Stefano Merler

• mathematician
• Principal Investigator at Fondazione Bruno Kessler

Background Local transmission of dengue, chikungunya, and Zika infection is an emerging public health threat in Europe. Monitoring the epidemiological trends can help define the intervention strategy. The aim of this work was to analyse epidemiological characteristics of autochthonous transmission of Aedes-borne arboviruses in Europe. Methods A sy...

Introduction: Here we reported the virological, entomological and epidemiological characteristics of the large autochthonous outbreak of dengue (DENV) occurred in a small village of the Lombardy region (Northern Italy) during summer 2023. Methods: After the diagnosis of the first autochthonous case on August 18, 2023, public health measures, includ...

The collection of updated data on social contact patterns following the COVID-19 pandemic disruptions is crucial for future epidemiological assessments and evaluating non-pharmaceutical interventions (NPIs) based on physical distancing. We conducted two waves of an online survey in March 2022 and March 2023 in Italy, gathering data from a represent...

Between August and 28 October 2024, 199 autochthonous cases of dengue virus serotype 2 were notified in the city of Fano, central Italy. We describe the ongoing epidemiological and microbiological investigation and public health measures implemented to contain the outbreak. The high transmissibility and the extension of the outbreak suggest that de...

We used published data from outbreak investigations of monkeypox virus clade I in the Democratic Republic of the Congo to estimate the distributions of critical epidemiological parameters. We estimated a mean incubation period of 9.9 days (95% credible interval [CrI] 8.5-11.5 days) and a mean generation time of 17.2 days (95% CrI 14.1-20.9 days) or...

Collaborative hubs that integrate multiple teams to generate ensemble projections and forecasts for shared targets are now regarded as state-of-the-art in epidemic predictive modeling. In this paper, we introduce Influcast, Italy's first epidemic forecasting hub for influenza-like illness. During the 2023/2024 winter season, Influcast provided 20 r...

Background The time-varying reproduction number R is a critical variable for situational awareness during infectious disease outbreaks; however, delays between infection and reporting of cases hinder its accurate estimation in real-time. A number of nowcasting methods, leveraging available information on data consolidation delays, have been propose...

Introduction. Here we reported the virological, entomological and epidemiological characteristics of the large autochthonous outbreak of dengue (DENV) occurred in a small village of the Lombardy region (Northern Italy) during summer 2023. Methods. After the diagnosis of the first autochthonous case on 18 August 2023, public health measures, includi...

Background Surveillance data and vaccination registries are widely used to provide real-time vaccine effectiveness (VE) estimates, which can be biased due to underreported (i.e. under-ascertained and under-notified) infections. Here, we investigate how the magnitude and direction of this source of bias in retrospective cohort studies vary under dif...

We estimate that the generation time of mpox clade I is distinctly longer than clade IIb and may depend on the transmission route (mean 17.5 days in households vs. 11.4 in hospitals). We estimate a mean reproduction number of 1.22-1.33 in the Democratic Republic of the Congo between August 2023-March 2024.

Quantifying the potential spatial spread of an infectious pathogen is key to defining effective containment and control strategies. The aim of this study is to estimate the risk of SARS-CoV-2 transmission at different distances in Italy before the first regional lockdown was imposed, identifying important sources of national spreading. To do this,...

In 2022, a global outbreak of mpox occurred, predominantly impacting men who have sex with men (MSM). The rapid decline of this epidemic is yet to be fully understood. We investigated the Italian outbreak by means of an individual-based mathematical model calibrated to surveillance data. The model accounts for transmission within the MSM sexual con...

Background Estimates of the spatiotemporal distribution of different mosquito vector species and the associated risk of transmission of arboviruses are key to design adequate policies for preventing local outbreaks and reducing the number of human infections in endemic areas. In this study, we quantified the abundance of Aedes albopictus and Aedes...

