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Targeted Virome Sequencing Enhances Unbiased Detection and Genome Assembly of Known and Emerging Viruses-The Example of SARS-CoV-2. Viruses 2022; 14:v14061272. [PMID: 35746743 PMCID: PMC9227943 DOI: 10.3390/v14061272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 12/10/2022] Open
Abstract
Targeted virome enrichment and sequencing (VirCapSeq-VERT) utilizes a pool of oligos (baits) to enrich all known—up to 2015—vertebrate-infecting viruses, increasing their detection sensitivity. The hybridisation of the baits to the target sequences can be partial, thus enabling the detection and genomic reconstruction of novel pathogens with <40% genetic diversity compared to the strains used for the baits’ design. In this study, we deploy this method in multiplexed mixes of viral extracts, and we assess its performance in the unbiased detection of DNA and RNA viruses after cDNA synthesis. We further assess its efficiency in depleting various background genomic material. Finally, as a proof-of-concept, we explore the potential usage of the method for the characterization of unknown, emerging human viruses, such as SARS-CoV-2, which may not be included in the baits’ panel. We mixed positive samples of equimolar DNA/RNA viral extracts from SARS-CoV-2, coronavirus OC43, cytomegalovirus, influenza A virus H3N2, parvovirus B19, respiratory syncytial virus, adenovirus C and coxsackievirus A16. Targeted virome enrichment was performed on a dsDNA mix, followed by sequencing on the NextSeq500 (Illumina) and the portable MinION sequencer, to evaluate its usability as a point-of-care (PoC) application. Genome mapping assembly was performed using viral reference sequences. The untargeted libraries contained less than 1% of total reads mapped on most viral genomes, while RNA viruses remained undetected. In the targeted libraries, the percentage of viral-mapped reads were substantially increased, allowing full genome assembly in most cases. Targeted virome sequencing can enrich a broad range of viruses, potentially enabling the discovery of emerging viruses.
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Oliveras T, Revuelta-López E, García-García C, Cserkóová A, Rueda F, Labata C, Ferrer M, Montero S, El-Ouaddi N, Martínez MJ, Roura S, Gálvez-Montón C, Bayes-Genis A. Circulating virome and inflammatory proteome in patients with ST-elevation myocardial infarction and primary ventricular fibrillation. Sci Rep 2022; 12:7910. [PMID: 35552514 PMCID: PMC9098642 DOI: 10.1038/s41598-022-12075-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Primary ventricular fibrillation (PVF) is a life-threatening complication of ST-segment elevation myocardial infarction (STEMI). It is unclear what roles viral infection and/or systemic inflammation may play as underlying triggers of PVF, as a second hit in the context of acute ischaemia. Here we aimed to evaluate whether the circulating virome and inflammatory proteome were associated with PVF development in patients with STEMI. Blood samples were obtained from non-PVF and PVF STEMI patients at the time of primary PCI, and from non-STEMI healthy controls. The virome profile was analysed using VirCapSeq-VERT (Virome Capture Sequencing Platform for Vertebrate Viruses), a sequencing platform targeting viral taxa of 342,438 representative sequences, spanning all virus sequence records. The inflammatory proteome was explored with the Olink inflammation panel, using the Proximity Extension Assay technology. After analysing all viral taxa known to infect vertebrates, including humans, we found that non-PVF and PVF patients only significantly differed in the frequencies of viruses in the Gamma-herpesvirinae and Anelloviridae families. In particular, most showed a significantly higher relative frequency in non-PVF STEMI controls. Analysis of systemic inflammation revealed no significant differences between the inflammatory profiles of non-PVF and PVF STEMI patients. Inflammatory proteins associated with cell adhesion, chemotaxis, cellular response to cytokine stimulus, and cell activation proteins involved in immune response (IL6, IL8 CXCL-11, CCL-11, MCP3, MCP4, and ENRAGE) were significantly higher in STEMI patients than non-STEMI controls. CDCP1 and IL18-R1 were significantly higher in PVF patients compared to healthy subjects, but not compared to non-PVF patients. The circulating virome and systemic inflammation were not associated with increased risk of PVF development in acute STEMI. Accordingly, novel strategies are needed to elucidate putative triggers of PVF in the setting of acute ischaemia, in order to reduce STEMI-driven sudden death burden.
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Affiliation(s)
- Teresa Oliveras
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain. .,Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain.
| | - Elena Revuelta-López
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Cosme García-García
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
| | - Adriana Cserkóová
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Ferran Rueda
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain
| | - Carlos Labata
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain
| | - Marc Ferrer
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain
| | - Santiago Montero
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain
| | - Nabil El-Ouaddi
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain
| | - Maria José Martínez
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain
| | - Santiago Roura
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain.,Faculty of Medicine, University of Vic-Central University of Catalonia (UVic-UCC), Vic, Barcelona, Spain
| | - Carolina Gálvez-Montón
- Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain.,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain
| | - Antoni Bayes-Genis
- Heart Failure Unit and Cardiology Department, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain. .,Heart Failure and Cardiac Regeneration (ICREC) Research Program, Health Sciences Research Institute Germans Trias i Pujol (IGTP), Badalona, Barcelona, Spain. .,CIBERCV, Instituto de Salud Carlos III, Madrid, Spain. .,Department of Medicine, Universitat Autònoma de Barcelona, Barcelona, Spain. .,Heart Institute, Hospital Universitari Germans Trias i Pujol, Carretera de Canyet s/n, Badalona, 08916, Barcelona, Spain.
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Ludowyke N, Phumiphanjarphak W, Apiwattanakul N, Manopwisedjaroen S, Pakakasama S, Sensorn I, Pasomsub E, Chantratita W, Hongeng S, Aiewsakun P, Thitithanyanont A. Target Enrichment Metagenomics Reveals Human Pegivirus-1 in Pediatric Hematopoietic Stem Cell Transplantation Recipients. Viruses 2022; 14:v14040796. [PMID: 35458526 PMCID: PMC9025367 DOI: 10.3390/v14040796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 11/17/2022] Open
Abstract
Human pegivirus-1 (HPgV-1) is a lymphotropic human virus, typically considered nonpathogenic, but its infection can sometimes cause persistent viremia both in immunocompetent and immunosuppressed individuals. In a viral discovery research program in hematopoietic stem cell transplant (HSCT) pediatric patients, HPgV-1 was detected in 3 out of 14 patients (21.4%) using a target enrichment next-generation sequencing method, and the presence of the viruses was confirmed by agent-specific qRT-PCR assays. For the first time in this patient cohort, complete genomes of HPgV-1 were acquired and characterized. Phylogenetic analyses indicated that two patients had HPgV-1 genotype 2 and one had HPgV-1 genotype 3. Intra-host genomic variations were described and discussed. Our results highlight the necessity to screen HSCT patients and blood and stem cell donors to reduce the potential risk of HPgV-1 transmission.
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Affiliation(s)
- Natali Ludowyke
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
| | - Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Nopporn Apiwattanakul
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Suwimon Manopwisedjaroen
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
| | - Samart Pakakasama
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Insee Sensorn
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (I.S.); (W.C.)
| | - Ekawat Pasomsub
- Virology and Molecular Microbiology Unit, Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand;
| | - Wasun Chantratita
- Center for Medical Genomics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (I.S.); (W.C.)
| | - Suradej Hongeng
- Department of Pediatrics, Division of Hematology and Oncology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand; (N.A.); (S.P.); (S.H.)
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (P.A.); (A.T.); Tel.: +66-22015676 (P.A.); +66-22015528 (A.T.)
| | - Arunee Thitithanyanont
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; (N.L.); (W.P.); (S.M.)
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand
- Correspondence: (P.A.); (A.T.); Tel.: +66-22015676 (P.A.); +66-22015528 (A.T.)
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Sanchez-Vicente S, Jain K, Tagliafierro T, Gokden A, Kapoor V, Guo C, Horn EJ, Lipkin WI, Tokarz R. Capture Sequencing Enables Sensitive Detection of Tick-Borne Agents in Human Blood. Front Microbiol 2022; 13:837621. [PMID: 35330765 PMCID: PMC8940530 DOI: 10.3389/fmicb.2022.837621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Assay sensitivity can be a limiting factor in the use of PCR as a tool for the detection of tick-borne pathogens in blood. We evaluated the performance of Tick-borne disease Capture Sequencing Assay (TBDCapSeq), a capture sequencing assay targeting tick-borne agents, to test 158 whole blood specimens obtained from the Lyme Disease Biobank. These included samples from 98 individuals with signs and symptoms of acute Lyme disease, 25 healthy individuals residing in Lyme disease endemic areas, and 35 samples collected from patients admitted to the Massachusetts General Hospital or referred to the infectious disease clinic. Compared to PCR, TBDCapSeq had better sensitivity and could identify infections with a wider range of tick-borne agents. TBDCapSeq identified a higher rate of samples positive for Borrelia burgdorferi (8 vs. 1 by PCR) and Babesia microti (26 vs. 15 by PCR). TBDCapSeq also identified previously unknown infections with Borrelia miyamotoi, Ehrlichia, and Rickettsia species. Overall, TBDCapSeq identified a pathogen in 43 samples vs. 23 using PCR, with four co-infections detected versus zero by PCR. We conclude that capture sequencing enables superior detection of tick-borne agents relative to PCR.
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Affiliation(s)
- Santiago Sanchez-Vicente
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Teresa Tagliafierro
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Alper Gokden
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Vishal Kapoor
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | | | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York City, NY, United States
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York City, NY, United States.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York City, NY, United States
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55
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Habibi N, Uddin S, Behbehani M, Abdul Razzack N, Zakir F, Shajan A. SARS-CoV-2 in hospital air as revealed by comprehensive respiratory viral panel sequencing. Infect Prev Pract 2022; 4:100199. [PMID: 34977533 PMCID: PMC8711137 DOI: 10.1016/j.infpip.2021.100199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 12/16/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Nosocomially acquired severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection has become the most significant pandemic of our lifetime. Though its transmission was essentially attributed to droplets from an infected person, with recent advancements in knowledge, aerosol transmission seems to be a viable pathway, as well. Because of the lower biological load in ambient aerosol, detection of SARS-CoV-2 is challenging. A few recent attempts of sampling large aerosol volumes and using next-generation sequencing (NGS) to detect the presence of SARS-CoV-2 in the air at very low levels gave positive results. These results suggest the potential of using this technique to detect the presence of SARS-CoV-2 and use it as an early warning signal for possible outbreak or recurrence of coronavirus disease 2019 (COVID-19). AIM To assess efficacy of comprehensive respiratory viral panel (CRVP) sequencing and RT-PCR for low-level identification of SARS-CoV-2 and other respiratory viruses in indoor air. METHODS A large volume of indoor aerosol samples from three major hospitals involved in COVID-19 care in Kuwait was collected. Viral RNA was isolated and subjected to comprehensive respiratory viral panel sequencing (CRVP) as per the standard protocol to detect the SARS-CoV-2 and other respiratory viruses in the hospital aerosol and monitor variations within the sequences. RT-PCR was also employed to estimate the viral load of SARS-CoV-2. FINDINGS 13 of 15 (86.7%) samples exhibited SARS-CoV-2 with a relative abundance of 0.2-33.3%. The co-occurrence of human adenoviruses (type C1, C2, C5, C4), respiratory syncytial virus (RSV), influenza B, and non-SARS-CoV-229E were also recorded. Alignment of SARS-CoV-2 sequences against the reference strain of Wuhan China revealed variations in the form of single nucleotide polymorphisms (SNPs-17), insertions and deletions (indels-1). These variations were predicted to create missense (16), synonymous (15), frameshift (1) and stop-gained (1) mutations with a high (2), low (15), and moderate (16) impact. CONCLUSIONS Our results suggest that using CRVP on a large volume aerosol sample was a valuable tool for detecting SARS-CoV-2 in indoor aerosols of health care settings. Owing to its higher sensitivity, it can be employed as a surveillance strategy in the post COVID times to act as an early warning system to possibly control future outbreaks.
