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Timsit S, Armand-Lefèvre L, Le Goff J, Salmona M. The clinical and epidemiological impacts of whole genomic sequencing on bacterial and virological agents. Infect Dis Now 2024; 54:104844. [PMID: 38101516 DOI: 10.1016/j.idnow.2023.104844] [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: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
Whole Genome Sequencing (WGS) is a molecular biology tool consisting in the sequencing of the entire genome of a given organism. Due to its ability to provide the finest available resolution of bacterial and virological genetics, it is used at several levels in the field of infectiology. On an individual scale and through application of a single technique, it enables the typological identification and characterization of strains, the characterization of plasmids, and enhanced search for resistance genes and virulence factors. On a collective scale, it enables the characterization of strains and the determination of phylogenetic links between different microorganisms during community outbreaks and healthcare-associated epidemics. The information provided by WGS enables real-time monitoring of strain-level epidemiology on a worldwide scale, and facilitates surveillance of the resistance dissemination and the introduction or emergence of pathogenic variants in humans or their environment. There are several possible approaches to completion of an entire genome. The choice of one method rather than another is essentially dictated by the matrix, either a clinical sample or a culture isolate, and the clinical objective. WGS is an advanced technology that remains costly despite a gradual decrease in its expenses, potentially hindering its implementation in certain laboratories and thus its use in routine microbiology. Even though WGS is making steady inroads as a reference method, efforts remain needed in view of so harmonizing its interpretations and decreasing the time to generation of conclusive results.
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Affiliation(s)
- Sarah Timsit
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France
| | - Laurence Armand-Lefèvre
- Service de Bactériologie, Hôpital Bichat-Claude Bernard, APHP, Paris, France; IAME UMR 1137, INSERM, Université Paris Cité, Paris, France
| | - Jérôme Le Goff
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France
| | - Maud Salmona
- Service de Virologie, Hôpital Saint-Louis, APHP, Paris, France; INSERM U976, Insight Team, Université Paris Cité, Paris, France.
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2
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Rose R, Feehan A, Lain BN, Ashcraft D, Nolan DJ, Velez-Climent L, Huston C, LaFleur T, Rosenthal S, Fogel GB, Miele L, Pankey G, Garcia-Diaz J, Lamers SL. Whole-genome sequencing of carbapenem-resistant Enterobacterales isolates in southeast Louisiana reveals persistent genetic clusters spanning multiple locations. J Infect Public Health 2023; 16:1911-1917. [PMID: 37866269 DOI: 10.1016/j.jiph.2023.10.013] [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: 05/01/2023] [Revised: 10/02/2023] [Accepted: 10/08/2023] [Indexed: 10/24/2023] Open
Abstract
BACKGROUND We investigated 51 g-negative carbapenem-resistant Enterobacterales (CRE) isolates collected from 22 patients over a five-year period from six health care institutions in the Ochsner Health network in southeast Louisiana. METHODS Short genomic reads were generated using Illumina sequencing and assembled for each isolate. Isolates were classified as Enterobacter spp. (n = 20), Klebsiella spp. (n = 30), and Escherichia coli (n = 1) and grouped into 19 different multi-locus sequence types (MLST). Species and patient-specific core genomes were constructed representing ∼50% of the chromosomal genome. RESULTS We identified two sets of patients with genetically related infections; in both cases, the related isolates were collected > 6 months apart, and in one case, the isolates were collected in different locations. On the other hand, we identified four sets of patients with isolates of the same species collected within 21 days from the same location; however, none had genetically related infections. Genes associated with resistance to carbapenem drugs (blaKPC and/or blaCTX-M-15) were found in 76% of the isolates. We found three blaKPC variants (blaKPC-2, blaKPC-3, and blaKPC-4) associated with four different Enterobacter MLST variants, and two blaKPC variants (blaKPC-2, blaKPC-3) associated with seven different Klebsiella MLST variants. CONCLUSIONS Molecular surveillance is increasingly becoming a powerful tool to understand bacterial spread in both community and clinical settings. This study provides evidence that genetically related infections in clinical settings do not necessarily reflect temporal associations, and vice versa. Our results also highlight the regional genomic and resistance diversity within related bacterial lineages.
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Affiliation(s)
- Rebecca Rose
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA.
| | - Amy Feehan
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | - Deborah Ashcraft
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | | | | | | | | | | | | | - Lucio Miele
- Translational Science and Genetics at LSU Health Science Center, New Orleans, LA, USA
| | - George Pankey
- Infectious Disease Translational Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Julia Garcia-Diaz
- Infectious Disease Clinical Research, Ochsner Clinic Foundation, New Orleans, LA, USA
| | - Susanna L Lamers
- BioInfoExperts, LLC, Thibodaux, LA, USA; FoxSeq, LLC, Thibodaux, LA, USA
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3
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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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4
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Anderegg N, Schwab T, Borcard L, Mugglin C, Keune-Dübi B, Ramette A, Fenner L. Population-Based Severe Acute Respiratory Syndrome Coronavirus 2 Whole-Genome Sequencing and Contact Tracing During the Coronavirus Disease 2019 Pandemic in Switzerland. J Infect Dis 2023; 228:251-260. [PMID: 36967680 PMCID: PMC10420393 DOI: 10.1093/infdis/jiad074] [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: 11/30/2022] [Accepted: 03/23/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND Testing and contact tracing (CT) can interrupt transmission chains of SARS-CoV-2. Whole-genome sequencing (WGS) can potentially strengthen these investigations and provide insights on transmission. METHODS We included all laboratory-confirmed COVID-19 cases diagnosed between 4 June and 26 July 2021, in a Swiss canton. We defined CT clusters based on epidemiological links reported in the CT data and genomic clusters as sequences with no single-nucleotide polymorphism (SNP) differences between any 2 pairs of sequences being compared. We assessed the agreement between CT clusters and genomic clusters. RESULTS Of 359 COVID-19 cases, 213 were sequenced. Overall, agreement between CT and genomic clusters was low (Cohen's κ = 0.13). Of 24 CT clusters with ≥2 sequenced samples, 9 (37.5%) were also linked based on genomic sequencing but in 4 of these, WGS found additional cases in other CT clusters. Household was most often reported source of infection (n = 101 [28.1%]) and home addresses coincided well with CT clusters: In 44 of 54 CT clusters containing ≥2 cases (81.5%), all cases in the cluster had the same reported home address. However, only a quarter of household transmission was confirmed by WGS (6 of 26 genomic clusters [23.1%]). A sensitivity analysis using ≤1-SNP differences to define genomic clusters resulted in similar results. CONCLUSIONS WGS data supplemented epidemiological CT data, supported the detection of potential additional clusters missed by CT, and identified misclassified transmissions and sources of infection. Household transmission was overestimated by CT.
