Real-time nowcasting and forecasting of COVID-19 dynamics in England: the first wave.
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ABSTRACT:
SUBMITTER: Birrell P
PROVIDER: S-EPMC8165585 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:ObjectivesSARS-CoV-2 emerged in South Asia in 2019 and has resulted in a global pandemic. Public Health England (PHE) Manchester rapidly escalated testing for SARS-CoV-2 in the highest COVID-19 incidence location in England. The results of the PHE Manchester SARS-CoV-2 surveillance during the first wave are presented.MethodsRetrospective data were collected for patients fitting the PHE SARS-CoV-2 case definition from 11th February to 31st August 2020. Respiratory tract, tissue, faecal, fluid and cerebrospinal (CSF) samples were tested for SARS-CoV-2 by a semi-quantitative real-time reverse-transcription PCR.ResultsOf the 204,083 tests for SARS-CoV-2, 18,011 were positive demonstrating a positivity of 8.90%. Highest positivity was in nasal swabs (20.99%) followed by broncheo-alveolar lavage samples (12.50%). None of the faecal, fluid or CSF samples received were positive for SARS-CoV-2.ConclusionsThere was a high incidence of SARS-CoV-2 patients in the North-West of England during the first UK wave of the Covid-19 pandemic. Highest positivity rate was in nasal specimens suggesting this is the optimum sample type within this dataset for detecting SARS-CoV-2. Further studies are warranted to assess the utility of testing faecal, fluid and CSF samples. Rapid escalation of testing via multiple platforms was required to ensure prompt diagnosis and isolate infected cases to reduce transmission of the virus.
| S-EPMC8058098 | biostudies-literature
Project description:To account for delays between specimen collection and report, the New York City Department of Health and Mental Hygiene used a time-correlated Bayesian nowcasting approach to support real-time COVID-19 situational awareness. We retrospectively evaluated nowcasting performance for case counts among residents diagnosed during March-May 2020, a period when the median reporting delay was 2 days. Nowcasts with a 2-week moving window and a negative binomial distribution had lower mean absolute error, lower relative root mean square error, and higher 95% prediction interval coverage than nowcasts conducted with a 3-week moving window or with a Poisson distribution. Nowcasts conducted toward the end of the week outperformed nowcasts performed earlier in the week, given fewer patients diagnosed on weekends and lack of day-of-week adjustments. When estimating case counts for weekdays only, metrics were similar across days the nowcasts were conducted, with Mondays having the lowest mean absolute error, of 183 cases in the context of an average daily weekday case count of 2,914. Nowcasting ensured that recent decreases in observed case counts were not overinterpreted as true declines and supported health department leadership in anticipating the magnitude and timing of hospitalizations and deaths and allocating resources geographically.
| S-EPMC7587834 | biostudies-literature
Project description:A novel parametric regression model is proposed to fit incidence data typically collected during epidemics. The proposal is motivated by real-time monitoring and short-term forecasting of the main epidemiological indicators within the first outbreak of COVID-19 in Italy. Accurate short-term predictions, including the potential effect of exogenous or external variables are provided. This ensures to accurately predict important characteristics of the epidemic (e.g., peak time and height), allowing for a better allocation of health resources over time. Parameter estimation is carried out in a maximum likelihood framework. All computational details required to reproduce the approach and replicate the results are provided.
| S-EPMC8242495 | biostudies-literature
Project description:In 2020, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spread across the world within a few months. The SARS-CoV-2 pandemic has had a devastating effect on humanity, with social and economic consequences. The continents of Europe and America have been hit the hardest. However, there has also been a huge loss of life in India, with the country having the fourth highest number of total deaths worldwide. Nevertheless, the infection and death rates per million and the case fatality ratio in India are substantially lower than those in many developed nations. Several explanations for this have been proposed, including genetics. Mathematical modelling has suggested that the actual number of infections is much higher than the number of reported cases. Therefore, to understand the dynamics of actual infection and the population-level immunity against SARS-CoV-2, a serosurvey (antibody testing) was performed among 2301 individuals in urban regions of 14 districts in six states of India. A notable outcome of this study was that a large proportion of the Indian population had an asymptomatic SARS-CoV-2 infection. The real infection rate in India was several fold higher than the reported number of cases. Therefore, a large number of people in the country have developed SARS-CoV-2-specific antibodies. In this survey, the seroprevalence (frequency antibody-positive) varied between 0.01 (95% CI 0.002-0.054) and 0.477 (95% CI 0.392-0.563), suggesting a high variability in viral transmission between the states and the possibility of future waves. In this study population, the frequency of asymptomatic infection was highest in the younger age groups. It was also found that the numbers of cases reported by the government were several-fold lower than the real incidence of infection. It is likely that the high number of asymptomatic cases was the main driver of this discrepancy.
