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Background The COVID-19 pandemic has placed an unprecedented strain on health systems, with rapidly increasing demand for healthcare in hospitals and intensive care units (ICUs) worldwide. As the pandemic escalates, determining the resulting needs for healthcare resources (beds, staff, equipment) has become a key priority for many countries. Projecting future demand requires estimates of how long patients with COVID-19 need different levels of hospital care. Methods We performed a systematic review of early evidence on length of stay (LoS) of patients with COVID-19 in hospital and in ICU. We subsequently developed a method to generate LoS distributions which combines summary statistics reported in multiple studies, accounting for differences in sample sizes. Applying this approach, we provide distributions for total hospital and ICU LoS from studies in China and elsewhere, for use by the community. Results We identified 52 studies, the majority from China (46/52). Median hospital LoS ranged from 4 to 53 days within China, and 4 to 21 days outside of China, across 45 studies. ICU LoS was reported by eight studies—four each within and outside China—with median values ranging from 6 to 12 and 4 to 19 days, respectively. Our summary distributions have a median hospital LoS of 14 (IQR 10–19) days for China, compared with 5 (IQR 3–9) days outside of China. For ICU, the summary distributions are more similar (median (IQR) of 8 (5–13) days for China and 7 (4–11) days outside of China). There was a visible difference by discharge status, with patients who were discharged alive having longer LoS than those who died during their admission, but no trend associated with study date. Conclusion Patients with COVID-19 in China appeared to remain in hospital for longer than elsewhere. This may be explained by differences in criteria for admission and discharge between countries, and different timing within the pandemic. In the absence of local data, the combined summary LoS distributions provided here can be used to model bed demands for contingency planning and then updated, with the novel method presented here, as more studies with aggregated statistics emerge outside China.

Tuberculosis (TB) transmission and prevalence are dynamic over time , and heterogeneous within populations . Public health programmes therefore require up-to-date , accurate epidemiological data to appropriately allocate resources , target interventions , and track progress towards End TB goals . Current methods of TB surveillance often rely on case notifications , which are biased by access to healthcare , and TB disease prevalence surveys , which are highly resource-intensive , requiring many tens of thousands of people to be tested to identify high-risk groups or capture trends . Surveys of “latent TB infection” , or immunoreactivity to Mycobacterium tuberculosis (Mtb) , using tests such as interferon-gamma release assays (IGRAs) could provide a way to identify TB transmission hotspots , supplementing information from disease notifications , and with greater spatial and temporal resolution than is possible to achieve in disease prevalence surveys . This cross-sectional survey will investigate the prevalence of Mtb immunoreactivity amongst young children , adolescents and adults in Blantyre , Malawi , a high HIV-prevalence city in southern Africa . Through this study we will estimate the annual risk of TB infection (ARTI) in Blantyre and explore individual- and area-level risk factors for infection, as well as investigating geospatial heterogeneity of Mtb infection (and its determinants), and comparing these to the distribution of TB disease case-notifications. We will also evaluate novel diagnostics for Mtb infection (QIAreach QFT) and sampling methodologies (convenience sampling in healthcare settings and community sampling based on satellite imagery), which may increase the feasibility of measuring Mtb infection at large scale. The overall aim is to provide high-resolution epidemiological data and provide new insights into methodologies which may be used by TB programmes globally.

The elimination programme for visceral leishmaniasis (VL) in India has seen great progress, with total cases decreasing by over 80% since 2010 and many blocks now reporting zero cases from year to year. Prompt diagnosis and treatment is critical to continue progress and avoid epidemics in the increasingly susceptible population. Short-term forecasts could be used to highlight anomalies in incidence and support health service logistics. The model which best fits the data is not necessarily most useful for prediction, yet little empirical work has been done to investigate the balance between fit and predictive performance. We developed statistical models of monthly VL case counts at block level. By evaluating a set of randomly-generated models, we found that fit and one-month-ahead prediction were strongly correlated and that rolling updates to model parameters as data accrued were not crucial for accurate prediction. The final model incorporated auto-regression over four months, spatial correlation between neighbouring blocks, and seasonality. Ninety-four percent of 10-90% prediction intervals from this model captured the observed count during a 24-month test period. Comparison of one-, three- and four-month-ahead predictions from the final model fit demonstrated that a longer time horizon yielded only a small sacrifice in predictive power for the vast majority of blocks. The model developed is informed by routinely-collected surveillance data as it accumulates, and predictions are sufficiently accurate and precise to be useful. Such forecasts could, for example, be used to guide stock requirements for rapid diagnostic tests and drugs. More comprehensive data on factors thought to influence geographic variation in VL burden could be incorporated, and might better explain the heterogeneity between blocks and improve uniformity of predictive performance. Integration of the approach in the management of the VL programme would be an important step to ensuring continued successful control.

