1
|
Oltean HN, Black A, Lunn SM, Smith N, Templeton A, Bevers E, Kibiger L, Sixberry M, Bickel JB, Hughes JP, Lindquist S, Baseman JG, Bedford T. Changing genomic epidemiology of COVID-19 in long-term care facilities during the 2020-2022 pandemic, Washington State. BMC Public Health 2024; 24:182. [PMID: 38225567 PMCID: PMC10789038 DOI: 10.1186/s12889-023-17461-2] [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: 08/28/2023] [Accepted: 12/12/2023] [Indexed: 01/17/2024] Open
Abstract
BACKGROUND Long-term care facilities (LTCFs) are vulnerable to disease outbreaks. Here, we jointly analyze SARS-CoV-2 genomic and paired epidemiologic data from LTCFs and surrounding communities in Washington state (WA) to assess transmission patterns during 2020-2022, in a setting of changing policy. We describe sequencing efforts and genomic epidemiologic findings across LTCFs and perform in-depth analysis in a single county. METHODS We assessed genomic data representativeness, built phylogenetic trees, and conducted discrete trait analysis to estimate introduction sizes over time, and explored selected outbreaks to further characterize transmission events. RESULTS We found that transmission dynamics among cases associated with LTCFs in WA changed over the course of the COVID-19 pandemic, with variable introduction rates into LTCFs, but decreasing amplification within LTCFs. SARS-CoV-2 lineages circulating in LTCFs were similar to those circulating in communities at the same time. Transmission between staff and residents was bi-directional. CONCLUSIONS Understanding transmission dynamics within and between LTCFs using genomic epidemiology on a broad scale can assist in targeting policies and prevention efforts. Tracking facility-level outbreaks can help differentiate intra-facility outbreaks from high community transmission with repeated introduction events. Based on our study findings, methods for routine tree building and overlay of epidemiologic data for hypothesis generation by public health practitioners are recommended. Discrete trait analysis added valuable insight and can be considered when representative sequencing is performed. Cluster detection tools, especially those that rely on distance thresholds, may be of more limited use given current data capture and timeliness. Importantly, we noted a decrease in data capture from LTCFs over time. Depending on goals for use of genomic data, sentinel surveillance should be increased or targeted surveillance implemented to ensure available data for analysis.
Collapse
Affiliation(s)
- Hanna N Oltean
- Department of Health, Washington State, 1610 NE 150th St, Shoreline, Washington, 98155, USA.
- University of Washington, 1410 NE Campus Parkway, Seattle, Washington, 98195, USA.
| | - Allison Black
- Department of Health, Washington State, 1610 NE 150th St, Shoreline, Washington, 98155, USA
| | - Stephanie M Lunn
- Department of Health, Washington State, 1610 NE 150th St, Shoreline, Washington, 98155, USA
| | - Nailah Smith
- Department of Health, Washington State, 1610 NE 150th St, Shoreline, Washington, 98155, USA
| | - Allison Templeton
- Department of Health, Washington State, 1610 NE 150th St, Shoreline, Washington, 98155, USA
| | - Elyse Bevers
- Department of Health, Washington State, 1610 NE 150th St, Shoreline, Washington, 98155, USA
| | - Lynae Kibiger
- Department of Health, Washington State, 1610 NE 150th St, Shoreline, Washington, 98155, USA
| | - Melissa Sixberry
- Yakima Health District, 1210 Ahtanum Ridge Dr, Union Gap, Washington, 98903, USA
| | - Josina B Bickel
- Yakima Health District, 1210 Ahtanum Ridge Dr, Union Gap, Washington, 98903, USA
| | - James P Hughes
- University of Washington, 1410 NE Campus Parkway, Seattle, Washington, 98195, USA
| | - Scott Lindquist
- Department of Health, Washington State, 1610 NE 150th St, Shoreline, Washington, 98155, USA
- University of Washington, 1410 NE Campus Parkway, Seattle, Washington, 98195, USA
| | - Janet G Baseman
- University of Washington, 1410 NE Campus Parkway, Seattle, Washington, 98195, USA
| | - Trevor Bedford
- Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, Washington, 98109, USA
| |
Collapse
|
2
|
Kain DC, Isabel S, Abdulnoor M, Boissinot K, De Borja R, Filkin A, Lam B, Li J, Lungu I, McCreight L, McGeer A, Mazzulli T, Paterson A, Zuzarte P, Vincelli F, Bergwerff C, Fattouh R, Simpson JT, Johnstone J. Coronavirus disease 2019 (COVID-19) outbreak on an in-patient medical unit associated with unrecognized exposures in common areas-Epidemiological and whole-genome sequencing investigation. Infect Control Hosp Epidemiol 2023; 44:1829-1833. [PMID: 36912329 PMCID: PMC10665866 DOI: 10.1017/ice.2023.34] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/31/2023] [Accepted: 02/04/2023] [Indexed: 03/14/2023]
Abstract
