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

• Main Authors: Tran Thi Ngoc Dung, Pham Thanh Duy, October M. Sessions, Uma K. Sangumathi, Voong Vinh Phat, Pham Thi Thanh Tam, Nguyen Thi Nguyen To, Tran My Phuc, Tran Thi Hong Chau, Nguyen Ngoc Minh Chau, Ngoc Nguyen Minh, Guy E. Thwaites, Maia A. Rabaa, Stephen Baker
• Format: Article
• Language: English
• Published: BMC 2017-04-01
• Series: BMC Genomics
• Subjects: Rotavirus A; Genomics; Phylogenetics; Genome sequencing; Reassortment; Co-infection
• Online Access: http://link.springer.com/article/10.1186/s12864-017-3714-6
• ISSN: 1471-2164

Abstract 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