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Ji CM, Feng XY, Huang YW, Chen RA. The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research. Viruses 2024; 16:798. [PMID: 38793679 PMCID: PMC11125791 DOI: 10.3390/v16050798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
In recent years, an increasing number of viruses have triggered outbreaks that pose a severe threat to both human and animal life, as well as caused substantial economic losses. It is crucial to understand the genomic structure and epidemiology of these viruses to guide effective clinical prevention and treatment strategies. Nanopore sequencing, a third-generation sequencing technology, has been widely used in genomic research since 2014. This technology offers several advantages over traditional methods and next-generation sequencing (NGS), such as the ability to generate ultra-long reads, high efficiency, real-time monitoring and analysis, portability, and the ability to directly sequence RNA or DNA molecules. As a result, it exhibits excellent applicability and flexibility in virus research, including viral detection and surveillance, genome assembly, the discovery of new variants and novel viruses, and the identification of chemical modifications. In this paper, we provide a comprehensive review of the development, principles, advantages, and applications of nanopore sequencing technology in animal and human virus research, aiming to offer fresh perspectives for future studies in this field.
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Affiliation(s)
- Chun-Miao Ji
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Xiao-Yin Feng
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
| | - Yao-Wei Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
- Department of Veterinary Medicine, Zhejiang University, Hangzhou 310058, China
| | - Rui-Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; (C.-M.J.); (X.-Y.F.)
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China;
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2
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Chen PY, Wang JT, Chang SC. Antiviral therapy of coronavirus disease 2019 (COVID-19). J Formos Med Assoc 2024; 123 Suppl 1:S47-S54. [PMID: 37661527 DOI: 10.1016/j.jfma.2023.08.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/05/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has reached a turning point. The non-pharmaceutical interventions for preventing COVID-19 are lifting. Vaccination uptake is increasing in general, but this strategy is continuously challenged by the rapid evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Of note, the Omicron subvariants spread globally for at least one year, and the most recently developed subvariants show strong immune evasion to preexisting immunity, either from previous infection, vaccination or both. Therefore, early and appropriate antiviral agents to treat patients at risk for severe COVID-19 or death is crucial to decrease morbidities and mortalities, to restore the healthcare capacities and to facilitate a return to the new normal. Current antiviral therapy for COVID-19 consist of neutralizing monoclonal antibodies (mAbs) and direct antiviral agents. Each agent has been proved for early ambulatory treatment of COIVD-19, but suffer from variable effectiveness and limitations due to patients' comorbidities, drug properties, or antiviral resistance. Besides, some specific mAbs are indicated for prophylaxis of COVID-19 before or after close contact with confirmed COVID-19 patients. This review article summarizes the evidence and unmet needs of the currently available antiviral agents for management of COVID-19 in the context of the Omicron subvariants.
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Affiliation(s)
- Pao-Yu Chen
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Jann-Tay Wang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; National Institutes of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli, Taiwan.
| | - Shan-Chwen Chang
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; School of Medicine, National Taiwan University College of Medicine, Taipei, Taiwan
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Chin H, Benton MC, Yang L, Poon KS, Tan KML, Jamuar SS, Foo R, Law HY, Goh DL, Chong SS, de Sessions PF. Clinical application of targeted long read sequencing in prenatal beta-thalassemia testing and genetic counseling. Mol Genet Genomic Med 2024; 12:e2285. [PMID: 37740604 PMCID: PMC10767580 DOI: 10.1002/mgg3.2285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 08/18/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Beta thalassemia, related to HBB mutation and associated with elevated hemoglobin A2 (HbA2), is an important genetic hemoglobinopathy with high incidences of disease and carrier rates in Singapore. Carrier screening is essential to facilitate prenatal counseling and testing. However, when individuals with elevated HbA2 do not have an identifiable HBB disease-associated variant, there is ambiguity on risk to their offspring. METHODS We describe a case report of a proband with elevated HbA2, no identifiable HBB disease-associated variant, whose partner was a beta thalassemia carrier. Through clinical HBB gene sequencing, multiplex ligation-dependent probe amplification (MLPA) analysis, as well as targeted Nanopore long read sequencing of selected genes, we performed a complete analysis of HBB including the promoter region, 5'UTR and coding gene sequence, as well as evaluation for potential modifier variants and other rare structural variants. RESULTS This process identified that the proband was heterozygous for KLF1:c.544T>C (p.Phe182Leu), a potential functional polymorphism previously known to be associated with benign elevated HbA2 levels. The presence of disease variants in the HBB locus was excluded. CONCLUSION This finding provided clarity and enabled family planning for the proband and her family.