OBJECTIVE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) hospital outbreaks have been common and devastating during the coronavirus disease 2019 (COVID-19) pandemic. Understanding SARS-CoV-2 transmission in these environments is critical for preventing and managing outbreaks. DESIGN Outbreak investigation through epidemiological mapping and whole-genome sequencing phylogeny. SETTING Hospital in-patient medical unit outbreak in Toronto, Canada, from November 2020 to January 2021. PARTICIPANTS The outbreak involved 8 patients and 10 staff and was associated with 3 patient deaths. RESULTS Patients being cared for in geriatric chairs at the nursing station were at high risk for both acquiring and transmitting SARS-CoV-2 to other patients and staff. Furthermore, given the informal nature of these transmissions, they were not initially recognized, which led to further transmission and missing the opportunity for preventative COVID-19 therapies. CONCLUSIONS During outbreak prevention and management, the risk of informal patient care settings, such as geriatric chairs, should be considered. During high-risk periods or during outbreaks, efforts should be made to care for patients in their rooms when possible.
Collapse
Affiliation(s)
- Dylan C. Kain
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sandra Isabel
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Mariana Abdulnoor
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Sick Kids Hospital, Department of Infectious Disease, Toronto, Ontario, Canada
| | - Karel Boissinot
- Department of Laboratory Medicine, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
| | | | - Amanda Filkin
- Occupational Health, Sinai Health, Toronto, Ontario, Canada
| | - Bernard Lam
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jason Li
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ilinca Lungu
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Liz McCreight
- Infection Prevention and Control, Sinai Health, Toronto, Ontario, Canada
| | - Allison McGeer
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Microbiology, Sinai Health System/University Health Network, Toronto, Ontario, Canada
| | - Tony Mazzulli
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Microbiology, Sinai Health System/University Health Network, Toronto, Ontario, Canada
| | - Aimee Paterson
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Philip Zuzarte
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | - Ramzi Fattouh
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Laboratory Medicine, St. Michael’s Hospital, Unity Health Toronto, Toronto, Ontario, Canada
- Li Ka Shing Knowledge Institute, Unity Health Toronto, Toronto, Ontario, Canada
| | - Jared T. Simpson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jennie Johnstone
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Infection Prevention and Control, Sinai Health, Toronto, Ontario, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
3
|
Sullivan SG, Sadewo GRP, Brotherton JM, Kaufman C, Goldsmith JJ, Whiting S, Wu L, Canevari JT, Lusher D. The spread of coronavirus disease 2019 (COVID-19) via staff work and household networks in residential aged-care services in Victoria, Australia, May-October 2020. Infect Control Hosp Epidemiol 2023; 44:1334-1341. [PMID: 36263465 DOI: 10.1017/ice.2022.243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
OBJECTIVE Morbidity and mortality from coronavirus disease 2019 (COVID-19) have been significant among elderly residents of residential aged-care services (RACS). To prevent incursions of COVID-19 in RACS in Australia, visitors were banned and aged-care workers were encouraged to work at a single site. We conducted a review of case notes and a social network analysis to understand how workplace and social networks enabled the spread of severe acute respiratory coronavirus virus 2 (SARS-CoV-2) among RACS. DESIGN Retrospective outbreak review. SETTING AND PARTICIPANTS Staff involved in COVID-19 outbreaks in RACS in Victoria, Australia, May-October 2020. METHODS The Victorian Department of Health COVID-19 case and contact data were reviewed to construct 2 social networks: (1) a work network connecting RACS through workers and (2) a household network connecting to RACS through households. Probable index cases were reviewed to estimate the number and size (number of resident cases and deaths) of outbreaks likely initiated by multisite work versus transmission via households. RESULTS Among 2,033 cases linked to an outbreak as staff, 91 (4.5%) were multisite staff cases. Forty-three outbreaks were attributed to multisite work and 35 were deemed potentially preventable had staff worked at a single site. In addition, 99 staff cases were linked to another RACS outbreak through their household contacts, and 21 outbreaks were attributed to staff-household transmission. CONCLUSIONS Limiting worker mobility through single-site policies could reduce the chances of SARS-CoV-2 spreading from one RACS to another. However, initiatives that reduce the chance of transmission via household networks would also be needed.
