Publications
127 results found
Abbas M, Cori A, Cordey S, et al., 2022, Reconstructing transmission chains of SARS-CoV-2 amid multiple outbreaks in a geriatric acute-care hospital
<jats:title>Abstract</jats:title><jats:sec><jats:title>Background</jats:title><jats:p>There is ongoing uncertainty regarding transmission chains and the respective roles of healthcare workers (HCWs) and elderly patients in nosocomial outbreaks of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in geriatric settings.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>We performed a retrospective cohort study including patients with nosocomial coronavirus disease 2019 (COVID-19) in four outbreak-affected wards, and all SARS-CoV-2 RT-PCR positive HCWs from a Swiss university-affiliated geriatric acute-care hospital that admitted both Covid-19 and non-Covid-19 patients during the first pandemic wave in Spring 2020. We combined epidemiological and genetic sequencing data using a Bayesian modelling framework, and reconstructed transmission dynamics of SARS-CoV-2 involving patients and HCWs, in order to determine who infected whom. We evaluated general transmission patterns according to type of case (HCWs working in dedicated Covid-19 cohorting wards: HCW<jats:sub>covid</jats:sub>; HCWs working in non-Covid-19 wards where outbreaks occurred: HCW<jats:sub>outbreak</jats:sub>; patients with nosocomial Covid-19: patient<jats:sub>noso</jats:sub>) by deriving the proportion of infections attributed to each type of case across all posterior trees and comparing them to random expectations.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>During the study period (March 1 to May 7, 2020) we included 180 SARS-CoV-2 positive cases: 127 HCWs (91 HCW<jats:sub>covid</jats:sub>, 36 HCW<jats:sub>outbreak</jats:sub>) and 53 patients. The attack rates ranged from 10-19% for patients, and 21% for HCWs. We estimated that there were 16 importation events (3 patients, 13 HCWs) th
Ferguson N, Ghani A, Cori A, et al., 2021, Report 49: Growth, population distribution and immune escape of Omicron in England
To estimate the growth of the Omicron variant of concern (1) and its immune escape (2–9) characteristics, we analysed data from all PCR-confirmed SARS-CoV-2 cases in England excluding those with a history of recent international travel. We undertook separate analyses according to two case definitions. For the first definition, we included all cases with a definitive negative S-gene Target Failure (SGTF) result and specimen dates between 29/11/2021 and 11/12/2021 inclusive. For the second definition, we included cases with a positive genotype result and specimen date between 23/11/2021 and 11/12/2021 inclusive. We chose a later start date for the SGTF definition to ensure greater specificity of SGTF for Omicron.We used logistic and Poisson regression to identify factors associated with testing positive for Omicron compared to non-Omicron (mostly Delta) cases. We explored the following predictors: day, region, symptomatic status, sex, ethnicity, age band and vaccination status. Our results suggest rapid growth of the frequency of the Omicron variant relative to Delta, with the exponential growth rate of its frequency estimated to be 0.34/day (95% CI: 0.33-0.35) [2.0 day doubling time] over the study period from both SGTF and genotype data. The distribution of Omicron by age, region and ethnicity currently differs markedly from Delta, with 18–29-year-olds, residents in the London region, and those of African ethnicity having significantly higher rates of infection with Omicron relative to Delta.Hospitalisation and asymptomatic infection indicators were not significantly associated with Omicron infection, suggesting at most limited changes in severity compared with Delta.To estimate the impact of Omicron on vaccine effectiveness (VE) for symptomatic infection we used conditional Poisson regression to estimate the hazard ratio of being an Omicron case (using SGTF definition) compared with Delta, restricting our analysis to symptomatic cases and matching by da
Bosse NI, Abbott S, Bracher J, et al., 2021, Comparing human and model-based forecasts of COVID-19 in Germany and Poland
<jats:label>1</jats:label><jats:title>Abstract</jats:title><jats:p>Forecasts based on epidemiological modelling have played an important role in shaping public policy throughout the COVID-19 pandemic. This modelling combines knowledge about infectious disease dynamics with the subjective opinion of the researcher who develops and refines the model and often also adjusts model outputs. Developing a forecast model is difficult, resource- and time-consuming. It is therefore worth asking what modelling is able to add beyond the subjective opinion of the researcher alone. To investigate this, we analysed different real-time forecasts of cases of and deaths from COVID-19 in Germany and Poland over a 1-4 week horizon submitted to the German and Polish Forecast Hub. We compared crowd forecasts elicited from researchers and volunteers, against a) forecasts from two semi-mechanistic models based on common epidemiological assumptions and b) the ensemble of all other models submitted to the Forecast Hub. We found crowd forecasts, despite being overconfident, to outperform all other methods across all forecast horizons when forecasting cases (weighted interval score relative to the Hub ensemble 2 weeks ahead: 0.89). Forecasts based on computational models performed comparably better when predicting deaths (rel. WIS 1.26), suggesting that epidemiological modelling and human judgement can complement each other in important ways.</jats:p>
Bhatia S, Wardle J, Nash RK, et al., 2021, A generic method and software to estimate the transmission advantage of pathogen variants in real-time : SARS-CoV-2 as a case-study
