Genomic epidemiology of COVID-19 in care homes in the east of England.
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ABSTRACT:
SUBMITTER: Hamilton WL
PROVIDER: S-EPMC7997667 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundWe investigated six London care homes experiencing a COVID-19 outbreak and found high rates of SARS-CoV-2 infection among residents and staff. Here we report follow-up investigations including antibody testing in the same care homes five weeks later.MethodsResidents and staff in the initial investigation had a repeat nasal swab for SARS-CoV-2 RT-PCR and a blood test for SARS CoV-2 antibodies using ELISA based on SARS-CoV-2 native viral antigens derived from infected cells and virus neutralisation.FindingsOf the 518 residents and staff in the initial investigation, 186/241 (77.2%) surviving residents and 208/254 (81.9%) staff underwent serological testing. Almost all SARS-CoV-2 RT-PCR positive residents and staff were seropositive five weeks later, whether symptomatic (residents 35/35, 100%; staff, 22/22, 100%) or asymptomatic (residents 32/33, 97.0%; staff 21/22, 95.5%). Symptomatic but SARS-CoV-2 RT-PCR negative residents and staff also had high seropositivity rates (residents 23/27, 85.2%; staff 18/21, 85.7%), as did asymptomatic RT-PCR negative individuals (residents 61/91, 67.0%; staff 95/143, 66.4%). Neutralising antibody was detected in 118/132 (89.4%) seropositive individuals and was not associated with age or symptoms. Ten residents (10/79 re-tested, 12.7%) remained RT-PCR positive but with higher RT-PCR cycle threshold values; 7/10 had serological testing and all were seropositive. New infections were detected in three residents and one staff.InterpretationRT-PCR provides a point prevalence of SARS-CoV-2 infection but significantly underestimates total exposure in outbreak settings. In care homes experiencing large COVID-19 outbreaks, most residents and staff had neutralising SARS-CoV-2 antibodies, which was not associated with age or symptoms.FundingPHE.
| S-EPMC7644437 | biostudies-literature
Project description:PurposeTo describe critical care patients with COVID-19 across England, Wales and Northern Ireland and compare them with a historic cohort of patients with other viral pneumonias (non-COVID-19) and with international cohorts of COVID-19.MethodsExtracted data on patient characteristics, acute illness severity, organ support and outcomes from the Case Mix Programme, the national clinical audit for adult critical care, for a prospective cohort of patients with COVID-19 (February to August 2020) are compared with a recent retrospective cohort of patients with other viral pneumonias (non-COVID-19) (2017-2019) and with other international cohorts of critical care patients with COVID-19, the latter identified from published reports.Results10,834 patients with COVID-19 (70.1% male, median age 60 years, 32.6% non-white ethnicity, 39.4% obese, 8.2% at least one serious comorbidity) were admitted across 289 critical care units. Of these, 36.9% had a PaO2/FiO2 ratio of ≤ 13.3 kPa (≤ 100 mmHg) consistent with severe ARDS and 72% received invasive ventilation. Acute hospital mortality was 42%, higher than for 5782 critical care patients with other viral pneumonias (non-COVID-19) (24.7%), and most COVID-19 deaths (88.7%) occurred before 30 days. Meaningful international comparisons were limited due to lack of standardised reporting.ConclusionCritical care patients with COVID-19 were disproportionately non-white, from more deprived areas and more likely to be male and obese. Conventional severity scoring appeared not to adequately reflect their acute severity, with the distribution across PaO2/FiO2 ratio categories indicating acutely severe respiratory disease. Critical care patients with COVID-19 experience high mortality and place a great burden on critical care services.
