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A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43

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Maurier, Florence | Beury, Delphine | Fléchon, Léa | Varré, Jean-Stéphane | Touzet, Hélène | Goffard, Anne | Hot, David | Caboche, Ségolène

Edité par CCSD ; Elsevier -

International audience. Genome sequencing of virus has become a useful tool for better understanding of virus pathogenicity and epidemiological surveillance. Obtaining virus genome sequence 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. Here we introduce a complete sequencing and analyzing protocol called V-ASAP for Virus Amplicon Sequencing Assembly Pipeline. Our protocol is able to generate the viral dominant genome sequence starting from clinical samples. It is based on a multiplex PCR amplicon sequencing coupled with a reference-free analytical pipeline. This protocol was applied to 11 clinical samples infected with coronavirus OC43 (HcoV-OC43), and led to seven complete and two nearly complete genome assemblies. The protocol introduced here is shown to be robust, to produce a reliable sequence, and could be applied to other virus.

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