The emergence of a more transmissible variant of SARS-CoV-2 (B1.1.7) in the United Kingdom (UK) during late 2020 has raised major public health concerns. Several mutations have been reported in the genome of the B.1.1.7 variant including the N501Y and 69-70deletion in the Spike that has implications on virus transmissibility and diagnostics. Although the B.1.1.7 variant has been reported from several countries, only two cases have been identified through whole-genome sequencing from Pakistan. We used a two-step strategy for the detection of B.1.1.7 with initial screening through ThermoFisher TaqPathTM SARS-CoV-2 kit followed by partial sequencing of Spike (S) gene of samples having spike gene target failure (SGTF) on real-time PCR. From January 01, 2021, to February 21, 2021, a total of 2,650 samples were tested for the presence of SARS-CoV-2 using TaqPathTM kit and 70.4% (n=1,867) showed amplification of all the 3 genes (S, N, and ORF). Notably, 29.6% (n=783) samples had the spike gene target failure (SGTF). The SGTF cases were detected at a low frequency during the first three weeks of January (n=10, n=13, and n=1 respectively) however, the cases started to increase in the last week. During February, 726 (93%) cases of SGTF was reported with a peak (n=345) found during the 3rd week. Based on the partial sequencing of spike gene of SGTF samples (n=15), 93% (n=14) showed the characteristic N501Y, A570D, P681H, and T716I mutations found in the B.1.1.7 variant. Our findings highlight the high prevalence of B.1.1.7 in Pakistan and warrant large scale genomic surveillance and strengthening of laboratory network in the country.
An upsurge of SARS CoV-2 B.1.1.7 Variant in Pakistan