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  1. Article ; Online: Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission.

    Ellingford, Jamie M / George, Ryan / McDermott, John H / Ahmad, Shazaad / Edgerley, Jonathan J / Gokhale, David / Newman, William G / Ball, Stephen / Machin, Nicholas / Black, Graeme Cm

    eLife

    2021  Volume 10

    Abstract: ... transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and ... of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight ... Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 ...

    Abstract Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.
    MeSH term(s) Aged ; COVID-19/transmission ; COVID-19/virology ; Contact Tracing ; Cross Infection/transmission ; Cross Infection/virology ; Female ; Health Personnel ; Humans ; Infectious Disease Transmission, Patient-to-Professional ; Infectious Disease Transmission, Professional-to-Patient ; Male ; SARS-CoV-2/genetics ; SARS-CoV-2/isolation & purification ; Whole Genome Sequencing
    Language English
    Publishing date 2021-03-17
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.65453
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission

    Jamie M Ellingford / Ryan George / John H McDermott / Shazaad Ahmad / Jonathan J Edgerley / David Gokhale / William G Newman / Stephen Ball / Nicholas Machin / Graeme CM Black

    eLife, Vol

    2021  Volume 10

    Abstract: ... transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and ... of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight ... Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 ...

    Abstract Understanding the effectiveness of infection control methods in reducing and preventing SARS-CoV-2 transmission in healthcare settings is of high importance. We sequenced SARS-CoV-2 genomes for patients and healthcare workers (HCWs) across multiple geographically distinct UK hospitals, obtaining 173 high-quality SARS-CoV-2 genomes. We integrated patient movement and staff location data into the analysis of viral genome data to understand spatial and temporal dynamics of SARS-CoV-2 transmission. We identified eight patient contact clusters (PCC) with significantly increased similarity in genomic variants compared to non-clustered samples. Incorporation of HCW location further increased the number of individuals within PCCs and identified additional links in SARS-CoV-2 transmission pathways. Patients within PCCs carried viruses more genetically identical to HCWs in the same ward location. SARS-CoV-2 genome sequencing integrated with patient and HCW movement data increases identification of outbreak clusters. This dynamic approach can support infection control management strategies within the healthcare setting.
    Keywords SARS-CoV-2 ; genome ; sequencing ; healthcare worker ; healthcare-associated ; nosocomial ; Medicine ; R ; Science ; Q ; Biology (General) ; QH301-705.5
    Subject code 360
    Language English
    Publishing date 2021-03-01T00:00:00Z
    Publisher eLife Sciences Publications Ltd
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  3. Article ; Online: Reconstruction of transmission chains of SARS-CoV-2 amidst multiple outbreaks in a geriatric acute-care hospital: a combined retrospective epidemiological and genomic study.

    Abbas, Mohamed / Cori, Anne / Cordey, Samuel / Laubscher, Florian / Robalo Nunes, Tomás / Myall, Ashleigh / Salamun, Julien / Huber, Philippe / Zekry, Dina / Prendki, Virginie / Iten, Anne / Vieux, Laure / Sauvan, Valérie / Graf, Christophe E / Harbarth, Stephan

    eLife

    2022  Volume 11

    Abstract: ... dynamics of SARS-CoV-2 involving patients and HCWs, to determine who infected whom. We evaluated general ... of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome ... coronavirus 2 (SARS-CoV-2) in geriatric settings.: Methods: We performed a retrospective cohort study ...