<jats:title>Abstract</jats:title><jats:p>Recent months have demonstrated that emerging variants may set back the global COVID-19 response. The ability to rapidly assess the threat of new variants in real-time is critical for timely optimisation of control strategies.</jats:p><jats:p>We extend the EpiEstim R package, designed to estimate the time-varying reproduction number (<jats:italic>R</jats:italic><jats:sub><jats:italic>t</jats:italic></jats:sub>), to estimate in real-time the effective transmission advantage of a new variant compared to a reference variant. Our method can combine information across multiple locations and over time and was validated using an extensive simulation study, designed to mimic a variety of real-time epidemic contexts.</jats:p><jats:p>We estimate that the SARS-CoV-2 Alpha variant is 1.46 (95% Credible Interval 1.44-1.47) and 1.29, (95% CrI 1.29-1.30) times more transmissible than the wild type, using data from England and France respectively. We further estimate that Beta and Gamma combined are 1.25 (95% CrI 1.24-1.27) times more transmissible than the wildtype (France data). All results are in line with previous estimates from literature, but could have been obtained earlier and more easily with our off-the-shelf open-source tool.</jats:p><jats:p>Our tool can be used as an important first step towards quantifying the threat of new variants in real-time. Given the popularity of EpiEstim, this extension will likely be used widely to monitor the co-circulation and/or emergence of multiple variants of infectious pathogens.</jats:p><jats:sec><jats:title>Significance Statement</jats:title><jats:p>Early assessment of the transmissibility of new variants of an infectious pathogen is critical for anticipating their impact and designing appropriate interventions. However, this often requires complex and bespoke analyses relying
Limbada M, Macleod D, Situmbeko V, et al., 2021, Rates of viral suppression in a cohort of people with stable HIV from two community models of ART delivery versus facility-based HIV care in Lusaka, Zambia: a cluster-randomised, non-inferiority trial nested in the HPTN 071 (PopART) trial, The Lancet HIV, Vol: 9, Pages: E13-E23, ISSN: 2405-4704
BackgroundNon-facility-based antiretroviral therapy (ART) delivery for people with stable HIV might increase sustainable ART coverage in low-income and middle-income countries. Within the HPTN 071 (PopART) trial, two interventions, home-based delivery (HBD) and adherence clubs (AC), which included groups of 15–30 participants who met at a communal venue, were compared with standard of care (SoC). In this trial we looked at the effectiveness and feasibility of these alternative models of care. Specifically, this trial aimed to assess whether these models of care had similar virological suppression to that of SoC 12 months after enrolment.MethodsThis was a three-arm, cluster-randomised, non-inferiority trial, done in two urban communities in Lusaka, Zambia included in the HPTN 071 trial. The two communities were split into zones, which were randomly assigned (1:1:1) to the three treatment strategies: 35 zones to the SoC group, 35 zones to the HBD group, and 34 zones to the AC group. ART and adherence support were delivered once every 3 months at home for the HBD group, in groups of 15–30 people in the AC group, or in the clinic for the SoC group. Adults with HIV who were receiving first-line ART for at least 6 months, virally suppressed using national HIV guidelines in the last 12 months, had no other health conditions requiring the clinicians attention, live in the study catchment area, and provided written informed consent, were eligible for inclusion. The primary endpoint was viral suppression at 12 months (with a 6 month final measurement window [ie, 9–15 months]), defined as less than 1000 HIV RNA copies per mL, with a non-inferiority margin of 5%.FindingsBetween May 5 and Dec 19, 2017, 9900 individuals were screened for inclusion, of whom 2489 (25·1%) participants were enrolled into the trial: 781 (31%) in the SoC group, 852 (34%) in the HBD group, and 856 (34%) in the AC group. A higher proportion of participants had viral load measurem
Bhatia S, Wardle J, Nash R, et al., 2021, Report 47: A generic method and software to estimate the transmission advantage of pathogen variants in real-time : SARS-CoV-2 as a case-study
Recent months have demonstrated that emerging variants may set back the global COVID-19 response.The ability to rapidly assess the threat of new variants in real-time is critical for timely optimisation ofcontrol strategies.We extend the EpiEstim R package, designed to estimate the time-varying reproduction number (Rt),to estimate in real-time the e ective transmission advantage of a new variant compared to a referencevariant. Our method can combine information across multiple locations and over time and was validatedusing an extensive simulation study, designed to mimic a variety of real-time epidemic contexts.We estimate that the SARS-CoV-2 Alpha variant is 1.46 (95% Credible Interval 1.44-1.47) and 1.29,(95% CrI 1.29-1.30) times more transmissible than the wild type, using data from England and Francerespectively. We further estimate that Beta and Gamma combined are 1.25 (95% CrI 1.24-1.27) timesmore transmissible than the wildtype (France data). All results are in line with previous estimates fromliterature, but could have been obtained earlier and more easily with our o -the-shelf open-source tool.Our tool can be used as an important rst step towards quantifying the threat of new variants inreal-time. Given the popularity of EpiEstim, this extension will likely be used widely to monitor theco-circulation and/or emergence of multiple variants of infectious pathogens.
