Background: We aim to fill a genomic surveillance gap by exploring the diversity of SARS-CoV-2 during the sixth wave (June–September 2022) and the post-sixth wave period (since October 2022) in Pakistan. Materials and methods: We sequenced 1398 samples (Ct <30) using Illumina COVIDSeq assay and analyzed them using CDC USA guidelines and Nextstrain. Results: The predominant variant during the sixth wave was BA.5.2 (62.43%), impacting Islamabad and Karachi. Post-sixth wave, a resurgence occurred from January 2023 to May 2023, driven by XBB.1.9.1 (16.13%), XBB.1.19.1 (15.62%) and XBB.1.5 (8.49%), with either Islamabad or Karachi, estimated as initial transmission point. Conclusion: The study highlights the link between phylogeography, regional case surges, impact of relaxed policies and vaccination efforts, providing vital insights for future strategies.
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Jamal et al. (2024) studied this question.
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