    Abstract Background: There is ongoing uncertainty regarding transmission chains and the respective roles of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in geriatric settings.
    Methods: We performed a retrospective cohort study including patients with nosocomial coronavirus disease 2019 (COVID-19) in four outbreak-affected wards, and all SARS-CoV-2 RT-PCR positive HCWs from a Swiss university-affiliated geriatric acute-care hospital that admitted both Covid-19 and non-Covid-19 patients during the first pandemic wave in Spring 2020. We combined epidemiological and genetic sequencing data using a Bayesian modelling framework, and reconstructed transmission dynamics of SARS-CoV-2 involving patients and HCWs, to determine who infected whom. We evaluated general transmission patterns according to case type (HCWs working in dedicated Covid-19 cohorting wards: HCW
    Results: During the study period (1 March to 7 May 2020), we included 180 SARS-CoV-2 positive cases: 127 HCWs (91 HCW
    Conclusions: Most importation events were linked to HCW. Unexpectedly, transmission between HCW
    Funding: This study was supported by a grant from the Swiss National Science Foundation under the NRP78 funding scheme (Grant no. 4078P0_198363).
    MeSH term(s) Aged ; Bayes Theorem ; COVID-19/epidemiology ; Cross Infection/epidemiology ; Disease Outbreaks ; Genomics ; Hospitals ; Humans ; Retrospective Studies ; SARS-CoV-2/genetics
    Language English
    Publishing date 2022-07-19
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2687154-3
    ISSN 2050-084X ; 2050-084X
    ISSN (online) 2050-084X
    ISSN 2050-084X
    DOI 10.7554/eLife.76854
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France

    Quéromès, Grégory / Destras, Grégory / Bal, Antonin / Regue, Hadrien / Burfin, Gwendolyne / Brun, Solenne / Fanget, Rémi / Morfin, Florence / Valette, Martine / Lina, Bruno / Frobert, Emilie / Josset, Laurence

    bioRxiv

    Abstract: ... paramount to detect strain prevalence and transmission dynamics. Given the role of ORF6 in interferon ... Through routine genomic surveillance of the novel SARS-CoV-2 virus (n=229 whole genome sequences ... deletion variants in the same ORF6 region. Importance While the SARS-CoV-2 genome has remained relatively ...

    Abstract Through routine genomic surveillance of the novel SARS-CoV-2 virus (n=229 whole genome sequences), 2 different frameshifting deletions were newly detected in the open reading frame (ORF) 6, starting at the same position (27267). While the 26-nucleotide deletion variant was only found in one sample in March 2020, the 34-nucleotide deletion variant was found within a single geriatric hospital unit in 5/9 patients sequenced and one health care worker with samples collected between April 2nd and 9th, 2020. Both the presence of the 34-nucleotide deletion variant limited to this unit and the clustering of the corresponding whole genome sequences by phylogeny analysis strongly suggested a nosocomial transmission between patients. Interestingly, prolonged viral excretion of the 34-nucleotide deletion variant was identified in a stool sample 14 days after initial diagnosis for one patient. Clinical data revealed no significant difference in disease severity between patients harboring the wild-type or the 34-nucleotide deletion variants. The in vitro infection of the two deletion variants on primate endothelial kidney cells (BGM) and human lung adenocarcinoma cells (Calu-3) yielded comparable replication kinetics with the wild-type strain. Furthermore, high viral loads were found in vivo regardless of the presence or absence of the ORF6 deletion. Our study highlights the transmission and replication capacity of two newly described deletion variants in the same ORF6 region. Importance While the SARS-CoV-2 genome has remained relatively stable since its emergence in the human population, genomic deletions are an evolutionary pattern previously described for the related SARS-CoV. Real-time genomic monitoring of the circulating variants is paramount to detect strain prevalence and transmission dynamics. Given the role of ORF6 in interferon modulation, further characterization, such as mechanistic interactions and interferon monitoring in patients, is crucial in understanding the viral-host factors driving disease evolution.
    Keywords covid19
    Publisher BioRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.08.07.241653
    Database COVID19

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  5. Article ; Online: Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 transmission identifies community social distancing as the dominant intervention reducing outbreaks

    Snell, L. B. / Fisher, C. L. / Taj, U. / Merrick, B. / Alcolea-Medina, A. / Charalampous, T. / Signell, A. W. / Wilson, H. D. / Betancor, G. / Tan Kia Ik, M. / Cunningham, E. / Cliff, P. R. / Pickering, S. / Galao, R. P. / Batra, R. / Neil, S. J. D. / Malim, M. H. / Doores, K. J. / Douthwaite, S. T. /
    Nebbia, G. / Edgeworth, J. D. / Awan, A. R. / consortium, The COVID-19 Genomics UK

    Abstract: Many healthcare facilities report SARS-CoV-2 outbreaks but analysis of transmission during ... surgical facemask-use by healthcare-workers (HCW). Incidence of nosocomial cases, community SARS-CoV-2 ... consecutive patients with a PCR positive SARS-CoV-2 test between March 13th and March 31st, when the pandemic ...

