Predicting Yellow Fever Through Species Distribution Modeling of Virus, Vector, and Monkeys

Potential effects of brown howler monkey extinction on dispersal services in fragmented forests void of large dispersers

The dispersal of large-seeded species strongly depends on medium-sized and large frugivores, such as primates, which are highly susceptible to population declines. In the Atlantic Forest, brown howler monkeys Alouatta guariba are medium-sized folivorous-frugivorous species that are likely to occur in small to large fragments where the largest frugivores are extinct. However, populations of this primate have been suffering from forest fragmentation, habitat loss, hunting, and the direct and indirect effects of yellow fever outbreaks, which increase the importance of understanding their role as seed dispersers and the impacts of their potential loss. The richness and abundance of large-seeded species might also be reduced in smaller fragments, which could directly affect the magnitude of the potential impact of disperser extinction on plant recruitment. Here, we tested the following mutually exclusive predictions on the effect of fragment size on plant richness and relative density of medium- and large-seeded species consumed by brown howler monkeys in fragments smaller than 1500 ha: the number and the relative density of plant species potentially affected by the local extinction of these monkeys will be (1) directly related to forest fragment size, or (2) not related to forest fragment size. Plant richness and the relative density of large- and medium-sized seed species consumed by brown howler monkeys did not vary with fragment size, corroborating our second prediction. Thus, the local extinction of brown howler monkeys would have a similar potentially negative impact on plant regeneration for the range of tested fragment sizes. We discuss the limitations of our results and suggest other lines of enquiry for the refinement of our conclusions.

Mechanisms of Yellow Fever Transmission: Gleaning the Overlooked Records of Importance and Identifying Problems, Puzzles, Serious Issues, Surprises and Research Questions

In viral disease research, few diseases can compete with yellow fever for the volume of literature, historical significance, richness of the topics and the amount of strong interest among both scientists and laypersons. While the major foci of viral disease research shifted to other more pressing new diseases in recent decades, many critically important basic tasks still remain unfinished for yellow fever. Some of the examples include the mechanisms of transmission, the process leading to outbreak occurrence, environmental factors, dispersal, and viral persistence in nature. In this review, these subjects are analyzed in depth, based on information not only in old but in modern literatures, to fill in blanks and to update the current understanding on these topics. As a result, many valuable facts, ideas, and other types of information that complement the present knowledge were discovered. Very serious questions about the validity of the arbovirus concept and some research practices were also identified. The characteristics of YFV and its pattern of transmission that make this virus unique among viruses transmitted by Ae. aegypti were also explored. Another emphasis was identification of research questions. The discovery of a few historical surprises was an unexpected benefit.

Weekly Forecasting of Yellow Fever Occurrence and Incidence via Eco-Meteorological Dynamics

Yellow Fever (YF), a mosquito-borne disease, requires ongoing surveillance and prevention due to its persistence and ability to cause major epidemics, including one that began in Brazil in 2016. Forecasting based on factors influencing YF risk can improve efficiency in prevention. This study aimed to produce weekly forecasts of YF occurrence and incidence in Brazil using weekly meteorological and ecohydrological conditions. Occurrence was forecast as the probability of observing any cases, and incidence was forecast to represent morbidity if YF occurs. We fit gamma hurdle models, selecting predictors from several meteorological and ecohydrological factors, based on forecast accuracy defined by receiver operator characteristic curves and mean absolute error. We fit separate models for data before and after the start of the 2016 outbreak, forecasting occurrence and incidence for all municipalities of Brazil weekly. Different predictor sets were found to produce most accurate forecasts in each time period, and forecast accuracy was high for both time periods. Temperature, precipitation, and previous YF burden were most influential predictors among models. Minimum, maximum, mean, and range of weekly temperature, precipitation, and humidity contributed to forecasts, with optimal lag times of 2, 6, and 7 weeks depending on time period. Results from this study show the use of environmental predictors in providing regular forecasts of YF burden and producing nationwide forecasts. Weekly forecasts, which can be produced using the forecast model developed in this study, are beneficial for informing immediate preparedness measures.