| S-EPMC9851738 | biostudies-literature
Project description:This paper develops a methodology for tracking in real-time the impact of shocks (such as natural disasters, financial crises or pandemics) on gross domestic product (GDP) by analyzing high-frequency electricity market data. As an illustration, we estimate the GDP loss caused by COVID-19 in twelve European countries during the first wave of the pandemic. Our results are almost indistinguishable from the official statistics during the first two quarters of 2020 (the correlation coefficient is 0.98) and are validated by several robustness tests. We provide estimates that are more chronologically disaggregated and up-to-date than standard macroeconomic indicators and, therefore, can provide timely information for policy evaluation in time of crisis. Our results show that pursuing "herd immunity" did not shelter from the harmful economic impacts of the first wave of the pandemic. They also suggest that coordinating policies internationally is fundamental for minimizing spillover effects from non-pharmaceutical interventions across countries.
| S-EPMC8433055 | biostudies-literature
Project description:Risk factors for increased risk of death from COVID-19 have been identified, but less is known on characteristics that make communities resilient or vulnerable to the mortality impacts of the pandemic. We applied a two-stage Bayesian spatial model to quantify inequalities in excess mortality in people aged 40 years and older at the community level during the first wave of the pandemic in England, March-May 2020 compared with 2015-2019. Here we show that communities with an increased risk of excess mortality had a high density of care homes, and/or high proportion of residents on income support, living in overcrowded homes and/or with a non-white ethnicity. We found no association between population density or air pollution and excess mortality. Effective and timely public health and healthcare measures that target the communities at greatest risk are urgently needed to avoid further widening of inequalities in mortality patterns as the pandemic progresses.
| S-EPMC8213785 | 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
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:BackgroundThere have been concerns that the COVID-19 pandemic may lead to an increase in suicide. The coronial system in England is not suitable for timely monitoring of suicide because of the delay of several months before inquests are held.MethodsWe used data from established systems of "real time surveillance" (RTS) of suspected suicides, in areas covering a total population of around 13 million, to test the hypothesis that the suicide rate rose after the first national lockdown began in England.FindingsThe number of suicides in April-October 2020, after the first lockdown began, was 121•3 per month, compared to 125•7 per month in January-March 2020 (-4%; 95% CI-19% to 13%, p = 0•59). Incidence rate ratios did not show a significant rise in individual months after lockdown began and were not raised during the 2-month lockdown period April-May 2020 (IRR: 1•01 [0•81-1•25]) or the 5-month period after the easing of lockdown, June-October 2020 (0•94 [0•81-1•09]). Comparison of the suicide rates after lockdown began in 2020 for the same months in selected areas in 2019 showed no difference.InterpretationWe did not find a rise in suicide rates in England in the months after the first national lockdown began in 2020, despite evidence of greater distress. However, a number of caveats apply. These are early figures and may change. Any effect of the pandemic may vary by population group or geographical area. The use of RTS in this way is new and further development is needed before it can provide full national data.FundingThis study was funded by the Healthcare Quality Improvement Partnership (HQIP).The HQIP is led by a consortium of the Academy of Medical Royal Colleges, the Royal College of Nursing, and National Voices. Its aim is to promote quality improvement in patient outcomes, and in particular, to increase the impact that clinical audit, outcome review programs and registries have on healthcare quality in England and Wales. HQIP holds the contract to commission, manage, and develop the National Clinical Audit and Patient Outcomes Program (NCAPOP), comprising around 40 projects covering care provided to people with a wide range of medical, surgical and mental health conditions. The program is funded by NHS England, the Welsh Government and, with some individual projects, other devolved administrations, and crown dependencies.
| S-EPMC8454726 | biostudies-literature
Project description:ObjectivesWe describe COVID-19 mortality among people with and without HIV during the first wave of the pandemic in England.MethodsNational surveillance data on adults (aged ≥ 15 years) with diagnosed HIV resident in England were linked to national COVID-19 mortality surveillance data (2 March 2020-16 June 2020); HIV clinicians verified linked cases and provided information on the circumstances of death. We present COVID-19 mortality rates by HIV status, using negative binomial regression to assess the association between HIV and mortality, adjusting for gender, age and ethnicity.ResultsOverall, 99 people with HIV, including 61 of black ethnicity, died of/with COVID-19 (107/100 000) compared with 49 483 people without HIV (109/100 000). Compared to people without HIV, higher COVID-19 mortality rates were observed in people with HIV of black (188 vs. 122/100 000) and Asian (131 vs. 77.0/100 000) ethnicity, and in both younger (15-59 years: 58.3 vs. 10.2/100 000) and older (≥ 60 years: 434 vs. 355/100 000) people. After adjustment for demographic factors, people with HIV had a higher COVID-19 mortality risk than those without (2.18; 95% CI: 1.76-2.70). Most people with HIV who died of/with COVID-19 had suppressed HIV viraemia (91%) and at least one comorbidity reported to be associated with poor COVID-19 outcomes (87%).ConclusionsIn the first wave of the pandemic in England, COVID-19 mortality among people with HIV was low, but was higher than in those without HIV, after controlling for demographic factors. This supports the strategy of prioritizing COVID-19 vaccination for people with HIV and strongly encouraging its uptake, especially in those of black and Asian ethnicity.
| S-EPMC8652768 | biostudies-literature