A Platform for Data-Centric, Continuous Epidemiological Analyses (EpiGraphHub): Descriptive Analysis.

BACKGROUND: Guaranteeing durability, provenance, accessibility, and trust in open data sets can be challenging for researchers and organizations that rely on public repositories of data critical for epidemiology and other health analytics. The required data repositories are often difficult to locate and may require conversion to a standard data format. Data-hosting websites may also change or become unavailable without warning. A single change to the rules in one repository can hinder updating a public dashboard reliant on data pulled from external sources. These concerns are particularly challenging at the international level, because policies on systems aimed at harmonizing health and related data are typically dictated by national governments to serve their individual needs. OBJECTIVE: In this paper, we introduce a comprehensive public health data platform, EpiGraphHub, that aims to provide a single interoperable repository for open health and related data. METHODS: The platform, curated by the international research community, allows secure local integration of sensitive data while facilitating the development of data-driven applications and reports for decision-makers. Its main components include centrally managed databases with fine-grained access control to data, fully automated and documented data collection and transformation, and a powerful web-based data exploration and visualization tool. RESULTS: EpiGraphHub is already being used for hosting a growing collection of open data sets and for automating epidemiological analyses based on them. The project has also released an open-source software library with the analytical methods used in the platform. CONCLUSIONS: The platform is fully open source and open to external users. It is in active development with the goal of maximizing its value for large-scale public health studies.

Dengue, Chikungunya, and Zika: Spatial and Temporal Distribution in Rio de Janeiro State, 2015-2019.

Simultaneous spatial circulation of urban arboviral diseases, such as dengue, chikungunya, and Zika, is a major challenge. In this ecological study of urban arboviruses performed from 2015 to 2019, we analyzed the spatial and temporal dynamics of these arboviruses in all 92 municipalities and nine health regions of Rio de Janeiro state. Annual cumulative incidences are presented for all three arboviruses throughout the study period. Spatial analyses of the three studied arboviruses showed distinct behaviors among municipalities and health regions. Co-circulation of the three arboviruses in the state and a heterogeneous spatiotemporal pattern was observed for each disease and region, with dengue having a higher annual incidence during the five years of the study, as well as two consecutive epidemic years in the state. The increase in transmission in different regions of the state in one year culminated in an epidemic in the state in the following year. A high annual cumulative incidence of chikungunya occurred in municipalities from 2017 to 2019 and of Zika only in 2016. Some municipalities with higher population densities showed higher incidences for some arboviruses and appeared to contribute to the dissemination to cities of lower demographic density and maintenance of these urban arboviruses. Thus, regions recording increased incidences of the three diseases in their territories for long periods should be considered municipal poles, as they initiated and sustained high transmission within their region.

An in-depth statistical analysis of the COVID-19 pandemic's initial spread in the WHO African region.

During the first wave of the COVID-19 pandemic, sub-Saharan African countries experienced comparatively lower rates of SARS-CoV-2 infections and related deaths than in other parts of the world, the reasons for which remain unclear. Yet, there was also considerable variation between countries. Here, we explored potential drivers of this variation among 46 of the 47 WHO African region Member States in a cross-sectional study. We described five indicators of early COVID-19 spread and severity for each country as of 29 November 2020: delay in detection of the first case, length of the early epidemic growth period, cumulative and peak attack rates and crude case fatality ratio (CFR). We tested the influence of 13 pre-pandemic and pandemic response predictor variables on the country-level variation in the spread and severity indicators using multivariate statistics and regression analysis. We found that wealthier African countries, with larger tourism industries and older populations, had higher peak (p<0.001) and cumulative (p<0.001) attack rates, and lower CFRs (p=0.021). More urbanised countries also had higher attack rates (p<0.001 for both indicators). Countries applying more stringent early control policies experienced greater delay in detection of the first case (p<0.001), but the initial propagation of the virus was slower in relatively wealthy, touristic African countries (p=0.023). Careful and early implementation of strict government policies were likely pivotal to delaying the initial phase of the pandemic, but did not have much impact on other indicators of spread and severity. An over-reliance on disruptive containment measures in more resource-limited contexts is neither effective nor sustainable. We thus urge decision-makers to prioritise the reduction of resource-based health disparities, and surveillance and response capacities in particular, to ensure global resilience against future threats to public health and economic stability.

Toxoplasma gondii in domiciled dogs and cats in urban areas of Brazil: risk factors and spatial distribution.

