{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["531"],"submitter":["Maurier F"],"funding":["Lille Hospital University"],"pubmed_abstract":["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 complet"],"journal":["Virology"],"pagination":["141-148"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC7112119"],"repository":["biostudies-literature"],"pubmed_title":["A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43."],"pmcid":["PMC7112119"],"pubmed_authors":["Varre JS","Touzet H","Caboche S","Beury D","Flechon L","Maurier F","Hot D","Goffard A"],"additional_accession":[]},"is_claimable":false,"name":"A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43.","description":"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 complet","dates":{"release":"2019-01-01T00:00:00Z","publication":"2019 May","modification":"2026-04-28T22:39:35.18Z","creation":"2020-05-22T18:54:25Z"},"accession":"S-EPMC7112119","cross_references":{"pubmed":["30878524"],"doi":["10.1016/j.virol.2019.03.006"]}}