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Affiliation(s)
- Nanina Anderegg
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, School of Public Health, University of Cape Town, Cape Town, South Africa
| | - Tiana Schwab
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Loïc Borcard
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Catrina Mugglin
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Department of Infectious Diseases, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Bettina Keune-Dübi
- Cantonal Physician’s Office, Gesundheitsamt, Canton of Solothurn, Solothurn, Switzerland
| | - Alban Ramette
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
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Barrett PM, Bruton O, Hanrahan M, White PF, Brennan A, Ertz K, Chu RW, Keogh S, Dean J, O'Mahony MT, O'Sullivan MB, Sheahan A, Murray D. A large outbreak of the Kappa mutation of COVID-19 in Cork, Ireland, April-May 2021. Ir J Med Sci 2023; 192:1573-1579. [PMID: 36369600 PMCID: PMC9651878 DOI: 10.1007/s11845-022-03212-6] [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: 05/23/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
BACKGROUND In May 2021, the B.1.617 variant of SARS-CoV-2 emerged in Ireland, and both Delta and Kappa sub-lineages were initially deemed variants of concern (VOCs) on a precautionary basis. We describe a large outbreak of SARS-CoV-2 B.1.617.1 (Kappa mutation) linked to a private gathering among third level students in Cork, Ireland. METHODS Surveillance data were available from the Health Service Executive COVID Care Tracker. The epidemiological sequence of infection for each new case in this outbreak was tracked and whole genome sequencing was requested on all linked cases. Enhanced public health control measures were implemented by the Department of Public Health HSE-South to contain onward spread of VOCs, including retrospective contact tracing, lengthy isolation and quarantine periods for cases and close contacts. Extensive surveillance efforts were used to describe and control onward transmission. RESULTS There were 146 confirmed SARS-CoV-2 cases linked to the outbreak. All sequenced cases (53/146; 36%) confirmed Kappa mutation. The median age was 21 years (range 17-65). The majority (88%) had symptoms of SARS-CoV-2 infection. There were 407 close contacts; the median was 3 per case (range 0-14). There were no known hospitalisations, ICU admissions or deaths. Vaccination data was unavailable, but the outbreak pre-dated routine availability of COVID-19 vaccines among younger adults in Ireland. CONCLUSION Enhanced public health control measures for new and emerging variants of SARS-CoV-2 may be burdensome for cases and close contacts. The overall public health benefit of enhanced controls may only become apparent when evidence on disease transmissibility and severity becomes more complete.
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Affiliation(s)
- P M Barrett
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland.
| | - O Bruton
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
| | - M Hanrahan
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
| | - P F White
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
| | - A Brennan
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
- National Cancer Registry Ireland, Kinsale Road, Cork, Ireland
| | - K Ertz
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
| | - R W Chu
- School of Medicine, University College Cork, Cork, Ireland
| | - S Keogh
- Cork Complex Contact Tracing Centre, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
| | - J Dean
- National Virus Reference Laboratory, University College Dublin, Dublin, Ireland
| | - M T O'Mahony
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
| | - M B O'Sullivan
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
| | - A Sheahan
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
| | - D Murray
- Department of Public Health HSE-South, St. Finbarr's Hospital, Douglas Road, Cork, Ireland
- National Cancer Registry Ireland, Kinsale Road, Cork, Ireland
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Cotton S, McHugh MP, Dewar R, Haas JG, Templeton K. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. J Hosp Infect 2023; 135:28-36. [PMID: 36906180 PMCID: PMC9997060 DOI: 10.1016/j.jhin.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/09/2023] [Accepted: 02/12/2023] [Indexed: 03/13/2023]
Abstract
BACKGROUND The first epidemic wave of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over a third of care homes reported an outbreak while there was limited testing of hospital patients discharged to care homes. AIM Investigate hospital discharges as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. METHODS A clinical review was performed for all discharges from hospitals to care homes starting 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease (COVID-19) test history, clinical assessment at discharge, whole genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis by cluster investigation and virus epidemiological tool (CIVET). Patient timelines were obtained using electronic hospital records. FINDINGS In total 787 hospital discharges to care homes were identified. Out of these 776 (99%) were ruled out for hospital discharge introduction. However, for 10 episodes the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission leading to 10 further positive cases in the care home. CONCLUSION Majority of hospital discharges were ruled out for introduction into Lothian care homes highlighting the importance of screening all new admissions when faced with a novel emerging virus and no vaccine available.
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Affiliation(s)
- S Cotton
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK; Infection Medicine, Edinburgh Medical School, University of Edinburgh, UK.
| | - M P McHugh
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK; School of Medicine, University of St Andrews, UK
| | - R Dewar
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK
| | - J G Haas
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK; Infection Medicine, Edinburgh Medical School, University of Edinburgh, UK
| | - K Templeton
- Specialist Virology Centre, Royal Infirmary Edinburgh, NHS Lothian, UK; Infection Medicine, Edinburgh Medical School, University of Edinburgh, UK
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7
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Bosworth A, Robson J, Lawrence B, Casey AL, Fair A, Khanam S, Hudson C, O'Shea MK. Deployment of whole genome next-generation sequencing of SARS-CoV-2 in a military maritime setting. BMJ Mil Health 2023:e002296. [PMID: 36759003 DOI: 10.1136/military-2022-002296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/20/2023] [Indexed: 02/11/2023]
Abstract
BACKGROUND SARS-CoV-2 can spread rapidly on maritime platforms. Several outbreaks of SARS-CoV-2 have been reported on warships at sea, where transmission is facilitated by living and working in close quarters. Core components of infection control measures such as social distancing, patient isolation and quarantine of exposed persons are extremely difficult to implement. Whole genome sequencing (WGS) of SARS-CoV-2 has facilitated epidemiological investigations of outbreaks, impacting on outbreak management in real time by identifying transmission patterns, clusters of infection and guiding control measures. We suggest such a capability could mitigate against the impact of SARS-CoV-2 in maritime settings. METHODS We set out to establish SARS-CoV-2 WGS using miniaturised nanopore sequencing technology aboard the Royal Fleet Auxiliary ARGUS while at sea. Objectives included designing a simplified protocol requiring minimal reagents and processing steps, the use of miniaturised equipment compatible for use in limited space, and a streamlined and standalone data analysis capability to allow rapid in situ data acquisition and interpretation. RESULTS Eleven clinical samples with blinded SARS-CoV-2 status were tested at sea. Following viral RNA extraction and ARTIC sequencing library preparation, reverse transcription and ARTIC PCR-tiling were performed. Samples were subsequently barcoded and sequenced using the Oxford Nanopore MinION Mk1B. An offline version of the MinKNOW software was used followed by CLC Genomics Workbench for downstream analysis for variant identification and phylogenetic tree construction. All samples were correctly classified, and relatedness identified. CONCLUSIONS It is feasible to establish a small footprint sequencing capability to conduct SARS-CoV-2 WGS in a military maritime environment at sea with limited access to reach-back support. This proof-of-concept study has highlighted the potential of deploying such technology in the future to military environments, both maritime and land-based, to provide meaningful clinical data to aid outbreak investigations.
