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Boulton W, Fidan FR, Denise H, De Maio N, Goldman N. SWAMPy: simulating SARS-CoV-2 wastewater amplicon metagenomes. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae532. [PMID: 39226177 PMCID: PMC11401744 DOI: 10.1093/bioinformatics/btae532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 06/19/2024] [Accepted: 08/31/2024] [Indexed: 09/05/2024]
Abstract
MOTIVATION Tracking SARS-CoV-2 variants through genomic sequencing has been an important part of the global response to the pandemic and remains a useful tool for surveillance of the virus. As well as whole-genome sequencing of clinical samples, this surveillance effort has been aided by amplicon sequencing of wastewater samples, which proved effective in real case studies. Because of its relevance to public healthcare decisions, testing and benchmarking wastewater sequencing analysis methods is also crucial, which necessitates a simulator. Although metagenomic simulators exist, none is fit for the purpose of simulating the metagenomes produced through amplicon sequencing of wastewater. RESULTS Our new simulation tool, SWAMPy (Simulating SARS-CoV-2 Wastewater Amplicon Metagenomes with Python), is intended to provide realistic simulated SARS-CoV-2 wastewater sequencing datasets with which other programs that rely on this type of data can be evaluated and improved. Our tool is suitable for simulating Illumina short-read RT-PCR amplified metagenomes. AVAILABILITY AND IMPLEMENTATION The code for this project is available at https://github.com/goldman-gp-ebi/SWAMPy. It can be installed on any Unix-based operating system and is available under the GPL-v3 license.
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Affiliation(s)
- William Boulton
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambs CB10 1SD, United Kingdom
- Department of Computing Sciences, University of East Anglia, Norwich, Norfolk NR4 7TJ, United Kingdom
| | - Fatma Rabia Fidan
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambs CB10 1SD, United Kingdom
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Cancer Dynamics Laboratory, Francis Crick Institute, London NW1 1AT, United Kingdom
| | - Hubert Denise
- Department of Health and Social Care, UK Health Security Agency, London SW1P 3HX, United Kingdom
| | - Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambs CB10 1SD, United Kingdom
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambs CB10 1SD, United Kingdom
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2
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Goldswain H, Penrice-Randal R, Donovan-Banfield I, Duffy CW, Dong X, Randle N, Ryan Y, Rzeszutek AM, Pilgrim J, Keyser E, Weller SA, Hutley EJ, Hartley C, Prince T, Darby AC, Aye Maung N, Nwume H, Hiscox JA, Emmett SR. SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection. Genome Med 2024; 16:89. [PMID: 39014481 PMCID: PMC11251137 DOI: 10.1186/s13073-024-01360-1] [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: 09/23/2023] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND SARS-CoV-2 remains rapidly evolving, and many biologically important genomic substitutions/indels have characterised novel SARS-CoV-2 lineages, which have emerged during successive global waves of the pandemic. Worldwide genomic sequencing has been able to monitor these waves, track transmission clusters, and examine viral evolution in real time to help inform healthcare policy. One school of thought is that an apparent greater than average divergence in an emerging lineage from contemporary variants may require persistent infection, for example in an immunocompromised host. Due to the nature of the COVID-19 pandemic and sampling, there were few studies that examined the evolutionary trajectory of SARS-CoV-2 in healthy individuals. METHODS We investigated viral evolutionary trends and participant symptomatology within a cluster of 16 SARS-CoV-2 infected, immunocompetent individuals with no co-morbidities in a closed transmission chain. Longitudinal nasopharyngeal swab sampling allowed characterisation of SARS-CoV-2 intra-host variation over time at both the dominant and minor genomic variant levels through Nimagen-Illumina sequencing. RESULTS A change in viral lineage assignment was observed in individual infections; however, there was only one indel and no evidence of recombination over the period of an acute infection. Minor and dominant genomic modifications varied between participants, with some minor genomic modifications increasing in abundance to become the dominant viral sequence during infection. CONCLUSIONS Data from this cohort of SARS-CoV-2-infected participants demonstrated that long-term persistent infection in an immunocompromised host was not necessarily a prerequisite for generating a greater than average frequency of amino acid substitutions. Amino acid substitutions at both the dominant and minor genomic sequence level were observed in immunocompetent individuals during infection showing that viral lineage changes can occur generating viral diversity.
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Affiliation(s)
- Hannah Goldswain
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Rebekah Penrice-Randal
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - I'ah Donovan-Banfield
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Craig W Duffy
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Xiaofeng Dong
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Nadine Randle
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Yan Ryan
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | | | - Jack Pilgrim
- Centre for Genomic Research, University of Liverpool, Liverpool, L69 3BX, UK
| | - Emma Keyser
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK
| | - Simon A Weller
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK
| | - Emma J Hutley
- Centre for Defence Pathology, Royal Centre for Defence Medicine, OCT Centre, Birmingham, B15 2WB, UK
| | - Catherine Hartley
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Tessa Prince
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Alistair C Darby
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Niall Aye Maung
- British Army, Hunter House, St Omer Barracks, Aldershot, Hampshire, GU11 2BG, UK
| | - Henry Nwume
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK
| | - Julian A Hiscox
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK.
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Connexis North Tower, 1 Fusionopolis Way, Singapore, #20-10138632, Singapore.
| | - Stevan R Emmett
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK.
