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:BackgroundThe COVID-19 pandemic intensified the risk factors for poor mental health among care workers in the UK. However, there is inadequate evidence on the mental health impact of COVID-19 on Black, Asian, and minority ethnic (BAME) care workers in particular. This study seeks to explore mental health experiences and coping strategies of BAME care workers who worked in nursing and residential care homes during the COVID-19 pandemic.MethodThis is a qualitative study conducted between February and May, 2021 in Luton, England. A sample of n = 15 care workers from BAME background working in nursing and residential care homes were recruited purposively using the snowball sampling technique. In-depth interviews were conducted around topics such as views on COVID-19, the impact of the COVID-19 pandemic on mental health and coping during the COVID-19 pandemic. Data from the interviews was analysed using the Framework Analysis Approach.ResultsThe COVID-19 pandemic had a negative impact on the participants' mental health as they experienced stress, depression, anxiety, trauma and paranoia. The majority of the participants explained that they managed their mental health by belief in God and religious practices, by keeping themselves busy doing activities they were passionate about, following government guidelines on the prevention of COVID-19, seeing the service users happy and some participants managed through support that was offered by the government. However, some participants did not have any support for their mental health.ConclusionIssues such as increased workload associated with COVID-19 restrictions engendered mental health problems among BAME care workers, however, the workload only further increased during the pandemic, but the health and social care sector was already affected by heavy workload due to staff shortages and this needs to be addressed through increasing their wages to encourage more people to work in the health and social care sector. In addition, some BAME care workers never received any support for their mental health during the pandemic. Hence, integrating mental health services such as counselling, supportive psychotherapy and recreational therapies in care homes could help to support the mental health of care workers in the COVID-19 era.
| S-EPMC10054189 | biostudies-literature
Project description:BackgroundLong-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.MethodsWe 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.ResultsWe 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.ConclusionsUnderstanding 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.
| S-EPMC10789038 | biostudies-literature
Project description:BackgroundCare 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.MethodsFive 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.FindingsAcross 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.InterpretationWe 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.FundingPHE.
| 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:PurposeTo report the experiences of End of Life (EoL) care in UK care homes during the COVID-19 pandemic.MethodsUK care home staff and family carers of residents in care home took part in remote, semi-structured interviews from October to November 2020, with 20 participants followed-up in March 2021. Interviews were conducted via telephone or online platforms and qualitatively analysed using inductive thematic analysis.ResultsForty-two participants (26 family carers and 16 care home staff) were included in a wider qualitative study exploring the impact on dementia care homes during the pandemic. Of these, 11 family carers and 9 care home staff participated in a follow-up interview. Following descriptive thematic analysis, three central themes concerning EoL care during the pandemic specifically, were conceptualised and redefined through research team discussions: 1) Wasting or losing time; 2) Maintaining control, plans and routine; and 3) Coping with loss and lack of support. Lack of suitable, meaningful visits with people with dementia in care homes resulted in negative feelings of guilt and abandonment with both family carers and care home staff. Where families experienced positive EoL visits, these appeared to breach public health restrictions at that time.ConclusionIt is recommended that care homes receive clear guidance from the government offering equitable contact with relatives at EoL to all family members, to support their grieving and avoid subsequent negative impacts to emotional wellbeing.
| S-EPMC9155982 | biostudies-literature