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Affiliation(s)
- Andrew Bosworth
- Department of Microbiology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Institute for Immunology and Immunotherapy, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
| | - J Robson
- Department of Microbiology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
- Defence Pathology, Royal Centre for Defence Medicine, Birmingham, UK
| | - B Lawrence
- Defence Pathology, Royal Centre for Defence Medicine, Birmingham, UK
- Department of Pathology, Portsmouth Hospitals University NHS Trust, Portsmouth, UK
| | - A L Casey
- Department of Microbiology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - A Fair
- Molecular Pathology Diagnostic Service, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - S Khanam
- Department of Microbiology, University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - C Hudson
- Department of Microbiology, Frimley Park Hospital, Camberley, UK
| | - M K O'Shea
- Institute for Immunology and Immunotherapy, University of Birmingham College of Medical and Dental Sciences, Birmingham, UK
- Defence Pathology, Royal Centre for Defence Medicine, Birmingham, UK
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Killough N, Patterson L, The Covid-Genomics Uk Cog-Uk Consortium, Peacock SJ, Bradley DT. How public health authorities can use pathogen genomics in health protection practice: a consensus-building Delphi study conducted in the United Kingdom. Microb Genom 2023; 9:mgen000912. [PMID: 36745548 PMCID: PMC9997744 DOI: 10.1099/mgen.0.000912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Pathogen sequencing guided understanding of SARS-CoV-2 evolution during the COVID-19 pandemic. Many health systems developed pathogen genomics services to monitor SARS-CoV-2. There are no agreed guidelines about how pathogen genomic information should be used in public health practice. We undertook a modified Delphi study in three rounds to develop expert consensus statements about how genomic information should be used. Our aim was to inform health protection policy, planning and practice. Participants were from organisations that produced or used pathogen genomics information in the United Kingdom. The first round posed questions derived from a rapid literature review. Responses informed statements for the subsequent rounds. Consensus was accepted when 70 % or more of the responses were strongly agree/agree, or 70 % were disagree/strongly disagree on the five-point Likert scale. Consensus was achieved in 26 (96 %) of 27 statements. We grouped the statements into six categories: monitoring the emergence of new variants; understanding the epidemiological context of genomic data; using genomic data in outbreak risk assessment and risk management; prioritising the use of limited sequencing capacity; sequencing service performance; and sequencing service capability. The expert consensus statements will help guide public health authorities and policymakers to integrate pathogen genomics in health protection practice.
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Affiliation(s)
| | - Lynsey Patterson
- Public Health Agency, Belfast, UK.,Centre for Public Health, Queen's University Belfast, Belfast, UK
| | | | | | - Declan T Bradley
- Public Health Agency, Belfast, UK.,Centre for Public Health, Queen's University Belfast, Belfast, UK
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9
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Colton H, Parker M, Stirrup O, Blackstone J, Loose M, McClure C, Roy S, Williams C, McLeod J, Smith D, Taha Y, Zhang P, Hsu S, Kele B, Harris K, Mapp F, Williams R, Flowers P, Breuer J, Partridge D, de Silva T. Factors affecting turnaround time of SARS-CoV-2 sequencing for inpatient infection prevention and control decision making: analysis of data from the COG-UK HOCI study. J Hosp Infect 2023; 131:34-42. [PMID: 36228768 PMCID: PMC9550290 DOI: 10.1016/j.jhin.2022.09.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Barriers to rapid return of sequencing results can affect the utility of sequence data for infection prevention and control decisions. AIM To undertake a mixed-methods analysis to identify challenges that sites faced in achieving a rapid turnaround time (TAT) in the COVID-19 Genomics UK Hospital-Onset COVID-19 Infection (COG-UK HOCI) study. METHODS For the quantitative analysis, timepoints relating to different stages of the sequencing process were extracted from both the COG-UK HOCI study dataset and surveys of study sites. Qualitative data relating to the barriers and facilitators to achieving rapid TATs were included from thematic analysis. FINDINGS The overall TAT, from sample collection to receipt of sequence report by infection control teams, varied between sites (median 5.1 days, range 3.0-29.0 days). Most variation was seen between reporting of a positive COVID-19 polymerase chain reaction (PCR) result to sequence report generation (median 4.0 days, range 2.3-27.0 days). On deeper analysis, most of this variability was accounted for by differences in the delay between the COVID-19 PCR result and arrival of the sample at the sequencing laboratory (median 20.8 h, range 16.0-88.7 h). Qualitative analyses suggest that closer proximity of sequencing laboratories to diagnostic laboratories, increased staff flexibility and regular transport times facilitated a shorter TAT. CONCLUSION Integration of pathogen sequencing into diagnostic laboratories may help to improve sequencing TAT to allow sequence data to be of tangible value to infection control practice. Adding a quality control step upstream to increase capacity further down the workflow may also optimize TAT if lower quality samples are removed at an earlier stage.