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Drouin N, Elfrink HL, Boers SA, van Hugten S, Wessels E, de Vries JJC, Groeneveld GH, Miggiels P, Van Puyvelde B, Dhaenens M, Budding AE, Ran L, Masius R, Takats Z, Boogaerds A, Bulters M, Muurlink W, Oostvogel P, Harms AC, van der Lubben M, Hankemeier T. A Targeted LC-MRM 3 Proteomic Approach for the Diagnosis of SARS-CoV-2 Infection in Nasopharyngeal Swabs. Mol Cell Proteomics 2024; 23:100805. [PMID: 38897290 PMCID: PMC11284538 DOI: 10.1016/j.mcpro.2024.100805] [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: 12/09/2023] [Revised: 05/30/2024] [Accepted: 06/16/2024] [Indexed: 06/21/2024] Open
Abstract
Since its first appearance, severe acute respiratory syndrome coronavirus 2 quickly spread around the world and the lack of adequate PCR testing capacities, especially during the early pandemic, led the scientific community to explore new approaches such as mass spectrometry (MS). We developed a proteomics workflow to target several tryptic peptides of the nucleocapsid protein. A highly selective multiple reaction monitoring-cubed (MRM3) strategy provided a sensitivity increase in comparison to conventional MRM acquisition. Our MRM3 approach was first tested on an Amsterdam public health cohort (alpha-variant, 760 participants) detecting viral nucleocapsid protein peptides from nasopharyngeal swabs samples presenting a cycle threshold value down to 35 with sensitivity and specificity of 94.2% and 100.0%, without immunopurification. A second iteration of the MS-diagnostic test, able to analyze more than 400 samples per day, was clinically validated on a Leiden-Rijswijk public health cohort (delta-variant, 2536 participants) achieving 99.9% specificity and 93.1% sensitivity for patients with cycle threshold values up to 35. In this manuscript, we also developed and brought the first proof of the concept of viral variant monitoring in a complex matrix using targeted MS.
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Affiliation(s)
- Nicolas Drouin
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
| | - Hyung L Elfrink
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Stefan A Boers
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands
| | - Sam van Hugten
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands
| | - Els Wessels
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands
| | - Jutte J C de Vries
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands
| | - Geert H Groeneveld
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center, Leiden, The Netherlands; Department of Internal Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Paul Miggiels
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | | | | | | | - Zoltan Takats
- Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | | | | | | | - Paul Oostvogel
- Regional Laboratory, Municipal Health Service (GGD) Amsterdam, Amsterdam, The Netherlands
| | - Amy C Harms
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands
| | - Mariken van der Lubben
- Regional Laboratory, Municipal Health Service (GGD) Amsterdam, Amsterdam, The Netherlands
| | - Thomas Hankemeier
- Metabolomics and Analytics Centre, Leiden Academic Center for Drug Research, Leiden University, Leiden, The Netherlands.
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Penrice-Randal R, Bentley EG, Sharma P, Kirby A, Donovan-Banfield I, Kipar A, Mega DF, Bramwell C, Sharp J, Owen A, Hiscox JA, Stewart JP. The effect of molnupiravir and nirmatrelvir on SARS-CoV-2 genome diversity in severe models of COVID-19. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.27.582110. [PMID: 38464327 PMCID: PMC10925244 DOI: 10.1101/2024.02.27.582110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Objectives Immunocompromised individuals are susceptible to severe COVID-19 and potentially contribute to the emergence of variants with altered pathogenicity due to persistent infection. This study investigated the impact of immunosuppression on SARS-CoV-2 infection in k18-hACE2 mice and the effectiveness of antiviral treatments in this context during the first 7 days of infection. Methods Mice were immunosuppressed using cyclophosphamide and infected with a B lineage of SARS-CoV-2. Molnupiravir and nirmatrelvir, alone and in combination, were administered and viral load and viral sequence diversity was assessed. Results Treatment of infected but immune compromised mice with both compounds either singly or in combination resulted in decreased viral loads and pathological changes compared to untreated animals. Treatment also abrogated infection of neuronal tissue. However, no consistent changes in the viral consensus sequence were observed, except for the emergence of the S:H655Y mutation. Molnupiravir, but not nirmatrelvir or immunosuppression alone, increased the transition/transversion (Ts/Tv) ratio, representative of A>G and C>U mutations and this increase was not altered by the co-administration of nirmatrelvir with molnupiravir.Notably, immunosuppression itself did not appear to promote the emergence of mutational characteristic of variants of concern (VOCs). Conclusions Further investigations are warranted to fully understand the role of immunocompromised individuals in VOC development, especially by taking persistence into consideration, and to inform optimised public health strategies. It is more likely that immunodeficiency promotes viral persistence but does not necessarily lead to substantial consensus-level changes in the absence of antiviral selection pressure. Consistent with mechanisms of action, molnupiravir showed a stronger mutagenic effect than nirmatrelvir in this model.
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Affiliation(s)
| | - Eleanor G. Bentley
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Parul Sharma
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Adam Kirby
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - I’ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Anja Kipar
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Laboratory for Animal Model Pathology, Institute of Veterinary Pathology, Vetsuisse Faculty, University of Zurich, Switzerland
| | - Daniele F. Mega
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Chloe Bramwell
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
| | - Joanne Sharp
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Andrew Owen
- Department of Pharmacology and Therapeutics, University of Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
| | - Julian A. Hiscox
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - James P. Stewart
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
- Centre of Excellence in Long-acting Therapeutics (CELT), University of Liverpool, UK
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5
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Li J, Zhang K, Lin G, Li J. CRISPR-Cas system: A promising tool for rapid detection of SARS-CoV-2 variants. J Med Virol 2024; 96:e29356. [PMID: 38180237 DOI: 10.1002/jmv.29356] [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: 06/04/2023] [Revised: 12/05/2023] [Accepted: 12/17/2023] [Indexed: 01/06/2024]
Abstract
COVID-19, caused by SARS-CoV-2, remains a global health crisis. The emergence of multiple variants with enhanced characteristics necessitates their detection and monitoring. Genome sequencing, the gold standard, faces implementation challenges due to complexity, cost, and limited throughput. The CRISPR-Cas system offers promising potential for rapid variant detection, with advantages such as speed, sensitivity, specificity, and programmability. This review provides an in-depth examination of the applications of CRISPR-Cas in mutation detection specifically for SARS-CoV-2. It begins by introducing SARS-CoV-2 and existing variant detection platforms. The principles of the CRISPR-Cas system are then clarified, followed by an exploration of three CRISPR-Cas-based mutation detection platforms, which are evaluated from different perspectives. The review discusses strategies for mutation site selection and the utilization of CRISPR-Cas, offering valuable insights for the development of mutation detection methods. Furthermore, a critical analysis of the clinical applications, advantages, disadvantages, challenges, and prospects of the CRISPR-Cas system is provided.
