ArticleBMC genomics2023
Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave.
Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 15 citations in OpenAlex.
- Acute SARS-CoV-2 viral load and systemic inflammation are associated with neuropsychiatric and musculoskeletal symptoms in long COVID.PloS one · 2026Article
- Validation of polyester nasal swabs for post-mortem SARS-CoV-2 diagnosis in Karachi, Pakistan: a prospective surveillance analysis.Journal of global health · 2025Observational
- Individuals with latent tuberculosis in a high TB endemic country show mild COVID-19.PloS one · 2025Article
- SARS-CoV-2 introductions to the island of Ireland: a phylogenetic and geospatiotemporal study of infection dynamics.Genome medicine · 2024Article
- Shift in SARS-CoV-2 variants of concern from Delta to Omicron was associated with reduced hospitalizations, increased risk of breakthrough infections but lesser disease severity.Journal of infection and public health · 2024Article
- Comparison of antibody responses of heterologous and homologous Covid-19 booster vaccination: an observational study.Frontiers in immunology · 2024Observational
- Genomic epidemiology and evolutionary dynamics of the Omicron variant of SARS-CoV-2 during the fifth wave of COVID-19 in Pakistan.Frontiers in cellular and infection microbiology · 2024Article
- Substitution spectra of SARS-CoV-2 genome from Pakistan reveals insights into the evolution of variants across the pandemic.Scientific reports · 2023Article
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Authors and funding
17 authors at 5 institutions in 2 countries.
Funding
Abstract
backgroundCOVID-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.
methodsWe 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.
resultsThe 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.
conclusionsPhylogenetic 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.
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