MOOD project is at the forefront of European research of infectious disease surveillance and modelling from a data science perspective, investigating the impact of global warming on disease outbreaks, and proposing innovations for building of One Health systems across Europe and the world.
In the table below all publications to which the MOOD project contributed are listed. Use the filter to select the most relevant articles.
Colosi, Elisabetta; Bassignana, Giulia; Barrat, Alain; Lina, Bruno; Vanhems, Philippe; Bielicki, Julia; Colizza, Vittoria
Minimizing school disruption under high incidence conditions due to the Omicron variant in France, Switzerland, Italy in January 2022 Journal Article
In: 2023.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Minimizing school disruption under high incidence conditions due to the Omicron variant in France, Switzerland, Italy in January 2022},
author = {Elisabetta Colosi and Giulia Bassignana and Alain Barrat and Bruno Lina and Philippe Vanhems and Julia Bielicki and Vittoria Colizza
},
url = {https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2023.28.5.2200192#abstract_content},
doi = {10.2807/1560-7917.ES.2023.28.5.2200192},
year = {2023},
date = {2023-02-02},
urldate = {2023-02-02},
abstract = {Background
As record cases of Omicron variant were registered in Europe in early 2022, schools remained a vulnerable setting undergoing large disruption.
Aim
Through mathematical modelling, we compared school protocols of reactive screening, regular screening, and reactive class closure implemented in France, in Baselland (Switzerland), and in Italy, respectively, and assessed them in terms of case prevention, testing resource demand, and schooldays lost.
Methods
We used a stochastic agent-based model of SARS-CoV-2 transmission in schools accounting for within- and across-class contacts from empirical contact data. We parameterised it to the Omicron BA.1 variant to reproduce the French Omicron wave in January 2022. We simulated the three protocols to assess their costs and effectiveness for varying peak incidence rates in the range experienced by European countries.
Results
We estimated that at the high incidence rates registered in France during the Omicron BA.1 wave in January 2022, the reactive screening protocol applied in France required higher test resources compared with the weekly screening applied in Baselland (0.50 vs 0.45 tests per student-week), but achieved considerably lower control (8% vs 21% reduction of peak incidence). The reactive class closure implemented in Italy was predicted to be very costly, leading to > 20% student-days lost.
Conclusions
At high incidence conditions, reactive screening protocols generate a large and unplanned demand in testing resources, for marginal control of school transmissions. Comparable or lower resources could be more efficiently used through weekly screening. Our findings can help define incidence levels triggering school protocols and optimise their cost-effectiveness.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
As record cases of Omicron variant were registered in Europe in early 2022, schools remained a vulnerable setting undergoing large disruption.
Aim
Through mathematical modelling, we compared school protocols of reactive screening, regular screening, and reactive class closure implemented in France, in Baselland (Switzerland), and in Italy, respectively, and assessed them in terms of case prevention, testing resource demand, and schooldays lost.
Methods
We used a stochastic agent-based model of SARS-CoV-2 transmission in schools accounting for within- and across-class contacts from empirical contact data. We parameterised it to the Omicron BA.1 variant to reproduce the French Omicron wave in January 2022. We simulated the three protocols to assess their costs and effectiveness for varying peak incidence rates in the range experienced by European countries.
Results
We estimated that at the high incidence rates registered in France during the Omicron BA.1 wave in January 2022, the reactive screening protocol applied in France required higher test resources compared with the weekly screening applied in Baselland (0.50 vs 0.45 tests per student-week), but achieved considerably lower control (8% vs 21% reduction of peak incidence). The reactive class closure implemented in Italy was predicted to be very costly, leading to > 20% student-days lost.
Conclusions
At high incidence conditions, reactive screening protocols generate a large and unplanned demand in testing resources, for marginal control of school transmissions. Comparable or lower resources could be more efficiently used through weekly screening. Our findings can help define incidence levels triggering school protocols and optimise their cost-effectiveness.
Mulchandani, Ranya; Wang, Yu; Gilbert, Marius; Boeckel, Thomas P Van
Global trends in antimicrobial use in food-producing animals: 2020 to 2030 Journal Article
In: PLOS Global Public Health, vol. 3, no. 2, pp. e0001305, 2023.
Abstract | Links | BibTeX | Tags: ASF (African Swine Fever), OpenDataSet
@article{nokey,
title = {Global trends in antimicrobial use in food-producing animals: 2020 to 2030},
author = {Ranya Mulchandani and Yu Wang and Marius Gilbert and Thomas P Van Boeckel},
editor = {Ismail Ayoade Odetokun, University of Ilorin, NIGERIA},
url = {https://journals.plos.org/globalpublichealth/article?id=10.1371/journal.pgph.0001305#abstract0},
doi = {10.1371/journal.pgph.0001305},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {PLOS Global Public Health},
volume = {3},
number = {2},
pages = {e0001305},
abstract = {Use of antimicrobials in farming has enabled the growth of intensive animal production and helped in meeting the global increase in demand for animal protein. However, the widespread use of veterinary antimicrobials drives antimicrobial resistance, with important consequences for animal health, and potentially human health. Global monitoring of antimicrobial use is essential: first, to track progress in reducing the reliance of farming on antimicrobials. Second, to identify countries where antimicrobial-stewardship efforts should be targeted to curb antimicrobial resistance. Data on usage of antimicrobials in food animals were collected from 42 countries. Multivariate regression models were used in combination with projections of animal counts for cattle, sheep, chicken, and pigs from the Food and Agriculture Organization to estimate global antimicrobial usage of veterinary antimicrobials in 2020 and 2030. Maps of animal densities were used to identify geographic hotspots of antimicrobial use. In each country, estimates of antimicrobial use (tonnes) were calibrated to match continental-level reports of antimicrobial use intensity (milligrams per kilogram of animal) from the World Organization for Animal Health, as well as country-level reports of antimicrobial use from countries that made this information publicly available. Globally, antimicrobial usage was estimated at 99,502 tonnes (95% CI 68,535–198,052) in 2020 and is projected, based on current trends, to increase by 8.0% to 107,472 tonnes (95% CI: 75,927–202,661) by 2030. Hotspots of antimicrobial use were overwhelmingly in Asia (67%), while <1% were in Africa. Findings indicate higher global antimicrobial usage in 2030 compared to prior projections that used data from 2017; this is likely associated with an upward revision of antimicrobial use in Asia/Oceania (~6,000 tonnes) and the Americas (~4,000 tonnes). National-level reporting of antimicrobial use should be encouraged to better evaluate the impact of national policies on antimicrobial use levels.},
keywords = {ASF (African Swine Fever), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Kyöttinen, Anniina
Vector-borne diseases stakeholder mapping in Finland - a one health approach Masters Thesis
Tampere University - Faculty of Social Sciences, 2023.
Abstract | Links | BibTeX | Tags:
@mastersthesis{nokey,
title = {Vector-borne diseases stakeholder mapping in Finland - a one health approach},
author = {Anniina Kyöttinen},
url = {https://mood-h2020.eu/wp-content/uploads/2023/04/VECTOR-BORNE-DISEASES-STAKEHOLDER-MAPPING-IN-FINLAND-a-one-health-approach-1.pdf},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
school = {Tampere University - Faculty of Social Sciences},
abstract = {Climate change, increasing human population, urbanization, industrialization and the gradual depletion of natural resources affects the health of humans, animals, and ecosystems around the globe. The complex and wicked health problems arising at the human-animal-ecosystem interphase, such as the (re)emergence, transmission, and management of both novel and traditional zoonoses and vector-born-diseases, requires enhanced multisectoral and multi-leveled interactions and collaboration between different One Health stakeholders.
