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

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 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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https://hal.archives-ouvertes.fr/hal-02167880
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Soumis le : mardi 15 octobre 2019 - 14:30:06
Dernière modification le : jeudi 24 mars 2022 - 03:43:01
Archivage à long terme le : : vendredi 17 janvier 2020 - 11:14:30

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Distributed under a Creative Commons Paternité 4.0 International License

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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, Elsevier, 2019, 531, pp.141-148. ⟨10.1016/j.virol.2019.03.006⟩. ⟨hal-02167880⟩

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