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Affiliation(s)
- H. Colton
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK,Directorate of Laboratory Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK,Corresponding author. Address: Department of Infection, Immunity and Cardiovascular Disease, Faculty of Medicine, Dentistry & Health, University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - M.D. Parker
- Sheffield Biomedical Research Centre, University of Sheffield, Sheffield, UK,Sheffield Bioinformatics Core, University of Sheffield, Sheffield, UK
| | - O. Stirrup
- Institute for Global Health, University College London, London, UK
| | - J. Blackstone
- The Comprehensive Clinical Trials Unit, University College London, London, UK
| | - M. Loose
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - C.P. McClure
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - S. Roy
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - C. Williams
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - J. McLeod
- School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK
| | - D. Smith
- Department of Applied Biology, Cellular and Molecular Sciences/Microbiology Group, Northumbria University, Newcastle, UK
| | - Y. Taha
- Department of Infection and Tropical Medicine, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Royal Victoria Infirmary, Newcastle Upon Tyne, UK
| | - P. Zhang
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - S.N. Hsu
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK,Sheffield Bioinformatics Core, University of Sheffield, Sheffield, UK
| | - B. Kele
- Virology Department, East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - K. Harris
- Virology Department, East and South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London, UK
| | - F. Mapp
- Institute for Global Health, University College London, London, UK
| | - R. Williams
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | | | - P. Flowers
- School of Psychological Sciences and Health, University of Strathclyde, Glasgow, UK
| | - J. Breuer
- Department of Infection, Immunity and Inflammation, Institute of Child Health, University College London, London, UK
| | - D.G. Partridge
- Directorate of Laboratory Medicine, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - T.I. de Silva
- Department of Infection, Immunity and Cardiovascular Disease, University of Sheffield, Sheffield, UK
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10
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Berggreen H, Løvestad AH, Helmersen K, Jørgensen SB, Aamot HV. Lessons learned: use of WGS in real-time investigation of suspected intrahospital SARS-CoV-2 outbreaks. J Hosp Infect 2023; 131:81-88. [PMID: 36404573 PMCID: PMC9617632 DOI: 10.1016/j.jhin.2022.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 11/18/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been a continuing source of hospital-acquired infection and outbreaks. At Akershus University Hospital in Norway, traditional contact tracing has been combined with whole-genome sequencing (WGS) surveillance in real-time to investigate potential hospital outbreaks. AIM To describe the advantages and challenges encountered when using WGS as a real-time tool in hospital outbreak investigation and surveillance during the SARS-CoV-2 pandemic. METHODS Routine contact tracing in the hospital was performed for all healthcare workers (HCWs) who tested positive for SARS-CoV-2. Viral RNA from all positive patient and HCW samples was sequenced in real-time using nanopore sequencing and the ARTIC Network protocol. Suspected outbreaks involving five or more individuals with viral sequences were described. FINDINGS Nine outbreaks were suspected based on contact tracing, and one outbreak was suspected based on WGS results. Five outbreaks were confirmed; of these, two outbreaks were supported but could not be confirmed by WGS with high confidence, one outbreak was found to consist of two different lineages, and two outbreaks were refuted. CONCLUSIONS WGS is a valuable tool in hospital outbreak investigations when combined with traditional contact tracing. Inclusion of WGS data improved outbreak demarcation, identified unknown transmission chains, and highlighted weaknesses in existing infection control measures.
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Affiliation(s)
- H Berggreen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - A H Løvestad
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway; Faculty of Health Sciences, Oslo Metropolitan University, Oslo, Norway
| | - K Helmersen
- 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
| | - S B Jørgensen
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
| | - H V Aamot
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
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11
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Bendall EE, Paz-Bailey G, Santiago GA, Porucznik CA, Stanford JB, Stockwell MS, Duque J, Jeddy Z, Veguilla V, Major C, Rivera-Amill V, Rolfes MA, Dawood FS, Lauring AS. SARS-CoV-2 Genomic Diversity in Households Highlights the Challenges of Sequence-Based Transmission Inference. mSphere 2022; 7:e0040022. [PMID: 36377913 PMCID: PMC9769559 DOI: 10.1128/msphere.00400-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The reliability of sequence-based inference of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission is not clear. Sequence data from infections among household members can define the expected genomic diversity of a virus along a defined transmission chain. SARS-CoV-2 cases were identified prospectively among 2,369 participants in 706 households. Specimens with a reverse transcription-PCR cycle threshold of ≤30 underwent whole-genome sequencing. Intrahost single-nucleotide variants (iSNV) were identified at a ≥5% frequency. Phylogenetic trees were used to evaluate the relationship of household and community sequences. There were 178 SARS-CoV-2 cases in 706 households. Among 147 specimens sequenced, 106 yielded a whole-genome consensus with coverage suitable for identifying iSNV. Twenty-six households had sequences from multiple cases within 14 days. Consensus sequences were indistinguishable among cases in 15 households, while 11 had ≥1 consensus sequence that differed by 1 to 2 mutations. Sequences from households and the community were often interspersed on phylogenetic trees. Identification of iSNV improved inference in 2 of 15 households with indistinguishable consensus sequences and in 6 of 11 with distinct ones. In multiple-infection households, whole-genome consensus sequences differed by 0 to 1 mutations. Identification of shared iSNV occasionally resolved linkage, but the low genomic diversity of SARS-CoV-2 limits the utility of "sequence-only" transmission inference. IMPORTANCE We performed whole-genome sequencing of SARS-CoV-2 from prospectively identified cases in three longitudinal household cohorts. In a majority of multi-infection households, SARS-CoV-2 consensus sequences were indistinguishable, and they differed by 1 to 2 mutations in the rest. Importantly, even with modest genomic surveillance of the community (3 to 5% of cases sequenced), it was not uncommon to find community sequences interspersed with household sequences on phylogenetic trees. Identification of shared minority variants only occasionally resolved these ambiguities in transmission linkage. Overall, the low genomic diversity of SARS-CoV-2 limits the utility of "sequence-only" transmission inference. Our work highlights the need to carefully consider both epidemiologic linkage and sequence data to define transmission chains in households, hospitals, and other transmission settings.