Previous research in Finland around the topic of vector-borne diseases has primarily been focused on vector, host, and disease epidemiology: changes in disease occurrence and distribution of hosts and vectors, nationally. However very little attention has been given to stakeholder networks studies, information- and resource sharing, nor on how different VBD actors and stakeholders interact in Finland.
Thus, the aim of this master’s thesis is to map and analyze the current and missing stakeholder/actor interactions and information flow related to vector-borne diseases and their management in Finland, within a One Health context. In addition, the objective is also to discuss and reflect on the future of a possible formal VBD/One Health-network in Finland and what are the chances, challenges and means of establishing one. In conclusion, this research plays a pivotal role in addressing the growing issue of vector- borne diseases nationally and globally, in addition to enhancing VBD research, management, surveillance, control and prevention in Finland.
Qualitative semi-structured interviews were chosen as the primary methodology for this master’s thesis. More specifically, a qualitative research method, focusing on identifying actors, resources, multi-actor dynamics and multi-actor interactions (ARDI) was used to analyze the data. The qualitative data in this research consists of 10 semi-structured VBD/OH stakeholder interviews of Finnish professionals collected between October 2021 - December 2021.
The results of this study indicate the importance of multisectoral and multi-leveled
stakeholder collaboration related to vector-borne disease research, management, surveillance, control and prevention in Finland. In total 139 potential direct and indirect VBD and One Health stakeholders were identified in this research. Twenty (20) stakeholders, from varying fields were recognized as key VBD/OH actors in Finland. The results in this study suggest that VBD/OH stakeholders in Finland are to some extent interdisciplinary and multisectoral, but the biggest emphasis among different stakeholders still remains in human health, resulting in neglect of other fields of study, especially social sciences and humanities. Currently VBD/OH networks in Finland are mostly built upon unofficial personal connections relying heavily on a few Finnish individual key experts and research projects with external funding, resulting in uncertainty in the continuity of collaborations. There also seems to be a lack of higher-level coordination of VBD/OH collaboration activities in addition to the lack of collaboration between Finnish governmental agencies and other lower-level stakeholders, mainly due to lack of fiscal and human resources. The results of this research indicate that stakeholders’ collaboration with the private sector, independent agencies, NGOs, professional and scientific associations and other foundations in Finland is very limited. Furthermore, all ten interviewed stakeholders unanimously support the formation of a formal VBD/OH network in Finland to enhance stakeholder collaboration, information sharing and data management related to vector-borne diseases in Finland.
The findings of this research strongly suggest the establishment of a formal
multidisciplinary and multi-leveled OH vector-borne disease expert network in Finland with higher level coordination and sufficient fiscal and skilled human resources. However, further investigations are still needed to gain a deeper understanding of formal One Health networks in Europe, private actor engagement and public-private partnerships in strengthening VBD management, in addition to investigations on
(re)emerging vectors, vector-borne diseases and climate change in Finland.},
keywords = {},
pubstate = {published},
tppubtype = {mastersthesis}
}
Previous research in Finland around the topic of vector-borne diseases has primarily been focused on vector, host, and disease epidemiology: changes in disease occurrence and distribution of hosts and vectors, nationally. However very little attention has been given to stakeholder networks studies, information- and resource sharing, nor on how different VBD actors and stakeholders interact in Finland.
Thus, the aim of this master’s thesis is to map and analyze the current and missing stakeholder/actor interactions and information flow related to vector-borne diseases and their management in Finland, within a One Health context. In addition, the objective is also to discuss and reflect on the future of a possible formal VBD/One Health-network in Finland and what are the chances, challenges and means of establishing one. In conclusion, this research plays a pivotal role in addressing the growing issue of vector- borne diseases nationally and globally, in addition to enhancing VBD research, management, surveillance, control and prevention in Finland.
Qualitative semi-structured interviews were chosen as the primary methodology for this master’s thesis. More specifically, a qualitative research method, focusing on identifying actors, resources, multi-actor dynamics and multi-actor interactions (ARDI) was used to analyze the data. The qualitative data in this research consists of 10 semi-structured VBD/OH stakeholder interviews of Finnish professionals collected between October 2021 - December 2021.
The results of this study indicate the importance of multisectoral and multi-leveled
stakeholder collaboration related to vector-borne disease research, management, surveillance, control and prevention in Finland. In total 139 potential direct and indirect VBD and One Health stakeholders were identified in this research. Twenty (20) stakeholders, from varying fields were recognized as key VBD/OH actors in Finland. The results in this study suggest that VBD/OH stakeholders in Finland are to some extent interdisciplinary and multisectoral, but the biggest emphasis among different stakeholders still remains in human health, resulting in neglect of other fields of study, especially social sciences and humanities. Currently VBD/OH networks in Finland are mostly built upon unofficial personal connections relying heavily on a few Finnish individual key experts and research projects with external funding, resulting in uncertainty in the continuity of collaborations. There also seems to be a lack of higher-level coordination of VBD/OH collaboration activities in addition to the lack of collaboration between Finnish governmental agencies and other lower-level stakeholders, mainly due to lack of fiscal and human resources. The results of this research indicate that stakeholders’ collaboration with the private sector, independent agencies, NGOs, professional and scientific associations and other foundations in Finland is very limited. Furthermore, all ten interviewed stakeholders unanimously support the formation of a formal VBD/OH network in Finland to enhance stakeholder collaboration, information sharing and data management related to vector-borne diseases in Finland.
The findings of this research strongly suggest the establishment of a formal
multidisciplinary and multi-leveled OH vector-borne disease expert network in Finland with higher level coordination and sufficient fiscal and skilled human resources. However, further investigations are still needed to gain a deeper understanding of formal One Health networks in Europe, private actor engagement and public-private partnerships in strengthening VBD management, in addition to investigations on
(re)emerging vectors, vector-borne diseases and climate change in Finland.
Borm, Steven Van; Boseret1, Géraldine; Dellicour1, Simon; Steensels, Mieke; Roupie, Virginie; Vandenbussche, Frank; Mathijs, Elisabeth; Vilain, Aline; Driesen, Michèle; Dispas, Marc; Delcloo, Andy W.; Lemey, Philippe; Mertens, Ingeborg; Gilbert, Marius; Lambrecht, Bénédicte; van den Berg, Thierry
2023.
