Nanopore Sequencing Reveals Genomic Diversity of COVID-19 Variants in Pakistan

Strategic Insights -

Researchers from the Korea Research Institute of Standards and Science conducted a comprehensive study to understand the genomic epidemiology of SARS-CoV-2 strains circulating in Pakistan during the country's third and fourth pandemic waves. The study analyzed 1,052 confirmed COVID-19 patient samples collected from multiple cities across Pakistan between March and October 2021. The researchers used the GridION platform (Oxford Nanopore Technologies) for whole genome sequencing, which revealed a clear temporal shift in variant dominance. The Alpha variant (B.1.1.7 lineage) predominated in the first half of 2021, while the Delta variant (B.1.617.2) became most prevalent in the latter half.

Key Takeaways:

  • The study analyzed 1,052 confirmed COVID-19 patient samples collected from multiple cities across Pakistan between March and October 2021.
  • The researchers used the GridION platform (Oxford Nanopore Technologies) for whole genome sequencing, which revealed a clear temporal shift in variant dominance.
  • The Alpha variant (B.1.1.7 lineage) predominated in the first half of 2021, while the Delta variant (B.1.617.2) became most prevalent in the latter half.
  • The study found that the most frequent nucleotide mutations in Pakistani SARS-CoV-2 samples were A23403G, C3037T, C14408T, and C241T, potentially contributing to increased disease transmission and evasion of host immune responses.
  • The AY.108 lineage, which has been reported at relatively low frequencies globally, was found to be present in approximately 34% of global cases in Pakistan, suggesting potential regional evolution or specific introduction events.
  • The study highlights the dynamic nature of SARS-CoV-2 and emphasizes the critical importance of ongoing, large-scale genomic surveillance in Pakistan.
  • The research demonstrates the feasibility and utility of using nanopore sequencing for comprehensive viral monitoring in Pakistan's public health context.
  • The study's findings could inform future public health strategies, including vaccine updates and targeted interventions.

Statistics:

  • 1,052 confirmed COVID-19 patient samples were analyzed in the study.
  • The samples were collected from multiple cities across Pakistan between March and October 2021.
  • The study found that the Alpha variant (B.1.1.7 lineage) predominated in the first half of 2021.
  • The Delta variant (B.1.617.2) became most prevalent in the latter half of 2021.
  • The AY.108 lineage was found to be present in approximately 34% of global cases in Pakistan.

Sources:

  • Nanopore sequencing reveals the genomic diversity of the variants of concern of SARS-CoV-2 during 2021 disease outbreak in Pakistan. Scientific Reports, 2025;15(1):28129.
  • Medical Letter on the CDC & FDA. August 24, 2025; p 114.
  • Korea Research Institute of Standards and Science.
  • Oxford Nanopore Technologies.
  • Nature Portfolio.
  • Nature Publishing Group.