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

Ali Raza Bukhari, Javaria Ashraf, Akbar Kanji, Yusra Abdul Rahman, Nídia S. Trovão, Peter M. Thielen, Maliha Yameen, Samiah Kanwar, Waqasuddin Khan, Furqan Kabir, Muhammad Imran Nisar, Brian Merritt, Rumina Hasan, David Spiro, Zeba Rasmussen, Uzma Bashir Aamir, Zahra Hasan

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


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.

Original languageEnglish
Article number432
JournalBMC Genomics
Issue number1
Publication statusPublished - Dec 2023


  • Omicron
  • Phylogenetics
  • SARS-CoV-2
  • Transmission dynamics
  • Variants of concern


Dive into the research topics of 'Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave'. Together they form a unique fingerprint.

Cite this