Sonabend R, Whittles LK, Imai N, et al., 2021, Non-pharmaceutical interventions, vaccination, and the SARS-CoV-2 delta variant in England: a mathematical modelling study, The Lancet, Vol: 398, Pages: 1825-1835, ISSN: 0140-6736
Background:England's COVID-19 roadmap out of lockdown policy set out the timeline and conditions for the stepwise lifting of non-pharmaceutical interventions (NPIs) as vaccination roll-out continued, with step one starting on March 8, 2021. In this study, we assess the roadmap, the impact of the delta (B.1.617.2) variant of SARS-CoV-2, and potential future epidemic trajectories.Methods:This mathematical modelling study was done to assess the UK Government's four-step process to easing lockdown restrictions in England, UK. We extended a previously described model of SARS-CoV-2 transmission to incorporate vaccination and multi-strain dynamics to explicitly capture the emergence of the delta variant. We calibrated the model to English surveillance data, including hospital admissions, hospital occupancy, seroprevalence data, and population-level PCR testing data using a Bayesian evidence synthesis framework, then modelled the potential trajectory of the epidemic for a range of different schedules for relaxing NPIs. We estimated the resulting number of daily infections and hospital admissions, and daily and cumulative deaths. Three scenarios spanning a range of optimistic to pessimistic vaccine effectiveness, waning natural immunity, and cross-protection from previous infections were investigated. We also considered three levels of mixing after the lifting of restrictions.Findings:The roadmap policy was successful in offsetting the increased transmission resulting from lifting NPIs starting on March 8, 2021, with increasing population immunity through vaccination. However, because of the emergence of the delta variant, with an estimated transmission advantage of 76% (95% credible interval [95% CrI] 69–83) over alpha, fully lifting NPIs on June 21, 2021, as originally planned might have led to 3900 (95% CrI 1500–5700) peak daily hospital admissions under our central parameter scenario. Delaying until July 19, 2021, reduced peak hospital admissions by three fol
Desai A, Nouvellet P, Bhatia S, et al., 2021, Data journalism and the COVID-19 pandemic: opportunities and challenges, The Lancet Digital Health, Vol: 3, Pages: e619-e621, ISSN: 2589-7500
Pickles M, Cori A, Probert WJM, et al., 2021, PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial, PLOS COMPUTATIONAL BIOLOGY, Vol: 17, ISSN: 1553-734X
Mathematical models are powerful tools in HIV epidemiology, producing quantitative projections of key indicators such as HIV incidence and prevalence. In order to improve the accuracy of predictions, such models need to incorporate a number of behavioural and biological heterogeneities, especially those related to the sexual network within which HIV transmission occurs. An individual-based model, which explicitly models sexual partnerships, is thus often the most natural type of model to choose. In this paper we present PopART-IBM, a computationally efficient individual-based model capable of simulating 50 years of an HIV epidemic in a large, high-prevalence community in under a minute. We show how the model calibrates within a Bayesian inference framework to detailed age- and sex-stratified data from multiple sources on HIV prevalence, awareness of HIV status, ART status, and viral suppression for an HPTN 071 (PopART) study community in Zambia, and present future projections of HIV prevalence and incidence for this community in the absence of trial intervention.
Miller KJ, Mueller K-R, Hermes D, 2021, Basis profile curve identification to understand electrical stimulation effects in human brain networks, PLOS COMPUTATIONAL BIOLOGY, Vol: 17, ISSN: 1553-734X
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Mishra S, Scott JA, Laydon DJ, et al., 2021, Comparing the responses of the UK, Sweden and Denmark to COVID-19 using counterfactual modelling, SCIENTIFIC REPORTS, Vol: 11, Pages: 1-9, ISSN: 2045-2322
The UK and Sweden have among the worst per-capita COVID-19 mortality in Europe. Sweden stands out for its greater reliance on voluntary, rather than mandatory, control measures. We explore how the timing and effectiveness of control measures in the UK, Sweden and Denmark shaped COVID-19 mortality in each country, using a counterfactual assessment: what would the impact have been, had each country adopted the others’ policies? Using a Bayesian semi-mechanistic model without prior assumptions on the mechanism or effectiveness of interventions, we estimate the time-varying reproduction number for the UK, Sweden and Denmark from daily mortality data. We use two approaches to evaluate counterfactuals which transpose the transmission profile from one country onto another, in each country’s first wave from 13th March (when stringent interventions began) until 1st July 2020. UK mortality would have approximately doubled had Swedish policy been adopted, while Swedish mortality would have more than halved had Sweden adopted UK or Danish strategies. Danish policies were most effective, although differences between the UK and Denmark were significant for one counterfactual approach only. Our analysis shows that small changes in the timing or effectiveness of interventions have disproportionately large effects on total mortality within a rapidly growing epidemic.