A real-world population-based longitudinal study, aimed at determining the magnitude and duration of immunity induced by different types of vaccines against COVID-19, started in 2021 by enrolling a cohort of 2,497 individuals at time of their first vaccination. The study cohort included both healthy adults aged ≤65 years and elderly subjects aged >...

Background Emerging arboviral diseases in Europe pose a challenge due to difficulties in detecting and diagnosing cases during the initial circulation of the pathogen. Early outbreak detection enables public health authorities to take effective actions to reduce disease transmission. Quantification of the reporting delays of cases is vital to plan...

Background: The difficulty in identifying SARS-CoV-2 infections has not only been the major obstacle to control the COVID-19 pandemic but also to quantify changes in the proportion of infections resulting in hospitalization, intensive care unit (ICU) admission, or death. Methods: We developed a model of SARS-CoV-2 transmission and vaccination in...

Background: Respiratory syncytial virus (RSV) is a leading cause of hospitalisation and mortality in young children globally. The social distancing measures implemented against COVID-19 in Lombardy (Italy) disrupted the typically seasonal RSV circulation during 2019-2021 and caused substantially more hospitalisations during 2021-2022. The primary...

Different monitoring and control policies have been implemented in schools to minimize the spread of SARS-CoV-2. Transmission in schools has been hard to quantify due to the large proportion of asymptomatic carriers in young individuals. We applied a Bayesian approach to reconstruct the transmission chains between 284 SARS-CoV-2 infections ascertai...

Importance: Estimates of the rate of waning of vaccine effectiveness (VE) against COVID-19 are key to assess population levels of protection and future needs for booster doses to face the resurgence of epidemic waves. Objective: To quantify the progressive waning of VE associated with the Delta and Omicron variants of SARS-CoV-2 by number of rec...

The worldwide inequitable access to vaccination claims for a re-assessment of policies that could minimize the COVID-19 burden in low-income countries. Nine months after the launch of the national vaccination program in March 2021, only 3.4% of the Ethiopian population received two doses of COVID-19 vaccine. We used a SARS-CoV-2 transmission model...

Mosquito-borne diseases are a major global public health concern and mosquito surveillance systems are essential for the implementation of effective mosquito control strategies. The objective of our study is to determine the spatiotemporal distribution of vector mosquito species in Maricopa County, AZ from 2011 to 2021, and to identify the hotspot...

Quantitative information on epidemiological quantities such as the incubation period and generation time of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants is scarce. We analysed a dataset collected during contact tracing activities in the province of Reggio Emilia, Italy, throughout 2021. We determined the distributions of th...

Background The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021. Aim To comprehensively describe Omicron spread in Italy in the 2 subsequent months and its impact on the overall SARS-CoV-2 circulation at population level. Methods We analyse data from four genomic surveys conducted across the country between Decem...

To date there has been limited head-to-head evaluation of immune responses to different types of COVID-19 vaccines. A real-world population-based longitudinal study was designed with the aim to define the magnitude and duration of immunity induced by each of four different COVID-19 vaccines available in Italy at the time of this study. Overall, 249...

Background: School closures and distance learning have been extensively adopted to counter the COVID-19 pandemic. However, the contribution of school transmission to the spread of SARS-CoV-2 remains poorly quantified. Methods: We analyzed transmission patterns associated with 976 SARS-CoV-2 exposure events, involving 460 positive individuals, as...

We analyzed the first 255 PCR-confirmed cases of monkeypox in Italy in 2022. Preliminary estimates indicate mean incubation period of 9.1 (95% CI 6.5-10.9) days, mean generation time of 12.5 (95% CI 7.5-17.3) days, and reproduction number among men who have sex with men of 2.43 (95% CI 1.82-3.26).

Background: Starting from the final months of 2021, the SARS-CoV-2 Omicron variant expanded globally, swiftly replacing Delta, the variant that was dominant at the time. Many uncertainties remain about the epidemiology of Omicron; here, we aim to estimate its generation time. Methods: We used a Bayesian approach to analyze 23,122 SARS-CoV-2 infe...

