| Publication | Publication Date | Authors | Summary | Covid-19 |
|---|---|---|---|---|
| Are people excessively pessimistic about the risk of coronavirus infection? | 01/2021 | Jocelyn Raude, Marion Debin, Cecile Souty, Caroline Guerrisi, Clement Turbelin, Alessandra Falchi, Isabelle Bonmarin, Daniela Paolotti, Yamir Moreno,Chinelo Obi, Jim Duggan, Ania Wisniak, Antoine Flahault, Thierry Blanchon, Vittoria Colizza, 2020. | 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. | |
| Assessing spread risk of Wuhan novel coronavirus within and beyond China, January-April 2020: a travel network-based modelling study | 03/2020 | Shengjie Lai, Isaac I. Bogoch, Nick W Ruktanonchai, Alexander Watts, Xin Lu, Weizhong Yang, Hongjie Yu, Kamran Khan, Andrew J Tatem, 2020. | Background:?A novel coronavirus (2019-nCoV) emerged in Wuhan City, China, at the end of 2019 and has caused an outbreak of human-to-human transmission with a Public Health Emergency of International Concern declared by the World Health Organization on January 30, 2020. Aim:?We aimed to estimate the potential risk and geographic range of Wuhan novel coronavirus (2019-nCoV) spread within and beyond China from January through to April, 2020. Methods:?A series of domestic and international travel network-based connectivity and risk analyses were performed, by using de-identified and aggregated mobile phone data, air passenger itinerary data, and case reports. Results: The cordon sanitaire of Wuhan is likely to have occurred during the latter stages of peak population numbers leaving the city before Lunar New Year (LNY), with travellers departing into neighbouring cities and other megacities in China. We estimated that 59,912 air passengers, of which 834 (95% UI: 478 - 1349) had 2019-nCoV infection, travelled from Wuhan to 382 cities outside of mainland China during the two weeks prior to Wuhan’s lockdown. The majority of these cities were in Asia, but major hubs in Europe, the US and Australia were also prominent, with strong correlation seen between predicted importation risks and reported cases. Because significant spread has already occurred, a large number of airline travellers (3.3 million under the scenario of 75% travel reduction from normal volumes) may be required to be screened at origin high-risk cities in China and destinations across the globe for the following three months of February to April, 2020 to effectively limit spread beyond its current extent. Conclusion:?Further spread of 2019-nCoV within China and international exportation is likely to occur. All countries, especially vulnerable regions, should be prepared for efforts to contain the 2019-nCoV infection. | |
| Assessing the impact of coordinated COVID-19 exit strategies across Europe. | 09/2020 | N. W. Ruktanonchai, J. R. Floyd, S. Lai, C. W. Ruktanonchai, A. Sadilek, P. Rente-Lourenco, X. Ben, A. Carioli, J. Gwinn, J. E. Steele, O. Prosper, A. Schneider, A. Oplinger, P. Eastham, A. J. Tatem, 2020. | As rates of new coronavirus disease 2019 (COVID-19) cases decline across Europe owing to nonpharmaceutical interventions such as social distancing policies and lockdown measures, countries require guidance on how to ease restrictions while minimizing the risk of resurgent outbreaks. We use mobility and case data to quantify how coordinated exit strategies could delay continental resurgence and limit community transmission of COVID-19. We find that a resurgent continental epidemic could occur as many as 5 weeks earlier when well-connected countries with stringent existing interventions end their interventions prematurely. Further, we find that appropriate coordination can greatly improve the likelihood of eliminating community transmission throughout Europe. In particular, synchronizing intermittent lockdowns across Europe means that half as many lockdown periods would be required to end continent-wide community transmission. | X |
| Automated Processing of Multilingual Online News for the Monitoring of Animal Infectious Diseases | 05/2020 | Sarah Valentin, Renaud Lancelot, Mathieu Roche, 2020. | The Platform for Automated extraction of animal Disease Information from the web (PADI-web) is an automated system which monitors the web for monitoring and detecting emerging animal infectious diseases. The tool automatically collects news via customised multilingual queries, classifies them and extracts epidemiological information. We detail the processing of multilingual online sources by PADI-web and analyse the translated outputs in a case study. | |
