Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave

Authors

Ali Raza Bukhari, Aga Khan University
Javaria Ashraf, Aga Khan UniversityFollow
Akber Kanji, Aga Khan UniversityFollow
Yusra Abdul Rehman, Aga Khan UniversityFollow
Maliha Yameen, Aga Khan UniversityFollow
Samiah Kanwar, Aga Khan UniversityFollow
Waqasuddin Khan, Aga Khan UniversityFollow
Furqan Kabir, Aga Khan UniversityFollow
Muhammad Imran Nisar, Aga Khan UniversityFollow
Rumina Hasan, Aga Khan UniversityFollow
Zahra Hasan, Aga Khan UniversityFollow

Document Type

Article

Department

Pathology and Laboratory Medicine; Paediatrics and Child Health

Abstract

Background: COVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan.
Methods: We studied 276,525 COVID-19 cases and 1,031 genomes sequenced from December 2021 to August 2022. Sequences were analyzed and visualized using phylogenetic trees.
Results: The highest case numbers and deaths were recorded in Sindh and Punjab, the most populous provinces in Pakistan. Omicron variants comprised 93% of all genomes, with BA.2 (32.6%) and BA.5 (38.4%) predominating. The first Omicron wave was associated with the sequential identification of BA.1 in Sindh, then Islamabad Capital Territory, Punjab, Khyber Pakhtunkhwa (KP), Azad Jammu Kashmir (AJK), Gilgit-Baltistan (GB) and Balochistan. Phylogenetic analysis revealed Sindh to be the source of BA.1 and BA.2 introductions into Punjab and Balochistan during early 2022. BA.4 was first introduced in AJK and BA.5 in Punjab. Most recent common ancestor (MRCA) analysis revealed relatedness between the earliest BA.1 genome from Sindh with Balochistan, AJK, Punjab and ICT, and that of first BA.1 from Punjab with strains from KPK and GB.
Conclusions: Phylogenetic analysis provides insights into the introduction and transmission dynamics of the Omicron variant in Pakistan, identifying Sindh as a hotspot for viral dissemination. Such data linked with public health efforts can help limit surges of new infections.

Comments

Pagination are not provided by author/publisher.

Publication (Name of Journal)

BMC Genomics

Recommended Citation

Bukhari, A. R., Ashraf, J., Kanji, A., Rehman, Y. A., Yameen, M., Kanwar, S., Khan, W., Kabir, F., Nisar, M. I., Hasan, R., Hasan, Z. (2023). Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave. BMC Genomics, 24(1).
Available at: https://ecommons.aku.edu/pakistan_fhs_mc_pathol_microbiol/1462