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Affiliation(s)
- Jing Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital/National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
- Graduate School, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
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Leontidou K, Abad-Recio IL, Rubel V, Filker S, Däumer M, Thielen A, Lanzén A, Stoeck T. Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection. Environ Microbiol 2023; 25:3484-3501. [PMID: 37974518 DOI: 10.1111/1462-2920.16530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 10/19/2023] [Indexed: 11/19/2023]
Abstract
Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one-fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)-PCR-based assay that amplifies seven out of the nine hypervariable regions of the 16S rRNA gene, to interrogate bacterial communities in sediment samples collected from different coastal marine sites with an impact gradient. In parallel, we employed a traditional one-fragment analysis of the hypervariable V3-V4 region to investigate whether the RC-PCR reveals more of the 'unseen' diversity obtained by the one-fragment approach. As a benchmark for the full deck of diversity, we subjected the samples to PCR-free metagenomic sequencing. None of the two PCR-based approaches recorded the full taxonomic repertoire obtained from the metagenomics datasets. However, the RC-PCR approach detected 2.8 times more bacterial genera compared to the near-saturation sequenced V3-V4 samples. RC-PCR is an ideal compromise between the standard one-fragment approach and metagenomics sequencing and may guide future environmental sequencing studies, in which bacterial diversity is a central subject.
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Affiliation(s)
- Kleopatra Leontidou
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Ion L Abad-Recio
- Marine Ecosystems Functioning, AZTI, Marine Research, Basque Research and Technology Alliance, Pasia, Gipuzkoa, Spain
| | - Verena Rubel
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Sabine Filker
- Molecular Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
| | - Martin Däumer
- SeqIT, Laboratory for Molecular Diagnostics and Services, Kaiserslautern, Germany
| | - Alexander Thielen
- SeqIT, Laboratory for Molecular Diagnostics and Services, Kaiserslautern, Germany
| | - Anders Lanzén
- Marine Ecosystems Functioning, AZTI, Marine Research, Basque Research and Technology Alliance, Pasia, Gipuzkoa, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Bizkaia, Spain
| | - Thorsten Stoeck
- Ecology Group, Rheinland-Pfälzische Technische Universität Kaiserslautern-Landau, Kaiserslautern, Germany
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7
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Hare D, Dembicka KM, Brennan C, Campbell C, Sutton-Fitzpatrick U, Stapleton PJ, De Gascun CF, Dunne CP. Whole-genome sequencing to investigate transmission of SARS-CoV-2 in the acute healthcare setting: a systematic review. J Hosp Infect 2023; 140:139-155. [PMID: 37562592 DOI: 10.1016/j.jhin.2023.08.002] [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: 05/30/2023] [Revised: 07/03/2023] [Accepted: 08/04/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Whole-genome sequencing (WGS) has been used widely to elucidate transmission of SARS-CoV-2 in acute healthcare settings, and to guide infection, prevention, and control (IPC) responses. AIM To systematically appraise available literature, published between January 1st, 2020 and June 30th, 2022, describing the implementation of WGS in acute healthcare settings to characterize nosocomial SARS-CoV-2 transmission. METHODS Searches of the PubMed, Embase, Ovid MEDLINE, EBSCO MEDLINE, and Cochrane Library databases identified studies in English reporting the use of WGS to investigate SARS-CoV-2 transmission in acute healthcare environments. Publications involved data collected up to December 31st, 2021, and findings were reported in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. FINDINGS In all, 3088 non-duplicate records were retrieved; 97 met inclusion criteria, involving 62 outbreak analyses and 35 genomic surveillance studies. No publications from low-income countries were identified. In 87/97 (90%), WGS supported hypotheses for nosocomial transmission, while in 46 out of 97 (47%) suspected transmission events were excluded. An IPC intervention was attributed to the use of WGS in 18 out of 97 (18%); however, only three (3%) studies reported turnaround times ≤7 days facilitating near real-time IPC action, and none reported an impact on the incidence of nosocomial COVID-19 attributable to WGS. CONCLUSION WGS can elucidate transmission of SARS-CoV-2 in acute healthcare settings to enhance epidemiological investigations. However, evidence was not identified to support sequencing as an intervention to reduce the incidence of SARS-CoV-2 in hospital or to alter the trajectory of active outbreaks.
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Affiliation(s)
- D Hare
- UCD National Virus Reference Laboratory, University College Dublin, Ireland; School of Medicine, University of Limerick, Limerick, Ireland.
| | - K M Dembicka
- School of Medicine, University of Limerick, Limerick, Ireland
| | - C Brennan
- UCD National Virus Reference Laboratory, University College Dublin, Ireland
| | - C Campbell
- UCD National Virus Reference Laboratory, University College Dublin, Ireland
| | | | | | - C F De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, Ireland
| | - C P Dunne
- School of Medicine, University of Limerick, Limerick, Ireland; Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
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8
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Moorlag SJCFM, Coolen JPM, van den Bosch B, Jin EHM, Buil JB, Wertheim HFL, Melchers WJG. Targeting the 16S rRNA Gene by Reverse Complement PCR Next-Generation Sequencing: Specific and Sensitive Detection and Identification of Microbes Directly in Clinical Samples. Microbiol Spectr 2023; 11:e0448322. [PMID: 37227289 PMCID: PMC10269728 DOI: 10.1128/spectrum.04483-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/09/2023] [Indexed: 05/26/2023] Open
Abstract
The detection and accurate identification of bacterial species in clinical samples are crucial for diagnosis and appropriate antibiotic treatment. To date, sequencing of the 16S rRNA gene has been widely used as a complementary molecular approach when identification by culture fails. The accuracy and sensitivity of this method are highly affected by the selection of the 16S rRNA gene region targeted. In this study, we assessed the clinical utility of 16S rRNA reverse complement PCR (16S RC-PCR), a novel method based on next-generation sequencing (NGS), for the identification of bacterial species. We investigated the performance of 16S RC-PCR on 11 bacterial isolates, 2 polymicrobial community samples, and 59 clinical samples from patients suspected of having a bacterial infection. The results were compared to culture results, if available, and to the results of Sanger sequencing of the 16S rRNA gene (16S Sanger sequencing). By 16S RC-PCR, all bacterial isolates were accurately identified to the species level. Furthermore, in culture-negative clinical samples, the rate of identification increased from 17.1% (7/41) to 46.3% (19/41) when comparing 16S Sanger sequencing to 16S RC-PCR. We conclude that the use of 16S RC-PCR in the clinical setting leads to an increased sensitivity of detection of bacterial pathogens, resulting in a higher number of diagnosed bacterial infections, and thereby can improve patient care. IMPORTANCE The identification of the causative infectious pathogen in patients suspected of having a bacterial infection is essential for diagnosis and the start of appropriate treatment. Over the past 2 decades, molecular diagnostics have improved the ability to detect and identify bacteria. However, novel techniques that can accurately detect and identify bacteria in clinical samples and that can be implemented in clinical diagnostics are needed. Here, we demonstrate the clinical utility of bacterial identification in clinical samples by a novel method called 16S RC-PCR. Using 16S RC-PCR, we reveal a significant increase in the number of clinical samples in which a potentially clinically relevant pathogen is identified compared to the commonly used 16S Sanger method. Moreover, RC-PCR allows automation and is well suited for implementation in a diagnostic laboratory. In conclusion, the implementation of this method as a diagnostic tool is expected to result in an increased number of diagnosed bacterial infections, and in combination with adequate treatment, this could improve clinical outcomes for patients.