Knock ES, Whittles LK, Lees JA, et al., 2021, Key epidemiological drivers and impact of interventions in the 2020 SARS-CoV-2 epidemic in England, Science Translational Medicine, Vol: 13, Pages: 1-12, ISSN: 1946-6234
We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional surveillance data for England. Compared with other approaches, our model provides a synthesis of multiple surveillance data streams into a single coherent modelling framework allowing transmission and severity to be disentangled from features of the surveillance system. Of the control measures implemented, only national lockdown brought the reproduction number (Rteff ) below 1 consistently; if introduced one week earlier it could have reduced deaths in the first wave from an estimated 48,600 to 25,600 (95% credible interval [95%CrI]: 15,900-38,400). The infection fatality ratio decreased from 1.00% (95%CrI: 0.85%-1.21%) to 0.79% (95%CrI: 0.63%-0.99%), suggesting improved clinical care. The infection fatality ratio was higher in the elderly residing in care homes (23.3%, 95%CrI: 14.7%-35.2%) than those residing in the community (7.9%, 95%CrI: 5.9%-10.3%). On 2nd December 2020 England was still far from herd immunity, with regional cumulative infection incidence between 7.6% (95%CrI: 5.4%-10.2%) and 22.3% (95%CrI: 19.4%-25.4%) of the population. Therefore, any vaccination campaign will need to achieve high coverage and a high degree of protection in vaccinated individuals to allow non-pharmaceutical interventions to be lifted without a resurgence of transmission.
O'Driscoll M, Harry C, Donnelly CA, et al., 2021, A comparative analysis of statistical methods to estimate the reproduction number in emerging epidemics with implications for the current COVID-19 pandemic, Clinical Infectious Diseases, Vol: 73, Pages: e215-e223, ISSN: 1058-4838
As the SARS-CoV-2 pandemic continues its rapid global spread, quantification of local transmission patterns has been, and will continue to be, critical for guiding pandemic response. Understanding the accuracy and limitations of statistical methods to estimate the reproduction number, R0, in the context of emerging epidemics is therefore vital to ensure appropriate interpretation of results and the subsequent implications for control efforts. Using simulated epidemic data we assess the performance of 6 commonly-used statistical methods to estimate R0 as they would be applied in a real-time outbreak analysis scenario - fitting to an increasing number of data points over time and with varying levels of random noise in the data. Method comparison was also conducted on empirical outbreak data, using Zika surveillance data from the 2015-2016 epidemic in Latin America and the Caribbean. We find that all methods considered here frequently over-estimate R0 in the early stages of epidemic growth on simulated data, the magnitude of which decreases when fitted to an increasing number of time points. This trend of decreasing bias over time can easily lead to incorrect conclusions about the course of the epidemic or the need for control efforts. We show that true changes in pathogen transmissibility can be difficult to disentangle from changes in methodological accuracy and precision, particularly for data with significant over-dispersion. As localised epidemics of SARS-CoV-2 take hold around the globe, awareness of this trend will be important for appropriately cautious interpretation of results and subsequent guidance for control efforts.