Background The worldwide inequitable access to vaccination claims for a re-assessment of policies that could minimize the COVID-19 burden in low-income countries. An illustrative example is what occurred in Ethiopia, where nine months after the launch of the national vaccination program in March 2021, only 3% of the population received two doses of...

Mosquito-borne diseases are a major global public health concern and mosquito surveillance systems are essential for the implementation of effective mosquito control strategies. The objective of our study is to determine the spatiotemporal distribution of vector mosquito species in Maricopa County, AZ from 2011 to 2021, and to identify the hotspot...

We analyzed the first 255 PCR-confirmed cases of monkeypox occurred in Italy in 2022. Preliminary estimates indicate: mean incubation period of 9.1 days (95%CI of the mean: 6.5-10.9); mean generation time of 12.5 days (95%CI of the mean: 7.5-17.3); reproduction number in the MSM community of 2.43 (95%CI: 1.82-3.26).

Background The emergence of Omicron (B.1.1.529) variant of SARS-CoV-2 in late 2021 was followed by a marked increase of breakthrough infections. Estimates of vaccine effectiveness (VE) in the long term are key to assess potential resurgence of COVID-19 cases in the future. Methods We conducted a systematic review of manuscripts published until Jun...

Undernotification of SARS-CoV-2 infections has been a major obstacle to the tracking of critical quantities such as infection attack rates and the probability of severe and lethal outcomes. We use a model of SARS-CoV-2 transmission and vaccination informed by epidemiological and genomic surveillance data to estimate the number of daily infections o...

Undernotification of SARS-CoV-2 infections has been a major obstacle to the tracking of critical quantities such as infection attack rates and the probability of severe and lethal outcomes. We use a model of SARS-CoV-2 transmission and vaccination informed by epidemiological and genomic surveillance data to estimate the number of daily infections o...

Background: After a rapid upsurge of COVID-19 cases in Italy during the fall of 2020, the government introduced a three-tiered restriction system aimed at increasing physical distancing. The Ministry of Health, after periodic epidemiological risk assessments, assigned a tier to each of the 21 Italian regions and autonomous provinces. It is still u...

Introduction EURO2020 generated a growing media and population interest across the month period, that peaked with large spontaneous celebrations across the country upon winning the tournament. Methods We retrospectively analysed data from the national surveillance system (indicator-based) and from event-based surveillance to assess how the epidemi...

Introduction SARS-CoV-2 was declared a pandemic by the WHO on March 11th, 2020. Public protective measures were enforced in every country to limit the diffusion of SARS-CoV-2. Its transmission, mainly by droplets, has been measured by the effective reproduction number (Rt) that counts the number of secondary cases caused in a population by an avera...

Besides the timely detection of different SARS-CoV-2 variants through surveillance systems, functional and modelling studies are essential to better inform public health response and preparedness. Here, the knowledge available so far on SARS-CoV-2 variants is discussed from different perspectives, in order to highlight the relevance of a multidisci...

Background: The elderly, commonly defined as subjects aged ≥65 years, are among the at-risk subjects recommended for annual influenza vaccination in European countries. Currently, two new vaccines are available for this population: the MF59-adjuvanted quadrivalent influenza vaccine (aQIV) and the high-dose quadrivalent influenza vaccine (hdQIV). T...

Background School closures and distance learning have been extensively applied to control SARS-CoV-2 transmission. Despite evidence of viral circulation in schools, the contribution of students and of in-person schooling to the transmission remains poorly quantified. Methods We analyze 976 exposure events, involving 460 positive individuals, as ide...

Background. During 2021, the COVID-19 pandemic was characterized by the emergence of lineages with increased fitness. For most of these variants, quantitative information is scarce on epidemiological quantities such as the incubation period and generation time, which are critical for both public health decisions and scientific research. Method. We...

Background Several SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains. Aim We aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility. Met...

