Yellow fever transmission in non-human primates, Bahia, Northeastern Brazil

Yellow fever virus (YFV) causes a clinical syndrome of acute hemorrhagic hepatitis. YFV transmission involves non-human primates (NHP), mosquitoes and humans. By late 2016, Brazil experienced the largest YFV outbreak of the last 100 years, with 2050 human confirmed cases, with 681 cases ending in death and 764 confirmed epizootic cases in NHP. Among affected areas, Bahia state in Northeastern was the only region with no autochthonous human cases. By using next generation sequence approach, we investigated the molecular epidemiology of YFV in NHP in Bahia and discuss what factors might have prevented human cases. We investigated 47 YFV positive tissue samples from NHP cases to generate 8 novel YFV genomes. ML phylogenetic tree reconstructions and automated subtyping tools placed the newly generated genomes within the South American genotype I (SA I). Our analysis revealed that the YFV genomes from Bahia formed two distinct well-supported phylogenetic clusters that emerged most likely of an introduction from Minas Gerais and Espírito Santo states. Vegetation coverage analysis performed shows predominantly low to medium vegetation coverage in Bahia state. Together, our findings support the hypothesis of two independent YFV SA-I introductions. We also highlighted the effectiveness of the actions taken by epidemiological surveillance team of the state to prevented human cases.

Genomic Surveillance of Yellow Fever Virus Epizootic in São Paulo, Brazil, 2016 - 2018

São Paulo, a densely inhabited state in southeast Brazil that contains the fourth most populated city in the world, recently experienced its largest yellow fever virus (YFV) outbreak in decades. YFV does not normally circulate extensively in São Paulo, so most people were unvaccinated when the outbreak began. Surveillance in non-human primates (NHPs) is important for determining the magnitude and geographic extent of an epizootic, thereby helping to evaluate the risk of YFV spillover to humans. Data from infected NHPs can give more accurate insights into YFV spread than when using data from human cases alone. To contextualise human cases, identify epizootic foci and uncover the rate and direction of YFV spread in São Paulo, we generated and analysed virus genomic data and epizootic case data from NHPs in São Paulo. We report the occurrence of three spatiotemporally distinct phases of the outbreak in São Paulo prior to February 2018. We generated 51 new virus genomes from YFV positive cases identified in 23 different municipalities in São Paulo, mostly sampled from NHPs between October 2016 and January 2018. Although we observe substantial heterogeneity in lineage dispersal velocities between phylogenetic branches, continuous phylogeographic analyses of generated YFV genomes suggest that YFV lineages spread in São Paulo at a mean rate of approximately 1km per day during all phases of the outbreak. Viral lineages from the first epizootic phase in northern São Paulo subsequently dispersed towards the south of the state to cause the second and third epizootic phases there. This alters our understanding of how YFV was introduced into the densely populated south of São Paulo state. Our results shed light on the sylvatic transmission of YFV in highly fragmented forested regions in São Paulo state and highlight the importance of continued surveillance of zoonotic pathogens in sentinel species.

Epidemiological and clinical characteristics of the COVID-19 epidemic in Brazil

The first case of COVID-19 was detected in Brazil on 25 February 2020. We report and contextualize epidemiological, demographic and clinical findings for COVID-19 cases during the first 3 months of the epidemic. By 31 May 2020, 514,200 COVID-19 cases, including 29,314 deaths, had been reported in 75.3% (4,196 of 5,570) of municipalities across all five administrative regions of Brazil. The R₀ value for Brazil was estimated at 3.1 (95% Bayesian credible interval = 2.4-5.5), with a higher median but overlapping credible intervals compared with some other seriously affected countries. A positive association between higher per-capita income and COVID-19 diagnosis was identified. Furthermore, the severe acute respiratory infection cases with unknown aetiology were associated with lower per-capita income. Co-circulation of six respiratory viruses was detected but at very low levels. These findings provide a comprehensive description of the ongoing COVID-19 epidemic in Brazil and may help to guide subsequent measures to control virus transmission.

