Non-invasive SARS-CoV-2 genome surveillance and its utility in resource-poor settings during the Delta wave of the COVID-19 pandemic

Abstract

Voluntary participation of the public in disease surveillance can be encouraged by deploying user-friendly sample collection processes that can minimise the discomfort to the participants. This study evaluated the suitability of saline gargle-based sample collection for genomic surveillance of SARS-CoV-2, which included 589 SARS-CoV-2 positive samples collected from Nagpur city in central India from March to December 2021. The SARS-CoV-2 positive samples were subjected to whole genome sequencing (WGS) using the oxford nanopore technologies next-generation sequencing platform. Out of 589 samples, 500 samples qualified for the WGS, and the results revealed eight different clades of SARS-CoV-2 encompassing 37 different Pango-lineage types. The mutation mapping analysis of the variants identified in this study showed six mutations of interest and one mutation of concern E484K in the spike glycoprotein region. Our findings indicate that non-invasive gargle-based genomic surveillance is scalable and does not need significant changes to the existing workflow post-sample collection.