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Affiliation(s)
- Simone J. C. F. M. Moorlag
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Bart van den Bosch
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Elisabeth Hui-Mei Jin
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Jochem B. Buil
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Heiman F. L. Wertheim
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboudumc, Nijmegen, The Netherlands
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9
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Maschietto C, Otto G, Rouzé P, Debortoli N, Bihin B, Nyinkeu L, Denis O, Huang TD, Mullier F, Bogaerts P, Degosserie J. Minimal requirements for ISO15189 validation and accreditation of three next generation sequencing procedures for SARS-CoV-2 surveillance in clinical setting. Sci Rep 2023; 13:6934. [PMID: 37117393 PMCID: PMC10140720 DOI: 10.1038/s41598-023-34088-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 04/24/2023] [Indexed: 04/30/2023] Open
Abstract
Rapid and recurrent breakthroughs of new SARS-CoV-2 strains (variants) have prompted public health authorities worldwide to set up surveillance networks to monitor the circulation of variants of concern. The use of next-generation sequencing technologies has raised the need for quality control assessment as required in clinical laboratories. The present study is the first to propose a validation guide for SARS-CoV-2 typing using three different NGS methods fulfilling ISO15189 standards. These include the assessment of the risk, specificity, accuracy, reproducibility, and repeatability of the methods. Among the three methods used, two are amplicon-based involving reverse transcription polymerase chain reaction (Artic v3 and Midnight v1) on Oxford Nanopore Technologies while the third one is amplicon-based using reverse complement polymerase chain reaction (Nimagen) on Illumina technology. We found that all methods met the quality requirement (e.g., 100% concordant typing results for accuracy, reproducibility, and repeatability) for SARS-CoV-2 typing in clinical setting. Additionally, the typing results emerging from each of the three sequencing methods were compared using three widely known nomenclatures (WHO, Pangolineage, and Nextclade). They were also compared regarding single nucleotide variations. The outcomes showed that Artic v3 and Nimagen should be privileged for outbreak investigation as they provide higher quality results for samples that do not meet inclusion criteria for analysis in a clinical setting. This study is a first step towards validation of laboratory developed NGS tests in the context of the new European regulation for medical devices and in vitro diagnostics.
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Affiliation(s)
- Céline Maschietto
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
| | - Gaëtan Otto
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
| | - Pauline Rouzé
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Nicolas Debortoli
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Benoît Bihin
- Scientific Support Unit, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Lesly Nyinkeu
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
- Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Olivier Denis
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Te-Din Huang
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - François Mullier
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium
| | - Pierre Bogaerts
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium
- Laboratory of Microbiology, CHU UCL Namur, 5530, Yvoir, Belgium
| | - Jonathan Degosserie
- Department of Laboratory Medicine, UCLouvain, CHU UCL Namur, 5530, Yvoir, Belgium.
- COVID-19 Federal Testing Platform Bis, CHU UCL Namur & UNamur, 5530, Yvoir, Belgium.
- Namur Molecular Tech, CHU UCL Namur, 5530, Yvoir, Belgium.
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10
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Child HT, O’Neill PA, Moore K, Rowe W, Denise H, Bass D, Wade MJ, Loose M, Paterson S, van Aerle R, Jeffries AR. Optimised protocol for monitoring SARS-CoV-2 in wastewater using reverse complement PCR-based whole-genome sequencing. PLoS One 2023; 18:e0284211. [PMID: 37058515 PMCID: PMC10104291 DOI: 10.1371/journal.pone.0284211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/24/2023] [Indexed: 04/15/2023] Open
Abstract
Monitoring the spread of viral pathogens in the population during epidemics is crucial for mounting an effective public health response. Understanding the viral lineages that constitute the infections in a population can uncover the origins and transmission patterns of outbreaks and detect the emergence of novel variants that may impact the course of an epidemic. Population-level surveillance of viruses through genomic sequencing of wastewater captures unbiased lineage data, including cryptic asymptomatic and undiagnosed infections, and has been shown to detect infection outbreaks and novel variant emergence before detection in clinical samples. Here, we present an optimised protocol for quantification and sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in influent wastewater, used for high-throughput genomic surveillance in England during the COVID-19 pandemic. This protocol utilises reverse compliment PCR for library preparation, enabling tiled amplification across the whole viral genome and sequencing adapter addition in a single step to enhance efficiency. Sequencing of synthetic SARS-CoV-2 RNA provided evidence validating the efficacy of this protocol, while data from high-throughput sequencing of wastewater samples demonstrated the sensitivity of this method. We also provided guidance on the quality control steps required during library preparation and data analysis. Overall, this represents an effective method for high-throughput sequencing of SARS-CoV-2 in wastewater which can be applied to other viruses and pathogens of humans and animals.
