@article{cc473f7c79b34a3d9247469631f8b324,
title = "Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave",
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.",
keywords = "Omicron, Phylogenetics, SARS-CoV-2, Transmission dynamics, Variants of concern",
author = "Bukhari, {Ali Raza} and Javaria Ashraf and Akbar Kanji and Rahman, {Yusra Abdul} and Trov{\~a}o, {N{\'i}dia S.} and Thielen, {Peter M.} and Maliha Yameen and Samiah Kanwar and Waqasuddin Khan and Furqan Kabir and Nisar, {Muhammad Imran} and Brian Merritt and Rumina Hasan and David Spiro and Zeba Rasmussen and Aamir, {Uzma Bashir} and Zahra Hasan",
note = "Funding Information: It is a limitation of this study that interpretations of the impact of Omicron subvariants in the different provinces of Pakistan was dependent on genome submissions from each region, and that these were not consistent. For instance, despite having identified Sindh as the entry-point of viral strains, this could be skewed by the limited data from other provinces. Another consequence of the limited genomic surveillance is delayed sampling, testing, and reporting. We used the sample collection dates for phylodynamic analysis and are able to provide insights regarding strain variations across the study period. Additionally, the sequencing was not consistent over the entire study period, as more samples were sequenced in the wave between December 2021 and February 2022. This makes it difficult to analyze the data in the context of burden of disease with age and gender stratification. However, given that most of the COVID-19 cases reported from Pakistan are from those aged 40 years and below, it is not surprising that we found that there was a greater representation of Omicron variants in this age group. This is in keeping with the younger age of the population of Pakistan, with 65% of individuals aged below 30 years. Another limitation of the study is that only the first Omicron subvariant, BA.1, was studied in terms of phylogenetic relatedness. Overall, it is likely that BA.5 samples had a greater representation in this study selection as the increase in this VoC occurred during a period in 2022 when there had been an increase in sequencing capacity for SARS-CoV-2 genomics. In the context of Aga Khan University, this was due to a contribution of institutional (Aga Khan University), national (GCF grant no.913, Higher Education Commission, Pakistan; World Health Organization, Pakistan) and international (Health Security Partners, USA; Fogarty International Center, NIH, USA; Bill and Melinda Gates Foundation) funding support for sequencing and bioinformatics initiatives. Publisher Copyright: {\textcopyright} 2023, The Author(s).",
year = "2023",
month = dec,
doi = "10.1186/s12864-023-09539-3",
language = "English",
volume = "24",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central Ltd.",
number = "1",
}
