ABSTRACT
Identifying linked cases of infection is a key part of the public health response to viral infectious disease. Viral genome sequence data is of great value in this task, but requires careful analysis, and may need to be complemented by additional types of data. The Covid-19 pandemic has highlighted the urgent need for analytical methods which bring together sources of data to inform epidemiological investigations. We here describe A2B-COVID, an approach for the rapid identification of linked cases of coronavirus infection. Our method combines knowledge about infection dynamics, data describing the movements of individuals, and novel approaches to genome sequence data to assess whether or not cases of infection are consistent or inconsistent with linkage via transmission. We apply our method to analyse and compare data collected from two wards at Cambridge University Hospitals, showing qualitatively different patterns of linkage between cases on designated Covid-19 and non-Covid-19 wards. Our method is suitable for the rapid analysis of data from clinical or other potential outbreak settings.
ABSTRACT
COVID-19 poses a major challenge to care homes, as SARS-CoV-2 is readily transmitted and causes disproportionately severe disease in older people. Here, 1,167 residents from 337 care homes were identified from a dataset of 6,600 COVID-19 cases from the East of England. Older age and being a care home resident were associated with increased mortality. SARS-CoV-2 genomes were available for 700 residents from 292 care homes. By integrating genomic and temporal data, 409 viral clusters within the 292 homes were identified, indicating two different patterns - outbreaks among care home residents and independent introductions with limited onward transmission. Approximately 70% of residents in the genomic analysis were admitted to hospital during the study, providing extensive opportunities for transmission between care homes and hospitals. Limiting viral transmission within care homes should be a key target for infection control to reduce COVID-19 mortality in this population. Impact statementSARS-CoV-2 can spread efficiently within care homes causing COVID-19 outbreaks among residents, who are at increased risk of severe disease, emphasising the importance of stringent infection control in this population.
ABSTRACT
BackgroundThere is urgent need for safe and efficient triage protocols for hospitalized COVID-19 suspects to appropriate isolation wards. A major barrier to timely discharge of patients from the emergency room and hospital is the turnaround time for many SARS-CoV-2 nucleic acid tests. We validated a point of care nucleic acid amplification based platform SAMBA II for diagnosis of COVID-19 and performed an implementation study to assess its impact on patient disposition at a major academic hospital. MethodsWe prospectively recruited COVID-19 suspects admitted to hospital (NCT04326387). In an initial pilot phase, individuals were tested using a nasal/throat swab with the SAMBA II SARS-CoV-2 rapid diagnostic platform in parallel with a combined nasal/throat swab for standard central laboratory RT-PCR testing. In the second implementation phase, we examined the utility of adding the SAMBA platform to routine care. In the pilot phase, we measured concordance and assay validity using the central laboratory as the reference standard and assessed assay turnaround time. In the implementation phase, we assessed 1) time to definitive bed placement from admission, 2) time spent on COVID-19 holding wards, 3) proportion of patients in isolation versus COVID negative areas following a test, comparing the implementation phase with the 10 days prior to implementation. ResultsIn phase I, 149 participants were included in the pilot. By central laboratory RT-PCR testing, 32 (21.5%) tested positive and 117 (78.5%). Sensitivity and specificity of the SAMBA assay compared to RT-PCR lab test were 96.9% (95% CI 0.838-0.999) and 99.1% (0.953-0.999), respectively. Median time to result was 2.6 hours (IQR 2.3 to 4.8) for SAMBA II SARS-CoV-2 test and 26.4 hours (IQR 21.4 to 31.4) for the standard lab RT-PCR test (p<0.001). In the first 10 days of the SAMBA implementation phase, we conducted 992 tests, with the majority (59.8%) used for hospital admission, and the remainder for pre-operative screening (11.3%), discharge planning (10%), in-hospital screening of new symptoms (9.7%). Comparing the pre-implementation (n=599) with the implementation phase, median time to definitive bed placement from admission was reduced from 23.4 hours (8.6-41.9) to 17.1 hours (9.0-28.8), P=0.02 in Cox analysis, adjusted for age, sex, comorbidities and clinical severity at presentation. Mean length of stay on a COVID-19 holding ward decreased from 58.5 hours to 29.9 hours (P<0.001). Use of single occupancy rooms amongst those tested fell from 30.8% before to 21.2% (P=0.03) and 11 hospital bay closures (on average 6 beds each) were avoided after implementation of the POC assay. ConclusionsThe SAMBA II SARS-CoV-2 rapid assay performed well compared to a centralized laboratory RT-PCR platform and demonstrated shorter time to result both in trial and real-world settings. It was also associated with faster time to definitive bed placement from the emergency room, greater availability of isolation rooms, avoidance of hospital bay closures, and greater movement of patients to COVID negative open "green" category wards. Rapid testing in hospitals has the potential to transform ability to deal with the COVID-19 epidemic.
