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1.
Epidemiol Infect ; 150: e100, 2022 05 12.
Article in English | MEDLINE | ID: covidwho-1947140

ABSTRACT

This paper presents a method used to rapidly assess the incursion and the establishment of community transmission of suspected SARS-CoV-2 variant of concern Delta (lineage B.1.617.2) into the UK in April and May 2021. The method described is independent of any genetically sequenced data, and so avoids the inherent lag times involved in sequencing of cases. We show that, between 1 April and 12 May 2021, there was a strong correlation between local authorities with high numbers of imported positive cases from India and high COVID-19 case rates, and that this relationship holds as we look at finer geographic detail. Further, we also show that Bolton was an outlier in the relationship, having the highest COVID-19 case rates despite relatively few importations. We use an artificial neural network trained on demographic data, to show that observed importations in Bolton were consistent with similar areas. Finally, using an SEIR transmission model, we show that imported positive cases were a contributing factor to persistent transmission in a number of local authorities, however they could not account for increased case rates observed in Bolton. As such, the outbreak of Delta variant in Bolton was likely not a result of direct importation from overseas, but rather secondary transmission from other regions within the UK.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Disease Outbreaks , Humans , SARS-CoV-2/genetics , United Kingdom/epidemiology
2.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-334159

ABSTRACT

The roll-out of COVID-19 vaccines in the England has generally been very good – with over 80% of over 12s having received two doses of vaccine by the start of February 2022, and 67% having received a further booster dose. Despite this, there is a small section of the population who remain unvaccinated, either due to lack of access, hesitancy or resistant to vaccination. In this report we estimate that, during 2021, there were approximately 3,500 deaths in unvaccinated people, who could otherwise have reasonably been expected to receive a vaccination. Further, we show that if all of the remaining unvaccinated population in England were to become infected (or reinfected) with the Omicron variant of COVID-19, we would expect to see approximately 11,700 further deaths and 29,600 hospitalisations. These number could fall to 5,300 and 19,600 respectively, if all but the most vaccine resistant individuals become fully vaccinated.

3.
SSRN; 2022.
Preprint in English | SSRN | ID: ppcovidwho-333480

ABSTRACT

Background: Paediatric Multisystem Inflammatory Syndrome (PIMS-TS) is a rare life-threatening complication that typically occurs several weeks after SARS-CoV-2 infection in children and young people (CYP). We used national and regional-level data from the COVID-19 pandemic wave in England to develop and optimise a model to predict PIMS-TS cases in subsequent waves. Methods: SARS-CoV-2 infections in CYP aged 0-15 years in England were estimated using the PHE-Cambridge real-time model. PIMS-TS cases were identified through the British Paediatric Surveillance Unit during the first pandemic wave (March-June 2020). Since November 2020, cases were identified through Secondary Uses Services (SUS), a national healthcare activity dataset. A predictive model was developed to estimate PIMS-TS risk and lag times after SARS-CoV-2 infection for the Alpha (weeks 1-10, 2021) and Delta (weeks 22-30, 2022) waves. Findings: During the Alpha wave, the model accurately predicted PIMS-TS cases (506 (95% CI: 491-531) vs 502 observed cases), with a median estimated the risk of 0·038% (IQR, 0·037-0·041%;38/100,000 infections) of paediatric SARS-CoV-2 infections. For the Delta wave, the median risk of PIMS-TS was significantly lower at 0·026% (IQR, 0·025-0·029%;27/100,000 infections) , with 212 observed PIMS-TS cases compared to 450 predicted by the model during June-October 2021. Interpretation: We developed a model that accurately predicted national and regional PIMS-TS cases in CYP during the Alpha wave. PIMS-TS cases were, however, 53% lower than predicted during the Delta wave. Further studies are needed to understand the mechanisms of the observed lower risk with the Delta variant.

4.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327788

ABSTRACT

Understanding the scale of the threat posed by SARS-CoV2 B.1.1.529, or Omicron , variant formed a key problem in public health in the early part of 2022. Early evidence indicated that the variant was more transmissible and less severe than previous variants. As the virus was expected to spread quickly through the population of England, it was important that some understanding of the immunological landscape of the country was developed. This paper attempts to estimate the number of people with good immunity to the Omicron variant, defined as either recent infection with two doses of vaccine, or two doses of vaccine with a recent booster dose. To achieve this, we use a process of iterative proportional fitting to estimate the cell values of a contingency table, using national immunisation records and real-time model infection estimates as marginal values. Our results indicate that, despite the increased risk of immune evasion with the Omicron variant, a high proportion of England’s population had good immunity to the virus, particularly in older age groups. However, low rates of immunity in younger populations may allow endemic infection to persist for some time.