    Abstract Many healthcare facilities report SARS-CoV-2 outbreaks but analysis of transmission during the first wave is complicated by the high prevalence of infection and limited viral genetic diversity. Furthermore, there is limited evidence on the contribution of different vectors for nosocomial infection or on the effectiveness of interventions. Detailed epidemiological and viral nanopore sequence data were analysed from 574 consecutive patients with a PCR positive SARS-CoV-2 test between March 13th and March 31st, when the pandemic first impacted on a large, multisite healthcare institution in London. During this time the first major preventative interventions were introduced including progressive community social distancing (CSD) policies leading to mandatory national lockdown, exclusion of hospital visitors, and introduction of universal surgical facemask-use by healthcare-workers (HCW). Incidence of nosocomial cases, community SARS-CoV-2 cases, and infection in a cohort of 228 HCWs followed the same dynamic course, decreasing subsequent to CSD and prior to introduction of the main hospital-based interventions. We investigated clusters involving nosocomial cases based on overlapping ward-stays during the 14-day incubation period and SARS-CoV-2 genome sequence similarity. Our method placed 80 (89%) of all 90 probable and definite nosocomial cases into 14 clusters containing a median of 4 patients (min 2, max 19) No genetic support was found for the majority of epidemiological clusters (31/44 70%) and genomics revealed multiple contemporaneous outbreaks within single epidemiological clusters. We included a measure of hospital enrichment compared to community cases to increase confidence in our clusters, which were 1-14 fold enriched. Applying genomics, we could provide a robust estimate of the incubation period for nosocomial transmission, with a median lower bound and upper bound of 6 and 9 days respectively. Six (43%) clusters spanned multiple wards, with evidence of cryptic transmission, and community-onset cases could not be identified in more than half the clusters, particularly on the elective hospital site, implicating HCW as vectors of transmission. Taken together these findings suggest that CSD had the dominant impact on reducing nosocomial transmission by reducing HCWs infection.
    Keywords covid19
    Publisher MedRxiv; WHO
    Document type Article ; Online
    DOI 10.1101/2020.11.17.20232827
    Database COVID19

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  6. Article ; Online: Combined epidemiological and genomic analysis of nosocomial SARS-CoV-2 transmission identifies community social distancing as the dominant intervention reducing outbreaks

    Snell, Luke B / Fisher, Chloe L / Taj, Usman / Merrick, Blair / Alcolea-Medina, Adela / Charalampous, Themoula / Signell, Adrian W / Wilson, Harry D / Betancor, Gilberto / Tan Kia Ik, Mark / Cunningham, Emma / Cliff, Penelope R / Pickering, Suzanne / Galao, Rui Pedro / Batra, Rahul / Neil, Stuart J D / Malim, Michael H / Doores, Katie J / Douthwaite, Sam T /
    Nebbia, Gaia / Edgeworth, Jonathan D / Awan, Ali R / The COVID-19 Genomics UK (COG-UK) consortium

    medRxiv

    Abstract: Many healthcare facilities report SARS-CoV-2 outbreaks but analysis of transmission during ... surgical facemask-use by healthcare-workers (HCW). Incidence of nosocomial cases, community SARS-CoV-2 ... consecutive patients with a PCR positive SARS-CoV-2 test between March 13th and March 31st, when the pandemic ...