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Affiliation(s)
- Emily E. Bendall
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Gabriela Paz-Bailey
- Centers for Disease Control and Preventiongrid.416738.f, Atlanta, Georgia, USA
| | | | - Christina A. Porucznik
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Joseph B. Stanford
- Division of Public Health, Department of Family and Preventive Medicine, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Melissa S. Stockwell
- Division of Child and Adolescent Health, Department of Pediatrics, Columbia University Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Population and Family Health, Mailman School of Public Health, Columbia University, New York, New York, USA
| | | | - Zuha Jeddy
- Abt Associates, Rockville, Maryland, USA
| | - Vic Veguilla
- Centers for Disease Control and Preventiongrid.416738.f, Atlanta, Georgia, USA
| | - Chelsea Major
- Centers for Disease Control and Preventiongrid.416738.f, Atlanta, Georgia, USA
| | - Vanessa Rivera-Amill
- Ponce Research Institute, Ponce Health Sciences University, Ponce, Puerto Rico, USA
| | - Melissa A. Rolfes
- Centers for Disease Control and Preventiongrid.416738.f, Atlanta, Georgia, USA
| | - Fatimah S. Dawood
- Centers for Disease Control and Preventiongrid.416738.f, Atlanta, Georgia, USA
| | - Adam S. Lauring
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
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12
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Optimized conditions for Listeria, Salmonella and Escherichia whole genome sequencing using the Illumina iSeq100 platform with point-and-click bioinformatic analysis. PLoS One 2022; 17:e0277659. [PMID: 36449522 PMCID: PMC9710801 DOI: 10.1371/journal.pone.0277659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/01/2022] [Indexed: 12/05/2022] Open
Abstract
Whole-genome sequencing (WGS) data have become an integral component of public health investigations and clinical diagnostics. Still, many veterinary diagnostic laboratories cannot afford to implement next generation sequencing (NGS) due to its high cost and the lack of bioinformatic knowledge of the personnel to analyze NGS data. Trying to overcome these problems, and make NGS accessible to every diagnostic laboratory, thirteen veterinary diagnostic laboratories across the United States (US) initiated the assessment of Illumina iSeq100 sequencing platform for whole genome sequencing of important zoonotic foodborne pathogens Escherichia coli, Listeria monocytogenes, and Salmonella enterica. The work presented in this manuscript is a continuation of this multi-laboratory effort. Here, seven AAVLD accredited diagnostic laboratories explored a further reduction in sequencing costs and the usage of user-friendly platforms for genomic data analysis. Our investigation showed that the same genomic library quality could be achieved by using a quarter of the recommended reagent volume and, therefore a fraction of the actual price, and confirmed that Illumina iSeq100 is the most affordable sequencing technology for laboratories with low WGS demand. Furthermore, we prepared step-by-step protocols for genomic data analysis in three popular user-friendly software (BaseSpace, Geneious, and GalaxyTrakr), and we compared the outcomes in terms of genome assembly quality, and species and antimicrobial resistance gene (AMR) identification. No significant differences were found in assembly quality, and the three analysis methods could identify the target bacteria species. However, antimicrobial resistance genes were only identified using BaseSpace and GalaxyTrakr; and GalaxyTrakr was the best tool for this task.
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13
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Hanney SR, Straus SE, Holmes BJ. Saving millions of lives but some resources squandered: emerging lessons from health research system pandemic achievements and challenges. Health Res Policy Syst 2022; 20:99. [PMID: 36088365 PMCID: PMC9464102 DOI: 10.1186/s12961-022-00883-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/27/2022] [Indexed: 12/15/2022] Open
Abstract
During the SARS-CoV-2 pandemic, astonishingly rapid research averted millions of deaths worldwide through new vaccines and repurposed and new drugs. Evidence use informed life-saving national policies including non-pharmaceutical interventions. Simultaneously, there was unprecedented waste, with many underpowered trials on the same drugs. We identified lessons from COVID-19 research responses by applying WHO's framework for research systems. It has four functions-governance, securing finance, capacity-building, and production and use of research-and nine components. Two linked questions focused the analysis. First, to what extent have achievements in knowledge production and evidence use built on existing structures and capacity in national health research systems? Second, did the features of such systems mitigate waste? We collated evidence on seven countries, Australia, Brazil, Canada, Germany, New Zealand, the United Kingdom and the United States, to identify examples of achievements and challenges.We used the data to develop lessons for each framework component. Research coordination, prioritization and expedited ethics approval contributed to rapid identification of new therapies, including dexamethasone in the United Kingdom and Brazil. Accelerated vaccines depended on extensive funding, especially through the Operation Warp Speed initiative in the United States, and new platforms created through long-term biomedical research capacity in the United Kingdom and, for messenger ribonucleic acid (mRNA) vaccines, in Canada, Germany and the United States. Research capacity embedded in the United Kingdom's healthcare system resulted in trial acceleration and waste avoidance. Faster publication of research saved lives, but raised challenges. Public/private collaborations made major contributions to vastly accelerating new products, available worldwide, though unequally. Effective developments of living (i.e. regularly updated) reviews and guidelines, especially in Australia and Canada, extended existing expertise in meeting users' needs. Despite complexities, effective national policy responses (less evident in Brazil, the United Kingdom and the United States) also saved lives by drawing on health research system features, including collaboration among politicians, civil servants and researchers; good communications; and willingness to use evidence. Comprehensive health research strategies contributed to success in research production in the United Kingdom and in evidence use by political leadership in New Zealand. In addition to waste, challenges included equity issues, public involvement and non-COVID research. We developed recommendations, but advocate studies of further countries.
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Affiliation(s)
- Stephen R Hanney
- Health Economics Research Group, Department of Health Sciences, Brunel University London, London, United Kingdom.
| | - Sharon E Straus
- St Michael's Hospital, Unity Health Toronto, Toronto, ON, Canada
| | - Bev J Holmes
- Michael Smith Health Research BC, Vancouver, BC, Canada
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14
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Chmel M, Bartoš O, Kabíčková H, Pajer P, Kubíčková P, Novotná I, Bartovská Z, Zlámal M, Burantová A, Holub M, Jiřincová H, Nagy A, Černíková L, Zákoucká H, Dresler J. Retrospective Analysis Revealed an April Occurrence of Monkeypox in the Czech Republic. Viruses 2022; 14:v14081773. [PMID: 36016395 PMCID: PMC9412638 DOI: 10.3390/v14081773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/16/2022] Open
Abstract
Herein, we present our findings of an early appearance of the Monkeypox virus in Prague, Czech Republic. A retrospective analysis of biological samples, carried out on the 28th of April, revealed a previously unrecognized case of Monkeypox virus (MPxV) infection. Subsequent data analysis confirmed that the virus strain belongs to the ongoing outbreak. Combined with clinical and epidemiological investigations, we extended the roots of the current outbreak at least back to 16th of April, 2022.