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Affiliation(s)
- Nazima Habibi
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Saif Uddin
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Montaha Behbehani
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Nasreem Abdul Razzack
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Farhana Zakir
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
| | - Anisha Shajan
- Environment and Life Sciences Research Center, Kuwait Institute for Scientific Research, Kuwait
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56
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Mishra N, Ng J, Strom MA, Jain K, Thakkar R, Joshi S, Pereira M, Shah L, Grossman ME, Lee MJ, De Michele S, Silvers DN, Faust PL, Lipkin WI, Gallitano SM. Human Polyomavirus 9-An Emerging Cutaneous and Pulmonary Pathogen in Solid Organ Transplant Recipients. JAMA Dermatol 2022; 158:293-298. [PMID: 35138364 PMCID: PMC8829745 DOI: 10.1001/jamadermatol.2021.5853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
IMPORTANCE We describe the first report to our knowledge of cutaneous and systemic pathogenicity of human polyomavirus 9 in solid organ transplant recipients. OBJECTIVE Three solid organ transplant recipients developed a widespread, progressive, violaceous, and hyperkeratotic skin eruption. All died from pulmonary and multiorgan failure around 1 year from onset of the rash. Routine clinical diagnostic testing could not identify any causative agent; therefore, samples and autopsies were investigated for novel pathogens using high-throughput sequencing. DESIGN, SETTING, AND PARTICIPANTS This case series, including 3 solid organ transplant recipients who developed characteristic pink, violaceous, or brown hyperkeratotic papules and plaques throughout the body, was conducted at the Columbia University Medical Center. Lesional skin biopsies were collected from all 3 patients and subjected to high-throughput illumina sequencing for identification of microbial pathogens. Human polyomavirus 9 was identified in lesional skin biopsies. We subsequently collected ocular swabs, oral swabs, urine samples, and blood samples from patients, and organ tissues at autopsy in 1 patient. We investigated these samples for the presence of human polyomavirus 9 using in situ hybridization and quantitative polymerase chain reaction (PCR) assays. MAIN OUTCOMES AND MEASURES A description of the clinical and pathologic findings of 3 patients. RESULTS This case series study found that human polyomavirus 9 was detected in the skin biopsies of all 3 patients by a capture-based high-throughput sequencing method platform (VirCapSeq-VERT). Human polyomavirus 9 was also detected in blood, oral, ocular swabs, and urine by real-time polymerase chain reaction (PCR) assay. In situ hybridization and quantitative PCR assays were performed on the skin biopsies from 3 patients and lung autopsy of 1 patient, which showed the presence of human polyomavirus 9 messenger RNA transcripts, indicating active viral replication and pathogenesis in the skin and lungs. CONCLUSIONS AND RELEVANCE Human polyomavirus 9 was associated with the widespread cutaneous eruption. All 3 patients had progression of cutaneous disease, accompanied by clinical deterioration, pulmonary failure, and death. One patient underwent autopsy and human polyomavirus 9 was identified in the lungs and paratracheal soft tissue. These findings suggest that human polyomavirus 9 may be associated with cutaneous and possibly pulmonary infection and death in solid organ transplant recipients.
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Affiliation(s)
- Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Mark A. Strom
- Department of Dermatology, Mount Sinai Hospital, New York, New York
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Riddhi Thakkar
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Shreyas Joshi
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Marcus Pereira
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Lori Shah
- Department of Medicine, Columbia University Irving Medical Center, New York, New York
| | - Marc E. Grossman
- Department of Dermatology, Yale University School of Medicine, New Haven, Connecticut,Hofstra/Northwell Donald and Barbara Zucker School of Medicine, New Hyde Park, New York
| | - Michael J. Lee
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - Simona De Michele
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - David N. Silvers
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York,Department of Dermatology, Columbia University Irving Medical Center, New York, New York
| | - Phyllis L. Faust
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York
| | - Stephanie M. Gallitano
- Department of Dermatology, Columbia University Irving Medical Center, New York, New York
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Abstract
Cost-effective, rapid, and accurate virus detection technologies play key roles in reducing viral transmission. Prompt and accurate virus detection enables timely treatment and effective quarantine of virus carrier, and therefore effectively reduces the possibility of large-scale spread. However, conventional virus detection techniques often suffer from slow response, high cost or sophisticated procedures. Recently, two-dimensional (2D) materials have been used as promising sensing platforms for the high-performance detection of a variety of chemical and biological substances. The unique properties of 2D materials, such as large specific area, active surface interaction with biomolecules and facile surface functionalization, provide advantages in developing novel virus detection technologies with fast response and high sensitivity. Furthermore, 2D materials possess versatile and tunable electronic, electrochemical and optical properties, making them ideal platforms to demonstrate conceptual sensing techniques and explore complex sensing mechanisms in next-generation biosensors. In this review, we first briefly summarize the virus detection techniques with an emphasis on the current efforts in fighting again COVID-19. Then, we introduce the preparation methods and properties of 2D materials utilized in biosensors, including graphene, transition metal dichalcogenides (TMDs) and other 2D materials. Furthermore, we discuss the working principles of various virus detection technologies based on emerging 2D materials, such as field-effect transistor-based virus detection, electrochemical virus detection, optical virus detection and other virus detection techniques. Then, we elaborate on the essential works in 2D material-based high-performance virus detection. Finally, our perspective on the challenges and future research direction in this field is discussed.
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Abstract
The COVID-19 pandemic has given the study of virus evolution and ecology new relevance. Although viruses were first identified more than a century ago, we likely know less about their diversity than that of any other biological entity. Most documented animal viruses have been sampled from just two phyla - the Chordata and the Arthropoda - with a strong bias towards viruses that infect humans or animals of economic and social importance, often in association with strong disease phenotypes. Fortunately, the recent development of unbiased metagenomic next-generation sequencing is providing a richer view of the animal virome and shedding new light on virus evolution. In this Review, we explore our changing understanding of the diversity, composition and evolution of the animal virome. We outline the factors that determine the phylogenetic diversity and genomic structure of animal viruses on evolutionary timescales and show how this impacts assessment of the risk of disease emergence in the short term. We also describe the ongoing challenges in metagenomic analysis and outline key themes for future research. A central question is how major events in the evolutionary history of animals, such as the origin of the vertebrates and periodic mass extinction events, have shaped the diversity and evolution of the viruses they carry.
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Compassionate-use pocapavir and immunoglobulin therapy for treatment of rituximab-associated enterovirus meningoencephalitis. J Neurovirol 2022; 28:329-334. [PMID: 34981437 DOI: 10.1007/s13365-021-01038-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 11/12/2021] [Accepted: 12/09/2021] [Indexed: 10/19/2022]
Abstract
A 71-year-old woman previously on rituximab treatment for rheumatoid arthritis presented with 2 years of progressive neurologic symptoms. She was found to have persistent hypogammaglobulinemia and B cell depletion despite rituximab discontinuation a year prior. MRI revealed diffuse meningeal enhancement along the entire neuroaxis. LP showed a CSF lymphocytic pleocytosis, elevated protein, and presence of enterovirus by PCR. The patient was hospitalized several times for progressive clinical and radiologic decline, though she had transient improvements following treatment with immunoglobulin therapy. Her CSF remained positive for enterovirus PCR for at least 12 months. Though two brain biopsies were non-diagnostic, pan-Enterovirus was ultimately identified using a high-throughput next-generation sequencing technique. She was treated with compassionate-use pocapavir with clinical stabilization at 4-month follow-up; however, she expired 8 months later from a bacterial pneumonia.
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McGill F, Tokarz R, Thomson EC, Filipe A, Sameroff S, Jain K, Bhuva N, Ashraf S, Lipkin WI, Corless C, Pattabiraman C, Gibney B, Griffiths MJ, Geretti AM, Michael BD, Beeching NJ, McKee D, Hart IJ, Mutton K, Jung A, Miller A, Solomon T. Viral capture sequencing detects unexpected viruses in the cerebrospinal fluid of adults with meningitis. J Infect 2022; 84:499-510. [PMID: 34990710 DOI: 10.1016/j.jinf.2021.12.042] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/20/2021] [Accepted: 12/29/2021] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Many patients with meningitis have no aetiology identified leading to unnecessary antimicrobials and prolonged hospitalisation. We used viral capture sequencing to identify possible pathogenic viruses in adults with community-acquired meningitis. METHODS Cerebrospinal fluid (CSF) from 73 patients was tested by VirCapSeq-VERT, a probe set designed to capture viral targets using high throughput sequencing. Patients were categorised as suspected viral meningitis - CSF pleocytosis, no pathogen identified (n = 38), proven viral meningitis - CSF pleocytosis with a pathogen identified (n = 15) or not meningitis - no CSF pleocytosis (n = 20). RESULTS VirCapSeq-VERT detected virus in the CSF of 16/38 (42%) of those with suspected viral meningitis, including twelve individual viruses. A potentially clinically relevant virus was detected in 9/16 (56%). Unexpectedly Toscana virus, rotavirus and Saffold virus were detected and assessed to be potential causative agents. CONCLUSION VirCapSeq-VERT increases the probability of detecting a virus. Using this agnostic approach we identified Toscana virus and, for the first time in adults, rotavirus and Saffold virus, as potential causative agents in adult meningitis. Further work is needed to determine the prevalence of atypical viral candidates as well as the clinical impact of using sequencing methods in real time. This knowledge can help to reduce antimicrobial use and hospitalisations leading to both patient and health system benefits.
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Affiliation(s)
- Fiona McGill
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Leeds Teaching Hospitals NHS Trust, Leeds, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
| | - Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Emma C Thomson
- Institute of infection, immunity and inflammation, University of Glasgow, Glasgow, UK
| | - Ana Filipe
- Institute of infection, immunity and inflammation, University of Glasgow, Glasgow, UK
| | - Stephen Sameroff
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Komal Jain
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Nishit Bhuva
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Shirin Ashraf
- Institute of infection, immunity and inflammation, University of Glasgow, Glasgow, UK
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, NY, USA
| | - Caroline Corless
- Liverpool Specialist virology centre, Department of Infection and Immunity, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Chitra Pattabiraman
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; National Institute for Mental Health and Neurosciences, Bangalore, India
| | - Barry Gibney
- UK Health Security Agency (previously Public Health England), UK
| | - Michael J Griffiths
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Alder Hey Children's NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Anna Maria Geretti
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Faculty of Medicine, University of Rome Tor Vergata
| | - Benedict D Michael
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Nicholas J Beeching
- Tropical and Infectious Disease Unit, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK; Liverpool School of Tropical Medicine, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - David McKee
- Central Manchester Foundation Trust, Manchester, UK
| | - Ian J Hart
- Liverpool Specialist virology centre, Department of Infection and Immunity, Liverpool Clinical Laboratories, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Ken Mutton
- University of Manchester, Manchester, UK
| | - Agam Jung
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Alastair Miller
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tom Solomon
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK; Department of Neurology, The Walton Centre NHS Foundation Trust, Liverpool, UK; National Institute for Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK.
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Cassidy H, Schuele L, Lizarazo-Forero E, Couto N, Rossen JWA, Friedrich AW, van Leer-Buter C, Niesters HGM. OUP accepted manuscript. Virus Evol 2022; 8:veab109. [PMID: 35317350 PMCID: PMC8932292 DOI: 10.1093/ve/veab109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 12/16/2021] [Accepted: 02/16/2022] [Indexed: 11/12/2022] Open
Abstract
Chronic enterovirus infections can cause significant morbidity, particularly in immunocompromised patients. This study describes a fatal case associated with a chronic untypeable enterovirus infection in an immunocompromised patient admitted to a Dutch university hospital over nine months. We aimed to identify the enterovirus genotype responsible for the infection and to determine potential evolutionary changes. Long-read sequencing was performed using viral targeted sequence capture on four respiratory and one faecal sample. Phylogenetic analysis was performed using a maximum likelihood method, along with a root-to-tip regression and time-scaled phylogenetic analysis to estimate evolutionary changes between sample dates. Intra-host variant detection, using a Fixed Ploidy algorithm, and selection pressure, using a Fixed Effect Likelihood and a Mixed Effects Model of Evolution, were also used to explore the patient samples. Near-complete genomes of enterovirus C104 (EV-C104) were recovered in all respiratory samples but not in the faecal sample. The recovered genomes clustered with a recently reported EV-C104 from Belgium in August 2018. Phylodynamic analysis including ten available EV-C104 genomes, along with the patient sequences, estimated the most recent common ancestor to occur in the middle of 2005 with an overall estimated evolution rate of 2.97 × 10−3 substitutions per year. Although positive selection pressure was identified in the EV-C104 reference sequences, the genomes recovered from the patient samples alone showed an overall negative selection pressure in multiple codon sites along the genome. A chronic infection resulting in respiratory failure from a relatively rare enterovirus was observed in a transplant recipient. We observed an increase in single-nucleotide variations between sample dates from a rapidly declining patient, suggesting mutations are weakly deleterious and have not been purged during selection. This is further supported by the persistence of EV-C104 in the patient, despite the clearance of other viral infections. Next-generation sequencing with viral enrichment could be used to detect and characterise challenging samples when conventional workflows are insufficient.
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Affiliation(s)
| | | | - Erley Lizarazo-Forero
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, UK
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
- Department of Pathology, University of Utah School of Medicine, 15 North Medical Drive East, Salt Lake City, UT 84112, USA
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
| | - Coretta van Leer-Buter
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, Hanzeplein 1, Groningen 9713 GZ, The Netherlands
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62
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Vannella KM, Oguz C, Stein SR, Pittaluga S, Dikoglu E, Kanwal A, Ramelli SC, Briese T, Su L, Wu X, Ramos-Benitez MJ, Perez-Valencia LJ, Babyak A, Cha NR, Chung JY, Ylaya K, Madathil RJ, Saharia KK, Scalea TM, Tran QK, Herr DL, Kleiner DE, Hewitt SM, Notarangelo LD, Grazioli A, Chertow DS. Evidence of SARS-CoV-2-Specific T-Cell-Mediated Myocarditis in a MIS-A Case. Front Immunol 2021; 12:779026. [PMID: 34956207 PMCID: PMC8695925 DOI: 10.3389/fimmu.2021.779026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 11/23/2021] [Indexed: 01/14/2023] Open
Abstract
A 26-year-old otherwise healthy man died of fulminant myocarditis. Nasopharyngeal specimens collected premortem tested negative for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Histopathological evaluation of the heart showed myocardial necrosis surrounded by cytotoxic T-cells and tissue-repair macrophages. Myocardial T-cell receptor (TCR) sequencing revealed hyper-dominant clones with highly similar sequences to TCRs that are specific for SARS-CoV-2 epitopes. SARS-CoV-2 RNA was detected in the gut, supporting a diagnosis of multisystem inflammatory syndrome in adults (MIS-A). Molecular targets of MIS-associated inflammation are not known. Our data indicate that SARS-CoV-2 antigens selected high-frequency T-cell clones that mediated fatal myocarditis.