Abstract | Links | BibTeX | Tags: HPAI (Avian Influenza), OpenDataSet
@bachelorthesis{nokey,
title = {Combined Phylogeographic Analyses and Epidemiologic Contact Tracing to Characterize Atypically Pathogenic Avian Influenza (H3N1) Epidemic, Belgium, 2019},
author = {Steven Van Borm and Géraldine Boseret1 and Simon Dellicour1 and Mieke Steensels and Virginie Roupie and Frank Vandenbussche and Elisabeth Mathijs and Aline Vilain and Michèle Driesen and Marc Dispas and Andy W. Delcloo and Philippe Lemey and Ingeborg Mertens and Marius Gilbert and Bénédicte Lambrecht and Thierry van den Berg},
url = {https://wwwnc.cdc.gov/eid/article/29/2/22-0765_article},
doi = {10.3201/eid2902.220765},
year = {2023},
date = {2023-02-01},
urldate = {2023-02-01},
journal = {Center for Disease Control and Prevention},
volume = {19},
number = {2},
abstract = {The high economic impact and zoonotic potential of avian influenza call for detailed investigations of dispersal dynamics of epidemics. We integrated phylogeographic and epidemiologic analyses to investigate the dynamics of a low pathogenicity avian influenza (H3N1) epidemic that occurred in Belgium during 2019. Virus genomes from 104 clinical samples originating from 85% of affected farms were sequenced. A spatially explicit phylogeographic analysis confirmed a dominating northeast to southwest dispersal direction and a long-distance dispersal event linked to direct live animal transportation between farms. Spatiotemporal clustering, transport, and social contacts strongly correlated with the phylogeographic pattern of the epidemic. We detected only a limited association between wind direction and direction of viral lineage dispersal. Our results highlight the multifactorial nature of avian influenza epidemics and illustrate the use of genomic analyses of virus dispersal to complement epidemiologic and environmental data, improve knowledge of avian influenza epidemiologic dynamics, and enhance control strategies.},
keywords = {HPAI (Avian Influenza), OpenDataSet},
pubstate = {published},
tppubtype = {bachelorthesis}
}
Bonacina, Francesco; Boëlle, Pierre-Yves; Colizza, Vittoria; Lopez, Olivier; Thomas, Maud; Poletto, Chiara
Global patterns and drivers of influenza decline during the COVID-19 pandemic Journal Article
In: 2023.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), HPAI (Avian Influenza), OpenDataSet
@article{nokey,
title = {Global patterns and drivers of influenza decline during the COVID-19 pandemic},
author = {Francesco Bonacina and Pierre-Yves Boëlle and Vittoria Colizza and Olivier Lopez and Maud Thomas and Chiara Poletto
},
url = {https://www.ijidonline.com/article/S1201-9712(22)00682-8/fulltext},
doi = {10.1016/j.ijid.2022.12.042},
year = {2023},
date = {2023-01-03},
urldate = {2023-01-03},
abstract = {Objectives
The influenza circulation reportedly declined during the COVID-19 pandemic in many countries. The occurrence of this change has not been studied worldwide nor its potential drivers.
Methods
The change in the proportion of positive influenza samples reported by country and trimester was computed relative to the 2014-2019 period using the FluNet database. Random forests were used to determine predictors of change from demographical, weather, pandemic preparedness, COVID-19 incidence, and pandemic response characteristics. Regression trees were used to classify observations according to these predictors.
Results
During the COVID-19 pandemic, the influenza decline relative to prepandemic levels was global but heterogeneous across space and time. It was more than 50% for 311 of 376 trimesters-countries and even more than 99% for 135. COVID-19 incidence and pandemic preparedness were the two most important predictors of the decline. Europe and North America initially showed limited decline despite high COVID-19 restrictions; however, there was a strong decline afterward in most temperate countries, where pandemic preparedness, COVID-19 incidence, and social restrictions were high; the decline was limited in countries where these factors were low. The “zero-COVID” countries experienced the greatest decline.
Conclusion
Our findings set the stage for interpreting the resurgence of influenza worldwide.},
keywords = {Covid-19 (Coronavirus), HPAI (Avian Influenza), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
The influenza circulation reportedly declined during the COVID-19 pandemic in many countries. The occurrence of this change has not been studied worldwide nor its potential drivers.
Methods
The change in the proportion of positive influenza samples reported by country and trimester was computed relative to the 2014-2019 period using the FluNet database. Random forests were used to determine predictors of change from demographical, weather, pandemic preparedness, COVID-19 incidence, and pandemic response characteristics. Regression trees were used to classify observations according to these predictors.
Results
During the COVID-19 pandemic, the influenza decline relative to prepandemic levels was global but heterogeneous across space and time. It was more than 50% for 311 of 376 trimesters-countries and even more than 99% for 135. COVID-19 incidence and pandemic preparedness were the two most important predictors of the decline. Europe and North America initially showed limited decline despite high COVID-19 restrictions; however, there was a strong decline afterward in most temperate countries, where pandemic preparedness, COVID-19 incidence, and social restrictions were high; the decline was limited in countries where these factors were low. The “zero-COVID” countries experienced the greatest decline.
Conclusion
Our findings set the stage for interpreting the resurgence of influenza worldwide.
Valentin, Sarah; Arsevska, Elena; Mercier, Alizé; Falala, Sylvain; Rabatel, Julien; Lancelot, Renaud; Roche, Mathieu
PADI-web: An Event-Based Surveillance System for Detecting, Classifying and Processing Online News Conference
Human Language Technology. Challenges for Computer Science and Linguistics, vol. 12598, Springer International Publishing, 2022, ISBN: 978-3-030-66526-5.
Abstract | Links | BibTeX | Tags: ASF (African Swine Fever), HPAI (Avian Influenza), Text mining
@conference{@InProceedings{10.1007/978-3-030-66527-2_7,
title = {PADI-web: An Event-Based Surveillance System for Detecting, Classifying and Processing Online News},
author = {Sarah Valentin and Elena Arsevska and Alizé Mercier and Sylvain Falala and Julien Rabatel and Renaud Lancelot and Mathieu Roche},
editor = {Vetulani, Zygmunt and Paroubek, Patrick and Kubis, Marek},
url = {https://link.springer.com/chapter/10.1007/978-3-030-66527-2_7},
doi = {https://doi.org/10.1007/978-3-030-66527-2_7},
isbn = {978-3-030-66526-5},
year = {2022},
date = {2022-12-31},
urldate = {2022-12-31},
booktitle = {Human Language Technology. Challenges for Computer Science and Linguistics},
volume = {12598},
pages = {87-101},
publisher = {Springer International Publishing},
abstract = {The Platform for Automated Extraction of Animal Disease Information from the Web (PADI-web) is a multilingual text mining tool for automatic detection, classification, and extraction of disease outbreak information from online news articles. PADI-web currently monitors the Web for nine animal infectious diseases and eight syndromes in five animal hosts. The classification module is based on a supervised machine learning approach to filter the relevant news with an overall accuracy of 0.94. The classification of relevant news between 5 topic categories (confirmed, suspected or unknown outbreak, preparedness and impact) obtained an overall accuracy of 0.75. In the first six months of its implementation (January--June 2016), PADI-web detected 73{%} of the outbreaks of African swine fever; 20{%} of foot-and-mouth disease; 13{%} of bluetongue, and 62{%} of highly pathogenic avian influenza. The information extraction module of PADI-web obtained F-scores of 0.80 for locations, 0.85 for dates, 0.95 for diseases, 0.95 for hosts, and 0.85 for case numbers},
keywords = {ASF (African Swine Fever), HPAI (Avian Influenza), Text mining},
pubstate = {published},
tppubtype = {conference}
}
Mencattelli, Giulia; Silverj, Andrea; Iapaolo, Federica; Ippoliti, Carla; Teodori, Liana; Gennaro, Annapia Di; Curini, Valentina; Candeloro, Luca; Conte, Annamaria; Polci, Andrea; Morelli, Daniela; Perrotta, Maria Gabriella; Marini, Giovanni; Rosà, Roberto; Monaco, Federica; Segata, Nicola; Rizzoli, Annapaola; Rota-Stabelli, Omar; Savini, Giovanni; Group, West Nile Working
Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy Journal Article
In: Viruses, vol. 15, no. 35, 2022, ISSN: 1999-4915.
