Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations

Abstract

Background: Global real-time monitoring of SARS-CoV-2 variants is crucial to controlling the COVID-19 outbreak. The purpose of this study was to set up a Sanger-based platform for massive SARS-CoV-2 variant tracking in laboratories in low-resource settings.Methods: We used nested RT-PCR assay, Sanger sequencing and lineage assignment for 930-bp of the SARS-CoV-2 spike gene, which harbors specific variants of concern (VOCs) mutations. We set up our platform by comparing its results with whole genome sequencing (WGS) data on 137 SARS-CoV-2 positive samples. Then, we applied it on 1028 samples from March-September 2021.Results: In total, 125 out of 137 samples showed 91.24 concordance in mutation detection. In lineage assignment, 123 out of 137 samples demonstrated 89.78 concordance, 65 of which were assigned as VOCs and showed 100 concordance. Of 1028 samples screened by our in-house method, 78 distinct mutations were detected. The most common mutations were: S:D614G (21.91), S:P681R (12.19), S:L452R (12.15), S:T478K (12.15), S:N501Y (8.91), S:A570D (8.89), S:P681H (8.89), S:T716I (8.74), S:L699I (3.50) and S:S477N (0.28). Of 1028 samples, 980 were attributed as VOCs, which include the Delta (B.1.617.2) and Alpha (B.1.1.7) variants. Conclusion: Our proposed in-house Sanger-based assay for SARS-CoV-2 lineage assignment is an accessible strategy in countries with poor infrastructure facilities. It can be applied in the rapid tracking of SARS-CoV-2 VOCs in the SARS-CoV-2 pandemic.