A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection
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 gen...
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| Format: | Article |
| Language: | English |
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BMC
2017-04-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3714-6 |
| _version_ | 1811303065750339584 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Tran Thi Ngoc Dung |
| collection | DOAJ |
| description | 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 |
| first_indexed | 2024-04-13T07:41:09Z |
| format | Article |
| id | doaj.art-4afc1fc5aaed4a1fb7d2c381fe16a30b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T07:41:09Z |
| publishDate | 2017-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-4afc1fc5aaed4a1fb7d2c381fe16a30b2022-12-22T02:55:54ZengBMCBMC Genomics1471-21642017-04-0118111610.1186/s12864-017-3714-6A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infectionTran Thi Ngoc Dung0Pham Thanh Duy1October M. Sessions2Uma K. Sangumathi3Voong Vinh Phat4Pham Thi Thanh Tam5Nguyen Thi Nguyen To6Tran My Phuc7Tran Thi Hong Chau8Nguyen Ngoc Minh Chau9Ngoc Nguyen Minh10Guy E. Thwaites11Maia A. Rabaa12Stephen Baker13The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitDuke – National University of SingaporeDuke – National University of SingaporeThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitChildren’s Hospital 2 (CH2)The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitThe Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University, Clinical Research UnitAbstract 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: 14/06/2012http://link.springer.com/article/10.1186/s12864-017-3714-6Rotavirus AGenomicsPhylogeneticsGenome sequencingReassortmentCo-infection |
| spellingShingle | 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 A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection BMC Genomics Rotavirus A Genomics Phylogenetics Genome sequencing Reassortment Co-infection |
| title | A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection |
| title_full | A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection |
| title_fullStr | A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection |
| title_full_unstemmed | A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection |
| title_short | A universal genome sequencing method for rotavirus A from human fecal samples which identifies segment reassortment and multi-genotype mixed infection |
| title_sort | universal genome sequencing method for rotavirus a from human fecal samples which identifies segment reassortment and multi genotype mixed infection |
| topic | Rotavirus A Genomics Phylogenetics Genome sequencing Reassortment Co-infection |
| url | http://link.springer.com/article/10.1186/s12864-017-3714-6 |
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