Abstract

Objective: The study was performed for a comparative analysis between primers from Japan’s and US’s disease control centers as well as to investigate the virus sequence alignment with primers’ oligonucleotide to introduce primer sets of high detectability with reduce false negative results.

Design or methods: 11,652 samples from Japanese population were tested for Novel Severe Acute Respiratory Syndrome Corona Virus-2 (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). Primer-probe sensitivity was analyzed for higher detectability for SARSCoV- 2 positive cases.

Results: Of 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. Our results revealed that CDC recommended primer-probe sets showed relatively higher detection sensitivity and accuracy. Further, virus sequence alignment analysis showed evidences for virus mutation occurred at primer’s binding sites.

Conclusion: The inconsistency in the RT-PCR results for SARS-CoV-2 detection using JPN-N1, JPN-N2, CDC-N1, and CDC-N2 primer-probe sets could be attributed to differences in primer efficiency or/and virus mutation at primer-probe’ binding sites. The use of JPN-N2 combined with CDC-N2 and CDC-N1 primer-probe sets produce the most effective results as well as may reduce the false negatives results in Japan and overseas.

Keywords: COVID-19; SARS-CoV-2; RT-PCR performance; Genomic variants; Primers; Sensitivity