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Affiliation(s)
- Kevin M Vannella
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States.,Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Cihan Oguz
- National Institute of Allergy and Infectious Diseases Collaborative Bioinformatics Resource, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, United States.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Sydney R Stein
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States.,Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Stefania Pittaluga
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Esra Dikoglu
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Arjun Kanwal
- Division of Cardiology, Westchester Medical Center, Valhalla, NY, United States
| | - Sabrina C Ramelli
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Thomas Briese
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, NY, United States
| | - Ling Su
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Xiaolin Wu
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Marcos J Ramos-Benitez
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States.,Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States.,Postdoctoral Research Associate Training Program, National Institute of General Medical Sciences, National Institutes of Health, Bethesda, MD, United States
| | - Luis J Perez-Valencia
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States.,Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Ashley Babyak
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States.,Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Nu Ri Cha
- Department of Transfusion Medicine, Clinical Center, National Institutes of Health, Bethesda, MD, United States
| | - Joon-Yong Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Kris Ylaya
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Ronson J Madathil
- Department of Surgery, Division of Cardiac Surgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Kapil K Saharia
- Department of Medicine, Division of Infectious Disease, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Thomas M Scalea
- Department of Surgery, Program in Trauma, R. Adams Cowley Shock Trauma Center, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Quincy K Tran
- Department of Emergency Medicine, R. Adams Cowley Shock Trauma Center, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Daniel L Herr
- Department of Medicine, Program in Trauma, R. Adams Cowley Shock Trauma Center, University of Maryland School of Medicine, Baltimore, MD, United States
| | - David E Kleiner
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Stephen M Hewitt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Alison Grazioli
- Kidney Diseases Branch, Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Daniel S Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD, United States.,Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
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63
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Bonny P, Schaeffer J, Besnard A, Desdouits M, Ngang JJE, Le Guyader FS. Human and Animal RNA Virus Diversity Detected by Metagenomics in Cameroonian Clams. Front Microbiol 2021; 12:770385. [PMID: 34917052 PMCID: PMC8669915 DOI: 10.3389/fmicb.2021.770385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Many recent pandemics have been recognized as zoonotic viral diseases. While their origins remain frequently unknown, environmental contamination may play an important role in emergence. Thus, being able to describe the viral diversity in environmental samples contributes to understand the key issues in zoonotic transmission. This work describes the use of a metagenomic approach to assess the diversity of eukaryotic RNA viruses in river clams and identify sequences from human or potentially zoonotic viruses. Clam samples collected over 2years were first screened for the presence of norovirus to verify human contamination. Selected samples were analyzed using metagenomics, including a capture of sequences from viral families infecting vertebrates (VirCapSeq-VERT) before Illumina NovaSeq sequencing. The bioinformatics analysis included pooling of data from triplicates, quality filtering, elimination of bacterial and host sequences, and a deduplication step before de novo assembly. After taxonomic assignment, the viral fraction represented 0.8–15% of reads with most sequences (68–87%) remaining un-assigned. Yet, several mammalian RNA viruses were identified. Contigs identified as belonging to the Astroviridae were the most abundant, with some nearly complete genomes of bastrovirus identified. Picobirnaviridae sequences were related to strains infecting bats, and few others to strains infecting humans or other hosts. Hepeviridae sequences were mostly related to strains detected in sponge samples but also strains from swine samples. For Caliciviridae and Picornaviridae, most of identified sequences were related to strains infecting bats, with few sequences close to human norovirus, picornavirus, and genogroup V hepatitis A virus. Despite a need to improve the sensitivity of our method, this study describes a large diversity of RNA virus sequences from clam samples. To describe all viral contaminants in this type of food, and being able to identify the host infected by viral sequences detected, may help to understand some zoonotic transmission events and alert health authorities of possible emergence.
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Affiliation(s)
- Patrice Bonny
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France.,Département de Microbiologie, Université de Yaoundé I, Yaoundé, Cameroon.,Centre de Recherche en Alimentation et Nutrition, IMPM, Yaoundé, Cameroon
| | - Julien Schaeffer
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Alban Besnard
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
| | - Marion Desdouits
- Laboratoire de Microbiologie, LSEM/SG2M, Ifremer, Nantes, France
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64
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Martínez-Puchol S, Itarte M, Rusiñol M, Forés E, Mejías-Molina C, Andrés C, Antón A, Quer J, Abril JF, Girones R, Bofill-Mas S. Exploring the diversity of coronavirus in sewage during COVID-19 pandemic: Don't miss the forest for the trees. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 800:149562. [PMID: 34391155 PMCID: PMC8349739 DOI: 10.1016/j.scitotenv.2021.149562] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 05/07/2023]
Abstract
In the wake of the COVID-19 pandemic, the use of next generation sequencing (NGS) has proved to be an important tool for the genetic characterization of SARS-CoV-2 from clinical samples. The use of different available NGS tools applied to wastewater samples could be the key for an in-depth study of the excreted virome, not only focusing on SARS-CoV-2 circulation and typing, but also to detect other potentially pandemic viruses within the same family. With this aim, 24-hours composite wastewater samples from March and July 2020 were sequenced by applying specific viral NGS as well as target enrichment NGS. The full virome of the analyzed samples was obtained, with human Coronaviridae members (CoV) present in one of those samples after applying the enrichment. One contig was identified as HCoV-OC43 and 8 contigs as SARS-CoV-2. CoVs from other animal hosts were also detected when applying this technique. These contigs were compared with those obtained from contemporary clinical specimens by applying the same target enrichment approach. The results showed that there is a co-circulation in urban areas of human and animal coronaviruses infecting domestic animals and rodents. NGS enrichment-based protocols might be crucial to describe the occurrence and genetic characteristics of SARS-CoV-2 and other Coronaviridae family members within the excreted virome present in wastewater.
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Affiliation(s)
- Sandra Martínez-Puchol
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain.
| | - Marta Itarte
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Marta Rusiñol
- Institute of Environmental Assessment & Water Research (IDAEA), CSIC, Barcelona, Catalonia, Spain
| | - Eva Forés
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Mejías-Molina
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain
| | - Cristina Andrés
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Andrés Antón
- Respiratory Viruses Unit, Virology Section, Microbiology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Josep Quer
- Liver Unit, Liver Diseases - Viral Hepatitis, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Hospital Universitari, Vall d'Hebron Barcelona Hospital Campus, Passeig Vall d'Hebron 119-129, 08035 Barcelona, Spain
| | - Josep F Abril
- Computational Genomics Lab, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona; Institut de Biomedicina (IBUB), Barcelona, Catalonia, Spain
| | - Rosina Girones
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Sílvia Bofill-Mas
- Laboratory of Viruses Contaminants of Water and Food, Genetics, Microbiology & Statistics Dept., Universitat de Barcelona. Barcelona, Catalonia, Spain; The Water Research Institute (IdRA), Universitat de Barcelona, Barcelona, Catalonia, Spain
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65
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Cell Culture Isolation and Whole Genome Characterization of Hepatitis E Virus Strains from Wild Boars in Germany. Microorganisms 2021; 9:microorganisms9112302. [PMID: 34835427 PMCID: PMC8624179 DOI: 10.3390/microorganisms9112302] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 11/16/2022] Open
Abstract
Infection with hepatitis E virus (HEV) can cause acute and chronic hepatitis in humans. The HEV genotype 3 can be zoonotically transmitted from animals to humans, with wild boars representing an important reservoir species. Cell culture isolation of HEV is generally difficult and mainly described for human isolates so far. Here, five sera and five liver samples from HEV-RNA-positive wild boar samples were inoculated onto PLC/PRF/5 cells, incubated for 3 months and thereafter passaged for additional 6 weeks. As demonstrated by RT-qPCR, immunofluorescence and immune electron microscopy, virus was successfully isolated from two liver samples, which originally contained high HEV genome copy numbers. Both isolates showed slower growth than the culture-adapted HEV strain 47832c. In contrast to this strain, the isolated strains had no insertions in their hypervariable genome region. Next generation sequencing using an HEV sequence-enriched library enabled full genome sequencing. Strain Wb108/17 belongs to subtype 3f and strain Wb257/17 to a tentative novel subtype recently described in Italian wild boars. The results indicate that HEV can be successfully isolated in cell culture from wild boar samples containing high HEV genome copy numbers. The isolates may be used further to study the zoonotic potential of wild boar-derived HEV subtypes.
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66
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Huang C, Chen H, Ding Y, Ma X, Zhu H, Zhang S, Du W, Summah HD, Shi G, Feng Y. A Microbial World: Could Metagenomic Next-Generation Sequencing Be Involved in Acute Respiratory Failure? Front Cell Infect Microbiol 2021; 11:738074. [PMID: 34671569 PMCID: PMC8522648 DOI: 10.3389/fcimb.2021.738074] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/10/2021] [Indexed: 11/13/2022] Open
Abstract
Background The usefulness of metagenomic next-generation sequencing (mNGS) in identifying pathogens is being investigated. We aimed to compare the power of microbial identification between mNGS and various methods in patients with acute respiratory failure. Methods We reviewed 130 patients with respiratory failure, and 184 specimens including blood, bronchoalveolar lavage fluid (BALF), sputum, pleural effusion, ascitic fluid, and urine were tested by mNGS and conventional methods (culture, PCR). We also enrolled 13 patients to evaluate the power of mNGS and pathogen targets NGS (ptNGS) in microbial identifications. Clinical features and microbes detected were analyzed. Results mNGS outperformed the conventional method in the positive detection rate of Mycobacterium tuberculosis (MTB) (OR, ∞; 95% CI, 1–∞; P < 0.05), bacteria (OR, 3.7; 95% CI, 2.4–5.8; P < 0.0001), fungi (OR, 4.37; 95% CI, 2.7–7.2; P < 0.0001), mycoplasma (OR, 10.5; 95% CI, 31.8–115; P = 0.005), and virus (OR, ∞; 95% CI, 180.7–∞; P < 0.0001). We showed that 20 patients (28 samples) were detected with Pneumocystis jirovecii (P. jirovecii) by mNGS, but not by the conventional method, and most of those patients were immunocompromised. Read numbers of Klebsiella pneumoniae (K. pneumoniae), Acinetobacter baumannii (A. baumannii), Pseudomonas aeruginosa (P. aeruginosa), P. jirovecii, cytomegalovirus (CMV), and Herpes simplex virus 1 (HSV1) in BALF were higher than those in other sample types, and the read number of Candida albicans (C. albicans) in blood was higher than that in BALF. We found that orotracheal intubation and type 2 diabetes mellitus (T2DM) were associated with a higher detection rate of bacteria and virus by mNGS, immunosuppression was associated with a higher detection rate of fungi and virus by mNGS, and inflammatory markers were associated with mNGS-positive detection rate of bacteria. In addition, we observed preliminary results of ptNGS. Conclusion mNGS outperformed the conventional method in the detection of MTB, bacteria, fungi, mycoplasma, and virus. Orotracheal intubation, T2DM, immunosuppression, and inflammatory markers were associated with a higher detection rate of bacteria, fungi, and virus by mNGS. In addition, ptNGS results were consistent with the detection of abundant bacteria, fungi, and mycoplasma in our specimens.
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Affiliation(s)
- Chunrong Huang
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Hong Chen
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Yongjie Ding
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Xiaolong Ma
- Department of Respiratory and Critical Care Medicine, The First Hospital of Jiaxing, Jiaxing, China
| | - Haixing Zhu
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Shengxiong Zhang
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Wei Du
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Hanssa Dwarka Summah
- Department of Respiratory and Critical Care Medicine, Poudre D'Or Chest Hospital, Rivière du Rempart, Mauritius
| | - Guochao Shi
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
| | - Yun Feng
- Department of Respiratory and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Ruijin Hospital, Shanghai, China
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67
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Carbo EC, Blankenspoor I, Goeman JJ, Kroes ACM, Claas ECJ, De Vries JJC. Viral metagenomic sequencing in the diagnosis of meningoencephalitis: a review of technical advances and diagnostic yield. Expert Rev Mol Diagn 2021; 21:1139-1146. [PMID: 34607520 DOI: 10.1080/14737159.2021.1985467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Meningoencephalitis patients are often severely impaired and benefit from early etiological diagnosis, though many cases remain without identified cause. Metagenomics as pathogen agnostic approach can result in additional etiological findings; however, the exact diagnostic yield when used as a secondary test remains unknown. AREAS COVERED This review aims to highlight recent advances with regard to wet and dry lab methodologies of metagenomic testing and technical milestones that have been achieved. A selection of procedures currently applied in accredited diagnostic laboratories is described in more detail to illustrate best practices. Furthermore, a meta-analysis was performed to assess the additional diagnostic yield utilizing metagenomic sequencing in meningoencephalitis patients. Finally, the remaining challenges for successful widespread implementation of metagenomic sequencing for the diagnosis of meningoencephalitis are addressed in a future perspective. EXPERT OPINION The last decade has shown major advances in technical possibilities for using mNGS in diagnostic settings including cloud-based analysis. An additional advance may be the current established infrastructure of platforms for bioinformatic analysis of SARS-CoV-2, which may assist to pave the way for global use of clinical metagenomics.