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Affiliation(s)
- Harry T. Child
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Paul A. O’Neill
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Karen Moore
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - William Rowe
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
| | - Hubert Denise
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Weymouth, United Kingdom
| | - Matthew J. Wade
- Analytics & Data Science Directorate, UK Health Security Agency, London, United Kingdom
| | - Matt Loose
- Deep Seq, Centre for Genetics and Genomics, Queen’s Medical Centre, The University of Nottingham, Nottingham, United Kingdom
| | - Steve Paterson
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ronny van Aerle
- International Centre of Excellence for Aquatic Animal Health, Weymouth, United Kingdom
| | - Aaron R. Jeffries
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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11
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Carbo EC, Mourik K, Boers SA, Munnink BO, Nieuwenhuijse D, Jonges M, Welkers MRA, Matamoros S, van Harinxma Thoe Slooten J, Kraakman MEM, Karelioti E, van der Meer D, Veldkamp KE, Kroes ACM, Sidorov I, de Vries JJC. A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2. Eur J Clin Microbiol Infect Dis 2023; 42:701-713. [PMID: 37017810 PMCID: PMC10075175 DOI: 10.1007/s10096-023-04590-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 03/14/2023] [Indexed: 04/06/2023]
Abstract
Rapid identification of the rise and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern remains critical for monitoring of the efficacy of diagnostics, therapeutics, vaccines, and control strategies. A wide range of SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over the last years, but cross-sequence technology benchmarking studies have been scarce. In the current study, 26 clinical samples were sequenced using five protocols: AmpliSeq SARS-CoV-2 (Illumina), EasySeq RC-PCR SARS-CoV-2 (Illumina/NimaGen), Ion AmpliSeq SARS-CoV-2 (Thermo Fisher), custom primer sets (Oxford Nanopore Technologies (ONT)), and capture probe-based viral metagenomics (Roche/Illumina). Studied parameters included genome coverage, depth of coverage, amplicon distribution, and variant calling. The median SARS-CoV-2 genome coverage of samples with cycle threshold (Ct) values of 30 and lower ranged from 81.6 to 99.8% for, respectively, the ONT protocol and Illumina AmpliSeq protocol. Correlation of coverage with PCR Ct values varied per protocol. Amplicon distribution signatures differed across the methods, with peak differences of up to 4 log10 at disbalanced positions in samples with high viral loads (Ct values ≤ 23). Phylogenetic analyses of consensus sequences showed clustering independent of the workflow used. The proportion of SARS-CoV-2 reads in relation to background sequences, as a (cost-)efficiency metric, was the highest for the EasySeq protocol. The hands-on time was the lowest when using EasySeq and ONT protocols, with the latter additionally having the shortest sequence runtime. In conclusion, the studied protocols differed on a variety of the studied metrics. This study provides data that assist laboratories when selecting protocols for their specific setting.
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Affiliation(s)
- Ellen C Carbo
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Kees Mourik
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Stefan A Boers
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Bas Oude Munnink
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - David Nieuwenhuijse
- Department of Viroscience, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Marcel Jonges
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Matthijs R A Welkers
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Sebastien Matamoros
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Joost van Harinxma Thoe Slooten
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Margriet E M Kraakman
- Clinical Microbiological Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Karin Ellen Veldkamp
- Clinical Microbiological Laboratory, Department of Medical Microbiology, 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
| | - Igor Sidorov
- 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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12
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Khoo SH, FitzGerald R, Saunders G, Middleton C, Ahmad S, Edwards CJ, Hadjiyiannakis D, Walker L, Lyon R, Shaw V, Mozgunov P, Periselneris J, Woods C, Bullock K, Hale C, Reynolds H, Downs N, Ewings S, Buadi A, Cameron D, Edwards T, Knox E, Donovan-Banfield I, Greenhalf W, Chiong J, Lavelle-Langham L, Jacobs M, Northey J, Painter W, Holman W, Lalloo DG, Tetlow M, Hiscox JA, Jaki T, Fletcher T, Griffiths G, Hayden F, Darbyshire J, Lucas A, Lorch U, Freedman A, Knight R, Julious S, Byrne R, Cubas Atienzar A, Jones J, Williams C, Song A, Dixon J, Alexandersson A, Hatchard P, Tilt E, Titman A, Doce Carracedo A, Chandran Gorner V, Davies A, Woodhouse L, Carlucci N, Okenyi E, Bula M, Dodd K, Gibney J, Dry L, Rashid Gardner Z, Sammour A, Cole C, Rowland T, Tsakiroglu M, Yip V, Osanlou R, Stewart A, Parker B, Turgut T, Ahmed A, Starkey K, Subin S, Stockdale J, Herring L, Baker J, Oliver A, Pacurar M, Owens D, Munro A, Babbage G, Faust S, Harvey M, Pratt D, Nagra D, Vyas A. Molnupiravir versus placebo in unvaccinated and vaccinated patients with early SARS-CoV-2 infection in the UK (AGILE CST-2): a randomised, placebo-controlled, double-blind, phase 2 trial. THE LANCET. INFECTIOUS DISEASES 2023; 23:183-195. [PMID: 36272432 PMCID: PMC9662684 DOI: 10.1016/s1473-3099(22)00644-2] [Citation(s) in RCA: 44] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 09/06/2022] [Accepted: 09/12/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The antiviral drug molnupiravir was licensed for treating at-risk patients with COVID-19 on the basis of data from unvaccinated adults. We aimed to evaluate the safety and virological efficacy of molnupiravir in vaccinated and unvaccinated individuals with COVID-19. METHODS This randomised, placebo-controlled, double-blind, phase 2 trial (AGILE CST-2) was done at five National Institute for Health and Care Research sites in the UK. Eligible participants were adult (aged ≥18 years) outpatients with PCR-confirmed, mild-to-moderate SARS-CoV-2 infection who were within 5 days of symptom onset. Using permuted blocks (block size 2 or 4) and stratifying by site, participants were randomly assigned (1:1) to receive either molnupiravir (orally; 800 mg twice daily for 5 days) plus standard of care or matching placebo plus standard of care. The primary outcome was the time from randomisation to SARS-CoV-2 PCR negativity on nasopharyngeal swabs and was analysed by use of a Bayesian Cox proportional hazards model for estimating the probability of a superior virological response (hazard ratio [HR]>1) for molnupiravir versus placebo. Our primary model used a two-point prior based on equal prior probabilities (50%) that the HR was 1·0 or 1·5. We defined a priori that if the probability of a HR of more than 1 was more than 80% molnupiravir would be recommended for further testing. The primary outcome was analysed in the intention-to-treat population and safety was analysed in the safety population, comprising participants who had received at least one dose of allocated treatment. This trial is registered in ClinicalTrials.gov, NCT04746183, and the ISRCTN registry, ISRCTN27106947, and is ongoing. FINDINGS Between Nov 18, 2020, and March 16, 2022, 1723 patients were assessed for eligibility, of whom 180 were randomly assigned to receive either molnupiravir (n=90) or placebo (n=90) and were included in the intention-to-treat analysis. 103 (57%) of 180 participants were female and 77 (43%) were male and 90 (50%) participants had received at least one dose of a COVID-19 vaccine. SARS-CoV-2 infections with the delta (B.1.617.2; 72 [40%] of 180), alpha (B.1.1.7; 37 [21%]), omicron (B.1.1.529; 38 [21%]), and EU1 (B.1.177; 28 [16%]) variants were represented. All 180 participants received at least one dose of treatment and four participants discontinued the study (one in the molnupiravir group and three in the placebo group). Participants in the molnupiravir group had a faster median time from randomisation to negative PCR (8 days [95% CI 8-9]) than participants in the placebo group (11 days [10-11]; HR 1·30, 95% credible interval 0·92-1·71; log-rank p=0·074). The probability of molnupiravir being superior to placebo (HR>1) was 75·4%, which was less than our threshold of 80%. 73 (81%) of 90 participants in the molnupiravir group and 68 (76%) of 90 participants in the placebo group had at least one adverse event by day 29. One participant in the molnupiravir group and three participants in the placebo group had an adverse event of a Common Terminology Criteria for Adverse Events grade 3 or higher severity. No participants died (due to any cause) during the trial. INTERPRETATION We found molnupiravir to be well tolerated and, although our predefined threshold was not reached, we observed some evidence that molnupiravir has antiviral activity in vaccinated and unvaccinated individuals infected with a broad range of SARS-CoV-2 variants, although this evidence is not conclusive. FUNDING Ridgeback Biotherapeutics, the UK National Institute for Health and Care Research, the Medical Research Council, and the Wellcome Trust.
