Detection of SARS-CoV-2 N501Y mutation by RT-PCR to identify the UK and the South African strains in the population of South Indian state of Telangana

Abstract

ObjectiveTo detect N501Y mutation of the SARS-CoV-2 spike protein by RT-PCR to distinguish (B.1.1.7) UK and (501Y.V2) South African strains from others in the population of Telangana and to determine its clinical implications.MethodsA primer-probe mix that specifically detects the mutated N501Y strain by real time RT-PCR was designed. 93 samples that were reported positive for COVID-19 by our laboratory in the month of February 2021 were tested using our own primer-probe mix for the presence of N501Y by RT-PCR. The results of RT-PCR were validated by Sanger sequencing in representative samples. Sanger sequencing of other defining spike mutations of B.1.1.7 (del 69-70, del 144, N501Y, A570D, D614G, P681H, T716I, S982A and D1118H) and 501Y.V2 (K417N, E484K, N501Y and D614G) was also investigated.FindingsOut of 93 COVID-19 positive samples, 12 samples are detected positive for N501Y by RT-PCR. Sanger sequencing of these 12 samples further confirmed the presence of N501Y and other mutations that are characteristic of UK strain (B.1.1.7). The South African strain (501Y.V2) is not detected in any of our samples in this study. But, the E484K mutation that is characteristic of 501Y.V2 is detected in one N501Y negative sample.ConclusionStrain-specific RT-PCR for N501Y was developed and validated with Sanger sequencing. Such strategy facilitates quick surveillance for more transmissible and more vaccine resistant strains.

Molecular Analysis and Genome Sequencing of SARS-CoV-2 during Second Wave 2021 Revealed Variant Diversity in India

“…Among them N440K, P681H considered to be powerful having more virulence, infectious and have higher immune escape than the wild type strain. 20,33 N440K mutation in SARS-CoV-2 became the reason behind the major destruction caused by the SARS-CoV-2 in Visakhapatnam, Karnataka, Telangana and other southern parts of India. 20 N501Y mutation found in this study was also detected in Telangana, the southern parts of India.…”

“…20 N501Y mutation found in this study was also detected in Telangana, the southern parts of India. 33 Occurrence of re-infections and rapid transmission is mainly due to the emergence of all these new variants, either after natural infection or after vaccination. 24 A recent study confirmed that re-infections are already happening in India.…”