Collapse
Affiliation(s)
- Sheena G Sullivan
- Public Health Division, Victorian Department of Health, Melbourne, Victoria, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, Royal Melbourne Hospital, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Giovanni Radhitio P Sadewo
- Social Network Research Laboratory, Centre for Transformative Innovation, Swinburne University of Technology, Melbourne, Victoria, Australia
| | - Julia M Brotherton
- Australian Centre for the Prevention of Cervical Cancer, Melbourne, Victoria, Australia
| | - Claire Kaufman
- Public Health Division, Victorian Department of Health, Melbourne, Victoria, Australia
| | - Jessie J Goldsmith
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Logan Wu
- Public Health Division, Victorian Department of Health, Melbourne, Victoria, Australia
| | - Jose T Canevari
- Public Health Division, Victorian Department of Health, Melbourne, Victoria, Australia
| | - Dean Lusher
- Social Network Research Laboratory, Centre for Transformative Innovation, Swinburne University of Technology, Melbourne, Victoria, Australia
| |
Collapse
|
4
|
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.
Collapse
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
| | | |
Collapse
|
5
|
Luterbach CL, Chen L, Komarow L, Ostrowsky B, Kaye KS, Hanson B, Arias CA, Desai S, Gallagher JC, Novick E, Pagkalinawan S, Lautenbach E, Wortmann G, Kalayjian RC, Eilertson B, Farrell JJ, McCarty T, Hill C, Fowler VG, Kreiswirth BN, Bonomo RA, van Duin D. Transmission of Carbapenem-Resistant Klebsiella pneumoniae in US Hospitals. Clin Infect Dis 2023; 76:229-237. [PMID: 36173830 PMCID: PMC10202433 DOI: 10.1093/cid/ciac791] [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: 05/04/2022] [Revised: 09/08/2022] [Accepted: 09/23/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKp) is the most prevalent carbapenem-resistant Enterobacterales in the United States. We evaluated CRKp clustering in patients in US hospitals. METHODS From April 2016 to August 2017, 350 patients with clonal group 258 CRKp were enrolled in the Consortium on Resistance Against Carbapenems in Klebsiella and other Enterobacteriaceae, a prospective, multicenter, cohort study. A maximum likelihood tree was constructed using RAxML. Static clusters shared ≤21 single-nucleotide polymorphisms (SNP) and a most recent common ancestor. Dynamic clusters incorporated SNP distance, culture timing, and rates of SNP accumulation and transmission using the R program TransCluster. RESULTS Most patients were admitted from home (n = 150, 43%) or long-term care facilities (n = 115, 33%). Urine (n = 149, 43%) was the most common isolation site. Overall, 55 static and 47 dynamics clusters were identified involving 210 of 350 (60%) and 194 of 350 (55%) patients, respectively. Approximately half of static clusters were identical to dynamic clusters. Static clusters consisted of 33 (60%) intrasystem and 22 (40%) intersystem clusters. Dynamic clusters consisted of 32 (68%) intrasystem and 15 (32%) intersystem clusters and had fewer SNP differences than static clusters (8 vs 9; P = .045; 95% confidence interval [CI]: -4 to 0). Dynamic intersystem clusters contained more patients than dynamic intrasystem clusters (median [interquartile range], 4 [2, 7] vs 2 [2, 2]; P = .007; 95% CI: -3 to 0). CONCLUSIONS Widespread intrasystem and intersystem transmission of CRKp was identified in hospitalized US patients. Use of different methods for assessing genetic similarity resulted in only minor differences in interpretation.