Risher K, Cori A, Reniers G, et al., 2021, Age patterns of HIV incidence in eastern and southern Africa: a collaborative analysis of observational general population cohort studies, The Lancet HIV, Vol: 8, Pages: e429-e439, ISSN: 2405-4704
Background: As the HIV epidemic in sub-Saharan Africa matures, evidence about the age distribution of new HIV infections and how this has changed over the epidemic is needed to guide HIV prevention. We assessed trends in age-specific HIV incidence in six population-based cohort studies in eastern and southern Africa, reporting changes in average age at infection, age distribution of new infections, and birth cohort cumulative incidence. Methods: We used a Bayesian model to reconstruct age-specific HIV incidence from repeated observations of individuals’ HIV serostatus and survival collected among population HIV cohorts in rural Malawi, South Africa, Tanzania, Uganda, and Zimbabwe. The HIV incidence rate by age, time and sex was modelled using smooth splines functions. Incidence trends were estimated separately by sex and study. Estimated incidence and prevalence results for 2000-2017, standardised to study population distribution, were used to estimate average age at infection and proportion of new infections by age. Findings: Age-specific incidence declined at all ages, though the timing and pattern of decline varied by study. The average age at infection was higher in men (cohort means: 27·8-34·6 years) than women (cohort means: 24·8-29·6 years). Between 2000 and 2017, the average age at infection increased slightly: cohort means 0·5-2·8 years among men and -0·2-2·5 years among women. Across studies, between 38-63%(cohort means)of women’s infections were among 15-24-year-olds and between 30-63% of men’s infections were in 20-29-year-olds. Lifetime risk of HIV declined for successive birth cohorts. Interpretation: HIV incidence declined in all age groups and shifted slightly, but not dramatically, to older ages. Disproportionate new HIV infections occur among 15-24-year-old 4women and20-29-year-oldmen, supporting focused prevention in these groups. But 40-60% of infections were outside these
FitzJohn RG, Knock ES, Whittles LK, et al., 2021, Reproducible parallel inference and simulation of stochastic state space models using odin, dust, and mcstate [version 2; peer review: 2 approved], Wellcome Open Research, Vol: 5, ISSN: 2398-502X
State space models, including compartmental models, are used to model physical, biological and social phenomena in a broad range of scientific fields. A common way of representing the underlying processes in these models is as a system of stochastic processes which can be simulated forwards in time. Inference of model parameters based on observed time-series data can then be performed using sequential Monte Carlo techniques. However, using these methods for routine inference problems can be made difficult due to various engineering considerations: allowing model design to change in response to new data and ideas, writing model code which is highly performant, and incorporating all of this with up-to-date statistical techniques. Here, we describe a suite of packages in the R programming language designed to streamline the design and deployment of state space models, targeted at infectious disease modellers but suitable for other domains. Users describe their model in a familiar domain-specific language, which is converted into parallelised C++ code. A fast, parallel, reproducible random number generator is then used to run large numbers of model simulations in an efficient manner. We also provide standard inference and prediction routines, though the model simulator can be used directly if these do not meet the user's needs. These packages provide guarantees on reproducibility and performance, allowing the user to focus on the model itself, rather than the underlying computation. The ability to automatically generate high-performance code that would be tedious and time-consuming to write and verify manually, particularly when adding further structure to compartments, is crucial for infectious disease modellers. Our packages have been critical to the development cycle of our ongoing real-time modelling efforts in the COVID-19 pandemic, and have the potential to do the same for models used in a number of different domains.
Thomas R, Probert W, Sauter R, et al., 2021, Cost and cost-effectiveness of a universal HIV testing and treatment intervention in Zambia and South Africa: evidence and projections from the HPTN 071 (PopART) trial, The Lancet Global Health, Vol: 9, Pages: e668-e680, ISSN: 2214-109X
BackgroundThe HPTN 071 (PopART) trial showed that a combination HIV prevention package including universal HIV testing and treatment (UTT) reduced population-level incidence of HIV compared with standard care. However, evidence is scarce on the costs and cost-effectiveness of such an intervention.MethodsUsing an individual-based model, we simulated the PopART intervention and standard care with antiretroviral therapy (ART) provided according to national guidelines for the 21 trial communities in Zambia and South Africa (for all individuals aged >14 years), with model parameters and primary cost data collected during the PopART trial and from published sources. Two intervention scenarios were modelled: annual rounds of PopART from 2014 to 2030 (PopART 2014–30; as the UNAIDS Fast-Track target year) and three rounds of PopART throughout the trial intervention period (PopART 2014–17). For each country, we calculated incremental cost-effectiveness ratios (ICERs) as the cost per disability-adjusted life-year (DALY) and cost per HIV infection averted. Cost-effectiveness acceptability curves were used to indicate the probability of PopART being cost-effective compared with standard care at different thresholds of cost per DALY averted. We also assessed budget impact by projecting undiscounted costs of the intervention compared with standard care up to 2030.FindingsDuring 2014–17, the mean cost per person per year of delivering home-based HIV counselling and testing, linkage to care, promotion of ART adherence, and voluntary medical male circumcision via community HIV care providers for the simulated population was US$6·53 (SD 0·29) in Zambia and US$7·93 (0·16) in South Africa. In the PopART 2014–30 scenario, median ICERs for PopART delivered annually until 2030 were $2111 (95% credible interval [CrI] 1827–2462) per HIV infection averted in Zambia and $3248 (2472–3963) per HIV infection averted in South Afric
Bhatia S, Lassmann B, Cohn E, et al., 2021, Using digital surveillance tools for near real-time mapping of the risk of infectious disease spread, npj Digital Medicine, Vol: 4, ISSN: 2398-6352
Data from digital disease surveillance tools such as ProMED and HealthMap can complement the field surveillance during ongoing outbreaks. Our aim was to investigate the use of data collected through ProMED and HealthMap in real-time outbreak analysis. We developed a flexible statistical model to quantify spatial heterogeneity in the risk of spread of an outbreak and to forecast short term incidence trends. The model was applied retrospectively to data collected by ProMED and HealthMap during the 2013–2016 West African Ebola epidemic and for comparison, to WHO data. Using ProMED and HealthMap data, the model was able to robustly quantify the risk of disease spread 1–4 weeks in advance and for countries at risk of case importations, quantify where this risk comes from. Our study highlights that ProMED and HealthMap data could be used in real-time to quantify the spatial heterogeneity in risk of spread of an outbreak.
