MOOD publications

@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 = {Agoti, Charles N and Ochola-Oyier, Lynette Isabella and Dellicour, Simon and Mohammed, Khadija Said and Lambisia, Arnold W and de Laurent, Zaydah R and Morobe, John M and Mburu, Maureen W and Omuoyo, Donwilliams O and Ongera, Edidah M and Ndwiga, Leonard and Maitha, Eric and Kitole, Benson and Suleiman, Thani and Mwakinangu, Mohamed and Nyambu, John K and Otieno, John and Salim, Barke and Musyoki, Jennifer and Murunga, Nickson and Otieno, Edward and Kiiru, John N and Kasera, Kadondi and Amoth, Patrick and Mwangangi, Mercy and Aman, Rashid and Kinyanjui, Samson and Warimwe, George and Phan, My and Agweyu, Ambrose and Cotten, Matthew and Barasa, Edwine and Tsofa, Benjamin and Nokes, D James and Bejon, Philip and Githinji, George},

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 = {Africa, COVID-19, epidemiology, genome, transmission},

pubstate = {published},

tppubtype = {article}

}

@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 = {Climate, culex, Emerging infectious diseases, Europe, Mediterranean, West Nile Virus},

pubstate = {published},

tppubtype = {article}

}

@article{@article{10.1093/ve/veac041,

title = {Accommodating sampling location uncertainty in continuous phylogeography},

author = {Dellicour, Simon and Lemey, Philippe and Suchard, Marc A and Gilbert, Marius and Baele, Guy},

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 = {Bayesian inference, BEAST, continuous phylogeography, host species, sampling precision, virus},

pubstate = {published},

tppubtype = {article}

}

@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 = {Climate, climate change, disease ecology, France, infectious diseases, ixodes, ticks, vector},

pubstate = {published},

tppubtype = {article}

}

@article{@article{colosi2022screening,,

title = {Screening and vaccination against COVID-19 to minimise school closure: a modelling study},

author = {Colosi, Elisabetta and Bassignana, Giulia and Contreras, Diego Andrés and Poirier, Canelle and Boëlle, Pierre-Yves and Cauchemez, Simon and Yazdanpanah, Yazdan and Lina, Bruno and Fontanet, Arnaud and Barrat, Alain 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 = {},

pubstate = {published},

tppubtype = {article}

}

@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 = {iterative screening, modelling, Non-pharmaceutical interventions, SARS-CoV-2, school},

pubstate = {published},

tppubtype = {article}

}

@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 = {Animal disease surveillance, fusion, ranking, Text mining},

pubstate = {published},

tppubtype = {article}

}

@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 = {COVID-19},

pubstate = {published},

tppubtype = {article}

}

@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 = {Bianco, Luca and Moser, Mirko and Silverj, Andrea and Micheletti, Diego and Lorenzin, Giovanni and Collini, Lucia and Barbareschi, Mattia and Lanzafame, Paolo and Segata, Nicola and Pindo, Massimo and Franceschi, Pietro and Rota-Stabelli, Omar and Rizzoli, Annapaola and Fontana, Paolo and Donati, Claudio},

url = {https://www.mdpi.com/1999-4915/14/3/580},

doi = {10.3390/v14030580},

issn = {1999-4915},

year  = {2022},

date = {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, genome, SARS-CoV-2, transmission},

pubstate = {published},

tppubtype = {article}

}

@article{@article{10.1093/ve/veac015,

title = {Phycova — a tool for exploring covariates of pathogen spread},

author = {Blokker, Tim and Baele, Guy and Lemey, Philippe and Dellicour, Simon},

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 = {BEAST, covariates, discrete phylogeography, generalized linear model, linear regression, pathogen spread, PhyCovA, visualization},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Epidemiology of West Nile virus in Africa: An underestimated threat},

author = {Mencattelli, Giulia AND Ndione, Marie Henriette Dior AND Rosà, Roberto AND Marini, Giovanni AND Diagne, Cheikh Tidiane AND Diagne, Moussa Moise AND Fall, Gamou AND Faye, Ousmane AND Diallo, Mawlouth AND Faye, Oumar AND Savini, Giovanni AND Rizzoli, Annapaola},

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},

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 = {Africa, birds, culex quiquefasciatus, egypt, Europe, mosquitoes, virus testing, West Nile Virus},

pubstate = {published},

tppubtype = {article}

}

@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 = {Li, Sabrina L. AND Acosta, André L. AND Hill, Sarah C. AND Brady, Oliver J. AND de Almeida, Marco A. B. AND Cardoso, Jader da C. AND Hamlet, Arran AND Mucci, Luis F. AND Telles de Deus, Juliana AND Iani, Felipe C. M. AND Alexander, Neil S. AND Wint, G. R. William AND Pybus, Oliver G. AND Kraemer, Moritz U. G. AND Faria, Nuno R. AND Messina, Jane P.},

