Since March-2020, after WHO announced that novel coronavirus (COVID-19) outbreak, a global pandemic, the virus has caused significant causalities more than 200 countries across the world. Recently there has been surge in the infections due to mutation of the SARS Covid-19 virus of which delta mutants with its lineages have been prominent. At present, mutations are monitored by a consortium using NGS (Next-generation sequencing) technology which is accurate but expensive and time consuming. As a rapid, inexpensive but accurate method we have explored RT-PCR (Real Time-Polymerase Chain Reaction) to detect the mutants. This would help in the early diagnosis and surveillance of this pandemic. One hundred Covid positive samples archived with us between Jan-2021 to July-2021 were studied by RT-PCR using commercial delta mutant kit. Sanger sequencing was done to confirm the RT-PCR findings. RT-PCR method was able to detect delta mutants in 08 of the 100 samples studied (8%). The simple RT-PCR technique is found to be sensitive and specific for the detection of Cov-19 delta mutant with less turnaround time than NGS. This technique may be deployed in all the approved laboratories for Screening and surveillance to contain the spread of delta mutant in the community. This simple method can be exploited to detect other published mutants of Covid-19, when the situation arises.

Keywords : Covid-19, Delta Mutant, Gene Sequencing, RTPCR, Surveillance.