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Affiliation(s)
- Ellen C Carbo
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ivar Blankenspoor
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jelle J Goeman
- Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, The Netherlands
| | - Aloys C M Kroes
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric C J Claas
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C De Vries
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
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Zhang C, Burch M, Wylie K, Herter B, Franklin CL, Ericsson AC. Characterization of the Eukaryotic Virome of Mice from Different Sources. Microorganisms 2021; 9:microorganisms9102064. [PMID: 34683385 PMCID: PMC8538372 DOI: 10.3390/microorganisms9102064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Accumulating studies show that the host microbiome influences the development or progression of many diseases. The eukaryotic virome, as a key component of the microbiome, plays an important role in host health and disease in humans and animals, including research animals designed to model human disease. To date, the majority of research on the microbiome has focused on bacterial populations, while less attention has been paid to the viral component. Members of the eukaryotic virome interact with the commensal bacterial microbiome through trans-kingdom interactions, and influence host immunity and disease phenotypes as a collective microbial ecosystem. As such, differences in the virome may affect the reproducibility of animal models, and supplementation of the virome may enhance the translatability of animal models of human disease. However, there are minimal empirical data regarding differences in the virome of mice from different commercial sources. Our hypotheses were that the mice obtained from pet store sources and lab mice differ in their eukaryotic virome, and that lab mice from different sources would also have different viromes. To test this hypothesis, the ViroCap platform was used to characterize the eukaryotic virome in multiple tissues of mice from different sources including three sources of laboratory mice and two pet stores. As expected, pet store mice harbored a much greater diversity within the virome compared to lab mice. This included an ostensibly novel norovirus strain identified in one source of these mice. Viruses found in both laboratory and pet store populations included four strains of endogenous retroviruses and murine astrovirus with the latter being restricted to one source of lab mice. Considering the relatively high richness virome within different samples from healthy humans, these data suggest that mouse models from alternative sources may be more translational to the human condition. Moreover, these data demonstrate that, by characterizing the eukaryotic murine virome from different sources, novel viruses may be identified for use as field strains in biomedical research.
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Affiliation(s)
- Chunye Zhang
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (C.Z.); (M.B.)
| | - Matt Burch
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (C.Z.); (M.B.)
| | - Kristine Wylie
- Department of Pediatrics, Washington University, St. Louis, MO 63110, USA; (K.W.); (B.H.)
- McDonnell Genome Institute, Washington University, St. Louis, MO 63110, USA
| | - Brandi Herter
- Department of Pediatrics, Washington University, St. Louis, MO 63110, USA; (K.W.); (B.H.)
| | - Craig L. Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (C.Z.); (M.B.)
- Metagenomics Center, University of Missouri, Columbia, MO 65201, USA
- Mutant Mouse Resource and Research Center, University of Missouri, Columbia, MO 65201, USA
- Correspondence: (C.L.F.); (A.C.E.)
| | - Aaron C. Ericsson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA; (C.Z.); (M.B.)
- Metagenomics Center, University of Missouri, Columbia, MO 65201, USA
- Mutant Mouse Resource and Research Center, University of Missouri, Columbia, MO 65201, USA
- Correspondence: (C.L.F.); (A.C.E.)
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69
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Faulkner CL, Luo YX, Isaacs S, Rawlinson WD, Craig ME, Kim KW. The virome in early life and childhood and development of islet autoimmunity and type 1 diabetes: A systematic review and meta-analysis of observational studies. Rev Med Virol 2021; 31:1-14. [PMID: 33378601 PMCID: PMC8518965 DOI: 10.1002/rmv.2209] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022]
Abstract
Viruses are postulated as primary candidate triggers of islet autoimmunity (IA) and type 1 diabetes (T1D), based on considerable epidemiological and experimental evidence. Recent studies have investigated the association between all viruses (the 'virome') and IA/T1D using metagenomic next-generation sequencing (mNGS). Current associations between the early life virome and the development of IA/T1D were analysed in a systematic review and meta-analysis of human observational studies from Medline and EMBASE (published 2000-June 2020), without language restriction. Inclusion criteria were as follows: cohort and case-control studies examining the virome using mNGS in clinical specimens of children ≤18 years who developed IA/T1D. The National Health and Medical Research Council level of evidence scale and Newcastle-Ottawa scale were used for study appraisal. Meta-analysis for exposure to specific viruses was performed using random-effects models, and the strength of association was measured using odds ratios (ORs) and 95% confidence intervals (CIs). Eligible studies (one case-control, nine nested case-control) included 1,425 participants (695 cases, 730 controls) and examined IA (n = 1,023) or T1D (n = 402). Meta-analysis identified small but significant associations between IA and number of stool samples positive for all enteroviruses (OR 1.14, 95% CI 1.00-1.29, p = 0.05; heterogeneity χ2 = 1.51, p = 0.68, I2 = 0%), consecutive positivity for enteroviruses (1.55, 1.09-2.20, p = 0.01; χ2 = 0.19, p = 0.91, I2 = 0%) and number of stool samples positive specifically for enterovirus B (1.20, 1.01-1.42, p = 0.04; χ2 = 0.03, p = 0.86, I2 = 0%). Virome analyses to date have demonstrated associations between enteroviruses and IA that may be clinically significant. However, larger prospective mNGS studies with more frequent sampling and follow-up from pregnancy are required to further elucidate associations between early virus exposure and IA/T1D.
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Affiliation(s)
- Clare L. Faulkner
- School of Women's and Children's HealthUniversity of New South Wales Faculty of MedicineSydneyNew South WalesAustralia
- Serology and Virology DivisionNSW Health PathologyVirology Research LaboratoryPrince of Wales HospitalSydneyNew South WalesAustralia
| | - Yi Xuan Luo
- School of Women's and Children's HealthUniversity of New South Wales Faculty of MedicineSydneyNew South WalesAustralia
- Serology and Virology DivisionNSW Health PathologyVirology Research LaboratoryPrince of Wales HospitalSydneyNew South WalesAustralia
| | - Sonia Isaacs
- School of Women's and Children's HealthUniversity of New South Wales Faculty of MedicineSydneyNew South WalesAustralia
- Serology and Virology DivisionNSW Health PathologyVirology Research LaboratoryPrince of Wales HospitalSydneyNew South WalesAustralia
| | - William D. Rawlinson
- School of Women's and Children's HealthUniversity of New South Wales Faculty of MedicineSydneyNew South WalesAustralia
- Serology and Virology DivisionNSW Health PathologyVirology Research LaboratoryPrince of Wales HospitalSydneyNew South WalesAustralia
- School of Medical SciencesUniversity of New South WalesSydneyNew South WalesAustralia
- Faculty of ScienceSchool of Biotechnology and Biomolecular SciencesUniversity of New South WalesSydneyNew South WalesAustralia
| | - Maria E. Craig
- School of Women's and Children's HealthUniversity of New South Wales Faculty of MedicineSydneyNew South WalesAustralia
- Serology and Virology DivisionNSW Health PathologyVirology Research LaboratoryPrince of Wales HospitalSydneyNew South WalesAustralia
- Institute of Endocrinology and DiabetesChildren's Hospital at WestmeadSydneyNew South WalesAustralia
- Discipline of Child and Adolescent HealthUniversity of SydneySydneyNew South WalesAustralia
| | - Ki Wook Kim
- School of Women's and Children's HealthUniversity of New South Wales Faculty of MedicineSydneyNew South WalesAustralia
- Serology and Virology DivisionNSW Health PathologyVirology Research LaboratoryPrince of Wales HospitalSydneyNew South WalesAustralia
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70
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Doddapaneni H, Cregeen SJ, Sucgang R, Meng Q, Qin X, Avadhanula V, Chao H, Menon V, Nicholson E, Henke D, Piedra FA, Rajan A, Momin Z, Kottapalli K, Hoffman KL, Sedlazeck FJ, Metcalf G, Piedra PA, Muzny DM, Petrosino JF, Gibbs RA. Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. PLoS One 2021; 16:e0244468. [PMID: 34432798 PMCID: PMC8386831 DOI: 10.1371/journal.pone.0244468] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 08/09/2021] [Indexed: 02/06/2023] Open
Abstract
The newly emerged and rapidly spreading SARS-CoV-2 causes coronavirus disease 2019 (COVID-19). To facilitate a deeper understanding of the viral biology we developed a capture sequencing methodology to generate SARS-CoV-2 genomic and transcriptome sequences from infected patients. We utilized an oligonucleotide probe-set representing the full-length genome to obtain both genomic and transcriptome (subgenomic open reading frames [ORFs]) sequences from 45 SARS-CoV-2 clinical samples with varying viral titers. For samples with higher viral loads (cycle threshold value under 33, based on the CDC qPCR assay) complete genomes were generated. Analysis of junction reads revealed regions of differential transcriptional activity among samples. Mixed allelic frequencies along the 20kb ORF1ab gene in one sample, suggested the presence of a defective viral RNA species subpopulation maintained in mixture with functional RNA in one sample. The associated workflow is straightforward, and hybridization-based capture offers an effective and scalable approach for sequencing SARS-CoV-2 from patient samples.
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Affiliation(s)
- Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Sara Javornik Cregeen
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard Sucgang
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Qingchang Meng
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Xiang Qin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vasanthi Avadhanula
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hsu Chao
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Vipin Menon
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Erin Nicholson
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - David Henke
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Felipe-Andres Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Anubama Rajan
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Zeineen Momin
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kavya Kottapalli
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Kristi L. Hoffman
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Pedro A. Piedra
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
| | - Joseph F. Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States of America
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71
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Reyes A, Carbo EC, Harinxma Thoe Slooten JSV, Kraakman MEM, Sidorov IA, Claas ECJ, Kroes ACM, Visser LG, de JJCV. Viral metagenomic sequencing in a cohort of international travellers returning with febrile illness. J Clin Virol 2021; 143:104940. [PMID: 34416523 DOI: 10.1016/j.jcv.2021.104940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/17/2021] [Accepted: 07/29/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Diagnosis of infections in returning international travellers can be challenging because of the broad spectrum of potential infectious etiologies potentially involved. Viral metagenomic next-generation sequencing (mNGS) has the potential to detect any virus present in a patient sample and is increasingly being used for difficult to diagnose cases. The aim of this study was to analyze the performance of mNGS for viral pathogen detection in the clinical setting of international travellers returning with febrile illness. METHODS Thirty-eight serum samples from international travellers returning with febrile illness and presenting at the outpatient clinic of the Leiden University Medical Center in the Netherlands in the time period 2015-2016 were selected retrospectively. Samples were processed for viral metagenomic sequencing using a probe panel capturing all known vertebrate viruses. Bioinformatic analysis was performed using Genome Detective software for metagenomic virus detection. Metagenomic virus findings were compared with viral pathogen detection using conventional methods. RESULTS In 8 out of the 38 patients (21%), a pathogenic virus was detected by mNGS. All viral pathogens detected by conventional assays were also detected by mNGS: dengue virus (n=4 patients), Epstein-Barr virus (n=2), hepatitis B virus (n=1). In addition, mNGS resulted in additional pathogenic findings in 2 patients (5%): dengue virus (n=1), and hepatitis C virus (n=1). Non-pathogenic viruses detected were: GB virus C (n=1) and torque teno viruses (n=3). High genome coverage and depth using capture probes enabled typing of the dengue viruses detected. CONCLUSIONS Viral metagenomics has the potential to assist the detection of viral pathogens and co-infections in one step in international travellers with a febrile syndrome. Furthermore, viral enrichment by probes resulted in high genome coverage and depth which enabled dengue virus typing.
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Affiliation(s)
- Alhena Reyes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands; Current affiliation: Microbiology Department, Hospital Universitario 12 de Octubre, Madrid, Spain.
| | - Ellen C Carbo
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | | | - Margriet E M Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Igor A Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Aloys C M Kroes
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Leo G Visser
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, the Netherlands.
| | - Jutte J C Vries de
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands.