Collapse
Affiliation(s)
- Courtney L Luterbach
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Lauren Komarow
- Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Belinda Ostrowsky
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Keith S Kaye
- Division of Infectious Diseases, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Blake Hanson
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, USA
- Center for Infectious Diseases, UTHealth School of Public Health, Houston, Texas, USA
| | - Cesar A Arias
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, USA
- Center for Infectious Diseases, UTHealth School of Public Health, Houston, Texas, USA
- Molecular Genetics and Antimicrobial Resistance Unit–International Center for Microbial Genomics, Universidad El Bosque, Bogota, Columbia
| | - Samit Desai
- Division of Infectious Diseases, Hackensack University Medical Center, Hackensack, New Jersey, USA
| | - Jason C Gallagher
- Temple University School of Pharmacy, Philadelphia, Pennsylvania, USA
| | - Elizabeth Novick
- Temple University School of Pharmacy, Philadelphia, Pennsylvania, USA
| | | | - Ebbing Lautenbach
- Division of Infectious Diseases, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Glenn Wortmann
- Section of Infectious Diseases, MedStar Washington Hospital Center, Washington, District of Columbia, USA
| | - Robert C Kalayjian
- Department of Medicine, MetroHealth Medical Center, Cleveland, Ohio, USA
| | - Brandon Eilertson
- Division of Infectious Diseases, Department of Medicine, State University of New York Downstate, Brooklyn, NY, USA
| | - John J Farrell
- Division of Infectious Disease, Department of Internal Medicine, OSF Saint Francis Medical Center, University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - Todd McCarty
- Division of Infectious Disease, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Carol Hill
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Vance G Fowler
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
| | - Robert A Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Case Western Reserve University-Cleveland Veterans Affairs Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | | |
Collapse
|
6
|
Brainard DJ, Bunn DD, Watts ML, Killett DA, O'Brien PSJ, Lake PIR, Mumford MS, Lane DK. English care home staff morale and preparedness during the Covid pandemic: A longitudinal analysis. Am J Infect Control 2022:S0196-6553(22)00778-7. [PMID: 36332725 PMCID: PMC9626402 DOI: 10.1016/j.ajic.2022.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 10/26/2022] [Accepted: 10/26/2022] [Indexed: 11/05/2022]
Abstract
BACKGROUND : Staff actions to prevent infection introduction and transmission in long-term care facilities (LTCFs) were key to reducing morbidity and mortality from COVID-19. Implementing infection control measures (ICMs) requires training, adherence and complex decision making while trying to deliver high quality care. We surveyed LTCF staff in England about their preparedness and morale at three timepoints during the COVID-19 epidemic. METHODS : Online structured survey targeted at LTCF workers (any role) administered at three timepoints (November 2020-January 2021; August-November 2021; March-May 2022). Narrative summary of answers, narrative and statistical summary (proportionality with Pearson's chi-square or Fisher's Exact Test) of possible differences in answers between waves. RESULTS : Across all three survey waves, 387 responses were received. Morale, attitudes towards working environment and perception about colleague collaboration were mostly positive at all survey points. Infection control training was perceived as adequate. Staff felt mostly positive emotions at work. The working environment remained challenging. Masks were the single form of PPE most consistently used; eye protection the least used. Mask-wearing was linked to poorer communication and resident discomfort as well as mild negative health impacts on many staff, such as dehydration and adverse skin reactions. Hand sanitiser caused skin irritation. CONCUSIONS : Staff morale and working practices were generally good even though the working environment provided many new challenges that did not exist pre-pandemic.
Collapse
|
7
|
Nguyen-Kim H, Beckmann C, Redondo M, Ziliox J, Vallett V, Berger-Sturm K, Overbeck JV, Alberi Auber L. COVID Salivary diagnostics: a comparative technical study. J Med Virol 2022; 94:4277-4286. [PMID: 35614569 PMCID: PMC9347777 DOI: 10.1002/jmv.27883] [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: 03/25/2022] [Revised: 05/11/2022] [Accepted: 05/23/2022] [Indexed: 12/02/2022]
Abstract
Since the beginning of the coronavirus disease 2019 (COVID‐19) pandemic, molecular diagnostics of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) have taken center stage in the detection of infected individuals for isolation purposes but also in the mass surveillance as a preventive strategy to contain the virus spread. While nasopharyngeal swabs (NPS) have remained the golden standard substrate, salivary diagnostic for SARS‐CoV‐2 has been proposed as an alternative and noninvasive measure in vulnerable individuals. Nevertheless, there is a widespread assumption that salivary reverse‐transcription polymerase chain reaction (RT‐PCR) does not match the quality of testing using NPS and particular care should be taken in respect to food or beverage intake, when sampling saliva. Our study indicates that without any precaution in the selection of 190 patients, nor restriction over the time window of sampling, there is 99% match in the COVID‐19 positivity between NPS and saliva when using RT‐PCR, with a reported Delta in thermal cycles (Cts) values for the viral genes Envelope (E) and Open reading frame 1ab (Orf1ab) between 0 and 2, a 98.7% sensitivity and 100% specificity. This high accuracy is maintained in pooling configurations that can be used for mass‐testing purposes in professional and educational settings. The further advantage to using crude saliva as compared to NPS or mouthwash is that direct methods yield robust results. Overall, our study validates and promotes the use of salivary diagnostic for COVID‐19 eliminating the need of a medical practitioner for the sampling, resolving the unpleasantness of the NPS intervention and empowering the patient to do self‐testing in times of need.
