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

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

doi:10.1186/s12864-023-09539-3

Cited by 4 publications

(2 citation statements)

References 24 publications

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“…The second period, B (10th December 2020–9th December 2021) covered the pandemic waves in 2021 associated with Alpha, Beta, Gamma and Delta variants in Pakistan 26 , 27 . The third period, C (10th December 2021–15th August 2022) associated with the Omicron wave in 2022 17 . Mortality due to COVID-19 increased at the beginning of the pandemic in 2020 (A) and then during 2021 (B), peaking in July.…”

Section: Resultsmentioning

confidence: 99%

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Substitution spectra of SARS-CoV-2 genome from Pakistan reveals insights into the evolution of variants across the pandemic

Ashraf,

Bukhari,

Kanji

et al. 2023

Sci Rep

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Changing morbidity and mortality due to COVID-19 across the pandemic has been linked with factors such as the emergence of SARS-CoV-2 variants and vaccination. Mutations in the Spike glycoprotein enhanced viral transmission and virulence. We investigated whether SARS-CoV-2 mutation rates and entropy were associated COVID-19 in Pakistan, before and after the introduction of vaccinations. We analyzed 1,705 SARS-CoV-2 genomes using the Augur phylogenetic pipeline. Substitution rates and entropy across the genome, and in the Spike glycoprotein were compared between 2020, 2021 and 2022 (as periods A, B and C). Mortality was greatest in B whilst cases were highest during C. In period A, G clades were predominant, and substitution rate was 5.25 × 10–4 per site per year. In B, Delta variants dominated, and substitution rates increased to 9.74 × 10–4. In C, Omicron variants led to substitution rates of 5.02 × 10–4. Genome-wide entropy was the highest during B particularly, at Spike E484K and K417N. During C, genome-wide mutations increased whilst entropy was reduced. Enhanced SARS-CoV-2 genome substitution rates were associated with a period when more virulent SARS-CoV-2 variants were prevalent. Reduced substitution rates and stabilization of genome entropy was subsequently evident when vaccinations were introduced. Whole genome entropy analysis can help predict virus evolution to guide public health interventions.

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Section: Resultsmentioning

confidence: 99%

“…The Omicron BA.2 lineage subvariant XBB, first identified in India in August 2022, became the most dominant by the end of 2022 15 , 16 . Phylogenetic analysis of Omicron variants in provinces across Pakistan revealed that BA.1 and BA.2 variants were first introduced in the province of Sindh 17 .…”

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confidence: 99%