Background: Interventions are now in place worldwide to reduce transmission of the novel coronavirus. Assessing temporal variations in transmission in different countries is essential for evaluating the effectiveness of public health interventions and the impact of changes in policy. Methods: We use case notification data to generate daily estimates of the time-dependent reproduction number in different regions and countries. Our modelling framework, based on open source tooling, accounts for reporting delays, so that temporal variations in reproduction number estimates can be compared directly with the times at which interventions are implemented. Results: We provide three example uses of our framework. First, we demonstrate how the toolset displays temporal changes in the reproduction number. Second, we show how the framework can be used to reconstruct case counts by date of infection from case counts by date of notification, as well as to estimate the reproduction number. Third, we show how maps can be generated to clearly show if case numbers are likely to decrease or increase in different regions. Results are shown for regions and countries worldwide on our website (https://epiforecasts.io/covid/) and are updated daily. Our tooling is provided as an open-source R package to allow replication by others. Conclusions: This decision-support tool can be used to assess changes in virus transmission in different regions and countries worldwide. This allows policymakers to assess the effectiveness of current interventions, and will be useful for inferring whether or not transmission will increase when interventions are lifted. As well as providing daily updates on our website, we also provide adaptable computing code so that our approach can be used directly by researchers and policymakers on confidential datasets. We hope that our tool will be used to support decisions in countries worldwide throughout the ongoing COVID-19 pandemic.

Background: Assessing temporal variations in transmission in different countries is essential for monitoring the epidemic, evaluating the effectiveness of public health interventions and estimating the impact of changes in policy. Methods: We use case and death notification data to generate daily estimates of the time-varying reproduction number globally, regionally, nationally, and subnationally over a 12-week rolling window. Our modelling framework, based on open source tooling, accounts for uncertainty in reporting delays, so that the reproduction number is estimated based on underlying latent infections. Results: Estimates of the reproduction number, trajectories of infections, and forecasts are displayed on a dedicated website as both maps and time series, and made available to download in tabular form. Conclusions:  This decision-support tool can be used to assess changes in virus transmission both globally, regionally, nationally, and subnationally. This allows public health officials and policymakers to track the progress of the outbreak in near real-time using an epidemiologically valid measure. As well as providing regular updates on our website, we also provide an open source tool-set so that our approach can be used directly by researchers and policymakers on confidential data-sets. We hope that our tool will be used to support decisions in countries worldwide throughout the ongoing COVID-19 pandemic.

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.

Emerging evidence suggests that contact tracing has had limited success in the UK in reducing the R number across the COVID-19 pandemic. We investigate potential pitfalls and areas for improvement by extending an existing branching process contact tracing model, adding diagnostic testing and refining parameter estimates. Our results demonstrate that reporting and adherence are the most important predictors of programme impact but tracing coverage and speed plus diagnostic sensitivity also play an important role. We conclude that well-implemented contact tracing could bring small but potentially important benefits to controlling and preventing outbreaks, providing up to a 15% reduction in R. We reaffirm that contact tracing is not currently appropriate as the sole control measure.

Background Predicting bed occupancy for hospitalised patients with COVID-19 requires understanding of length of stay (LoS) in particular bed types. LoS can vary depending on the patient’s “bed pathway” - the sequence of transfers of individual patients between bed types during a hospital stay. In this study, we characterise these pathways, and their impact on predicted hospital bed occupancy. Methods We obtained data from University College Hospital (UCH) and the ISARIC4C COVID-19 Clinical Information Network (CO-CIN) on hospitalised patients with COVID-19 who required care in general ward or critical care (CC) beds to determine possible bed pathways and LoS. We developed a discrete-time model to examine the implications of using either bed pathways or only average LoS by bed type to forecast bed occupancy. We compared model-predicted bed occupancy to publicly available bed occupancy data on COVID-19 in England between March and August 2020. Results In both the UCH and CO-CIN datasets, 82% of hospitalised patients with COVID-19 only received care in general ward beds. We identified four other bed pathways, present in both datasets: “Ward, CC, Ward”, “Ward, CC”, “CC” and “CC, Ward”. Mean LoS varied by bed type, pathway, and dataset, between 1.78 and 13.53 days. For UCH, we found that using bed pathways improved the accuracy of bed occupancy predictions, while only using an average LoS for each bed type underestimated true bed occupancy. However, using the CO-CIN LoS dataset we were not able to replicate past data on bed occupancy in England, suggesting regional LoS heterogeneities. Conclusions We identified five bed pathways, with substantial variation in LoS by bed type, pathway, and geography. This might be caused by local differences in patient characteristics, clinical care strategies, or resource availability, and suggests that national LoS averages may not be appropriate for local forecasts of bed occupancy for COVID-19. Trial registration The ISARIC WHO CCP-UK study ISRCTN66726260 was retrospectively registered on 21/04/2020 and designated an Urgent Public Health Research Study by NIHR.