Ragonnet-Cronin M, Boyd O, Geidelberg L, et al., 2021, Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions, Nature Communications, Vol: 12, Pages: 1-7, ISSN: 2041-1723
Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non- pharmaceutical interventions is still debated. We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were examined in relation to the dates of the most stringent interventions in each location as well as to the number of cumulative COVID-19 deaths and phylodynamic estimates of epidemic size. Here we report that the time elapsed between epidemic origin and maximum intervention is associated with different measures of epidemic severity and explains 11% of the variance in reported deaths one month after the most stringent intervention. Locations where strong non-pharmaceutical interventions were implemented earlier experienced 30 much less severe COVID-19 morbidity and mortality during the period of study.
Nouvellet P, Bhatia S, Cori A, et al., 2021, Reduction in mobility and COVID-19 transmission, Nature Communications, Vol: 12, ISSN: 2041-1723
In response to the COVID-19 pandemic, countries have sought to control SARS-CoV-2 transmission by restricting population movement through social distancing interventions, thus reducing the number of contacts.Mobility data represent an important proxy measure of social distancing, and here, we characterise the relationship between transmission and mobility for 52 countries around the world.Transmission significantly decreased with the initial reduction in mobility in 73% of the countries analysed, but we found evidence of decoupling of transmission and mobility following the relaxation of strict control measures for 80% of countries. For the majority of countries, mobility explained a substantial proportion of the variation in transmissibility (median adjusted R-squared: 48%, interquartile range - IQR - across countries [27-77%]). Where a change in the relationship occurred, predictive ability decreased after the relaxation; from a median adjusted R-squared of 74% (IQR across countries [49-91%]) pre-relaxation, to a median adjusted R-squared of 30% (IQR across countries [12-48%]) post-relaxation.In countries with a clear relationship between mobility and transmission both before and after strict control measures were relaxed, mobility was associated with lower transmission rates after control measures were relaxed indicating that the beneficial effects of ongoing social distancing behaviours were substantial.
Abbas M, Robalo Nunes T, Cori A, et al., 2021, Explosive Nosocomial Outbreak of SARS-CoV-2 in a Rehabilitation Clinic: The Limits of Genomics for Outbreak Reconstruction, SSRN
Knock E, Whittles L, Lees J, et al., 2020, Report 41: The 2020 SARS-CoV-2 epidemic in England: key epidemiological drivers and impact of interventions
England has been severely affected by COVID-19. We fitted a model of SARS-CoV-2 transmission in care homes and the community to regional 2020 surveillance data. Only national lockdown brought the reproduction number below 1 consistently; introduced one week earlier in the first wave it could have reduced mortality by 23,300 deaths on average. The mean infection fatality ratio was initially ~1.3% across all regions except London and halved following clinical care improvements. The infection fatality ratio was two-fold lower throughout in London, even when adjusting for demographics. The infection fatality ratio in care homes was 2.5-times that in the elderly in the community. Population-level infection-induced immunity in England is still far from herd immunity, with regional mean cumulative attack rates ranging between 4.4% and 15.8%.
Djaafara B, Imai N, Hamblion E, et al., 2020, A quantitative framework for defining the end of an infectious disease outbreak: application to Ebola virus disease, American Journal of Epidemiology, Vol: 190, Pages: 642-651, ISSN: 0002-9262
The end-of-outbreak declaration is an important step in controlling infectious disease outbreaks. Objective estimation of the confidence level that an outbreak is over is important to reduce the risk of postdeclaration flare-ups. We developed a simulation-based model with which to quantify that confidence and tested it on simulated Ebola virus disease data. We found that these confidence estimates were most sensitive to the instantaneous reproduction number, the reporting rate, and the time between the symptom onset and death or recovery of the last detected case. For Ebola virus disease, our results suggested that the current World Health Organization criterion of 42 days since the recovery or death of the last detected case is too short and too sensitive to underreporting. Therefore, we suggest a shift to a preliminary end-of-outbreak declaration after 63 days from the symptom onset day of the last detected case. This preliminary declaration should still be followed by 90 days of enhanced surveillance to capture potential flare-ups of cases, after which the official end of the outbreak can be declared. This sequence corresponds to more than 95% confidence that an outbreak is over in most of the scenarios examined. Our framework is generic and therefore could be adapted to estimate end-of-outbreak confidence for other infectious diseases.
