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Fomsgaard AS, Tahas SA, Spiess K, Polacek C, Fonager J, Belsham GJ. Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System. Viruses 2023; 15:1399. [PMID: 37376698 DOI: 10.3390/v15061399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human-animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time.
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Affiliation(s)
- Anna S Fomsgaard
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
| | | | - Katja Spiess
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Charlotta Polacek
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Jannik Fonager
- Department of Virus & Microbiological Special Diagnostics, Statens Serum Institut, 5 Artillerivej, 2300 Copenhagen, Denmark
| | - Graham J Belsham
- Department of Veterinary and Animal Sciences, University of Copenhagen, 4 Stigboejlen, 1870 Frederiksberg, Denmark
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Khan MAA, Ghosh P, Chowdhury R, Hossain F, Mahmud A, Faruque ASG, Ahmed T, Abd El Wahed A, Mondal D. Feasibility of MinION Nanopore Rapid Sequencing in the Detection of Common Diarrhea Pathogens in Fecal Specimen. Anal Chem 2022; 94:16658-16666. [DOI: 10.1021/acs.analchem.2c02771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Md Anik Ashfaq Khan
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
- Institute of Animal Hygiene and Veterinary Public Health, University of Leipzig, An den Tierkliniken 1, 04103Leipzig, Germany
| | - Prakash Ghosh
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Rajashree Chowdhury
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Faria Hossain
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Araf Mahmud
- Laboratory Sciences and Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Abu S. G. Faruque
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Tahmeed Ahmed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Ahmed Abd El Wahed
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
| | - Dinesh Mondal
- Nutrition and Clinical Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
- Laboratory Sciences and Services Division, International Centre for Diarrheal Disease Research, Bangladesh, Dhaka-1212, Bangladesh
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Whittle E, Yonkus JA, Jeraldo P, Alva-Ruiz R, Nelson H, Kendrick ML, Grys TE, Patel R, Truty MJ, Chia N. Optimizing Nanopore Sequencing for Rapid Detection of Microbial Species and Antimicrobial Resistance in Patients at Risk of Surgical Site Infections. mSphere 2022; 7:e0096421. [PMID: 35171692 PMCID: PMC8849348 DOI: 10.1128/msphere.00964-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Surgical site infections (SSI) are a significant burden to patients and health care systems. We evaluated the use of Nanopore sequencing (NS) to rapidly detect microbial species and antimicrobial resistance (AMR) genes present in intraoperative bile aspirates. Bile aspirates from 42 patients undergoing pancreatic head resection were included. Three methods of DNA extraction using mechanical cell lysis or protease cell lysis were compared to determine the optimum method of DNA extraction. The impact of host DNA depletion, sequence run duration, and use of different AMR gene databases was also assessed. To determine clinical value, NS results were compared to standard culture (SC) results. NS identified microbial species in all culture positive samples. Mechanical lysis improved NS detection of cultured species from 60% to 76%, enabled detection of fungal species, and increased AMR predictions. Host DNA depletion improved detection of streptococcal species and AMR correlation with SC. Selection of AMR database influenced the number of AMR hits and resistance profile of 13 antibiotics. AMR prediction using CARD and ResFinder 4.1 correctly predicted 79% and 81% of the bile antibiogram, respectively. Sequence run duration positively correlated with detection of AMR genes. A minimum of 6 h was required to characterize the biliary microbes, resulting in a turnaround time of 14 h. Rapid identification of microbial species and AMR genes can be achieved by NS. NS results correlated with SC, suggesting that NS may be useful in guiding early antimicrobial therapy postsurgery. IMPORTANCE Surgical site infections (SSI) are a significant burden to patients and health care systems. They increase mortality rates, length of hospital stays, and associated health care costs. To reduce the risk of SSI, surgical patients are administered broad-spectrum antibiotics that are later adapted to target microbial species detected at the site of surgical incision. Use of broad-spectrum antibiotics can be harmful to the patient. We wanted to develop a rapid method of detecting microbial species and their antimicrobial resistance phenotypes. We developed a method of detecting microbial species and predicting resistance phenotypes using Nanopore sequencing. Results generated using Nanopore sequencing were similar to current methods of detection but were obtained in a significantly shorter amount of time. This suggests that Nanopore sequencing could be used to tailor antibiotics in surgical patients and reduce use of broad-spectrum antibiotics.