Trends in mosquito species distribution modeling: insights for vector surveillance and disease control

Species distribution modeling (SDM) has become an increasingly common approach to explore questions about ecology, geography, outbreak risk, and global change as they relate to infectious disease vectors. Here, we conducted a systematic review of the scientific literature, screening 563 abstracts and identifying 204 studies that used SDMs to produce distribution estimates for mosquito species. While the number of studies employing SDM methods has increased markedly over the past decade, the overwhelming majority used a single method (maximum entropy modeling; MaxEnt) and focused on human infectious disease vectors or their close relatives. The majority of regional models were developed for areas in Africa and Asia, while more localized modeling efforts were most common for North America and Europe. Findings from this study highlight gaps in taxonomic, geographic, and methodological foci of current SDM literature for mosquitoes that can guide future efforts to study the geography of mosquito-borne disease risk.

The role of forest fragmentation in yellow fever virus dispersal

The intense process of deforestation in tropical forests poses serious challenges for the survival of biodiversity, as well as for the human species itself. This scenario is supported by the increase in the incidence of epidemics of zoonotic origin observed over the last few decades. In the specific case of sylvatic yellow fever (YF), it has already been shown that an increase in the transmission risk of the causative agent (yellow fever virus - YFV) is associated with areas with a high degree of forest fragmentation, which can facilitate the spread of the virus. In this study we tested the hypothesis that areas with more fragmented landscapes and a higher edge density (ED) but a high degree of connectivity between forest patches favor YFV spread. To this end, we used YF epizootics in non-human primates (NHPs) in the state of São Paulo to build direct networks, and used a multi-selection approach to analyze which landscape features could facilitate YFV spread. Our results showed that municipalities with the potential to spread the virus exhibited a higher amount of forest edge. Additionally, the models with greater empirical support showed a strong association between forest edge density and the risk of occurrence of epizootic diseases, as well as the need for a minimum threshold of native vegetation cover to restrict their transmission. These findings corroborate our hypothesis that more fragmented landscapes with a higher degree of connectivity favor the spread of YFV, while landscapes with fewer connections tend to act as dead zones for the circulation of the virus.

Applications and advances in acoustic monitoring for infectious disease epidemiology

Emerging infectious diseases continue to pose a significant burden on global public health, and there is a critical need to better understand transmission dynamics arising at the interface of human activity and wildlife habitats. Passive acoustic monitoring (PAM), more typically applied to questions of biodiversity and conservation, provides an opportunity to collect and analyse audio data in relative real time and at low cost. Acoustic methods are increasingly accessible, with the expansion of cloud-based computing, low-cost hardware, and machine learning approaches. Paired with purposeful experimental design, acoustic data can complement existing surveillance methods and provide a novel toolkit to investigate the key biological parameters and ecological interactions that underpin infectious disease epidemiology.

Ecological, Genetic, and Phylogenetic Aspects of YFV 2017-2019 Spread in Rio de Janeiro State

In Brazil, a yellow fever (YF) outbreak was reported in areas considered YF-free for decades. The low vaccination coverage and the increasing forest fragmentation, with the wide distribution of vector mosquitoes, have been related to yellow fever virus (YFV) transmission beyond endemic areas since 2016. Aiming to elucidate the molecular and phylogenetic aspects of YFV spread on a local scale, we generated 43 new YFV genomes sampled from humans, non-human primates (NHP), and primarily, mosquitoes from highly heterogenic areas in 15 localities from Rio de Janeiro (RJ) state during the YFV 2016-2019 outbreak in southeast Brazil. Our analysis revealed that the genetic diversity and spatial distribution of the sylvatic transmission of YFV in RJ originated from at least two introductions and followed two chains of dissemination, here named the YFV RJ-I and YFV RJ-II clades. They moved with similar dispersal speeds from the north to the south of the RJ state in parallel directions, separated by the Serra do Mar Mountain chain, with YFV RJ-I invading the north coast of São Paulo state. The YFV RJ-I clade showed a more significant heterogeneity across the entire polyprotein. The YFV RJ-II clade, with only two amino acid polymorphisms, mapped at NS1 (I1086V), present only in mosquitoes at the same locality and NS4A (I2176V), shared by all YFV clade RJ-II, suggests a recent clustering of YFV isolates collected from different hosts. Our analyses strengthen the role of surveillance, genomic analyses of YVF isolated from other hosts, and environmental studies into the strategies to forecast, control, and prevent yellow fever outbreaks.