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Affiliation(s)
- Martin Chmel
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
- Correspondence: ; Tel.: +420-722712999
| | - Oldřich Bartoš
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Hana Kabíčková
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Pavla Kubíčková
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Iva Novotná
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
| | - Zofia Bartovská
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
| | - Milan Zlámal
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
| | - Anna Burantová
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
| | - Michal Holub
- Department of Infectious Diseases, First Faculty of Medicine, Charles University and Military University Hospital Prague, 12108 Prague, Czech Republic
| | - Helena Jiřincová
- National Reference Laboratory for Influenza and Respiratory Viruses, National Institute for Public Health, 10042 Prague, Czech Republic
| | - Alexander Nagy
- National Reference Laboratory for Influenza and Respiratory Viruses, National Institute for Public Health, 10042 Prague, Czech Republic
- State Veterinary Institute, 16503 Prague, Czech Republic
| | | | - Hana Zákoucká
- Department of Sexually Transmitted Infections, National Institute for Public Health, 10042 Prague, Czech Republic
| | - Jiří Dresler
- Military Health Institute, Military Medical Agency, 16200 Prague, Czech Republic
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15
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Watt AE, Sherry NL, Andersson P, Lane CR, Johnson S, Wilmot M, Horan K, Sait M, Ballard SA, Crachi C, Beck DJ, Marshall C, Kainer MA, Stuart R, McGrath C, Kwong JC, Bass P, Kelley PG, Crowe A, Guy S, Macesic N, Smith K, Williamson DA, Seemann T, Howden BP. State-wide genomic epidemiology investigations of COVID-19 in healthcare workers in 2020 Victoria, Australia: Qualitative thematic analysis to provide insights for future pandemic preparedness. THE LANCET REGIONAL HEALTH - WESTERN PACIFIC 2022; 25:100487. [PMID: 35677391 PMCID: PMC9168175 DOI: 10.1016/j.lanwpc.2022.100487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background COVID-19 has affected many healthcare workers (HCWs) globally. We performed state-wide SARS-CoV-2 genomic epidemiological investigations to identify HCW transmission dynamics and provide recommendations to optimise healthcare system preparedness for future outbreaks. Methods Genome sequencing was attempted on all COVID-19 cases in Victoria, Australia. We combined genomic and epidemiologic data to investigate the source of HCW infections across multiple healthcare facilities (HCFs) in the state. Phylogenetic analysis and fine-scale hierarchical clustering were performed for the entire dataset including community and healthcare cases. Facilities provided standardised epidemiological data and putative transmission links. Findings Between March-October 2020, approximately 1,240 HCW COVID-19 infection cases were identified; 765 are included here, requested for hospital investigations. Genomic sequencing was successful for 612 (80%) cases. Thirty-six investigations were undertaken across 12 HCFs. Genomic analysis revealed that multiple introductions of COVID-19 into facilities (31/36) were more common than single introductions (5/36). Major contributors to HCW acquisitions included mobility of staff and patients between wards and facilities, and characteristics and behaviours of patients that generated numerous secondary infections. Key limitations at the HCF level were identified. Interpretation Genomic epidemiological analyses enhanced understanding of HCW infections, revealing unsuspected clusters and transmission networks. Combined analysis of all HCWs and patients in a HCF should be conducted, supported by high rates of sequencing coverage for all cases in the population. Established systems for integrated genomic epidemiological investigations in healthcare settings will improve HCW safety in future pandemics. Funding The Victorian Government, the National Health and Medical Research Council Australia, and the Medical Research Future Fund.
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Affiliation(s)
- Anne E. Watt
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Norelle L. Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Courtney R. Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Sandra Johnson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Mathilda Wilmot
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Christina Crachi
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Dianne J. Beck
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Caroline Marshall
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Infectious Diseases, The University of Melbourne at the Doherty Institute, Melbourne, Victoria, Australia
| | - Marion A. Kainer
- Department of Infectious Diseases, Western Health, Footscray, Victoria, Australia
| | - Rhonda Stuart
- Monash Infectious Diseases, Monash Health, Clayton, Victoria, Australia
- South East Public Health Unit, Monash Health, Clayton, Victoria, Australia
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
| | - Christian McGrath
- Department of Infectious Diseases, The Northern Hospital, Epping, Victoria, Australia
| | - Jason C. Kwong
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
| | - Pauline Bass
- Infection Prevention and Healthcare Epidemiology Department, Alfred Health, Prahran, Victoria, Australia
| | - Peter G. Kelley
- Department of Infectious Diseases, Peninsula Health, Frankston, Victoria, Australia
| | - Amy Crowe
- Department of Microbiology, St Vincent's Hospital Melbourne, Fitzroy, Victoria, Australia
| | - Stephen Guy
- Department of Infectious Diseases, Eastern Health, Box Hill, Victoria, Australia
- Eastern Health Clinical School, Monash University, Victoria, Australia
| | - Nenad Macesic
- Department of Infectious Diseases, Epworth Hospital, Richmond, Victoria, Australia
| | - Karen Smith
- Centre for Research and Evaluation, Ambulance Victoria, Victoria, Australia
- Department of Epidemiology and Preventive Medicine, Monash University, Victoria, Australia
| | - Deborah A. Williamson
- Department of Infectious Diseases, The University of Melbourne at the Doherty Institute, Melbourne, Victoria, Australia
- Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
- Corresponding author at: Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, 792 Elizabeth St, Melbourne, Victoria 3000, Australia.
