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.
101.
Agoti, Charles N; Ochola-Oyier, Lynette Isabella; Dellicour, Simon; Mohammed, Khadija Said; Lambisia, Arnold W; de Laurent, Zaydah R; Morobe, John M; Mburu, Maureen W; Omuoyo, Donwilliams O; Ongera, Edidah M; Ndwiga, Leonard; Maitha, Eric; Kitole, Benson; Suleiman, Thani; Mwakinangu, Mohamed; Nyambu, John K; Otieno, John; Salim, Barke; Musyoki, Jennifer; Murunga, Nickson; Otieno, Edward; Kiiru, John N; Kasera, Kadondi; Amoth, Patrick; Mwangangi, Mercy; Aman, Rashid; Kinyanjui, Samson; Warimwe, George; Phan, My; Agweyu, Ambrose; Cotten, Matthew; Barasa, Edwine; Tsofa, Benjamin; Nokes, D James; Philip, Philip Bejon; Githinji, George
Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study Journal Article
In: eLife, vol. 11, pp. e71703, 2022, ISSN: 2050-084X.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{@article{10.7554/eLife.71703,
title = {Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study},
author = {Charles N Agoti and Lynette Isabella Ochola-Oyier and Simon Dellicour and Khadija Said Mohammed and Arnold W Lambisia and Zaydah R de Laurent and John M Morobe and Maureen W Mburu and Donwilliams O Omuoyo and Edidah M Ongera and Leonard Ndwiga and Eric Maitha and Benson Kitole and Thani Suleiman and Mohamed Mwakinangu and John K Nyambu and John Otieno and Barke Salim and Jennifer Musyoki and Nickson Murunga and Edward Otieno and John N Kiiru and Kadondi Kasera and Patrick Amoth and Mercy Mwangangi and Rashid Aman and Samson Kinyanjui and George Warimwe and My Phan and Ambrose Agweyu and Matthew Cotten and Edwine Barasa and Benjamin Tsofa and D James Nokes and Philip Bejon Philip and George Githinji},
editor = {Grabowski, Mary Kate and van der Meer, Jos W},},
url = {https://doi.org/10.7554/eLife.71703},
doi = {10.7554/eLife.71703},
issn = {2050-084X},
year = {2022},
date = {2022-06-14},
urldate = {2022-06-14},
journal = {eLife},
volume = {11},
pages = {e71703},
abstract = {Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic. textbf{Methods:} Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction, and virus dispersal between counties was estimated using discrete phylogeographic analysis. textbf{Results:} During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; 9 of which occurred in both waves and 4 seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1, and N.8). Most of the sequenced infections belonged to lineage B.1 (n = 723, 63%), which predominated in both Wave 1 (73%, followed by lineages N.8 [6%] and B.1.1 [6%]) and Wave 2 (56%, followed by lineages B.1.549 [21%] and B.1.530 [5%]). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many Coronavirus Disease 2019 (COVID-19) government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity. textbf{Conclusions:} Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission. textbf{Funding:} This work was funded by The Wellcome (grant numbers: 220985, 203077/Z/16/Z, 220977/Z/20/Z, and 222574/Z/21/Z) and the National Institute for Health and Care Research (NIHR), project references: 17/63/and 16/136/33 using UK Aid from the UK government to support global health research, The UK Foreign, Commonwealth and Development Office. The views expressed in this publication are those of the author(s) and not necessarily those of the funding agencies.},},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic. textbf{Methods:} Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties of Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, and Lamu) to infer virus introductions and local transmission patterns during the first two waves of infections. Virus importations were inferred using ancestral state reconstruction, and virus dispersal between counties was estimated using discrete phylogeographic analysis. textbf{Results:} During Wave 1, 23 distinct Pango lineages were detected across the six counties, while during Wave 2, 29 lineages were detected; 9 of which occurred in both waves and 4 seemed to be Kenya specific (B.1.530, B.1.549, B.1.596.1, and N.8). Most of the sequenced infections belonged to lineage B.1 (n = 723, 63%), which predominated in both Wave 1 (73%, followed by lineages N.8 [6%] and B.1.1 [6%]) and Wave 2 (56%, followed by lineages B.1.549 [21%] and B.1.530 [5%]). Over the study period, we estimated 280 SARS-CoV-2 virus importations into Coastal Kenya. Mombasa City, a vital tourist and commercial centre for the region, was a major route for virus imports, most of which occurred during Wave 1, when many Coronavirus Disease 2019 (COVID-19) government restrictions were still in force. In Wave 2, inter-county transmission predominated, resulting in the emergence of local transmission chains and diversity. textbf{Conclusions:} Our analysis supports moving COVID-19 control strategies in the region from a focus on international travel to strategies that will reduce local transmission. textbf{Funding:} This work was funded by The Wellcome (grant numbers: 220985, 203077/Z/16/Z, 220977/Z/20/Z, and 222574/Z/21/Z) and the National Institute for Health and Care Research (NIHR), project references: 17/63/and 16/136/33 using UK Aid from the UK government to support global health research, The UK Foreign, Commonwealth and Development Office. The views expressed in this publication are those of the author(s) and not necessarily those of the funding agencies.},
102.
Moussaoui, Majdouline El; Maes, Nathalie; Hong, Samuel L.; Lambert, Nicolas; Gofflot, Stéphanie; Dellot, Patricia; Belhadj, Yasmine; Huynen, Pascale; Hayette, Marie-Pierre; Meex, Cécile; Bontems, Sébastien; Defêche, Justine; Godderis, Lode; Molenberghs, Geert; Meuris, Christelle; Artesi, Maria; Durkin, Keith; Rahmouni, Souad; Grégoire, Céline; Beguin, Yves; Moutschen, Michel; Dellicour, Simon; Darcis, Gilles
Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium Journal Article
In: MDPI, 2022.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{nokey,
title = {Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium},
author = {Majdouline El Moussaoui and Nathalie Maes and Samuel L. Hong and Nicolas Lambert and Stéphanie Gofflot and Patricia Dellot and Yasmine Belhadj and Pascale Huynen and Marie-Pierre Hayette and Cécile Meex and Sébastien Bontems and Justine Defêche and Lode Godderis and Geert Molenberghs and Christelle Meuris and Maria Artesi and Keith Durkin and Souad Rahmouni and Céline Grégoire and Yves Beguin and Michel Moutschen and Simon Dellicour and Gilles Darcis },
url = {https://www.mdpi.com/1999-4915/14/6/1302},
doi = {10.3390/v14061302 },
year = {2022},
date = {2022-06-09},
urldate = {2022-06-09},
journal = {MDPI},
abstract = {first_pagesettingsOrder Article Reprints
Open AccessArticle
Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium
by Majdouline El Moussaoui 1,*ORCID,Nathalie Maes 2ORCID,Samuel L. Hong 3ORCID,Nicolas Lambert 4,Stéphanie Gofflot 5,Patricia Dellot 1,Yasmine Belhadj 1ORCID,Pascale Huynen 6,Marie-Pierre Hayette 6ORCID,Cécile Meex 6,Sébastien Bontems 6,Justine Defêche 6,Lode Godderis 7ORCID,Geert Molenberghs 8,Christelle Meuris 1,Maria Artesi 9,Keith Durkin 9,Souad Rahmouni 10,Céline Grégoire 11,Yves Beguin 11ORCID,Michel Moutschen 1,Simon Dellicour 3,12ORCID andGilles Darcis 1ORCIDremove Hide full author list
1
Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 4000 Liege, Belgium
2
Department of Biostatistics and Medico-Economic Information, University Hospital of Liège, 4000 Liege, Belgium
3
Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
4
Department of Neurology, University Hospital of Liège, 4000 Liege, Belgium
5
Department of Biothèque Hospitalo-Universitaire de Liège (BHUL), University Hospital of Liège, 4000 Liege, Belgium
6
Department of Clinical Microbiology, University Hospital of Liège, 4000 Liege, Belgium
7
Centre for Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
8
Institute for Biostatistics and Statistical Bioinformatics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
9
Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4000 Liege, Belgium
10
Laboratory of Animal Genomics, GIGA-Medical Genomics, GIGA-Institute, University of Liège, 4000 Liege, Belgium
add Show full affiliation list
*
Author to whom correspondence should be addressed.
