SARS-CoV-2 variants and genomic surveillance in the low-resource north-west region of Pakistan

Abstract

During January and February 2022, a huge spike in the cases of COVID-19 was recorded in the Khyber Pakhtunkhwa (KP) province of Pakistan prompting the civil administration to institute new restrictions. To investigate the underlying causes of this surge, the regional Public Health Reference Lab (PHRL) launched a screening effort throughout the Province’s remote and urban areas. Herein, we present our survey results during the peak months of the pandemic. The data indicated the prevalence of highly transmissible delta- and Omicron-like virus variants, which may explain the rise in positive cases. Phylogenetic analysis revealed the genetic association between the sequences from this study and those found in Pakistan as well as from geographically distant countries, suggesting a complex evolutionary history. For screening, we deployed an easy-to-use single primer-based polymerase chain reaction (PCR) assay to identify the circulation of SARS-CoV-2. The assay was validated using clinical swabs of COVID-19 patients and obtained consistent results with Sanger sequencing. Our survey identified a patient simultaneously infected with two variants of concern, indicating the presence of the Deltacron variant, although we cannot discount the possibility of sequencing errors. We recommend that SARS-CoV-2 be continuously monitored to detect single nucleotide polymorphisms (SNPs) that are causally linked to the emergence of new lineages. Our method provides a rapid and cost-effective detection assay for SARS-CoV-2 in a resource-constrained setting.

Keywords

• COVID-19
• molecular testing
• delta
• omicron
• co-infection