5.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-307507

ABSTRACT

Background: Paediatric Multisystem Inflammatory Syndrome (PIMS-TS) is a rare life-threatening complication that occurs in some children two to four weeks after SARS-CoV-2 infection. Although the precise causal mechanisms underpinning the relationship between SARS-CoV-2 and PIMS-TS are unclear, several recent studies have confirmed a strong temporal association. This study provides further evidence in support of a causal and temporal link. A novel methodology is presented whereby PIMS-TS incidence parameters estimated from data published on SARS-CoV-2 in the first wave of the COVID-19 pandemic in England were used to make accurate projections of PIMS-TS cases in the second wave. Methods: Case classifications and data on PIMS-TS cases were obtained from the British Paediatric Surveillance Unit (BPSU) in an endeavour initiated by Public Heath England (PHE). The dataset contained all PIMS-TS cases presenting as symptomatic in England in the first wave of the pandemic. PIMS-TS incidence rates in children aged <15 years were estimated for the first wave and expressed as a fraction of SARS-CoV-2 cases. Data on SARS-CoV-2 cases were extracted from the PHE-Cambridge real-time model. Temporal analysis was performed to estimate the lag-time between peak SARS-CoV-2 incidence and peak PIMS-TS. The incidence and lag-time parameters estimated during the first wave were used to produce weekly projections of PIMS-TS cases in the second wave. These projections were then employed operationally in a clinical setting. Statistical analyses were performed to assess the accuracy of the forecasts once data on PIMS-TS cases were published by the BPSU approximately three months after the PIMS-TS forecasts were generated. Findings: Statistical analyses show that the PIMS-TS parameters estimated from the first wave produced accurate projections of PIMS-TS incidence in the second wave. Results at the aggregated national level showed there were no statistically significant differences observed between the PIMS-TS admission data and forecasts in England. Forecasts generated at the disaggregated regional level were also accurate, with no statistically significant differences observed between the PIMS-TS admissions data and forecasts in five of the nine Public Health England Centres (PHECs). However, a statistically significant divergence was observed between the PIMS-TS admissions data and the second wave forecasts in the regions of London and in the East, North West, and South West of England.Interpretation: This study provides further evidence in support of a causal and temporal association between SARS-CoV-2 and PIMS-TS, since data on SARS-CoV-2 incidence in the first wave of the COVID-19 pandemic in England have been shown to be a good baseline from which to generate forecasts of PIMS-TS incidence in the second wave, at both aggregated national and disaggregated regional levels.Funding Information: : Department of Health and Social Care (DHSC) Grant-in-aid funding to Public Health England (PHE).Declaration of Interests: None;this study did not receive any specific grant funding from external agencies in the public, commercial or not-for-profit sectors.Ethics Approval Statement: : PHE has legal permission under Regulation 3 of The Health Service (Control of Patient Information) Regulations 2002, to conduct national surveillance of communicable diseases in England and, as such, individual patient consent is not required. Public Health Wales, through the established order legislation, is required to conduct surveillance of communicable diseases in Wales and, as such, individual patient consent is not required. The surveillance protocol was approved by the Public Benefit and Privacy Panel for Health and Social Care in Scotland (Ref: 20210041, 19 May 2020).

6.
Philos Trans R Soc Lond B Biol Sci ; 376(1829): 20200277, 2021 07 19.
Article in English | MEDLINE | ID: covidwho-1309695

ABSTRACT

We investigate the effect of school closure and subsequent reopening on the transmission of COVID-19, by considering Denmark, Norway, Sweden and German states as case studies. By comparing the growth rates in daily hospitalizations or confirmed cases under different interventions, we provide evidence that school closures contribute to a reduction in the growth rate approximately 7 days after implementation. Limited school attendance, such as older students sitting exams or the partial return of younger year groups, does not appear to significantly affect community transmission. In countries where community transmission is generally low, such as Denmark or Norway, a large-scale reopening of schools while controlling or suppressing the epidemic appears feasible. However, school reopening can contribute to statistically significant increases in the growth rate in countries like Germany, where community transmission is relatively high. In all regions, a combination of low classroom occupancy and robust test-and-trace measures were in place. Our findings underscore the need for a cautious evaluation of reopening strategies. This article is part of the theme issue 'Modelling that shaped the early COVID-19 pandemic response in the UK'.


