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

Abstract

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 world’s largest populations, of over 200 million people and is experiencing a severe third wave of infections caused by SARS-CoV-2 that began in March 2021. In Pakistan, during the third wave until now only 12 SARS-CoV-2 genomes have been collected and among these nine are from Islamabad. This highlights the need for more genome sequencing to allow surveillance of variants in circulation. In fact, more genomes are available among travellers with a travel history from Pakistan, than from within the country itself. We thus aimed to provide a snapshot assessment of circulating lineages in Lahore and surrounding areas with a combined population of 11.1 million. Within a week of April 2021, 102 samples were sequenced. The samples were randomly collected from two hospitals with a diagnostic PCR cutoff value of less than 25 cycles. Analysis of the lineages shows that the Alpha variant of concern (first identified in the UK) dominates, accounting for 97.9 % (97/99) of cases, with the Beta variant of concern (first identified in South Africa) accounting for 2.0 % (2/99) of cases. No other lineages were observed. In depth analysis of the Alpha lineages indicated multiple separate introductions and subsequent establishment within the region. Eight samples were identical to genomes observed in Europe (seven UK, one 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 Alpha, however, the low level of Beta against which some vaccines are less effective demonstrates the requirement for continued prospective genomic surveillance.

Circulating Dynamics of SARS-CoV-2 Variants between April 2021 and February 2022 in Turkey

“…In a recent study conducted in Turkey between March 2021 and December 2021, B.1.1.7 was dominant in April 2021 [ 16 ]. B.1.1.7 was reported as the most common lineage in Pakistan, one of the most populated countries in that month [ 17 ]. Similarly, the most common variant during Spring 2021 was reported Alpha in the United States [ 18 ].…”

Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan

“…Out of these 1725 mutations, 1058 were present in ORF1ab which transcribe into 16 nonstructural proteins (NSPs). Among the ORF1ab proteins, NSP3 had the largest number of missense (210), silent (111), in-frame deletions (2), frameshift deletions (17), frameshift insertion (11), and stop-gain mutations (4). It was followed by the NSP2 which had the second highest number of mutations with 86 missense, 52 silent, 02 in-frame deletions, 02 frameshift deletions, 03 frameshift insertions, and 1 stop-gain mutation.…”

“…According to RT-PCR based diagnostic assay, the incidence of B.1.1.7 in Lahore -the 2 nd largest city of Pakistan- during the April 2021 (peak month of 3 rd wave) was 97.9%. Moreover, out of eight samples of SARS-CoV-2 which were sequenced in the start of the 3 rd wave of COVID-19 in Pakistan, 7 were found identical with the genomes reported from UK and one with that of Switzerland, suggesting the transmission of disease in Pakistan from these European countries [ 17 ].…”

Development and validation of a clinical predictive model for severe and critical pediatric COVID-19 infection

“…For example, the Delta variant (B.1.617.2) of SARS-CoV-2 was dominant in Singapore by May 31 st 2021, whereas in Indonesia and Malaysia, it became dominant by July 8 th and 23 rd 2021, respectively [ 48 – 50 ]. Moreover, availability of sequencing data in some regions was limited and may be subject to sampling bias [ 51 ]. Due to the retrospective nature of data collection, the perceived severity of disease may be biased and there was no standardized reporting, laboratory testing or management protocol.…”