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Article Dans Une Revue Virology Année : 2019

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

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Résumé

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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Origine : Publication financée par une institution
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Dates et versions

hal-02167880 , version 1 (15-10-2019)

Licence

Paternité - CC BY 4.0

Identifiants

Citer

Florence Maurier, Delphine Beury, Léa Fléchon, Jean-Stéphane Varré, Hélène Touzet, et al.. A complete protocol for whole-genome sequencing of virus from clinical samples: Application to coronavirus OC43. Virology, 2019, 531, pp.141-148. ⟨10.1016/j.virol.2019.03.006⟩. ⟨hal-02167880⟩
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