Subject(s)
COVID-19/epidemiology , Pandemics , SARS-CoV-2/pathogenicity , Adolescent , COVID-19/transmission , COVID-19/virology , Denmark/epidemiology , Europe/epidemiology , Germany/epidemiology , Humans , Norway/epidemiology , Schools/trends , Sweden/epidemiology
7.
Bull World Health Organ ; 99(3): 178-189, 2021 Mar 01.
Article in English | MEDLINE | ID: covidwho-1256313

ABSTRACT

OBJECTIVE: To describe the clinical presentation, course of disease and health-care seeking behaviour of the first few hundred cases of coronavirus disease 2019 (COVID-19) in the United Kingdom of Great Britain and Northern Ireland. METHODS: We implemented the World Health Organization's First Few X cases and contacts investigation protocol for COVID-19. Trained public health professionals collected information on 381 virologically confirmed COVID-19 cases from 31 January 2020 to 9 April 2020. We actively followed up cases to identify exposure to infection, symptoms and outcomes. We also collected limited data on 752 symptomatic people testing negative for COVID-19, as a control group for analyses of the sensitivity, specificity and predictive value of symptoms. FINDINGS: Approximately half of the COVID-19 cases were imported (196 cases; 51.4%), of whom the majority had recent travel to Italy (140 cases; 71.4%). Of the 94 (24.7%) secondary cases, almost all reported close contact with a confirmed case (93 cases; 98.9%), many through household contact (37 cases; 39.8%). By age, a lower proportion of children had COVID-19. Most cases presented with cough, fever and fatigue. The sensitivity and specificity of symptoms varied by age, with nonlinear relationships with age. Although the proportion of COVID-19 cases with fever increased with age, for those with other respiratory infections the occurrence of fever decreased with age. The occurrence of shortness of breath also increased with age in a greater proportion of COVID-19 cases. CONCLUSION: The study has provided useful evidence for generating case definitions and has informed modelling studies of the likely burden of COVID-19.


Subject(s)
COVID-19/epidemiology , COVID-19/physiopathology , Adolescent , Adult , Age Distribution , Aged , Child , Child, Preschool , Dyspnea/epidemiology , Female , Humans , Infant , Male , Middle Aged , Respiratory Tract Infections/epidemiology , SARS-CoV-2 , Travel , United Kingdom/epidemiology , Young Adult
8.
Lancet Reg Health Eur ; 3: 100075, 2021 Apr.
Article in English | MEDLINE | ID: covidwho-1144857

ABSTRACT

BACKGROUND: Paediatric Multisystem Inflammatory Syndrome temporally associated with SARS-CoV-2 (PIMS-TS), first identified in April 2020, shares features of both Kawasaki disease (KD) and toxic shock syndrome (TSS). The surveillance describes the epidemiology and clinical characteristics of PIMS-TS in the United Kingdom and Ireland. METHODS: Public Health England initiated prospective national surveillance of PIMS-TS through the British Paediatric Surveillance Unit. Paediatricians were contacted monthly to report PIMS-TS, KD and TSS cases electronically and complete a detailed clinical questionnaire. Cases with symptom onset between 01 March and 15 June 2020 were included. FINDINGS: There were 216 cases with features of PIMS-TS alone, 13 with features of both PIMS-TS and KD, 28 with features of PIMS-TS and TSS and 11 with features of PIMS-TS, KD and TSS, with differences in age, ethnicity, clinical presentation and disease severity between the phenotypic groups. There was a strong geographical and temporal association between SARS-CoV-2 infection rates and PIMS-TS cases. Of those tested, 14.8% (39/264) children had a positive SARS-CoV-2 RT-PCR, and 63.6% (75/118) were positive for SARS-CoV-2 antibodies. In total 44·0% (118/268) required intensive care, which was more common in cases with a TSS phenotype. Three of five children with cardiac arrest had TSS phenotype. Three children (1·1%) died. INTERPRETATION: The strong association between SARS-CoV-2 infection and PIMS-TS emphasises the importance of maintaining low community infection rates to reduce the risk of this rare but severe complication in children and adolescents. Close follow-up will be important to monitor long-term complications in children with PIMS-TS. FUNDING: PHE.

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