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

Sarwar, M. B.; Yasir, M.; Alikhan, N.-F.; Afzal, N.; de Oliveria Martins, L.; Le Viet, T.; Trotter, A. J.; Prosolek, S. J.; Kay, G. L.; Foster-Nyarko, E.; Rudder, S.; Baker, D. J.; Tul-Muntaha, S.; Roman, M.; Webber, M. A.; Shafiq, A.; Shabir, B.; Akram, J.; Page, A. J.; Jahan, S.

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 beginning in March 2021. Currently very few SARS-CoV-2 genomes collected in Pakistan are available, with just 12 covering the third wave, 9 of which are from Islamabad. This highlights the need for more genome sequencing to allow surveillance of variants in circulation. In fact more genomes are available for travellers with a travel history from Pakistan, than from within the country itself. For an understanding of the circulating variants in Lahore and surrounding areas with a combined population of 11.1 million, 102 samples were sequenced, covering one week period from April 2021. The samples were randomly chosen from 2 hospitals with a diagnostic polymerase chain reaction (PCR) cutoff value of less than 25 cycles. Analysis of the lineages shows that B.1.1.7 (first identified in the UK, Alpha variant) dominates, accounting for 97.9% (97/99) of cases, with B.1.351 (first identified in South Africa, Beta variant) 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. Genomes of other samples show evidence that these 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.