biostudies-literatureUnknown531Maurier FLille Hospital UniversityGenome 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 completVirology141-148https://www.ebi.ac.uk/biostudies/studies/S-EPMC7112119biostudies-literatureA complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43.PMC7112119Varre JSTouzet HCaboche SBeury DFlechon LMaurier FHot DGoffard AfalseA complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43.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 complet2019-01-01T00:00:00Z2019 May2026-04-28T22:39:35.18Z2020-05-22T18:54:25ZS-EPMC71121193087852410.1016/j.virol.2019.03.006