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1.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-319931

ABSTRACT

Background: The duration of immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still uncertain, but it is of key clinical and epidemiological importance. Seasonal human coronaviruses (HCoV) have been circulating for longer and, therefore, may offer insights into the long-term dynamics of reinfection for such viruses. Methods: Combining historical seroprevalence data from five studies covering the four circulating HCoVs with an age-structured reverse catalytic model, we estimated the likely duration of seropositivity following seroconversion. Results: We estimated that antibody persistence lasted between 0.9 (95% Credible interval: 0.6 - 1.6) and 3.8 (95% CrI: 2.0 - 7.4) years. Furthermore, we found the force of infection in older children and adults (those over 8.5 [95% CrI: 7.5 - 9.9] years) to be higher compared with young children in the majority of studies. Conclusions: These estimates of endemic HCoV dynamics could provide an indication of the future long-term infection and reinfection patterns of SARS-CoV-2.

2.
PLoS Biol ; 20(2): e3001531, 2022 02.
Article in English | MEDLINE | ID: covidwho-1686076

ABSTRACT

Identifying the potential for SARS-CoV-2 reinfection is crucial for understanding possible long-term epidemic dynamics. We analysed longitudinal PCR and serological testing data from a prospective cohort of 4,411 United States employees in 4 states between April 2020 and February 2021. We conducted a multivariable logistic regression investigating the association between baseline serological status and subsequent PCR test result in order to calculate an odds ratio for reinfection. We estimated an odds ratio for reinfection ranging from 0.14 (95% CI: 0.019 to 0.63) to 0.28 (95% CI: 0.05 to 1.1), implying that the presence of SARS-CoV-2 antibodies at baseline is associated with around 72% to 86% reduced odds of a subsequent PCR positive test based on our point estimates. This suggests that primary infection with SARS-CoV-2 provides protection against reinfection in the majority of individuals, at least over a 6-month time period. We also highlight 2 major sources of bias and uncertainty to be considered when estimating the relative risk of reinfection, confounders and the choice of baseline time point, and show how to account for both in reinfection analysis.


Subject(s)
Antibodies, Viral/blood , COVID-19/immunology , Reinfection/immunology , Adolescent , Adult , Aged , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Nucleic Acid Testing , COVID-19 Serological Testing , Humans , Logistic Models , Middle Aged , Polymerase Chain Reaction , Prospective Studies , Reinfection/prevention & control , SARS-CoV-2/immunology , Seroepidemiologic Studies , Time Factors , United States/epidemiology , Workplace/statistics & numerical data , Young Adult
3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-296879

ABSTRACT

Background: The COVID-19 epidemic has differentially impacted communities across England, with regional variation in rates of confirmed cases, hospitalisations and deaths. Measurement of this burden changed substantially over the first months, as surveillance was expanded to accommodate the escalating epidemic. Laboratory confirmation was initially restricted to clinical need (“pillar 1”) before expanding to community-wide symptomatics (“pillar 2”). This study aimed to ascertain whether inconsistent measurement of case data resulting from varying testing coverage could be reconciled by drawing inference from COVID-19-related deaths. MethodsWe fit a Bayesian spatio-temporal model to weekly COVID-19-related deaths per local authority (LTLA) throughout the first wave (1 January - 30 June 2020), adjusting for the local epidemic timing and the age, deprivation and ethnic composition of its population. We combined predictions from this model with case data under community-wide, symptomatic testing and infection prevalence estimates from the ONS infection survey, to infer the likely trajectory of infections implied by the deaths in each LTLA.ResultsA model including temporally- and spatially-correlated random effects was found to best accommodate the observed variation in COVID-19-related deaths, after accounting for local population characteristics. Predicted case counts under community-wide symptomatic testing suggest a total of 275,000-420,000 cases over the first wave - a median of over 100,000 additional to the total confirmed in practice under varying testing coverage. This translates to a peak incidence of around 200,000 total infections per week across England. The extent to which estimated total infections are reflected in confirmed case counts was found to vary substantially across LTLAs, ranging from 7% in Leicester to 96% in Gloucester with a median of 23%. ConclusionsLimitations in testing capacity biased the observed trajectory of COVID-19 infections throughout the first wave. Basing inference on COVID-19-related mortality and higher-coverage testing later in the time period, we could explore the extent of this bias more explicitly. Evidence points towards substantial under-representation of initial growth and peak magnitude of infections nationally, to which different parts of the country contribute unequally.