Collapse
Affiliation(s)
- Hanh Nguyen-Kim
- Swiss Integrative Center for Human Health, Fribourg, Switzerland
| | | | | | | | | | | | | | | |
Collapse
|
8
|
Sims S, Harris R, Hussein S, Rafferty AM, Desai A, Palmer S, Brearley S, Adams R, Rees L, Fitzpatrick JM. Social Distancing and Isolation Strategies to Prevent and Control the Transmission of COVID-19 and Other Infectious Diseases in Care Homes for Older People: An International Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19063450. [PMID: 35329137 PMCID: PMC8955170 DOI: 10.3390/ijerph19063450] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/02/2022] [Accepted: 03/06/2022] [Indexed: 12/18/2022]
Abstract
Older people living in care homes are at high risk of poor health outcomes and mortality if they contract COVID-19 or other infectious diseases. Measures used to protect residents include social distancing and isolation, although implementation is challenging. This review aimed to assess the social distancing and isolation strategies used by care homes to prevent and control the transmission of COVID-19 and other infectious diseases. Seven electronic databases were searched: Medline, CINAHL, Embase, PsycINFO, HMIC, Social Care Online, and Web of Science Core Collection. Grey literature was searched using MedRxiv, PDQ-Evidence, NICE Evidence Search, LTCCovid19.org and TRIP. Extracted data were synthesised using narrative synthesis and tabulation. 103 papers were included (10 empirical studies, seven literature reviews, and 86 policy documents). Strategies used to prevent and control the transmission of COVID-19 and other infectious diseases included social distancing and isolation of residents and staff, zoning and cohorting of residents, restriction of resident movement/activities, restriction of visitors and restriction of staff working patterns. This review demonstrates a lack of empirical evidence and the limited nature of policy documentation around social distancing and isolation measures in care homes. Evaluative research on these interventions is needed urgently, focusing on the well-being of all residents, particularly those with hearing, vision or cognitive impairments.
Collapse
Affiliation(s)
- Sarah Sims
- The Florence Nightingale Faculty of Nursing, Midwifery and Palliative Care, King’s College London, London SE1 8WA, UK; (S.S.); (R.H.); (A.M.R.); (A.D.)
| | - Ruth Harris
- The Florence Nightingale Faculty of Nursing, Midwifery and Palliative Care, King’s College London, London SE1 8WA, UK; (S.S.); (R.H.); (A.M.R.); (A.D.)
| | - Shereen Hussein
- London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK;
| | - Anne Marie Rafferty
- The Florence Nightingale Faculty of Nursing, Midwifery and Palliative Care, King’s College London, London SE1 8WA, UK; (S.S.); (R.H.); (A.M.R.); (A.D.)
| | - Amit Desai
- The Florence Nightingale Faculty of Nursing, Midwifery and Palliative Care, King’s College London, London SE1 8WA, UK; (S.S.); (R.H.); (A.M.R.); (A.D.)
| | - Sinead Palmer
- Personal Social Services Research Unit, University of Kent, Canterbury CT2 7NZ, UK;
| | - Sally Brearley
- School of Nursing, Kingston University and St George’s University London, London SW17 0RE, UK;
| | | | - Lindsay Rees
- Encore Care Homes Management Ltd., Bournemouth BH8 9RL, UK;
| | - Joanne M. Fitzpatrick
- The Florence Nightingale Faculty of Nursing, Midwifery and Palliative Care, King’s College London, London SE1 8WA, UK; (S.S.); (R.H.); (A.M.R.); (A.D.)
