SARS-CoV-2 UK, South African and Brazilian Variants in Karachi- Pakistan (preprint)

ABSTRACT

COVID-19 pandemic has been evolving in Pakistan since the UK, South African and Brazilian variants have started surfacing which are known for increase transmissibility and can also be responsible for escape from immune responses. The gold standard to detect these variants of concern is sequencing, however routine genomic surveillance in resource limited countries like Pakistan is not always readily available. With the emergence of variants of concern and a dearth of facilities for genomic scrutiny leaves policy makers and health authorities an inconsistent and twisted image to make decisions. The inadvertent detection of B.1.1.7 by target failure because of a key deletion in spike {Delta}69-70 in the UK by commercially available COVID-19 PCR assay helps to understand target failures as an alternative approach to detect variants. It was ascertained further that a deletion in the ORF1a gene (ORF1a {Delta}3675-3677) found common in B.1.1.7, B.135 and P.1 variants of concern. The Real Time Quantitative PCR (RT-qPCR) assay for detection of emergence and spread of SARS-CoV-2 variants, by these target failures is used here. The positive samples archived in respective labs were divided in two groups used in the present study. Group I constitutes 261 positive samples out of 16964 (1.53%) collected from August till September 2020. Group II include 3501 positive samples out of 46041 (7.60%) from November 2020 till January 2021. In positive samples of group I, no variant of concern was found. A staggering difference in results was noted in group II where positivity ratio increased exponentially and the variants of concern started appearing in significant numbers (53.64% overall). This is indicative that the third wave in Pakistan is due to the importation of SARS-CoV-2 variants. This calls for measures to increase surveillance by RT-qPCR which would help authorities in decision making.