Problem: After Italy's first national restriction measures in 2020, a robust approach was needed to monitor the emerging epidemic of coronavirus disease 2019 (COVID-19) at subnational level and provide data to inform the strengthening or easing of epidemic control measures. Approach: We adapted the European Centre for Disease Prevention and Cont...

The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021. Data from three genomic surveys conducted in Italy between December 2021 and January 2022 suggest that Omicron became dominant in less than one month (prevalence on January 3: 78.6%-83.8%) with a doubling time of 2.7-3.1 days. The mean net reproduction number ro...

There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, we developed a data-driven computational model of SARS-CoV-2 transmission. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 17.3%...

During the COVID-19 pandemic, several countries have resorted to self-adaptive mechanisms that tailor non-pharmaceutical interventions to local epidemiological and health care indicators. These mechanisms reinforce the mutual influence between containment measures and the evolution of the epidemic. To account for such interplay, we develop an epide...

COVID-19 vaccination is allowing a progressive release of restrictions worldwide. Using a mathematical model, we assess the impact of vaccination in Italy since December 27, 2020 and evaluate prospects for societal reopening after emergence of the Delta variant. We estimate that by June 30, 2021, COVID-19 vaccination allowed the resumption of about...

Mechanisms for retrieving basic knowledge in the human mind are still unknown. Exploration is usually represented by cognitive units, i.e., concepts, linked together by associative relationships forming semantic networks. However, understanding how humans navigate such networks remains elusive, because the underlying topology of concepts cannot be...

Considerable uncertainty surrounds the timeline of introductions and onsets of local transmission of SARS-CoV-2 globally1–7. Although a limited number of SARS-CoV-2 introductions were reported in January and February 20208,9, the narrowness of the initial testing criteria, combined with a slow growth in testing capacity and porous travel screening1...

Background In the night of February 20, 2020, the first epidemic of the novel coronavirus disease (COVID-19) outside Asia was uncovered by the identification of its first patient in Lombardy region, Italy. In the following weeks, Lombardy experienced a sudden increase in the number of ascertained infections and strict measures were imposed to conta...

We investigated contact patterns in diverse social contexts in Kenya and the daily behaviours that may play a pivotal role in infection transmission to the most vulnerable leveraging novel data from a 2-day survey on social contacts and time use (TU) from a sample of 1407 individuals (for a total of 2705 person days) from rural, urban formal, and i...

Background After a rapid upsurge of COVID-19 cases in Italy during the fall of 2020, the government introduced a three-tiered restriction system aimed at increasing physical distancing. The Ministry of Health, after periodic epidemiological risk assessments, assigned a tier to each of the 21 Italian regions and autonomous provinces (AP). It is stil...

Solid estimates describing the clinical course of SARS-CoV-2 infections are still lacking due to under-ascertainment of asymptomatic and mild-disease cases. In this work, we quantify age-specific probabilities of transitions between stages defining the natural history of SARS-CoV-2 infection from 1,965 SARS-CoV-2 positive individuals identified in...

During the spring of 2020, the COVID-19 epidemic caused an unprecedented demand for intensive care resources in Lombardy, Italy. Using data on 43,538 hospitalized patients admitted between February 21 and July 12, 2020, we evaluated variations in intensive care unit (ICU) admissions and mortality over three periods: the early phase (February 20-Mar...

COVID-19 vaccination is being conducted in over 200 countries and regions to control SARS-CoV-2 transmission and return to a pre-pandemic lifestyle. However, understanding when non-pharmaceutical interventions (NPIs) can be lifted as immunity builds up remains a key question for policy makers. To address this, we built a data-driven model of SARS-C...

To counter the second COVID-19 wave in autumn 2020, the Italian government introduced a system of physical distancing measures organized in progressively restrictive tiers (coded as yellow, orange, and red) imposed on a regional basis according to real-time epidemiological risk assessments. We leverage the data from the Italian COVID-19 integrated...

