Trend estimation and short-term forecasting of COVID-19 cases and deaths worldwide (preprint)

Since the beginning of the COVID-19 pandemic, many dashboards have emerged as useful tools to monitor the evolution of the pandemic, inform the public, and assist governments in decision making. Our goal is to develop a globally applicable method, integrated in a twice daily updated dashboard that provides an estimate of the trend in the evolution of the number of cases and deaths from reported data of more than 200 countries and territories, as well as a seven-day forecast. One of the significant difficulties to manage a quickly propagating epidemic is that the details of the dynamic needed to forecast its evolution are obscured by the delays in the identification of cases and deaths and by irregular reporting. Our forecasting methodology substantially relies on estimating the underlying trend in the observed time series using robust seasonal trend decomposition techniques. This allows us to obtain forecasts with simple, yet effective extrapolation methods in linear or log scale. We present the results of an assessment of our forecasting methodology and discuss its application to the production of global and regional risk maps.

Seroprevalence of anti-SARS-CoV-2 IgG antibodies, risk factors for infection and associated symptoms in Geneva, Switzerland: a population-based study (preprint)

Background: Population-based serological surveys provide a means for assessing the immunologic landscape of a community, without the biases related to health-seeking behaviors and testing practices typically associated with rt-PCR testing. This study assesses SARS-CoV-2 seroprevalence over the first epidemic wave in Canton Geneva, Switzerland, as well as biological and socio-economic risk factors for infection and symptoms associated with IgG seropositivity. Methods and findings: Between April 6 and June 30, 2020, former participants of a yearly representative cross-sectional survey of the 20-75-year-old population of the canton of Geneva were invited to participate in a seroprevalence study, along with household members five years and older. We collected blood and tested it for anti-SARS-CoV-2 immunoglobulins G (IgG). Questionnaires were self-administered. We estimated seroprevalence with a Bayesian model accounting for test performance and sampling design. We included 8344 participants (53.5% women, mean age 46.9 years). The population-level seroprevalence over the 12-week study period was 7.8 % (95% Credible Interval (CrI) 6.8-8.9), accounting for sex, age and household random effects. Seroprevalence was highest among 18-49 year olds (9.5%, 95%CrI 8.1-10.9), with young children (5-9 years) and those >65 years having significantly lower seroprevalence (4.3% and 4.7-5.4% respectively). Men were more likely to be seropositive than women (relative risk 1.2, 95%CrI 1.1-1.4). Odds of seropositivity were reduced for female retirees (0.46, 95%CI 0.23-0.93) and unemployed men (0.35, 95%CI 0.13-1.0) compared to employed individuals, and for current smokers (0.36, 95%CI 0.23-0.55) compared to never-smokers. We found no significant association between occupation, level of education, neighborhood income and the risk of being seropositive. Symptoms most strongly associated with seropositivity were anosmia/dysgeusia, loss of appetite, fever, fatigue and myalgia and/or arthralgia. Thirteen percent of seropositive participants reported no symptoms. Conclusions: Our results confirm a low population seroprevalence of anti-SARS-CoV-2 antibodies after the first wave in Geneva, a region hard hit by the COVID-19 pandemic. Socioeconomic factors were not associated with seropositivity in this sample. The elderly and young children were less frequently seropositive, though it is not clear how biology and behaviors shape these differences. These specificities should be considered when assessing the need for targeted public health measures.

Household Transmission of SARS-COV-2: Insights from a Population-based Serological Survey (preprint)

Importance: Knowing the transmissibility of asymptomatic infections and risk of infection from household and community exposures is critical to SARS-CoV-2 control. Limited previous evidence is based primarily on virologic testing, which disproportionately misses mild and asymptomatic infections. Serologic measures are more likely to capture all previously infected individuals. Objective: Estimate the risk of SARS-CoV-2 infection from household and community exposures, and identify key risk factors for transmission and infection. Design: Household serosurvey and transmission model. Setting: Population-based serosurvey in Geneva, Switzerland Participants: 4,524 household members five years and older from 2,267 households enrolled April-June 2020. Exposures: SARS-CoV-2 infected (seropositive) household members and background risk of community transmission. Main outcomes and measures: Past SARS-CoV-2 infection confirmed through anti-SARS-CoV-2 IgG antibodies by ELISA. Chain-binomial models based on the number of infections within households were used to estimate extra-household infection risk by demographics and reported extra-household contacts, and infection risk from exposure to an infected household member by demographics and infector's symptoms. Infections attributable to exposure to different types of infectious individuals were estimated. Results: The chance of being infected by a single SARS-CoV-2 infected household member was 17.2% (95%CrI 13.6-21.5%) compared to a cumulative extra-household infection risk of 5.1% (95%CrI 4.5-5.8%). Infection risk from an infected household member increased with age, from 7.5% (95%CrI 1.3-20.3%) among 5-9 years to 30.2% (95%CrI 14.3-48.2%) among those [≥]65 years. Working-age adults (20-49 years) had the highest extra-household infection risk. Seropositive household members not reporting symptoms had 74.8% lower odds (95%CrI 43.8-90.3%) of infecting another household member compared to those reporting symptoms, accounting for 19.6% (95%CrI 12.9-24.5%) of all household infections. Conclusions and Relevance: The risk of infection from exposure to a single infected household member was four-times that of extra-household exposures over the first wave of the pandemic. Young children had a lower risk from infection from household members. Asymptomatic infections are far less likely to transmit than symptomatic ones but do cause infections. While the small households in Geneva limit the contribution of household spread, household transmission likely plays a greater role in other settings.

