Human coronavirus OC43 genome sequencing and assembly in clinical context with amplicon-seq data

Genome sequencing of virus has become an unavoidable tool for the better understanding of virus pathogenecity and epidemiological surveillance. However to sequence virus genome directly from clinical samples is still a challenging task due to the low load of virus genetic material compared to the host DNA and to the difficulty to get an accurate genome assembly. We developed a complete sequencing and analyzing protocol to obtain the viral dominant genome sequence starting from clinical samples. This method is based on a PCR multiplex amplicon sequencing coupled withan alignment-free analytical pipeline. This protocol was applied to 11 clinical samples infected with coronavirus OC43 (HCoV-OC43). Application of the protocol led to seven complete and two nearly complete genome assemblies. The protocol used here was shown to be robust and producing a reliable sequence, and could be applied to other virus.