Importance: Identifying health care settings and professionals at increased risk of SARS-CoV-2 infection is crucial to defining appropriate strategies, resource allocation, and protocols to protect health care workers (HCWs) and patients. Moreover, such information is crucial to decrease the risk that HCWs and health care facilities become amplifi...

We analyzed 221 COVID-19 cases identified between June 2020 and January 2021 in 6,074 individuals screened for IgG antibodies in May 2020, representing 77% of residents of five Italian municipalities. The adjusted relative risk of developing symptomatic infection in SARS-COV-2 seropositive participants was 0.055 (95%CI: 0.014 - 0.220)

There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, here we develop a data-driven computational model of SARS-CoV-2 transmission to investigate mechanistically the effect on COVID-19 outbreaks of school closure strategies based on syndromic surveillance and an...

To what extent infection with SARS-CoV-2 protects against subsequent reinfection or symptomatic reinfection is still unclear. In this cohort study, we analyzed surveillance records of COVID-19 cases identified between June 2020 and January 2021 in five Italian municipalities, where 77.7% of the entire population was screened for IgG antibodies in M...

Background COVID-19 spread may have a dramatic impact in countries with vulnerable economies and limited availability of, and access to, healthcare resources and infrastructures. However, in sub-Saharan Africa, a low prevalence and mortality have been observed so far. Methods We collected data on individuals’ social contacts in the South West Shew...

SARS-CoV-2 variants of concern (B.1.1.7, P.1 and B.1.351) have emerged in different continents of the world. To date, little information is available on their ecological interactions. Based on two genomic surveillance surveys conducted on February 18 and March 18, 2021 across the whole Italian territory and covering over 3,000 clinical samples, we...

Solid estimates describing the clinical course of SARS-CoV-2 infections are still lacking due to under-ascertainment of asymptomatic and mild-disease cases. In this work, we quantify age-specific probabilities of transitions between stages defining the natural history of SARS-CoV-2 infection from 1,965 SARS-CoV-2 positive individuals identified in...

Given the narrowness of the initial testing criteria, the SARS-CoV-2 virus spread through cryptic transmission in January and February, setting the stage for the epidemic wave experienced in March and April, 2020. We use a global metapopulation epidemic model to provide a mechanistic understanding of the global dynamic underlying the establishment...

Background Being unable to suppress SARS-CoV-2 transmission, the majority of countries worldwide have resorted to a mitigation approach, adjusting physical distancing restrictions (PDRs) to find a balance between viral circulation, individual freedoms and economic losses. Vaccination campaigns in many countries are allowing the progressive release...

Which are the characteristics of contact patterns in diverse social contexts in sub-Saharan Africa, and which types of individuals and daily behaviours may play a pivotal role in infection transmission to the most vulnerable, such as older adults? We address these questions using novel survey data on social contacts and time use from a sample of 14...

Importance Solid estimates of the risk of developing symptoms and of progressing to critical disease in individuals infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are key to interpreting coronavirus disease 2019 (COVID-19) dynamics, identifying the settings and the segments of the population where transmission is more li...

COVID-19 vaccination has been initiated in several countries to control SARS-CoV-2 transmission. Whether and when non-pharmaceutical interventions (NPIs) can be lifted as vaccination builds up remains key questions. To address them, we built a data-driven SARS-CoV-2 transmission model for China. We estimated that, to prevent local outbreaks to esca...

COVID-19 vaccination programs have been initiated in several countries to control SARS-CoV-2 transmission and return to a pre-pandemic lifestyle. However, understanding when non-pharmaceutical interventions (NPIs) can be lifted as vaccination builds up and how to update priority groups for vaccination in real-time remain key questions for policy ma...

Significance We use a mathematical model to evaluate the Italian exit strategy after the lockdown imposed against the COVID-19 epidemics, comparing it to a number of alternative scenarios. We highlight that a successful reopening requires two critical conditions: a low value of the reproduction number and a low incidence of infection. The first is...