Abstract | Links | BibTeX | Tags: OpenDataSet, WNV (West Nile Virus)
@article{nokey,
title = {Epidemiological and Evolutionary Analysis of West Nile Virus Lineage 2 in Italy},
author = {Giulia Mencattelli and Andrea Silverj and Federica Iapaolo and Carla Ippoliti and Liana Teodori and Annapia Di Gennaro and Valentina Curini and Luca Candeloro and Annamaria Conte and Andrea Polci and Daniela Morelli and Maria Gabriella Perrotta and Giovanni Marini and Roberto Rosà and Federica Monaco and Nicola Segata and Annapaola Rizzoli and Omar Rota-Stabelli and Giovanni Savini and West Nile Working Group},
url = {https://www.mdpi.com/1999-4915/15/1/35},
doi = {10.3390/v15010035},
issn = {1999-4915},
year = {2022},
date = {2022-12-22},
urldate = {2022-12-22},
journal = {Viruses},
volume = {15},
number = {35},
abstract = {West Nile virus (WNV) is a mosquito-borne virus potentially causing serious illness in humans and other animals. Since 2004, several studies have highlighted the progressive spread of WNV Lineage 2 (L2) in Europe, with Italy being one of the countries with the highest number of cases of West Nile disease reported. In this paper, we give an overview of the epidemiological and genetic features characterising the spread and evolution of WNV L2 in Italy, leveraging data obtained from national surveillance activities between 2011 and 2021, including 46 newly assembled genomes that were analysed under both phylogeographic and phylodynamic frameworks. In addition, to better understand the seasonal patterns of the virus, we used a machine learning model predicting areas at high-risk of WNV spread. Our results show a progressive increase in WNV L2 in Italy, clarifying the dynamics of interregional circulation, with no significant introductions from other countries in recent years. Moreover, the predicting model identified the presence of suitable conditions for the 2022 earlier and wider spread of WNV in Italy, underlining the importance of using quantitative models for early warning detection of WNV outbreaks. Taken together, these findings can be used as a reference to develop new strategies to mitigate the impact of the pathogen on human and other animal health in endemic areas and new regions.},
keywords = {OpenDataSet, WNV (West Nile Virus)},
pubstate = {published},
tppubtype = {article}
}
Lai, Shengjie; Bogoch, Isaac; Ruktanonchai, Nick; Watts, Alexander; Lu, Xin; Yang, Weizhong; Yu, Hongjie; Khan, Kamran; Tatem, Andrew J
Assessing spread risk of COVID-19 in early 2020 Journal Article
In: vol. 5, iss. 4, 2022.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Assessing spread risk of COVID-19 in early 2020},
author = {Shengjie Lai and Isaac Bogoch and Nick Ruktanonchai and Alexander Watts and Xin Lu and Weizhong Yang and Hongjie Yu and Kamran Khan and Andrew J Tatem
},
url = {https://www.sciencedirect.com/science/article/pii/S2666764922000340?via%3Dihub},
doi = {10.1016/j.dsm.2022.08.004},
year = {2022},
date = {2022-12-08},
urldate = {2022-12-08},
volume = {5},
issue = {4},
abstract = {A novel coronavirus emerged in late 2019, named as the coronavirus disease 2019 (COVID-19) by the World Health Organization (WHO). This study was originally conducted in January 2020 to estimate the potential risk and geographic range of COVID-19 spread at the early stage of the transmission. A series of connectivity and risk analyses based on domestic and international travel networks were conducted using historical aggregated mobile phone data and air passenger itinerary data. We found that the cordon sanitaire of the primary city was likely to have occurred during the latter stages of peak population numbers leaving the city, with travellers departing into neighbouring cities and other megacities in China. We estimated that there were 59,912 international air passengers, of which 834 (95% uncertainty interval: 478–1,349) had COVID-19 infection, with a strong correlation seen between the predicted risks of importation and the number of imported cases found. Given the limited understanding of emerging infectious diseases in the very early stages of outbreaks, our approaches and findings in assessing travel patterns and risk of transmission can help guide public health preparedness and intervention design for new COVID-19 waves caused by variants of concern and future pandemics to effectively limit transmission beyond its initial extent.
},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Zardini, Agnese; Galli, Margherita; Tirani, Marcello; Cereda, Danilo; Manica, Mattia; Trentini, Filippo; Guzzetta, Giorgio; Marziano, Valentina; Piccarreta, Raffaella; Melegaro, Alessia; Ajelli, Marco; Poletti, Piero; Merler, Stefano
A quantitative assessment of epidemiological parameters required to investigate COVID-19 burden Journal Article
In: Epidemics, vol. 37, pp. 100530, 2022, ISSN: 1755-4365.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{nokey,
title = {A quantitative assessment of epidemiological parameters required to investigate COVID-19 burden},
author = {Agnese Zardini and Margherita Galli and Marcello Tirani and Danilo Cereda and Mattia Manica and Filippo Trentini and Giorgio Guzzetta and Valentina Marziano and Raffaella Piccarreta and Alessia Melegaro and Marco Ajelli and Piero Poletti and Stefano Merler},
url = {https://www.sciencedirect.com/science/article/pii/S1755436521000748},
doi = {10.1016/j.epidem.2021.100530},
issn = {1755-4365},
year = {2022},
date = {2022-12-01},
urldate = {2022-12-01},
journal = {Epidemics},
volume = {37},
pages = {100530},
abstract = {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 1965 SARS-CoV-2 positive individuals identified in Italy between March and April 2020 among contacts of confirmed cases. Infected contacts of cases were confirmed via RT-PCR tests as part of contact tracing activities or retrospectively via IgG serological tests and followed-up for symptoms and clinical outcomes. In addition, we provide estimates of time intervals between key events defining the clinical progression of cases as obtained from a larger sample, consisting of 95,371 infections ascertained between February and July 2020. We found that being older than 60 years of age was associated with a 39.9% (95%CI: 36.2–43.6%) likelihood of developing respiratory symptoms or fever ≥ 37.5 °C after SARS-CoV-2 infection; the 22.3% (95%CI: 19.3–25.6%) of the infections in this age group required hospital care and the 1% (95%CI: 0.4–2.1%) were admitted to an intensive care unit (ICU). The corresponding proportions in individuals younger than 60 years were estimated at 27.9% (95%CI: 25.4–30.4%), 8.8% (95%CI: 7.3–10.5%) and 0.4% (95%CI: 0.1–0.9%), respectively. The infection fatality ratio (IFR) ranged from 0.2% (95%CI: 0.0–0.6%) in individuals younger than 60 years to 12.3% (95%CI: 6.9–19.7%) for those aged 80 years or more; the case fatality ratio (CFR) in these two age classes was 0.6% (95%CI: 0.1–2%) and 19.2% (95%CI: 10.9–30.1%), respectively. The median length of stay in hospital was 10 (IQR: 3–21) days; the length of stay in ICU was 11 (IQR: 6–19) days. The obtained estimates provide insights into the epidemiology of COVID-19 and could be instrumental to refine mathematical modeling work supporting public health decisions.},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
Marini, Giovanni; Pugliese, Andrea; Wint, William; Alexander, Neil S.; Rizzoli, Annapaola; Rosà, Roberto
Modelling the West Nile virus force of infection in the European human population Journal Article
In: One Health, vol. 15, pp. 100462, 2022, ISSN: 2352-7714.