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16
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Hare D, Meaney C, Powell J, Slevin B, O' Brien B, Power L, O' Connell N, De Gascun C, Dunne C, Stapleton P. Repeated transmission of SARS-CoV-2 in an overcrowded Irish emergency department elucidated by whole-genome sequencing. J Hosp Infect 2022; 126:1-9. [PMID: 35562074 PMCID: PMC9088210 DOI: 10.1016/j.jhin.2022.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/20/2022] [Accepted: 04/28/2022] [Indexed: 01/11/2023]
Abstract
AIM To provide a detailed genomic-epidemiological description of a complex multi-ward SARS-CoV-2 outbreak, which originated in the crowded emergency department (ED) in our hospital during the third wave of the COVID-19 pandemic, and was elucidated promptly by local whole-genome sequencing (WGS). METHODS SARS-CoV-2 was detected by reverse transcriptase real-time polymerase chain reaction on viral RNA extracted from nasopharyngeal swabs. WGS was performed using an Oxford MinION Mk1C instrument following the ARTIC v3 sequencing protocol. High-quality consensus genomes were assembled with the artic-ncov2019 bioinformatics pipeline and viral phylogenetic trees were built, inferred by maximum-likelihood. Clusters were defined using a threshold of 0-1 single nucleotide polymorphisms (SNPs) between epidemiologically linked sequences. RESULTS In April 2021, outbreaks of COVID-19 were declared on two wards at University Hospital Limerick after 4 healthcare-associated SARS-CoV-2 infections were detected by post-admission surveillance testing. Contact tracing identified 12 further connected cases; all with direct or indirect links to the ED 'COVID Zone'. All sequences were assigned to the Pangolin B.1.1.7 lineage by WGS, and SNP-level analysis revealed two distinct but simultaneous clusters of infections. Repeated transmission in the ED was demonstrated, involving patients accommodated on trolleys in crowded areas, resulting in multiple generations of infections across three inpatient hospital wards and subsequently to the local community. These findings informed mitigation efforts to prevent cross-transmission in the ED. CONCLUSION Cross-transmission of SARS-CoV-2 occurred repeatedly in an overcrowded emergency department. Viral WGS elucidated complex viral transmission networks in our hospital and informed infection, prevention and control practice.
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Affiliation(s)
- D. Hare
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland,School of Medicine, University of Limerick, Limerick, Ireland,UCD National Virus Reference Laboratory, University College Dublin, Dublin, Ireland,Corresponding author. Address: Department of Clinical Microbiology University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland
| | - C. Meaney
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland
| | - J. Powell
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland,Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
| | - B. Slevin
- Department of Infection, Prevention and Control, University Hospital Limerick, Limerick, Ireland
| | - B. O' Brien
- Department of Infection, Prevention and Control, University Hospital Limerick, Limerick, Ireland
| | - L. Power
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland
| | - N.H. O' Connell
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland,School of Medicine, University of Limerick, Limerick, Ireland,Centre for Interventions in Infection, Inflammation & Immunity (4i), University of Limerick, Limerick, Ireland
| | - C.F. De Gascun
- UCD National Virus Reference Laboratory, University College Dublin, 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
| | - P.J. Stapleton
- Department of Clinical Microbiology, University Hospital Limerick, St Nessan's Road, Dooradoyle, Limerick, Ireland,School of Medicine, University of Limerick, Limerick, Ireland
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17
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El Moussaoui M, Maes N, Hong SL, Lambert N, Gofflot S, Dellot P, Belhadj Y, Huynen P, Hayette MP, Meex C, Bontems S, Defêche J, Godderis L, Molenberghs G, Meuris C, Artesi M, Durkin K, Rahmouni S, Grégoire C, Beguin Y, Moutschen M, Dellicour S, Darcis G. Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium. Viruses 2022; 14:v14061302. [PMID: 35746774 PMCID: PMC9227503 DOI: 10.3390/v14061302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/16/2022] Open
Abstract
Healthcare workers (HCWs) are known to be at higher risk of developing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections although whether these risks are equal across all occupational roles is uncertain. Identifying these risk factors and understand SARS-CoV-2 transmission pathways in healthcare settings are of high importance to achieve optimal protection measures. We aimed to investigate the implementation of a voluntary screening program for SARS-CoV-2 infections among hospital HCWs and to elucidate potential transmission pathways though phylogenetic analysis before the vaccination era. HCWs of the University Hospital of Liège, Belgium, were invited to participate in voluntary reverse transcriptase-polymerase chain reaction (RT-PCR) assays performed every week from April to December 2020. Phylogenetic analysis of SARS-CoV-2 genomes were performed for a subgroup of 45 HCWs. 5095 samples were collected from 703 HCWs. 212 test results were positive, 15 were indeterminate, and 4868 returned negative. 156 HCWs (22.2%) tested positive at least once during the study period. All SARS-CoV-2 test results returned negative for 547 HCWs (77.8%). Nurses (p < 0.05), paramedics (p < 0.05), and laboratory staff handling respiratory samples (p < 0.01) were at higher risk for being infected compared to the control non-patient facing group. Our phylogenetic analysis revealed that most positive samples corresponded to independent introduction events into the hospital. Our findings add to the growing evidence of differential risks of being infected among HCWs and support the need to implement appropriate protection measures based on each individual’s risk profile to guarantee the protection of both HCWs and patients. Furthermore, our phylogenetic investigations highlight that most positive samples correspond to distinct introduction events into the hospital.
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Affiliation(s)
- Majdouline El Moussaoui
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 4000 Liege, Belgium; (P.D.); (Y.B.); (C.M.); (M.M.); (G.D.)
- Correspondence:
| | - Nathalie Maes
- Department of Biostatistics and Medico-Economic Information, University Hospital of Liège, 4000 Liege, Belgium;
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; (S.L.H.); (S.D.)
| | - Nicolas Lambert
- Department of Neurology, University Hospital of Liège, 4000 Liege, Belgium;
| | - Stéphanie Gofflot
- Department of Biothèque Hospitalo-Universitaire de Liège (BHUL), University Hospital of Liège, 4000 Liege, Belgium;
| | - Patricia Dellot
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 4000 Liege, Belgium; (P.D.); (Y.B.); (C.M.); (M.M.); (G.D.)
| | - Yasmine Belhadj
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 4000 Liege, Belgium; (P.D.); (Y.B.); (C.M.); (M.M.); (G.D.)
| | - Pascale Huynen
- Department of Clinical Microbiology, University Hospital of Liège, 4000 Liege, Belgium; (P.H.); (M.-P.H.); (C.M.); (S.B.); (J.D.)
| | - Marie-Pierre Hayette
- Department of Clinical Microbiology, University Hospital of Liège, 4000 Liege, Belgium; (P.H.); (M.-P.H.); (C.M.); (S.B.); (J.D.)
| | - Cécile Meex
- Department of Clinical Microbiology, University Hospital of Liège, 4000 Liege, Belgium; (P.H.); (M.-P.H.); (C.M.); (S.B.); (J.D.)