Routes for COVID-19 importation in Brazil

The global outbreak caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been declared a pandemic by the World Health Organization. As the number of imported SARS-CoV-2 cases is on the rise in Brazil, we use incidence and historical air travel data to estimate the most important routes of importation into the country.

Genomic evidence of yellow fever virus in Aedes scapularis, southeastern Brazil, 2016

The southeastern region of Brazil has recently experienced the largest yellow fever disease outbreak in decades. Since July 2016 epizootic events were reported in São Paulo state's north region, where 787 Culicidae were captured as part of public health surveillance efforts and tested using real-time quantitative PCR. One Aedes scapularis pool collected in November 2016 in an agriculture area in Urupês city tested positive for YFV-RNA. Using a validated multiplex PCR approach we were able to recover a complete virus genome sequence from this pool. Phylogenetic analysis of the novel strain and publicly available data indicates that the belongs to the South American genotype 1 clade circulating in Sao Paulo state and is basal to the recent outbreak clade in southeast Brazil. Our findings highlight the need of additional studies, including vector competence studies, to disentangle the role of Aedes scapularis in yellow fever transmission in the Americas.

OC 8477 MAKING RESEARCH EASIER, BETTER AND FASTER THROUGH KNOWLEDGE SHARING AND BUILDING COMMUNITIES OF PRACTICE

Background

The Global Health Network improves the health research capacity of low- and middle-income countries (LMICs) by facilitating know-how and knowledge exchange between organisations, disease areas, regions and roles. We show how we use the sharing phenomenon to transform and drive health research in resource-limited settings.

Methods

We harnessed cutting-edge technology that facilitates engagement of medical researchers and healthcare professionals in low-resource settings and creates opportunity for knowledge exchange and capacity development in global health. We built highly functional digital communities of practice (CoPs) that serve as learning and sharing tools for researchers, and a gateway for sharing experience about disease research. These CoPs are intertwined with regional activities such as training workshops with health care professionals, which helps to enhance engagement and impact.

Results

We disseminate resources with collaborators to enable research in LMICs via 37 CoPs. The data derived from these CoPs is used to identify knowledge-gaps in research capacity, as well as a guide to the development of resources and tools, such as standardised outcome measures. The network has developed 25 free peer-reviewed e-learning courses covering a wide range of topics, as well as high-quality professional development tools. We highlight the WHO-TDR Professional Development Scheme that tracks and guides training and career development. The network has trained over 33 500 professionals (with >400 k courses taken) across 119 LMICs on the principles of good clinical practices ensuring the safety of research participants and the integrity and validity of research data.

Conclusion

The Global Health Network is enabling research in areas where data is missing by providing tools, training, and resources whilst supporting and training research teams. The next step is to widen this impact and invite new researchers to drive and enable more and better clinical research in places and situations where evidence is still woefully lacking.

Spatial variation in leopard (Panthera pardus) site use across a gradient of anthropogenic pressure in Tanzania's Ruaha landscape

Understanding large carnivore occurrence patterns in anthropogenic landscapes adjacent to protected areas is central to developing actions for species conservation in an increasingly human-dominated world. Among large carnivores, leopards (Panthera pardus) are the most widely distributed felid. Leopards occupying anthropogenic landscapes frequently come into conflict with humans, which often results in leopard mortality. Leopards' use of anthropogenic landscapes, and their frequent involvement with conflict, make them an insightful species for understanding the determinants of carnivore occurrence across human-dominated habitats. We evaluated the spatial variation in leopard site use across a multiple-use landscape in Tanzania's Ruaha landscape. Our study region encompassed i) Ruaha National Park, where human activities were restricted and sport hunting was prohibited; ii) the Pawaga-Idodi Wildlife Management Area, where wildlife sport hunting, wildlife poaching, and illegal pastoralism all occurred at relatively low levels; and iii) surrounding village lands where carnivores and other wildlife were frequently exposed to human-carnivore conflict related-killings and agricultural habitat conversion and development. We investigated leopard occurrence across the study region via an extensive camera trapping network. We estimated site use as a function of environmental (i.e. habitat and anthropogenic) variables using occupancy models within a Bayesian framework. We observed a steady decline in leopard site use with downgrading protected area status from the national park to the Wildlife Management Area and village lands. Our findings suggest that human-related activities such as increased livestock presence and proximity to human households exerted stronger influence than prey availability on leopard site use, and were the major limiting factors of leopard distribution across the gradient of human pressure, especially in the village lands outside Ruaha National Park. Overall, our study provides valuable information about the determinants of spatial distribution of leopards in human-dominated landscapes that can help inform conservation strategies in the borderlands adjacent to protected areas.