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72
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van Doremalen N, Purushotham JN, Schulz JE, Holbrook MG, Bushmaker T, Carmody A, Port JR, Yinda CK, Okumura A, Saturday G, Amanat F, Krammer F, Hanley PW, Smith BJ, Lovaglio J, Anzick SL, Barbian K, Martens C, Gilbert SC, Lambe T, Munster VJ. Intranasal ChAdOx1 nCoV-19/AZD1222 vaccination reduces viral shedding after SARS-CoV-2 D614G challenge in preclinical models. Sci Transl Med 2021; 13:eabh0755. [PMID: 34315826 PMCID: PMC9267380 DOI: 10.1126/scitranslmed.abh0755] [Citation(s) in RCA: 147] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 07/16/2021] [Indexed: 12/17/2022]
Abstract
ChAdOx1 nCoV-19/AZD1222 is an approved adenovirus-based vaccine for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) currently being deployed globally. Previous studies in rhesus macaques revealed that intramuscular vaccination with ChAdOx1 nCoV-19/AZD1222 provided protection against pneumonia but did not reduce shedding of SARS-CoV-2 from the upper respiratory tract. Here, we investigated whether intranasally administered ChAdOx1 nCoV-19 reduces detection of virus in nasal swabs after challenging vaccinated macaques and hamsters with SARS-CoV-2 carrying a D614G mutation in the spike protein. Viral loads in swabs obtained from intranasally vaccinated hamsters were decreased compared to control hamsters, and no viral RNA or infectious virus was found in lung tissue after a direct challenge or after direct contact with infected hamsters. Intranasal vaccination of rhesus macaques resulted in reduced virus concentrations in nasal swabs and a reduction in viral loads in bronchoalveolar lavage and lower respiratory tract tissue. Intranasal vaccination with ChAdOx1 nCoV-19/AZD1222 reduced virus concentrations in nasal swabs in two different SARS-CoV-2 animal models, warranting further investigation as a potential vaccination route for COVID-19 vaccines.
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Affiliation(s)
- Neeltje van Doremalen
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Jyothi N Purushotham
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Jonathan E Schulz
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Myndi G Holbrook
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Trenton Bushmaker
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Aaron Carmody
- Research Technologies Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT 59840, USA
| | - Julia R Port
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Claude K Yinda
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Atsushi Okumura
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Fatima Amanat
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Florian Krammer
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Patrick W Hanley
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Brian J Smith
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Jamie Lovaglio
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Sarah L Anzick
- Research Technologies Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT 59840, USA
| | - Kent Barbian
- Research Technologies Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT 59840, USA
| | - Craig Martens
- Research Technologies Branch, Rocky Mountain Laboratories, National Institutes of Health, Hamilton, MT 59840, USA
| | - Sarah C Gilbert
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Teresa Lambe
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Vincent J Munster
- Laboratory of Virology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA.
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73
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NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water. Foods 2021; 10:foods10081820. [PMID: 34441597 PMCID: PMC8394881 DOI: 10.3390/foods10081820] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 02/07/2023] Open
Abstract
Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.
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74
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Schuele L, Lizarazo-Forero E, Strutzberg-Minder K, Schütze S, Löbert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Rossen JWA, Couto N. Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region. Transbound Emerg Dis 2021; 69:2306-2319. [PMID: 34347385 PMCID: PMC9540031 DOI: 10.1111/tbed.14249] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/16/2021] [Indexed: 12/22/2022]
Abstract
Porcine viruses have been emerging in recent decades, threatening animal and human health, as well as economic stability for pig farmers worldwide. Next‐generation sequencing (NGS) can detect and characterize known and unknown viruses but has limited sensitivity when an unbiased approach, such as shotgun metagenomics sequencing, is used. To increase the sensitivity of NGS for the detection of viruses, we applied and evaluated a broad viral targeted sequence capture (TSC) panel and compared it to an unbiased shotgun metagenomic approach. A cohort of 36 pooled porcine nasal swab and blood serum samples collected from both sides of the Dutch–German border region were evaluated. Overall, we detected 46 different viral species using TSC, compared to 40 viral species with a shotgun metagenomics approach. Furthermore, we performed phylogenetic analysis on recovered influenza A virus (FLUAV) genomes from Germany and revealed a close similarity to a zoonotic influenza strain previously detected in the Netherlands. Although TSC introduced coverage bias within the detected viruses, it improved sensitivity, genome sequence depth and contig length. In‐depth characterization of the swine virome, coupled with developing new enrichment techniques, can play a crucial role in the surveillance of circulating porcine viruses and emerging zoonotic pathogens.
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Affiliation(s)
- Leonard Schuele
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - Erley Lizarazo-Forero
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | | | - Sabine Schütze
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Sandra Löbert
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Claudia Lambrecht
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Jürgen Harlizius
- Animal Health Services, Chamber of Agriculture of North Rhine-Westphalia, Bad Sassendorf, Germany
| | - Alex W Friedrich
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tübingen, Tübingen, Germany
| | - John W A Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,The Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK
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75
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Yolken RH, Kinnunen PM, Vapalahti O, Dickerson F, Suvisaari J, Chen O, Sabunciyan S. Studying the virome in psychiatric disease. Schizophr Res 2021; 234:78-86. [PMID: 34016507 DOI: 10.1016/j.schres.2021.04.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/12/2022]
Abstract
An overlooked aspect of current microbiome studies is the role of viruses in human health. Compared to bacterial studies, laboratory and analytical methods to study the entirety of viral communities in clinical samples are rudimentary and need further refinement. In order to address this need, we developed Virobiome-Seq, a sequence capture method and an accompanying bioinformatics analysis pipeline, that identifies viral reads in human samples. Virobiome-Seq is able to enrich for and detect multiple types of viruses in human samples, including novel subtypes that diverge at the sequence level. In addition, Virobiome-Seq is able to detect RNA transcripts from DNA viruses and may provide a sensitive method for detecting viral activity in vivo. Since Virobiome-Seq also yields the viral sequence, it makes it possible to investigate associations between viral genotype and psychiatric illness. In this proof of concept study, we detected HIV1, Torque Teno, Pegi, Herpes and Papilloma virus sequences in Peripheral Blood Mononuclear Cells, plasma and stool samples collected from individuals with psychiatric disorders. We also detected the presence of numerous novel circular RNA viruses but were unable to determine whether these viruses originate from the sample or represent contaminants. Despite this challenge, we demonstrate that our knowledge of viral diversity is incomplete and opportunities for novel virus discovery exist. Virobiome-Seq will enable a more sophisticated analysis of the virome and has the potential of uncovering complex interactions between viral activity and psychiatric disease.
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Affiliation(s)
- Robert H Yolken
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
| | - Paula M Kinnunen
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Olli Vapalahti
- Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland; Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; HUS Diagnostic Center, HUSLAB, Clinical Microbiology, Helsinki University Hospital, Helsinki, Finland
| | - Faith Dickerson
- Stanley Research Program, Sheppard Pratt, Baltimore, MD, USA
| | - Jaana Suvisaari
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
| | - Ou Chen
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
| | - Sarven Sabunciyan
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA.
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76
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Alfano N, Dayaram A, Axtner J, Tsangaras K, Kampmann M, Mohamed A, Wong ST, Gilbert MTP, Wilting A, Greenwood AD. Non‐invasive surveys of mammalian viruses using environmental DNA. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13661] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Niccolò Alfano
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Department of Biology and Biotechnology University of Pavia Pavia Italy
| | - Anisha Dayaram
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Charité‐Universitätsmedizin Berlin Corporate Member of Freie Universitäts Berlin and Humboldt‐Universität of BerlinInstitut für Neurophysiologie Berlin Germany
| | - Jan Axtner
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Kyriakos Tsangaras
- Department of Life and Health Sciences University of Nicosia Nicosia Cyprus
| | - Marie‐Louise Kampmann
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Section of Forensic Genetics Department of Forensic Medicine Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark
| | - Azlan Mohamed
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- WWF‐MalaysiaPJCC Petaling Jaya Malaysia
| | - Seth T. Wong
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - M. Thomas P. Gilbert
- The GLOBE Institute University of Copenhagen Copenhagen Denmark
- University MuseumNTNU Trondheim Norway
| | - Andreas Wilting
- Department of Ecological Dynamics Leibniz Institute for Zoo and Wildlife Research Berlin Germany
| | - Alex D. Greenwood
- Department of Wildlife Diseases Leibniz Institute for Zoo and Wildlife Research Berlin Germany
- Department of Veterinary Medicine Freie Universität Berlin Berlin Germany
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77
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Zhan SH, Alamouti SM, Daneshpajouh H, Kwok BS, Lee MH, Khattra J, Houck HJ, Rand KH. Target capture sequencing of SARS-CoV-2 genomes using the ONETest Coronaviruses Plus. Diagn Microbiol Infect Dis 2021; 101:115508. [PMID: 34391075 PMCID: PMC8299291 DOI: 10.1016/j.diagmicrobio.2021.115508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/03/2021] [Accepted: 07/17/2021] [Indexed: 12/01/2022]
Abstract
We introduce a target capture next-generation sequencing methodology, the ONETest Coronaviruses Plus, to sequence the SARS-CoV-2 genome and select loci of other respiratory viruses. We applied the ONETest on 70 respiratory samples (collected in Florida, USA between May and July, 2020), in which SARS-CoV-2 had been detected by a PCR assay. For 48 of the samples, we also applied the ARTIC protocol. Of the 70 ONETest libraries, 45 (64%) had a (near-)complete sequence (>29,000 bases and >90% covered by >9 reads). Of the 48 ARTIC libraries, 25 (52%) had a (near-)complete sequence. In 19 out of 25 (76%) samples in which both the ONETest and ARTIC yielded (near-)complete sequences, the lineages assigned were identical. As a target capture approach, the ONETest is less prone to loss of sequence coverage than amplicon approaches, and thus can provide complete genomic information more often to track and monitor SARS-CoV-2 variants.
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Affiliation(s)
- Shing H Zhan
- Fusion Genomics Corporation, Burnaby, British Columbia, Canada.
| | | | | | - Brian S Kwok
- Fusion Genomics Corporation, Burnaby, British Columbia, Canada
| | - Meng-Hsun Lee
- Fusion Genomics Corporation, Burnaby, British Columbia, Canada
| | | | - Herbert J Houck
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Kenneth H Rand
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida College of Medicine, Gainesville, FL, USA
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78
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Tan MTH, Ho SX, Chu JJH, Li D. Application of virome capture sequencing in shellfish sold at retail level in Singapore. Lett Appl Microbiol 2021; 73:486-494. [PMID: 34268776 DOI: 10.1111/lam.13540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/25/2021] [Accepted: 07/13/2021] [Indexed: 12/01/2022]
Abstract
During the period from late 2019 to early 2020, we performed a foodborne virus detection from shellfish collected in Singapore at retail level. Multiple human enteric viruses were included as our targets including human noroviruses (NoVs) GI and GII, hepatitis A virus, hepatitis E virus and rotavirus. Out of the 60 shellfish samples, 23 (38·3%) were detected to be positive by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) with human enteric viruses. Six samples were selected to proceed with virome capture sequencing with positive control samples spiked with serially diluted NoV GII clinical samples in oyster extract. As a result, the natural sample with comparable Ct values (34·0-35·0) of the spiked sample as detected by RT-qPCR generated much lower read counts (>7-log2 cumulative sum scaling difference) and genome coverage (406 nt. vs 3715 nt.), suggesting that the RT-qPCR positive signals detected from the shellfish samples collected at the retail market were likely from degraded RNA derived from inactive virus particles.
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Affiliation(s)
- M T H Tan
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore
| | - S X Ho
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - J J H Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Collaborative and Translation Unit for HFMD, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - D Li
- Department of Food Science & Technology, Faculty of Science, National University of Singapore, Singapore
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79
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Isaacs SR, Foskett DB, Maxwell AJ, Ward EJ, Faulkner CL, Luo JYX, Rawlinson WD, Craig ME, Kim KW. Viruses and Type 1 Diabetes: From Enteroviruses to the Virome. Microorganisms 2021; 9:microorganisms9071519. [PMID: 34361954 PMCID: PMC8306446 DOI: 10.3390/microorganisms9071519] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 12/15/2022] Open
Abstract
For over a century, viruses have left a long trail of evidence implicating them as frequent suspects in the development of type 1 diabetes. Through vigorous interrogation of viral infections in individuals with islet autoimmunity and type 1 diabetes using serological and molecular virus detection methods, as well as mechanistic studies of virus-infected human pancreatic β-cells, the prime suspects have been narrowed down to predominantly human enteroviruses. Here, we provide a comprehensive overview of evidence supporting the hypothesised role of enteroviruses in the development of islet autoimmunity and type 1 diabetes. We also discuss concerns over the historical focus and investigation bias toward enteroviruses and summarise current unbiased efforts aimed at characterising the complete population of viruses (the “virome”) contributing early in life to the development of islet autoimmunity and type 1 diabetes. Finally, we review the range of vaccine and antiviral drug candidates currently being evaluated in clinical trials for the prevention and potential treatment of type 1 diabetes.
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Affiliation(s)
- Sonia R. Isaacs
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Dylan B. Foskett
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Anna J. Maxwell
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Emily J. Ward
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Faculty of Medicine and Health, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Clare L. Faulkner
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - Jessica Y. X. Luo
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
| | - William D. Rawlinson
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Faculty of Medicine and Health, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
- Faculty of Science, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Maria E. Craig
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Institute of Endocrinology and Diabetes, Children’s Hospital at Westmead, Sydney, NSW 2145, Australia
- Faculty of Medicine and Health, Discipline of Child and Adolescent Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Ki Wook Kim
- Faculty of Medicine and Health, School of Women’s and Children’s Health, University of New South Wales, Sydney, NSW 2031, Australia; (S.R.I.); (D.B.F.); (A.J.M.); (E.J.W.); (C.L.F.); (J.Y.X.L.); (W.D.R.); (M.E.C.)