Pickles M, Cori A, Probert W, et al., 2020, PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial
<jats:title>Abstract</jats:title><jats:p>Mathematical models are powerful tools in HIV epidemiology, producing quantitative projections of key indicators such as HIV incidence and prevalence. In order to improve the accuracy of predictions, such models need to incorporate a number of behavioural and biological heterogeneities, especially those related to the sexual network within which HIV transmission occurs. An individual-based model, which explicitly models sexual partnerships, is thus often the most natural type of model to choose. In this paper we present PopART-IBM, a computationally efficient individual-based model capable of simulating 50 years of an HIV epidemic in a large, high-prevalence community in under a minute. We show how the model calibrates within a Bayesian inference framework to detailed age- and sex-stratified data from multiple sources on HIV prevalence, awareness of HIV status, ART status, and viral suppression for an HPTN 071 (PopART) study community in Zambia, and present future projections of HIV prevalence and incidence for this community in the absence of trial intervention.</jats:p>
Bhatia S, Imai N, Cuomo-Dannenburg G, et al., 2020, Estimating the number of undetected COVID-19 cases among travellers from mainland China, Publisher: F1000 Research Ltd
Background: Since the start of the COVID-19 epidemic in late 2019, there have been more than 152 affected regions and countries with over 110,000 confirmed cases outside mainland China.Methods: We analysed COVID-19 cases among travellers from mainland China to different regions and countries, comparing the region- and country-specific rates of detected and confirmed cases per flight volume to estimate the relative sensitivity of surveillance in different regions and countries.Results: Although travel restrictions from Wuhan City and other cities across China may have reduced the absolute number of travellers to and from China, we estimated that more than two thirds (70%, 95% CI: 54% - 80%, compared to Singapore; 75%, 95% CI: 66% - 82%, compared to multiple countries) of cases exported from mainland China have remained undetected.Conclusions: These undetected cases potentially resulted in multiple chains of human-to-human transmission outside mainland China.
Nouvellet P, Bhatia S, Cori A, et al., 2020, Report 26: Reduction in mobility and COVID-19 transmission
In response to the COVID-19 pandemic, countries have sought to control transmission of SARS-CoV-2by restricting population movement through social distancing interventions, reducing the number ofcontacts.Mobility data represent an important proxy measure of social distancing. Here, we develop aframework to infer the relationship between mobility and the key measure of population-level diseasetransmission, the reproduction number (R). The framework is applied to 53 countries with sustainedSARS-CoV-2 transmission based on two distinct country-specific automated measures of humanmobility, Apple and Google mobility data.For both datasets, the relationship between mobility and transmission was consistent within andacross countries and explained more than 85% of the variance in the observed variation intransmissibility. We quantified country-specific mobility thresholds defined as the reduction inmobility necessary to expect a decline in new infections (R<1).While social contacts were sufficiently reduced in France, Spain and the United Kingdom to controlCOVID-19 as of the 10th of May, we find that enhanced control measures are still warranted for themajority of countries. We found encouraging early evidence of some decoupling of transmission andmobility in 10 countries, a key indicator of successful easing of social-distancing restrictions.Easing social-distancing restrictions should be considered very carefully, as small increases in contactrates are likely to risk resurgence even where COVID-19 is apparently under control. Overall, strongpopulation-wide social-distancing measures are effective to control COVID-19; however gradualeasing of restrictions must be accompanied by alternative interventions, such as efficient contacttracing, to ensure control.
