Abstract: The D614 mutation of the S gene of the new coronavirus (SARS-CoV-2) significantly increases the virus' infectivity, and is also the main source of the delta mutant strain. How to quickly type such high-risk SNPs in viral nucleic acid detection is a technical issue that researchers are very concerned about. However, the new coronavirus is a single-stranded RNA virus, and the genome is easily degraded. The existing point mutation identification technology is not suitable for highly degraded fragmented viral nucleic acid. In this study, a ligase detection reaction (LDR) technology combined with fluorescent quantitative PCR was used to establish a method to detect the fragmented new coronavirus S gene D614G. The results showed that this method had a good degree of discrimination for 5 pmol/L viral RNA templates, and the minimum point mutations carried by viral RNAs with a length of only 40 nt could be detected.

Key words: LDR, SARS-CoV-2, fragmentation, D614G mutation