Implementation of an In-House Platform for Rapid Screening of SARS-CoV-2 Genome Variations
Farzane Zare Ashrafi , Marzieh Mohseni , Maryam Beheshtian , Zohreh Fattahi , Fatemeh Ghodratpour , Fatemeh Keshavarzi , Hanieh Behravan , Marzieh Kalhor , Khadijeh Jalalvand , Maryam Azad , Mahdieh Koshki , Ali Jafarpour , Azam Ghaziasadi , Alireza Abdollahi , Seyed Jalal Kiani , Angila Ataei-Pirkooh , Iman Rezaei Azhar , Farah Bokharaei-Salim , Mohammad Reza Haghshenas
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.
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.
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.
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.