SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021. SARS-CoV-2 Pakistan in April 2021

The SARS-CoV-2 pandemic continues to expand globally, with case numbers rising in many areas of the world, including the Indian sub-continent. Pakistan has one of the worlds largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 in beginning in March 2021. To help gain an understanding of the circulating variants 102 samples from Lahore and surrounding areas were sequenced, covering a 1 week period from April 2021. The samples were randomly chosen from diagnostic positives from 2 hospitals. Analysis of the lineages shows that B.1.1.7 (first identified in the UK) dominates, accounting for 97.9% (97/99) of cases, with B.1.351 (first identified in South Africa) accounting for 2.0% (2/99) of cases. No other lineages were observed. In depth analysis of the B.1.1.7 lineages indicates multiple separate introductions and subsequent establishment within the region. Eight samples were identical to genomes observed in Europe (7 UK, 1 Switzerland), indicating recent transmission. Other genomes have evolved, indicating sustained transmission over a period of time either within Pakistan or other countries with low density genome sequencing. Vaccines remain effective against B.1.1.7, however the low level of B.1.351 against which some vaccines are less effective demonstrates the requirement for continued prospective genomic surveillance.