- Virology Research Laboratory, Serology and Virology Division, NSW Health Pathology, Prince of Wales Hospital, Sydney, NSW 2031, Australia
- Correspondence: ; Tel.: +61-2-9382-9096
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80
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Tokarz R, Lipkin WI. Discovery and Surveillance of Tick-Borne Pathogens. JOURNAL OF MEDICAL ENTOMOLOGY 2021; 58:1525-1535. [PMID: 33313662 PMCID: PMC8285023 DOI: 10.1093/jme/tjaa269] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Indexed: 05/06/2023]
Abstract
Within the past 30 yr molecular assays have largely supplanted classical methods for detection of tick-borne agents. Enhancements provided by molecular assays, including speed, throughput, sensitivity, and specificity, have resulted in a rapid increase in the number of newly characterized tick-borne agents. The use of unbiased high throughput sequencing has enabled the prompt identification of new pathogens and the examination of tick microbiomes. These efforts have led to the identification of hundreds of new tick-borne agents in the last decade alone. However, little is currently known about the majority of these agents beyond their phylogenetic classification. Our article outlines the primary methods involved in tick-borne agent discovery and the current status of our understanding of tick-borne agent diversity.
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Affiliation(s)
- Rafal Tokarz
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY
- Corresponding author, e-mail:
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY
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81
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Paulson JN, Williams BL, Hehnly C, Mishra N, Sinnar SA, Zhang L, Ssentongo P, Mbabazi-Kabachelor E, Wijetunge DSS, von Bredow B, Mulondo R, Kiwanuka J, Bajunirwe F, Bazira J, Bebell LM, Burgoine K, Couto-Rodriguez M, Ericson JE, Erickson T, Ferrari M, Gladstone M, Guo C, Haran M, Hornig M, Isaacs AM, Kaaya BN, Kangere SM, Kulkarni AV, Kumbakumba E, Li X, Limbrick DD, Magombe J, Morton SU, Mugamba J, Ng J, Olupot-Olupot P, Onen J, Peterson MR, Roy F, Sheldon K, Townsend R, Weeks AD, Whalen AJ, Quackenbush J, Ssenyonga P, Galperin MY, Almeida M, Atkins H, Warf BC, Lipkin WI, Broach JR, Schiff SJ. Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants. Sci Transl Med 2021; 12:12/563/eaba0565. [PMID: 32998967 DOI: 10.1126/scitranslmed.aba0565] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 05/06/2020] [Indexed: 12/14/2022]
Abstract
Postinfectious hydrocephalus (PIH), which often follows neonatal sepsis, is the most common cause of pediatric hydrocephalus worldwide, yet the microbial pathogens underlying this disease remain to be elucidated. Characterization of the microbial agents causing PIH would enable a shift from surgical palliation of cerebrospinal fluid (CSF) accumulation to prevention of the disease. Here, we examined blood and CSF samples collected from 100 consecutive infant cases of PIH and control cases comprising infants with non-postinfectious hydrocephalus in Uganda. Genomic sequencing of samples was undertaken to test for bacterial, fungal, and parasitic DNA; DNA and RNA sequencing was used to identify viruses; and bacterial culture recovery was used to identify potential causative organisms. We found that infection with the bacterium Paenibacillus, together with frequent cytomegalovirus (CMV) coinfection, was associated with PIH in our infant cohort. Assembly of the genome of a facultative anaerobic bacterial isolate recovered from cultures of CSF samples from PIH cases identified a strain of Paenibacillus thiaminolyticus This strain, designated Mbale, was lethal when injected into mice in contrast to the benign reference Paenibacillus strain. These findings show that an unbiased pan-microbial approach enabled characterization of Paenibacillus in CSF samples from PIH cases, and point toward a pathway of more optimal treatment and prevention for PIH and other proximate neonatal infections.
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Affiliation(s)
- Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Brent L Williams
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Christine Hehnly
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Nischay Mishra
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Shamim A Sinnar
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA.,Department of Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Lijun Zhang
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Paddy Ssentongo
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA.,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Public Health Sciences, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | | | - Dona S S Wijetunge
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Benjamin von Bredow
- Department of Pathology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ronnie Mulondo
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Julius Kiwanuka
- Department of Pediatrics, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda
| | - Francis Bajunirwe
- Department of Epidemiology, Mbarara University of Science and Technology, P.O. Box 1410, Mbarara, Uganda
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda
| | - Lisa M Bebell
- Division of Infectious Disease, Massachusetts Genereal Hospital, Harvard Medical School, 55 Fruit St, GRJ-504, Boston, MA 02114, USA
| | - Kathy Burgoine
- Neonatal Unit, Department of Paediatrics and Child Health, Mbale Regional Referral Hospital, Plot 29-33 Pallisa Road, P.O. Box 1966, Mbale, Uganda.,Mbale Clinical Research Institute, Mbale Regional Referral Hospital, Plot 29-33 Pallisa Road, P.O. Box 1966 Mbale, Uganda.,University of Liverpool, Liverpool, L69 3BX, UK
| | - Mara Couto-Rodriguez
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Biotia, 100 6th avenue, New York, NY 10013, USA
| | - Jessica E Ericson
- Division of Pediatric Infectious Disease, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Tim Erickson
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Matthew Ferrari
- Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.,Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Melissa Gladstone
- Institute for Translational Medicine, University of Liverpool, Liverpool, L12 2AP, UK
| | - Cheng Guo
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Murali Haran
- Department of Statistics, Pennsylvania State University, University Park, PA 16802, USA
| | - Mady Hornig
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Albert M Isaacs
- Department of Neuroscience, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Brian Nsubuga Kaaya
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Sheila M Kangere
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Abhaya V Kulkarni
- Division of Neurosurgery, Hospital for Sick Children, University of Toronto, Toronto, Ontario, M5G 1X8, Canada
| | - Elias Kumbakumba
- Department of Pediatrics, Mbarara University of Science and Technology, P.O. Box 1410 Mbarara, Uganda
| | - Xiaoxiao Li
- Institute for Translational Medicine, University of Liverpool, Liverpool, L12 2AP, UK
| | - David D Limbrick
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, MO 63130, USA
| | - Joshua Magombe
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Sarah U Morton
- Division of Newborn Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston MA 02115, USA
| | - John Mugamba
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - James Ng
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA
| | - Peter Olupot-Olupot
- Mbale Clinical Research Institute, Mbale Regional Referral Hospital, Plot 29-33 Pallisa Road, P.O. Box 1966 Mbale, Uganda.,Busitema University, Mbale Campus, Plot 29-33 Pallisa Road, P.O. Box 1966, Mbale, Uganda
| | - Justin Onen
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Mallory R Peterson
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA.,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA
| | - Farrah Roy
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kathryn Sheldon
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Reid Townsend
- Department of Medicine, Washington University School of Medicine , St. Louis, MO 63130, USA
| | - Andrew D Weeks
- Sanyu Research Unit, Liverpool Women's Hospital, University of Liverpool, Liverpool L8 7SS, UK
| | - Andrew J Whalen
- Department of Mechanical Engineering, Pennsylvania State University, University Park, PA 16802, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Peter Ssenyonga
- CURE Children's Hospital of Uganda, Plot 97-105, Bugwere Road, P.O. Box 903 Mbale, Uganda
| | - Michael Y Galperin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Mathieu Almeida
- Université Paris-Saclay, INRAE, MGP, Jouy-en-Josas, 78350, France
| | - Hannah Atkins
- Department of Comparative Medicine, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Benjamin C Warf
- Department of Neurosurgery, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, NY 10032, USA.,Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - James R Broach
- Institute for Personalized Medicine, Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Steven J Schiff
- Center for Neural Engineering, Pennsylvania State University, University Park, PA 16802, USA. .,Department of Engineering Science and Mechanics, Pennsylvania State University, University Park, PA 16802, USA.,Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA.,Department of Neurosurgery, Pennsylvania State University College of Medicine, Hershey, PA 17033, USA.,Department of Physics, Pennsylvania State University, University Park, PA 16802, USA
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82
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Damavandi F, Wang W, Shen WZ, Cetinel S, Jordan T, Jovel J, Montemagno C, Wong GKS. Enrichment of low abundance DNA/RNA by oligonucleotide-clicked iron oxide nanoparticles. Sci Rep 2021; 11:13053. [PMID: 34158543 PMCID: PMC8219684 DOI: 10.1038/s41598-021-92376-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 06/07/2021] [Indexed: 01/05/2023] Open
Abstract
Detection of low abundance target DNA/RNA for clinical or research purposes is challenging because the target sequences can be hidden under a large background of human genomic or non-human metagenomic sequences. We describe a probe-based capture method to enrich for target sequences with DNA-clicked iron oxide nanoparticles. Our method was tested against commercial capture assays using streptavidin beads, on a set of probes derived from a common genotype of the hepatitis C virus. We showed that our method is more specific and sensitive, most likely due to the combination of an inert silica coating and a high density of DNA probes clicked to the nanoparticles. This facilitates target capture below the limits of detection for TaqMan qPCR, and we believe that this method has the potential to transform management of infectious diseases.
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Affiliation(s)
- Fereshte Damavandi
- Ingenuity Lab, 1-070C, 11421 Saskatchewan Drive NW, Edmonton, AB, T6G 2M9, Canada.,Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | - Weiwei Wang
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada.,Geneis Inc., Bldg A, 5 Guangshun North Street, Beijing, China
| | - Wei-Zheng Shen
- Ingenuity Lab, 1-070C, 11421 Saskatchewan Drive NW, Edmonton, AB, T6G 2M9, Canada.,Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | - Sibel Cetinel
- Ingenuity Lab, 1-070C, 11421 Saskatchewan Drive NW, Edmonton, AB, T6G 2M9, Canada.,Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada.,Nanotechnology Research and Application Center (SUNUM), Sabanci University, Istanbul, 34956, Turkey
| | - Tracy Jordan
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Juan Jovel
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Carlo Montemagno
- Ingenuity Lab, 1-070C, 11421 Saskatchewan Drive NW, Edmonton, AB, T6G 2M9, Canada.,Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB, T6G 2V4, Canada
| | - Gane Ka-Shu Wong
- Department of Medicine, University of Alberta, Edmonton, AB, T6G 2E1, Canada. .,Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
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83
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O'Neal AJ, Hanson MR. The Enterovirus Theory of Disease Etiology in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Critical Review. Front Med (Lausanne) 2021; 8:688486. [PMID: 34222292 PMCID: PMC8253308 DOI: 10.3389/fmed.2021.688486] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/26/2021] [Indexed: 02/06/2023] Open
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex, multi-system disease whose etiological basis has not been established. Enteroviruses (EVs) as a cause of ME/CFS have sometimes been proposed, as they are known agents of acute respiratory and gastrointestinal infections that may persist in secondary infection sites, including the central nervous system, muscle, and heart. To date, the body of research that has investigated enterovirus infections in relation to ME/CFS supports an increased prevalence of chronic or persistent enteroviral infections in ME/CFS patient cohorts than in healthy individuals. Nevertheless, inconsistent results have fueled a decline in related studies over the past two decades. This review covers the aspects of ME/CFS pathophysiology that are consistent with a chronic enterovirus infection and critically reviews methodologies and approaches used in past EV-related ME/CFS studies. We describe the prior sample types that were interrogated, the methods used and the limitations to the approaches that were chosen. We conclude that there is considerable evidence that prior outbreaks of ME/CFS were caused by one or more enterovirus groups. Furthermore, we find that the methods used in prior studies were inadequate to rule out the presence of chronic enteroviral infections in individuals with ME/CFS. Given the possibility that such infections could be contributing to morbidity and preventing recovery, further studies of appropriate biological samples with the latest molecular methods are urgently needed.
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Affiliation(s)
- Adam J O'Neal
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
| | - Maureen R Hanson
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, United States
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Abstract
Neonatal sepsis (NS) kills 750,000 infants every year. Effectively treating NS requires timely diagnosis and antimicrobial therapy matched to the causative pathogens, but most blood cultures for suspected NS do not recover a causative pathogen. We refer to these suspected but unidentified pathogens as microbial dark matter. Given these low culture recovery rates, many non–culture-based technologies are being explored to diagnose NS, including PCR, 16S amplicon sequencing, and whole metagenomic sequencing. However, few of these newer technologies are scalable or sustainable globally. To reduce worldwide deaths from NS, one possibility may be performing population-wide pathogen discovery. Because pathogen transmission patterns can vary across space and time, computational models can be built to predict the pathogens responsible for NS by region and season. This approach could help to optimally treat patients, decreasing deaths from NS and increasing antimicrobial stewardship until effective diagnostics that are scalable become available globally.
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85
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Development of a capture sequencing assay for enhanced detection and genotyping of tick-borne pathogens. Sci Rep 2021; 11:12384. [PMID: 34117323 PMCID: PMC8196166 DOI: 10.1038/s41598-021-91956-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/31/2021] [Indexed: 02/05/2023] Open
Abstract
Inadequate sensitivity has been the primary limitation for implementing high-throughput sequencing for studies of tick-borne agents. Here we describe the development of TBDCapSeq, a sequencing assay that uses hybridization capture probes that cover the complete genomes of the eleven most common tick-borne agents found in the United States. The probes are used for solution-based capture and enrichment of pathogen nucleic acid followed by high-throughput sequencing. We evaluated the performance of TBDCapSeq to surveil samples that included human whole blood, mouse tissues, and field-collected ticks. For Borrelia burgdorferi and Babesia microti, the sensitivity of TBDCapSeq was comparable and occasionally exceeded the performance of agent-specific quantitative PCR and resulted in 25 to > 10,000-fold increase in pathogen reads when compared to standard unbiased sequencing. TBDCapSeq also enabled genome analyses directly within vertebrate and tick hosts. The implementation of TBDCapSeq could have major impact in studies of tick-borne pathogens by improving detection and facilitating genomic research that was previously unachievable with standard sequencing approaches.