Genomic and epidemiological monitoring of yellow fever virus transmission potential

The yellow fever virus (YFV) epidemic in Brazil is the largest in decades. The recent discovery of YFV in Brazilian Aedes species mosquitos highlights a need to monitor the risk of reestablishment of urban YFV transmission in the Americas. We use a suite of epidemiological, spatial, and genomic approaches to characterize YFV transmission. We show that the age and sex distribution of human cases is characteristic of sylvatic transmission. Analysis of YFV cases combined with genomes generated locally reveals an early phase of sylvatic YFV transmission and spatial expansion toward previously YFV-free areas, followed by a rise in viral spillover to humans in late 2016. Our results establish a framework for monitoring YFV transmission in real time that will contribute to a global strategy to eliminate future YFV epidemics.

The many faces of fear: a synthesis of the methodological variation in characterizing predation risk

Predators affect prey by killing them directly (lethal effects) and by inducing costly antipredator behaviours in living prey (risk effects). Risk effects can strongly influence prey populations and cascade through trophic systems. A prerequisite for assessing risk effects is characterizing the spatiotemporal variation in predation risk. Risk effects research has experienced rapid growth in the last several decades. However, preliminary assessments of the resultant literature suggest that researchers characterize predation risk using a variety of techniques. The implications of this methodological variation for inference and comparability among studies have not been well recognized or formally synthesized. We couple a literature survey with a hierarchical framework, developed from established theory, to quantify the methodological variation in characterizing risk using carnivore-ungulate systems as a case study. Via this process, we documented 244 metrics of risk from 141 studies falling into at least 13 distinct subcategories within three broader categories. Both empirical and theoretical work suggest risk and its effects on prey constitute a complex, multi-dimensional process with expressions varying by spatiotemporal scale. Our survey suggests this multi-scale complexity is reflected in the literature as a whole but often underappreciated in any given study, which complicates comparability among studies and leads to an overemphasis on documenting the presence of risk effects rather than their mechanisms or scale of influence. We suggest risk metrics be placed in a more concrete conceptual framework to clarify inference surrounding risk effects and their cascading effects throughout ecosystems. We recommend studies (i) take a multi-scale approach to characterizing risk; (ii) explicitly consider 'true' predation risk (probability of predation per unit time); and (iii) use risk metrics that facilitate comparison among studies and the evaluation of multiple competing hypotheses. Addressing the pressing questions in risk effects research, including how, to what extent and on what scale they occur, requires leveraging the advantages of the many methods available to characterize risk while minimizing the confusion caused by variability in their application.

Zika virus in the Americas: Early epidemiological and genetic findings

Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015, and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. We performed next-generation sequencing to generate seven Brazilian ZIKV genomes sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Results of phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, which we estimated to have occurred between May and December 2013, more than 12 months before the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV-endemic areas, as well as with reported outbreaks in the Pacific Islands. ZIKV genomes from Brazil are phylogenetically interspersed with those from other South American and Caribbean countries. Mapping mutations onto existing structural models revealed the context of viral amino acid changes present in the outbreak lineage; however, no shared amino acid changes were found among the three currently available virus genomes from microcephaly cases. Municipality-level incidence data indicate that reports of suspected microcephaly in Brazil best correlate with ZIKV incidence around week 17 of pregnancy, although this correlation does not demonstrate causation. Our genetic description and analysis of ZIKV isolates in Brazil provide a baseline for future studies of the evolution and molecular epidemiology of this emerging virus in the Americas.