AUTHOR=Khan Adnan , Hanif Muhammad , Ahmed Akhtar , Syed Sarosh , Ghazali Saqib , Khanani Rafiq 

TITLE=SARS-CoV-2 UK, South African and Brazilian Variants in Karachi- Pakistan

JOURNAL=Frontiers in Molecular Biosciences

VOLUME=Volume 8 - 2021

YEAR=2021

URL=https://www.frontiersin.org/journals/molecular-biosciences/articles/10.3389/fmolb.2021.724208

DOI=10.3389/fmolb.2021.724208

ISSN=2296-889X

ABSTRACT=COVID-19 pandemic has been evolving in Pakistan with the emergence of UK, South African and Brazilian variants. These variants of concern (VOC) are known for increase transmissibility and can also be responsible for escape from immune responses. The gold standard to detect the VOC is sequencing, however routine genomic surveillance in resource limited countries like Pakistan is not always readily available. The inadvertent detection of B.1.1.7 (UK) 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 which can distinguish target failures and can discriminate SARS-CoV-2 VOC. The study uses positive samples archived in respective labs. Samples were divided in two groups. Group I constitutes 261 positive samples out of total 16964 (1.53%) performed from August till September 2020, while group II consist of 3501 positive samples out of total 46041 performed (7.60%), 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 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.