Viruses 2022, 14(6), 1302; https://doi.org/10.3390/v14061302
Submission received: 16 April 2022 / Revised: 3 June 2022 / Accepted: 9 June 2022 / Published: 14 June 2022
(This article belongs to the Special Issue SARS-CoV-2 Research in Belgium)
Downloadkeyboard_arrow_down Browse Figures Review Reports Versions Notes
Abstract
Healthcare workers (HCWs) are known to be at higher risk of developing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections although whether these risks are equal across all occupational roles is uncertain. Identifying these risk factors and understand SARS-CoV-2 transmission pathways in healthcare settings are of high importance to achieve optimal protection measures. We aimed to investigate the implementation of a voluntary screening program for SARS-CoV-2 infections among hospital HCWs and to elucidate potential transmission pathways though phylogenetic analysis before the vaccination era. HCWs of the University Hospital of Liège, Belgium, were invited to participate in voluntary reverse transcriptase-polymerase chain reaction (RT-PCR) assays performed every week from April to December 2020. Phylogenetic analysis of SARS-CoV-2 genomes were performed for a subgroup of 45 HCWs. 5095 samples were collected from 703 HCWs. 212 test results were positive, 15 were indeterminate, and 4868 returned negative. 156 HCWs (22.2%) tested positive at least once during the study period. All SARS-CoV-2 test results returned negative for 547 HCWs (77.8%). Nurses (p < 0.05), paramedics (p < 0.05), and laboratory staff handling respiratory samples (p < 0.01) were at higher risk for being infected compared to the control non-patient facing group. Our phylogenetic analysis revealed that most positive samples corresponded to independent introduction events into the hospital. Our findings add to the growing evidence of differential risks of being infected among HCWs and support the need to implement appropriate protection measures based on each individual’s risk profile to guarantee the protection of both HCWs and patients. Furthermore, our phylogenetic investigations highlight that most positive samples correspond to distinct introduction events into the hospital.},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
first_pagesettingsOrder Article Reprints
Open AccessArticle
Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium
by Majdouline El Moussaoui 1,*ORCID,Nathalie Maes 2ORCID,Samuel L. Hong 3ORCID,Nicolas Lambert 4,Stéphanie Gofflot 5,Patricia Dellot 1,Yasmine Belhadj 1ORCID,Pascale Huynen 6,Marie-Pierre Hayette 6ORCID,Cécile Meex 6,Sébastien Bontems 6,Justine Defêche 6,Lode Godderis 7ORCID,Geert Molenberghs 8,Christelle Meuris 1,Maria Artesi 9,Keith Durkin 9,Souad Rahmouni 10,Céline Grégoire 11,Yves Beguin 11ORCID,Michel Moutschen 1,Simon Dellicour 3,12ORCID andGilles Darcis 1ORCIDremove Hide full author list
1
Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 4000 Liege, Belgium
2
Department of Biostatistics and Medico-Economic Information, University Hospital of Liège, 4000 Liege, Belgium
3
Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
4
Department of Neurology, University Hospital of Liège, 4000 Liege, Belgium
5
Department of Biothèque Hospitalo-Universitaire de Liège (BHUL), University Hospital of Liège, 4000 Liege, Belgium
6
Department of Clinical Microbiology, University Hospital of Liège, 4000 Liege, Belgium
7
Centre for Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
8
Institute for Biostatistics and Statistical Bioinformatics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
9
Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4000 Liege, Belgium
10
Laboratory of Animal Genomics, GIGA-Medical Genomics, GIGA-Institute, University of Liège, 4000 Liege, Belgium
add Show full affiliation list
*
Author to whom correspondence should be addressed.
Viruses 2022, 14(6), 1302; https://doi.org/10.3390/v14061302
Submission received: 16 April 2022 / Revised: 3 June 2022 / Accepted: 9 June 2022 / Published: 14 June 2022
(This article belongs to the Special Issue SARS-CoV-2 Research in Belgium)
Downloadkeyboard_arrow_down Browse Figures Review Reports Versions Notes
Abstract
Healthcare workers (HCWs) are known to be at higher risk of developing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections although whether these risks are equal across all occupational roles is uncertain. Identifying these risk factors and understand SARS-CoV-2 transmission pathways in healthcare settings are of high importance to achieve optimal protection measures. We aimed to investigate the implementation of a voluntary screening program for SARS-CoV-2 infections among hospital HCWs and to elucidate potential transmission pathways though phylogenetic analysis before the vaccination era. HCWs of the University Hospital of Liège, Belgium, were invited to participate in voluntary reverse transcriptase-polymerase chain reaction (RT-PCR) assays performed every week from April to December 2020. Phylogenetic analysis of SARS-CoV-2 genomes were performed for a subgroup of 45 HCWs. 5095 samples were collected from 703 HCWs. 212 test results were positive, 15 were indeterminate, and 4868 returned negative. 156 HCWs (22.2%) tested positive at least once during the study period. All SARS-CoV-2 test results returned negative for 547 HCWs (77.8%). Nurses (p < 0.05), paramedics (p < 0.05), and laboratory staff handling respiratory samples (p < 0.01) were at higher risk for being infected compared to the control non-patient facing group. Our phylogenetic analysis revealed that most positive samples corresponded to independent introduction events into the hospital. Our findings add to the growing evidence of differential risks of being infected among HCWs and support the need to implement appropriate protection measures based on each individual’s risk profile to guarantee the protection of both HCWs and patients. Furthermore, our phylogenetic investigations highlight that most positive samples correspond to distinct introduction events into the hospital.
Open AccessArticle
Evaluation of Screening Program and Phylogenetic Analysis of SARS-CoV-2 Infections among Hospital Healthcare Workers in Liège, Belgium
by Majdouline El Moussaoui 1,*ORCID,Nathalie Maes 2ORCID,Samuel L. Hong 3ORCID,Nicolas Lambert 4,Stéphanie Gofflot 5,Patricia Dellot 1,Yasmine Belhadj 1ORCID,Pascale Huynen 6,Marie-Pierre Hayette 6ORCID,Cécile Meex 6,Sébastien Bontems 6,Justine Defêche 6,Lode Godderis 7ORCID,Geert Molenberghs 8,Christelle Meuris 1,Maria Artesi 9,Keith Durkin 9,Souad Rahmouni 10,Céline Grégoire 11,Yves Beguin 11ORCID,Michel Moutschen 1,Simon Dellicour 3,12ORCID andGilles Darcis 1ORCIDremove Hide full author list
1
Department of Infectious Diseases and General Internal Medicine, University Hospital of Liège, 4000 Liege, Belgium
2
Department of Biostatistics and Medico-Economic Information, University Hospital of Liège, 4000 Liege, Belgium
3
Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
4
Department of Neurology, University Hospital of Liège, 4000 Liege, Belgium
5
Department of Biothèque Hospitalo-Universitaire de Liège (BHUL), University Hospital of Liège, 4000 Liege, Belgium
6
Department of Clinical Microbiology, University Hospital of Liège, 4000 Liege, Belgium
7
Centre for Environment and Health, Department of Public Health and Primary Care, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
8
Institute for Biostatistics and Statistical Bioinformatics, Katholieke Universiteit Leuven, 3000 Leuven, Belgium
9
Laboratory of Human Genetics, GIGA-Institute, University of Liège, 4000 Liege, Belgium
10
Laboratory of Animal Genomics, GIGA-Medical Genomics, GIGA-Institute, University of Liège, 4000 Liege, Belgium
add Show full affiliation list
*
Author to whom correspondence should be addressed.
Viruses 2022, 14(6), 1302; https://doi.org/10.3390/v14061302
Submission received: 16 April 2022 / Revised: 3 June 2022 / Accepted: 9 June 2022 / Published: 14 June 2022
(This article belongs to the Special Issue SARS-CoV-2 Research in Belgium)
Downloadkeyboard_arrow_down Browse Figures Review Reports Versions Notes
Abstract
Healthcare workers (HCWs) are known to be at higher risk of developing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections although whether these risks are equal across all occupational roles is uncertain. Identifying these risk factors and understand SARS-CoV-2 transmission pathways in healthcare settings are of high importance to achieve optimal protection measures. We aimed to investigate the implementation of a voluntary screening program for SARS-CoV-2 infections among hospital HCWs and to elucidate potential transmission pathways though phylogenetic analysis before the vaccination era. HCWs of the University Hospital of Liège, Belgium, were invited to participate in voluntary reverse transcriptase-polymerase chain reaction (RT-PCR) assays performed every week from April to December 2020. Phylogenetic analysis of SARS-CoV-2 genomes were performed for a subgroup of 45 HCWs. 5095 samples were collected from 703 HCWs. 212 test results were positive, 15 were indeterminate, and 4868 returned negative. 156 HCWs (22.2%) tested positive at least once during the study period. All SARS-CoV-2 test results returned negative for 547 HCWs (77.8%). Nurses (p < 0.05), paramedics (p < 0.05), and laboratory staff handling respiratory samples (p < 0.01) were at higher risk for being infected compared to the control non-patient facing group. Our phylogenetic analysis revealed that most positive samples corresponded to independent introduction events into the hospital. Our findings add to the growing evidence of differential risks of being infected among HCWs and support the need to implement appropriate protection measures based on each individual’s risk profile to guarantee the protection of both HCWs and patients. Furthermore, our phylogenetic investigations highlight that most positive samples correspond to distinct introduction events into the hospital.
103.
