A framework for estimating and visualising excess mortality during the COVID-19 pandemic (preprint)

COVID-19 related deaths underestimate the pandemic burden on mortality because they suffer from completeness and accuracy issues. Excess mortality is a popular alternative, as it compares observed with expected deaths based on the assumption that the pandemic did not occur. Expected deaths had the pandemic not occurred depend on population trends, temperature, and spatio-temporal patterns. In addition to this, high geographical resolution is required to examine within country trends and the effectiveness of the different public health policies. In this tutorial, we propose a framework using R to estimate and visualise excess mortality at high geographical resolution. We show a case study estimating excess deaths during 2020 in Italy. The proposed framework is fast to implement and allows combining different models and presenting the results in any age, sex, spatial and temporal aggregation desired. This makes it particularly powerful and appealing for online monitoring of the pandemic burden and timely policy making.

Regional excess mortality during the 2020 COVID-19 pandemic: a study of five European countries (preprint)

The impact of the COVID-19 pandemic on excess mortality from all causes in 2020 varied across and within European countries. Using data for 2015-2019, we applied Bayesian spatio-temporal models to quantify the expected weekly deaths at the regional level had the pandemic not occurred in England, Greece, Italy, Spain, and Switzerland. With around 30%, Madrid, Castile-La Mancha, Castile-Leon (Spain) and Lombardia (Italy) were the regions with the highest excess mortality. In England, Greece and Switzerland, the regions most affected were Outer London and the West Midlands (England), Eastern, Western and Central Macedonia (Greece), and Ticino (Switzerland), with 15-20% excess mortality in 2020. Our study highlights the importance of the large transportation hubs for establishing community transmission in the first stages of the pandemic. Acting promptly to limit transmission around these hubs is essential to prevent spread to other regions and countries.

Monitoring occurrence of SARS-CoV-2 in school populations: a wastewater-based approach (preprint)

Clinical testing of children in schools is challenging, with economic implications limiting its frequent use as a monitoring tool of the risks assumed by children and staff during the COVID-19 pandemic. Here, a wastewater based epidemiology approach has been used to monitor 16 schools (10 primary, 5 secondary and 1 post-16 and further education for a total of 17 sites) in England. A total of 296 samples over 9 weeks have been analysed for N1 and E genes using qPCR methods. Of the samples returned, 47.3% were positive for one or both genes with a frequency of detection in line with the respective community. WBE offers a promising low cost, non-invasive approach for supplementing clinical testing and can offer longitudinal insights that are impractical with traditional clinical testing.

Estimating weekly excess mortality at subnational level in Italy during the COVID-19 pandemic (preprint)

ObjectivesTo provide a sub-national analysis of excess mortality during the COVID-19 pandemic in Italy. DesignPopulation-based on all-cause mortality official data, available as counts by age and sex. SettingThe 7,904 municipalities in Italy. ParticipantsAll residents in Italy in the years 2016 to 2020. Main outcome measuresAll-cause mortality weekly rates for each municipality, based on the first four months of 2016 - 2019. Predicted all-cause weekly deaths and mortality rates at municipality level for 2020, based on the modelled spatio-temporal trends. ResultsThere was strong evidence of excess mortality for Northern Italy; Lombardia showed higher mortality rates than expected from the end of February, with 23,946 (23,013 to 24,786) total excess deaths. North-West and North-East regions showed higher mortality from the beginning of March, with 6,942 (6,142 to 7,667) and 8,033 (7,061 to 9,044) total excess deaths respectively. After discounting for the number of COVID-19-confirmed deaths, Lombardia still registered 10,197 (9,264 to 11,037) excess deaths, while regions in the North-West and North-East had 2,572 (1,772 to 3,297) and 2,047 (1,075 to 3,058) extra deaths, respectively. We observed marked geographical differences at municipality level. The city of Bergamo (Lombardia) showed the largest percent excess 88.9% (81.9% to 95.2%) at the peak of the pandemic. An excess of 84.2% (73.8% to 93.4%) was also estimated at the same time for the city of Pesaro (Central Italy), in stark contrast with the rest of the region, which does not show evidence of excess deaths. ConclusionsOur study gives a comprehensive picture of the evolution of all-cause mortality in Italy from 2016 to 2020 and describes the spatio-temporal differences in excess mortality during the COVID-19 pandemic. Our model shows heterogeneous impact of COVID-19, and it can be used to help policy- makers target measures to limit the burden on the health-care system as well as reducing social and economic consequences. Our probabilistic methodology is useful for real-time mortality surveillance, continuously monitoring local temporal trends and flagging where and when mortality rates deviate from the expected range, which might suggest a second wave of the pandemic.