Back to Where It Was First Described: Vectors of Sylvatic Yellow Fever Transmission in the 2017 Outbreak in Espírito Santo, Brazil

Evidence of sylvatic yellow fever was first reported in Atlantic Forest areas in Espírito Santo, Brazil, during a yellow fever virus (YFV) outbreak in 1931. An entomological survey was conducted in six forest sites during and after an outbreak reported ~80 years after the last case in the area. Among 10,658 mosquitoes of 78 species, Haemagogus leucocelaenus, and Hg. janthinomys/capricornii were considered the main vectors as they had a relatively high abundance, co-occurred in essentially all areas, and showed high YFV infection rates. Sabethes chloropterus, Sa. soperi, Sa. identicus, Aedes aureolineatus, and Shannoniana fluviatilis may have a secondary role in transmission. This is the first report of Sa. identicus, Ae. aureolineatus, and Sh. fluviatilis infected with YFV. Our study emphasizes the importance of entomological monitoring and maintenance of high vaccination coverage in receptive areas to YFV transmission.

Synthesizing the connections between environmental disturbances and zoonotic spillover

Zoonotic spillover is a phenomenon characterized by the transfer of pathogens between different animal species. Most human emerging infectious diseases originate from non-human animals, and human-related environmental disturbances are the driving forces of the emergence of new human pathogens. Synthesizing the sequence of basic events involved in the emergence of new human pathogens is important for guiding the understanding, identification, and description of key aspects of human activities that can be changed to prevent new outbreaks, epidemics, and pandemics. This review synthesizes the connections between environmental disturbances and increased risk of spillover events based on the One Health perspective. Anthropogenic disturbances in the environment (e.g., deforestation, habitat fragmentation, biodiversity loss, wildlife exploitation) lead to changes in ecological niches, reduction of the dilution effect, increased contact between humans and other animals, changes in the incidence and load of pathogens in animal populations, and alterations in the abiotic factors of landscapes. These phenomena can increase the risk of spillover events and, potentially, facilitate new infectious disease outbreaks. Using Brazil as a study model, this review brings a discussion concerning anthropogenic activities in the Amazon region and their potential impacts on spillover risk and spread of emerging diseases in this region.

An ecological niche model to predict the geographic distribution of Haemagogus janthinomys, Dyar, 1921 a yellow fever and Mayaro virus vector, in South America

Yellow fever virus (YFV) has a long history of impacting human health in South America. Mayaro virus (MAYV) is an emerging arbovirus of public health concern in the Neotropics and its full impact is yet unknown. Both YFV and MAYV are primarily maintained via a sylvatic transmission cycle but can be opportunistically transmitted to humans by the bites of infected forest dwelling Haemagogus janthinomys Dyar, 1921. To better understand the potential risk of YFV and MAYV transmission to humans, a more detailed understanding of this vector species’ distribution is critical. This study compiled a comprehensive database of 177 unique Hg. janthinomys collection sites retrieved from the published literature, digitized museum specimens and publicly accessible mosquito surveillance data. Covariate analysis was performed to optimize a selection of environmental (topographic and bioclimatic) variables associated with predicting habitat suitability, and species distributions modelled across South America using a maximum entropy (MaxEnt) approach. Our results indicate that suitable habitat for Hg. janthinomys can be found across forested regions of South America including the Atlantic forests and interior Amazon.

Mayaro virus is a neglected tropical disease and there is insufficient evidence to define its geographic range. The mosquito Haemagogus janthinomys is a primary vector of Mayaro and its distribution is largely unknown at a sub-country scale. Building compendiums of collection data and creating ecological niche models provides a more precise estimation of vector species potential habitat. Our dataset stands as one of the most expansive existing for collection data of this species combining data published in literature, publicly available data repositories and digitized museum specimen records. Comparing results of niche models with near real time environmental data can give even better predictions of areas where Mayaro virus exposure could occur. The methods and results of this study can be replicated for any disease/vector of interest so long as there is data discoverable through the scientific literature, public repositories, or other civilian and governmental agencies willing to share.