Ge, Yong; Zhang, Wen-Bin; Wu, Xilin; amd Haiyan Liu, Corrine W Ruktanonchai; amd Yongze Song, Jianghao Wang; Liu, Mengxiao; Yan, Wei; Yang, Juan; amd Sarchil H Qader amd Fatumah Atuhaire, Eimear Cleary; amd Andrew J Tatem amd Shengjie Lai, Nick W Ruktanonchai
Untangling the changing impact of non-pharmaceutical interventions and vaccination on European COVID-19 trajectories Journal Article
In: Nature Commun, vol. 13, no. 3106, 2022.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Untangling the changing impact of non-pharmaceutical interventions and vaccination on European COVID-19 trajectories},
author = {Yong Ge and Wen-Bin Zhang and Xilin Wu and Corrine W Ruktanonchai amd Haiyan Liu and Jianghao Wang amd Yongze Song and Mengxiao Liu and Wei Yan and Juan Yang and Eimear Cleary amd Sarchil H Qader amd Fatumah Atuhaire and Nick W Ruktanonchai amd Andrew J Tatem amd Shengjie Lai},
url = {https://www.nature.com/articles/s41467-022-30897-1#citeas},
doi = {10.1038/s41467-022-30897-1},
year = {2022},
date = {2022-06-03},
urldate = {2022-06-03},
journal = {Nature Commun},
volume = {13},
number = {3106},
abstract = {Non-pharmaceutical interventions (NPIs) and vaccination are two fundamental approaches for mitigating the coronavirus disease 2019 (COVID-19) pandemic. However, the real-world impact of NPIs versus vaccination, or a combination of both, on COVID-19 remains uncertain. To address this, we built a Bayesian inference model to assess the changing effect of NPIs and vaccination on reducing COVID-19 transmission, based on a large-scale dataset including epidemiological parameters, virus variants, vaccines, and climate factors in Europe from August 2020 to October 2021. We found that (1) the combined effect of NPIs and vaccination resulted in a 53% (95% confidence interval: 42–62%) reduction in reproduction number by October 2021, whereas NPIs and vaccination reduced the transmission by 35% and 38%, respectively; (2) compared with vaccination, the change of NPI effect was less sensitive to emerging variants; (3) the relative effect of NPIs declined 12% from May 2021 due to a lower stringency and the introduction of vaccination strategies. Our results demonstrate that NPIs were complementary to vaccination in an effort to reduce COVID-19 transmission, and the relaxation of NPIs might depend on vaccination rates, control targets, and vaccine effectiveness concerning extant and emerging variants.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Non-pharmaceutical interventions (NPIs) and vaccination are two fundamental approaches for mitigating the coronavirus disease 2019 (COVID-19) pandemic. However, the real-world impact of NPIs versus vaccination, or a combination of both, on COVID-19 remains uncertain. To address this, we built a Bayesian inference model to assess the changing effect of NPIs and vaccination on reducing COVID-19 transmission, based on a large-scale dataset including epidemiological parameters, virus variants, vaccines, and climate factors in Europe from August 2020 to October 2021. We found that (1) the combined effect of NPIs and vaccination resulted in a 53% (95% confidence interval: 42–62%) reduction in reproduction number by October 2021, whereas NPIs and vaccination reduced the transmission by 35% and 38%, respectively; (2) compared with vaccination, the change of NPI effect was less sensitive to emerging variants; (3) the relative effect of NPIs declined 12% from May 2021 due to a lower stringency and the introduction of vaccination strategies. Our results demonstrate that NPIs were complementary to vaccination in an effort to reduce COVID-19 transmission, and the relaxation of NPIs might depend on vaccination rates, control targets, and vaccine effectiveness concerning extant and emerging variants.
104.
Giesen, Christine; Herrador, Zaida; Fernandez-Martinez, Beatriz; Figuerola, Jordi; Gangoso, Laura; Vazquez, Ana; Gómez-Barroso, Diana
A systematic review of environmental factors related to WNV circulation in European and Mediterranean countries Journal Article
In: One Health, vol. 16, pp. 100478, 2022, ISSN: 2352-7714.
Abstract | Links | BibTeX | Tags: WNV (West Nile Virus)
@article{nokey,
title = {A systematic review of environmental factors related to WNV circulation in European and Mediterranean countries},
author = {Christine Giesen and Zaida Herrador and Beatriz Fernandez-Martinez and Jordi Figuerola and Laura Gangoso and Ana Vazquez and Diana Gómez-Barroso},
url = {https://www.sciencedirect.com/science/article/pii/S2352771422001100},
doi = {10.1016/j.onehlt.2022.100478},
issn = {2352-7714},
year = {2022},
date = {2022-06-01},
journal = {One Health},
volume = {16},
pages = {100478},
abstract = {Introduction/objective
West Nile virus (WNV) is one of the most widely distributed flaviviruses worldwide. It is considered an endemic and emerging pathogen in different areas of the Europe and Mediterranean countries (MR). Mosquitoes of the genus Culex spp. are the main vectors, and birds its main vertebrate hosts. It can occasionally infect mammals, including humans. Different environmental factors can influence its distribution and transmission through its effects on vector or host populations. Our objective was to determine environmental factors associated with changes in vector distribution and WNV transmission in Europe and MR.
Material & methods
Systematic peer review of articles published between 2000 and 2020. We selected studies on WNV, and its vectors carried out in Europe and MR. The search included terms referring to climatic and environmental factors.
Results
We included 65 studies, of which 21 (32%) were conducted in Italy. Culex spp. was studied in 26 papers (40%), humans in 19 papers (29%) and host animals (mainly horses) in 16 papers (25%), whereas bird reservoirs were addressed in 5 studies (8%). A significant positive relationship was observed between changes in temperature and precipitation patterns and the epidemiology of WNV, although contrasting results were found among studies. Other factors positively related to WNV dynamics were the normalized difference vegetation index (NDVI] and expansion of anthropized habitats.
Conclusion
The epidemiology of WNV seems to be related to climatic factors that are changing globally due to ongoing climate change. Unfortunately, the complete zoonotic cycle was not analyzed in most papers, making it difficult to determine the independent impact of environment on the different components of the transmission cycle. Given the current expansion and endemicity of WNV in the area, it is important to adopt holistic approaches to understand WNV epidemiology and to improve WNV surveillance and control.},
keywords = {WNV (West Nile Virus)},
pubstate = {published},
tppubtype = {article}
}
Introduction/objective
West Nile virus (WNV) is one of the most widely distributed flaviviruses worldwide. It is considered an endemic and emerging pathogen in different areas of the Europe and Mediterranean countries (MR). Mosquitoes of the genus Culex spp. are the main vectors, and birds its main vertebrate hosts. It can occasionally infect mammals, including humans. Different environmental factors can influence its distribution and transmission through its effects on vector or host populations. Our objective was to determine environmental factors associated with changes in vector distribution and WNV transmission in Europe and MR.
Material & methods
Systematic peer review of articles published between 2000 and 2020. We selected studies on WNV, and its vectors carried out in Europe and MR. The search included terms referring to climatic and environmental factors.
Results
We included 65 studies, of which 21 (32%) were conducted in Italy. Culex spp. was studied in 26 papers (40%), humans in 19 papers (29%) and host animals (mainly horses) in 16 papers (25%), whereas bird reservoirs were addressed in 5 studies (8%). A significant positive relationship was observed between changes in temperature and precipitation patterns and the epidemiology of WNV, although contrasting results were found among studies. Other factors positively related to WNV dynamics were the normalized difference vegetation index (NDVI] and expansion of anthropized habitats.
Conclusion
The epidemiology of WNV seems to be related to climatic factors that are changing globally due to ongoing climate change. Unfortunately, the complete zoonotic cycle was not analyzed in most papers, making it difficult to determine the independent impact of environment on the different components of the transmission cycle. Given the current expansion and endemicity of WNV in the area, it is important to adopt holistic approaches to understand WNV epidemiology and to improve WNV surveillance and control.
West Nile virus (WNV) is one of the most widely distributed flaviviruses worldwide. It is considered an endemic and emerging pathogen in different areas of the Europe and Mediterranean countries (MR). Mosquitoes of the genus Culex spp. are the main vectors, and birds its main vertebrate hosts. It can occasionally infect mammals, including humans. Different environmental factors can influence its distribution and transmission through its effects on vector or host populations. Our objective was to determine environmental factors associated with changes in vector distribution and WNV transmission in Europe and MR.
Material & methods
Systematic peer review of articles published between 2000 and 2020. We selected studies on WNV, and its vectors carried out in Europe and MR. The search included terms referring to climatic and environmental factors.
Results
We included 65 studies, of which 21 (32%) were conducted in Italy. Culex spp. was studied in 26 papers (40%), humans in 19 papers (29%) and host animals (mainly horses) in 16 papers (25%), whereas bird reservoirs were addressed in 5 studies (8%). A significant positive relationship was observed between changes in temperature and precipitation patterns and the epidemiology of WNV, although contrasting results were found among studies. Other factors positively related to WNV dynamics were the normalized difference vegetation index (NDVI] and expansion of anthropized habitats.
Conclusion
The epidemiology of WNV seems to be related to climatic factors that are changing globally due to ongoing climate change. Unfortunately, the complete zoonotic cycle was not analyzed in most papers, making it difficult to determine the independent impact of environment on the different components of the transmission cycle. Given the current expansion and endemicity of WNV in the area, it is important to adopt holistic approaches to understand WNV epidemiology and to improve WNV surveillance and control.
105.
Dellicour, Simon; Lemey, Philippe; Suchard, Marc A; Gilbert, Marius; Baele, Guy
Accommodating sampling location uncertainty in continuous phylogeography Journal Article
In: Virus Evolution, vol. 8, iss. 1, no. 1, 2022, ISSN: 2057-1577.
Abstract | Links | BibTeX | Tags:
@article{@article{10.1093/ve/veac041,
title = {Accommodating sampling location uncertainty in continuous phylogeography},
author = {Simon Dellicour and Philippe Lemey and Marc A Suchard and Marius Gilbert and Guy Baele},
url = {https://academic.oup.com/ve/article/8/1/veac041/6588218},
doi = {10.1093/ve/veac041},
issn = {2057-1577},
year = {2022},
date = {2022-05-18},
urldate = {2022-05-18},
journal = {Virus Evolution},
volume = {8},
number = {1},
issue = {1},
abstract = {Phylogeographic inference of the dispersal history of viral lineages offers key opportunities to tackle epidemiological questions about the spread of fast-evolving pathogens across human, animal and plant populations. In continuous space, i.e. when locations are specified by longitude and latitude, these reconstructions are however often limited by the availability or accessibility of precise sampling locations required for such spatially explicit analyses. We here review the different approaches that can be considered when genomic sequences are associated with a geographic area of sampling instead of precise coordinates. In particular, we describe and compare the approaches to define homogeneous and heterogeneous prior ranges of sampling coordinates.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Phylogeographic inference of the dispersal history of viral lineages offers key opportunities to tackle epidemiological questions about the spread of fast-evolving pathogens across human, animal and plant populations. In continuous space, i.e. when locations are specified by longitude and latitude, these reconstructions are however often limited by the availability or accessibility of precise sampling locations required for such spatially explicit analyses. We here review the different approaches that can be considered when genomic sequences are associated with a geographic area of sampling instead of precise coordinates. In particular, we describe and compare the approaches to define homogeneous and heterogeneous prior ranges of sampling coordinates.
106.