| Changes in contact patterns shape the dynamics of the COVID-19 outbreak in China. | 06/2020 | Juanjuan Zhang, Maria Litvinova, Yuxia Liang, Yan Wang, Wei Wang, Shanlu Zhao, Qianhui Wu, Stefano Merler, C?cile Viboud, Alessandro Vespignani, Marco Ajelli, Hongjie Yu, 2020 | Intense nonpharmaceutical interventions were put in place in China to stop transmission of the novel coronavirus disease 2019 (COVID-19). As transmission intensifies in other countries, the interplay between age, contact patterns, social distancing, susceptibility to infection, and COVID-19 dynamics remains unclear. To answer these questions, we analyze contact survey data for Wuhan and Shanghai before and during the outbreak and contact-tracing information from Hunan province. Daily contacts were reduced seven- to eightfold during the COVID-19 social distancing period, with most interactions restricted to the household. We find that children 0 to 14 years of age are less susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection than adults 15 to 64 years of age (odds ratio 0.34, 95% confidence interval 0.24 to 0.49), whereas individuals more than 65 years of age are more susceptible to infection (odds ratio 1.47, 95% confidence interval 1.12 to 1.92). Based on these data, we built a transmission model to study the impact of social distancing and school closure on transmission. We find that social distancing alone, as implemented in China during the outbreak, is sufficient to control COVID-19. Although proactive school closures cannot interrupt transmission on their own, they can reduce peak incidence by 40 to 60% and delay the epidemic. | |
| COVID-19 and Media Datasets: Period- and location-specific textual data mining. | 12/2020 | Mathieu Roche, 2020. | The vocabulary used in news on a disease such as COVID-19 changes according the period. This aspect is discussed on the basis of MEDISYS-sourced media datasets via two studies. The first focuses on terminology extraction and the second on period prediction according to the textual content using machine learning approaches. | |
| Crowding and the shape of COVID-19 epidemics. | 10/2020 | Benjamin Rader, Samuel V. Scarpino, Anjalika Nande, Alison L. Hill, Ben Adlam, Robert C. Reiner, David M. Pigott, Bernardo Gutierrez, Alexander E. Zarebski, Munik Shrestha, John S. Brownstein, Marcia C. Castro, Christopher Dye, Huaiyu Tian, Oliver G. Pybus & Moritz U. G. Kraemer , 2020. | The coronavirus disease 2019 (COVID-19) pandemic is straining public health systems worldwide, and major non-pharmaceutical interventions have been implemented to slow its spread1,2,3,4. During the initial phase of the outbreak, dissemination of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was primarily determined by human mobility from Wuhan, China5,6. Yet empirical evidence on the effect of key geographic factors on local epidemic transmission is lacking7. In this study, we analyzed highly resolved spatial variables in cities, together with case count data, to investigate the role of climate, urbanization and variation in interventions. We show that the degree to which cases of COVID-19 are compressed into a short period of time (peakedness of the epidemic) is strongly shaped by population aggregation and heterogeneity, such that epidemics in crowded cities are more spread over time, and crowded cities have larger total attack rates than less populated cities. Observed differences in the peakedness of epidemics are consistent with a meta-population model of COVID-19 that explicitly accounts for spatial hierarchies. We paired our estimates with globally comprehensive data on human mobility and predict that crowded cities worldwide could experience more prolonged epidemics. | |
| Effect of non-pharmaceutical interventions to contain COVID-19 in China. | 05/2020 | Lai, S., Ruktanonchai, N.W., Zhou, L. et al., 2020 | On 11 March 2020, the World Health Organization (WHO) declared coronavirus disease 2019 (COVID-19) a pandemic. The strategies based on non-pharmaceutical interventions that were used to contain the outbreak in China appear to be effective, but quantitative research is still needed to assess the efficacy of non-pharmaceutical interventions and their timings.Here, using epidemiological data on COVID-19 and anonymized data on human movement, we develop a modelling framework that uses daily travel networks to simulate different outbreak and intervention scenarios across China. We estimate that there were a total of 114,325 cases of COVID-19 (interquartile range 76,776–164,576) in mainland China as of 29 February 2020. Without non-pharmaceutical interventions, we predict that the number of cases would have been 67-fold higher (interquartile range 44–94-fold) by 29 February 2020, and we find that the effectiveness of different interventions varied. We estimate that early detection and isolation of cases prevented more infections than did travel restrictions and contact reductions, but that a combination of non-pharmaceutical interventions achieved the strongest and most rapid effect. According to our model, the lifting of travel restrictions from 17 February 2020 does not lead to an increase in cases across China if social distancing interventions can be maintained, even at a limited level of an on average 25% reduction in contact between individuals that continues until late April. These findings improve our understanding of the effects of non-pharmaceutical interventions on COVID-19, and will inform response efforts across the world. | X |
| Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework. | 11/2020 | Simon Dellicour, Sebastian Lequime, Bram Vrancken, Mandev S. Gill, Paul Bastide, Karthik Gangavarapu, Nathaniel L. Matteson, Yi Tan, Louis du Plessis, Alexander A. Fisher, Martha I. Nelson, Marius Gilbert, Marc A. Suchard, Kristian G. Andersen, Nathan D. Grubaugh, Oliver G. Pybus & Philippe Lemey, 2020. | Computational analyses of pathogen genomes are increasingly used to unravel the dispersal history and transmission dynamics of epidemics. Here, we show how to go beyond historical reconstructions and use spatially-explicit phylogeographic and phylodynamic approaches to formally test epidemiological hypotheses. We illustrate our approach by focusing on the West Nile virus (WNV) spread in North America that has substantially impacted public, veterinary, and wildlife health. We apply an analytical workflow to a comprehensive WNV genome collection to test the impact of environmental factors on the dispersal of viral lineages and on viral population genetic diversity through time. We find that WNV lineages tend to disperse faster in areas with higher temperatures and we identify temporal variation in temperature as a main predictor of viral genetic diversity through time. By contrasting inference with simulation, we find no evidence for viral lineages to preferentially circulate within the same migratory bird flyway, suggesting a substantial role for non-migratory birds or mosquito dispersal along the longitudinal gradient. | |
| Evaluating the effect of demographic factors, socioeconomic factors, and risk aversion on mobility during the COVID-19 epidemic in France under lockdown: a population-based study. | 10/2020 | Giulia Pullano, Eugenio Valdano, Nicola Scarpa, Stefania Rubrichi, Vittoria Colizza, 2020 | On March 17, 2020, French authorities implemented a nationwide lockdown to respond to the COVID-19 epidemic and curb the surge of patients requiring critical care. Assessing the effect of lockdown on individual displacements is essential to quantify achievable mobility reductions and identify the factors driving the changes in social dynamics that affected viral diffusion. We aimed to use mobile phone data to study how mobility in France changed before and during lockdown, breaking down our findings by trip distance, user age and residency, and time of day, and analysing regional data and spatial heterogeneities. | X |
| Evolution and epidemic spread of SARS-CoV-2 in Brazil. | 09/2020 | Darlan S. Candido, Ingra M. Claro, Jaqueline G. de Jesus, William M. Souza, et al., 2020 | Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in S?o Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country. | |
| Evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside Hubei province, China: a descriptive and modelling study. | 06/2020 | Juanjuan Zhang, Maria Litvinova, Wei Wang, Yan Wang, Xiaowei Deng, Xinghui Chen, et al., 2020 | The coronavirus disease 2019 (COVID-19) epidemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), began in Wuhan city, Hubei province, in December, 2019, and has spread throughout China. Understanding the evolving epidemiology and transmission dynamics of the outbreak beyond Hubei would provide timely information to guide intervention policy. We aimed to describe the epidemiological characteristics of the COVID-19 outbreak 50 days after it was recognised in Chinese provinces outside Hubei. We also estimated changes in key time-to-event intervals and reproduction numbers to assess whether the strict control measures put in place in China have been successful in slowing transmission. | |
| Global Trends in Antimicrobial Use in Food Animals from 2017 to 2030. | 11/2020 | Katie Tiseo, Laura Huber, Marius Gilbert, Timothy P. Robinson, Thomas P. Van Boeckel, 2020. | Demand for animal protein is rising globally and has been facilitated by the expansion of intensive farming. However, intensive animal production relies on the regular use of antimicrobials to maintain health and productivity on farms. The routine use of antimicrobials fuels the development of antimicrobial resistance, a growing threat for the health of humans and animals. Monitoring global trends in antimicrobial use is essential to track progress associated with antimicrobial stewardship efforts across regions. We collected antimicrobial sales data for chicken, cattle, and pig systems in 41 countries in 2017 and projected global antimicrobial consumption from 2017 to 2030. We used multivariate regression models and estimated global antimicrobial sales in 2017 at 93,309 tonnes (95% CI: 64,443, 149,886). Globally, sales are expected to rise by 11.5% in 2030 to 104,079 tonnes (95% CI: 69,062, 172,711). All continents are expected to increase their antimicrobial use. Our results show lower global antimicrobial sales in 2030 compared to previous estimates, owing to recent reports of decrease in antimicrobial use, in particular in China, the world’s largest consumer. Countries exporting a large proportion of their production are more likely to report their antimicrobial sales data than countries with small export markets. | |