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86
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Allnutt TR, Roth-Schulze AJ, Harrison LC. Expanding the taxonomic range in the fecal metagenome. BMC Bioinformatics 2021; 22:312. [PMID: 34107881 PMCID: PMC8188691 DOI: 10.1186/s12859-021-04212-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 05/20/2021] [Indexed: 11/10/2022] Open
Abstract
Background Except for bacteria, the taxonomic diversity of the human fecal metagenome has not been widely studied, despite the potential importance of viruses and eukaryotes. Widely used bioinformatic tools contain limited numbers of non-bacterial species in their databases compared to available genomic sequences and their methodologies do not favour classification of rare sequences which may represent only a small fraction of their parent genome. In seeking to optimise identification of non-bacterial species, we evaluated five widely-used metagenome classifier programs (BURST, Kraken2, Centrifuge, MetaPhlAn2 and CCMetagen) for their ability to correctly assign and count simulations of bacterial, viral and eukaryotic DNA sequence reads, including the effect of taxonomic order of analysis of bacteria, viruses and eukaryotes and the effect of sequencing depth. Results We found that the precision of metagenome classifiers varied significantly between programs and between taxonomic groups. When classifying viruses and eukaryotes, ordering the analysis such that bacteria were classified first significantly improved classification precision. Increasing sequencing depth decreased classification precision and did not improve recall of rare species. Conclusions Choice of metagenome classifier program can have a marked effect on results with respect to precision of species assignment in different taxonomic groups. The order of taxonomic classification can markedly improve precision. Increasing sequencing depth can decrease classification precision and yields diminishing returns in probability of species detection. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04212-6.
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Affiliation(s)
- Theo R Allnutt
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.
| | - Alexandra J Roth-Schulze
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Leonard C Harrison
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, Melbourne, VIC, 3052, Australia. .,Department of Medical Biology, University of Melbourne, Melbourne, VIC, 3010, Australia.
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87
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Tan CW, Yang X, Anderson DE, Wang LF. Bat virome research: the past, the present and the future. Curr Opin Virol 2021; 49:68-80. [PMID: 34052731 DOI: 10.1016/j.coviro.2021.04.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 04/30/2021] [Indexed: 02/07/2023]
Abstract
Bats have been increasingly recognised as an exceptional reservoir for emerging zoonotic viruses for the past few decades. Recent studies indicate that the unique bat immune system may be partially responsible for their ability to co-exist with viruses with minimal or no clinical diseases. In this review, we discuss the history and importance of bat virome studies and contrast the vast difference between such studies before and after the introduction of next generation sequencing (NGS) in this area of research. We also discuss the role of discovery serology and high-throughput single cell RNA-seq in future bat virome research.
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Affiliation(s)
- Chee Wah Tan
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Xinglou Yang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 169857, Singapore; SingHealth Duke-NUS Global Health Institute, 169857, Singapore.
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88
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Filkins LM, Bryson AL, Miller SA, Mitchell SL. Navigating Clinical Utilization of Direct-from-Specimen Metagenomic Pathogen Detection: Clinical Applications, Limitations, and Testing Recommendations. Clin Chem 2021; 66:1381-1395. [PMID: 33141913 DOI: 10.1093/clinchem/hvaa183] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/16/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Metagenomic next generation sequencing (mNGS) is becoming increasingly available for pathogen detection directly from clinical specimens. These tests use target-independent, shotgun sequencing to detect potentially unlimited organisms. The promise of this methodology to aid infection diagnosis is demonstrated through early case reports and clinical studies. However, the optimal role of mNGS in clinical microbiology remains uncertain. CONTENT We reviewed studies reporting clinical use of mNGS for pathogen detection from various specimen types, including cerebrospinal fluid, plasma, lower respiratory specimens, and others. Published clinical study data were critically evaluated and summarized to identify promising clinical indications for mNGS-based testing, to assess the clinical impact of mNGS for each indication, and to recognize test limitations. Based on these clinical studies, early testing recommendations are made to guide clinical utilization of mNGS for pathogen detection. Finally, current barriers to routine clinical laboratory implementation of mNGS tests are highlighted. SUMMARY The promise of direct-from-specimen mNGS to enable challenging infection diagnoses has been demonstrated through early clinical studies of patients with meningitis or encephalitis, invasive fungal infections, community acquired pneumonia, and other clinical indications. However, the proportion of patient cases with positive clinical impact due to mNGS testing is low in published studies and the cost of testing is high, emphasizing the importance of improving our understanding of 'when to test' and for which patients mNGS testing is appropriate.
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Affiliation(s)
- Laura M Filkins
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Alexandra L Bryson
- Department of Pathology, Virginia Commonwealth University Health System, Richmond, VA
| | - Steve A Miller
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA
| | - Stephanie L Mitchell
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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89
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Fulci V, Stronati L, Cucchiara S, Laudadio I, Carissimi C. Emerging Roles of Gut Virome in Pediatric Diseases. Int J Mol Sci 2021; 22:4127. [PMID: 33923593 PMCID: PMC8073368 DOI: 10.3390/ijms22084127] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 12/15/2022] Open
Abstract
In the last decade, the widespread application of shotgun metagenomics provided extensive characterization of the bacterial "dark matter" of the gut microbiome, propelling the development of dedicated, standardized bioinformatic pipelines and the systematic collection of metagenomic data into comprehensive databases. The advent of next-generation sequencing also unravels a previously underestimated viral population (virome) present in the human gut. Despite extensive efforts to characterize the human gut virome, to date, little is known about the childhood gut virome. However, alterations of the gut virome in children have been linked to pathological conditions such as inflammatory bowel disease, type 1 diabetes, malnutrition, diarrhea and celiac disease.
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Affiliation(s)
- Valerio Fulci
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Laura Stronati
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Salvatore Cucchiara
- Department of Women’s and Children’s Health, Sapienza University of Rome, 00161 Rome, Italy;
| | - Ilaria Laudadio
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
| | - Claudia Carissimi
- Department of Molecular Medicine, Sapienza University of Rome, 00161 Rome, Italy; (V.F.); (L.S.)
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90
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Maina S, Zheng L, Rodoni BC. Targeted Genome Sequencing (TG-Seq) Approaches to Detect Plant Viruses. Viruses 2021; 13:583. [PMID: 33808381 PMCID: PMC8066983 DOI: 10.3390/v13040583] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 12/18/2022] Open
Abstract
Globally, high-throughput sequencing (HTS) has been used for virus detection in germplasm certification programs. However, sequencing costs have impeded its implementation as a routine diagnostic certification tool. In this study, the targeted genome sequencing (TG-Seq) approach was developed to simultaneously detect multiple (four) viral species of; Pea early browning virus (PEBV), Cucumber mosaic virus (CMV), Bean yellow mosaic virus (BYMV) and Pea seedborne mosaic virus (PSbMV). TG-Seq detected all the expected viral amplicons within multiplex PCR (mPCR) reactions. In contrast, the expected PCR amplicons were not detected by gel electrophoresis (GE). For example, for CMV, GE only detected RNA1 and RNA2 while TG-Seq detected all the three RNA components of CMV. In an mPCR to amplify all four viruses, TG-Seq readily detected each virus with more than 732,277 sequence reads mapping to each amplicon. In addition, TG-Seq also detected all four amplicons within a 10-8 serial dilution that were not detectable by GE. Our current findings reveal that the TG-Seq approach offers significant potential and is a highly sensitive targeted approach for detecting multiple plant viruses within a given biological sample. This is the first study describing direct HTS of plant virus mPCR products. These findings have major implications for grain germplasm healthy certification programs and biosecurity management in relation to pathogen entry into Australia and elsewhere.
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Affiliation(s)
- Solomon Maina
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham, Victoria 3400, Australia
| | - Linda Zheng
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
| | - Brendan C. Rodoni
- Microbial Sciences, Pests & Diseases, Agriculture Victoria, AgriBio, 5 Ring Road, Bundoora, Victoria 3083, Australia; (L.Z.); (B.C.R.)
- School of Applied Systems Biology (SASB), La Trobe University, Bundoora, Victoria 3083, Australia
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91
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Mwesigwa S, Williams L, Retshabile G, Katagirya E, Mboowa G, Mlotshwa B, Kyobe S, Kateete DP, Wampande EM, Wayengera M, Mpoloka SW, Mirembe AN, Kasvosve I, Morapedi K, Kisitu GP, Kekitiinwa AR, Anabwani G, Joloba ML, Matovu E, Mulindwa J, Noyes H, Botha G, Brown CW, Mardon G, Matshaba M, Hanchard NA. Unmapped exome reads implicate a role for Anelloviridae in childhood HIV-1 long-term non-progression. NPJ Genom Med 2021; 6:24. [PMID: 33741997 PMCID: PMC7979878 DOI: 10.1038/s41525-021-00185-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 01/25/2021] [Indexed: 01/31/2023] Open
Abstract
Human immunodeficiency virus (HIV) infection remains a significant public health burden globally. The role of viral co-infection in the rate of progression of HIV infection has been suggested but not empirically tested, particularly among children. We extracted and classified 42 viral species from whole-exome sequencing (WES) data of 813 HIV-infected children in Botswana and Uganda categorised as either long-term non-progressors (LTNPs) or rapid progressors (RPs). The Ugandan participants had a higher viral community diversity index compared to Batswana (p = 4.6 × 10-13), and viral sequences were more frequently detected among LTNPs than RPs (24% vs 16%; p = 0.008; OR, 1.9; 95% CI, 1.6-2.3), with Anelloviridae showing strong association with LTNP status (p = 3 × 10-4; q = 0.004, OR, 3.99; 95% CI, 1.74-10.25). This trend was still evident when stratified by country, sex, and sequencing platform, and after a logistic regression analysis adjusting for age, sex, country, and the sequencing platform (p = 0.02; q = 0.03; OR, 7.3; 95% CI, 1.6-40.5). Torque teno virus (TTV), which made up 95% of the Anelloviridae reads, has been associated with reduced immune activation. We identify an association between viral co-infection and prolonged AIDs-free survival status that may have utility as a biomarker of LTNP and could provide mechanistic insights to HIV progression in children, demonstrating the added value of interrogating off-target WES reads in cohort studies.
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Affiliation(s)
| | | | | | - Eric Katagirya
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Samuel Kyobe
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - David P Kateete
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Misaki Wayengera
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Angella N Mirembe
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | | | | | - Grace P Kisitu
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | - Adeodata R Kekitiinwa
- Baylor College of Medicine Children's Foundation Uganda (Baylor Uganda), Kampala, Uganda
| | - Gabriel Anabwani
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
| | - Moses L Joloba
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Julius Mulindwa
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Harry Noyes
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Gerrit Botha
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Chester W Brown
- University of Tennessee Health Science Center, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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92
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Fitzpatrick AH, Rupnik A, O'Shea H, Crispie F, Keaveney S, Cotter P. High Throughput Sequencing for the Detection and Characterization of RNA Viruses. Front Microbiol 2021; 12:621719. [PMID: 33692767 PMCID: PMC7938315 DOI: 10.3389/fmicb.2021.621719] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
This review aims to assess and recommend approaches for targeted and agnostic High Throughput Sequencing of RNA viruses in a variety of sample matrices. HTS also referred to as deep sequencing, next generation sequencing and third generation sequencing; has much to offer to the field of environmental virology as its increased sequencing depth circumvents issues with cloning environmental isolates for Sanger sequencing. That said however, it is important to consider the challenges and biases that method choice can impart to sequencing results. Here, methodology choices from RNA extraction, reverse transcription to library preparation are compared based on their impact on the detection or characterization of RNA viruses.
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Affiliation(s)
- Amy H. Fitzpatrick
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
- Shellfish Microbiology, Marine Institute, Oranmore, Ireland
- Biological Sciences, Munster Technological University, Cork, Ireland
| | | | - Helen O'Shea
- Biological Sciences, Munster Technological University, Cork, Ireland
| | - Fiona Crispie
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
| | | | - Paul Cotter
- Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
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93
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Yinda CK, Seifert SN, Macmenamin P, van Doremalen N, Kim L, Bushmaker T, de Wit E, Quinones M, Munster VJ. A Novel Field-Deployable Method for Sequencing and Analyses of Henipavirus Genomes From Complex Samples on the MinION Platform. J Infect Dis 2021; 221:S383-S388. [PMID: 31784761 DOI: 10.1093/infdis/jiz576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Viruses in the genus Henipavirus encompass 2 highly pathogenic emerging zoonotic pathogens, Hendra virus (HeV) and Nipah virus (NiV). Despite the impact on human health, there is currently limited full-genome sequence information available for henipaviruses. This lack of full-length genomes hampers our ability to understand the molecular drivers of henipavirus emergence. Furthermore, rapidly deployable viral genome sequencing can be an integral part of outbreak response and epidemiological investigations to study transmission chains. In this study, we describe the development of a reverse-transcription, long-range polymerase chain reaction (LRPCR) assay for efficient genome amplification of NiV, HeV, and a related non-pathogenic henipavirus, Cedar virus (CedPV). We then demonstrated the utility of our method by amplifying partial viral genomes from 6 HeV-infected tissue samples from Syrian hamsters and 4 tissue samples from a NiV-infected African green monkey with viral loads as low as 52 genome copies/mg. We subsequently sequenced the amplified genomes on the portable Oxford Nanopore MinION platform and analyzed the data using a newly developed field-deployable bioinformatic pipeline. Our LRPCR assay allows amplification and sequencing of 2 or 4 amplicons in semi-nested reactions. Coupled with an easy-to-use bioinformatics pipeline, this method is particularly useful in the field during outbreaks in resource-poor environments.