- Correspondence:
| |
Collapse
|
9
|
Lindsey BB, Villabona-Arenas CJ, Campbell F, Keeley AJ, Parker MD, Shah DR, Parsons H, Zhang P, Kakkar N, Gallis M, Foulkes BH, Wolverson P, Louka SF, Christou S, State A, Johnson K, Raza M, Hsu S, Jombart T, Cori A, Evans CM, Partridge DG, Atkins KE, Hué S, de Silva TI. Characterising within-hospitalSARS-CoV-2 transmission events using epidemiological and viral genomic data across two pandemic waves. Nat Commun 2022; 13:671. [PMID: 35115517 PMCID: PMC8814040 DOI: 10.1038/s41467-022-28291-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 01/17/2022] [Indexed: 01/24/2023] Open
Abstract
Hospital outbreaks of COVID19 result in considerable mortality and disruption to healthcare services and yet little is known about transmission within this setting. We characterise within hospital transmission by combining viral genomic and epidemiological data using Bayesian modelling amongst 2181 patients and healthcare workers from a large UK NHS Trust. Transmission events were compared between Wave 1 (1st March to 25th J'uly 2020) and Wave 2 (30th November 2020 to 24th January 2021). We show that staff-to-staff transmissions reduced from 31.6% to 12.9% of all infections. Patient-to-patient transmissions increased from 27.1% to 52.1%. 40%-50% of hospital-onset patient cases resulted in onward transmission compared to 4% of community-acquired cases. Control measures introduced during the pandemic likely reduced transmissions between healthcare workers but were insufficient to prevent increasing numbers of patient-to-patient transmissions. As hospital-acquired cases drive most onward transmission, earlier identification of nosocomial cases will be required to break hospital transmission chains.
Collapse
Affiliation(s)
- Benjamin B Lindsey
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.,Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Ch Julián Villabona-Arenas
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Finlay Campbell
- Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Alexander J Keeley
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.,Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Matthew D Parker
- Sheffield Biomedical Research Centre, The University of Sheffield, Sheffield, UK.,Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK.,The Department of Neuroscience/Neuroscience Institute, The University of Sheffield, Sheffield, UK
| | - Dhruv R Shah
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Helena Parsons
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.,Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Peijun Zhang
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Nishchay Kakkar
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Marta Gallis
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Benjamin H Foulkes
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Paige Wolverson
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Stavroula F Louka
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Stella Christou
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Amy State
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Katie Johnson
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Mohammad Raza
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.,Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Sharon Hsu
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.,Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, UK
| | - Thibaut Jombart
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK.,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.,MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK
| | | | | | | | - Cariad M Evans
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.,Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - David G Partridge
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK.,Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Katherine E Atkins
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK. .,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK. .,Usher Institute, The University of Edinburgh, Edinburgh, UK.
| | - Stéphane Hué
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, UK. .,Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
| | - Thushan I de Silva
- The Florey Institute for Host-Pathogen Interactions & Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK. .,Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK. .,MRC Unit The Gambia at the London School of Hygiene and Tropical Medicine, Fajara, The Gambia.
| |
Collapse
|
10
|
Illingworth CJR, Hamilton WL, Jackson C, Warne B, Popay A, Meredith L, Hosmillo M, Jahun A, Fieldman T, Routledge M, Houldcroft CJ, Caller L, Caddy S, Yakovleva A, Hall G, Khokhar FA, Feltwell T, Pinckert ML, Georgana I, Chaudhry Y, Curran M, Parmar S, Sparkes D, Rivett L, Jones NK, Sridhar S, Forrest S, Dymond T, Grainger K, Workman C, Gkrania-Klotsas E, Brown NM, Weekes MP, Baker S, Peacock SJ, Gouliouris T, Goodfellow I, Angelis DD, Török ME. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events. Mol Biol Evol 2022; 39:6519868. [PMID: 35106603 PMCID: PMC8892943 DOI: 10.1093/molbev/msac025] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Identifying linked cases of infection is a critical component of the public health response to viral infectious diseases. In a clinical context, there is a need to make rapid assessments of whether cases of infection have arrived independently onto a ward, or are potentially linked via direct transmission. Viral genome sequence data are of great value in making these assessments, but are often not the only form of data available. Here, we describe A2B-COVID, a method for the rapid identification of potentially linked cases of COVID-19 infection designed for clinical settings. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and evolutionary analysis of genome sequences to assess whether data collected from cases of infection are consistent or inconsistent with linkage via direct transmission. A retrospective analysis of data from two wards at Cambridge University Hospitals NHS Foundation Trust during the first wave of the pandemic showed qualitatively different patterns of linkage between cases on designated COVID-19 and non-COVID-19 wards. The subsequent real-time application of our method to data from the second epidemic wave highlights its value for monitoring cases of infection in a clinical context.