Wongnak, Phrutsamon; Bord, Séverine; Jacquot, Maude; Agoulon, Albert; Beugnet, Frédéric; Bournez, Laure; Cèbe, Nicolas; Chevalier, Adélie; Cosson, Jean-François; Dambrine, Naïma; Hoch, Thierry; Huard, Frédéric; Korboulewsky, Nathalie; Lebert, Isabelle; Madouasse, Aurélien; Mårell, Anders; Moutailler, Sara; Plantard, Olivier; Pollet, Thomas; Poux, Valérie; René-Martellet, Magalie; Vayssier-Taussat, Muriel; Verheyden, Hélène; Vourc’h, Gwenaël; Chalvet-Monfray, Karine
Meteorological and climatic variables predict the phenology of Ixodes ricinus nymph activity in France, accounting for habitat heterogeneity. Journal Article
In: Nature Scientific Reports, vol. 7833, iss. 12, 2022.
Abstract | Links | BibTeX | Tags: OpenDataSet
@article{nokey,
title = { Meteorological and climatic variables predict the phenology of Ixodes ricinus nymph activity in France, accounting for habitat heterogeneity.},
author = {Phrutsamon Wongnak and Séverine Bord and Maude Jacquot and Albert Agoulon and Frédéric Beugnet and Laure Bournez and Nicolas Cèbe and Adélie Chevalier and Jean-François Cosson and Naïma Dambrine and Thierry Hoch and Frédéric Huard and Nathalie Korboulewsky and Isabelle Lebert and Aurélien Madouasse and Anders Mårell and Sara Moutailler and Olivier Plantard and Thomas Pollet and Valérie Poux and Magalie René-Martellet and Muriel Vayssier-Taussat and Hélène Verheyden and Gwenaël Vourc’h and Karine Chalvet-Monfray},
url = {https://www.nature.com/articles/s41598-022-11479-z},
doi = {https://doi.org/10.1038/s41598-022-11479-z},
year = {2022},
date = {2022-05-12},
urldate = {2022-05-12},
journal = {Nature Scientific Reports},
volume = {7833},
issue = {12},
abstract = {Ixodes ricinus ticks (Acari: Ixodidae) are the most important vector for Lyme borreliosis in Europe. As climate change might affect their distributions and activities, this study aimed to determine the effects of environmental factors, i.e., meteorological, bioclimatic, and habitat characteristics on host-seeking (questing) activity of I. ricinus nymphs, an important stage in disease transmissions, across diverse climatic types in France over 8 years. Questing activity was observed using a repeated removal sampling with a cloth-dragging technique in 11 sampling sites from 7 tick observatories from 2014 to 2021 at approximately 1-month intervals, involving 631 sampling campaigns. Three phenological patterns were observed, potentially following a climatic gradient. The mixed-effects negative binomial regression revealed that observed nymph counts were driven by different interval-average meteorological variables, including 1-month moving average temperature, previous 3-to-6-month moving average temperature, and 6-month moving average minimum relative humidity. The interaction effects indicated that the phenology in colder climates peaked differently from that of warmer climates. Also, land cover characteristics that support the highest baseline abundance were moderate forest fragmentation with transition borders with agricultural areas. Finally, our model could potentially be used to predict seasonal human-tick exposure risks in France that could contribute to mitigating Lyme borreliosis risk.},
keywords = {OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Ixodes ricinus ticks (Acari: Ixodidae) are the most important vector for Lyme borreliosis in Europe. As climate change might affect their distributions and activities, this study aimed to determine the effects of environmental factors, i.e., meteorological, bioclimatic, and habitat characteristics on host-seeking (questing) activity of I. ricinus nymphs, an important stage in disease transmissions, across diverse climatic types in France over 8 years. Questing activity was observed using a repeated removal sampling with a cloth-dragging technique in 11 sampling sites from 7 tick observatories from 2014 to 2021 at approximately 1-month intervals, involving 631 sampling campaigns. Three phenological patterns were observed, potentially following a climatic gradient. The mixed-effects negative binomial regression revealed that observed nymph counts were driven by different interval-average meteorological variables, including 1-month moving average temperature, previous 3-to-6-month moving average temperature, and 6-month moving average minimum relative humidity. The interaction effects indicated that the phenology in colder climates peaked differently from that of warmer climates. Also, land cover characteristics that support the highest baseline abundance were moderate forest fragmentation with transition borders with agricultural areas. Finally, our model could potentially be used to predict seasonal human-tick exposure risks in France that could contribute to mitigating Lyme borreliosis risk.
107.
Syed, Mehtab Alam; Arsevska, Elena; Roche, Mathieu; Teisseire, Maguelonne
A Data-Driven Score Model to Assess Online News Articles in Event-Based Surveillance System Conference
Information Management and Big Data, vol. 1577, Springer International Publishing, 2022.
Abstract | BibTeX | Tags: Text mining
@conference{@InProceedings{10.1007/978-3-031-04447-2_18,
title = {A Data-Driven Score Model to Assess Online News Articles in Event-Based Surveillance System},
author = {Mehtab Alam Syed and Elena Arsevska and Mathieu Roche and Maguelonne Teisseire},
editor = {Juan Antonio Lossio-Ventura, Eduardo Díaz, Carlos Gavidia-Calderon, Alan Demétrius Baria Valejo, Hugo Alatrista-Salas
},
year = {2022},
date = {2022-04-20},
urldate = {2022-04-20},
booktitle = {Information Management and Big Data},
volume = {1577},
pages = {264-280},
publisher = {Springer International Publishing},
abstract = {Online news sources are popular resources for learning about current health situations and developing event-based surveillance (EBS) systems. However, having access to diverse information originating from multiple sources can misinform stakeholders, eventually leading to false health risks. The existing literature contains several techniques for performing data quality evaluation to minimize the effects of misleading information. However, these methods only rely on the extraction of spatiotemporal information for representing health events. To address this research gap, a score-based technique is proposed to quantify the data quality of online news articles through three assessment measures: 1) news article metadata, 2) content analysis, and 3) epidemiological entity extraction with NLP to weight the contextual information. The results are calculated using classification metrics with two evaluation approaches: 1) a strict approach and 2) a flexible approach. The obtained results show significant enhancement in the data quality by filtering irrelevant news, which can potentially reduce false alert generation in EBS systems.},
keywords = {Text mining},
pubstate = {published},
tppubtype = {conference}
}
Online news sources are popular resources for learning about current health situations and developing event-based surveillance (EBS) systems. However, having access to diverse information originating from multiple sources can misinform stakeholders, eventually leading to false health risks. The existing literature contains several techniques for performing data quality evaluation to minimize the effects of misleading information. However, these methods only rely on the extraction of spatiotemporal information for representing health events. To address this research gap, a score-based technique is proposed to quantify the data quality of online news articles through three assessment measures: 1) news article metadata, 2) content analysis, and 3) epidemiological entity extraction with NLP to weight the contextual information. The results are calculated using classification metrics with two evaluation approaches: 1) a strict approach and 2) a flexible approach. The obtained results show significant enhancement in the data quality by filtering irrelevant news, which can potentially reduce false alert generation in EBS systems.
108.
Colosi, Elisabetta; Bassignana, Giulia; Contreras, Diego Andrés; Poirier, Canelle; Boëlle, Pierre-Yves; Cauchemez, Simon; Yazdanpanah, Yazdan; Lina, Bruno; Fontanet, Arnaud; Barrat, Alain; others,
Screening and vaccination against COVID-19 to minimise school closure: a modelling study Journal Article
In: The Lancet Infectious Diseases, vol. 2, iss. 7, pp. Pages 977-989, 2022.
Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{@article{colosi2022screening,,
title = {Screening and vaccination against COVID-19 to minimise school closure: a modelling study},
author = {Elisabetta Colosi and Giulia Bassignana and Diego Andrés Contreras and Canelle Poirier and Pierre-Yves Boëlle and Simon Cauchemez and Yazdan Yazdanpanah and Bruno Lina and Arnaud Fontanet and Alain Barrat and others},
url = {https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(22)00138-4/fulltext},
doi = {https://doi.org/10.1016/S1473-3099(22)00138-4},
year = {2022},
date = {2022-04-01},
urldate = {2022-04-01},
journal = {The Lancet Infectious Diseases},
volume = {2},
issue = {7},
pages = {Pages 977-989},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
109.
Colosi, Elisabetta; Bassignana, Giulia; Barrat, Alain; Colizza, Vittoria
Modelling COVID-19 in school settings to evaluate prevention and control protocols Journal Article
In: Anaesthesia Critical Care & Pain Medicine, vol. 41, no. 2, pp. 101047, 2022, ISSN: 2352-5568.
Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{@article{COLOSI2022101047,
title = {Modelling COVID-19 in school settings to evaluate prevention and control protocols},
author = {Elisabetta Colosi and Giulia Bassignana and Alain Barrat and Vittoria Colizza},
url = {https://www.sciencedirect.com/science/article/pii/S2352556822000285},
doi = {https://doi.org/10.1016/j.accpm.2022.101047},
issn = {2352-5568},
year = {2022},
date = {2022-04-01},
urldate = {2022-04-01},
journal = {Anaesthesia Critical Care & Pain Medicine},
volume = {41},
number = {2},
pages = {101047},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
110.
Valentin, Sarah; Lancelot, Renaud; Roche, Mathieu
Fusion of spatiotemporal and thematic features of textual data for animal disease surveillance Journal Article
In: Information Processing in Agriculture, 2022, ISSN: 2214-3173.