| S-EPMC7545019 | biostudies-literature
Project description:BackgroundOlder people living in care homes in England have complex health needs due to a range of medical conditions, mental health needs and frailty. Despite an increasing policy expectation that professionals should operate in an integrated way across organisational boundaries, there is a lack of understanding between care homes and the National Health Service (NHS) about how the two sectors should work together, meaning that residents can experience a poor "fit" between their needs, and services they can access. This paper describes a survey to establish the current extent of integrated working that exists between care homes and primary and community health and social services.MethodsA self-completion, online questionnaire was designed by the research team. Items on the different dimensions of integration (funding, administrative, organisational, service delivery, clinical care) were included. The survey was sent to a random sample of residential care homes with more than 25 beds (n?=?621) in England in 2009. Responses were analysed using quantitative and qualitative methods.ResultsThe survey achieved an overall response rate of 15.8%. Most care homes (78.7%) worked with more than one general practice. Respondents indicated that a mean of 14.1 professionals/ services (other than GPs) had visited the care homes in the last six months (SD 5.11, median 14); a mean of .39 (SD.163) professionals/services per bed. The most frequent services visiting were district nursing, chiropody and community psychiatric nurses. Many (60%) managers considered that they worked with the NHS in an integrated way, including sharing documents, engaging in integrated care planning and joint learning and training. However, some care home managers cited working practices dictated by NHS methods of service delivery and priorities for care, rather than those of the care home or residents, a lack of willingness by NHS professionals to share information, and low levels of respect for the experience and knowledge of care home staff.ConclusionsCare homes are a hub for a wide range of NHS activity, but this is ad hoc with no recognised way to support working together. Integration between care homes and local health services is only really evident at the level of individual working relationships and reflects patterns of collaborative working rather than integration. More integrated working between care homes and primary health services has the potential to improve quality of care in a cost-effective manner, but strategic decisions to create more formal arrangements are required to bring this about. Commissioners of services for older people need to capitalise on good working relationships and address idiosyncratic patterns of provision to care homes.The low response rate is indicative of the difficulty of undertaking research in care homes.
| S-EPMC3534387 | biostudies-literature
Project description:BackgroundCare home residents have complex healthcare needs but may have faced barriers to accessing hospital treatment during the first wave of the COVID-19 pandemic.ObjectivesTo examine trends in the number of hospital admissions for care home residents during the first months of the COVID-19 outbreak.MethodsRetrospective analysis of a national linked dataset on hospital admissions for residential and nursing home residents in England (257,843 residents, 45% in nursing homes) between 20 January 2020 and 28 June 2020, compared to admissions during the corresponding period in 2019 (252,432 residents, 45% in nursing homes). Elective and emergency admission rates, normalised to the time spent in care homes across all residents, were derived across the first three months of the pandemic between 1 March and 31 May 2020 and primary admission reasons for this period were compared across years.ResultsHospital admission rates rapidly declined during early March 2020 and remained substantially lower than in 2019 until the end of June. Between March and May, 2,960 admissions from residential homes (16.2%) and 3,295 admissions from nursing homes (23.7%) were for suspected or confirmed COVID-19. Rates of other emergency admissions decreased by 36% for residential and by 38% for nursing home residents (13,191 fewer admissions in total). Emergency admissions for acute coronary syndromes fell by 43% and 29% (105 fewer admission) and emergency admissions for stroke fell by 17% and 25% (128 fewer admissions) for residential and nursing home residents, respectively. Elective admission rates declined by 64% for residential and by 61% for nursing home residents (3,762 fewer admissions).ConclusionsThis is the first study showing that care home residents' hospital use declined during the first wave of COVID-19, potentially resulting in substantial unmet health need that will need to be addressed alongside ongoing pressures from COVID-19.
