A proposal of an alternative primer for the ARTIC Network’s multiplex PCR to improve coverage of SARS-CoV-2 genome sequencing

A group of biologists, ARTIC Network, has proposed a multiplexed PCR primer set for whole genome analysis of the novel corona virus, SARS-CoV-2, soon after the epidemics of this pathogen was revealed. The primer set seems to have been adapted already by many researchers worldwide and contributed for the high-quality and prompt genome epidemiology of this potential pandemic virus. We have also seen the great performance of their primer set and protocol; the primer set was able to amplify all desired PCR products with fairy small amplification bias from clinical samples with relatively high viral load. However, we observed acute drop of reads derived from two particular PCR products, 18 and 76, out of the 98 designated products as sample9s viral load decreases. We suspected the reason for this low coverage issue was due to dimer formation between primers used to amplify those two PCR products. Here, we propose replacing just one of those primers, nCoV-2019_76_RIGHT(-), to a newly designed primer. The result of the replacement of primer showed improvement in coverage at both regions targeted by the products, 18 and 76. We expect this simple modification will extend the limit for whole SARS-CoV-2 genome analysis to samples with lower viral load and enhance genomic epidemiology of this pathogen.