| Impact of a Nationwide Lockdown on SARS-CoV-2 Transmissibility, Italy | 01/2021 | Giorgio Guzzetta, Flavia Riccardo1, Valentina Marziano, Piero Poletti, Filippo Trentini, Antonino Bella, Xanthi Andrianou, Martina Del Manso, Massimo Fabiani, Stefania Bellino, Stefano Boros, Alberto Mateo Urdiales, Maria Fenicia Vescio, Andrea Piccioli, Silvio Brusaferro, Giovanni Rezza, Patrizio Pezzotti, Marco AjelliComments to Author , Stefano Merler, and COVID-19 Working Group, 2020. | 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. On February 21, 2020, the earliest known case of locally transmitted severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) infection was reported in Italy (1; D. Cereda et al., unpub. data, https://arxiv.org/abs/2003.09320External Link). Since then, several interventions have been deployed to control disease spread in regions with sustained transmission, including quarantine of most-affected municipalities, ban of mass gatherings, and local school closures. School closure at the national level was mandated on March 5, and a national lockdown (stay-home mandate and closure of all nonessential productive activities) was issued on March 11 (2,3), then eased after May 4, 2020 (Appendix). The aim of this study is to evaluate the impact of these interventions on SARS-CoV-2 transmissibility in Italy. | |
| Influence of Temperature on the Life-Cycle Dynamics of Aedes albopictus Population Established at Temperate Latitudes: A Laboratory Experiment | 10/2020 | Marini, Giovanni; Manica, Manica; Arnoldi, Daniele; Inama, Enrico; Ros?, Roberto; Rizzoli, Annapaola, 2020. | Mosquitoes represent a potential major public health concern, as they are capable of transmitting several pathogens when biting humans. It is well known that temperature is a crucial factor affecting mosquito biology: for instance, warmer conditions can increase survival and fecundity. Here, we quantify the influence of different temperatures on the bionomics of Aedes albopictus, which is a mosquito species native to Southeast Asia that has been able to spread worldwide during the last forty years. We used specimens collected from northern Italy to assess if temperate individuals are characterized, possibly thanks to an adaptation process, by a different thermal response with respect to subtropical individuals. We found that immature stages are well adapted to colder temperatures, which nonetheless seem to prevent any blood-feeding activity. Adult longevity and fecundity were substantially greater at mild conditions. This thermal adaptation might increase the length of the breeding season and could allow the colonization of areas at higher altitude, resulting in an overall increased risk for potential transmission of Ae. albopictus-borne pathogens. | |
| Lessons learnt from 288 COVID-19 international cases: importations over time, effect of interventions, underdetection of imported cases | 02/2020 | Francesco Pinotti, Laura Di Domenico, Ernesto Ortega, Marco Mancastroppa, Giulia Pullano, Eugenio Valdano, Pierre-Yves Boelle, Chiara Poletto, Vittoria Colizza, 2020. | 288 cases have been confirmed out of China from January 3 to February 13, 2020. We collected and synthesized all available information on these cases from official sources and media. We analyzed importations that were successfully isolated and those leading to onward transmission. We modeled their number over time, in relation to the origin of travel (Hubei province, other Chinese provinces, other countries) and interventions. We characterized importations timeline to assess the rapidity of isolation, and epidemiologically linked clusters to estimate the rate of detection. We found a rapid exponential growth of importations from Hubei, combined with a slower growth from the other areas. We predicted a rebound of importations from South East Asia in the upcoming weeks. Time from travel to detection has considerably decreased since the first importation, however 6 cases out of 10 were estimated to go undetected. Countries outside China should be prepared for the possible emergence of several undetected clusters of chains of local transmissions. | |
| Monitoring online media reports for early detection of unknown diseases: Insight from a retrospective study of COVID_19 emergence | 07/2020 | Sarah Valentin, Aliz? Mercier, Renaud Lancelot, Mathieu Roche, Elena Arsevska, 2020. | Event_based surveillance (EBS) systems monitor a broad range of information sources to detect early signals of disease emergence, including new and unknown diseases. In December 2019, a newly identified coronavirus emerged in Wuhan (China), causing a global coronavirus disease (COVID_19) pandemic. A retrospective study was conducted to evaluate the capacity of three event_based surveillance (EBS) systems (ProMED, HealthMap and PADI_web) to detect early COVID_19 emergence signals. We focused on changes in online news vocabulary over the period before/after the identification of COVID_19, while also assessing its contagiousness and pandemic potential. ProMED was the timeliest EBS, detecting signals one day before the official notification. At this early stage, the specific vocabulary used was related to ‘pneumonia symptoms’ and ‘mystery illness’. Once COVID_19 was identified, the vocabulary changed to virus family and specific COVID_19 acronyms. Our results suggest that the three EBS systems are complementary regarding data sources, and all require timeliness improvements. EBS methods should be adapted to the different stages of disease emergence to enhance early detection of future unknown disease outbreaks. | |