As of 2021, the National Kala-azar Elimination Programme (NKAEP) in India has achieved visceral leishmaniasis (VL) elimination (<1 case / 10,000 population/year per block) in 625 of the 633 endemic blocks (subdistricts) in four states. The programme needs to sustain this achievement and target interventions in the remaining blocks to achieve the WHO 2030 target of VL elimination as a public health problem. An effective tool to analyse programme data and predict/ forecast the spatial and temporal trends of VL incidence, elimination threshold, and risk of resurgence will be of use to the programme management at this juncture. We employed spatiotemporal models incorporating environment, climatic and demographic factors as covariates to describe monthly VL cases for 8-years (2013-2020) in 491 and 27 endemic and non-endemic blocks of Bihar and Jharkhand states. We fitted 37 models of spatial, temporal, and spatiotemporal interaction random effects with covariates to monthly VL cases for 6-years (2013-2018, training data) using Bayesian inference via Integrated Nested Laplace Approximation (INLA) approach. The best-fitting model was selected based on deviance information criterion (DIC) and Watanabe-Akaike Information Criterion (WAIC) and was validated with monthly cases for 2019-2020 (test data). The model could describe observed spatial and temporal patterns of VL incidence in the two states having widely differing incidence trajectories, with >93% and 99% coverage probability (proportion of observations falling inside 95% Bayesian credible interval for the predicted number of VL cases per month) during the training and testing periods. PIT (probability integral transform) histograms confirmed consistency between prediction and observation for the test period. Forecasting for 2021-2023 showed that the annual VL incidence is likely to exceed elimination threshold in 16-18 blocks in 4 districts of Jharkhand and 33-38 blocks in 10 districts of Bihar. The risk of VL in non-endemic neighbouring blocks of both Bihar and Jharkhand are less than 0.5 during the training and test periods, and for 2021-2023, the probability that the risk greater than 1 is negligible (P<0.1). Fitted model showed that VL occurrence was positively associated with mean temperature, minimum temperature, enhanced vegetation index, precipitation, and isothermality, and negatively with maximum temperature, land surface temperature, soil moisture and population density. The spatiotemporal model incorporating environmental, bioclimatic, and demographic factors demonstrated that the KAMIS database of the national programmme can be used for block level predictions of long-term spatial and temporal trends in VL incidence and risk of outbreak / resurgence in endemic and non-endemic settings. The database integrated with the modelling framework and a dashboard facility can facilitate such analysis and predictions. This could aid the programme to monitor progress of VL elimination at least one-year ahead, assess risk of resurgence or outbreak in post-elimination settings, and implement timely and targeted interventions or preventive measures so that the NKAEP meet the target of achieving elimination by 2030.

The kala-azar elimination programme has resulted in a significant reduction in visceral leishmaniasis (VL) cases across the Indian Subcontinent. To detect any resurgence of transmission, a sensitive cost-effective surveillance system is required. Molecular xenomonitoring (MX), detection of pathogen DNA/RNA in vectors, provides a proxy of human infection in the lymphatic filariasis elimination programme. To determine whether MX can be used for VL surveillance in a low transmission setting, large numbers of the sand fly vector Phlebotomus argentipes are required. This study will determine the best method for capturing P. argentipes females for MX. The field study was performed in two programmatic and two non-programmatic villages in Bihar, India. A total of 48 households (12/village) were recruited. Centers for Disease Control and Prevention light traps (CDC-LTs) were compared with Improved Prokopack (PKP) and mechanical vacuum aspirators (MVA) using standardised methods. Four 12x12 Latin squares, 576 collections, were attempted (12/house, 144/village,192/method). Molecular analyses of collections were conducted to confirm identification of P. argentipes and to detect human and Leishmania DNA. Operational factors, such as time burden, acceptance to householders and RNA preservation, were also considered. A total of 562 collections (97.7%) were completed with 6,809 sand flies captured. Females comprised 49.0% of captures, of which 1,934 (57.9%) were identified as P. argentipes. CDC-LTs collected 4.04 times more P. argentipes females than MVA and 3.62 times more than PKP (p<0.0001 for each). Of 21,735 mosquitoes in the same collections, no significant differences between collection methods were observed. CDC-LTs took less time to install and collect than to perform aspirations and their greater yield compensated for increased sorting time. No significant differences in Leishmania RNA detection and quantitation between methods were observed in experimentally infected sand flies maintained in conditions simulating field conditions. CDC-LTs were favoured by householders. CDC-LTs are the most useful collection tool of those tested for MX surveillance since they collected higher numbers of P. argentipes females without compromising mosquito captures or the preservation of RNA. However, capture rates are still low.

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. Methods We fit a Bayesian spatio-temporal model to weekly COVID-19-related deaths per local authority (LTLA) throughout the first wave (1 January 2020–30 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. Results A 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%. Conclusions Limitations 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.