Peaks of Fine Particulate Matter May Modulate the Spreading and Virulence of COVID-19 (preprint)

A probe of a patient, seeking help in an emergency ward of a French hospital in late December 2019 because of Influenza like symptoms, was retrospectively tested positive to COVID-19. Despite the early appearance of the virus in Europe, the prevalence and virulence appeared to be low for several weeks, before the spread and severity of symptoms increased exponentially, yet with marked spatial and temporal differences. Here, we compare the possible linkages between peaks of fine particulate matter (PM2.5) and the sudden, explosive increase of hospitalizations and mortality rates in the Swiss Canton of Ticino, and the Greater Paris and London regions. We also discuss the influence of Saharan dust intrusions on the COVID-19 outbreak observed in early 2020 on the Canary Islands. We find that high PM2.5 concentrations – possibly favored by air temperature inversions or Saharan dust intrusions – are not only modulating but even more so boosting severe outbreaks of COVID-19. We conclude that the overburdening of the health services and hospitals as well as the high over-mortality observed in various regions of Europe in spring 2020 can be linked to peaks of PM2.5 and likely particular weather situations that have favored the spread and enhanced the virulence of the virus. In the future, we recommend to monitor not only the prevalence of the virus, but also to consider the occurrence of weather situations that can lead to sudden, very explosive COVID-19 outbreaks.

Future scenarios for the SARS-CoV-2 epidemic in Switzerland: an age-structured model (preprint)

The recent lifting of COVID-19 related restrictions in Switzerland causes uncertainty about the future of the epidemic. We developed a compartmental model for SARS-CoV-2 transmission in Switzerland and projected the course of the epidemic until the end of year 2020 under various scenarios. The model was age-structured with three categories, children (0-17), adults (18-64) and seniors (65- years). Lifting all restrictions according to the plans disclosed by the Swiss federal authorities by mid-May resulted in a rapid rebound in the epidemic, with the peak expected in July. Measures equivalent to at least 90% reduction in all contacts were able to eradicate the epidemic; 56% reduction in contacts could keep the intensive care unit occupancy under the critical level, and delay the next wave until October. Scenarios where strong contact reductions were only applied in selected age groups could not suppress the epidemic, increasing the risk of a next wave in July, and another stronger wave in September. Future interventions need to cover all age groups to keep the SARS-CoV-2 epidemic under control.

Repeated seroprevalence of anti-SARS-CoV-2 IgG antibodies in a population-based sample from Geneva, Switzerland (preprint)

BackgroundAssessing the burden of COVID-19 based on medically-attended case counts is suboptimal given its reliance on testing strategy, changing case definitions and the wide spectrum of disease presentation. Population-based serosurveys provide one avenue for estimating infection rates and monitoring the progression of the epidemic, overcoming many of these limitations. MethodsTaking advantage of a pool of adult participants from population-representative surveys conducted in Geneva, Switzerland, we implemented a study consisting of 8 weekly serosurveys among these participants and their household members older than 5 years. We tested each participant for anti-SARS-CoV-2-IgG antibodies using a commercially available enzyme-linked immunosorbent assay (Euroimmun AG, Lubeck, Germany). We estimated seroprevalence using a Bayesian regression model taking into account test performance and adjusting for the age and sex of Genevas population. ResultsIn the first three weeks, we enrolled 1335 participants coming from 633 households, with 16% <20 years of age and 53.6% female, a distribution similar to that of Geneva. In the first week, we estimated a seroprevalence of 3.1% (95% CI 0.2-5.99, n=343). This increased to 6.1% (95% CI 2.69.33, n=416) in the second, and to 9.7% (95% CI 6.1-13.11, n=576) in the third week. We found that 5-19 year-olds (6.0%, 95% CI 2.3-10.2%) had similar seroprevalence to 20-49 year olds (8.5%, 95%CI 4.99-11.7), while significantly lower seroprevalence was observed among those 50 and older (3.7%, 95% CI 0.99-6.0, p=0.0008). InterpretationAssuming that the presence of IgG antibodies is at least in the short-term associated with immunity, these results highlight that the epidemic is far from burning out simply due to herd immunity. Further, no differences in seroprevalence between children and middle age adults are observed. These results must be considered as Switzerland and the world look towards easing restrictions aimed at curbing transmission.

Are people excessively pessimistic about the risk of coronavirus infection? (preprint)

The recent emergence of the SARS-CoV-2 in China has raised the spectre of a novel, potentially catastrophic pandemic in both scientific and lay communities throughout the world. In this particular context, people have been accused of being excessively pessimistic regarding the future consequences of this emerging health threat. However, consistent with previous research in social psychology, a large survey conducted in Europe in the early stage of the COVID-19 epidemic shows that the majority of respondents was actually overly optimistic about the risk of infection.