Collapse
Affiliation(s)
- Christopher J R Illingworth
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom,MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom,Institut für Biologische Physik, Universität zu Köln, Köln, Germany,Corresponding author: E-mail:
| | - William L Hamilton
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | - Ben Warne
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ashley Popay
- Public Health England Field Epidemiology Unit, Cambridge Institute of Public Health, Cambridge, United Kingdom
| | - Luke Meredith
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Myra Hosmillo
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Aminu Jahun
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Tom Fieldman
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Matthew Routledge
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | | | | | - Sarah Caddy
- Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Anna Yakovleva
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Grant Hall
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Fahad A Khokhar
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Theresa Feltwell
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Malte L Pinckert
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Iliana Georgana
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Yasmin Chaudhry
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Martin Curran
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Surendra Parmar
- Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Dominic Sparkes
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Lucy Rivett
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Nick K Jones
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Sushmita Sridhar
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom,Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | - Tom Dymond
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Kayleigh Grainger
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Chris Workman
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Effrossyni Gkrania-Klotsas
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,MRC Epidemiology Unit, University of Cambridge, Level 3 Institute of Metabolic Science, Cambridge, United Kingdom,School of Clinical Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nicholas M Brown
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Michael P Weekes
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Stephen Baker
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge Institute for Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge, United Kingdom
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Clinical Microbiology and Public Health Laboratory, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Ian Goodfellow
- Department of Pathology, Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Daniela De Angelis
- MRC Biostatistics Unit, University of Cambridge, Cambridge, United Kingdom,Public Health England, National Infection Service, London, United Kingdom
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom,Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| |
Collapse
|
11
|
Aggarwal D, Myers R, Hamilton WL, Bharucha T, Tumelty NM, Brown CS, Meader EJ, Connor T, Smith DL, Bradley DT, Robson S, Bashton M, Shallcross L, Zambon M, Goodfellow I, Chand M, O'Grady J, Török ME, Peacock SJ, Page AJ. The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. THE LANCET. MICROBE 2022; 3:e151-e158. [PMID: 34608459 PMCID: PMC8480962 DOI: 10.1016/s2666-5247(21)00208-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We reviewed all genomic epidemiology studies on COVID-19 in long-term care facilities (LTCFs) that had been published to date. We found that staff and residents were usually infected with identical, or near identical, SARS-CoV-2 genomes. Outbreaks usually involved one predominant cluster, and the same lineages persisted in LTCFs despite infection control measures. Outbreaks were most commonly due to single or few introductions followed by a spread rather than a series of seeding events from the community into LTCFs. The sequencing of samples taken consecutively from the same individuals at the same facilities showed the persistence of the same genome sequence, indicating that the sequencing technique was robust over time. When combined with local epidemiology, genomics allowed probable transmission sources to be better characterised. The transmission between LTCFs was detected in multiple studies. The mortality rate among residents was high in all facilities, regardless of the lineage. Bioinformatics methods were inadequate in a third of the studies reviewed, and reproducing the analyses was difficult because sequencing data were not available in many facilities.
Collapse
Affiliation(s)
- Dinesh Aggarwal
- Department of Medicine, University of Cambridge, Cambridge, UK
- Public Health England, London, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | | | - William L Hamilton
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Tehmina Bharucha
- Public Health England, London, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital, Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Niamh M Tumelty
- Cambridge University Libraries, University of Cambridge, Cambridge, UK
| | - Colin S Brown
- Public Health England, London, UK
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford, UK
- Lao-Oxford-Mahosot Hospital, Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Emma J Meader
- Norfolk and Norwich University Hospital, Norwich, UK
| | - Tom Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff, Wales, UK
- Public Health Wales, University Hospital of Wales, Cardiff, UK
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Darren L Smith
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Declan T Bradley
