Genomic Diversity and Evolution of SARS-CoV-2 Lineages in Pakistan

Abstract

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.

Associations between genetic mutations in different SARS-CoV-2 strains and negative conversion time of viral RNA among imported cases in Hangzhou: A cross-sectional study

“…Previous studies have mainly reported that VOCs have more genetic mutations (such as T4685A, N4992N, and G5063S in RNA-dependent RNA polymerase [RdRp]; T19R and T19I in the spike N-terminal domain; and N440K, K444N, Q493R and N532H in the spike receptor-binding domain), ( Saifi et al, 2022 ) possibly contributing to increased transmission, virulence, mortality, and immune escape ( Carabelli et al, 2023 ; Aziz et al, 2023 ; Davies et al, 2021 ). Although NCT is known to be closely related to clinical manifestations in SARS-CoV-2 cases ( Yang et al, 2021 ; Zang et al, 2022 ; Wang et al, 2022 ; Atluri et al, 2022 ), there is a lack of evidence on the effects of mutations in different SARS-CoV-2 strains on NCT.…”