Abstract | Links | BibTeX | Tags: Text mining
@article{@article{VALENTIN2022,
title = {Fusion of spatiotemporal and thematic features of textual data for animal disease surveillance},
author = {Sarah Valentin and Renaud Lancelot and Mathieu Roche},
url = {https://www.sciencedirect.com/science/article/pii/S2214317322000312},
doi = {https://doi.org/10.1016/j.inpa.2022.03.004},
issn = {2214-3173},
year = {2022},
date = {2022-03-28},
journal = {Information Processing in Agriculture},
abstract = {Several internet-based surveillance systems have been created to monitor the web for animal health surveillance. These systems collect a large amount of news dealing with outbreaks related to animal diseases. Automatically identifying news articles that describe the same outbreak event is a key step to quickly detect relevant epidemiological information while alleviating manual curation of news content. This paper addresses the task of retrieving news articles that are related in epidemiological terms. We tackle this issue using text mining and feature fusion methods. The main objective of this paper is to identify a textual representation in which two articles that share the same epidemiological content are close. We compared two types of representations (i.e., features) to represent the documents: (i) morphosyntactic features (i.e., selection and transformation of all terms from the news, based on classical textual processing steps) and (ii) lexicosemantic features (i.e., selection, transformation and fusion of epidemiological terms including diseases, hosts, locations and dates). We compared two types of term weighing (i.e., Boolean and TF-IDF) for both representations. To combine and transform lexicosemantic features, we compared two data fusion techniques (i.e., early fusion and late fusion) and the effect of features generalisation, while evaluating the relative importance of each type of feature. We conducted our analysis using a corpus composed of a subset of news articles in English related to animal disease outbreaks. Our results showed that the combination of relevant lexicosemantic (epidemiological) features using fusion methods improves classical morphosyntactic representation in the context of disease-related news retrieval. The lexicosemantic representation based on TF-IDF and feature generalisation (F-measure = 0.92, r-precision = 0.58) outperformed the morphosyntactic representation (F-measure = 0.89, r-precision = 0.45), while reducing the features space. Converting the features into lower granular features (i.e., generalisation) contributed to improving the results of the lexicosemantic representation. Our results showed no difference between the early and late fusion approaches. Temporal features performed poorly on their own. Conversely, spatial features were the most discriminative features, highlighting the need for robust methods for spatial entity extraction, disambiguation and representation in internet-based surveillance systems.},
keywords = {Text mining},
pubstate = {published},
tppubtype = {article}
}
Several internet-based surveillance systems have been created to monitor the web for animal health surveillance. These systems collect a large amount of news dealing with outbreaks related to animal diseases. Automatically identifying news articles that describe the same outbreak event is a key step to quickly detect relevant epidemiological information while alleviating manual curation of news content. This paper addresses the task of retrieving news articles that are related in epidemiological terms. We tackle this issue using text mining and feature fusion methods. The main objective of this paper is to identify a textual representation in which two articles that share the same epidemiological content are close. We compared two types of representations (i.e., features) to represent the documents: (i) morphosyntactic features (i.e., selection and transformation of all terms from the news, based on classical textual processing steps) and (ii) lexicosemantic features (i.e., selection, transformation and fusion of epidemiological terms including diseases, hosts, locations and dates). We compared two types of term weighing (i.e., Boolean and TF-IDF) for both representations. To combine and transform lexicosemantic features, we compared two data fusion techniques (i.e., early fusion and late fusion) and the effect of features generalisation, while evaluating the relative importance of each type of feature. We conducted our analysis using a corpus composed of a subset of news articles in English related to animal disease outbreaks. Our results showed that the combination of relevant lexicosemantic (epidemiological) features using fusion methods improves classical morphosyntactic representation in the context of disease-related news retrieval. The lexicosemantic representation based on TF-IDF and feature generalisation (F-measure = 0.92, r-precision = 0.58) outperformed the morphosyntactic representation (F-measure = 0.89, r-precision = 0.45), while reducing the features space. Converting the features into lower granular features (i.e., generalisation) contributed to improving the results of the lexicosemantic representation. Our results showed no difference between the early and late fusion approaches. Temporal features performed poorly on their own. Conversely, spatial features were the most discriminative features, highlighting the need for robust methods for spatial entity extraction, disambiguation and representation in internet-based surveillance systems.
111.
Faucher, Benjamin; Assab, Rania; Roux, Jonathan; Levy-Bruhl, Daniel; Kiem, Cécile Tran; Cauchemez, Simon; Zanetti, Laura; Colizza, Vittoria; Boëlle, Pierre-Yves; Poletto, Chiara
Agent-based modelling of reactive vaccination of workplaces and schools against COVID-19 Journal Article
In: Nature Communications, vol. 13, no. 1414, 2022.
Abstract | Links | BibTeX | Tags: OpenDataSet
@article{nokey,
title = {Agent-based modelling of reactive vaccination of workplaces and schools against COVID-19},
author = {Benjamin Faucher and Rania Assab and Jonathan Roux and Daniel Levy-Bruhl and Cécile Tran Kiem and Simon Cauchemez and Laura Zanetti and Vittoria Colizza and Pierre-Yves Boëlle and Chiara Poletto},
url = {https://www.nature.com/articles/s41467-022-29015-y#Abs1},
doi = {10.1038/s41467-022-29015-y},
year = {2022},
date = {2022-03-17},
urldate = {2022-03-17},
journal = {Nature Communications},
volume = {13},
number = {1414},
abstract = {With vaccination against COVID-19 stalled in some countries, increasing vaccine accessibility and distribution could help keep transmission under control. Here, we study the impact of reactive vaccination targeting schools and workplaces where cases are detected, with an agent-based model accounting for COVID-19 natural history, vaccine characteristics, demographics, behavioural changes and social distancing. In most scenarios, reactive vaccination leads to a higher reduction in cases compared with non-reactive strategies using the same number of doses. The reactive strategy could however be less effective than a moderate/high pace mass vaccination program if initial vaccination coverage is high or disease incidence is low, because few people would be vaccinated around each case. In case of flare-ups, reactive vaccination could better mitigate spread if it is implemented quickly, is supported by enhanced test-trace-isolate and triggers an increased vaccine uptake. These results provide key information to plan an adaptive vaccination rollout.},
keywords = {OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
With vaccination against COVID-19 stalled in some countries, increasing vaccine accessibility and distribution could help keep transmission under control. Here, we study the impact of reactive vaccination targeting schools and workplaces where cases are detected, with an agent-based model accounting for COVID-19 natural history, vaccine characteristics, demographics, behavioural changes and social distancing. In most scenarios, reactive vaccination leads to a higher reduction in cases compared with non-reactive strategies using the same number of doses. The reactive strategy could however be less effective than a moderate/high pace mass vaccination program if initial vaccination coverage is high or disease incidence is low, because few people would be vaccinated around each case. In case of flare-ups, reactive vaccination could better mitigate spread if it is implemented quickly, is supported by enhanced test-trace-isolate and triggers an increased vaccine uptake. These results provide key information to plan an adaptive vaccination rollout.
112.
Bianco, Luca; Moser, Mirko; Silverjand, Andrea; Micheletti, Diego; Lorenzin, Giovanni; Collini, Lucia; Barbareschi, Mattia; Lanzafame, Paolo; Segata, Nicola; Pindo, Massimo; Franceschi, Pietro; Rota-Stabelli, Omar; Rizzoli, Annapaola; Fontana, Paolo; Donati, Claudio
On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy Journal Article
In: Viruses, vol. 14, iss. 3, no. 580, 2022, ISSN: 1999-4915.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy},
author = {Luca Bianco and Mirko Moser and Andrea Silverjand and Diego Micheletti and Giovanni Lorenzin and Lucia Collini and Mattia Barbareschi and Paolo Lanzafame and Nicola Segata and Massimo Pindo and Pietro Franceschi and Omar Rota-Stabelli and Annapaola Rizzoli and Paolo Fontana and Claudio Donati},
url = {https://www.mdpi.com/1999-4915/14/3/580},
doi = {10.3390/v14030580},
issn = {1999-4915},
year = {2022},
date = {2022-03-11},
urldate = {2022-03-11},
journal = {Viruses},
volume = {14},
number = {580},
issue = {3},
abstract = {Background: Trentino is an Italian province with a tourism-based economy, bordering the regions of Lombardy and Veneto, where the two earliest and largest outbreaks of COVID-19 occurred in Italy. The earliest cases in Trentino were reported in the first week of March 2020, with most of the cases occurring in the winter sport areas in the Dolomites mountain range. The number of reported cases decreased over the summer months and was followed by a second wave in the autumn and winter of 2020. Methods: we performed high-coverage Oxford Nanopore sequencing of 253 positive SARS-CoV-2 swabs collected in Trentino between March and December 2020. Results: in this work, we analyzed genome sequences to trace the routes through which the virus entered the area, and assessed whether the autumnal resurgence could be attributed to lineages persisting undetected during summer, or as a consequence of new introductions. Conclusions: Comparing the draft genomes analyzed with a large selection of European sequences retrieved from GISAID we found that multiple introductions of the virus occurred at the early stage of the epidemics; the two epidemic waves were unrelated; the second wave was due to reintroductions of the virus in summer when traveling restrictions were uplifted.},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Background: Trentino is an Italian province with a tourism-based economy, bordering the regions of Lombardy and Veneto, where the two earliest and largest outbreaks of COVID-19 occurred in Italy. The earliest cases in Trentino were reported in the first week of March 2020, with most of the cases occurring in the winter sport areas in the Dolomites mountain range. The number of reported cases decreased over the summer months and was followed by a second wave in the autumn and winter of 2020. Methods: we performed high-coverage Oxford Nanopore sequencing of 253 positive SARS-CoV-2 swabs collected in Trentino between March and December 2020. Results: in this work, we analyzed genome sequences to trace the routes through which the virus entered the area, and assessed whether the autumnal resurgence could be attributed to lineages persisting undetected during summer, or as a consequence of new introductions. Conclusions: Comparing the draft genomes analyzed with a large selection of European sequences retrieved from GISAID we found that multiple introductions of the virus occurred at the early stage of the epidemics; the two epidemic waves were unrelated; the second wave was due to reintroductions of the virus in summer when traveling restrictions were uplifted.