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Affiliation(s)
- Saye H Khoo
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK; Tropical and Infectious Disease Unit, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK.
| | - Richard FitzGerald
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK,NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Geoffrey Saunders
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Calley Middleton
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Shazaad Ahmad
- NIHR Manchester Clinical Research Facility, Manchester University NHS Foundation Trust, Manchester, UK
| | - Christopher J Edwards
- Human Development and Health School, University of Southampton, Southampton, UK,NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Dennis Hadjiyiannakis
- NIHR Lancashire Clinical Research Facility, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Lauren Walker
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK,NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Rebecca Lyon
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Victoria Shaw
- Clinical Directorate, University of Liverpool, Liverpool, UK
| | - Pavel Mozgunov
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Jimstan Periselneris
- NIHR Kings Clinical Research Facility, King's College Hospital NHS Foundation Trust, London, UK
| | - Christie Woods
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Katie Bullock
- Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Colin Hale
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK
| | - Helen Reynolds
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Nichola Downs
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Sean Ewings
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Amanda Buadi
- NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - David Cameron
- NIHR Lancashire Clinical Research Facility, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | | | - Emma Knox
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - I'ah Donovan-Banfield
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK,National Institute of Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - William Greenhalf
- Molecular & Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Justin Chiong
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | | | - Michael Jacobs
- Infectious Diseases, Royal Free London NHS Foundation Trust, London, UK
| | - Josh Northey
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | | | | | | | - Michelle Tetlow
- Pharmacology and Therapeutics, University of Liverpool, Liverpool, UK
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK,National Institute of Health Research Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool, Liverpool, UK
| | - Thomas Jaki
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK,Computational Statistics, University of Regensburg, Regensburg, Germany
| | - Thomas Fletcher
- Tropical and Infectious Disease Unit, Liverpool University Hospital NHS Foundation Trust, Liverpool, UK,Clinical Sciences, Liverpool, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
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13
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Li M, Ge H, Sun Z, Fu J, Cao L, Feng X, Meng G, Peng Y, Liu Y, Zhao C. A loop-mediated isothermal amplification-enabled analytical assay for the detection of SARS-CoV-2: A review. Front Cell Infect Microbiol 2022; 12:1068015. [PMID: 36619749 PMCID: PMC9816412 DOI: 10.3389/fcimb.2022.1068015] [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: 10/12/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The number of words: 4645, the number of figures: 4, the number of tables: 1The outbreak of COVID-19 in December 2019 caused a global pandemic of acute respiratory disease, and with the increasing virulence of mutant strains and the number of confirmed cases, this has resulted in a tremendous threat to global public health. Therefore, an accurate diagnosis of COVID-19 is urgently needed for rapid control of SARS-CoV-2 transmission. As a new molecular biology technology, loop-mediated isothermal amplification (LAMP) has the advantages of convenient operation, speed, low cost and high sensitivity and specificity. In the past two years, rampant COVID-19 and the continuous variation in the virus strains have demanded higher requirements for the rapid detection of pathogens. Compared with conventional RT-PCR and real-time RT-PCR methods, genotyping RT-LAMP method and LAMP plus peptide nucleic acid (PNA) probe detection methods have been developed to correctly identified SARS-CoV-2 variants, which is also why LAMP technology has attracted much attention. LAMP detection technology combined with lateral flow assay, microfluidic technology and other sensing technologies can effectively enhance signals by nucleic acid amplification and help to give the resulting output in a faster, more convenient and user-friendly way. At present, LAMP plays an important role in the detection of SARS-CoV-2.