The National Health Service (NHS) Pathways triage system collates data on enquiries to 111 and 999 services in England. Since the 18th of March 2020, these data have been made publically available for potential COVID-19 symptoms self-reported by members of the public. Trends in such reports over time are likely to reflect behaviour of the ongoing epidemic within the wider community, potentially capturing valuable information across a broader severity profile of cases than hospital admission data. We present a fully reproducible analysis of temporal trends in NHS Pathways reports until 14th May 2020, nationally and regionally, and demonstrate that rates of growth/decline and effective reproduction number estimated from these data may be useful in monitoring transmission. This is a particularly pressing issue as lockdown restrictions begin to be lifted and evidence of disease resurgence must be constantly reassessed. We further assess the correlation between NHS Pathways reports and a publicly available NHS dataset of COVID-19-associated deaths in England, finding that enquiries to 111/999 were strongly associated with daily deaths reported 16 days later. Our results highlight the potential of NHS Pathways as the basis of an early warning system. However, this dataset relies on self-reported symptoms, which are at risk of being severely biased. Further detailed work is therefore necessary to investigate potential behavioural issues which might otherwise explain our conclusions.

BackgroundVisceral leishmaniasis (VL) is a debilitating and—without treatment—fatal parasitic disease which burdens the most impoverished communities in northeastern India. Control and ultimately, elimination of VL depends heavily on prompt case detection. However, a proportion of VL cases remain undiagnosed many months after symptom onset. Delay to diagnosis increases the chance of onward transmission, and poses a risk of resurgence in populations with waning immunity. We analysed the spatial variation of delayed diagnosis of VL in Bihar, India and aimed to understand the potential driving factors of these delays.MethodsThe spatial distribution of time to diagnosis was explored using a Bayesian hierarchical model fit to 4270 geo-located cases notified between January 2018 and July 2019 through routine surveillance. Days between symptoms meeting clinical criteria (14-day fever) and diagnosis were assumed to be Poisson-distributed, adjusting for individual- and village-level characteristics. Residual variance was modelled with an explicit spatial structure. Cumulative delays were estimated under different scenarios of active case detection coverage.ResultsThe 4270 cases analysed were found to be prone to excessive delays in areas outside existing endemic ‘hot spots’. After accounting for differences associated with age, HIV status and mode of detection (active versus passive surveillance), cases diagnosed within recently affected (≥ 1 case reported in the previous year) blocks and villages experienced shorter delays on average (by 13% [2.9–21.7%] (95% credible interval) and 7% [1.3–13.1%], respectively) than those in non-recently-affected areas.ConclusionsDelays to VL diagnosis when incidence is low could influence whether transmission of the disease could be interrupted or resurges. Prioritising and narrowing surveillance to high-burden areas may increase the likelihood of excessive delays in diagnosis in peripheral areas. Active surveillance driven by observed incidence may lead to missing the risk posed by as-yet-undiagnosed cases in low-endemic areas, and such surveillance could be insufficient for achieving and sustaining elimination.

Background As cases of visceral leishmaniasis (VL) in India dwindle, there is motivation to monitor elimination progress on a finer geographic scale than sub-district (block). Low-incidence projections across geographically- and demographically- heterogeneous communities are difficult to act upon, and equitable elimination cannot be achieved if local pockets of incidence are overlooked. However, maintaining consistent surveillance at this scale is resource-intensive and not sustainable in the long-term. Methods We analysed VL incidence across 45,000 villages in Bihar state, exploring spatial autocorrelation and associations with local environmental conditions in order to assess the feasibility of inference at this scale. We evaluated a statistical disaggregation approach to infer finer spatial variation from routinely-collected, block-level data, validating against observed village-level incidence. Results This disaggregation approach does not estimate village-level incidence more accurately than a baseline assumption of block-homogeneity. Spatial auto-correlation is evident on a block-level but weak between neighbouring villages within the same block, possibly suggesting that longer-range transmission (e.g., due to population movement) may be an important contributor to village-level heterogeneity. Conclusions Increasing the range of reactive interventions to neighbouring villages may not improve their efficacy in suppressing transmission, but maintaining surveillance and diagnostic capacity in areas distant from recently observed cases - particularly along routes of population movement from endemic regions - could reduce reintroduction risk in currently unaffected villages. The reactive, spatially-targeted approach to VL surveillance limits interpretability of data observed at the village level, and hence the feasibility of routinely drawing and validating inference at this scale. Plain Language Summary Near elimination, it is important to understand how the remaining cases of disease are distributed on a local level. However, surveillance data are more easily collated according to larger administrative units. We investigated whether village-level patterns of visceral leishmaniasis (VL) incidence could be inferred from administrative-level data using a statistical modelling approach. We found strong similarity in incidence between neighbouring administrative units but not between neighbouring villages, and model predictions did not correspond well to observed village-level case data. This could suggest that longer-range transmission contributes more to the village-level pattern of incidence than short in this near-elimination context, which should be considered in intervention planning. However, increased surveillance effort in assumed high-risk villages makes interpretation of data at this level challenging. Nightingale et al. compare block-homogeneity and statistical disaggregation approaches to analyse visceral leishmaniasis incidence across 45,000 villages in Bihar state. Village-level incidence is not measured more accurately by the disaggregation approach and spatial auto-correlation is evident on a block-level but weak between neighbouring villages within the same block.