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Affiliation(s)
- Hui‐Lin Chin
- Division of Genetics and Metabolism, Department of PaediatricsKhoo Teck Puat‐National University Children's Medical Institute, National University HospitalSingaporeSingapore
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | | | - Lin Yang
- Oxford Nanopore TechnologiesSingaporeSingapore
| | - Kok Siong Poon
- Department of Laboratory MedicineNational University HospitalSingaporeSingapore
| | - Karen M. L. Tan
- Department of Laboratory MedicineNational University HospitalSingaporeSingapore
| | - Saumya S. Jamuar
- Genetics Service, Department of PaediatricsKK Women's and Children's HospitalSingaporeSingapore
| | - Roger Foo
- Cardiovascular Research Institute, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Hai Yang Law
- DNA Diagnostic and Research LaboratoryKK Women's and Children's HospitalSingaporeSingapore
| | - Denise Li‐Meng Goh
- Division of Genetics and Metabolism, Department of PaediatricsKhoo Teck Puat‐National University Children's Medical Institute, National University HospitalSingaporeSingapore
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Samuel S. Chong
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Laboratory MedicineNational University HospitalSingaporeSingapore
- Department of Obstetrics and GynaecologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
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Snell LB, McGreal-Bellone A, Nye C, Gage S, Bakrania P, Williams TGS, Aarons E, Botgros A, Douthwaite ST, Mallon P, Milligan I, Moore C, O’Kelly B, Underwood J, de Barra E, Nebbia G. A Multinational Case Series Describing Successful Treatment of Persistent Severe Acute Respiratory Syndrome Coronavirus 2 Infection Caused by Omicron Sublineages With Prolonged Courses of Nirmatrelvir/Ritonavir. Open Forum Infect Dis 2024; 11:ofad612. [PMID: 38269048 PMCID: PMC10807981 DOI: 10.1093/ofid/ofad612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/06/2023] [Indexed: 01/26/2024] Open
Abstract
The optimum treatment for persistent infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is not known. Our case series, across 5 hospitals in 3 countries, describes 11 cases where persistent SARS-CoV-2 infection was successfully treated with prolonged courses (median, 10 days [range, 10-18 days]) of nirmatrelvir/ritonavir (Paxlovid). Most cases (9/11) had hematological malignancy and 10 (10/11) had received CD20-depleting therapy. The median duration of infection was 103 days (interquartile range, 85-138 days). The majority (10/11) were hospitalized, and 7 (7/11) had severe/critical disease. All survived and 9 of 11 demonstrated viral clearance, almost half (4/9) of whom received nirmatrelvir/ritonavir as monotherapy. This case series suggests that prolonged nirmatrelvir/ritonavir has a role in treating persistent infection.