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Affiliation(s)
- Emma Whittle
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Jennifer A. Yonkus
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Patricio Jeraldo
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Roberto Alva-Ruiz
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Heidi Nelson
- Division of Research and Optimal Patient Care, Cancer Programs, American College of Surgeonsgrid.417954.a, Chicago, Illinois, USA
| | - Michael L. Kendrick
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Thomas E. Grys
- Department of Laboratory Medicine and Pathology, Mayo Clinicgrid.66875.3a, Phoenix, Arizona, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Mark J. Truty
- Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
| | - Nicholas Chia
- Division of Surgical Research, Department of Surgery, Mayo Clinicgrid.66875.3a, Rochester, Minnesota, USA
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Miller S, Chiu C. The Role of Metagenomics and Next-Generation Sequencing in Infectious Disease Diagnosis. Clin Chem 2021; 68:115-124. [PMID: 34969106 DOI: 10.1093/clinchem/hvab173] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) for pathogen detection is becoming increasingly available as a method to identify pathogens in cases of suspected infection. mNGS analyzes the nucleic acid content of patient samples with high-throughput sequencing technologies to detect and characterize microorganism DNA and/or RNA. This unbiased approach to organism detection enables diagnosis of a broad spectrum of infection types and can identify more potential pathogens than any single conventional test. This can lead to improved ability to diagnose patients, although there remains concern regarding contamination and detection of nonclinically significant organisms. CONTENT We describe the laboratory approach to mNGS testing and highlight multiple considerations that affect diagnostic performance. We also summarize recent literature investigating the diagnostic performance of mNGS assays for a variety of infection types and recommend further studies to evaluate the improvement in clinical outcomes and cost-effectiveness of mNGS testing. SUMMARY The majority of studies demonstrate that mNGS has sensitivity similar to specific PCR assays and will identify more potential pathogens than conventional methods. While many of these additional organism detections correlate with the expected pathogen spectrum based on patient presentations, there are relatively few formal studies demonstrating whether these are true-positive infections and benefits to clinical outcomes. Reduced specificity due to contamination and clinically nonsignificant organism detections remains a major concern, emphasizing the importance of careful interpretation of the organism pathogenicity and potential association with the clinical syndrome. Further research is needed to determine the possible improvement in clinical outcomes and cost-effectiveness of mNGS testing.
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Affiliation(s)
- Steve Miller
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Charles Chiu
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, Division of Infectious Diseases, University of California San Francisco, San Francisco, CA, USA
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"Answers in hours": A prospective clinical study using nanopore sequencing for bile duct cultures. Surgery 2021; 171:693-702. [PMID: 34973809 DOI: 10.1016/j.surg.2021.09.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/17/2021] [Accepted: 09/07/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Surgical site infection is a major source of morbidity in patients undergoing pancreatic head resection and is often from organisms in intraoperative bile duct cultures. As such, many institutions use prolonged prophylactic antibiotics and tailor based on bile duct cultures. However, standard cultures take days, leaving many patients unnecessarily on prolonged antibiotics. Nanopore sequencing can provide data in hours and, thus, has the potential to improve antibiotic stewardship. The present study investigates the feasibility of nanopore sequencing in intraoperative bile samples. METHODS Patients undergoing pancreatic head resection were included. Intra-operative bile microbial profiles were determined with standard cultures and nanopore sequencing. Antibiotic recommendations were generated, and time-to-results determined for both methods. Organism yields, resistance patterns, antibiotic recommendations, and costs were compared. RESULTS Out of 42 patients, 22 (52%) had samples resulting in positive standard cultures. All positive standard cultures had microbes detected using nanopore sequencing. All 20 patients with negative standard cultures had negative nanopore sequencing. Nanopore sequencing detected more bacterial species compared to standard cultures (10.5 vs 4.4, p < 0.05) and more resistance genotypes (10.3 vs 2.7, p < 0.05). Antimicrobial recommendations based on nanopore sequencing provided coverage for standard cultures in 27 out of 44 (61%) samples, with broader coverage recommended by nanopore sequencing in 13 out of 27 (48%) of these samples. Nanopore sequencing results were faster (8 vs 98 hours) than standard cultures but had higher associated costs ($165 vs $38.49). CONCLUSION Rapid microbial profiling with nanopore sequencing is feasible with broader organism and resistance profiling compared to standard cultures. Nanopore sequencing has perfect negative predictive value and can potentially improve antibiotic stewardship; thus, a randomized control trial is under development.