| Novel coronavirus (2019-nCoV) early-stage importation risk to Europe, January 2020. | 01/2020 | G. Pullano, F. Pinotti, E. Valdano, P.Y. Bo?lle, C. Poletto, V. Colizza, 2020. | As at 27 January 2020, 42 novel coronavirus (2019-nCoV) cases were confirmed outside China. We estimate the risk of case importation to Europe from affected areas in China via air travel. We consider travel restrictions in place, three reported cases in France, one in Germany. Estimated risk in Europe remains high. The United Kingdom, Germany and France are at highest risk. Importation from Beijing and Shanghai would lead to higher and widespread risk for Europe. | |
| PADI-web: an event-based surveillance system for detecting, classifying and processing online news. | 02/2020 | Sarah Valentin, Elena Arsevska, Alize Mercier, Sylvain Falala, Julien Rabatel, Renaud Lancelot, Mathieu Roche, 2020. | Global animal disease outbreak detection and monitoring rely on official sources, such as intergovernmental organisations, as well as digital media and other unofficial outlets. Manually extracting relevant information from unofficial sources is time-consuming. The Platform for Automated extraction of animal Disease Information from the web (PADI-web) is an automated biosurveillance system devoted to online news source monitoring for the detection of emerging/new animal infectious diseases by the French Epidemic Intelligence System. The tool automatically collects news via customised multilingual queries, classifies them and extracts epidemiological information. We detail each step of the PADI-web pipeline, with a focus on the new user-oriented features. | |
| Potential short-term outcome of an uncontrolled COVID-19 epidemic in Lombardy, Italy, February to March 2020. | 03/2020 | Giorgio Guzzetta1 , Piero Poletti1 , Marco Ajelli , Filippo Trentini, Valentina Marziano, Danilo Cereda, Marcello Tirani, Giulio Diurno, Annalisa Bodina, Antonio Barone, Lucia Crottogini, Maria Gramegna, Alessia Melegaro, Stefano Merler | On 20 February 2020, a case of coronavirus disease (COVID-19) was notified in Lombardy, Italy, uncovering ongoing transmission in at least two other regions (Emilia Romagna and Veneto) [1]. To rapidly assess risks of the current situation, we analysed the line list of reported cases in Lombardy to project the number of cases, should the epidemic be left uncontrolled. | |
| Preparedness and vulnerability of African countries against importations of COVID-19: a modelling study | 03/2020 | Marius Gilbert, Giulia Pullano, Francesco Pinotti, Eugenio Valdano, Chiara Poletto, Pierre-Yves Boëlle, Eric D’Ortenzio, Yazdan Yazdanpanah, Serge Paul Eholie, Mathias Altmann, Bernardo Gutierrez, Moritz U G Kraemer, Vittoria Colizza, 2020. | The novel coronavirus disease 2019 (COVID-19) epidemic has spread from China to 25 countries. Local cycles of transmission have already occurred in 12 countries after case importation. In Africa, Egypt has so far confirmed one case. The management and control of COVID-19 importations heavily rely on a country's health capacity. Here we evaluate the preparedness and vulnerability of African countries against their risk of importation of COVID-19. We used data on the volume of air travel departing from airports in the infected provinces in China and directed to Africa to estimate the risk of importation per country. We determined the country's capacity to detect and respond to cases with two indicators: preparedness, using the WHO International Health Regulations Monitoring and Evaluation Framework; and vulnerability, using the Infectious Disease Vulnerability Index. Countries were clustered according to the Chinese regions contributing most to their risk. Countries with the highest importation risk (ie, Egypt, Algeria, and South Africa) have moderate to high capacity to respond to outbreaks. Countries at moderate risk (ie, Nigeria, Ethiopia, Sudan, Angola, Tanzania, Ghana, and Kenya) have variable capacity and high vulnerability. We identified three clusters of countries that share the same exposure to the risk originating from the provinces of Guangdong, Fujian, and the city of Beijing, respectively. Many countries in Africa are stepping up their preparedness to detect and cope with COVID-19 importations. Resources, intensified surveillance, and capacity building should be urgently prioritised in countries with moderate risk that might be ill-prepared to detect imported cases and to limit onward transmission. | |