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Affiliation(s)
- Luke B Snell
- Department of Infectious Diseases, King’s College London, London, UK
- Directorate of Infection, Guy’s & St Thomas’ National Health Service Foundation Trust, London, UK
| | | | - Clemency Nye
- Microbiology Department, Public Health Wales, Cardiff, UK
| | - Sarah Gage
- Department of Infectious Diseases, University Hospital of Wales, Cardiff, UK
| | - Prijay Bakrania
- Directorate of Infection, Guy’s & St Thomas’ National Health Service Foundation Trust, London, UK
| | - Tom G S Williams
- Directorate of Infection, Guy’s & St Thomas’ National Health Service Foundation Trust, London, UK
| | - Emma Aarons
- Directorate of Infection, Guy’s & St Thomas’ National Health Service Foundation Trust, London, UK
| | - Alina Botgros
- Directorate of Infection, Guy’s & St Thomas’ National Health Service Foundation Trust, London, UK
| | - Samuel T Douthwaite
- Directorate of Infection, Guy’s & St Thomas’ National Health Service Foundation Trust, London, UK
| | - Patrick Mallon
- Centre for Experimental Pathogen Host Research, University College Dublin, Dublin, Ireland
| | - Iain Milligan
- Directorate of Infection, Guy’s & St Thomas’ National Health Service Foundation Trust, London, UK
| | - Catherine Moore
- Wales Specialist Virology Centre, Public Health Wales, Cardiff, UK
| | - Brendan O’Kelly
- Department of Infectious Diseases, Beaumont Hospital, Dublin, Ireland
- Infectious Diseases, Our Lady of Lourdes Hospital, Drogheda, Ireland
| | - Jonathan Underwood
- Department of Infectious Diseases, University Hospital of Wales, Cardiff, UK
- Division of Infection and Immunity, Cardiff University, Cardiff, UK
| | - Eoghan de Barra
- Department of Infectious Diseases, Beaumont Hospital, Dublin, Ireland
- Department of International Health and Tropical Medicine, Royal College of Surgeons in Ireland, University of Medicine and Health Sciences, Ireland
| | - Gaia Nebbia
- Department of Infectious Diseases, King’s College London, London, UK
- Directorate of Infection, Guy’s & St Thomas’ National Health Service Foundation Trust, London, UK
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Stewart DD. Can Nitazoxanide and/or other anti-viral medications be a solution to long COVID? Case report with a brief literature review. Clin Case Rep 2023; 11:e8162. [PMID: 38028066 PMCID: PMC10654558 DOI: 10.1002/ccr3.8162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/20/2023] [Accepted: 10/21/2023] [Indexed: 12/01/2023] Open
Abstract
Key Clinical Message Findings here imply lingering of virus, SARS-CoV-2, in the body for months. Thus, Nitazoxanide and/or other anti-viral medications might be potential options to combat long COVID. This could transform treatment for long COVID patients globally. Abstract Long COVID or post-acute sequelae of COVID-19 (PASC) continues to affect many people even after a relatively mild acute illness. Underlying causes of PASC are poorly understood. There is no particular treatment or management program developed yet. Thus, the possibility of well-known, safe anti-viral medications use against PASC is proposed here.
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Upasani V, Townsend K, Wu MY, Carr EJ, Hobbs A, Dowgier G, Ragno M, Herman LS, Sharma S, Shah D, Lee SFK, Chauhan N, Glanville JM, Neave L, Hanson S, Ravichandran S, Tynan A, O’Sullivan M, Moreira F, Workman S, Symes A, Burns SO, Tadros S, Hart JCL, Beale RCL, Gandhi S, Wall EC, McCoy L, Lowe DM. Commercial Immunoglobulin Products Contain Neutralizing Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein. Clin Infect Dis 2023; 77:950-960. [PMID: 37338118 PMCID: PMC10552578 DOI: 10.1093/cid/ciad368] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/05/2023] [Accepted: 06/16/2023] [Indexed: 06/21/2023] Open
Abstract
BACKGROUND Patients with antibody deficiency respond poorly to coronavirus disease 2019 (COVID-19) vaccination and are at risk of severe or prolonged infection. They are given long-term immunoglobulin replacement therapy (IRT) prepared from healthy donor plasma to confer passive immunity against infection. Following widespread COVID-19 vaccination alongside natural exposure, we hypothesized that immunoglobulin preparations will now contain neutralizing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike antibodies, which confer protection against COVID-19 disease and may help to treat chronic infection. METHODS We evaluated anti-SARS-CoV-2 spike antibody in a cohort of patients before and after immunoglobulin infusion. Neutralizing capacity of patient samples and immunoglobulin products was assessed using in vitro pseudovirus and live-virus neutralization assays, the latter investigating multiple batches against current circulating Omicron variants. We describe the clinical course of 9 patients started on IRT during treatment of COVID-19. RESULTS In 35 individuals with antibody deficiency established on IRT, median anti-spike antibody titer increased from 2123 to 10 600 U/mL postinfusion, with corresponding increase in pseudovirus neutralization titers to levels comparable to healthy donors. Testing immunoglobulin products directly in the live-virus assay confirmed neutralization, including of BQ1.1 and XBB variants, but with variation between immunoglobulin products and batches.Initiation of IRT alongside remdesivir in patients with antibody deficiency and prolonged COVID-19 infection (median 189 days, maximum >900 days with an ancestral viral strain) resulted in clearance of SARS-CoV-2 at a median of 20 days. CONCLUSIONS Immunoglobulin preparations now contain neutralizing anti-SARS-CoV-2 antibodies that are transmitted to patients and help to treat COVID-19 in individuals with failure of humoral immunity.
