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Kim JH, Yi DY, Lim I, Ward AC, Kim W. Detection of an unusual G8P[8] rotavirus in a Rotarix-vaccinated child with acute gastroenteritis using Nanopore MinION sequencing: A case report. Medicine (Baltimore) 2020; 99:e22641. [PMID: 33019489 PMCID: PMC7535698 DOI: 10.1097/md.0000000000022641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 07/08/2020] [Accepted: 09/09/2020] [Indexed: 12/29/2022] Open
Abstract
RATIONALE Rotavirus is routinely diagnosed by the detection of antigens or the viral genome. However, these tests have limitations, in that they do not detect all rotavirus strains. PATIENT CONCERNS We present a case of a 27-month-old girl who was hospitalized for 4 days with severe gastroenteritis, including high fever, vomiting, diarrhea, mild dehydration, and periumbilical pain. Notably, the patient previously received the Rotarix vaccine. DIAGNOSES The laboratory tests were negative for rotavirus, astrovirus, adenovirus, and norovirus as well as common diarrhea-causing bacteria. Human-bovine recombinant rotavirus was detected by MinION sequencing. INTERVENTIONS To investigate the cause agents from the unexplained severe gastroenteritis infant, the stool sample was prepared by random amplification for Nanopore MinION sequencing. OUTCOMES Treatment through the administration of ORS solution and galtase powder with probiotics was successful after the diagnosis of unusual rotavirus infection. LESSONS This case report is the first detection of an unusual human-bovine recombinant rotavirus in an idiopathic gastroenteritis using Nanopore MinION sequencing.
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Affiliation(s)
| | - Dae Yong Yi
- Department of Pediatrics, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Inseok Lim
- Department of Pediatrics, Chung-Ang University College of Medicine, Seoul, South Korea
| | - Alan C. Ward
- School of Biology, Newcastle University, Newcastle upon Tyne, UK
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Fuselli S, Baptista RP, Panziera A, Magi A, Guglielmi S, Tonin R, Benazzo A, Bauzer LG, Mazzoni CJ, Bertorelle G. A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra). Heredity (Edinb) 2018; 121:293-303. [PMID: 29572469 PMCID: PMC6133961 DOI: 10.1038/s41437-018-0070-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 01/24/2018] [Accepted: 02/25/2018] [Indexed: 12/13/2022] Open
Abstract
The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are challenging especially without a reference sequence. We designed a combination of long-range PCR, Illumina short-reads, and Oxford Nanopore MinION long-reads approaches to capture the genetic variation of the MHC II DRB locus in an Italian population of the Alpine chamois (Rupicapra rupicapra). We utilized long-range PCR to generate a 9 Kb fragment of the DRB locus. Amplicons from six different individuals were fragmented, tagged, and simultaneously sequenced with Illumina MiSeq. One of these amplicons was sequenced with the MinION device, which produced long reads covering the entire amplified fragment. A pipeline that combines short and long reads resolved several short tandem repeats and homopolymers and produced a de novo reference, which was then used to map and genotype the short reads from all individuals. The assembled DRB locus showed a high level of polymorphism and the presence of a recombination breakpoint. Our results suggest that an amplicon-based NGS approach coupled with single-molecule MinION nanopore sequencing can efficiently achieve both the assembly and the genotyping of complex genomic regions in multiple individuals in the absence of a reference sequence.
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Affiliation(s)
- S Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy.
| | - R P Baptista
- Center for Tropical & Emerging Global Diseases, University of Georgia, 107 Paul D. Coverdell Center, 500 D. W. Brooks Drive, Athens, GA, 30602-7394, USA
| | - A Panziera
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy.,Department of Biodiversity and Molecular Ecology, Research and Innovation Centre, Fondazione Edmund Mach, Via Edmund Mach 1, San Michele all'Adige, I-38010, Italy
| | - A Magi
- Department of Experimental and Clinical Medicine, University of Florence, Largo Brambilla, Florence, 3-50134, Italy
| | - S Guglielmi
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
| | - R Tonin
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy.,Faculty of Science and Technology, Free University of Bozen-Bolzano, Piazza Università 5, Bolzano, Italy
| | - A Benazzo
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
| | - L G Bauzer
- Laboratório de Fisiologia e Controle de Artrópodes Vetores, Instituto Oswaldo Cruz, Fiocruz, Rio de Janeiro, Brazil.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - C J Mazzoni
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Str. 6-8, Berlin, 14195, Germany
| | - G Bertorelle
- Department of Life Sciences and Biotechnology, University of Ferrara, Via L. Borsari 46, Ferrara, 44121, Italy
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Jain M, Olsen HE, Paten B, Akeson M. The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community. Genome Biol 2016; 17:239. [PMID: 27887629 PMCID: PMC5124260 DOI: 10.1186/s13059-016-1103-0] [Citation(s) in RCA: 716] [Impact Index Per Article: 89.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Nanopore DNA strand sequencing has emerged as a competitive, portable technology. Reads exceeding 150 kilobases have been achieved, as have in-field detection and analysis of clinical pathogens. We summarize key technical features of the Oxford Nanopore MinION, the dominant platform currently available. We then discuss pioneering applications executed by the genomics community.
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Affiliation(s)
- Miten Jain
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Hugh E Olsen
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Benedict Paten
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA
| | - Mark Akeson
- UC Santa Cruz Genomics Institute and Department of Biomolecular Engineering, University of California, Santa Cruz, CA, 95064, USA.
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Characterization of Two Multidrug-Resistant IncA/C Plasmids from the 1960s by Using the MinION Sequencer Device. Antimicrob Agents Chemother 2016; 60:6780-6786. [PMID: 27600047 DOI: 10.1128/aac.01121-16] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 08/22/2016] [Indexed: 01/13/2023] Open
Abstract
Two A/C incompatibility group (IncA/C family) plasmids from the 1960s have been sequenced and classified into the A/C2 type 1 group. R16a and IP40a contain novel antibiotic resistance islands and a complete GIsul2 genomic island not previously found in the family. In the 173.1-kb R16a, the 29.9-kb antibiotic resistance island (ARI) is located in a unique backbone position not utilized by ARIs. ARIR16a consists of Tn1, Tn6020, and Tn6333, harboring the resistance genes blaTEM-1D and aphA1b and a mer module, respectively; a truncated Tn5393 copy; and a gene cluster with unknown function. Plasmid IP40a is 170.4 kb in size and contains a 5.6-kb ARI inserted into the kfrA gene. ARIIP40a carrying blaTEM-1D and aphA1b genes is composed of Tn1 with a Tn6023 insertion. Additionally, IP40a harbors single IS2, IS186, and Tn1000 insertions scattered in the backbone; an IS150 copy in GIsul2; and a complete Tn6333 carrying a mer module at the position of ARIR16a Loss of resistance markers in R16a, IP40a, and R55 was observed during stability tests. Every phenotypic change proved to be the result of recombination events involving mobile elements. Intramolecular transposition of IS copies that generated IP40a derivatives lacking large parts of the backbone could account for the formation of other family members, too. The MinION platform proved to be a valuable tool in bacterial genome sequencing since it generates long reads that span repetitive elements and facilitates full-length plasmid or chromosome assembly. Nanopore technology enables rapid characterization of large, low-copy-number plasmids and their rearrangement products.
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