Author:
Bukhari Ali Raza,Ashraf Javaria,Kanji Akbar,Rahman Yusra Abdul,Trovão Nídia S.,Thielen Peter M.,Yameen Maliha,Kanwar Samiah,Khan Waqasuddin,Kabir Furqan,Nisar Muhammad Imran,Merritt Brian,Hasan Rumina,Spiro David,Rasmussen Zeba,Aamir Uzma Bashir,Hasan Zahra
Abstract
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.
Funder
Higher Education Commision, Pakistan
Bill and Melinda Gates Foundation
Publisher
Springer Science and Business Media LLC
Cited by
1 articles.
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