Toxoplasma gondii is a highly prevalent zoonotic parasite in Brazil capable of infecting mammals and birds. The increase in the urban populations of pets and the narrowing of the human-animal relationship can facilitate the transmission of important public health zoonoses, such as toxoplasmosis. This study aimed to evaluate the frequency and spatial distribution of T. gondii infection and its risk factors in domiciled dogs and cats attended at the Jorge Vaitsman Institute, Rio de Janeiro. Serum samples from 400 dogs and 272 cats were evaluated by an indirect fluorescent antibody test (IFAT) for IgG anti-T. gondii antibodies. Epidemiological questionnaires were used to interview the animals' owners to identify risk factors for infection. Of the total, 34% (136/400) of dogs and 8.1% (22/272) of cats had anti-T. gondii antibodies. Breed (OR: 2.10-95%, CI 1.27-3.46) was a risk factor for dogs, while sex (OR: 3.40-95%, CI 1.10-10.52) and homemade food consumption (OR: 8.49-95%, CI 2.48-29.05) were risk factors for cats. Offal consumption was considered a risk factor for both species evaluated (OR: 2.74-95%, CI 1.38-5.43 for dogs; OR: 7.66-95%, CI 1.24-47.29 for cats). The spatial analysis showed that T. gondii seropositive animals were widely distributed in the metropolitan region of Rio de Janeiro state, with a concentration observed mainly in the west and north zones of Rio de Janeiro city. The results emphasize the importance of adopting prophylactic measures to control T. gondii transmission in domiciled dogs and cats in Rio de Janeiro, contributing positively to public health.

TITLE: Toxoplasma gondii chez les chiens et les chats domiciliés dans des zones urbaines du Brésil : facteurs de risque et répartition spatiale. ABSTRACT: Toxoplasma gondii est un parasite zoonotique très répandu au Brésil, capable d'infecter les mammifères et les oiseaux. L'augmentation des populations urbaines d'animaux de compagnie et le rétrécissement de la relation homme-animal peuvent faciliter la transmission de zoonoses importantes pour la santé publique, telles que la toxoplasmose. Cette étude visait à évaluer la fréquence et la distribution spatiale de l'infection à T. gondii et ses facteurs de risque chez les chiens et les chats domiciliés qui ont fréquenté l'Institut Jorge Vaitsman de Rio de Janeiro. Des échantillons de sérum de 400 chiens et 272 chats ont été évalués par un test d'immunofluorescence indirecte (IFAT) pour les anticorps IgG anti-T. gondii. Des questionnaires épidémiologiques ont été appliqués aux propriétaires des animaux pour identifier les facteurs de risque d'infection. Sur le total, 34 % (136/400) des chiens et 8,1 % (22/272) des chats avaient des anticorps anti-T. gondii. La race (OR : 2,10-95 %, IC 1,27-3,46) était un facteur de risque pour les chiens, tandis que le sexe (OR : 3,40-95 %, IC 1,10-10,52) et la consommation d'aliments faits maison (OR : 8,49-95 % IC 2,48-29,05) l'étaient pour les chats. La consommation d'abats a été considérée comme un facteur de risque pour les deux espèces évaluées (OR : 2,74-95 %, IC 1,38-5,43 pour les chiens; OR : 7,66-95 %, IC 1,24-47,29 pour les chats). L'analyse spatiale a montré que les animaux séropositifs pour T. gondii étaient largement répartis dans la région métropolitaine de l'État de Rio de Janeiro, avec une concentration observée principalement dans les zones ouest et nord de la ville de Rio de Janeiro. Les résultats soulignent l'importance d'adopter des mesures prophylactiques pour contrôler la transmission de T. gondii chez les chiens et les chats domiciliés à Rio de Janeiro, contribuant positivement à la santé publique.

Intestinal parasites and risk factors in dogs and cats from Rio de Janeiro, Brazil.

The urban populations of pets, mainly dogs and cats, have been growing in recent years and, consequently, human-animal relationships have become increasingly closer. However, pets are vulnerable to infection by various parasites, as well are their owners due to the zoonotic potential of these agents. This study aimed to assess the frequency and risk factors of intestinal parasites in dogs and cats attended at the Municipal Institute of Veterinary Medicine Jorge Vaitsman, Rio de Janeiro, Brazil, as well as georeferencing the parasitized animals. A total of 608 animals (400 dogs and 208 cats) were enrolled from August 2017 to November 2018. Fecal samples were obtained from the animal's rectum during clinical examination. In addition, the owners of the enrolled dogs and cats were asked to complete an epidemiological questionnaire with questions about the animals' general information, lifestyle, and handling. Fecal samples were subjected to sedimentation and centrifugal-flotation in sucrose solution techniques. The frequencies of intestinal parasites total in dogs and cats were 11.3% and 24.5%, respectively, with hookworms being the most detected parasites in dogs (8.3%) and Dipylidium caninum in cats (12.5%). Sex was the only variable that showed statistical differences in the canine population males being more often infected than female (p < 0.05), while street access was associated with parasitic infections in cats (p < 0.05). The results obtained in this study demonstrate the need to control parasitic infections in domiciled dogs and cats in different municipalities in the metropolitan region of the state of Rio de Janeiro, including residents in the northern, western and central areas.

Entomo-virological surveillance strategy for dengue, Zika and chikungunya arboviruses in field-caught Aedes mosquitoes in an endemic urban area of the Northeast of Brazil.