Abstract | Links | BibTeX | Tags: WNV (West Nile Virus)
@article{@article{MARINI2022100462,
title = {Modelling the West Nile virus force of infection in the European human population},
author = {Giovanni Marini and Andrea Pugliese and William Wint and Neil S. Alexander and Annapaola Rizzoli and Roberto Rosà},
url = {https://www.sciencedirect.com/science/article/pii/S2352771422000945},
doi = {https://doi.org/10.1016/j.onehlt.2022.100462},
issn = {2352-7714},
year = {2022},
date = {2022-12-01},
urldate = {2022-12-01},
journal = {One Health},
volume = {15},
pages = {100462},
abstract = {West Nile virus (WNV) is among the most recent emerging mosquito-borne pathogens in Europe where each year hundreds of human cases are recorded. We developed a relatively simple technique to model the WNV force of infection (FOI) in the human population to assess its dependence on environmental and human demographic factors. To this aim, we collated WNV human case-based data reported to the European Surveillance System from 15 European Countries during the period 2010–2021. We modelled the regional WNV FOI for each year through normal distributions and calibrated the constituent parameters, namely average (peak timing), variance and overall intensity, to observed cases. Finally, we investigated through regression models how these parameters are associated to a set of climatic, environmental and human demographic covariates. Our modelling approach shows good agreement between expected and observed epidemiological curves. We found that FOI magnitude is positively associated with spring temperature and larger in more anthropogenic semi-natural areas, while FOI peak timing is negatively related to summer temperature. Unsurprisingly, FOI is estimated to be greater in regions with a larger fraction of elderly people, who are more likely to contract severe infections. Our results confirm that temperature plays a key role in shaping WNV transmission in Europe and provide some interesting hints on how human presence and demography might affect WNV burden. This simple yet reliable approach could be easily adopted for early warning and to address epidemiological investigations of other vector-borne diseases, especially where eco-epidemiological data are scarce.},
keywords = {WNV (West Nile Virus)},
pubstate = {published},
tppubtype = {article}
}
Claudel, Iris; Brouazin, Ronan; Lancelot, Renaud; Gouagna, Louis-Clément; Dupraz, Marlène; Baldet, Thierry; Bouyer, Jérémy
Optimization of adult mosquito trap settings to monitor populations of Aedes and Culex mosquitoes, vectors of arboviruses in La Reunion Journal Article
In: Nature Communications, iss. 12, no. 19544, 2022.
Abstract | Links | BibTeX | Tags: OpenDataSet
@article{nokey,
title = {Optimization of adult mosquito trap settings to monitor populations of Aedes and Culex mosquitoes, vectors of arboviruses in La Reunion},
author = { Iris Claudel and Ronan Brouazin and Renaud Lancelot and Louis-Clément Gouagna and Marlène Dupraz and Thierry Baldet and Jérémy Bouyer},
url = {https://www.nature.com/articles/s41598-022-24191-9},
doi = {10.1038/s41598-022-24191-9},
year = {2022},
date = {2022-11-15},
urldate = {2022-11-15},
journal = {Nature Communications},
number = {19544},
issue = {12},
abstract = {Competent arbovirus vectors are found in the culicid mosquito fauna of south-west Indian Ocean (SWIO) islands. In La Reunion, Aedes albopictus and Aedes aegypti mosquitoes are known vectors of dengue and chikungunya viruses. Culex quinquefasciatus is a potential vector of Rift Valley fever and West Nile viruses. To prepare a vector-control field trial against Ae. aegypti, this study aimed at identifying the best trapping strategy to catch adult Ae. aegypti, using BG-Sentinel traps (Biogents, Germany). It was implemented in two sites in southern La Reunion. Catches of Ae. albopictus and Cx. quinquefasciatus mosquitoes were also recorded. A Latin square design was used to estimate the detection probability and the apparent daily density—according to the BG-Sentinel trapping strategy: none, carbon dioxide (CO2), a commercial attractant—BG-Lure (Biogents, Germany), or both. The use of CO2 alone was associated with a higher detection probability for Ae. aegypti and Cx. quinquefasciatus mosquitoes, as well as a large increase in their apparent density. Traps with BG-Lure—alone or in combination with CO2, did not improve the detection probability of Ae. aegypti and Cx. quinquefasciatus mosquitoes. The same result was found for male Ae. albopictus. For females, baiting BG-Sentinel traps with CO2 or BG-Lure had no significant effect. The same apparent densities were found for Ae. aegypti and Ae. albopictus mosquitoes in both study sites—where Ae. aegypti mosquitoes were found at very low densities during previous surveys.},
keywords = {OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Stefanelli, Paola; Trentini, Filippo; Petrone, Daniele; Mammone, Alessia; Ambrosio, Luigiana; Manica, Mattia; Guzzetta, Giorgio; d'Andrea, Valeria; Marziano, Valentina; Zardini, Agnese; Molina, Carla Grane; Ajelli, Marco; Martino, Angela Di; Riccardo, Flavia; Bella, Antonino; Schepisi, Monica Sane; Maraglino, Francesco; amd Anna Teresa Palamara, Piero Poletti; Brusaferro, Silvio; Rezza, Giovanni; Patrizio, Patrizio Pezzotti; Merler, Stefano; the Genomic SARS–CoV–2 National Surveillance Working Group, the Italian Integrated Surveillance of COVID–19 Study Group
Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 to January 2022 Journal Article
In: 2022.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{nokey,
title = {Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 to January 2022},
author = {Paola Stefanelli and Filippo Trentini and Daniele Petrone and Alessia Mammone and Luigiana Ambrosio and Mattia Manica and Giorgio Guzzetta and Valeria d'Andrea and Valentina Marziano and Agnese Zardini and Carla Grane Molina and Marco Ajelli and Angela Di Martino and Flavia Riccardo and Antonino Bella and Monica Sane Schepisi and Francesco Maraglino and Piero Poletti amd Anna Teresa Palamara and Silvio Brusaferro and Giovanni Rezza and Patrizio Pezzotti Patrizio and Stefano Merler and the Genomic SARS–CoV–2 National Surveillance Working Group, the Italian Integrated Surveillance of COVID–19 Study Group
},
url = {https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2022.27.45.2200125#html_fulltext},
doi = {10.2807/1560-7917.ES.2022.27.45.2200125},
year = {2022},
date = {2022-11-10},
urldate = {2022-11-10},
abstract = {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 December 2021 and January 2022. Combining genomic sequencing results with epidemiological records collated by the National Integrated Surveillance System, the Omicron reproductive number and exponential growth rate are estimated, as well as SARS-CoV-2 transmissibility.
Results
Omicron became dominant in Italy less than 1 month after its first detection, representing on 3 January 76.9–80.2% of notified SARS-CoV-2 infections, with a doubling time of 2.7–3.3 days. As of 17 January 2022, Delta variant represented < 6% of cases. During the Omicron expansion in December 2021, the estimated mean net reproduction numbers respectively rose from 1.15 to a maximum of 1.83 for symptomatic cases and from 1.14 to 1.36 for hospitalised cases, while remaining relatively stable, between 0.93 and 1.21, for cases needing intensive care. Despite a reduction in relative proportion, Delta infections increased in absolute terms throughout December contributing to an increase in hospitalisations. A significant reproduction numbers’ decline was found after mid-January, with average estimates dropping below 1 between 10 and 16 January 2022.
