Targeted Whole Genome Sequencing of the Capripoxvirus Genome from Clinical Tissue Samples and Lyophilized Vaccine Batches.
Capripoxvirus
Targeted sequencing
Tiled PCR
Whole-genome sequencing
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2024
2024
Historique:
medline:
11
12
2023
pubmed:
7
12
2023
entrez:
7
12
2023
Statut:
ppublish
Résumé
Diseases caused by Capripoxviruses (CaPVs) are of great economic importance in sheep, goats, and cattle. Since CaPV strains are serologically indistinguishable and genetically highly homologous, typing of closely related strains can only be achieved by whole-genome sequencing. In this chapter, we describe a robust, cost-effective, and widely applicable protocol for reconstructing (nearly) complete CaPV genomes directly from clinical samples or commercial vaccine batches in less than a week. Taking advantage of the genetic similarity of CaPVs, a set of pan-CaPVs long-range PCRs was developed that covers the entire genome with only a limited number of tiled amplicons. The resulting amplicons can be sequenced on all currently available high-throughput sequencing platforms. As an example, we have included a detailed protocol for performing nanopore sequencing and a pipeline for assembling the resulting tiled amplicon data.
Identifiants
pubmed: 38060125
doi: 10.1007/978-1-0716-3515-5_12
doi:
Substances chimiques
Viral Vaccines
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
165-177Informations de copyright
© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.
Références
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pubmed: 21749675
Tuppurainen ES, Venter EH, Shisler JL et al (2017) Review. Capripoxvirus diseases: current status and opportunities for control. Transbound Emerg Dis 64:729–745
doi: 10.1111/tbed.12444
pubmed: 26564428
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pubmed: 27217175