4.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-295820

ABSTRACT

Background: The duration of immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still uncertain, but it is of key clinical and epidemiological importance. Seasonal human coronaviruses (HCoV) have been circulating for longer and, therefore, may offer insights into the long-term dynamics of reinfection for such viruses. Methods: Combining historical seroprevalence data from five studies covering the four circulating HCoVs with an age-structured reverse catalytic model, we estimated the likely duration of seropositivity following seroconversion. Results: We estimated that antibody persistence lasted between 0.9 (95% Credible interval: 0.6 - 1.6) and 3.8 (95% CrI: 2.0 - 7.4) years. Furthermore, we found the force of infection in older children and adults (those over 8.5 [95% CrI: 7.5 - 9.9] years) to be higher compared with young children in the majority of studies. Conclusions: These estimates of endemic HCoV dynamics could provide an indication of the future long-term infection and reinfection patterns of SARS-CoV-2.

6.
Wellcome Open Res ; 6: 138, 2021.
Article in English | MEDLINE | ID: covidwho-1481209

ABSTRACT

Background: The duration of immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still uncertain, but it is of key clinical and epidemiological importance. Seasonal human coronaviruses (HCoV) have been circulating for longer and, therefore, may offer insights into the long-term dynamics of reinfection for such viruses. Methods: Combining historical seroprevalence data from five studies covering the four circulating HCoVs with an age-structured reverse catalytic model, we estimated the likely duration of seropositivity following seroconversion. Results: We estimated that antibody persistence lasted between 0.9 (95% Credible interval: 0.6 - 1.6) and 3.8 (95% CrI: 2.0 - 7.4) years. Furthermore, we found the force of infection in older children and adults (those over 8.5 [95% CrI: 7.5 - 9.9] years) to be higher compared with young children in the majority of studies. Conclusions: These estimates of endemic HCoV dynamics could provide an indication of the future long-term infection and reinfection patterns of SARS-CoV-2.

7.
PLoS Med ; 18(10): e1003793, 2021 10.
Article in English | MEDLINE | ID: covidwho-1477510

ABSTRACT

BACKGROUND: The importance of infectious disease epidemic forecasting and prediction research is underscored by decades of communicable disease outbreaks, including COVID-19. Unlike other fields of medical research, such as clinical trials and systematic reviews, no reporting guidelines exist for reporting epidemic forecasting and prediction research despite their utility. We therefore developed the EPIFORGE checklist, a guideline for standardized reporting of epidemic forecasting research. METHODS AND FINDINGS: We developed this checklist using a best-practice process for development of reporting guidelines, involving a Delphi process and broad consultation with an international panel of infectious disease modelers and model end users. The objectives of these guidelines are to improve the consistency, reproducibility, comparability, and quality of epidemic forecasting reporting. The guidelines are not designed to advise scientists on how to perform epidemic forecasting and prediction research, but rather to serve as a standard for reporting critical methodological details of such studies. CONCLUSIONS: These guidelines have been submitted to the EQUATOR network, in addition to hosting by other dedicated webpages to facilitate feedback and journal endorsement.


