Assessing the impact of non-pharmaceutical interventions on SARS-CoV-2 transmission in Switzerland.

Following the rapid dissemination of COVID-19 cases in Switzerland, large-scale non-pharmaceutical interventions (NPIs) were implemented by the cantons and the federal government between 28 February and 20 March 2020. Estimates of the impact of these interventions on SARS-CoV-2 transmission are critical for decision making in this and future outbreaks. We here aim to assess the impact of these NPIs on disease transmission by estimating changes in the basic reproduction number (R0) at national and cantonal levels in relation to the timing of these NPIs. We estimated the time-varying R0 nationally and in eleven cantons by fitting a stochastic transmission model explicitly simulating within-hospital dynamics. We used individual-level data from more than 1000 hospitalised patients in Switzerland and public daily reports of hospitalisations and deaths. We estimated the national R0 to be 2.8 (95% confidence interval 2.1–3.8) at the beginning of the epidemic. Starting from around 7 March, we found a strong reduction in time-varying R0 with a 86% median decrease (95% quantile range [QR] 79–90%) to a value of 0.40 (95% QR 0.3–0.58) in the period of 29 March to 5 April. At the cantonal level, R0 decreased over the course of the epidemic between 53% and 92%. Reductions in time-varying R0 were synchronous with changes in mobility patterns as estimated through smartphone activity, which started before the official implementation of NPIs. We inferred that most of the reduction of transmission is attributable to behavioural changes as opposed to natural immunity, the latter accounting for only about 4% of the total reduction in effective transmission. As Switzerland considers relaxing some of the restrictions of social mixing, current estimates of time-varying R0 well below one are promising. However, as of 24 April 2020, at least 96% (95% QR 95.7–96.4%) of the Swiss population remains susceptible to SARS-CoV-2. These results warrant a cautious relaxation of social distance practices and close monitoring of changes in both the basic and effective reproduction numbers.

Spatial clustering and temporal trend analysis of international migrants diagnosed with tuberculosis in Brazil.

BACKGROUND: Tuberculosis (TB) in migrants is of concern to health authorities worldwide and is even more critical in Brazil, considering the country´s size and long land borders. The aim of the study was to identify critical areas in Brazil for migrants diagnosed with TB and to describe the temporal trend in this phenomenon in recent years. METHODS: This is an ecological study that used spatial analysis and time series analysis. As the study population, all cases of migrants diagnosed with TB from 2014 to 2019 were included, and Brazilian municipalities were considered as the unit of ecological analysis. The Getis-Ord Gi* technique was applied to identify critical areas, and based on the identified clusters, seasonal-trend decomposition based on loess (STL) and Prais-Winsten autoregression were used, respectively, to trace and classify temporal trend in the analyzed series. In addition, several municipal socioeconomic indicators were selected to verify the association between the identified clusters and social vulnerability. RESULTS: 2,471 TB cases were reported in migrants. Gi* analysis showed that areas with spatial association with TB in immigrants coincide with critical areas for TB in the general population (coast of the Southeast and North regions). Four TB clusters were identified in immigrants in the states of Amazonas, Roraima, São Paulo, and Rio de Janeiro, with an upward trend in most of these clusters. The temporal trend in TB in immigrants was classified as increasing in Brazil (+ 60.66% per year [95% CI: 27.21-91.85]) and in the clusters in the states of Amazonas, Roraima, and Rio de Janeiro (+1.01, +2.15, and + 2.90% per year, respectively). The cluster in the state of São Paulo was the only one classified as stationary. The descriptive data on the municipalities belonging to the clusters showed evidence of the association between TB incidence and conditions of social vulnerability. CONCLUSIONS: The study revealed the critical situation of TB among migrants in the country. Based on the findings, health authorities might focus on actions in regions identified, stablishing an intensive monitoring and following up, ensuring that these cases concluded their treatment and avoiding that they could spread the disease to the other regions or scenarios. The population of migrants are very dynamic, therefore strategies for following up them across Brazil are really urgent to manage the tuberculosis among international migrants in an efficient and proper way.

Fine-scale spatial clustering of measles nonvaccination that increases outbreak potential is obscured by aggregated reporting data.

