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

BMC Genomics

Methodology Article

Ngoc Nguyen Minh¹  October M. Sessions²  Uma K. Sangumathi²  Nguyen Ngoc Minh Chau³  Tran My Phuc³  Tran Thi Hong Chau³  Tran Thi Ngoc Dung³  Nguyen Thi Nguyen To³  Pham Thi Thanh Tam³  Pham Thanh Duy³  Voong Vinh Phat³  Guy E. Thwaites⁴  Maia A. Rabaa⁴  Stephen Baker⁵ 

[1] Children’s Hospital 2 (CH2), Ho Chi Minh City, Vietnam;Duke – National University of Singapore, Singapore, Singapore;The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam;The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam;Centre for Tropical Medicine, Oxford University, Oxford, UK;The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research Unit, 764 Vo Van Kiet, Quan 5, Ho Chi Minh City, Vietnam;Centre for Tropical Medicine, Oxford University, Oxford, UK;The London School of Hygiene and Tropical Medicine, London, UK;

关键词: Rotavirus A;    Genomics;    Phylogenetics;    Genome sequencing;    Reassortment;    Co-infection;    Antibody capture;   

DOI  :  10.1186/s12864-017-3714-6

 received in 2016-11-04, accepted in 2017-04-21,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundGenomic 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.MethodsTo 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.ResultsOur approach had a 100% success rate, producing >90% genome coverage for diverse RoV present in fecal samples (Ct < 30).ConclusionsThis 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

【 授权许可】

CC BY   
© The Author(s). 2017