Verity R, Okell LC, Dorigatti I, et al., 2020, Estimates of the severity of coronavirus disease 2019: a model-based analysis., Lancet Infectious Diseases, Vol: 20, Pages: 669-677, ISSN: 1473-3099
BACKGROUND: In the face of rapidly changing data, a range of case fatality ratio estimates for coronavirus disease 2019 (COVID-19) have been produced that differ substantially in magnitude. We aimed to provide robust estimates, accounting for censoring and ascertainment biases. METHODS: We collected individual-case data for patients who died from COVID-19 in Hubei, mainland China (reported by national and provincial health commissions to Feb 8, 2020), and for cases outside of mainland China (from government or ministry of health websites and media reports for 37 countries, as well as Hong Kong and Macau, until Feb 25, 2020). These individual-case data were used to estimate the time between onset of symptoms and outcome (death or discharge from hospital). We next obtained age-stratified estimates of the case fatality ratio by relating the aggregate distribution of cases to the observed cumulative deaths in China, assuming a constant attack rate by age and adjusting for demography and age-based and location-based under-ascertainment. We also estimated the case fatality ratio from individual line-list data on 1334 cases identified outside of mainland China. Using data on the prevalence of PCR-confirmed cases in international residents repatriated from China, we obtained age-stratified estimates of the infection fatality ratio. Furthermore, data on age-stratified severity in a subset of 3665 cases from China were used to estimate the proportion of infected individuals who are likely to require hospitalisation. FINDINGS: Using data on 24 deaths that occurred in mainland China and 165 recoveries outside of China, we estimated the mean duration from onset of symptoms to death to be 17·8 days (95% credible interval [CrI] 16·9-19·2) and to hospital discharge to be 24·7 days (22·9-28·1). In all laboratory confirmed and clinically diagnosed cases from mainland China (n=70 117), we estimated a crude case fatality ratio (adjusted for cen
Cori A, Kamvar ZN, Stockwin J, et al., 2020, mrc-ide/EpiEstim: 2.2-3
Fixed bugs in draw_one_set_of_ancestries resulting from incorrect lengths and an undefined variable (issue #92) (#93, @jstockwin)Fixed incorrect quantiles (issue #88) (#89, @jstockwin)
ODriscoll M, Harry C, Donnelly CA, et al., 2020, A comparative analysis of statistical methods to estimate the reproduction number in emerging epidemics with implications for the current COVID-19 pandemic
<jats:title>Abstract</jats:title><jats:p>As the SARS-CoV-2 pandemic continues its rapid global spread, quantification of local transmission patterns has been, and will continue to be, critical for guiding pandemic response. Understanding the accuracy and limitations of statistical methods to estimate the reproduction number, R<jats:sub>0</jats:sub>, in the context of emerging epidemics is therefore vital to ensure appropriate interpretation of results and the subsequent implications for control efforts. Using simulated epidemic data we assess the performance of 6 commonly-used statistical methods to estimate R<jats:sub>0</jats:sub> as they would be applied in a real-time outbreak analysis scenario – fitting to an increasing number of data points over time and with varying levels of random noise in the data. Method comparison was also conducted on empirical outbreak data, using Zika surveillance data from the 2015–2016 epidemic in Latin America and the Caribbean. We find that all methods considered here frequently over-estimate R0 in the early stages of epidemic growth on simulated data, the magnitude of which decreases when fitted to an increasing number of time points. This trend of decreasing bias over time can easily lead to incorrect conclusions about the course of the epidemic or the need for control efforts. We show that true changes in pathogen transmissibility can be difficult to disentangle from changes in methodological accuracy and precision, particularly for data with significant over-dispersion. As localised epidemics of SARS-CoV-2 take hold around the globe, awareness of this trend will be important for appropriately cautious interpretation of results and subsequent guidance for control efforts.</jats:p><jats:sec><jats:title>Significance Statement</jats:title><jats:p>In line with a real-time outbreak analysis we use simulated epidemic data to assess the performance of 6
Gaythorpe K, Imai N, Cuomo-Dannenburg G, et al., 2020, Report 8: Symptom progression of COVID-19
The COVID-19 epidemic was declared a Public Health Emergency of International Concern (PHEIC) by WHO on 30th January 2020 [1]. As of 8 March 2020, over 107,000 cases had been reported. Here, we use published and preprint studies of clinical characteristics of cases in mainland China as well as case studies of individuals from Hong Kong, Japan, Singapore and South Korea to examine the proportional occurrence of symptoms and the progression of symptoms through time.We find that in mainland China, where specific symptoms or disease presentation are reported, pneumonia is the most frequently mentioned, see figure 1. We found a more varied spectrum of severity in cases outside mainland China. In Hong Kong, Japan, Singapore and South Korea, fever was the most frequently reported symptom. In this latter group, presentation with pneumonia is not reported as frequently although it is more common in individuals over 60 years old. The average time from reported onset of first symptoms to the occurrence of specific symptoms or disease presentation, such as pneumonia or the use of mechanical ventilation, varied substantially. The average time to presentation with pneumonia is 5.88 days, and may be linked to testing at hospitalisation; fever is often reported at onset (where the mean time to develop fever is 0.77 days).
Thompson H, Imai N, Dighe A, et al., 2020, Report 7: Estimating infection prevalence in Wuhan City from repatriation flights
Since the end of January 2020, in response to the growing COVID-19 epidemic, 55 countries have repatriated over 8000 citizens from Wuhan City, China. In addition to quarantine measures for returning citizens, many countries implemented PCR screening to test for infection regardless of symptoms. These flights therefore give estimates of infection prevalence in Wuhan over time. Between 30th January and 1st February (close to the peak of the epidemic in Wuhan), infection prevalence was 0.87% (95% CI: 0.32% - 1.89%). As countries now start to repatriate citizens from Iran and northern Italy, information from repatriated citizens could help inform the level of response necessary to help control the outbreaks unfolding in newly affected areas.
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