| | - Sébastien Bontems
- Department of Clinical Microbiology, University Hospital of Liège, 4000 Liege, Belgium; (P.H.); (M.-P.H.); (C.M.); (S.B.); (J.D.)
| | - Justine Defêche
- Department of Clinical Microbiology, University Hospital of Liège, 4000 Liege, Belgium; (P.H.); (M.-P.H.); (C.M.); (S.B.); (J.D.)
| | - Lode Godderis
- Centre for Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit Leuven, 3000 Leuven, Belgium;
| | - Geert Molenberghs
- Institute for Biostatistics and Statistical Bioinformatics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium;
| | - Christelle Meuris
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 4000 Liege, Belgium; (P.D.); (Y.B.); (C.M.); (M.M.); (G.D.)
| | - Maria Artesi
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4000 Liege, Belgium; (M.A.); (K.D.)
| | - Keith Durkin
- Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4000 Liege, Belgium; (M.A.); (K.D.)
| | - Souad Rahmouni
- Laboratory of Animal Genomics, GIGA-Medical Genomics, GIGA-Institute, University of Liège, 4000 Liege, Belgium;
| | - Céline Grégoire
- Department of Haematology, University Hospital of Liège, 4000 Liege, Belgium; (C.G.); (Y.B.)
| | - Yves Beguin
- Department of Haematology, University Hospital of Liège, 4000 Liege, Belgium; (C.G.); (Y.B.)
| | - Michel Moutschen
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 4000 Liege, Belgium; (P.D.); (Y.B.); (C.M.); (M.M.); (G.D.)
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium; (S.L.H.); (S.D.)
- Spatial Epidemiology Lab, Université Libre de Bruxelles, 1000 Brussels, Belgium
| | - Gilles Darcis
- Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 4000 Liege, Belgium; (P.D.); (Y.B.); (C.M.); (M.M.); (G.D.)
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18
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Rosenthal SH, Gerasimova A, Ruiz-Vega R, Livingston K, Kagan RM, Liu Y, Anderson B, Owen R, Bernstein L, Smolgovsky A, Xu D, Chen R, Grupe A, Tanpaiboon P, Lacbawan F. Development and validation of a high throughput SARS-CoV-2 whole genome sequencing workflow in a clinical laboratory. Sci Rep 2022; 12:2054. [PMID: 35136154 PMCID: PMC8826425 DOI: 10.1038/s41598-022-06091-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 01/24/2022] [Indexed: 11/24/2022] Open
Abstract
Monitoring new mutations in SARS-CoV-2 provides crucial information for identifying diagnostic and therapeutic targets and important insights to achieve a more effective COVID-19 control strategy. Next generation sequencing (NGS) technologies have been widely used for whole genome sequencing (WGS) of SARS-CoV-2. While various NGS methods have been reported, one chief limitation has been the complexity of the workflow, limiting the scalability. Here, we overcome this limitation by designing a laboratory workflow optimized for high-throughput studies. The workflow utilizes modified ARTIC network v3 primers for SARS-CoV-2 whole genome amplification. NGS libraries were prepared by a 2-step PCR method, similar to a previously reported tailed PCR method, with further optimizations to improve amplicon balance, to minimize amplicon dropout for viral genomes harboring primer-binding site mutation(s), and to integrate robotic liquid handlers. Validation studies demonstrated that the optimized workflow can process up to 2688 samples in a single sequencing run without compromising sensitivity and accuracy and with fewer amplicon dropout events compared to the standard ARTIC protocol. We additionally report results for over 65,000 SARS-CoV-2 whole genome sequences from clinical specimens collected in the United States between January and September of 2021, as part of an ongoing national genomics surveillance effort.
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Affiliation(s)
| | | | | | | | - Ron M Kagan
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA.
| | - Yan Liu
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | - Ben Anderson
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | - Renius Owen
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | | | | | - Dong Xu
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | - Rebecca Chen
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
| | - Andrew Grupe
- Quest Diagnostics, San Juan Capistrano, CA, 92675, USA
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19
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Transmission of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) from pre and asymptomatic infected individuals: a systematic review. Clin Microbiol Infect 2022; 28:178-189. [PMID: 34757116 PMCID: PMC8555342 DOI: 10.1016/j.cmi.2021.10.015] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/13/2021] [Accepted: 10/23/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND The role of SARS-Cov-2-infected persons who develop symptoms after testing (presymptomatics) or not at all (asymptomatics) in the pandemic spread is unknown. OBJECTIVES To determine infectiousness and probable contribution of asymptomatic persons (at the time of testing) to pandemic SARS-CoV-2 spread. DATA SOURCES LitCovid, medRxiv, Google Scholar, and WHO Covid-19 databases (to 31 March 2021) and references in included studies. STUDY ELIGIBILITY CRITERIA Studies with a proven or hypothesized transmission chain based either on serial PCR cycle threshold readings and/or viral culture and/or gene sequencing, with adequate follow-up. PARTICIPANTS People exposed to SARS-CoV-2 within 2-14 days to index asymptomatic (at time of observation) infected individuals. INTERVENTIONS Reliability of symptom and signs was assessed within contemporary knowledge; transmission likelihood was assessed using adapted causality criteria. METHODS Systematic review. We contacted all included studies' corresponding authors requesting further details. RESULTS We included 18 studies from a diverse setting with substantial methodological variation (this field lacks standardized methodology). At initial testing, prevalence of asymptomatic cases was 12.5-100%. Of these, 6-100% were later determined to be presymptomatic, this proportion varying according to setting, methods of case ascertainment and population. Nursing/care home facilities reported high rates of presymptomatic: 50-100% (n = 3 studies). Fourteen studies were classified as high risk of, and four studies as at moderate risk of symptom ascertainment bias. High-risk studies may be less likely to distinguish between presymptomatic and asymptomatic cases. Six asymptomatic studies and four presymptomatic studies reported culturing infectious virus; data were too sparse to determine infectiousness duration. Three studies provided evidence of possible and three of probable/likely asymptomatic transmission; five studies provided possible and two probable/likely presymptomatic SARS-CoV-2 transmission. CONCLUSION High-quality studies provide probable evidence of SARS-CoV-2 transmission from presymptomatic and asymptomatic individuals, with highly variable estimated transmission rates.
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