ABSTRACT
Significant differences exist in the availability of healthcare worker (HCW) SARS-CoV-2 testing between countries, and existing programmes focus on screening symptomatic rather than asymptomatic staff. Over a 3-week period (April 2020), 1,032 asymptomatic HCWs were screened for SARS-CoV-2 in a large UK teaching hospital. Symptomatic staff and symptomatic household contacts were additionally tested. Real-time RT-PCR was used to detect viral RNA from a throat+nose self-swab. 3% of HCWs in the asymptomatic screening group tested positive for SARS-CoV-2. 17/30 (57%) were truly asymptomatic/pauci-symptomatic. 12/30 (40%) had experienced symptoms compatible with coronavirus disease 2019 (COVID-19) >7 days prior to testing, most self-isolating, returning well. Clusters of HCW infection were discovered on two independent wards. Viral genome sequencing showed that the majority of HCWs had the dominant lineage B{middle dot}1. Our data demonstrates the utility of comprehensive screening of HCWs with minimal or no symptoms. This approach will be critical for protecting patients and hospital staff. Appendix: The CITIID-NIHR COVID-19 BioResource CollaborationO_ST_ABSPrincipal InvestigatorsC_ST_ABSStephen Baker, John Bradley, Gordon Dougan, Ian Goodfellow, Ravi Gupta, Paul J. Lehner, Paul A. Lyons, Nicholas J. Matheson, Kenneth G.C. Smith, M. Estee Torok, Mark Toshner, Michael P. Weekes Infectious Diseases DepartmentNicholas K. Jones, Lucy Rivett, Matthew Routledge, Dominic Sparkes, Ben Warne SARS-CoV-2 testing teamJosefin Bartholdson Scott, Claire Cormie, Sally Forrest, Harmeet Gill, Iain Kean, Mailis Maes, Joana Pereira-Dias, Nicola Reynolds, Sushmita Sridhar, Michelle Wantoch, Jamie Young COG-UK Cambridge Sequencing TeamSarah Caddy, Laura Caller, Theresa Feltwell, Grant Hall, William Hamilton, Myra Hosmillo, Charlotte Houldcroft, Aminu Jahun, Fahad Khokhar, Luke Meredith, Anna Yakovleva NIHR BioResourceHelen Butcher, Daniela Caputo, Debra Clapham-Riley, Helen Dolling, Anita Furlong, Barbara Graves, Emma Le Gresley, Nathalie Kingston, Sofia Papadia, Hannah Stark, Kathleen E. Stirrups, Jennifer Webster Research nursesJoanna Calder, Julie Harris, Sarah Hewitt, Jane Kennet, Anne Meadows, Rebecca Rastall, Criona O,Brien, Jo Price, Cherry Publico, Jane Rowlands, Valentina Ruffolo, Hugo Tordesillas NIHR Cambridge Clinical Research FacilityKaren Brookes, Laura Canna, Isabel Cruz, Katie Dempsey, Anne Elmer, Naidine Escoffery, Stewart Fuller, Heather Jones, Carla Ribeiro, Caroline Saunders, Angela Wright Cambridge Cancer Trial CentreRutendo Nyagumbo, Anne Roberts Clinical Research Network EasternAshlea Bucke, Simone Hargreaves, Danielle Johnson, Aileen Narcorda, Debbie Read, Christian Sparke, Lucy Warboys Administrative staff, CUHKirsty Lagadu, Lenette Mactavous CUH NHS Foundation TrustTim Gould, Tim Raine, Ashley Shaw Cambridge Cancer Trials CentreClaire Mather, Nicola Ramenatte, Anne-Laure Vallier Legal/EthicsMary Kasanicki CUH Improvement and Transformation TeamPenelope-Jane Eames, Chris McNicholas, Lisa Thake Clinical Microbiology & Public Health Laboratory (PHE): Neil Bartholomew, Nick