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Affiliation(s)
- Mingna Li
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Hongjuan Ge
- College of public health, Jilin Medical University, Jilin, China
| | - Zhe Sun
- College of public health, Jilin Medical University, Jilin, China,College of medical technology, Beihua University, Jilin, China
| | - Jangshan Fu
- College of public health, Jilin Medical University, Jilin, China
| | - Lele Cao
- College of public health, Jilin Medical University, Jilin, China
| | - Xinrui Feng
- College of public health, Jilin Medical University, Jilin, China,Medical college, Yanbian University, Jilin, China
| | - Guixian Meng
- College of medical laboratory, Jilin Medical University, Jilin, China
| | - Yubo Peng
- Business School, The University of Adelaide, Adelaide, SA, Australia
| | - Yan Liu
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
| | - Chen Zhao
- College of public health, Jilin Medical University, Jilin, China,*Correspondence: Yan Liu, ; Chen Zhao,
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14
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Donovan-Banfield I, Penrice-Randal R, Goldswain H, Rzeszutek AM, Pilgrim J, Bullock K, Saunders G, Northey J, Dong X, Ryan Y, Reynolds H, Tetlow M, Walker LE, FitzGerald R, Hale C, Lyon R, Woods C, Ahmad S, Hadjiyiannakis D, Periselneris J, Knox E, Middleton C, Lavelle-Langham L, Shaw V, Greenhalf W, Edwards T, Lalloo DG, Edwards CJ, Darby AC, Carroll MW, Griffiths G, Khoo SH, Hiscox JA, Fletcher T. Characterisation of SARS-CoV-2 genomic variation in response to molnupiravir treatment in the AGILE Phase IIa clinical trial. Nat Commun 2022; 13:7284. [PMID: 36435798 PMCID: PMC9701236 DOI: 10.1038/s41467-022-34839-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 11/09/2022] [Indexed: 11/28/2022] Open
Abstract
Molnupiravir is an antiviral, currently approved by the UK Medicines and Healthcare products Regulatory Agency (MHRA) for treating at-risk COVID-19 patients, that induces lethal error catastrophe in SARS-CoV-2. How this drug-induced mechanism of action might impact the emergence of resistance mutations is unclear. To investigate this, we used samples from the AGILE Candidate Specific Trial (CST)-2 (clinical trial number NCT04746183). The primary outcomes of AGILE CST-2 were to measure the drug safety and antiviral efficacy of molnupiravir in humans (180 participants randomised 1:1 with placebo). Here, we describe the pre-specified exploratory virological endpoint of CST-2, which was to determine the possible genomic changes in SARS-CoV-2 induced by molnupiravir treatment. We use high-throughput amplicon sequencing and minor variant analysis to characterise viral genomics in each participant whose longitudinal samples (days 1, 3 and 5 post-randomisation) pass the viral genomic quality criteria (n = 59 for molnupiravir and n = 65 for placebo). Over the course of treatment, no specific mutations were associated with molnupiravir treatment. We find that molnupiravir significantly increased the transition:transversion mutation ratio in SARS-CoV-2, consistent with the model of lethal error catastrophe. This study highlights the utility of examining intra-host virus populations to strengthen the prediction, and surveillance, of potential treatment-emergent adaptations.
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Affiliation(s)
- I'ah Donovan-Banfield
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
| | - Rebekah Penrice-Randal
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Hannah Goldswain
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Aleksandra M Rzeszutek
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jack Pilgrim
- Department of Evolution, Ecology and Behaviour, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Katie Bullock
- GCPLab Facility, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Geoffrey Saunders
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Josh Northey
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Xiaofeng Dong
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Yan Ryan
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Helen Reynolds
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Michelle Tetlow
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lauren E Walker
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Richard FitzGerald
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Colin Hale
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Rebecca Lyon
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Christie Woods
- NIHR Royal Liverpool and Broadgreen Clinical Research Facility, Liverpool University Hospitals NHS Foundation Trust, Liverpool, UK
| | - Shazaad Ahmad
- NIHR Manchester Clinical Research Facility, Manchester University NHS Foundation Trust, Manchester, UK
| | - Dennis Hadjiyiannakis
- NIHR Lancashire Clinical Research Facility, Lancashire Teaching Hospitals NHS Foundation Trust, Preston, UK
| | - Jimstan Periselneris
- NIHR Kings Clinical Research Facility, King's College Hospital NHS Foundation Trust, London, UK
| | - Emma Knox
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Calley Middleton
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Lara Lavelle-Langham
- GCPLab Facility, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Victoria Shaw
- GCPLab Facility, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- The Clinical Directorate, University of Liverpool, Liverpool, UK
| | - William Greenhalf
- GCPLab Facility, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Thomas Edwards
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Christopher J Edwards
- Human Development and Health School, University of Southampton, Southampton, UK
- NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Alistair C Darby
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- NIHR Health Protection Research Unit in Gastrointestinal Infections, Liverpool, UK
| | - Miles W Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK
- Wellcome Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gareth Griffiths
- Southampton Clinical Trials Unit, University of Southampton, Southampton, UK
| | - Saye H Khoo
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Julian A Hiscox
- Department of Infection Biology and Microbiomes, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| | - Thomas Fletcher
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, UK.
- Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Liverpool, UK.
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15
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Evaluation and Clinical Validation of Guanidine-Based Inactivation Transport Medium for Preservation of SARS-CoV-2. Adv Pharmacol Pharm Sci 2022; 2022:1677621. [PMID: 35873075 PMCID: PMC9301760 DOI: 10.1155/2022/1677621] [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: 02/09/2022] [Revised: 06/02/2022] [Accepted: 06/10/2022] [Indexed: 12/02/2022] Open
Abstract
WHO declared the outbreak of COVID-19, caused by SARS-CoV-2, a pandemic in March 2020. More than 223 million cases and approximately 4.6 million deaths have been confirmed. Early diagnosis and immediate treatment became a priority during this pandemic. However, COVID-19 diagnostic testing resources are limited, especially early in the pandemic. Apart from being limited, the COVID-19 diagnostic tests using reverse transcription polymerase chain reaction (RT-PCR) have encountered storage, transportation, and safety issues. These problems are mainly experienced by developing poor countries, countries in the equatorial region, and archipelagic countries. VITPAD® is a guanidine-based inactivation transport medium (ITM) formulated to maintain the RNA quality of SARS-CoV-2 during transportation without cold chains. This study, conducted from September 2020 to March 2021, performed clinical validation of VITPAD® by comparing its performance with a globally commercially available ITM from the NEST brand. Its stability at room temperature, safety, and resistance at high temperatures was also tested using RT-PCR analysis. VITPAD® can reduce the infectious nature of the specimen, preserve the SARS-CoV-2 for 18 days at an ambient temperature, and resist high temperatures (40°C for 3 hours). A guanidine-based transport medium, such as VITPAD®, is compatible and recommended for RT-PCR-based molecular diagnosis of COVID-19.