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 = {},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Rapid epidemic expansion of the SARS-CoV-2 Omicron variant in southern Africa},

author = {Viana, Raquel and Moyo, Sikhulile and Amoako, Daniel G and Tegally, Houriiyah and Scheepers, Cathrine and Althaus, Christian L and Anyaneji, Ugochukwu J and Bester, Phillip A and Boni, Maciej F and Chand, Mohammed and others},

url = {https://www.nature.com/articles/s41586-022-04411-y#citeas},

doi = {10.1038/s41586-022-04411-y},

year  = {2022},

date = {2022-01-07},

journal = {Nature},

volume = {603},

number = {7902},

pages = {679-686},

abstract = {The SARS-CoV-2 epidemic in southern Africa has been characterized by three distinct waves. The first was associated with a mix of SARS-CoV-2 lineages, while the second and third waves were driven by the Beta (B.1.351) and Delta (B.1.617.2) variants, respectively1,2,3. In November 2021, genomic surveillance teams in South Africa and Botswana detected a new SARS-CoV-2 variant associated with a rapid resurgence of infections in Gauteng province, South Africa. Within three days of the first genome being uploaded, it was designated a variant of concern (Omicron, B.1.1.529) by the World Health Organization and, within three weeks, had been identified in 87 countries. The Omicron variant is exceptional for carrying over 30 mutations in the spike glycoprotein, which are predicted to influence antibody neutralization and spike function4. Here we describe the genomic profile and early transmission dynamics of Omicron, highlighting the rapid spread in regions with high levels of population immunity.},

keywords = {epidemiology, Molecular evolution, SARS-CoV-2},

pubstate = {published},

tppubtype = {article}

}

@article{@conference{healthinf22,,

title = {Feature Selection for Sentiment Classification of COVID-19 Tweets: H-TFIDF Featuring BERT},

author = {Mehtab Syed. and Elena Arsevska. and Mathieu Roche. and Maguelonne Teisseire.},

editor = {SciTePress},

url = {https://www.scitepress.org/Link.aspx?doi=10.5220/0010887800003123},

doi = {10.5220/0010887800003123},

isbn = {978-989-758-552-4},

year  = {2022},

date = {2022-01-01},

journal = {Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies - HEALTHINF},

pages = {648-656},

abstract = {In the first quarter of 2020, the World Health Organization (WHO) declared COVID-19 a public health emergency around the globe. Different users from all over the world shared their opinions about COVID-19 on social media platforms such as Twitter and Facebook. At the beginning of the pandemic, it became relevant to assess public opinions regarding COVID-19 using data available on social media. We used a recently proposed hierarchy-based measure for tweet analysis (H-TFIDF) for feature extraction over sentiment classification of tweets. We assessed how H-TFIDF and concatenation of H-TFIDF with bidirectional encoder representations from transformers (BH-TFIDF) perform over state-of-the-art bag-of-words (BOW) and term frequency-inverse document frequency (TF-IDF) features for sentiment classification of COVID-19 tweets. A uniform experimental setup of the training-test (90% and 10%) split scheme was used to train the classifier. Moreover, evaluation was performed with the gold standard expert labeled dataset to measure precision for each binary classified class. },

keywords = {Feature selection, sentiment analysis, Text mining, Twitter},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {The effect of COVID-19 vaccination in Italy and perspectives for living with the virus},

author = {Marziano, Valentina; Guzzetta, Giorgio; Mammone, Alessia; Riccardo, Flavia; Poletti, Piero; Trentini, Filippo; Manica, Mattia; Siddu, Andrea; Bella, Antonino; Stefanelli, Paola; Pezzotti, Patrizio; Ajelli, Marco; Brusaferro, Silvio; Rezza, Giovanni; Merler, Stefano},

url = {https://www.nature.com/articles/s41467-021-27532-w#citeas},

doi = {10.1038/s41467-021-27532-w},

year  = {2021},

date = {2021-12-14},

urldate = {2021-12-14},

volume = {12},

number = {7272},

abstract = {COVID-19 vaccination is allowing a progressive release of restrictions worldwide. Using a mathematical model, we assess the impact of vaccination in Italy since December 27, 2020 and evaluate prospects for societal reopening after emergence of the Delta variant. We estimate that by June 30, 2021, COVID-19 vaccination allowed the resumption of about half of pre-pandemic social contacts. In absence of vaccination, the same number of cases is obtained by resuming only about one third of pre-pandemic contacts, with about 12,100 (95% CI: 6,600-21,000) extra deaths (+27%; 95% CI: 15–47%). Vaccination offset the effect of the Delta variant in summer 2021. The future epidemic trend is surrounded by substantial uncertainty. Should a pediatric vaccine (for ages 5 and older) be licensed and a coverage >90% be achieved in all age classes, a return to pre-pandemic society could be envisioned. Increasing vaccination coverage will allow further reopening even in absence of a pediatric vaccine.},