Brown, Martin Curran, Surendra Parmar, Hongyi Zhang Occupational HealthAilsa Bowring, Mark Ferris, Geraldine Martell, Natalie Quinnell, Giles Wright, Jo Wright Health and SafetyHelen Murphy Department of Medicine Sample LogisticsBenjamin J. Dunmore, Ekaterina Legchenko, Stefan Graf, Christopher Huang, Josh Hodgson, Kelvin Hunter, Jennifer Martin, Federica Mescia, Ciara ODonnell, Linda Pointon, Joy Shih, Rachel Sutcliffe, Tobias Tilly, Zhen Tong, Carmen Treacy, Jennifer Wood Department of Medicine Sample Processing and Acquisition: Laura Bergamaschi, Ariana Betancourt, Georgie Bowyer, Aloka De Sa, Maddie Epping, Andrew Hinch, Oisin Huhn, Isobel Jarvis, Daniel Lewis, Joe Marsden, Simon McCallum, Francescsa Nice, Ommar Omarjee, Marianne Perera, Nika Romashova, Mateusz Strezlecki, Natalia Savoinykh Yarkoni, Lori Turner Epic team/other computing supportBarrie Bailey, Afzal Chaudhry, Rachel Doughton, Chris Workman Statistics/modellingRichard J. Samworth, Caroline Trotter
ABSTRACT
The COVID-19 pandemic is expanding at an unprecedented rate. As a result, diagnostic services are stretched to their limit, and there is a clear need for the provision of additional diagnostic capacity. Academic laboratories, many of which are closed due to governmental lockdowns, may be in a position to support local screening capacity by adapting their current laboratory practices. Here, we describe the process of developing a SARS-Cov2 diagnostic workflow in a conventional academic Containment Level 2 (CL2) laboratory. Our outline includes simple SARS-Cov2 deactivation upon contact, the methods for a quantitative real-time reverse transcriptase PCR (qRT-PCR) detecting SARS-Cov2, a description of process establishment and validation, and some considerations for establishing a similar workflow elsewhere. This was achieved under challenging circumstances through the collaborative efforts of scientists, clinical staff, and diagnostic staff to mitigate to the ongoing crisis. Within 14 days, we created a validated COVID-19 diagnostics service for healthcare workers in our local hospital. The described methods are not exhaustive, but we hope may offer support to other academic groups aiming to set up something comparable in a short time frame.
ABSTRACT
This paper examines whether corporate financial performance is affected by public endorsement of environmental and social performance. Event study methodology, which relies on the notion of market efficiency, is used to examine the relationship between positive and negative announcements and changes in share prices or daily returns. Inclusion in and deletion from the FTSE4Good UK Index is used as a proxy measure for good (poor) corporate social responsibility. The abnormal or unexpected daily returns associated with an event are calculated and their significance tested. The results show a trend towards positive and negative announcements having the expected effects on daily returns. But these movements are not significant and the data do not suggest that a firm's presence on the index brings it any significant financial return for signalling its corporate social responsibility.
