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A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection

BACKGROUND: Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS: To overcome these limitations, we developed a novel RoV capture and genome seq...

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Detalles Bibliográficos
Autores principales: Dung, Tran Thi Ngoc, Duy, Pham Thanh, Sessions, October M., Sangumathi, Uma K., Phat, Voong Vinh, Tam, Pham Thi Thanh, To, Nguyen Thi Nguyen, Phuc, Tran My, Hong Chau, Tran Thi, Chau, Nguyen Ngoc Minh, Minh, Ngoc Nguyen, Thwaites, Guy E., Rabaa, Maia A., Baker, Stephen
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5404283/
https://www.ncbi.nlm.nih.gov/pubmed/28438140
http://dx.doi.org/10.1186/s12864-017-3714-6
Descripción
Sumario:BACKGROUND: Genomic characterization of rotavirus (RoV) has not been adopted at large-scale due to the complexity of obtaining sequences for all 11 segments, particularly when feces are used as starting material. METHODS: To overcome these limitations, we developed a novel RoV capture and genome sequencing method combining commercial enzyme immunoassay plates and a set of routinely used reagents. RESULTS: Our approach had a 100% success rate, producing >90% genome coverage for diverse RoV present in fecal samples (Ct < 30). CONCLUSIONS: This method provides a novel, reproducible and comparatively simple approach for genomic RoV characterization and could be scaled-up for use in global RoV surveillance systems. TRIAL REGISTRATION (PROSPECTIVELY REGISTERED): Current Controlled Trials ISRCTN88101063. Date of registration: 14/06/2012 ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3714-6) contains supplementary material, which is available to authorized users.