Mathematical and computational modeling approaches are increasingly used as quantitative tools in the analysis and forecasting of infectious disease epidemics. The growing need for realism in addressing complex public health questions is, however, calling for accurate models of the human contact patterns that govern the disease transmission process...

To counter the second COVID-19 wave in autumn 2020, the Italian government introduced a system of physical distancing measures organized in progressively restrictive tiers (coded as yellow, orange, and red) and imposed on a regional basis according to epidemiological risk assessments. The individuals' attendance to locations outside the residential...

On March 11, 2020, Italy imposed a national lockdown to curtail the spread of severe acute respiratory syndrome coronavirus 2. We estimate that, 14 days after lockdown, the net reproduction number had dropped below 1 and remained stable at »0.76 (95% CI 0.67-0.85) in all regions for >3 of the following weeks.

In January 2020, a COVID-19 outbreak was detected in Sichuan Province of China. Six weeks later, the outbreak was successfully contained. The aim of this work is to characterize the epidemiology of the Sichuan outbreak and estimate the impact of interventions in limiting SARS-CoV-2 transmission. We analyzed patient records for all laboratory-confir...

Background On 20 February 2020, a locally acquired coronavirus disease (COVID-19) case was detected in Lombardy, Italy. This was the first signal of ongoing transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the country. The number of cases in Italy increased rapidly and the country became the first in Europe to experie...

Significance The recent increase in large-scale migration trends generates several concerns about public health in destination countries, especially in the presence of massive incoming human flows from countries with a disrupted healthcare system. Here, we analyze the flow of 3.5 M Syrian refugees toward Turkey to quantify the risk of measles outbr...

Background Despite thousands of influenza cases annually recorded by surveillance systems around the globe, estimating the transmission patterns of seasonal influenza is challenging. Methods We develop an age-structured mathematical model to influenza transmission to analyze ten consecutive seasons (from 2010-2011 to 2019-2020) of influenza epidem...

Background COVID-19 spread may have a dramatic impact in countries with vulnerable economies and limited availability of, and access to, healthcare resources and infrastructures. However, in sub-Saharan Africa a low prevalence and mortality have been observed so far. Methods We collected data on individuals’ social contacts in Ethiopia across geog...

Background During the spring of 2020, the SARS-CoV-2 epidemic has caused significant resource strain in hospitals of Lombardy, Italy, with the demand for intensive care beds for COVID-19 patients exceeding the overall pre-crisis capacity. In this study, we evaluate the effect of healthcare strain on ICU admission and survival. Methods We used data...

Objectives: A seroprevalence study of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was conducted in a high-incidence area located in northeastern Italy. Methods: All citizens above 10 years of age resident in five municipalities of the Autonomous Province of Trento, with the highest incidence of coronavirus disease 2019 (COVID-19...

Ministero della Salute - Istituto Superiore di Sanità Prevention and response to COVID-19: evolution of strategy and planning in the transition phase for the autumn-winter season. English version. vii, 109 p. With the beginning of the 2020 autumn-winter season, Italy, as other European countries, is experiencing a slow and progressive worsening of...

While severe social-distancing measures have proven effective in slowing the coronavirus disease 2019 (COVID-19) pandemic, second-wave scenarios are likely to emerge as restrictions are lifted. Here we integrate anonymized, geolocalized mobility data with census and demographic data to build a detailed agent-based model of severe acute respiratory...

Background: The spatial spread of many mosquito-borne diseases occurs by focal spread at the scale of a few hundred meters and over longer distances due to human mobility. The relative contributions of different spatial scales for transmission of chikungunya virus require definition to improve outbreak vector control recommendations. Methods: We...

We analysed 5,484 close contacts of coronavirus disease (COVID-19) cases in Italy, all tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Infection fatality ratio was 0.43% (95% confidence interval (CI): 0.21-0.79) for individuals younger than 70 years and 10.5% (95% CI: 8.0-13.6) for older individuals. Risk of death after inf...