The introduction of the SARS-CoV-2 BA.4 lineage into Pakistan

Abstract

Pakistan has experienced a total of six COVID-19 waves throughout the pandemic, each driven by distinct SARS-CoV-2 lineages. This study explores the introduction of Omicron lineage BA.4 into Pakistan, which contributed to the sixth wave between June and September 2022. A discrete phylogeographic reconstruction was conducted on a global dataset of 443 samples across 49 countries, of which 92 samples were collected in Pakistan. Samples collected in Pakistan were from 10 locations across the country: Balochistan, Gilgit Baltistan, Islamabad, Jhelum, Karachi, Khyber Pakhtunkhwa, Lahore, Mirpur, Punjab, and Swat. This analysis identified eight distinct introductions into Pakistan between May 2022 and January 2023. The majority of BA.4 cases in Pakistan descended from one introduction, indicating that most transmission occurred within the country rather than through multiple importations. Two exportation events were also identified. During this time, there were reduced public health interventions in place, following the lifting of international travel restrictions in March 2022. This work stems from a collaboration between the UKHSA New Variant Assessment Platform and the National Institute of Health of Pakistan to strengthen genomic surveillance in front-line public health laboratories for global pandemic preparedness and response. The benefit of such partnerships has been evidenced throughout the COVID-19 pandemic, where scientific collaboration through data sharing and knowledge exchange has facilitated risk assessment and action. As a result of this collaboration, we have conducted the first Bayesian phylodynamic analysis of SARS-CoV-2 in Pakistan. This work can lend evidence to support understanding of SARS-CoV-2 variant transmission patterns and inform public health containment measures for virus spread.

Keywords: 6th wave; Omicron; Pakistan; Phylodynamics; Phylogenetics; SARS-CoV-2.