Subject(s)
Commerce/economics , Environment , Investments/economics , Social Responsibility , Investments/statistics & numerical data , Organizational Policy , United KingdomABSTRACT
BACKGROUND: Community animal health services in low-income countries aim to improve the health of animals and directly improve the wealth and health or livelihood of their owners. These services have been promoted by aid organizations since the 1970s. OBJECTIVES: To summarize reliable research of community animal health services on indicators for household wealth and health. SEARCH STRATEGY: We searched the Cochrane Infectious Diseases Group Specialized Register (July 2005), CENTRAL (The Cochrane Library 2005, Issue 2), MEDLINE (1966 to July 2002), AGRIS (1975 to July 2005), Science Citation Index (2000 to July 2005), STN SIGLE database (1976 to 2002), and AGRICOLA (19 July 2005). We contacted relevant researchers and organizations, and also checked the reference lists of articles. SELECTION CRITERIA: Randomized controlled trials and controlled before-and-after studies comparing community animal health services with no community animal health services or with an alternative animal health service. DATA COLLECTION AND ANALYSIS: We independently assessed studies for inclusion in the review. MAIN RESULTS: No studies met the inclusion criteria. AUTHORS' CONCLUSIONS: Well-designed randomized controlled trials or controlled before-and-after studies that use standard pragmatic outcomes are needed to evaluate the positive results reported by observational studies.
Subject(s)
Animal Husbandry/organization & administration , Animals, Domestic , Community Health Services/organization & administration , Developing Countries , Animals , HumansABSTRACT
This study was carried out to assess the impact of animal healthcare services on poor donkey owners in Ethiopia. The services provided by the Donkey Sanctuary were used as a case study. A questionnaire survey was designed and carried out in the areas around Debre Zeit in the Highlands of Ethiopia. The staff carried out a survey at 10 sites. Six of these were in Donkey Sanctuary project areas and four were in control areas. The results showed that in project areas donkeys were significantly healthier and more productive than in non-project areas. Donkey owners in project sites felt better off for having access to animal healthcare services; donkey owners in non-project sites were less confident about their incomes and the health of their animals.
Subject(s)
Animal Welfare , Equidae , Veterinary Medicine , Agriculture , Animals , Ethiopia , Female , Humans , Male , Socioeconomic Factors , Surveys and QuestionnairesABSTRACT
This paper is based on an impact assessment of a donkey provision programme in Ethiopia. The work was carried out in 2001 as part of a DFID Livestock Production Programme project 'Use and management of donkeys by poor societies in peri-urban areas in Ethiopia'. In order to establish whether donkey ownership was a cause or an effect of improved livelihoods, an investigation was carried out that compared non-donkey-owning households with households that had owned no donkey until they were given one by a local NGO. Indicators that poor people use to express their well-being, wealth and health status (components of their livelihoods) were identified and used to compare communities. Guidelines were prepared for project managers for carrying out livelihood indicator identification and impact assessment. The results showed that the informants used a range of indicators to assess their livelihoods. A selection of these were investigated in depth, including number of children per household attending school, number of people per household earning an income, type and quantity of staple foods bought, and ability to save. A trend was identified that demonstrated that donkey owners' livelihoods were improved compared to non-donkey owners.
Subject(s)
Equidae , Ownership , Adolescent , Animals , Child , Child, Preschool , Ethiopia , Female , Humans , Income , Infant , Poverty , Schools , Social Class , Suburban Population , Surveys and QuestionnairesABSTRACT
This survey was conducted at three sites in Ethiopia. The purpose of the survey was to provide detailed information on donkey use in rural and peri-urban areas. The study revealed that donkeys are indeed of immense value to farmers and merchants, being used almost daily for income-generating activities. Unfortunately, they are rarely given any veterinary attention, they receive no feed supplements and their owners are often unaware of improved saddling techniques that would reduce the back sores their animals suffer from. An extension programme providing donkey owners with information on saddling, feeding and basic health care would improve the animals' productivity and improve the livelihoods of the owners.
Subject(s)
Animal Husbandry , Animal Welfare , Equidae/physiology , Animals , Equidae/growth & development , Ethiopia , Female , Humans , Longitudinal Studies , Male , Rural Population , Suburban Population , Surveys and QuestionnairesABSTRACT
A survey was conducted in central Ethiopia to elicit information on existing and potential dissemination pathways for technical information on donkey husbandry. A detailed socio-economic survey was also conducted to provide background information on the people and the region, and livelihood indicators were drawn out at the same time. The results showed that there are many opportunities for group dissemination by making use of existing social networks. There are also opportunities for dissemination through extension agents, farmer groups and radio broadcasting.