keywords = {COVID-19, vaccination},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {Adherence and sustainability of interventions informing optimal control against the COVID-19 pandemic},

author = {Di Domenico, Laura; E. Sabbatini, Chiara; Boëlle, Pierre-Yves; Poletto, Chiara; Crépey, Pascal; Paireau, Juliette; Cauchemez, Simon; Beck, François; Noel, Harold ; Lévy-Bruhl, Daniel; Colizza, Vittoria},

url = {https://www.nature.com/articles/s43856-021-00057-5},

doi = {10.1038/s43856-021-00057-5},

year  = {2021},

date = {2021-12-06},

urldate = {2021-12-06},

journal = {Nature Communications},

volume = {1},

number = {57},

abstract = {After one year of stop-and-go COVID-19 mitigation, in the spring of 2021 European countries still experienced sustained viral circulation due to the Alpha variant. As the prospect of entering a new pandemic phase through vaccination was drawing closer, a key challenge remained on how to balance the efficacy of long-lasting interventions and their impact on the quality of life.

We show that moderate interventions would require a much longer time to achieve the same result as high intensity lockdowns, with the additional risk of deteriorating control as adherence wanes. Shorter strict lockdowns are largely more effective than longer moderate lockdowns, for similar intermediate distress and infringement on individual freedom.},

keywords = {COVID-19, OpenDataSet},

pubstate = {published},

tppubtype = {article}

}

@article{@article{CEREDA2021100528,,

title = {The early phase of the COVID-19 epidemic in Lombardy, Italy},

author = {Danilo Cereda and Mattia Manica and Marcello Tirani and Francesca Rovida and Vittorio Demicheli and Marco Ajelli and Piero Poletti and Filippo Trentini and Giorgio Guzzetta and Valentina Marziano and Raffaella Piccarreta and Antonio Barone and Michele Magoni and Silvia Deandrea and Giulio Diurno and Massimo Lombardo and Marino Faccini and Angelo Pan and Raffaele Bruno and Elena Pariani and Giacomo Grasselli and Alessandra Piatti and Maria Gramegna and Fausto Baldanti and Alessia Melegaro and Stefano Merler},

url = {https://www.sciencedirect.com/science/article/pii/S1755436521000724},

doi = {https://doi.org/10.1016/j.epidem.2021.100528},

issn = {1755-4365},

year  = {2021},

date = {2021-12-01},

urldate = {2021-12-01},

journal = {Epidemics},

volume = {37},

pages = {100528},

abstract = {Background

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

Methods

We analyzed official records of cases occurred in Lombardy to characterize the epidemiology of SARS-CoV-2 during the early phase of the outbreak. A line list of laboratory-confirmed cases was set up and later retrospectively consolidated, using standardized interviews to ascertained cases and their close contacts. We provide estimates of the serial interval, of the basic reproduction number, and of the temporal variation of the net reproduction number of SARS-CoV-2.

Results

Epidemiological investigations detected over 500 cases (median age: 69, IQR: 57–78) before the first COVID-19 diagnosed patient (February 20, 2020), and suggested that SARS-CoV-2 was already circulating in at least 222 out of 1506 (14.7%) municipalities with sustained transmission across all the Lombardy provinces. We estimated the mean serial interval to be 6.6 days (95% CrI, 0.7–19). Our estimates of the basic reproduction number range from 2.6 in Pavia (95% CI, 2.1–3.2) to 3.3 in Milan (95% CI, 2.9–3.8). A decreasing trend in the net reproduction number was observed following the detection of the first case.

Conclusions

At the time of first case notification, COVID-19 was already widespread in the entire Lombardy region. This may explain the large number of critical cases experienced by this region in a very short timeframe. The slight decrease of the reproduction number observed in the early days after February 20, 2020 might be due to increased population awareness and early interventions implemented before the regional lockdown imposed on March 8, 2020.},

keywords = {Coronavirus, COVID-19, epidemiology, Lombardy outbreak, reproduction number, SARS-CoV-2, Transmission dynamics},

pubstate = {published},

tppubtype = {article}

}