - COVID-19 pandemic
KW - SARS-CoV-2 lineages
KW - genetic evolution
KW - spatiotemporal surveillance
KW - viral variants
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U2 - 10.1111/tbed.14586
DO - 10.1111/tbed.14586
M3 - Article
C2 - 35510932
AN - SCOPUS:85132617545
SN - 1865-1674
VL - 69
SP - e2418-e2430
JO - Transboundary and Emerging Diseases
JF - Transboundary and Emerging Diseases
IS - 5
ER -