| Retrospective analysis of the Italian exit strategy from COVID-19 lockdown | 09/2020 | Valentina Marziano, Giorgio Guzzetta, Bruna Maria Rondinone, Fabio Boccuni, Flavia Riccardo, Antonino Bella, Piero Poletti, Filippo Trentini, Patrizio Pezzotti, Silvio Brusaferro, Giovanni Rezza, Sergio Iavicoli, Marco Ajelli, and Stefano Merler, 2020. | 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 needed to allow some margin for expansion after the lifting of restrictions; the second is needed because the level of incidence will be maintained approximately constant after the reproduction number has grown to values close to one. Furthermore, we suggest that, even with significant reductions of transmission rates, resuming social contacts at prepandemic levels escalates quickly the COVID-19 burden. | |
| Spatial modes for transmission of chikungunya virus during a large chikungunya outbreak in Italy: a modeling analysis | 08/2020 | Giorgio Guzzetta, Francesco Vairo, Alessia Mammone, Simone Lanini, Piero Poletti, Mattia Manica, Roberto Rosa, Beniamino Caputo, Angelo Solimini, Alessandra Della Torre, Paola Scognamiglio, Alimuddin Zumla, Giuseppe Ippolito & Stefano Merler, 2020. | 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. Evidence suggest that human mobility contributes to seeding a relevant number of secondary cases and new foci of transmission over several kilometers. Reactive vector control based on current guidelines might allow a significant number of secondary clusters in untreated areas, especially if the outbreak is not detected early. Existing policies and guidelines for control during outbreaks should recommend the prioritization of preventive measures in neighboring territories with known mobility flows to the main areas of transmission. | |
| Spring temperature shapes West Nile virus transmission in Europe | 03/2021 | Giovanni Marini, Mattia Manica, Luca Delucchi, Andrea Pugliese, Roberto Rosa, 2020. | West Nile Virus (WNV) is now endemic in many European countries, causing hundreds of human cases every year, with a high spatial and temporal heterogeneity. Previous studies have suggested that spring temperature might play a key role at shaping WNV transmission. Specifically, warmer temperatures in April-May might amplify WNV circulation, thus increasing the risk for human transmission later in the year. To test this hypothesis, we collated publicly available data on the number of human infections recorded in Europe between 2011 and 2019. We then applied generalized linear models to quantify the relationship between human cases and spring temperature, considering both average conditions (over years 2003-2010) and deviations from the average for subsequent years (2011-2019). We found a significant positive association both spatial (average conditions) and temporal (deviations). The former indicates that WNV circulation is higher in usually warmer regions while the latter implies a predictive value of spring conditions over the coming season. We also found a positive association with WNV detection during the previous year, which can be interpreted as an indication of the reliability of the surveillance system but also of WNV overwintering capacity. Weather anomalies at the beginning of the mosquito breeding season might act as an early warning signal for public health authorities, enabling them to strengthen in advance ongoing surveillance and prevention strategies. | |
| The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak | 04/2020 | Chinazzi, M., Davis, J. T., Ajelli, M., Gioannini, C., Litvinova, M., Merler, S., … & Viboud, C., 2020. | Motivated by the rapid spread of coronavirus disease 2019 (COVID-19) in mainland China, we use a global metapopulation disease transmission model to project the impact of travel limitations on the national and international spread of the epidemic. The model is calibrated on the basis of internationally reported cases and shows that, at the start of the travel ban from Wuhan on 23 January 2020, most Chinese cities had already received many infected travelers. The travel quarantine of Wuhan delayed the overall epidemic progression by only 3 to 5 days in mainland China but had a more marked effect on the international scale, where case importations were reduced by nearly 80% until mid-February. Modeling results also indicate that sustained 90% travel restrictions to and from mainland China only modestly affect the epidemic trajectory unless combined with a 50% or higher reduction of transmission in the community. | |
