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- Ten-year performance of Influenzanet: ILI time series, risks, vaccine effects, and care-seeking behaviourPublication . van Noort, Sander P.; Codeço, Cláudia T.; Koppeschaar, Carl E.; van Ranst, Marc; Paolotti, Daniela; Gomes, M. Gabriela M.Recent public health threats have propelled major innovations on infectious disease monitoring, culminating in the development of innovative syndromic surveillance methods. Influenzanet is an internet-based system that monitors influenza-like illness (ILI) in cohorts of self-reporting volunteers in European countries since 2003. We investigate and confirm coherence through the first ten years in comparison with ILI data from the European Influenza Surveillance Network and demonstrate country-specific behaviour of participants with ILI regarding medical care seeking. Using regression analysis, we determine that chronic diseases, being a child, living with children, being female, smoking and pets at home, are all independent predictors of ILI risk, whereas practicing sports and walking or bicycling for locomotion are associated with a small risk reduction. No effect for using public transportation or living alone was found. Furthermore, we determine the vaccine effectiveness for ILI for each season.
- inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosisPublication . Soares, Patrícia; Alves, Renato J; Abecasis, Ana B; Penha-Gonçalves, Carlos; Gomes, M Gabriela M; Pereira-Leal, José BTuberculosis is currently the second highest cause of death from infectious diseases worldwide. The emergence of multi and extensive drug resistance is threatening to make tuberculosis incurable. There is growing evidence that the genetic diversity of Mycobacterium tuberculosis may have important clinical consequences. Therefore, combining genetic, clinical and socio-demographic data is critical to understand the epidemiology of this infectious disease, and how virulence and other phenotypic traits evolve over time. This requires dedicated bioinformatics platforms, capable of integrating and enabling analyses of this heterogeneous data.
- Comparative analysis of Streptococcus pneumoniae transmission in Portuguese and Finnish day-care centresPublication . Pessoa, Delphine; Hoti, Fabian; Syrjänen, Ritva; Sá-Leão, Raquel; Kaijalainen, Tarja; Gomes, M Gabriela M; Auranen, KariDay-care centre (DCC) attendees play a central role in maintaining the circulation of Streptococcus pneumoniae (pneumococcus) in the population. The prevalence of pneumococcal carriage is highest in DCC attendees but varies across countries and is found to be consistently lower in Finland than in Portugal. We compared key parameters underlying pneumococcal transmission in DCCs to understand which of these contributed to the observed differences in carriage prevalence.
- Unveiling time in dose-response models to infer host susceptibility to pathogensPublication . Pessoa, Delphine; Souto-Maior, Caetano; Gjini, Erida; Lopes, Joao S; Ceña, Bruno; Codeço, Cláudia T; Gomes, M Gabriela MThe biological effects of interventions to control infectious diseases typically depend on the intensity of pathogen challenge. As much as the levels of natural pathogen circulation vary over time and geographical location, the development of invariant efficacy measures is of major importance, even if only indirectly inferrable. Here a method is introduced to assess host susceptibility to pathogens, and applied to a detailed dataset generated by challenging groups of insect hosts (Drosophila melanogaster) with a range of pathogen (Drosophila C Virus) doses and recording survival over time. The experiment was replicated for flies carrying the Wolbachia symbiont, which is known to reduce host susceptibility to viral infections. The entire dataset is fitted by a novel quantitative framework that significantly extends classical methods for microbial risk assessment and provides accurate distributions of symbiont-induced protection. More generally, our data-driven modeling procedure provides novel insights for study design and analyses to assess interventions.
- Interpreting measures of tuberculosis transmission: a case study on the Portuguese populationPublication . Lopes, Joao; Rodrigues, Paula; Pinho, Suani TR; Andrade, Roberto FS; Duarte, Raquel; Gomes, M Gabriela MTuberculosis remains a high burden for Human society despite considerable investments in its control. Unique features in the history of infection and transmission dynamics of tuberculosis pose serious limitations on the direct interpretation of surveillance data and call for models that incorporate latent processes and simulate specific interventions.