- Public Health Agency, Belfast, UK
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Samuel Robson
- University of Portsmouth, Centre for Enzyme Innovation, Portsmouth, UK
| | - Matthew Bashton
- Hub for Biotechnology in the Built Environment, Department of Applied Sciences, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne, UK
| | - Laura Shallcross
- Institute of Health Informatics, University College London, London, UK
| | | | - Ian Goodfellow
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Meera Chand
- Public Health England, London, UK
- Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Justin O'Grady
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - M Estée Török
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospital NHS Foundation Trust, Cambridge, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Andrew J Page
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| |
Collapse
|
12
|
Gallego-García P, Varela N, Estévez-Gómez N, De Chiara L, Fernández-Silva I, Valverde D, Sapoval N, Treangen TJ, Regueiro B, Cabrera-Alvargonzález JJ, del Campo V, Pérez S, Posada D. OUP accepted manuscript. Virus Evol 2022; 8:veac008. [PMID: 35242361 PMCID: PMC8889950 DOI: 10.1093/ve/veac008] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/21/2021] [Accepted: 02/04/2022] [Indexed: 11/23/2022] Open
Abstract
A detailed understanding of how and when severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission occurs is crucial for designing effective prevention measures. Other than contact tracing, genome sequencing provides information to help infer who infected whom. However, the effectiveness of the genomic approach in this context depends on both (high enough) mutation and (low enough) transmission rates. Today, the level of resolution that we can obtain when describing SARS-CoV-2 outbreaks using just genomic information alone remains unclear. In order to answer this question, we sequenced forty-nine SARS-CoV-2 patient samples from ten local clusters in NW Spain for which partial epidemiological information was available and inferred transmission history using genomic variants. Importantly, we obtained high-quality genomic data, sequencing each sample twice and using unique barcodes to exclude cross-sample contamination. Phylogenetic and cluster analyses showed that consensus genomes were generally sufficient to discriminate among independent transmission clusters. However, levels of intrahost variation were low, which prevented in most cases the unambiguous identification of direct transmission events. After filtering out recurrent variants across clusters, the genomic data were generally compatible with the epidemiological information but did not support specific transmission events over possible alternatives. We estimated the effective transmission bottleneck size to be one to two viral particles for sample pairs whose donor–recipient relationship was likely. Our analyses suggest that intrahost genomic variation in SARS-CoV-2 might be generally limited and that homoplasy and recurrent errors complicate identifying shared intrahost variants. Reliable reconstruction of direct SARS-CoV-2 transmission based solely on genomic data seems hindered by a slow mutation rate, potential convergent events, and technical artifacts. Detailed contact tracing seems essential in most cases to study SARS-CoV-2 transmission at high resolution.
Collapse
Affiliation(s)
| | - Nair Varela
- CINBIO, Universidade de Vigo, Vigo 36310, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
| | - Nuria Estévez-Gómez
- CINBIO, Universidade de Vigo, Vigo 36310, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
| | - Loretta De Chiara
- CINBIO, Universidade de Vigo, Vigo 36310, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
| | - Iria Fernández-Silva
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo 36310, Spain
| | - Diana Valverde
- CINBIO, Universidade de Vigo, Vigo 36310, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
- Department of Biochemistry, Genetics, and Immunology, Universidade de Vigo, Vigo 36310, Spain
| | | | | | - Benito Regueiro
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
- Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), Sergas, Vigo 36213, Spain
- Microbiology and Parasitology Department, Medicine and Odontology, Universidade de Santiago, Santiago de Compostela 15782, Spain
| | - Jorge Julio Cabrera-Alvargonzález
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
- Department of Microbiology, Complexo Hospitalario Universitario de Vigo (CHUVI), Sergas, Vigo 36213, Spain
| | - Víctor del Campo
- Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO
- Department of Preventive Medicine, Complexo Hospitalario Universitario de Vigo (CHUVI), Sergas, Vigo 36213, Spain
| | | | | |
Collapse
|
13
|
Martinot M, Carnein S, Kempf C, Gantner P, Gallais F, Fafi-Kremer S. Outbreak of SARS-CoV-2 infection in a long-term care facility after COVID-19 BNT162b2 mRNA vaccination. Clin Microbiol Infect 2021; 27:1537-1539. [PMID: 34242805 PMCID: PMC9525170 DOI: 10.1016/j.cmi.2021.06.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/22/2021] [Accepted: 06/26/2021] [Indexed: 11/28/2022]
Affiliation(s)
- Martin Martinot
- Infectious Diseases Department, Hôpitaux Civils de Colmar 68000 France.
| | | | - Christian Kempf
- Clinical Research Department Hôpitaux Civils de Colmar, Colmar, France
| | - Pierre Gantner
- Virology Laboratory, Strasbourg University Hospital, Strasbourg, France; Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France
| | - Floriane Gallais
- Virology Laboratory, Strasbourg University Hospital, Strasbourg, France; Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France
| | - Samira Fafi-Kremer
- Virology Laboratory, Strasbourg University Hospital, Strasbourg, France; Strasbourg University, INSERM, IRM UMR-S 1109, F-67000 Strasbourg, France
| |
Collapse
|