| The emergence of SARS-CoV-2 in Europe and the US | 05/2020 | Michael Worobey, Jonathan Pekar, Brendan B. Larsen, Martha I. Nelson, Verity Hill, Jeffrey B. Joy, Andrew Rambaut, Marc A. Suchard, Joel O. Wertheim, Philippe Lemey, 2020. | Accurate understanding of the global spread of emerging viruses is critically important for public health response and for anticipating and preventing future outbreaks. Here, we elucidate when, where and how the earliest sustained SARS-CoV-2 transmission networks became established in Europe and the United States (US). Our results refute prior findings erroneously linking cases in January 2020 with outbreaks that occurred weeks later. Instead, rapid interventions successfully prevented onward transmission of those early cases in Germany and Washington State. Other, later introductions of the virus from China to both Italy and Washington State founded the earliest sustained European and US transmission networks. Our analyses reveal an extended period of missed opportunity when intensive testing and contact tracing could have prevented SARS-CoV-2 from becoming established in the US and Europe. | |
| Tracing and analysis of 288 early SARS-CoV-2 infections outside China: A modeling study | 07/2020 | Francesco Pinotti, Laura Di Domenico, Ernesto Ortega, Marco Mancastroppa, Giulia Pullano, Eugenio Valdano, Pierre-Yves Bo?lle, Chiara Polett, Vittoria Colizza, 2020. | Originating from China, COVID-19 outbreak has now become a global pandemic, with more than 4 million cases reported across all continents. Underdetection of imported cases from China in the early phase of the epidemic played a crucial role in the spreading of the virus across and within countries. We quantified importations over time in light of the implemented travel ban in China and assessed delay and rate of detection of the first imported cases responsible for seeding the epidemic across multiple countries. We collected information on all international cases outside China officially confirmed in the period from January 3 to February 13, 2020. We developed a statistical model to predict trends in importations and predicted a rebound effect in importations from South East Asia. By analyzing clusters of local transmission, we estimated the detection rate at 36%. Travel bans adopted in China contributed to reducing the growth rate of exportations; however, they did not prevent international seeding. The majority of imported cases went undetected, generating extensive chains of local transmission in countries outside China. This led to silently spreading epidemics in seeded countries. | |
| Annotation of epidemiological informationin animal disease-related news articles: guidelines | 01/2021 | Sarah Valentin, Elena Arsevska, Aline Vilain, Valérie De Waele, Renaud Lancelot, Mathieu Roche | This paper describes a method for annotation of epidemiological information in animal disease-related news articles. The annotation guidelines are generic and aim to embrace all animal or zoonotic infectious diseases, regardless of the pathogen involved or its way of transmission (e.g. vector-borne, airborne, by contact). The framework relies on the successive annotation of all the sentences from a news article. The annotator evaluates the sentences in a specific epidemiological context, corresponding to the publication of the news article. | |
| Modelling safe protocols for reopening schools during the COVID-19 pandemic in France | 01/2021 | Laura Di Domenico, Giulia Pullano, Chiara E. Sabbatini, Pierre-Yves Boëlle, Vittoria Colizza | As countries in Europe implement strategies to control COVID-19 pandemic, different options are chosen regarding schools. Through a stochastic age-structured transmission model calibrated to the observed epidemic in Île-de-France in the first wave, we explored scenarios of partial, progressive, or full school reopening. Given the uncertainty on children’s role, we found that reopening schools after lockdown may increase COVID-19 cases, yet protocols exist that maintain the epidemic controlled. Under a scenario with stable epidemic activity if schools were closed, reopening pre-schools and primary schools would lead up to 76% [67, 84]% occupation of ICU beds if no other school level reopened, or if middle and high schools reopened later. Immediately reopening all school levels may overwhelm the ICU system. Priority should be given to pre- and primary schools allowing younger children to resume learning and development, whereas full attendance in middle and high schools is not recommended for stable or increasing epidemic activity. Large-scale test and trace are required to maintain the epidemic under control. Ex-post assessment shows that progressive reopening of schools, limited attendance, and strong adoption of preventive measures contributed to a decreasing epidemic after lifting the first lockdown. | |
| Can a COVID-19 vaccination program guarantee the return to a pre-pandemic lifestyle? | 02/2021 | Juan Yang, Valentina Marziano, Xiaowei Deng, Giorgio Guzzetta, Juanjuan Zhang, Filippo Trentini, Jun Cai, Piero Poletti, Wen Zheng, Wei Wang, Qianhui Wu, Zeyao Zhao, Kaige Dong, Guangjie Zhong, Cécile Viboud, Stefano Merler, Marco Ajelli, Hongjie Yu | 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 escalate to major widespread epidemics, stringent NPIs need to remain in place at least one year after the start of vaccination. Should NPIs be capable to keep the reproduction number (Rt) around 1.3, vaccination could reduce up to 99% of COVID-19 burden and bring Rt below the epidemic threshold in 9 months. Maintaining strict NPIs throughout 2021 is of paramount importance to reduce COVID-19 burden while vaccines are distributed, especially in large populations with little natural immunity. | |