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Baloğlu B, Chen Z, Elbrecht V, Braukmann T, MacDonald S, Steinke D. A workflow for accurate metabarcoding using nanopore MinION sequencing. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13561] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Bilgenur Baloğlu
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Zhewei Chen
- California Institute of Technology Pasadena CA USA
| | - Vasco Elbrecht
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
- Centre for Biodiversity MonitoringZoological Research Museum Alexander Koenig Bonn Germany
| | - Thomas Braukmann
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Shanna MacDonald
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
| | - Dirk Steinke
- Centre for Biodiversity Genomics University of Guelph Guelph ON Canada
- Integrative Biology University of Guelph Guelph ON Canada
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Flesh ID: Nanopore Sequencing Combined with Offline BLAST Search for the Identification of Meat Source. Foods 2020; 9:foods9101392. [PMID: 33019679 PMCID: PMC7600754 DOI: 10.3390/foods9101392] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/28/2020] [Indexed: 11/17/2022] Open
Abstract
Detection of animal species in meat product is crucial to prevent adulterated and unnecessary contamination during processing, in addition to avoid allergy and religious consequences. Gold standard is the real-time PCR assays, which has a limited target capability. In this study, we have established a rapid sequencing protocol to identify animal species within hours. Sequencing was achieved by nanopore sequencing and data analysis via offline BLAST search. The whole procedure was conducted in a mobile suitcase lab. As per national and international regulations, the developed assay detected adulteration of pork meat with 0.1% of horse, chicken, turkey, cattle, sheep, duck, rabbit, goat, and donkey. The developed test could be used on-site as a rapid and mobile detection system to determine contamination of meat products.
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Point-Of-Care or Point-Of-Need Diagnostic Tests: Time to Change Outbreak Investigation and Pathogen Detection. Trop Med Infect Dis 2020; 5:tropicalmed5040151. [PMID: 32992688 PMCID: PMC7709694 DOI: 10.3390/tropicalmed5040151] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/20/2020] [Accepted: 09/21/2020] [Indexed: 12/23/2022] Open
Abstract
In the recent years, the progress of international trade and travel has led to an increased risk of emerging infections. Around 75 percent of the pathogens causing these infections are of animal origin. Point-of-care tests (POCT) and point-of-need tests (PONT) have been established in order to directly provide accurate and rapid diagnostics at field level, the patient bed-side or at the site of outbreaks. These assays can help physicians and decision makers to take the right action without delay. Typically, POCT and PONT rely on genomic identification of pathogens or track their immunological fingerprint. Recently, protocols for metagenomic diagnostics in the field have been developed. In this review, we give an overview of the latest developments in portable diagnostic methods. In addition, four mobile platforms for the implementation of these techniques at point-of-care and point-of-need are described. These approaches can provide reliable diagnostics and surveillance, especially in low resource settings as well as at the level of one health.
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Bezerra RDS, Diefenbach CF, Pereira DV, Kashima S, Slavov SN. Viral metagenomics performed in patients with acute febrile syndrome during Toxoplasma gondii outbreak in south Brazil. Braz J Infect Dis 2020; 24:250-255. [PMID: 32422120 PMCID: PMC9392116 DOI: 10.1016/j.bjid.2020.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/10/2020] [Accepted: 04/17/2020] [Indexed: 11/16/2022] Open
Abstract
Toxoplasmosis is a zoonotic infection caused by the protozoan parasite Toxoplasma gondii. The infection is widely disseminated in the human population and is usually benign or asymptomatic. Systemic T. gondii infection presents risks for pregnant women and AIDS patients. Although rare, T. gondii can cause outbreaks in urban centers. The origin of these outbreaks is not completely understood but probably results from introduction of zoonotic T. gondii strains in the population. During such outbreaks other pathogens which mimic T. gondii acute febrile syndrome may also circulate; therefore, detailed investigation of the outbreak is of extreme importance. In this study we performed viral metagenomics next-generation sequencing (mNGS) in patient samples obtained during T. gondii outbreak in Santa Maria city, South Brazil. Specific bioinformatics pipelines specialized in virus discovery were applied in order to identify co-circulating vial agents. Epstein Barr virus and Parvovirus B19 contigs were assembled and these viruses can cause symptoms similar to toxoplasmosis. In conclusion, our findings show the importance of Metagenomics next generation sequencing (mNGS) use to help characterize the outbreak more completely and in the management of the affected patients.