Aedes spp. are considered the main vectors of dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV) viruses in the world. Arbovirus detection in Aedes mosquitoes can alert authorities to possible outbreaks, reducing the impact of these diseases. The purpose of this study was to perform an operational strategy for virological surveillance of DENV, ZIKV and CHIKV in adult Aedes aegypti and Aedes albopictus mosquitoes captured at different key-sites in an endemic urban area of the Northeast Region of Brazil, with the prospect of discussing its role as part of an alert system for outbreaks in critical areas. Residential and non-residential premises located in areas of recent of transmission of these arboviruses were selected for adult mosquito collection in the rainy season (July) of 2018. A total of 1068 adult mosquitoes were collected: 946 Culex quinquefasciatus (88.6%), 118 Ae. aegypti (11.0%), two Ae. albopictus (0.2%) and two Aedes taeniorhynchus (0.2%). Among the premises surveyed, recycling points (N = 48, 40.7%), municipal schools (N = 36, 30.5%) and junkyards (N = 31, 26.2%) were the places with the highest frequency of adult Ae. aegypti. Health units (including primary health care facilities and one hospital) (N = 23; 19.5%) together with residential premises (N = 11; 9.3%) presented the lowest frequencies. Total RNAs of the samples were extracted from Aedes mosquitoes and a nested reverse transcription (RT) polymerase chain reaction (PCR) assay for detecting and typing DENV, ZIKV and CHIKV was performed. From the 37 Aedes spp. pools analyzed (35 Ae. aegypti, one Ae. albopictus and one Ae. taeniorhynchus), seven were positive for DENV-3, including three pools containing Ae. aegypti females, one containing an Ae. aegypti engorged female and three comprised of Ae. aegypti males. The positive pools were composed of mosquitoes collected in public schools, health units, junkyards, recycling points and residential premises. Our findings reinforce the importance of continuous virological surveillance in Aedes mosquitoes, as a useful tool for detecting arboviruses circulation in vulnerable areas, even in low infestation seasons.

Contribution of fish farming ponds to the production of immature Anopheles spp. in a malaria-endemic Amazonian town.

BACKGROUND: In the past decade fish farming has become an important economic activity in the Occidental Brazilian Amazon, where the number of new fish farms is rapidly increasing. One of the primary concerns with this phenomenon is the contribution of fishponds to the maintenance and increase of the anopheline mosquito population, and the subsequent increase in human malaria burden. This study reports the results of a 2-year anopheline abundance survey in fishponds and natural water bodies in a malaria-endemic area in northwest Brazil. The objective of this study was to investigate the contribution of natural water bodies (rivers, streams, creeks, ponds, and puddles) and artificial fishponds as breeding sites for Anopheles spp. in Mâncio Lima, Acre and to investigate the effect of limnological and environmental variables on Anopheles spp. larval abundance. METHODS: Natural water bodies and fishponds were sampled at eight different times over 2 years (early, mid and late rainy season, dry season) in the Amazonian town of Mâncio Lima, Acre. Anopheline larvae were collected with an entomological dipper, and physical, chemical and ecological characteristics of each water body were measured. Management practices of fishpond owners were ascertained with a systematic questionnaire. RESULTS: Fishponds were four times more infested with anopheline larvae than natural water bodies. Electrical conductivity and the distance to the nearest house were both significant inverse predictors of larval abundance in natural water bodies. The density of larvae in fishponds raised with increasing border vegetation. Fishponds owned by different farmers varied in the extent of anopheline larval infestation but ponds owned by the same individual had similar infestation patterns over time. Commercial fishponds were 1.7-times more infested with anopheline larvae compared to fishponds for family use. CONCLUSIONS: These results suggest that fishponds are important breeding sites for anopheline larvae, and that adequate management activities, such as removal of border vegetation could reduce the abundance of mosquito larvae, most importantly Anopheles darlingi.

Relevance of differentiating between residential and non-residential premises for surveillance and control of Aedes aegypti in Rio de Janeiro, Brazil.

Entomological surveys on Aedes aegypti (L.) often focus on residential premises, while ignoring non-residential premises. It has been proposed that the latter should be subject to specific monitoring strategies, since they have the potential to contribute a large proportion of the overall mosquito population. In this study, we used traps for ovipositing females to compare the levels of Ae. aegypti infestation in residential and non-residential premises and assess whether there was any evidence for a spatial association of infestation between non-residential premises and the surrounding homes. This information is important for designing specific surveillance programmes for these special sites and their surroundings. This study was conducted in three neighbourhoods of the city of Rio de Janeiro, Brazil, with distinct population densities, water services, dengue histories and vegetation coverage. Ae. aegypti abundance was measured using two types of traps (standard and sticky ovitraps) installed in five non-residential premises and 80 residential premises per neighbourhood. Mosquitoes were collected in the summer (January to March) and winter (June to September) of 2007. The distribution of captures per household per week did not differ significantly between the seasons, although larger numbers of eggs and adults were obtained during the summer. Most non-residential premises were not significantly more infested than homes, despite the larger quantities of containers. There were a few exceptions, including a transportation company, two recycling centres and a boat yard. These highly infested non-residential premises were also spatially associated with highly infested homes in the vicinity. Continuous monitoring with traps may be an effective way of evaluating non-residential premises as sources of dengue vectors for nearby communities.