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

• Published in: BMC genomics Vol. 18; no. 1; p. 324
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: England BioMed Central 24.04.2017; BMC
• Subjects: Acids; Bias; Co-infection; Diarrhea; DNA, Complementary - genetics; Enzyme immunoassay; Feces; Feces - virology; Gene sequencing; Genome sequencing; Genome, Viral - genetics; Genomes; Genomics; Genomics - methods; Genotype; Genotypes; Humans; Immunoassay; Infections; Methodology; Methods; Mixed infection; Phylogenetics; Phylogeny; Reagents; Reassortant Viruses - genetics; Reassortant Viruses - physiology; Reassortment; Rotavirus; Rotavirus - genetics; Rotavirus - physiology; Rotavirus A; Segments; Sequence Analysis, RNA - methods; Surveillance; Surveillance systems; Vaccines; Viral Load; Viruses; Co-infection; Rotavirus A; Genome sequencing; Genomics; Phylogenetics; Antibody capture; Reassortment
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-017-3714-6

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. 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. Our approach had a 100% success rate, producing >90% genome coverage for diverse RoV present in fecal samples (Ct < 30). 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. Current Controlled Trials ISRCTN88101063 . Date of registration: 14/06/2012.