113.
Manica, Mattia; Litvinova, Maria; Bellis, Alfredo De; Guzzetta, Giorgio; Mancuso, Pamela; Vicentini, Massimo; Venturelli, Francesco; Bisaccia, Eufemia; Bento, Ana I.; Poletti, Piero; Marziano, Valentina; Zardini, Agnese; d'Andrea, Valeria; Trentini, Filippo; Bella, Antonino; Riccardo, Flavia; Pezzotti, Patrizio; Ajelli, Marco; Rossi, Paolo Giorgi; Merler, Stefano; the Reggio Emilia COVID-19 Working Group,
Estimation of the incubation period and generation time of SARS-CoV-2 Alpha and Delta variants from contact tracing data Journal Article
In: arXiv, 2022.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{nokey,
title = {Estimation of the incubation period and generation time of SARS-CoV-2 Alpha and Delta variants from contact tracing data},
author = {Mattia Manica and Maria Litvinova and Alfredo De Bellis and Giorgio Guzzetta and Pamela Mancuso and Massimo Vicentini and Francesco Venturelli and Eufemia Bisaccia and Ana I. Bento and Piero Poletti and Valentina Marziano and Agnese Zardini and Valeria d'Andrea and Filippo Trentini and Antonino Bella and Flavia Riccardo and Patrizio Pezzotti and Marco Ajelli and Paolo Giorgi Rossi and Stefano Merler and the Reggio Emilia COVID-19 Working Group},
url = {https://arxiv.org/abs/2203.07063},
doi = {https://doi.org/10.48550/arXiv.2203.07063},
year = {2022},
date = {2022-03-11},
urldate = {2022-03-11},
journal = {arXiv},
abstract = {Background. During 2021, the COVID-19 pandemic was characterized by the emergence of lineages with increased fitness. For most of these variants, quantitative information is scarce on epidemiological quantities such as the incubation period and generation time, which are critical for both public health decisions and scientific research. Method. We analyzed a dataset collected during contact tracing activities in the province of Reggio Emilia, Italy, throughout 2021. We determined the distributions of the incubation period using information on negative PCR tests and the date of last exposure from 282 symptomatic cases. We estimated the distributions of the intrinsic generation time (the time between the infection dates of an infector and its secondary cases under a fully susceptible population) using a Bayesian inference approach applied to 4,435 SARS-CoV-2 cases clustered in 1,430 households where at least one secondary case was recorded. Results. We estimated a mean incubation period of 4.9 days (95% credible intervals, CrI, 4.4-5.4; 95 percentile of the mean distribution: 1-12) for Alpha and 4.5 days (95%CrI 4.0-5.0; 95 percentile: 1-10) for Delta. The intrinsic generation time was estimated to have a mean of 6.0 days (95% CrI 5.6-6.4; 95 percentile: 1-15) for Alpha and of 6.6 days (95%CrI 6.0-7.3; 95 percentile: 1-18) for Delta. The household serial interval was 2.6 days (95%CrI 2.4-2.7) for Alpha and 2.4 days (95%CrI 2.2-2.6) for Delta, and the estimated proportion of pre-symptomatic transmission was 54-55% for both variants. Conclusions. These results indicate limited differences in the incubation period and intrinsic generation time of SARS-CoV-2 variants Alpha and Delta compared to ancestral lineages. Funding. EU grant 874850 MOOD },
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
Background. During 2021, the COVID-19 pandemic was characterized by the emergence of lineages with increased fitness. For most of these variants, quantitative information is scarce on epidemiological quantities such as the incubation period and generation time, which are critical for both public health decisions and scientific research. Method. We analyzed a dataset collected during contact tracing activities in the province of Reggio Emilia, Italy, throughout 2021. We determined the distributions of the incubation period using information on negative PCR tests and the date of last exposure from 282 symptomatic cases. We estimated the distributions of the intrinsic generation time (the time between the infection dates of an infector and its secondary cases under a fully susceptible population) using a Bayesian inference approach applied to 4,435 SARS-CoV-2 cases clustered in 1,430 households where at least one secondary case was recorded. Results. We estimated a mean incubation period of 4.9 days (95% credible intervals, CrI, 4.4-5.4; 95 percentile of the mean distribution: 1-12) for Alpha and 4.5 days (95%CrI 4.0-5.0; 95 percentile: 1-10) for Delta. The intrinsic generation time was estimated to have a mean of 6.0 days (95% CrI 5.6-6.4; 95 percentile: 1-15) for Alpha and of 6.6 days (95%CrI 6.0-7.3; 95 percentile: 1-18) for Delta. The household serial interval was 2.6 days (95%CrI 2.4-2.7) for Alpha and 2.4 days (95%CrI 2.2-2.6) for Delta, and the estimated proportion of pre-symptomatic transmission was 54-55% for both variants. Conclusions. These results indicate limited differences in the incubation period and intrinsic generation time of SARS-CoV-2 variants Alpha and Delta compared to ancestral lineages. Funding. EU grant 874850 MOOD
114.
Mencattelli, Giulia
West Nile Virus in Africa: current epidemiological situation and knowledge gaps Journal Article
In: 2022.
Abstract | Links | BibTeX | Tags: WNV (West Nile Virus)
@article{nokey,
title = {West Nile Virus in Africa: current epidemiological situation and knowledge gaps},
author = {Giulia Mencattelli et al.},
url = {https://www.sciencedirect.com/science/article/pii/S1201971221011838},
doi = {10.1016/j.ijid.2021.12.291},
year = {2022},
date = {2022-03-08},
urldate = {2022-03-08},
abstract = {West Nile virus (WNV) is an arthropod-borne zoonotic pathogen which represents a continuous source of concern for public health worldwide due to its expansion and invasion into new regions. Its distribution and circulation intensity in African countries is only partially known. The aim of the present study is to provide an updated overview on the current knowledge of WNV epidemiology in Africa, providing available data on incidence in humans and animals, the circulating lineages and clades, other than an updated list of the principal arthropod vectors identified and the availability of vector competence studies.
},
keywords = {WNV (West Nile Virus)},
pubstate = {published},
tppubtype = {article}
}
West Nile virus (WNV) is an arthropod-borne zoonotic pathogen which represents a continuous source of concern for public health worldwide due to its expansion and invasion into new regions. Its distribution and circulation intensity in African countries is only partially known. The aim of the present study is to provide an updated overview on the current knowledge of WNV epidemiology in Africa, providing available data on incidence in humans and animals, the circulating lineages and clades, other than an updated list of the principal arthropod vectors identified and the availability of vector competence studies.
115.
Blokker, Tim; Baele, Guy; Lemey, Philippe; Dellicour, Simon
Phycova — a tool for exploring covariates of pathogen spread Journal Article
In: Virus Evolution, vol. 8, iss. 1, 2022, ISSN: 2057-1577, (veac015).
Abstract | Links | BibTeX | Tags: OpenDataSet
@article{@article{10.1093/ve/veac015,
title = {Phycova — a tool for exploring covariates of pathogen spread},
author = {Tim Blokker and Guy Baele and Philippe Lemey and Simon Dellicour},
url = {https://academic.oup.com/ve/article/8/1/veac015/6530450},
doi = {https://doi.org/10.1093/ve/veac015},
issn = {2057-1577},
year = {2022},
date = {2022-02-18},
urldate = {2022-02-18},
journal = {Virus Evolution},
volume = {8},
issue = {1},
abstract = {Genetic analyses of fast-evolving pathogens are frequently undertaken to test the impact of covariates on their dispersal. In particular, a popular approach consists of parameterizing a discrete phylogeographic model as a generalized linear model to identify and analyse the predictors of the dispersal rates of viral lineages among discrete locations. However, such a full probabilistic inference is often computationally demanding and time-consuming. In the face of the increasing amount of viral genomes sequenced in epidemic outbreaks, there is a need for a fast exploration of covariates that might be relevant to consider in formal analyses. We here present PhyCovA (short for ‘Phylogeographic Covariate Analysis’), a web-based application allowing users to rapidly explore the association between candidate covariates and the number of phylogenetically informed transition events among locations. Specifically, PhyCovA takes as input a phylogenetic tree with discrete state annotations at the internal nodes, or reconstructs those states if not available, to subsequently conduct univariate and multivariate linear regression analyses, as well as an exploratory variable selection analysis. In addition, the application can also be used to generate and explore various visualizations related to the regression analyses or to the phylogenetic tree annotated by the ancestral state reconstruction. PhyCovA is freely accessible at https://evolcompvir-kuleuven.shinyapps.io/PhyCovA/ and also distributed in a dockerized form obtainable from https://hub.docker.com/repository/docker/timblokker/phycova. The source code and tutorial are available from the GitHub repository https://github.com/TimBlokker/PhyCovA.},
note = {veac015},
keywords = {OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Genetic analyses of fast-evolving pathogens are frequently undertaken to test the impact of covariates on their dispersal. In particular, a popular approach consists of parameterizing a discrete phylogeographic model as a generalized linear model to identify and analyse the predictors of the dispersal rates of viral lineages among discrete locations. However, such a full probabilistic inference is often computationally demanding and time-consuming. In the face of the increasing amount of viral genomes sequenced in epidemic outbreaks, there is a need for a fast exploration of covariates that might be relevant to consider in formal analyses. We here present PhyCovA (short for ‘Phylogeographic Covariate Analysis’), a web-based application allowing users to rapidly explore the association between candidate covariates and the number of phylogenetically informed transition events among locations. Specifically, PhyCovA takes as input a phylogenetic tree with discrete state annotations at the internal nodes, or reconstructs those states if not available, to subsequently conduct univariate and multivariate linear regression analyses, as well as an exploratory variable selection analysis. In addition, the application can also be used to generate and explore various visualizations related to the regression analyses or to the phylogenetic tree annotated by the ancestral state reconstruction. PhyCovA is freely accessible at https://evolcompvir-kuleuven.shinyapps.io/PhyCovA/ and also distributed in a dockerized form obtainable from https://hub.docker.com/repository/docker/timblokker/phycova. The source code and tutorial are available from the GitHub repository https://github.com/TimBlokker/PhyCovA.
