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A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses

The diseases caused by capripoxviruses (CaPVs) are of major economic concern in sheep, goat and cattle as they are inexorably spreading into non-endemic regions. As CaPV strains are serologically indistinguishable and genetically highly homologous, typing closely related strains can only be achieved...

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Autores principales: Mathijs, Elisabeth, Haegeman, Andy, De Clercq, Kris, Van Borm, Steven, Vandenbussche, Frank
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier/North-Holland Biomedical Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8872832/
https://www.ncbi.nlm.nih.gov/pubmed/35032481
http://dx.doi.org/10.1016/j.jviromet.2022.114464
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author Mathijs, Elisabeth
Haegeman, Andy
De Clercq, Kris
Van Borm, Steven
Vandenbussche, Frank
author_facet Mathijs, Elisabeth
Haegeman, Andy
De Clercq, Kris
Van Borm, Steven
Vandenbussche, Frank
author_sort Mathijs, Elisabeth
collection PubMed
description The diseases caused by capripoxviruses (CaPVs) are of major economic concern in sheep, goat and cattle as they are inexorably spreading into non-endemic regions. As CaPV strains are serologically indistinguishable and genetically highly homologous, typing closely related strains can only be achieved by whole genome sequencing. Unfortunately the number of publicly available genomes remains low as most sequencing methods rely on virus isolation. Therefore, we developed a robust, cost-effective and widely applicable method that allows to generate (nearly) complete CaPV genomes directly from clinical samples or commercial vaccine batches. A set of pan-CaPVs long-range PCRs spanning the entire genome was designed to generate PCR amplicons that can be sequenced on commonly used high-throughput sequencing platforms: MiSeq (Illumina), RSII (PacBio) and MinION (Oxford Nanopore Technologies). The robustness of the LR-PCR strategy was evaluated for all 3 members of CaPV directly from a variety of samples, including clinical samples (N = 7), vaccine batches (N = 6), and virus isolates (N = 2). The sequencing method described here allows to reconstruct (nearly) complete CaPV genomes in less than a week and will aid researchers studying closely-related CaPV strains worldwide.
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spelling pubmed-88728322022-03-01 A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses Mathijs, Elisabeth Haegeman, Andy De Clercq, Kris Van Borm, Steven Vandenbussche, Frank J Virol Methods Protocols The diseases caused by capripoxviruses (CaPVs) are of major economic concern in sheep, goat and cattle as they are inexorably spreading into non-endemic regions. As CaPV strains are serologically indistinguishable and genetically highly homologous, typing closely related strains can only be achieved by whole genome sequencing. Unfortunately the number of publicly available genomes remains low as most sequencing methods rely on virus isolation. Therefore, we developed a robust, cost-effective and widely applicable method that allows to generate (nearly) complete CaPV genomes directly from clinical samples or commercial vaccine batches. A set of pan-CaPVs long-range PCRs spanning the entire genome was designed to generate PCR amplicons that can be sequenced on commonly used high-throughput sequencing platforms: MiSeq (Illumina), RSII (PacBio) and MinION (Oxford Nanopore Technologies). The robustness of the LR-PCR strategy was evaluated for all 3 members of CaPV directly from a variety of samples, including clinical samples (N = 7), vaccine batches (N = 6), and virus isolates (N = 2). The sequencing method described here allows to reconstruct (nearly) complete CaPV genomes in less than a week and will aid researchers studying closely-related CaPV strains worldwide. Elsevier/North-Holland Biomedical Press 2022-03 /pmc/articles/PMC8872832/ /pubmed/35032481 http://dx.doi.org/10.1016/j.jviromet.2022.114464 Text en © 2022 The Authors https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Protocols
Mathijs, Elisabeth
Haegeman, Andy
De Clercq, Kris
Van Borm, Steven
Vandenbussche, Frank
A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses
title A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses
title_full A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses
title_fullStr A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses
title_full_unstemmed A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses
title_short A robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses
title_sort robust, cost-effective and widely applicable whole-genome sequencing protocol for capripoxviruses
topic Protocols
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8872832/
https://www.ncbi.nlm.nih.gov/pubmed/35032481
http://dx.doi.org/10.1016/j.jviromet.2022.114464
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