Conclusion
Estimates suggest a marked growth advantage of Omicron compared with Delta variant, but lower disease severity at population level possibly due to residual immunity against severe outcomes acquired from vaccination and prior infection.},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
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 December 2021 and January 2022. Combining genomic sequencing results with epidemiological records collated by the National Integrated Surveillance System, the Omicron reproductive number and exponential growth rate are estimated, as well as SARS-CoV-2 transmissibility.
Results
Omicron became dominant in Italy less than 1 month after its first detection, representing on 3 January 76.9–80.2% of notified SARS-CoV-2 infections, with a doubling time of 2.7–3.3 days. As of 17 January 2022, Delta variant represented < 6% of cases. During the Omicron expansion in December 2021, the estimated mean net reproduction numbers respectively rose from 1.15 to a maximum of 1.83 for symptomatic cases and from 1.14 to 1.36 for hospitalised cases, while remaining relatively stable, between 0.93 and 1.21, for cases needing intensive care. Despite a reduction in relative proportion, Delta infections increased in absolute terms throughout December contributing to an increase in hospitalisations. A significant reproduction numbers’ decline was found after mid-January, with average estimates dropping below 1 between 10 and 16 January 2022.
Conclusion
Estimates suggest a marked growth advantage of Omicron compared with Delta variant, but lower disease severity at population level possibly due to residual immunity against severe outcomes acquired from vaccination and prior infection.
Brouazin, Ronan; Claudel, Iris; Lancelot, Renaud; Dupuy, Guillaume; Gouagna, Louis-Clément; Dupraz, Marlène; Baldet, Theirry; Bouyer, Jérémy
Optimization of oviposition trap settings to monitor populations of Aedes mosquitoes, vectors of arboviruses in La Reunion Journal Article
In: Nature Communications, iss. Sci Rep 12, no. 18450, 2022.
Abstract | Links | BibTeX | Tags: OpenDataSet
@article{nokey,
title = {Optimization of oviposition trap settings to monitor populations of Aedes mosquitoes, vectors of arboviruses in La Reunion},
author = {Ronan Brouazin and Iris Claudel and Renaud Lancelot and Guillaume Dupuy and Louis-Clément Gouagna and Marlène Dupraz and Theirry Baldet and Jérémy Bouyer},
url = {https://www.nature.com/articles/s41598-022-23137-5#citeas},
doi = {10.1038/s41598-022-23137-5},
year = {2022},
date = {2022-11-02},
urldate = {2022-11-02},
journal = {Nature Communications},
number = {18450},
issue = {Sci Rep 12},
abstract = {Several dengue epidemics recently occurred in La Reunion, an island harboring two dengue viruses (DVs) vectors: Aedes albopictus, and Ae. aegypti, the former being the main local DV vector. Aedes aegypti shows a peculiar ecology, compared to other tropical populations of the same species. This study aimed to provide researchers and public-health users with locally validated oviposition traps (ovitraps) to monitor Aedes populations. A field experiment was performed in Saint-Joseph to assess the effect of different settings on the detection probability and apparent density of Aedes mosquitoes. Black plastic ovitraps were identified as the best choice. Vacoa trees (Pandanus utilis) were the only observed breeding sites for Ae. aegypti, shared with Ae. albopictus. They were the experimental units in a Latin square design with three factors: trap position in the trees (ground vs canopy), oviposition surface in the trap (blotting paper vs. vacoa leaf), and addition of organic matter to the trap water. The latter factor was found unimportant. On the ground, Ae. aegypti eggs were only found with vacoa leaves as the oviposition surface. Their detection and apparent density increased when ovitraps were located in the tree canopy. The main factor for Ae. albopictus was the oviposition surface, with a preference for blotting paper. In all trap settings, their detection was close to 100%. Larval survival was lower for a high egg density, combined with blotting paper as the oviposition surface. When monitoring mixed Aedes populations in La Reunion, we recommend using black plastic ovitraps, placed at 1.50-to-2.00-m high in vacoa trees, with vacoa leaves as the oviposition surface.},
keywords = {OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Arınık, Nejat; Interdonato, Roberto; Roche, Mathieu; Teissere, Maguelonne
Inferring the transmission dynamics of Avian Influenza from news and environmental data Conference
NetSci (Network Science Society) , 2022.
Links | BibTeX | Tags: HPAI (Avian Influenza)
@conference{nokey,
title = {Inferring the transmission dynamics of Avian Influenza from news and environmental data},
author = {Nejat Arınık and Roberto Interdonato and Mathieu Roche and Maguelonne Teissere},
url = {https://hal.science/hal-03936660/document},
year = {2022},
date = {2022-11-01},
urldate = {2022-11-01},
booktitle = {NetSci (Network Science Society) },
keywords = {HPAI (Avian Influenza)},
pubstate = {published},
tppubtype = {conference}
}
Monteiro, Joao; Martins, Bruno; Costa, Miguel; Pires, Joao
A Co-Training Approach for Spatial Data Disaggregation Conference
no. 91, SIGSPATIAL '22 Association for Computing Machinery, New York, NY, USA, 2022, ISBN: 9781450395298.
Abstract | Links | BibTeX | Tags:
@conference{nokey,
title = {A Co-Training Approach for Spatial Data Disaggregation},
author = {Joao Monteiro and Bruno Martins and Miguel Costa and Joao Pires},
url = {https://doi.org/10.1145/3557915.3561475},
doi = {10.1145/3557915.3561475},
isbn = {9781450395298},
year = {2022},
date = {2022-11-01},
urldate = {2022-11-01},
number = {91},
pages = {1-10},
publisher = {Association for Computing Machinery},
address = {New York, NY, USA},
series = {SIGSPATIAL '22},
abstract = {Socio-demographic information is usually only accessible at relatively coarse spatial resolutions. However, its availability at thinner granularities is of substantial interest for several stakeholders, since it enhances the formulation of informed hypotheses on the distribution of population indicators. Spatial disaggregation methods aim to compute these fine-grained estimates, often using regression algorithms that employ ancillary data to re-distribute the aggregated information. However, since disaggregation tasks are ill-posed, and given that examples of disaggregated data at the target geospatial resolution are seldom available, model training is particularly challenging. We propose to address this problem through a self-supervision framework that iteratively refines initial estimates from seminal disaggregation heuristics. Specifically, we propose to co-train two different models, using the results from one model to train/refine the other. By doing so, we are able to explore complementary views from the data. We assessed the use of co-training with a fast regressor based on random forests that takes individual raster cells as input, together with a more expressive model, based on a fully-convolutional neural network, that takes raster patches as input. We also compared co-training against the use of self-training with a single model. In experiments involving the disaggregation of a socio-demographic variable collected for Continental Portugal, the results show that our co-training approach outperforms alternative disaggregation approaches, including methods based on self-training or co-training with two similar fully-convolutional models. Co-training is effective at exploring the characteristics of both regression algorithms, leading to a consistent improvement in different types of error metrics.},
keywords = {},
pubstate = {published},
tppubtype = {conference}
}
Valentin, Sarah; Arsevska, Elena; al.,
Elaboration of a new framework for fine-grained epidemiological annotation Journal Article
In: 2022.
