Abstract
The COVID-19 pandemic has been evolving in Pakistan with the emergence of the United Kingdom, South African, and Brazilian variants. These variants of concern (VOC) are known for increased transmissibility and can also be responsible for avoiding immune responses. The gold standard to detect VOC is sequencing, however routine genomic surveillance in resource-limited countries like Pakistan is not always readily available. The inadvertent detection of the B.1.1.7 (United Kingdom) VOC by a target failure due to the key deletion in spike Δ69-70 by commercially available PCR assay helps to understand target failures as an alternative approach to detect variants. In pursuit of VOC it was further discovered that a deletion in the ORF1a gene (ORF1a Δ3675-3677) is common in B.1.1.7, B.1.351 (South African), and P.1 (Brazilian) VOC. The Real-Time Quantitative PCR (RT-qPCR) assay can distinguish target failures and can discriminate SARS-CoV-2 VOC. The study uses positive samples archived in respective labs. Samples were divided into two groups. Group I constitutes 261 positive samples out of total of 16,964 (1.53%) performed from August till September 2020, while group II consists of 3501 positive samples out of a total of 46,041 (7.60%) performed, from November 2020 till January 2021. The RT-qPCR analysis showed that no VOC was present in positive samples of group I. However, a staggering difference in results was noted in group II where the positivity ratio increased exponentially and the VOC started appearing in significant numbers (53.64%). This concludes that the third wave in Pakistan is due to the importation of SARS-CoV-2 variants.
Highlights
The global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 disease, has ravaged the world by surprise
We firstly investigate mutations related to SARS-CoV-2 variants of concern (VOC) by reverse transcription (RT)-PCR method from SARS-CoV-2 positive samples, divided in two different quarters, of three different labs in Karachi
We identified that the total tests conducted in group I were 16,964 while in group II (Second quarter) were 46,041 respectively
Summary
The global outbreak of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19 disease, has ravaged the world by surprise. As of March 28, 2021, SARS-CoV-2 related infections have surpassed over 128,247,719, with 2,804,719 deaths globally. In Pakistan, the virus has affected more than 659,116 individuals, with more than 14,256 reported deaths to date (www.covid.gov.pk/stats/pakistan) (access date; 29-3-2021). SARS-CoV-2 has been responsible for overwhelmed health care systems, coerced shutting down of schools and gatherings, and pulling the planet into an economic recession. Despite the fact that 2020 was a challenging year, 2021 seems like it will not be easy either with the surfacing of multiple variants of SARS-CoV-2. One of the notorious variants of SARS-CoV-2 characterized as lineage B.1.1.7 became known in the United Kingdom in December 2020
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