| Reducing contacts to stop SARS-CoV-2 transmission during the second pandemic wave in Brussels, Belgium, August to November 2020 | 02/2021 | Brecht Ingelbeen, Laurène Peckeu, Marie Laga, Ilona Hendrix, Inge Neven, Marianne AB van der Sande, Esther van Kleef | Belgium reported per capita the highest number of coronavirus disease (COVID-19)-related deaths and near highest number of cases worldwide and was heavily affected during Europe’s first and second pandemic wave, reporting a total of 21,634 deaths and more than 700,000 cases on 13 February 2021 [1]. We describe the effect of physical distancing and school reopening on the number of contacts reported by each confirmed case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and on associated age-specific SARS-CoV-2 transmission patterns, using operational data from the COVID-19 contact tracing system of the Brussels region (Supplementary material) and case reports made available via the Belgian institute for health, Sciensano. | |
| Integrated vaccination and physical distancing interventions to prevent future COVID-19 waves in Chinese cities | 02/2021 | Bo Huang, Jionghua Wang, Jixuan Cai, Shiqi Yao, Paul Kay Sheung Chan, Tony Hong-wing Tam, Ying-Yi Hong, Corrine W. Ruktanonchai, Alessandra Carioli, Jessica R. Floyd, Nick W. Ruktanonchai, Weizhong Yang, Zhongjie Li, Andrew J. Tatem & Shengjie Lai | The coronavirus disease 2019 (COVID-19) pandemic has posed substantial challenges to the formulation of preventive interventions, particularly since the effects of physical distancing measures and upcoming vaccines on reducing susceptible social contacts and eventually halting transmission remain unclear. Here, using anonymized mobile geolocation data in China, we devise a mobility-associated social contact index to quantify the impact of both physical distancing and vaccination measures in a unified way. Building on this index, our epidemiological model reveals that vaccination combined with physical distancing can contain resurgences without relying on stay-at-home restrictions, whereas a gradual vaccination process alone cannot achieve this. Further, for cities with medium population density, vaccination can reduce the duration of physical distancing by 36% to 78%, whereas for cities with high population density, infection numbers can be well-controlled through moderate physical distancing. These findings improve our understanding of the joint effects of vaccination and physical distancing with respect to a city’s population density and social contact patterns. | |
| Retrospective analysis of the Italian exit strategy from COVID-19 lockdown | 02/2021 | Valentina Marzianoa, Giorgio Guzzettaa, Bruna Maria Rondinone, Fabio Boccuni, Flavia Riccardoc, Antonino Bellac, Piero Polettia, Filippo Trentinia, Patrizio Pezzottic, Silvio Brusaferroc, Giovanni Rezzac, Sergio Iavicolib, Marco Ajellid and Stefano Merler | After the national lockdown imposed on March 11, 2020, the Italian government has gradually resumed the suspended economic and social activities since May 4, while maintaining the closure of schools until September 14. We use a model of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission to estimate the health impact of different exit strategies. The strategy adopted in Italy kept the reproduction number Rt at values close to one until the end of September, with marginal regional differences. Based on the estimated postlockdown transmissibility, reopening of workplaces in selected industrial activities might have had a minor impact on the transmissibility. Reopening educational levels in May up to secondary schools might have influenced SARS-CoV-2 transmissibility only marginally; however, including high schools might have resulted in a marked increase of the disease burden. Earlier reopening would have resulted in disproportionately higher hospitalization incidence. Given community contacts in September, we project a large second wave associated with school reopening in the fall. | |
| Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK | 02/2021 | Louis du Plessis, John T. McCrone, Alexander E. Zarebski, Verity Hill, Christopher Ruis, Bernardo Gutierrez, Jayna Raghwani, Jordan Ashworth, Rachel Colquhoun, Thomas R. Connor, Nuno R. Faria, Ben Jackson, Nicholas J. Loman, Áine O’Toole, Samuel M. Nicholls, Kris V. Parag, Emily Scher, Tetyana I. Vasylyeva, ProfileErik M. Volz, Alexander Watts, ProfileIsaac I. Bogoch, Kamran Khan, the COVID-19 Genomics UK (COG-UK) Consortium, David M. Aanensen, Moritz U. G. Kraemer, Andrew Rambaut, Oliver G. Pybus | The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown were larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whilst lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control. |