116.
Stefanelli, Paola; Group, COVID-19 National Microbiology Surveillance Study
Co-circulation of SARS-CoV-2 Alpha and Gamma variants in Italy, February and March 2021 Journal Article
In: Eurosurveillance, vol. 27, no. 5, pp. 2100429, 2022.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus)
@article{nokey,
title = {Co-circulation of SARS-CoV-2 Alpha and Gamma variants in Italy, February and March 2021},
author = {Paola Stefanelli et al. and COVID-19 National Microbiology Surveillance Study Group},
url = {https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2022.27.5.2100429},
doi = {10.2807/1560-7917.ES.2022.27.5.2100429},
year = {2022},
date = {2022-02-03},
urldate = {2022-02-03},
journal = {Eurosurveillance},
volume = {27},
number = {5},
pages = {2100429},
abstract = {Background
Several SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains.
Aim
We aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility.
Methods
We conducted two genomic surveillance surveys on 18 February and 18 March 2021 across the whole Italian territory covering 3,243 clinical samples and developed a mathematical model that describes the dynamics of co-circulating strains.
Results
The Alpha variant was already dominant on 18 February in a majority of regions/autonomous provinces (national prevalence: 54%) and almost completely replaced historical lineages by 18 March (dominant across Italy, national prevalence: 86%). We found a substantial proportion of the Gamma variant on 18 February, almost exclusively in central Italy (prevalence: 19%), which remained similar on 18 March. Nationally, the mean relative transmissibility of Alpha ranged at 1.55–1.57 times the level of historical lineages (95% CrI: 1.45–1.66). The relative transmissibility of Gamma varied according to the assumed degree of cross-protection from infection with other lineages and ranged from 1.12 (95% CrI: 1.03–1.23) with complete immune evasion to 1.39 (95% CrI: 1.26–1.56) for complete cross-protection.
Conclusion
We assessed the relative advantage of competing viral strains, using a mathematical model assuming different degrees of cross-protection. We found substantial co-circulation of Alpha and Gamma in Italy. Gamma was not able to outcompete Alpha, probably because of its lower transmissibility.},
keywords = {Covid-19 (Coronavirus)},
pubstate = {published},
tppubtype = {article}
}
Background
Several SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains.
Aim
We aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility.
Methods
We conducted two genomic surveillance surveys on 18 February and 18 March 2021 across the whole Italian territory covering 3,243 clinical samples and developed a mathematical model that describes the dynamics of co-circulating strains.
Results
The Alpha variant was already dominant on 18 February in a majority of regions/autonomous provinces (national prevalence: 54%) and almost completely replaced historical lineages by 18 March (dominant across Italy, national prevalence: 86%). We found a substantial proportion of the Gamma variant on 18 February, almost exclusively in central Italy (prevalence: 19%), which remained similar on 18 March. Nationally, the mean relative transmissibility of Alpha ranged at 1.55–1.57 times the level of historical lineages (95% CrI: 1.45–1.66). The relative transmissibility of Gamma varied according to the assumed degree of cross-protection from infection with other lineages and ranged from 1.12 (95% CrI: 1.03–1.23) with complete immune evasion to 1.39 (95% CrI: 1.26–1.56) for complete cross-protection.
Conclusion
We assessed the relative advantage of competing viral strains, using a mathematical model assuming different degrees of cross-protection. We found substantial co-circulation of Alpha and Gamma in Italy. Gamma was not able to outcompete Alpha, probably because of its lower transmissibility.
Several SARS-CoV-2 variants of concern (VOC) have emerged through 2020 and 2021. There is need for tools to estimate the relative transmissibility of emerging variants of SARS-CoV-2 with respect to circulating strains.
Aim
We aimed to assess the prevalence of co-circulating VOC in Italy and estimate their relative transmissibility.
Methods
We conducted two genomic surveillance surveys on 18 February and 18 March 2021 across the whole Italian territory covering 3,243 clinical samples and developed a mathematical model that describes the dynamics of co-circulating strains.
Results
The Alpha variant was already dominant on 18 February in a majority of regions/autonomous provinces (national prevalence: 54%) and almost completely replaced historical lineages by 18 March (dominant across Italy, national prevalence: 86%). We found a substantial proportion of the Gamma variant on 18 February, almost exclusively in central Italy (prevalence: 19%), which remained similar on 18 March. Nationally, the mean relative transmissibility of Alpha ranged at 1.55–1.57 times the level of historical lineages (95% CrI: 1.45–1.66). The relative transmissibility of Gamma varied according to the assumed degree of cross-protection from infection with other lineages and ranged from 1.12 (95% CrI: 1.03–1.23) with complete immune evasion to 1.39 (95% CrI: 1.26–1.56) for complete cross-protection.
Conclusion
We assessed the relative advantage of competing viral strains, using a mathematical model assuming different degrees of cross-protection. We found substantial co-circulation of Alpha and Gamma in Italy. Gamma was not able to outcompete Alpha, probably because of its lower transmissibility.
117.
Liu, Quan-Hui; Zhang, Juanjuan; Peng, Cheng; Litvinova, Maria; Huang, Shudong; Poletti, Piero; Trentini, Filippo; Guzzetta, Giorgio; Marziano, Valentina; Zhou, Tao; Viboud, Cecile; Bento, Ana I.; Lv, Jiancheng; Vespignani, Alessandro; Merler, Stefano; Yu, Hongjie; Ajelli, Marco
Model-based evaluation of alternative reactive class closure strategies against COVID-19. Journal Article
In: 2022.
Abstract | Links | BibTeX | Tags: Covid-19 (Coronavirus), OpenDataSet
@article{nokey,
title = {Model-based evaluation of alternative reactive class closure strategies against COVID-19.},
author = {Quan-Hui Liu and Juanjuan Zhang and Cheng Peng and Maria Litvinova and Shudong Huang and Piero Poletti and Filippo Trentini and Giorgio Guzzetta and Valentina Marziano and Tao Zhou and Cecile Viboud and Ana I. Bento and Jiancheng Lv and Alessandro Vespignani and Stefano Merler and Hongjie Yu and Marco Ajelli
},
url = {https://www.nature.com/articles/s41467-021-27939-5#article-info},
doi = {10.1038/s41467-021-27939-5},
year = {2022},
date = {2022-01-14},
urldate = {2022-01-14},
abstract = {There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, we developed a data-driven computational model of SARS-CoV-2 transmission. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 17.3% (95%CI: 8.0–26.8%), due to the low probability of timely identification of infections in the young population. We thus investigated an alternative triggering mechanism based on repeated screening of students using antigen tests. Depending on the contribution of schools to transmission, this strategy can greatly reduce COVID-19 burden even when school contribution to transmission and immunity in the population is low. Moving forward, the adoption of antigen-based screenings in schools could be instrumental to limit COVID-19 burden while vaccines continue to be rolled out.
},
keywords = {Covid-19 (Coronavirus), OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
There are contrasting results concerning the effect of reactive school closure on SARS-CoV-2 transmission. To shed light on this controversy, we developed a data-driven computational model of SARS-CoV-2 transmission. We found that by reactively closing classes based on syndromic surveillance, SARS-CoV-2 infections are reduced by no more than 17.3% (95%CI: 8.0–26.8%), due to the low probability of timely identification of infections in the young population. We thus investigated an alternative triggering mechanism based on repeated screening of students using antigen tests. Depending on the contribution of schools to transmission, this strategy can greatly reduce COVID-19 burden even when school contribution to transmission and immunity in the population is low. Moving forward, the adoption of antigen-based screenings in schools could be instrumental to limit COVID-19 burden while vaccines continue to be rolled out.
118.
Roche, Mathieu; Teisseire, Maguelonne
Integrating Textual Data into Heterogeneous Data Ingestion Processing Conference
2021 IEEE International Conference on Big Data (Big Data), IEEE, Orlando, FL, USA, 2022, ISBN: 978-1-6654-3902-2.
Abstract | Links | BibTeX | Tags: Text mining
@conference{@INPROCEEDINGS{9671759,
title = {Integrating Textual Data into Heterogeneous Data Ingestion Processing},
author = {Mathieu Roche and Maguelonne Teisseire},
url = {https://ieeexplore.ieee.org/document/9671759},
doi = {10.1109/BigData52589.2021.9671759},
isbn = {978-1-6654-3902-2},
year = {2022},
date = {2022-01-13},
urldate = {2022-01-13},
booktitle = {2021 IEEE International Conference on Big Data (Big Data)},
pages = {6008-6010},
publisher = {IEEE},
address = {Orlando, FL, USA},
abstract = {In this abstract, two methods for integrating textual data and textual features into ingestion processing are summarized. The first method involves integrating all features, including textual features, into dedicated frameworks, such as by using machine learning techniques. In the second method, text and textual features, such as keywords, are used to explain results returned by heterogeneous data mining. In this context, it is necessary to link data (e.g., databases, images, etc.) and/or obtained results with textual data (e.g., documents and keywords).},
keywords = {Text mining},
pubstate = {published},
tppubtype = {conference}
}
In this abstract, two methods for integrating textual data and textual features into ingestion processing are summarized. The first method involves integrating all features, including textual features, into dedicated frameworks, such as by using machine learning techniques. In the second method, text and textual features, such as keywords, are used to explain results returned by heterogeneous data mining. In this context, it is necessary to link data (e.g., databases, images, etc.) and/or obtained results with textual data (e.g., documents and keywords).