| S-EPMC8267611 | biostudies-literature
Project description:Background Care homes have been disproportionately affected by the COVID-19 pandemic. We investigated the potential role of asymptomatic infection and silent transmission in London care homes that reported no cases of COVID-19 during the first wave of the pandemic. Methods Five care homes with no cases and two care homes reporting a single case of COVID-19 (non-outbreak homes) were investigated with nasal swabbing for SARS-CoV-2 RT-PCR and serology for SARS-CoV-2 antibodies five weeks later. Whole genome sequencing (WGS) was performed on RT-PCR positive samples. Serology results were compared with those of six care homes with recognised outbreaks. Findings Across seven non-outbreak homes, 718 (387 staff, 331 residents) individuals had a nasal swab and 651 (386 staff, 265 residents) had follow-up serology. Sixteen individuals (13 residents, 3 staff) in five care homes with no reported cases were RT-PCR positive (care home positivity rates, 0 to 7.6%) compared to 13 individuals (3.0 and 10.8% positivity) in two homes reporting a single case. Seropositivity across these seven homes varied between 10.7-56.5%, with four exceeding community seroprevalence in London (14.8%). Seropositivity rates for staff and residents correlated significantly (rs 0.84, [95% CI 0.51-0.95] p <0.001) across the 13 homes. WGS identified multiple introductions into some homes and silent transmission of a single lineage between staff and residents in one home. Interpretation We found high rates of asymptomatic infection and transmission even in care homes with no COVID-19 cases. The higher seropositivity rates compared to RT-PCR positivity highlights the true extent of the silent outbreak. Funding PHE
| S-EPMC7826003 | biostudies-literature
Project description:Analysis of genetic sequence data from the SARS-CoV-2 pandemic can provide insights into epidemic origins, worldwide dispersal, and epidemiological history. With few exceptions, genomic epidemiological analysis has focused on geographically distributed data sets with few isolates in any given location. Here, we report an analysis of 20 whole SARS- CoV-2 genomes from a single relatively small and geographically constrained outbreak in Weifang, People's Republic of China. Using Bayesian model-based phylodynamic methods, we estimate a mean basic reproduction number (R 0) of 3.4 (95% highest posterior density interval: 2.1-5.2) in Weifang, and a mean effective reproduction number (Rt) that falls below 1 on 4 February. We further estimate the number of infections through time and compare these estimates to confirmed diagnoses by the Weifang Centers for Disease Control. We find that these estimates are consistent with reported cases and there is unlikely to be a large undiagnosed burden of infection over the period we studied.
| S-EPMC7955981 | biostudies-literature
Project description:IntroductionCare home residents are at high risk of dying from coronavirus disease 2019 (COVID-19). Regular testing, producing rapid and reliable results is important in this population because infections spread quickly, and presentations are often atypical or asymptomatic. This study evaluated current testing pathways in care homes to explore the role of point-of-care tests (POCTs).MethodsA total of 10 staff from eight care homes, purposively sampled to reflect care organisational attributes that influence outbreak severity, underwent a semi-structured remote videoconference interview. Transcripts were analysed using process mapping tools and framework analysis focussing on perceptions about, gaps within and needs arising from current pathways.ResultsFour main steps were identified in testing: infection prevention, preparatory steps, swabbing procedure and management of residents. Infection prevention was particularly challenging for mobile residents with cognitive impairment. Swabbing and preparatory steps were resource-intensive, requiring additional staff resource. Swabbing required flexibility and staff who were familiar to the resident. Frequent approaches to residents were needed to ensure they would participate at a suitable time. After-test management varied between sites. Several homes reported deviating from government guidance to take more cautious approaches, which they perceived to be more robust.ConclusionSwab-based testing is organisationally complex and resource-intensive in care homes. It needs to be flexible to meet the needs of residents and provide care homes with rapid information to support care decisions. POCT could help address gaps but the complexity of the setting means that each technology must be evaluated in context before widespread adoption in care homes.
| S-EPMC7929459 | biostudies-literature
Project description:We performed the first population-based clinical and molecular genetic study of Leber hereditary optic neuropathy (LHON) in a population of 2,173,800 individuals in the North East of England. We identified 16 genealogically unrelated families who harbor one of the three primary mitochondrial DNA (mtDNA) mutations that cause LHON. Two of these families were found to be linked genetically to a common maternal founder. A de novo mtDNA mutation (G3460A) was identified in one family. The minimum point prevalence of visual failure due to LHON within this population was 3.22 per 100,000 (95% CI 2.47-3.97 per 100,000), and the minimum point prevalence for mtDNA LHON mutations was 11.82 per 100,000 (95% CI 10.38-13.27 per 100,000). These results indicate that LHON is not rare but has a population prevalence similar to autosomally inherited neurological disorders. The majority of individuals harbored only mutant mtDNA (homoplasmy), but heteroplasmy was detected in approximately 12% of individuals. Overall, however, approximately 33% of families with LHON had at least one heteroplasmic individual. The high incidence of heteroplasmy in pedigrees with LHON raises the possibility that a closely related maternal relative of an index case may not harbor the mtDNA mutation, highlighting the importance of molecular genetic testing for each maternal family member seeking advice about their risks of visual failure.