Subject(s)
Biomedical Research/standards , COVID-19/epidemiology , Checklist/standards , Epidemics , Guidelines as Topic/standards , Research Design , Biomedical Research/methods , Checklist/methods , Communicable Diseases/epidemiology , Epidemics/statistics & numerical data , Forecasting/methods , Humans , Reproducibility of Results
8.
Nat Commun ; 12(1): 5968, 2021 10 13.
Article in English | MEDLINE | ID: covidwho-1467102

ABSTRACT

There is conflicting evidence on the influence of weather on COVID-19 transmission. Our aim is to estimate weather-dependent signatures in the early phase of the pandemic, while controlling for socio-economic factors and non-pharmaceutical interventions. We identify a modest non-linear association between mean temperature and the effective reproduction number (Re) in 409 cities in 26 countries, with a decrease of 0.087 (95% CI: 0.025; 0.148) for a 10 °C increase. Early interventions have a greater effect on Re with a decrease of 0.285 (95% CI 0.223; 0.347) for a 5th - 95th percentile increase in the government response index. The variation in the effective reproduction number explained by government interventions is 6 times greater than for mean temperature. We find little evidence of meteorological conditions having influenced the early stages of local epidemics and conclude that population behaviour and government interventions are more important drivers of transmission.


Subject(s)
COVID-19/transmission , Meteorological Concepts , SARS-CoV-2/pathogenicity , Basic Reproduction Number , COVID-19/epidemiology , Cities , Cross-Sectional Studies , Humans , Meta-Analysis as Topic , Pandemics , Regression Analysis , Seasons , Temperature , Weather
9.
International Journal of Forecasting ; 2021.
Article in English | ScienceDirect | ID: covidwho-1433288

ABSTRACT

Weather forecasts, climate change projections, and epidemiological predictions all represent domains that are using forecast data to take early action for risk management. However, the methods and applications of the modeling efforts in each of these three fields have been developed and applied with little cross-fertilization. This perspective identifies best practices in each domain that can be adopted by the others, which can be used to inform each field separately as well as to facilitate a more effective combined use for the management of compound and evolving risks. In light of increased attention to predictive modeling during the COVID-19 pandemic, we identify three major areas that all three of these modeling fields should prioritize for future investment and improvement: (1) decision support, (2) conveying uncertainty, and (3) capturing vulnerability.

10.
J Epidemiol Community Health ; 76(2): 128-132, 2022 02.
Article in English | MEDLINE | ID: covidwho-1367464

ABSTRACT

This essay examines key aspects of social relationships that were disrupted by the COVID-19 pandemic. It focuses explicitly on relational mechanisms of health and brings together theory and emerging evidence on the effects of the COVID-19 pandemic to make recommendations for future public health policy and recovery. We first provide an overview of the pandemic in the UK context, outlining the nature of the public health response. We then introduce four distinct domains of social relationships: social networks, social support, social interaction and intimacy, highlighting the mechanisms through which the pandemic and associated public health response drastically altered social interactions in each domain. Throughout the essay, the lens of health inequalities, and perspective of relationships as interconnecting elements in a broader system, is used to explore the varying impact of these disruptions. The essay concludes by providing recommendations for longer term recovery ensuring that the social relational cost of COVID-19 is adequately considered in efforts to rebuild.


Subject(s)
COVID-19 , Pandemics , Humans , Interpersonal Relations , Public Health , SARS-CoV-2
12.
Am J Trop Med Hyg ; 105(1): 81-87, 2021 05 20.
Article in English | MEDLINE | ID: covidwho-1236889

ABSTRACT

Shortages of essential supplies used to prevent, diagnose, and treat COVID-19 have been a global concern, and price speculation and hikes may have negatively influenced access. This study identifies variability in prices of products acquired through government-driven contracts in Ecuador during the early pandemic response, when the highest mortality rates were registered in a single day. Data were obtained from the National Public Procurement Service (SERCOP) database between March 1 and July 31, 2020. A statistical descriptive analysis was conducted to extract relevant measures for commonly purchased products, medical devices, pharmaceutical drugs, and other goods. Among the most frequently purchased products, the greatest amounts were spent on face masks (US$4.5 million), acetaminophen (US$2.2 million), and reverse transcriptase quantitative polymerase chain reaction assay kits (US$1.8 million). Prices varied greatly, depending on each individual contract and on the number of units purchased; some were exceptionally higher than their market value. Compared with 2019, the mean price of medical examination gloves increased up to 1,307%, acetaminophen 500 mg pills, up to 796%, and oxygen flasks, 30.8%. In a context of budgetary constraints that actually required an effective use of available funds, speculative price hikes may have limited patient access to health care and the protection of the general population and health care workers. COVID-19 vaccine allocations to privileged individuals have also been widely reported. Price caps and other forms of regulation, as well as greater scrutiny and transparency of government-driven purchases, and investment in local production, are warranted in Ecuador for improved infectious disease prevention.