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Affiliation(s)
- Vinit Upasani
- Institute of Immunity and Transplantation, University College London (UCL), London, United Kingdom
| | - Katie Townsend
- Department of Clinical Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Mary Y Wu
- COVID Surveillance Unit, Francis Crick Institute, London, United Kingdom
| | - Edward J Carr
- Francis Crick Institute, London, United Kingdom
- Department of Renal Medicine, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Agnieszka Hobbs
- COVID Surveillance Unit, Francis Crick Institute, London, United Kingdom
| | - Giulia Dowgier
- COVID Surveillance Unit, Francis Crick Institute, London, United Kingdom
| | - Martina Ragno
- COVID Surveillance Unit, Francis Crick Institute, London, United Kingdom
| | - Lou S Herman
- COVID Surveillance Unit, Francis Crick Institute, London, United Kingdom
| | - Sonal Sharma
- Department of Elderly Medicine, Barnet Hospital, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Devesh Shah
- Department of Elderly Medicine, Barnet Hospital, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Simon F K Lee
- Department of Infectious Diseases, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Neil Chauhan
- Department of Haematology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Julie M Glanville
- Department of Haematology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Lucy Neave
- Department of Haematology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Steven Hanson
- Department of Haematology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Sriram Ravichandran
- Department of Haematology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Aoife Tynan
- Department of Pharmacy, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Mary O’Sullivan
- Department of Clinical Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Fernando Moreira
- Department of Clinical Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Sarita Workman
- Department of Clinical Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Andrew Symes
- Department of Clinical Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Siobhan O Burns
- Institute of Immunity and Transplantation, University College London (UCL), London, United Kingdom
- Department of Clinical Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Susan Tadros
- Department of Clinical Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
| | - Jennifer C L Hart
- Department of Virology, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Rupert C L Beale
- COVID Surveillance Unit, Francis Crick Institute, London, United Kingdom
- Department of Renal Medicine, Royal Free London NHS Foundation Trust, London, United Kingdom
| | - Sonia Gandhi
- COVID Surveillance Unit, Francis Crick Institute, London, United Kingdom
- UCL Hospitals Biomedical Research Centre, London, United Kingdom
| | - Emma C Wall
- COVID Surveillance Unit, Francis Crick Institute, London, United Kingdom
- UCL Hospitals Biomedical Research Centre, London, United Kingdom
| | - Laura McCoy
- Institute of Immunity and Transplantation, University College London (UCL), London, United Kingdom
| | - David M Lowe
- Institute of Immunity and Transplantation, University College London (UCL), London, United Kingdom
- Department of Clinical Immunology, Royal Free London National Health Service (NHS) Foundation Trust, London, United Kingdom
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Williams TGS, Snell LB, Alder C, Charalampous T, Alcolea-Medina A, Sehmi JK, Al-Yaakoubi N, Humayun G, Miah S, Lackenby A, Zambon M, Batra R, Douthwaite S, Edgeworth JD, Nebbia G. Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance. Microb Genom 2023; 9:mgen001083. [PMID: 37590039 PMCID: PMC10483427 DOI: 10.1099/mgen.0.001083] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 07/18/2023] [Indexed: 08/18/2023] Open
Abstract
Rapid respiratory viral whole genome sequencing (WGS) in a clinical setting can inform real-time outbreak and patient treatment decisions, but the feasibility and clinical utility of influenza A virus (IAV) WGS using Nanopore technology has not been demonstrated. A 24 h turnaround Nanopore IAV WGS protocol was performed on 128 reverse transcriptase PCR IAV-positive nasopharyngeal samples taken over seven weeks of the 2022-2023 winter influenza season, including 25 from patients with nosocomial IAV infections and 102 from patients attending the Emergency Department. WGS results were reviewed collectively alongside clinical details for interpretation and reported to clinical teams. All eight segments of the IAV genome were recovered for 97/128 samples (75.8 %) and the haemagglutinin gene for 117/128 samples (91.4 %). Infection prevention and control identified nosocomial IAV infections in 19 patients across five wards. IAV WGS