| S-EPMC379226 | biostudies-literature
Project description:BackgroundCOVID-19 has affected care home residents internationally, but detailed information on outbreaks is scarce. We aimed to describe the evolution of outbreaks of COVID-19 in all care homes in one large health region in Scotland.MethodsWe did a population analysis of testing, cases, and deaths in care homes in the National Health Service (NHS) Lothian health region of the UK. We obtained data for COVID-19 testing (PCR testing of nasopharyngeal swabs for severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) and deaths (COVID-19-related and non-COVID-19-related), and we analysed data by several variables including type of care home, number of beds, and locality. Outcome measures were timing of outbreaks, number of confirmed cases of COVID-19 in care home residents, care home characteristics associated with the presence of an outbreak, and deaths of residents in both care homes and hospitals. We calculated excess deaths (both COVID-19-related and non-COVID-19-related), which we defined as the sum of deaths over and above the historical average in the same period over the past 5 years.FindingsBetween March 10 and Aug 2, 2020, residents at 189 care homes (5843 beds) were tested for COVID-19 when symptomatic. A COVID-19 outbreak was confirmed at 69 (37%) care homes, of which 66 (96%) were care homes for older people. The size of care homes for older people was strongly associated with a COVID-19 outbreak (odds ratio per 20-bed increase 3·35, 95% CI 1·99-5·63). 907 confirmed cases of SARS-CoV-2 infection were recorded during the study period, and 432 COVID-19-related deaths. 229 (25%) COVID-19-related cases and 99 (24%) COVID-related deaths occurred in five (3%) of 189 care homes, and 441 (49%) cases and 207 (50%) deaths were in 13 (7%) care homes. 411 (95%) COVID-19-related deaths occurred in the 69 care homes with a confirmed COVID-19 outbreak, 19 (4%) deaths were in hospital, and two (<1%) were in one of the 120 care homes without a confirmed COVID-19 outbreak. At the 69 care homes with a confirmed COVID-19 outbreak, 74 excess non-COVID-19-related deaths were reported, whereas ten non-COVID-19-related excess deaths were observed in the 120 care homes without a confirmed COVID-19 outbreak. 32 fewer non-COVID-19-related deaths than expected were reported among care home residents in hospital.InterpretationThe effect of COVID-19 on care homes has been substantial but concentrated in care homes with known outbreaks. A key implication from our findings is that, if community incidence of COVID-19 increases again, many care home residents will be susceptible. Shielding care home residents from potential sources of SARS-CoV-2 infection, and ensuring rapid action to minimise outbreak size if infection is introduced, will be important for any second wave.FundingNone.
| S-EPMC7574931 | biostudies-literature
Project description:BackgroundThe Covid-19 pandemic has created an unprecedented challenge for health and social care systems globally. There is an urgent need for research on experiences of COVID-19 at different levels of health systems, including lessons from professional, organisational and local system responses, that can be used to inform managerial and policy responses.MethodsThis paper presents the findings from a thematic analysis of front-line staff experiences working across the Norfolk and Waveney integrated care system (ICS) in the East of England during April and October 2020 to address the question "What are the experiences and perceptions of partner organisations and practitioners at multiple levels of the health system in responding to COVID-19 during the first wave of the pandemic?" This question was posed to learn from how practitioners, interdependent partner organisations and the system experienced the pandemic and responded. 176 interview transcripts derived from one to one and focus group interviews, meeting notes and feedback from a "We Care Together" Instagram campaign were submitted for qualitative thematic analysis to an external research team at a regional University commissioned to undertake an independent evaluation. Three phases of qualitative analysis were systematically undertaken to derive the findings.FindingsThirty-one themes were distilled highlighting lessons learned from things that went well compared with those that did not; challenges compared with the celebrations and outcomes; learning and insights gained; impact on role; and system headlines. The analysis supported the ICS to inform and capitalise on system wide learning for integration, improvement and innovations in patient and care home resident safety, and staff wellbeing to deal with successive waves of the pandemic as well as prioritising workforce development priorities as part of its People Plan.ConclusionsThe findings contribute to a growing body of knowledge about what impact the pandemic has had on health and social care systems and front-line practitioners globally. It is important to understand the impact at all three levels of the system (micro, meso and macro) as it is the meso and macro system levels that ultimately impact front line staff experiences and the ability to deliver person centered safe and effective care in any context. The paper presents implications for future workforce and health services policy, practice innovation and research.
| S-EPMC9037583 | biostudies-literature