Subject(s)
COVID-19 Vaccines/economics , COVID-19/economics , COVID-19/epidemiology , Personal Protective Equipment/economics , SARS-CoV-2 , Acetaminophen/economics , Analgesics, Non-Narcotic/economics , COVID-19 Vaccines/supply & distribution , Economics, Hospital , Ecuador/epidemiology , Health Personnel , Humans , Masks/economics , Time Factors
13.
Trials ; 22(1): 286, 2021 Apr 16.
Article in English | MEDLINE | ID: covidwho-1190097

ABSTRACT

The LEAP-MS (Lifestyle, Exercise and Activity Package for People living with Progressive Multiple Sclerosis) study has developed an individualised supported self-management approach for physical activity for people with progressive multiple sclerosis (MS) and severe disability. The intervention has been evaluated in a single-arm feasibility study with embedded process evaluation. The feasibility study was due to open to recruitment during the COVID-19 2020-2021 pandemic, 1 month into the first UK-wide lockdown. We worked rapidly to implement adaptions to the trial procedures and intervention delivery that we believe are applicable to randomised controlled trials. Recruitment became predominantly via self-referral. Electronic consent was employed, with consent discussions occurring over the telephone. Registration, consent, eligibility assessment and data collection as well as the intervention (online physical activity tool) were via a secure, encrypted multi-user web-based platform for participants, physiotherapists and researchers accessible via various hardware. Physiotherapy consultations, as well as the process evaluation, were conducted remotely using video conferencing software or the telephone. A remote training package for physiotherapists and site initiations was also developed and electronic site files employed. Our adaptions are extremely topical given the COVID-19 situation, and whilst not what we had originally planned, have enabled successful delivery of the feasibility study and are relevant to conducting randomised controlled trials and meeting the needs of people with MS who are far more isolated than ever before. TRIAL REGISTRATION: ClinicalTrials.gov NCT03951181 . Registered on 15 May 2019.


Subject(s)
Exercise , Life Style , Multiple Sclerosis/therapy , Self Care , Telemedicine , COVID-19 , Disease Management , Humans , Pandemics , Patient Selection , Research Design , Videoconferencing
14.
Int J Infect Dis ; 105: 234-235, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1083229

ABSTRACT

Voluntary collective isolation has been proposed to be the best response to COVID-19 for indigenous populations. While the potential value of voluntary collective isolation is appealing, the feasibility of this approach needs empirical evidence to support it as the best response to protect indigenous communities from COVID-19. This paper describes our experience during SARS-CoV-2 surveillance among Waorani communities in the Ecuadorian Amazonian region, from June to September 2020. We found that self-isolation strategies failed to contain the spread of SARS-CoV-2 from main urban areas to remote and isolated comunities.


Subject(s)
COVID-19/prevention & control , SARS-CoV-2 , Social Isolation , COVID-19/diagnosis , COVID-19/epidemiology , Ecuador/epidemiology , Humans , Population Groups
15.
PLoS Negl Trop Dis ; 15(1): e0008958, 2021 01.
Article in English | MEDLINE | ID: covidwho-1067383

