Sequence mismatch in PCR probes may mask the COVID-19 detection in Nepal

ABSTRACT

•Most of the COVID-19 cases in Nepal are in the Southern districts of Nepal bordering India and many cases have travel history to India.•Very few positive cases of COVID-19 are detected in Nepal which could either be due to early national lockdown or inefficiency of PCR methods.•Whole genomes of 93 clinical samples from COVID-19 patients were analysed to find the primer and probe binding sites.•Mutations in probe binding sites were found and this could significantly impact PCR efficiency resulting in false negative results.