revealed two separate clusters on one ward and excluded transmission across different wards with contemporaneous outbreaks. IAV WGS also identified neuraminidase inhibitor resistance in a persistently infected patient and excluded avian influenza in a sample taken from an immunosuppressed patient with a history of travel to Singapore which had failed PCR subtyping. Accurate IAV genomes can be generated in 24 h using a Nanopore protocol accessible to any laboratory with SARS-CoV-2 Nanopore sequencing capacity. In addition to replicating reference laboratory surveillance results, IAV WGS can identify antiviral resistance and exclude avian influenza. IAV WGS also informs management of nosocomial outbreaks, though molecular and clinical epidemiology were concordant in this study, limiting the impact on decision-making.
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Affiliation(s)
- Tom G. S. Williams
- Department of Infection, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Luke B. Snell
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
| | - Christopher Alder
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Themoula Charalampous
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Adela Alcolea-Medina
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Infection Sciences, Synnovis, London, UK
| | | | - Noor Al-Yaakoubi
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Gul Humayun
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Shahjahan Miah
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Angie Lackenby
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Maria Zambon
- United Kingdom Health Security Agency (UKHSA), London, UK
| | - Rahul Batra
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Sam Douthwaite
- Department of Infection, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Jonathan D. Edgeworth
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
| | - Gaia Nebbia
- Department of Infection, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Centre for Clinical Diagnostics & Infectious Disease Research, Guy’s & St. Thomas’ NHS Foundation Trust, London, UK
- Department of Infectious Diseases, King’s College London, London, UK
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Zheng P, Zhou C, Ding Y, Liu B, Lu L, Zhu F, Duan S. Nanopore sequencing technology and its applications. MedComm (Beijing) 2023; 4:e316. [PMID: 37441463 PMCID: PMC10333861 DOI: 10.1002/mco2.316] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 07/15/2023] Open
Abstract
Since the development of Sanger sequencing in 1977, sequencing technology has played a pivotal role in molecular biology research by enabling the interpretation of biological genetic codes. Today, nanopore sequencing is one of the leading third-generation sequencing technologies. With its long reads, portability, and low cost, nanopore sequencing is widely used in various scientific fields including epidemic prevention and control, disease diagnosis, and animal and plant breeding. Despite initial concerns about high error rates, continuous innovation in sequencing platforms and algorithm analysis technology has effectively addressed its accuracy. During the coronavirus disease (COVID-19) pandemic, nanopore sequencing played a critical role in detecting the severe acute respiratory syndrome coronavirus-2 virus genome and containing the pandemic. However, a lack of understanding of this technology may limit its popularization and application. Nanopore sequencing is poised to become the mainstream choice for preventing and controlling COVID-19 and future epidemics while creating value in other fields such as oncology and botany. This work introduces the contributions of nanopore sequencing during the COVID-19 pandemic to promote public understanding and its use in emerging outbreaks worldwide. We discuss its application in microbial detection, cancer genomes, and plant genomes and summarize strategies to improve its accuracy.
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Affiliation(s)
- Peijie Zheng
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Chuntao Zhou
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Yuemin Ding
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
| | - Bin Liu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Liuyi Lu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Feng Zhu
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
| | - Shiwei Duan
- Department of Clinical MedicineSchool of MedicineZhejiang University City CollegeHangzhouChina
- Institute of Translational Medicine, School of MedicineZhejiang University City CollegeHangzhouChina
- Key Laboratory of Novel Targets and Drug Study for Neural Repair of Zhejiang Province, School of MedicineZhejiang University City CollegeHangzhouChina
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