High sensitivity detection of coronavirus SARS-CoV-2 using multiplex PCR and a multiplex-PCR-based metagenomic method

Chenyu Li; David N. Debruyne; Julia Spencer; Vidushi Kapoor; Lily Y. Liu; Bo Zhou; Lucie Lee; Rounak Feigelman; Grayson Burdon; Jeffrey Liu; Alejandra Oliva; Adam Borcherding; Hongdong Tan; Alexander E. Urban; Guoying Liu; Zhitong Liu

Here, we describe the development of a highly sensitive and robust detection assay incorporating the use of multiplex PCR technology to identify SARS-CoV-2. Theoretically, the multiplex PCR strategy, by amplifying hundreds of targets, has significantly higher sensitivity than RT-PCR and may even detect DNA molecules resulting from degraded virus genome fragments. Multiplex PCR has been shown to be an efficient and low-cost method to detect Plasmodium falciparum infections, with high coverage (median 99%), specificity (99.8%) and sensitivity. Moreover, this solution can be tailored to simultaneously address multiple questions of interest within various epidemiological settings 42 . Similar to a recently described metagenomic approach for SARS-CoV-2 identification 43 , we also establish a user-friendly multiplex-PCRbased metagenomic method that is not only able to detect SARS-CoV-2, but could also be applied for the identification of significant sequence mutations within known viruses and to uncover novel pathogens with a limited sequencing depth of approximately 1 million reads.