    Abstract Many healthcare facilities report SARS-CoV-2 outbreaks but analysis of transmission during the first wave is complicated by the high prevalence of infection and limited viral genetic diversity. Furthermore, there is limited evidence on the contribution of different vectors for nosocomial infection or on the effectiveness of interventions. Detailed epidemiological and viral nanopore sequence data were analysed from 574 consecutive patients with a PCR positive SARS-CoV-2 test between March 13th and March 31st, when the pandemic first impacted on a large, multisite healthcare institution in London. During this time the first major preventative interventions were introduced including progressive community social distancing (CSD) policies leading to mandatory national lockdown, exclusion of hospital visitors, and introduction of universal surgical facemask-use by healthcare-workers (HCW). Incidence of nosocomial cases, community SARS-CoV-2 cases, and infection in a cohort of 228 HCWs followed the same dynamic course, decreasing subsequent to CSD and prior to introduction of the main hospital-based interventions. We investigated clusters involving nosocomial cases based on overlapping ward-stays during the 14-day incubation period and SARS-CoV-2 genome sequence similarity. Our method placed 80 (89%) of all 90 probable and definite nosocomial cases into 14 clusters containing a median of 4 patients (min 2, max 19) No genetic support was found for the majority of epidemiological clusters (31/44 70%) and genomics revealed multiple contemporaneous outbreaks within single epidemiological clusters. We included a measure of hospital enrichment compared to community cases to increase confidence in our clusters, which were 1-14 fold enriched. Applying genomics, we could provide a robust estimate of the incubation period for nosocomial transmission, with a median lower bound and upper bound of 6 and 9 days respectively. Six (43%) clusters spanned multiple wards, with evidence of cryptic transmission, and community-onset cases could not be identified in more than half the clusters, particularly on the elective hospital site, implicating HCW as vectors of transmission. Taken together these findings suggest that CSD had the dominant impact on reducing nosocomial transmission by reducing HCWs infection.
    Keywords covid19
    Language English
    Publishing date 2020-11-18
    Publisher Cold Spring Harbor Laboratory Press
    Document type Article ; Online
    DOI 10.1101/2020.11.17.20232827
    Database COVID19

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  7. Article ; Online: Explosive nosocomial outbreak of SARS-CoV-2 in a rehabilitation clinic: the limits of genomics for outbreak reconstruction.

    Abbas, M / Robalo Nunes, T / Cori, A / Cordey, S / Laubscher, F / Baggio, S / Jombart, T / Iten, A / Vieux, L / Teixeira, D / Perez, M / Pittet, D / Frangos, E / Graf, C E / Zingg, W / Harbarth, S

    The Journal of hospital infection

    2021  Volume 117, Page(s) 124–134

    Abstract: ... This outbreak report highlights the essential role of HCWs in SARS-CoV-2 transmission dynamics in healthcare ... transmission chains and assess the role of healthcare workers (HCWs) in SARS-CoV-2 transmission.: Methods ... Background: Nosocomial outbreaks of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2 ...

    Abstract Background: Nosocomial outbreaks of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) are frequent despite implementation of conventional infection control measures. An outbreak investigation was undertaken using advanced genomic and statistical techniques to reconstruct likely transmission chains and assess the role of healthcare workers (HCWs) in SARS-CoV-2 transmission.
    Methods: A nosocomial SARS-CoV-2 outbreak in a university-affiliated rehabilitation clinic was investigated, involving patients and HCWs, with high coverage of pathogen whole-genome sequences (WGS). The time-varying reproduction number from epidemiological data (R
    Findings: The outbreak lasted from 14
    Interpretation: This outbreak report highlights the essential role of HCWs in SARS-CoV-2 transmission dynamics in healthcare settings. Limited genetic diversity in pathogen genomes hampered the reconstruction of individual transmission events, resulting in substantial uncertainty in who infected whom. However, this study shows that despite such uncertainty, significant transmission patterns can be observed.
    MeSH term(s) Bayes Theorem ; COVID-19 ; Case-Control Studies ; Cross Infection/epidemiology ; Disease Outbreaks ; Explosive Agents ; Genomics ; Health Personnel ; Humans ; Phylogeny ; SARS-CoV-2
    Chemical Substances Explosive Agents
    Language English
    Publishing date 2021-08-27
    Publishing country England
    Document type Journal Article
    ZDB-ID 779366-2
    ISSN 1532-2939 ; 0195-6701
    ISSN (online) 1532-2939
    ISSN 0195-6701
    DOI 10.1016/j.jhin.2021.07.013
    Database MEDical Literature Analysis and Retrieval System OnLINE

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