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16
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Zhang Y, Huang Z, Zhu J, Li C, Fang Z, Chen K, Zhang Y. An updated review of SARS-CoV-2 detection methods in the context of a novel coronavirus pandemic. Bioeng Transl Med 2022; 8:e10356. [PMID: 35942232 PMCID: PMC9349698 DOI: 10.1002/btm2.10356] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 01/21/2023] Open
Abstract
The World Health Organization has reported approximately 430 million confirmed cases of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), worldwide, including nearly 6 million deaths, since its initial appearance in China in 2019. While the number of diagnosed cases continues to increase, the need for technologies that can accurately and rapidly detect SARS-CoV-2 virus infection at early phases continues to grow, and the Federal Drug Administration (FDA) has licensed emergency use authorizations (EUAs) for virtually hundreds of diagnostic tests based on nucleic acid molecules and antigen-antibody serology assays. Among them, the quantitative real-time reverse transcription PCR (qRT-PCR) assay is considered the gold standard for early phase virus detection. Unfortunately, qRT-PCR still suffers from disadvantages such as the complex test process and the occurrence of false negatives; therefore, new nucleic acid detection devices and serological testing technologies are being developed. However, because of the emergence of strongly infectious mutants of the new coronavirus, such as Alpha (B.1.1.7), Delta (B.1.617.2), and Omicron (B.1.1.529), the need for the specific detection of mutant strains is also increasing. Therefore, this article reviews nucleic acid- and antigen-antibody-based serological assays, and compares the performance of some of the most recent FDA-approved and literature-reported assays and associated kits for the specific testing of new coronavirus variants.
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Affiliation(s)
- Yuxuan Zhang
- Shulan International Medical College, Zhejiang Shuren UniversityHangzhouChina
| | - Zhiwei Huang
- School of Laboratory Medicine and Life SciencesWenzhou Medical UniversityWenzhouChina
| | - Jiajie Zhu
- Shulan International Medical College, Zhejiang Shuren UniversityHangzhouChina
| | - Chaonan Li
- Shulan International Medical College, Zhejiang Shuren UniversityHangzhouChina
| | - Zhongbiao Fang
- Shulan International Medical College, Zhejiang Shuren UniversityHangzhouChina
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren UniversityHangzhouChina
| | - Yanjun Zhang
- Zhejiang Provincial Center for Disease Control and PreventionHangzhouChina
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17
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Wegner F, Roloff T, Huber M, Cordey S, Ramette A, Gerth Y, Bertelli C, Stange M, Seth-Smith HMB, Mari A, Leuzinger K, Cerutti L, Harshman K, Xenarios I, Le Mercier P, Bittel P, Neuenschwander S, Opota O, Fuchs J, Panning M, Michel C, Hallin M, Demuyser T, De Mendonca R, Savelkoul P, Dingemans J, van der Veer B, Boers SA, Claas ECJ, Coolen JPM, Melchers WJG, Gunell M, Kallonen T, Vuorinen T, Hakanen AJ, Bernhoff E, Hetland MAK, Golan Berman H, Adar S, Moran-Gilad J, Wolf DG, Leib SL, Nolte O, Kaiser L, Schmutz S, Kufner V, Zaheri M, Trkola A, Aamot HV, Hirsch HH, Greub G, Egli A. External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories. J Clin Microbiol 2022; 60:e0169821. [PMID: 34757834 PMCID: PMC8769736 DOI: 10.1128/jcm.01698-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/05/2021] [Indexed: 12/01/2022] Open
Abstract
This first pilot trial on external quality assessment (EQA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) whole-genome sequencing, initiated by the European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Genomic and Molecular Diagnostics (ESGMD) and the Swiss Society for Microbiology (SSM), aims to build a framework between laboratories in order to improve pathogen surveillance sequencing. Ten samples with various viral loads were sent out to 15 clinical laboratories that had free choice of sequencing methods and bioinformatic analyses. The key aspects on which the individual centers were compared were the identification of (i) single nucleotide polymorphisms (SNPs) and indels, (ii) Pango lineages, and (iii) clusters between samples. The participating laboratories used a wide array of methods and analysis pipelines. Most were able to generate whole genomes for all samples. Genomes were sequenced to various depths (up to a 100-fold difference across centers). There was a very good consensus regarding the majority of reporting criteria, but there were a few discrepancies in lineage and cluster assignments. Additionally, there were inconsistencies in variant calling. The main reasons for discrepancies were missing data, bioinformatic choices, and interpretation of data. The pilot EQA was overall a success. It was able to show the high quality of participating laboratories and provide valuable feedback in cases where problems occurred, thereby improving the sequencing setup of laboratories. A larger follow-up EQA should, however, improve on defining the variables and format of the report. Additionally, contamination and/or minority variants should be a further aspect of assessment.
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Affiliation(s)
- Fanny Wegner
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Yannick Gerth
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Claire Bertelli
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Madlen Stange
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Helena M. B. Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Alfredo Mari
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Karoline Leuzinger
- Clinical Virology, University Hospital Basel, Basel, Switzerland
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
| | | | | | | | | | - Pascal Bittel
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | | | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jonas Fuchs
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marcus Panning
- Institute of Virology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Charlotte Michel
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Marie Hallin
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles, Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Paul Savelkoul
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jozef Dingemans
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Brian van der Veer
- Department of Medical Microbiology, Maastricht University, Maastricht, Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Willem J. G. Melchers
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Marianne Gunell
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Teemu Kallonen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Tytti Vuorinen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Antti J. Hakanen
- Department of Clinical Microbiology, Turku University Hospital, Turku, Finland
- Department of Clinical Microbiology, University of Turku, Turku, Finland
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | | | - Hadar Golan Berman
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Sheera Adar
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel Canada, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Jacob Moran-Gilad
- School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Dana G. Wolf
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
- Lautenberg Center for General and Tumor Immunology, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - Stephen L. Leib
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Oliver Nolte
- Center for Laboratory Medicine, Saint Gall, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, University Hospital Geneva, Geneva, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Maryam Zaheri
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Zurich, Switzerland
| | - Hege Vangstein Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Clinical Molecular Biology (EPIGEN), Akershus University Hospital and University of Oslo, Lørenskog, Norway
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Hans H. Hirsch
- Transplantation and Clinical Virology, Department of Biomedicine, University of Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Infectious Diseases and Hospital Epidemiology, University of Basel, Basel, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital, Lausanne, Switzerland
- Institute of Microbiology, University of Lausanne, Lausanne, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD), Basel, Switzerland
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