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Affiliation(s)
- Rafael Dos Santos Bezerra
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Ciências Biológicas e da Saúde, Riberão Preto,SP, Brazil; Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro, Ribeirão Preto, SP, Brazil
| | - Cristiane Fração Diefenbach
- Hospital De Caridade Dr. Astrogildo De Azevedo, Departamento de Hematologia e Oncologia, Rio Grande do Sul, RS, Brazil
| | - Dalnei Veiga Pereira
- Hospital De Caridade Dr. Astrogildo De Azevedo, Departamento de Hematologia e Oncologia, Rio Grande do Sul, RS, Brazil
| | - Simone Kashima
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro, Ribeirão Preto, SP, Brazil
| | - Svetoslav Nanev Slavov
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Hemocentro, Ribeirão Preto, SP, Brazil; Universidade de São Paulo, Faculdade de Medicina de Ribeirão Preto, Departamento de Medicina Interna, Ribeirão Preto, SP, Brazil.
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How Cities Cope in Outbreak Events? THE CITY IN NEED 2020. [PMCID: PMC7278263 DOI: 10.1007/978-981-15-5487-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
An outbreak can cause more problems than just the spread of disease. It can be an antagonistic nemesis to our cities and communities, particularly if we lack preparedness and resilience. Its progress is usually unclear as it can be completely different from case to case, and can react differently in different contexts and with different groups of people. Such reactions may purely relate to climatic conditions, hygienic status, and environmental attributes of the context. Those reactions can also differ from one group of people to another, while the disease has to find its correct host as well the way it can transmit and evolve. Consequently, the magnitude of impacts would depend on many factors, of which the nature of the disease is very important during the whole outbreak progress.
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Ji P, Aw TG, Van Bonn W, Rose JB. Evaluation of a portable nanopore-based sequencer for detection of viruses in water. J Virol Methods 2019; 278:113805. [PMID: 31891731 DOI: 10.1016/j.jviromet.2019.113805] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/18/2019] [Accepted: 12/19/2019] [Indexed: 12/20/2022]
Abstract
The newly emerged nanopore sequencing technology such as MinION™ allows for real-time detection of long DNA/RNA fragments on a portable device, yet few have examined its performance for environmental viromes. Here we seeded one RNA virus bacteriophage MS2 and one DNA virus bacteriophage PhiX174 into 10 L well water at three levels ranging from 1 to 21,100 plaque-forming units (PFU)/mL. Two workflows were established to maximize the number of sequencing reads of RNA and DNA viruses using MinION™. With dead-end ultrafiltration, PEG precipitation, and random amplification, MinION™ was capable of detecting MS2 at 155 PFU/mL and PhiX174 at 1-2 PFU/mL. While the DNA workflow only detected PhiX174, the RNA workflow detected both MS2 and PhiX174. The virus concentration, or relative abundance of viral nucleic acids in total nucleic acids, is critical to the proportion of viral reads in sequencing results. Our findings also highlight the importance of including control samples in sequencing runs for environmental water samples with low virus abundance.
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Affiliation(s)
- Pan Ji
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Tiong Gim Aw
- Department of Environmental Health Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA 70112, USA
| | - William Van Bonn
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA; A. Watson Armour III Center for Animal Health and Welfare, John G. Shedd Aquarium, Chicago, IL 60605, USA
| | - Joan B Rose
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA.
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Midha MK, Wu M, Chiu KP. Long-read sequencing in deciphering human genetics to a greater depth. Hum Genet 2019; 138:1201-1215. [PMID: 31538236 DOI: 10.1007/s00439-019-02064-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 09/13/2019] [Indexed: 12/12/2022]
Abstract
Through four decades' development, DNA sequencing has inched into the era of single-molecule sequencing (SMS), or the third-generation sequencing (TGS), as represented by two distinct technical approaches developed independently by Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT). Historically, each generation of sequencing technologies was marked by innovative technological achievements and novel applications. Long reads (LRs) are considered as the most advantageous feature of SMS shared by both PacBio and ONT to distinguish SMS from next-generation sequencing (NGS, or the second-generation sequencing) and Sanger sequencing (the first-generation sequencing). Long reads overcome the limitations of NGS and drastically improves the quality of genome assembly. Besides, ONT also contributes several unique features including ultra-long reads (ULRs) with read length above 300 kb and some close to 1 million bp, direct RNA sequencing and superior portability as made possible by pocket-sized MinION sequencer. Here, we review the history of DNA sequencing technologies and associated applications, with a special focus on the advantages as well as the limitations of ULR sequencing in genome assembly.
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Affiliation(s)
- Mohit K Midha
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang District, Taipei, 115, Taiwan.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan
| | - Mengchu Wu
- Health GeneTech, 22F No. 99, Xin Pu 6th St., Taoyuan, Taiwan
| | - Kuo-Ping Chiu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Sec. 2, Nankang District, Taipei, 115, Taiwan. .,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan. .,Department of Life Sciences, College of Life Sciences, National Taiwan University, Taipei, Taiwan.
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