Abstract | Links | BibTeX | Tags: OpenDataSet, Text mining
@article{nokey,
title = {Elaboration of a new framework for fine-grained epidemiological annotation},
author = {Sarah Valentin and Elena Arsevska and al.
},
url = {https://www.nature.com/articles/s41597-022-01743-2},
doi = {10.1038/s41597-022-01743-2},
year = {2022},
date = {2022-10-26},
urldate = {2022-10-26},
abstract = {Event-based surveillance (EBS) gathers information from a variety of data sources, including online news articles. Unlike the data from formal reporting, the EBS data are not structured, and their interpretation can overwhelm epidemic intelligence (EI) capacities in terms of available human resources. Therefore, diverse EBS systems that automatically process (all or part of) the acquired nonstructured data from online news articles have been developed. These EBS systems (e.g., GPHIN, HealthMap, MedISys, ProMED, PADI-web) can use annotated data to improve the surveillance systems. This paper describes a framework for the annotation of epidemiological information in animal disease-related news articles. We provide annotation guidelines that are generic and applicable to both animal and zoonotic infectious diseases, regardless of the pathogen involved or its mode 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 date of the news article.
},
keywords = {OpenDataSet, Text mining},
pubstate = {published},
tppubtype = {article}
}
Cuypers, Lize; Dellicour, Simon; Hong, Samuel L.; l. Potter, Barney; Verhasselt, Bruno; Vereecke, Nick; Lambrechts, Laurens; Durkin, Keith; Bours, Vincent; Klamer, Sofieke; Bayon-Vicente, Guillaume; Vael, Carl; Ariën, Kevin K.; Mendonca, Ricardo De; Soetens, Oriane; Michel, Charlotte; Bearzatto, Bertrand; Naesens, Reinout; Gras, Jeremie; Vankeerberghen, Anne; Matheeussen, Veerle; Martens, Geert; Obbels, Dagmar; Lemmens, Ann; den Poel, Bea Van; Even, Ellen Van; Rauw, Klara De; Waumans, Luc; Reynders, Marijke; Degosserie, Jonathan; Maes, Piet; André, Emmanuel; Baele, Guy
In: Viruses, vol. 14, no. 10, pp. 2301, 2022, ISSN: 1999-4915.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{@article{2022b,
title = {Two Years of Genomic Surveillance in Belgium during the SARS-CoV-2 Pandemic to Attain Country-Wide Coverage and Monitor the Introduction and Spread of Emerging Variants},
author = {Lize Cuypers and Simon Dellicour and Samuel L. Hong and Barney l. Potter and Bruno Verhasselt and Nick Vereecke and Laurens Lambrechts and Keith Durkin and Vincent Bours and Sofieke Klamer and Guillaume Bayon-Vicente and Carl Vael and Kevin K. Ariën and Ricardo De Mendonca and Oriane Soetens and Charlotte Michel and Bertrand Bearzatto and Reinout Naesens and Jeremie Gras and Anne Vankeerberghen and Veerle Matheeussen and Geert Martens and Dagmar Obbels and Ann Lemmens and Bea Van den Poel and Ellen Van Even and Klara De Rauw and Luc Waumans and Marijke Reynders and Jonathan Degosserie and Piet Maes and Emmanuel André and Guy Baele},
url = {https://www.mdpi.com/1999-4915/14/10/2301},
doi = {https://doi.org/10.3390/v14102301},
issn = {1999-4915},
year = {2022},
date = {2022-10-20},
urldate = {2022-10-20},
journal = {Viruses},
volume = {14},
number = {10},
pages = {2301},
abstract = {An adequate SARS-CoV-2 genomic surveillance strategy has proven to be essential for countries to obtain a thorough understanding of the variants and lineages being imported and successfully established within their borders. During 2020, genomic surveillance in Belgium was not structurally implemented but performed by individual research laboratories that had to acquire the necessary funds themselves to perform this important task. At the start of 2021, a nationwide genomic surveillance consortium was established in Belgium to markedly increase the country’s genomic sequencing efforts (both in terms of intensity and representativeness), to perform quality control among participating laboratories, and to enable coordination and collaboration of research projects and publications. We here discuss the genomic surveillance efforts in Belgium before and after the establishment of its genomic sequencing consortium, provide an overview of the specifics of the consortium, and explore more details regarding the scientific studies that have been published as a result of the increased number of Belgian SARS-CoV-2 genomes that have become available.},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
Gonçalves, Bronner P; Hall, Matthew; Jassat, Waasila; Balan, Valeria; Murthy, Srinivas; Kartsonaki, Christiana; Semple, Malcolm G; Rojek, Amanda; Baruch, Joaquín; Reyes, Luis Felipe; Dasgupta, Abhishek; Dunning, Jake; Citarella, Barbara Wanjiru; Pritchard, Mark; Martín-Quiros, Alejandro; Baillie, Uluhan SiliJ Kenneth; Aryal, Diptesh; Arabi, Yaseen; Rashan, Aasiyah; Nor, Andrea AnghebenJanice CaoiliFrançois Martin CarrierEwen M HarrisonJoan Gómez-JunyentClaudia Figueiredo-MelloJames Joshua DouglasMohd Basri Mat; Chow, Yock Ping; Wong, Xin Ci; Bertagnolio, Silvia; Thwin, Soe Soe; Streinu-Cercel, Anca; Salazar, Leonardo; Rishu, Asgar; Rangappa, Rajavardhan; Ong, David SY; Hashmi, Madiha; Carson, Gail; Diaz, Janet; Fowler, Rob; Kraemer, Moritz UG; Wils, Evert-Jan; Horby, Peter; Merson, Laura; Olliaro, Piero L; Group, ISARIC Clinical Characterisation
In: elife, 2022.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients},
author = {Bronner P Gonçalves and Matthew Hall and Waasila Jassat and Valeria Balan and Srinivas Murthy and Christiana Kartsonaki and Malcolm G Semple and Amanda Rojek and Joaquín Baruch and Luis Felipe Reyes and Abhishek Dasgupta and Jake Dunning and Barbara Wanjiru Citarella and Mark Pritchard and Alejandro Martín-Quiros and Uluhan SiliJ Kenneth Baillie and Diptesh Aryal and Yaseen Arabi and Aasiyah Rashan and Andrea AnghebenJanice CaoiliFrançois Martin CarrierEwen M HarrisonJoan Gómez-JunyentClaudia Figueiredo-MelloJames Joshua DouglasMohd Basri Mat Nor and Yock Ping Chow and Xin Ci Wong and Silvia Bertagnolio and Soe Soe Thwin and Anca Streinu-Cercel and Leonardo Salazar and Asgar Rishu and Rajavardhan Rangappa and David SY Ong and Madiha Hashmi and Gail Carson and Janet Diaz and Rob Fowler and Moritz UG Kraemer and Evert-Jan Wils and Peter Horby and Laura Merson and Piero L Olliaro and ISARIC Clinical Characterisation Group},
url = {https://elifesciences.org/articles/80556},
doi = {https://doi.org/10.7554/eLife.80556},
year = {2022},
date = {2022-10-05},
urldate = {2022-10-05},
journal = {elife},
abstract = {Background:
Whilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings.
