Detecting and isolating false negatives ofSARS-CoV-2 primers and probe sets among the Japanese Population: A laboratory testing methodology and study

Tsutae, Wataru; Chaochaisit, Wirawit; Aoshima, Hideyuki; Ida, Chiharu; Miyakawa, Shino; Sekine, Hiroko; Baran, Iri Sato; Furukawa, Toshiharu; Sekine, Akihiro

ObjectivesIn this study, a comparative study between primers from Japans and USs disease control centers was conducted. As further investigation, virus sequence alignment with primers oligonucleotide was analyzed. Design or methods11,652 samples from Japanese population were tested for SARS-CoV-2 positive using recommended RT-PCR primer-probe sets from Japan National Institute of Infectious Disease (NIID) and US Centers for Disease Control and Prevention (CDC). ResultsOf the 102 positive samples, 17 samples (16.7% of total positives) showed inconsistent results when tested simultaneously for the following primers: JPN-N2, JPN-N1, CDC-N1, and CDC-N2. As a result, CDC recommended primer-probe sets showed relatively higher sensitivity and accuracy. Further virus sequence alignment analysis showed evidences for virus mutation happening at primers binding sites. ConclusionsThe inconsistency in the RT-PCR results for JPN-N1, JPN-N2, CDC-N1, and CDC-N2 primer-probe sets could be attributed to differences in virus mutation at primers binding site as observed in sequence analysis. The use of JPN-N2 combined with CDC-N2 primer produces the most effective result to reduce false negatives in Japan region. In addition, adding CDC-N1 will also help to detect false negatives.