Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment.

Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods: Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results: Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies

Deriving fine-scale models of human mobility from aggregated origin-destination flow data.

The spatial dynamics of epidemics are fundamentally affected by patterns of human mobility. Mobile phone call detail records (CDRs) are a rich source of mobility data, and allow semi-mechanistic models of movement to be parameterised even for resource-poor settings. While the gravity model typically reproduces human movement reasonably well at the administrative level spatial scale, past studies suggest that parameter estimates vary with the level of spatial discretisation at which models are fitted. Given that privacy concerns usually preclude public release of very fine-scale movement data, such variation would be problematic for individual-based simulations of epidemic spread parametrised at a fine spatial scale. We therefore present new methods to fit fine-scale mathematical mobility models (here we implement variants of the gravity and radiation models) to spatially aggregated movement data and investigate how model parameter estimates vary with spatial resolution. We use gridded population data at 1km resolution to derive population counts at different spatial scales (down to ∼ 5km grids) and implement mobility models at each scale. Parameters are estimated from administrative-level flow data between overnight locations in Kenya and Namibia derived from CDRs: where the model spatial resolution exceeds that of the mobility data, we compare the flow data between a particular origin and destination with the sum of all model flows between cells that lie within those particular origin and destination administrative units. Clear evidence of over-dispersion supports the use of negative binomial instead of Poisson likelihood for count data with high values. Radiation models use fewer parameters than the gravity model and better predict trips between overnight locations for both considered countries. Results show that estimates for some parameters change between countries and with spatial resolution and highlight how imperfect flow data and spatial population distribution can influence model fit

SARS-CoV-2 antibody dynamics and transmission from community-wide serological testing in the Italian municipality of Vo'

none36In February and March 2020, two mass swab testing campaigns were conducted in Vo', Italy. In May 2020, we tested 86% of the Vo' population with three immuno-assays detecting antibodies against the spike and nucleocapsid antigens, a neutralisation assay and Polymerase Chain Reaction (PCR). Subjects testing positive to PCR in February/March or a serological assay in May were tested again in November. Here we report on the results of the analysis of the May and November surveys. We estimate a seroprevalence of 3.5% (95% Credible Interval (CrI): 2.8-4.3%) in May. In November, 98.8% (95% Confidence Interval (CI): 93.7-100.0%) of sera which tested positive in May still reacted against at least one antigen; 18.6% (95% CI: 11.0-28.5%) showed an increase of antibody or neutralisation reactivity from May. Analysis of the serostatus of the members of 1,118 households indicates a 26.0% (95% CrI: 17.2-36.9%) Susceptible-Infectious Transmission Probability. Contact tracing had limited impact on epidemic suppression.restrictedDorigatti, Ilaria; Lavezzo, Enrico; Manuto, Laura; Ciavarella, Constanze; Pacenti, Monia; Boldrin, Caterina; Cattai, Margherita; Saluzzo, Francesca; Franchin, Elisa; Del Vecchio, Claudia; Caldart, Federico; Castelli, Gioele; Nicoletti, Michele; Nieddu, Eleonora; Salvadoretti, Elisa; Labella, Beatrice; Fava, Ludovico; Guglielmo, Simone; Fascina, Mariateresa; Grazioli, Marco; Alvisi, Gualtiero; Vanuzzo, Maria Cristina; Zupo, Tiziano; Calandrin, Reginetta; Lisi, Vittoria; Rossi, Lucia; Castagliuolo, Ignazio; Merigliano, Stefano; Unwin, H Juliette T; Plebani, Mario; Padoan, Andrea; Brazzale, Alessandra R; Toppo, Stefano; Ferguson, Neil M; Donnelly, Christl A; Crisanti, AndreaDorigatti, Ilaria; Lavezzo, Enrico; Manuto, Laura; Ciavarella, Constanze; Pacenti, Monia; Boldrin, Caterina; Cattai, Margherita; Saluzzo, Francesca; Franchin, Elisa; Del Vecchio, Claudia; Caldart, Federico; Castelli, Gioele; Nicoletti, Michele; Nieddu, Eleonora; Salvadoretti, Elisa; Labella, Beatrice; Fava, Ludovico; Guglielmo, Simone; Fascina, Mariateresa; Grazioli, Marco; Alvisi, Gualtiero; Vanuzzo, Maria Cristina; Zupo, Tiziano; Calandrin, Reginetta; Lisi, Vittoria; Rossi, Lucia; Castagliuolo, Ignazio; Merigliano, Stefano; Unwin, H Juliette T; Plebani, Mario; Padoan, Andrea; Brazzale, Alessandra R; Toppo, Stefano; Ferguson, Neil M; Donnelly, Christl A; Crisanti, Andre

Suppression of a SARS-CoV-2 outbreak in the Italian municipality of Vo'

On the 21st of February 2020 a resident of the municipality of Vo', a small town near Padua, died of pneumonia due to SARS-CoV-2 infection1. This was the first COVID-19 death detected in Italy since the emergence of SARS-CoV-2 in the Chinese city of Wuhan, Hubei province2. In response, the regional authorities imposed the lockdown of the whole municipality for 14 days3. We collected information on the demography, clinical presentation, hospitalization, contact network and presence of SARS-CoV-2 infection in nasopharyngeal swabs for 85.9% and 71.5% of the population of Vo' at two consecutive time points. On the first survey, which was conducted around the time the town lockdown started, we found a prevalence of infection of 2.6% (95% confidence interval (CI) 2.1-3.3%). On the second survey, which was conducted at the end of the lockdown, we found a prevalence of 1.2% (95% Confidence Interval (CI) 0.8-1.8%). Notably, 42.5% (95% CI 31.5-54.6%) of the confirmed SARS-CoV-2 infections detected across the two surveys were asymptomatic (i.e. did not have symptoms at the time of swab testing and did not develop symptoms afterwards). The mean serial interval was 7.2 days (95% CI 5.9-9.6). We found no statistically significant difference in the viral load of symptomatic versus asymptomatic infections (p-values 0.62 and 0.74 for E and RdRp genes, respectively, Exact Wilcoxon-Mann-Whitney test). This study sheds new light on the frequency of asymptomatic SARS-CoV-2 infection, their infectivity (as measured by the viral load) and provides new insights into its transmission dynamics and the efficacy of the implemented control measures