Methods:
Here, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries.
Results:
Our analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61–0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population.
Conclusions:
Although clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Whilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings.
Methods:
Here, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries.
Results:
Our analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61–0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population.
Conclusions:
Although clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome.
Klitting, Raphaëlle; Kafetzopoulou, Liana E.; Thiery, Wim; Dudas, Gytis; Gryseels, Sophie; Kotamarthi, Anjali; Gangavarapu, Bram Vranckenand Karthik; Momoh, Mambu; Sandi, John Demby; Goba, Augustine; Alhasan, Foday; Grant, Donald S.; Okogbenin, Sylvanus; Ogbaini-Emovo, Ephraim; Garry, Robert F.; Smither, Allison R.; Zeller, Mark; Pauthner, Matthias G.; McGraw, Michelle; Hughes, Laura D.; Duraffour, Sophie; Günther, Stephan; Suchard, Marc A.; Lemey, Philippe; Andersen, Kristian G.; Dellicour, Simon
Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades Journal Article
In: Nature Communications, vol. 13, no. 5596, 2022.
Abstract | Links | BibTeX | Tags: OpenDataSet
@article{nokey,
title = {Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades},
author = {Raphaëlle Klitting and Liana E. Kafetzopoulou and Wim Thiery and Gytis Dudas and Sophie Gryseels and Anjali Kotamarthi and Bram Vranckenand Karthik Gangavarapu and Mambu Momoh and John Demby Sandi and Augustine Goba and Foday Alhasan and Donald S. Grant and Sylvanus Okogbenin and Ephraim Ogbaini-Emovo and Robert F. Garry and Allison R. Smither and Mark Zeller and Matthias G. Pauthner and Michelle McGraw and Laura D. Hughes and Sophie Duraffour and Stephan Günther and Marc A. Suchard and Philippe Lemey and Kristian G. Andersen and Simon Dellicour},
url = {https://www.nature.com/articles/s41467-022-33112-3#citeas},
doi = {https://doi.org/10.1038/s41467-022-33112-3},
year = {2022},
date = {2022-09-27},
urldate = {2022-09-27},
journal = {Nature Communications},
volume = {13},
number = {5596},
abstract = {Lassa fever is a severe viral hemorrhagic fever caused by a zoonotic virus that repeatedly spills over to humans from its rodent reservoirs. It is currently not known how climate and land use changes could affect the endemic area of this virus, currently limited to parts of West Africa. By exploring the environmental data associated with virus occurrence using ecological niche modelling, we show how temperature, precipitation and the presence of pastures determine ecological suitability for virus circulation. Based on projections of climate, land use, and population changes, we find that regions in Central and East Africa will likely become suitable for Lassa virus over the next decades and estimate that the total population living in ecological conditions that are suitable for Lassa virus circulation may drastically increase by 2070. By analysing geotagged viral genomes using spatially-explicit phylogeography and simulating virus dispersal, we find that in the event of Lassa virus being introduced into a new suitable region, its spread might remain spatially limited over the first decades.},
keywords = {OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Zeller, Mark; Gangavarapu, Karthik; Anderson, Catelyn; Smither, Allison R.; Vanchiere, John A.; Rose, Rebecca; Snyder, Daniel J.; Dudas, Gytis; Watts, Alexander; Matteson, Nathaniel L.; Robles-Sikisaka, Refugio; Marshall, Maximilian; Feehan, Amy K.; Sabino-Santos, Gilberto; Bell-Kareem, Antoinette R.; Hughes, Laura D.; Alkuzweny, Manar; Snarski, Patricia; Garcia-Diaz, Julia; Scott, Rona S.; Melnik, Lilia I.; Klitting, Raphaëlle; McGraw, Michelle; Belda-Ferre, Pedro; DeHoff, Peter; Sathe, Shashank; Marotz, Clarisse; Grubaugh, Nathan D.; Nolan, David J.; Drouin, Arnaud C.; Genemaras, Kaylynn J.; Chao, Karissa; Topol, Sarah; Spencer, Emily; Nicholson, Laura; Aigner, Stefan; Yeo, Gene W.; Farnaes, Lauge; Hobbs, Charlotte A.; Laurent, Louise C.; Knight, Rob; Hodcroft, Emma B.; Khan, Kamran; Fusco, Dahlene N.; Cooper, Vaughn S.; Lemey, Phillipe; Gardner, Lauren; Lamers, Susanna L.; Kamil, Jeremy P.; Garry, Robert F.; Suchard, Marc A.; Andersen, Kristian G.
Emergence of an early SARS-CoV-2 epidemic in the United States Journal Article
In: Cell, vol. 184, iss. 19, pp. 4939-4952.e15, 2022, ISSN: 0092-8674.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Emergence of an early SARS-CoV-2 epidemic in the United States},
author = {Mark Zeller and Karthik Gangavarapu and Catelyn Anderson and Allison R. Smither and John A. Vanchiere and Rebecca Rose and Daniel J. Snyder and Gytis Dudas and Alexander Watts and Nathaniel L. Matteson and Refugio Robles-Sikisaka and Maximilian Marshall and Amy K. Feehan and Gilberto Sabino-Santos and Antoinette R. Bell-Kareem and Laura D. Hughes and Manar Alkuzweny and Patricia Snarski and Julia Garcia-Diaz and Rona S. Scott and Lilia I. Melnik and Raphaëlle Klitting and Michelle McGraw and Pedro Belda-Ferre and Peter DeHoff and Shashank Sathe and Clarisse Marotz and Nathan D. Grubaugh and David J. Nolan and Arnaud C. Drouin and Kaylynn J. Genemaras and Karissa Chao and Sarah Topol and Emily Spencer and Laura Nicholson and Stefan Aigner and Gene W. Yeo and Lauge Farnaes and Charlotte A. Hobbs and Louise C. Laurent and Rob Knight and Emma B. Hodcroft and Kamran Khan and Dahlene N. Fusco and Vaughn S. Cooper and Phillipe Lemey and Lauren Gardner and Susanna L. Lamers and Jeremy P. Kamil and Robert F. Garry and Marc A. Suchard and Kristian G. Andersen},
url = {https://www.sciencedirect.com/science/article/pii/S0092867421008898},
doi = {10.1016/j.cell.2021.07.030},
issn = {0092-8674},
year = {2022},
date = {2022-09-16},
urldate = {2022-09-16},
journal = {Cell},
volume = {184},
issue = {19},
pages = {4939-4952.e15},
abstract = {The emergence of the COVID-19 epidemic in the United States (U.S.) went largely undetected due to inadequate testing. New Orleans experienced one of the earliest and fastest accelerating outbreaks, coinciding with Mardi Gras. To gain insight into the emergence of SARS-CoV-2 in the U.S. and how large-scale events accelerate transmission, we sequenced SARS-CoV-2 genomes during the first wave of the COVID-19 epidemic in Louisiana. We show that SARS-CoV-2 in Louisiana had limited diversity compared to other U.S. states and that one introduction of SARS-CoV-2 led to almost all of the early transmission in Louisiana. By analyzing mobility and genomic data, we show that SARS-CoV-2 was already present in New Orleans before Mardi Gras, and the festival dramatically accelerated transmission. Our study provides an understanding of how superspreading during large-scale events played a key role during the early outbreak in the U.S. and can greatly accelerate epidemics.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}