119.
Mencattelli, Giulia; Ndione, Marie Henriette Dior; Rosà, Roberto; Marini, Giovanni; Diagne, Cheikh Tidiane; Moussa, Moise; Fall, Gamou; Faye, Ousmane; Diallo, Mawlouth; Faye, Oumar; Savini, Giovanni; Rizzoli, Annapaola
Epidemiology of West Nile virus in Africa: An underestimated threat Journal Article
In: PLOS Neglected Tropical Diseases, vol. 16, no. 1, pp. 1-31, 2022.
Abstract | Links | BibTeX | Tags: OpenDataSet, WNV (West Nile Virus)
@article{nokey,
title = {Epidemiology of West Nile virus in Africa: An underestimated threat},
author = {Giulia Mencattelli and Marie Henriette Dior Ndione and Roberto Rosà and Giovanni Marini and Cheikh Tidiane Diagne and Moise Moussa and Gamou Fall and Ousmane Faye and Mawlouth Diallo and Oumar Faye and Giovanni Savini and Annapaola Rizzoli},
url = {https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0010075#abstract0},
doi = {10.1371/journal.pntd.0010075},
year = {2022},
date = {2022-01-10},
urldate = {2022-01-10},
journal = {PLOS Neglected Tropical Diseases},
volume = {16},
number = {1},
pages = {1-31},
abstract = {Background West Nile virus is a mosquito-borne flavivirus which has been posing continuous challenges to public health worldwide due to the identification of new lineages and clades and its ability to invade and establish in an increasing number of countries. Its current distribution, genetic variability, ecology, and epidemiological pattern in the African continent are only partially known despite the general consensus on the urgency to obtain such information for quantifying the actual disease burden in Africa other than to predict future threats at global scale. Methodology and principal findings References were searched in PubMed and Google Scholar electronic databases on January 21, 2020, using selected keywords, without language and date restriction. Additional manual searches of reference list were carried out. Further references have been later added accordingly to experts’ opinion. We included 153 scientific papers published between 1940 and 2021. This review highlights: (i) the co-circulation of WNV-lineages 1, 2, and 8 in the African continent; (ii) the presence of diverse WNV competent vectors in Africa, mainly belonging to the Culex genus; (iii) the lack of vector competence studies for several other mosquito species found naturally infected with WNV in Africa; (iv) the need of more competence studies to be addressed on ticks; (iv) evidence of circulation of WNV among humans, animals and vectors in at least 28 Countries; (v) the lack of knowledge on the epidemiological situation of WNV for 19 Countries and (vii) the importance of carrying out specific serological surveys in order to avoid possible bias on WNV circulation in Africa. Conclusions This study provides the state of art on WNV investigation carried out in Africa, highlighting several knowledge gaps regarding i) the current WNV distribution and genetic diversity, ii) its ecology and transmission chains including the role of different arthropods and vertebrate species as competent reservoirs, and iii) the real disease burden for humans and animals. This review highlights the needs for further research and coordinated surveillance efforts on WNV in Africa.},
keywords = {OpenDataSet, WNV (West Nile Virus)},
pubstate = {published},
tppubtype = {article}
}
Background West Nile virus is a mosquito-borne flavivirus which has been posing continuous challenges to public health worldwide due to the identification of new lineages and clades and its ability to invade and establish in an increasing number of countries. Its current distribution, genetic variability, ecology, and epidemiological pattern in the African continent are only partially known despite the general consensus on the urgency to obtain such information for quantifying the actual disease burden in Africa other than to predict future threats at global scale. Methodology and principal findings References were searched in PubMed and Google Scholar electronic databases on January 21, 2020, using selected keywords, without language and date restriction. Additional manual searches of reference list were carried out. Further references have been later added accordingly to experts’ opinion. We included 153 scientific papers published between 1940 and 2021. This review highlights: (i) the co-circulation of WNV-lineages 1, 2, and 8 in the African continent; (ii) the presence of diverse WNV competent vectors in Africa, mainly belonging to the Culex genus; (iii) the lack of vector competence studies for several other mosquito species found naturally infected with WNV in Africa; (iv) the need of more competence studies to be addressed on ticks; (iv) evidence of circulation of WNV among humans, animals and vectors in at least 28 Countries; (v) the lack of knowledge on the epidemiological situation of WNV for 19 Countries and (vii) the importance of carrying out specific serological surveys in order to avoid possible bias on WNV circulation in Africa. Conclusions This study provides the state of art on WNV investigation carried out in Africa, highlighting several knowledge gaps regarding i) the current WNV distribution and genetic diversity, ii) its ecology and transmission chains including the role of different arthropods and vertebrate species as competent reservoirs, and iii) the real disease burden for humans and animals. This review highlights the needs for further research and coordinated surveillance efforts on WNV in Africa.
120.
Li, Sabrina L.; Acosta, André L.; Hill, Sarah C.; Brady, Oliver J.; Almeida, Marco A. B. de; da C. Cardoso, Jader; Hamlet, Arran; Mucci, Luis F.; de Deus, Juliana Telles; Iani, Felipe C.; Alexander, Neil S.; Wint, William G. R.; Pybus, Oliver G.; Kraemer, Moritz; Messina, Nuno R. Fariaand Jane P.
In: PLOS Neglected Tropical Diseases, vol. 16, pp. 1-21, 2022.
Abstract | Links | BibTeX | Tags: OpenDataSet
@article{@article{10.1371/journal.pntd.0010019,,
title = {Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil},
author = {Sabrina L. Li and André L. Acosta and Sarah C. Hill and Oliver J. Brady and Marco A.B.de Almeida and Jader da C. Cardoso and Arran Hamlet and Luis F. Mucci and Juliana Telles de Deus and Felipe C. Iani and Neil S. Alexander and William G. R. Wint and Oliver G. Pybus and Moritz Kraemer and Nuno R. Fariaand Jane P. Messina},
editor = {Public Library of Science},
url = {https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0010019},
doi = {https://doi.org/10.1371/journal.pntd.0010019},
year = {2022},
date = {2022-01-07},
urldate = {2022-01-07},
journal = {PLOS Neglected Tropical Diseases},
volume = {16},
pages = {1-21},
abstract = {Background Yellow fever (YF) is an arboviral disease which is endemic to Brazil due to a sylvatic transmission cycle maintained by infected mosquito vectors, non-human primate (NHP) hosts, and humans. Despite the existence of an effective vaccine, recent sporadic YF epidemics have underscored concerns about sylvatic vector surveillance, as very little is known about their spatial distribution. Here, we model and map the environmental suitability of YF’s main vectors in Brazil, Haemagogus spp. and Sabethes spp., and use human population and NHP data to identify locations prone to transmission and spillover risk. Methodology/Principal findings We compiled a comprehensive set of occurrence records on Hg. janthinomys, Hg. leucocelaenus, and Sabethes spp. from 1991–2019 using primary and secondary data sources. Linking these data with selected environmental and land-cover variables, we adopted a stacked regression ensemble modelling approach (elastic-net regularized GLM, extreme gradient boosted regression trees, and random forest) to predict the environmental suitability of these species across Brazil at a 1 km x 1 km resolution. We show that while suitability for each species varies spatially, high suitability for all species was predicted in the Southeastern region where recent outbreaks have occurred. By integrating data on NHP host reservoirs and human populations, our risk maps further highlight municipalities within the region that are prone to transmission and spillover. Conclusions/Significance Our maps of sylvatic vector suitability can help elucidate potential locations of sylvatic reservoirs and be used as a tool to help mitigate risk of future YF outbreaks and assist in vector surveillance. Furthermore, at-risk regions identified from our work could help disease control and elucidate gaps in vaccination coverage and NHP host surveillance.},
keywords = {OpenDataSet},
pubstate = {published},
tppubtype = {article}
}
Background Yellow fever (YF) is an arboviral disease which is endemic to Brazil due to a sylvatic transmission cycle maintained by infected mosquito vectors, non-human primate (NHP) hosts, and humans. Despite the existence of an effective vaccine, recent sporadic YF epidemics have underscored concerns about sylvatic vector surveillance, as very little is known about their spatial distribution. Here, we model and map the environmental suitability of YF’s main vectors in Brazil, Haemagogus spp. and Sabethes spp., and use human population and NHP data to identify locations prone to transmission and spillover risk. Methodology/Principal findings We compiled a comprehensive set of occurrence records on Hg. janthinomys, Hg. leucocelaenus, and Sabethes spp. from 1991–2019 using primary and secondary data sources. Linking these data with selected environmental and land-cover variables, we adopted a stacked regression ensemble modelling approach (elastic-net regularized GLM, extreme gradient boosted regression trees, and random forest) to predict the environmental suitability of these species across Brazil at a 1 km x 1 km resolution. We show that while suitability for each species varies spatially, high suitability for all species was predicted in the Southeastern region where recent outbreaks have occurred. By integrating data on NHP host reservoirs and human populations, our risk maps further highlight municipalities within the region that are prone to transmission and spillover. Conclusions/Significance Our maps of sylvatic vector suitability can help elucidate potential locations of sylvatic reservoirs and be used as a tool to help mitigate risk of future YF outbreaks and assist in vector surveillance. Furthermore, at-risk regions identified from our work could help disease control and elucidate gaps in vaccination coverage and NHP host surveillance.