ABSTRACT

The SARS-CoV-2 virus has spread rapidly around the globe. Nevertheless, there is limited information describing the characteristics and outcomes of COVID-19 patients in Latin America. We conducted a cross-sectional analysis of 9,468 confirmed COVID-19 cases reported in Ecuador. We calculated overall incidence, mortality, case fatality rates, disability adjusted life years, attack and crude mortality rates, as well as relative risk and relative odds of death, adjusted for age, sex and presence of comorbidities. A total of 9,468 positive COVID-19 cases and 474 deaths were included in the analysis. Men accounted for 55.4% (n = 5, 247) of cases and women for 44.6% (n = 4, 221). We found the presence of comorbidities, being male and older than 65 years were important determinants of mortality. Coastal regions were most affected by COVID-19, with higher mortality rates than the highlands. Fatigue was reported in 53.2% of the patients, followed by headache (43%), dry cough (41.7%), ageusia (37.1%) and anosmia (36.1%). We present an analysis of the burden of COVID-19 in Ecuador. Our findings show that men are at higher risk of dying from COVID-19 than women, and risk increases with age and the presence of comorbidities. We also found that blue-collar workers and the unemployed are at greater risk of dying. These early observations offer clinical insights for the medical community to help improve patient care and for public health officials to strengthen Ecuador's response to the outbreak.


Subject(s)
COVID-19/mortality , Disease Outbreaks , Adolescent , Adult , Age Distribution , Aged , Aged, 80 and over , Child , Child, Preschool , Cost of Illness , Cross-Sectional Studies , Ecuador/epidemiology , Female , Geography , Humans , Infant , Infant, Newborn , Logistic Models , Male , Middle Aged , Occupations , Risk Factors , Sex Distribution , Social Class , Symptom Assessment , Unemployment , Young Adult
16.
BMC Med ; 19(1): 40, 2021 02 05.
Article in English | MEDLINE | ID: covidwho-1067227

ABSTRACT

BACKGROUND: Non-pharmaceutical interventions (NPIs) are used to reduce transmission of SARS coronavirus 2 (SARS-CoV-2) that causes coronavirus disease 2019 (COVID-19). However, empirical evidence of the effectiveness of specific NPIs has been inconsistent. We assessed the effectiveness of NPIs around internal containment and closure, international travel restrictions, economic measures, and health system actions on SARS-CoV-2 transmission in 130 countries and territories. METHODS: We used panel (longitudinal) regression to estimate the effectiveness of 13 categories of NPIs in reducing SARS-CoV-2 transmission using data from January to June 2020. First, we examined the temporal association between NPIs using hierarchical cluster analyses. We then regressed the time-varying reproduction number (Rt) of COVID-19 against different NPIs. We examined different model specifications to account for the temporal lag between NPIs and changes in Rt, levels of NPI intensity, time-varying changes in NPI effect, and variable selection criteria. Results were interpreted taking into account both the range of model specifications and temporal clustering of NPIs. RESULTS: There was strong evidence for an association between two NPIs (school closure, internal movement restrictions) and reduced Rt. Another three NPIs (workplace closure, income support, and debt/contract relief) had strong evidence of effectiveness when ignoring their level of intensity, while two NPIs (public events cancellation, restriction on gatherings) had strong evidence of their effectiveness only when evaluating their implementation at maximum capacity (e.g. restrictions on 1000+ people gathering were not effective, restrictions on < 10 people gathering were). Evidence about the effectiveness of the remaining NPIs (stay-at-home requirements, public information campaigns, public transport closure, international travel controls, testing, contact tracing) was inconsistent and inconclusive. We found temporal clustering between many of the NPIs. Effect sizes varied depending on whether or not we included data after peak NPI intensity. CONCLUSION: Understanding the impact that specific NPIs have had on SARS-CoV-2 transmission is complicated by temporal clustering, time-dependent variation in effects, and differences in NPI intensity. However, the effectiveness of school closure and internal movement restrictions appears robust across different model specifications, with some evidence that other NPIs may also be effective under particular conditions. This provides empirical evidence for the potential effectiveness of many, although not all, actions policy-makers are taking to respond to the COVID-19 pandemic.


Subject(s)
COVID-19/prevention & control , COVID-19/transmission , Contact Tracing/trends , Physical Distancing , Quarantine/trends , Schools/trends , COVID-19/epidemiology , Contact Tracing/methods , Humans , Pandemics , Quarantine/methods , SARS-CoV-2 , Time Factors
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