The United States experienced historically high numbers of measles cases in 2019, despite achieving national measles vaccination rates above the World Health Organization recommendation of 95% coverage with two doses. Since the COVID-19 pandemic began, resulting in suspension of many clinical preventive services, pediatric vaccination rates in the United States have fallen precipitously, dramatically increasing risk of measles resurgence. Previous research has shown that measles outbreaks in high-coverage contexts are driven by spatial clustering of nonvaccination, which decreases local immunity below the herd immunity threshold. However, little is known about how to best conduct surveillance and target interventions to detect and address these high-risk areas, and most vaccination data are reported at the state-level-a resolution too coarse to detect community-level clustering of nonvaccination characteristic of recent outbreaks. In this paper, we perform a series of computational experiments to assess the impact of clustered nonvaccination on outbreak potential and magnitude of bias in predicting disease risk posed by measuring vaccination rates at coarse spatial scales. We find that, when nonvaccination is locally clustered, reporting aggregate data at the state- or county-level can result in substantial underestimates of outbreak risk. The COVID-19 pandemic has shone a bright light on the weaknesses in US infectious disease surveillance and a broader gap in our understanding of how to best use detailed spatial data to interrupt and control infectious disease transmission. Our research clearly outlines that finer-scale vaccination data should be collected to prevent a return to endemic measles transmission in the United States.

Daily surveillance of COVID-19 using the prospective space-time scan statistic in the United States.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first discovered in late 2019 in Wuhan City, China. The virus may cause novel coronavirus disease 2019 (COVID-19) in symptomatic individuals. Since December of 2019, there have been over 7,000,000 confirmed cases and over 400,000 confirmed deaths worldwide. In the United States (U.S.), there have been over 2,000,000 confirmed cases and over 110,000 confirmed deaths. COVID-19 case data in the United States has been updated daily at the county level since the first case was reported in January of 2020. There currently lacks a study that showcases the novelty of daily COVID-19 surveillance using space-time cluster detection techniques. In this paper, we utilize a prospective Poisson space-time scan statistic to detect daily clusters of COVID-19 at the county level in the contiguous 48 U.S. and Washington D.C. As the pandemic progresses, we generally find an increase of smaller clusters of remarkably steady relative risk. Daily tracking of significant space-time clusters can facilitate decision-making and public health resource allocation by evaluating and visualizing the size, relative risk, and locations that are identified as COVID-19 hotspots.

Impact and trend of COVID-19 in the Brazilian prison system: an ecological study. / Impacto e tendência da COVID-19 no sistema penitenciário do Brasil: um estudo ecológico.

Given the rapid spread of new coronavirus within the prison system, this study's objective was to identify spatial clusters for the occurrence of COVID-19 in the incarcerated population and analyze temporal trends of confirmed cases in the Brazilian prison system. This ecological study considered the five Brazilian macro-regions to be units of analysis, with its 26 states and the Federal District. The population was composed of all COVID-19 cases confirmed from April 14th to August 31st, 2020. The source used to collect data was the COVID-19 Monitoring Panel from the National Prison Department. Descriptive analysis, scan statistics, and time series were performed. A total of 18,767 COVID-19 cases were reported among the incarcerated population, 4,724 in São Paulo. The scan statistic analysis resulted in 14 spatial risk clusters for COVID-19 among persons deprived of liberty; the highest-risk cluster was in the Federal District. Although the country ends the series with a decreasing behavior, a growing trend was verified in most of the study period. The conclusion is that there is a need to implement mass testing among the incarcerated population while continually monitoring and recording COVID-19 cases.

Tendo em vista a rápida disseminação do novo coronavírus no sistema prisional, o presente trabalho teve como objetivos identificar aglomerados espaciais para ocorrência da COVID-19 na população privada de liberdade (PPL) e analisar a tendência temporal dos casos confirmados no sistema penitenciário do Brasil. Estudo ecológico que considerou como unidades de análise as cinco macrorregiões do Brasil, seus 26 estados e o Distrito Federal. A população foi composta por todos os casos de COVID-19 confirmados, no período de 14 de abril a 31 de agosto de 2020. A fonte de dados utilizada foi o Painel de Monitoramento dos casos de COVID-19 nos sistemas prisionais do Departamento Penitenciário Nacional. Realizou-se análise descritiva, estatística de varredura e análise da tendência temporal. Foram notificados 18.767 casos de COVID-19 na PPL, dos quais 4.724 ocorreram no estado de São Paulo. A estatística de varredura possibilitou a identificação de 14 clusters espaciais de risco para COVID-19 na PPL, sendo o aglomerado de maior risco formado pelo Distrito Federal. Embora o país finalize a série com um comportamento decrescente, observa-se que no período de investigação a tendência apresentou um comportamento maioritariamente crescente. Evidencia-se a necessidade de testagem em massa, monitoramento e registro contínuo dos casos de COVID-19 na PPL do país.