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Affiliation(s)
- Claude Kwe Yinda
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Stephanie N Seifert
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Philip Macmenamin
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Neeltje van Doremalen
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Lewis Kim
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Trenton Bushmaker
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Emmie de Wit
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - Mariam Quinones
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Vincent J Munster
- Laboratory of Virology, Rocky Mountain Laboratories, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
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Wylezich C, Calvelage S, Schlottau K, Ziegler U, Pohlmann A, Höper D, Beer M. Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2. MICROBIOME 2021; 9:51. [PMID: 33610182 DOI: 10.1186/s40168-020-00973-z/figures/4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/07/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. METHODS A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. RESULTS The VirBaits set consists of 177,471 RNA baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also points to the risk of cross-contamination between samples. CONCLUSIONS The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2. Video abstract.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
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Wylezich C, Calvelage S, Schlottau K, Ziegler U, Pohlmann A, Höper D, Beer M. Next-generation diagnostics: virus capture facilitates a sensitive viral diagnosis for epizootic and zoonotic pathogens including SARS-CoV-2. MICROBIOME 2021; 9:51. [PMID: 33610182 PMCID: PMC7896545 DOI: 10.1186/s40168-020-00973-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 12/07/2020] [Indexed: 05/15/2023]
Abstract
BACKGROUND The detection of pathogens in clinical and environmental samples using high-throughput sequencing (HTS) is often hampered by large amounts of background information, which is especially true for viruses with small genomes. Enormous sequencing depth can be necessary to compile sufficient information for identification of a certain pathogen. Generic HTS combining with in-solution capture enrichment can markedly increase the sensitivity for virus detection in complex diagnostic samples. METHODS A virus panel based on the principle of biotinylated RNA baits was developed for specific capture enrichment of epizootic and zoonotic viruses (VirBaits). The VirBaits set was supplemented by a SARS-CoV-2 predesigned bait set for testing recent SARS-CoV-2-positive samples. Libraries generated from complex samples were sequenced via generic HTS (without enrichment) and afterwards enriched with the VirBaits set. For validation, an internal proficiency test for emerging epizootic and zoonotic viruses (African swine fever virus, Ebolavirus, Marburgvirus, Nipah henipavirus, Rift Valley fever virus) was conducted. RESULTS The VirBaits set consists of 177,471 RNA baits (80-mer) based on about 18,800 complete viral genomes targeting 35 epizootic and zoonotic viruses. In all tested samples, viruses with both DNA and RNA genomes were clearly enriched ranging from about 10-fold to 10,000-fold for viruses including distantly related viruses with at least 72% overall identity to viruses represented in the bait set. Viruses showing a lower overall identity (38% and 46%) to them were not enriched but could nonetheless be detected based on capturing conserved genome regions. The internal proficiency test supports the improved virus detection using the combination of HTS plus targeted enrichment but also points to the risk of cross-contamination between samples. CONCLUSIONS The VirBaits approach showed a high diagnostic performance, also for distantly related viruses. The bait set is modular and expandable according to the favored diagnostics, health sector, or research question. The risk of cross-contamination needs to be taken into consideration. The application of the RNA-baits principle turned out to be user friendly, and even non-experts can easily use the VirBaits workflow. The rapid extension of the established VirBaits set adapted to actual outbreak events is possible as shown for SARS-CoV-2. Video abstract.
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Affiliation(s)
- Claudia Wylezich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany.
| | - Sten Calvelage
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Kore Schlottau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Ute Ziegler
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Dirk Höper
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, 17493, Greifswald-Insel Riems, Germany
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96
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Characterization of oral virome and microbiome revealed distinctive microbiome disruptions in paediatric patients with hand, foot and mouth disease. NPJ Biofilms Microbiomes 2021; 7:19. [PMID: 33608551 PMCID: PMC7895916 DOI: 10.1038/s41522-021-00190-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 01/20/2021] [Indexed: 01/01/2023] Open
Abstract
While the underlying determinants are unclear, hand, foot and mouth disease (HFMD) presents a wide spectrum of clinical manifestations with varying severity in different individuals. Recently, many studies identified the human microbiome as a critical factor in the pathogenesis of various diseases. Therefore, we here investigated the ecological dynamics of the oral microbiome changes during the HFMD infection. After targeted enrichment of all known vertebrate viruses, the virome profiles of symptomatic and asymptomatic HFMD patients were examined and revealed to be significantly altered from those of healthy individuals, with nine discriminative viruses detected. Further characterization of the prokaryotic microbiome revealed an elevated level of Streptococcus sp. as the most important signature of the symptomatic HFMD cohort, positively correlating to the level of enterovirus A RNA. In addition, we found that while coxsackievirus A5 is detected in saliva RNA of all asymptomatic cases, coxsackievirus A6 dominates the majority of the symptomatic cohort.
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97
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Hartley PD, Tillett RL, AuCoin DP, Sevinsky JR, Xu Y, Gorzalski A, Pandori M, Buttery E, Hansen H, Picker MA, Rossetto CC, Verma SC. Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene. J Genet Genomics 2021; 48:40-51. [PMID: 33820739 PMCID: PMC7891100 DOI: 10.1016/j.jgg.2021.01.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 12/28/2022]
Abstract
Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs. To determine the variants of SARS-CoV-2 circulating in the state of Nevada, specimens from 200 COVID-19 patients were sequenced through our robust sequencing platform, which enabled sequencing of SARS-CoV-2 from specimens with even very low viral loads, without the need of culture-based amplification. High genome coverage allowed the identification of single and multi-nucleotide variants in SARS-CoV-2 in the community and their phylogenetic relationships with other variants present during the same period of the outbreak. We report the occurrence of a novel mutation at 323aa (314aa of orf1b) of nsp12 (RNA-dependent RNA polymerase) changed to phenylalanine (F) from proline (P), in the first reported isolate of SARS-CoV-2, Wuhan-Hu-1. This 323F variant was present at a very high frequency in Northern Nevada. Structural modeling determined this mutation in the interface domain, which is important for the association of accessory proteins required for the polymerase. In conclusion, we report the introduction of specific SARS-CoV-2 variants at very high frequency in distinct geographic locations, which is important for understanding the evolution and circulation of SARS-CoV-2 variants of public health importance, while it circulates in humans.
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Affiliation(s)
- Paul D Hartley
- Nevada Genomics Center, Reno, NV 89557, USA; University of Nevada, Reno, Reno, NV 89557, USA
| | - Richard L Tillett
- Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, NV 89154, USA
| | - David P AuCoin
- University of Nevada, Reno, Reno, NV 89557, USA; Department of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA
| | | | - Yanji Xu
- University of Nevada, Reno, Reno, NV 89557, USA; Nevada Center for Bioinformatics, Reno, NV 89557, USA
| | - Andrew Gorzalski
- University of Nevada, Reno, Reno, NV 89557, USA; Nevada State Public Health Laboratory, Reno, NV 89503, USA
| | - Mark Pandori
- University of Nevada, Reno, Reno, NV 89557, USA; Nevada State Public Health Laboratory, Reno, NV 89503, USA
| | - Erin Buttery
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89107, USA
| | - Holly Hansen
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89107, USA
| | - Michael A Picker
- Southern Nevada Public Health Laboratory of the Southern Nevada Health District, Las Vegas, NV 89107, USA
| | - Cyprian C Rossetto
- University of Nevada, Reno, Reno, NV 89557, USA; Department of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
| | - Subhash C Verma
- University of Nevada, Reno, Reno, NV 89557, USA; Department of Microbiology & Immunology, University of Nevada, Reno School of Medicine, Reno, NV 89557, USA.
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98
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Respiratory viral co-infections among SARS-CoV-2 cases confirmed by virome capture sequencing. Sci Rep 2021; 11:3934. [PMID: 33594223 PMCID: PMC7887263 DOI: 10.1038/s41598-021-83642-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 02/03/2021] [Indexed: 02/07/2023] Open
Abstract
Accumulating evidence supports the high prevalence of co-infections among Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) patients, and their potential to worsen the clinical outcome of COVID-19. However, there are few data on Southern Hemisphere populations, and most studies to date have investigated a narrow spectrum of viruses using targeted qRT-PCR. Here we assessed respiratory viral co-infections among SARS-CoV-2 patients in Australia, through respiratory virome characterization. Nasopharyngeal swabs of 92 SARS-CoV-2-positive cases were sequenced using pan-viral hybrid-capture and the Twist Respiratory Virus Panel. In total, 8% of cases were co-infected, with rhinovirus (6%) or influenzavirus (2%). Twist capture also achieved near-complete sequencing (> 90% coverage, > tenfold depth) of the SARS-CoV-2 genome in 95% of specimens with Ct < 30. Our results highlight the importance of assessing all pathogens in symptomatic patients, and the dual-functionality of Twist hybrid-capture, for SARS-CoV-2 whole-genome sequencing without amplicon generation and the simultaneous identification of viral co-infections with ease.
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99
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Dulanto Chiang A, Dekker JP. From the Pipeline to the Bedside: Advances and Challenges in Clinical Metagenomics. J Infect Dis 2021; 221:S331-S340. [PMID: 31538184 DOI: 10.1093/infdis/jiz151] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) technologies have revolutionized multiple areas in the field of infectious diseases, from pathogen discovery to characterization of genes mediating drug resistance. Consequently, there is much anticipation that NGS technologies may be harnessed in the realm of diagnostic methods to complement or replace current culture-based and molecular microbiologic techniques. In this context, much consideration has been given to hypothesis-free, culture-independent tests that can be performed directly on primary clinical samples. The closest realizations of such universal diagnostic methods achieved to date are based on targeted amplicon and unbiased metagenomic shotgun NGS approaches. Depending on the exact details of implementation and analysis, these approaches have the potential to detect viruses, bacteria, fungi, parasites, and archaea, including organisms that were previously undiscovered and those that are uncultivatable. Shotgun metagenomics approaches additionally can provide information on the presence of virulence and resistance genetic elements. While many limitations to the use of NGS in clinical microbiology laboratories are being overcome with decreasing technology costs, expanding curated pathogen sequence databases, and better data analysis tools, there remain many challenges to the routine use and implementation of these methods. This review summarizes recent advances in applications of targeted amplicon and shotgun-based metagenomics approaches to infectious disease diagnostic methods. Technical and conceptual challenges are considered, along with expectations for future applications of these techniques.
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Affiliation(s)
- Augusto Dulanto Chiang
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, Bethesda, Maryland
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100
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Maljkovic Berry I, Melendrez MC, Bishop-Lilly KA, Rutvisuttinunt W, Pollett S, Talundzic E, Morton L, Jarman RG. Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity. J Infect Dis 2021; 221:S292-S307. [PMID: 31612214 DOI: 10.1093/infdis/jiz286] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Next generation sequencing (NGS) combined with bioinformatics has successfully been used in a vast array of analyses for infectious disease research of public health relevance. For instance, NGS and bioinformatics approaches have been used to identify outbreak origins, track transmissions, investigate epidemic dynamics, determine etiological agents of a disease, and discover novel human pathogens. However, implementation of high-quality NGS and bioinformatics in research and public health laboratories can be challenging. These challenges mainly include the choice of the sequencing platform and the sequencing approach, the choice of bioinformatics methodologies, access to the appropriate computation and information technology infrastructure, and recruiting and retaining personnel with the specialized skills and experience in this field. In this review, we summarize the most common NGS and bioinformatics workflows in the context of infectious disease genomic surveillance and pathogen discovery, and highlight the main challenges and considerations for setting up an NGS and bioinformatics-focused infectious disease research public health laboratory. We describe the most commonly used sequencing platforms and review their strengths and weaknesses. We review sequencing approaches that have been used for various pathogens and study questions, as well as the most common difficulties associated with these approaches that should be considered when implementing in a public health or research setting. In addition, we provide a review of some common bioinformatics tools and procedures used for pathogen discovery and genome assembly, along with the most common challenges and solutions. Finally, we summarize the bioinformatics of advanced viral, bacterial, and parasite pathogen characterization, including types of study questions that can be answered when utilizing NGS and bioinformatics.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | | | - Kimberly A Bishop-Lilly
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, Maryland
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland.,Department of Preventive Medicine and Biostatistics, Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Eldin Talundzic
- Division of Parasitic Diseases and Malaria, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, Maryland
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland
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