- A Missing Dimension in Measures of Vaccination ImpactsPublication . Gomes, M. Gabriela M.; Lipsitch, Marc; Wargo, Andrew R.; Kurath, Gael; Rebelo, Carlota; Medley, Graham F.; Coutinho, Antonio
- Controlling malaria using livestock-based interventions: a one health approachPublication . Franco, Ana O; Gomes, M Gabriela M; Rowland, Mark; Coleman, Paul G; Davies, Clive RWhere malaria is transmitted by zoophilic vectors, two types of malaria control strategies have been proposed based on animals: using livestock to divert vector biting from people (zooprophylaxis) or as baits to attract vectors to insecticide sources (insecticide-treated livestock). Opposing findings have been obtained on malaria zooprophylaxis, and despite the success of an insecticide-treated livestock trial in Pakistan, where malaria vectors are highly zoophilic, its effectiveness is yet to be formally tested in Africa where vectors are more anthropophilic. This study aims to clarify the different effects of livestock on malaria and to understand under what circumstances livestock-based interventions could play a role in malaria control programmes. This was explored by developing a mathematical model and combining it with data from Pakistan and Ethiopia. Consistent with previous work, a zooprophylactic effect of untreated livestock is predicted in two situations: if vector population density does not increase with livestock introduction, or if livestock numbers and availability to vectors are sufficiently high such that the increase in vector density is counteracted by the diversion of bites from humans to animals. Although, as expected, insecticide-treatment of livestock is predicted to be more beneficial in settings with highly zoophilic vectors, like South Asia, we find that the intervention could also considerably decrease malaria transmission in regions with more anthropophilic vectors, like Anopheles arabiensis in Africa, under specific circumstances: high treatment coverage of the livestock population, using a product with stronger or longer lasting insecticidal effect than in the Pakistan trial, and with small (ideally null) repellency effect, or if increasing the attractiveness of treated livestock to malaria vectors. The results suggest these are the most appropriate conditions for field testing insecticide-treated livestock in an Africa region with moderately zoophilic vectors, where this intervention could contribute to the integrated control of malaria and livestock diseases.
- The representativeness of a European multi-center network for influenza-like-illness participatory surveillancePublication . Cantarelli, Pietro; Debin, Marion; Turbelin, Clément; Poletto, Chiara; Blanchon, Thierry; Falchi, Alessandra; Hanslik, Thomas; Bonmarin, Isabelle; Levy-Bruhl, Daniel; Micheletti, Alessandra; Paolotti, Daniela; Vespignani, Alessandro; Edmunds, John; Eames, Ken; Smallenburg, Ronald; Koppeschaar, Carl; Franco, Ana O; Faustino, Vitor; Carnahan, AnnaSara; Rehn, Moa; Colizza, VittoriaThe Internet is becoming more commonly used as a tool for disease surveillance. Similarly to other surveillance systems and to studies using online data collection, Internet-based surveillance will have biases in participation, affecting the generalizability of the results. Here we quantify the participation biases of Influenzanet, an ongoing European-wide network of Internet-based participatory surveillance systems for influenza-like-illness.
- Modeling Malaria Infection and Immunity against Variant Surface Antigens in Príncipe Island, West AfricaPublication . Trovoada, Maria Jesus; Gonçalves, Lígia A.; Marinho, Cláudio R. F.; Turner, Louise; Hviid, Lars; Penha-Gonçalves, Carlos; Gomes, M. Gabriela M.After remarkable success of vector control campaigns worldwide, concerns about loss of immunity against Plasmodium falciparum due to lack of exposure to the parasite are relevant since an increase of severe cases in less immune individuals is expected. We present a mathematical model to investigate the impact of reducing exposure to the parasite on the immune repertoire against P. falciparum erythrocyte membrane protein 1 (PfEMP1) variants. The model was parameterized with data from Príncipe Island, West Africa, and applied to simulate two alternative transmission scenarios: one where control measures are continued to eventually drive the system to elimination; and another where the effort is interrupted after 6 years of its initiation and the system returns to the initial transmission potential. Population dynamics of parasite prevalence predict that in a few years infection levels return to the pre-control values, while the re-acquisition of the immune repertoire against PfEMP1 is slower, creating a window for increased severity. The model illustrates the consequences of loss of immune repertoire against PfEMP1 in a given setting and can be applied to other regions where similar data may be available.
- Association between Recruitment Methods and Attrition in Internet-Based StudiesPublication . Bajardi, Paolo; Paolotti, Daniela; Vespignani, Alessandro; Eames, Ken; Funk, Sebastian; Edmunds, W. John; Turbelin, Clement; Debin, Marion; Colizza, Vittoria; Smallenburg, Ronald; Koppeschaar, Carl; Franco, Ana O.; Faustino, Vitor; Carnahan, AnnaSara; Rehn, Moa; Merletti, Franco; Douwes, Jeroen; Firestone, Ridvan; Richiardi, LorenzoInternet-based systems for epidemiological studies have advantages over traditional approaches as they can potentially recruit and monitor a wider range of individuals in a relatively inexpensive fashion. We studied the association between communication strategies used for recruitment (offline, online, face-to-face) and follow-up participation in nine Internet-based cohorts: the Influenzanet network of platforms for influenza surveillance which includes seven cohorts in seven different European countries, the Italian birth cohort Ninfea and the New Zealand birth cohort ELF. Follow-up participation varied from 43% to 89% depending on the cohort. Although there were heterogeneities among studies, participants who became aware of the study through an online communication campaign compared with those through traditional offline media seemed to have a lower follow-up participation in 8 out of 9 cohorts. There were no clear differences in participation between participants enrolled face-to-face and those enrolled through other offline strategies. An Internet-based campaign for Internet-based epidemiological studies seems to be less effective than an offline one in enrolling volunteers who keep participating in follow-up questionnaires. This suggests that even for Internet-based epidemiological studies an offline enrollment campaign would be helpful in order to achieve a higher participation proportion and limit the cohort attrition.
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