Study of SARS-CoV-2 genomes from Pakistan in the post-pandemic period 2023-2024 shows unique phylogenetic diversity as compared with other global data

Introduction SARS-CoV-2 infections caused a global pandemic between 2019 and 2023. Omicron variants continued to emerge but morbidity and mortality were reduced likely due to vaccinations and increasing host immunity. COVID-19 case numbers reported from Pakistan as was genomic epidemiology of SARS-CoV-2. We studied SARS-CoV-2 variants reported between 2023 and 2024 and compare these with variants in other countries. Methodology We studied SARS-CoV-2 genomes submitted from Pakistan available in public databases as well as those reported by our facility, the Aga Khan University Hospital, Karachi.  Phylogenetic analysis was performed. Viral variants reported from other countries were compared. Results In Pakistan, SARS-CoV-2 genomic epidemiology identified predominant types to be: XBB.1 and its subvariants in 2023 and JN.1 and its subvariants in 2024.  Although variants such as KP.2, LB.1, and LA.1 emerged by mid-2024, JN.1 remained the dominant variant in Pakistan.  Global data (USA, UK, France, Germany, Italy) showed XBB.1.5 transitioned to JN.1 and KP.3.3 by September 2024. Notably, JN.1 strains persisted in India until 2024. Conclusions We show differing trends between the evolution of SARS-CoV-2 variants in different countries. Strains in Pakistan differed from four countries in the North. These findings suggest the importance of continued genomic surveillance and epidemiological monitoring to track variant evolution. Different strains likely impact disease severity across regions and may contribute to differences observed in COVID-19 associated morbidity observed globally.