Environmental determinants predicting population vulnerability to high yellow fever incidence

Yellow fever (YF) is an endemic mosquito-borne disease in Brazil, though many locations have not observed cases in recent decades. Some locations with low disease burden may resemble locations with higher disease burden through environmental and ecohydrological characteristics, which are known to impact YF burden, motivating increased or continued prevention measures such as vaccination, mosquito control or surveillance. This study aimed to use environmental characteristics to estimate vulnerability to observing high YF burden among all Brazilian municipalities. Vulnerability was defined in three categories based on yearly incidence between 2000 and 2017: minimal, low and high vulnerability. A cumulative logit model was fit to these categories using environmental and ecohydrological predictors, selecting those that provided the most accurate model fit. Per cent of days with precipitation, mean temperature, biome, population density, elevation, vegetation and nearby disease occurrence were included in best-fitting models. Model results were applied to estimate vulnerability nationwide. Municipalities with highest probability of observing high vulnerability was found in the North and Central-West (2000-2016) as well as the Southeast (2017) regions. Results of this study serve to identify specific locations to prioritize new or ongoing surveillance and prevention of YF based on underlying ecohydrological conditions.

Ecological and environmental factors affecting transmission of sylvatic yellow fever in the 2017-2019 outbreak in the Atlantic Forest, Brazil

BACKGROUND

Yellow fever virus (YFV) is an arbovirus that, despite the existence of a safe and effective vaccine, continues to cause outbreaks of varying dimensions in the Americas and Africa. Between 2017 and 2019, Brazil registered un unprecedented sylvatic YFV outbreak whose severity was the result of its spread into zones of the Atlantic Forest with no signals of viral circulation for nearly 80 years.

METHODS

To investigate the influence of climatic, environmental, and ecological factors governing the dispersion and force of infection of YFV in a naïve area such as the landscape mosaic of Rio de Janeiro (RJ), we combined the analyses of a large set of data including entomological sampling performed before and during the 2017-2019 outbreak, with the geolocation of human and nonhuman primates (NHP) and mosquito infections.

RESULTS

A greater abundance of Haemagogus mosquitoes combined with lower richness and diversity of mosquito fauna increased the probability of finding a YFV-infected mosquito. Furthermore, the analysis of functional traits showed that certain functional groups, composed mainly of Aedini mosquitoes which includes Aedes and Haemagogus mosquitoes, are also more representative in areas where infected mosquitoes were found. Human and NHP infections were more common in two types of landscapes: large and continuous forest, capable of harboring many YFV hosts, and patches of small forest fragments, where environmental imbalance can lead to a greater density of the primary vectors and high human exposure. In both, we show that most human infections (~ 62%) occurred within an 11-km radius of the finding of an infected NHP, which is in line with the flight range of the primary vectors.

CONCLUSIONS

Together, our data suggest that entomological data and landscape composition analyses may help to predict areas permissive to yellow fever outbreaks, allowing protective measures to be taken to avoid human cases.

Mapping environmental suitability of Haemagogus and Sabethes spp. mosquitoes to understand sylvatic transmission risk of yellow fever virus in Brazil

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.

Necropsies disclose a low helminth parasite diversity in periurban howler monkeys

Primate-parasite interactions are often investigated via coprological studies given ethical and conservation restrictions of collecting primate hosts. Yet, these studies are inadequate to recover adult helminths for taxonomic identification and to accurately assess their prevalence, intensity, abundance, and site of infection. Fresh carcasses found in anthropogenic landscapes come as informative and reliable alternatives. In this study, we identified the helminths of brown howler monkeys (Alouatta guariba clamitans) and their sites of infection, and measured their prevalence, intensity, and abundance of infection. We necropsied 18 adult males, 11 adult females, and 7 juvenile males that died in conflicts with the anthropogenic environment (domestic dog attacks, n = 11; electrocutions and road-kills, n = 10 each; unknown, n = 5) in periurban landscapes of southern Brazil between 2013 and 2019. We found three nematodes (Trypanoxyuris minutus, Dipetalonema gracile, and Parabronema bonnei) and one cestode (Bertiella cf. studeri), a diversity estimated to account for a sampling completeness of 99%. Prevalence ranged from 3% for P. bonnei to 100% for T. minutus. Mean abundance ranged from 2 (D. gracile and B. cf. studeri) to 55,116 (T. minutus) and mean intensity of infection ranged from 4 (B. cf. studeri) to 55,116 (T. minutus). Trypanoxyuris minutus sex ratio was strongly male-biased. The intensity of infection with T. minutus was higher in juvenile males and adult females than in adult males. The low parasite diversity and the helminths' mode of transmission are compatible with howlers' arboreality and folivorous-frugivorous diet. The howlers were not infected with soil-transmitted helminth parasites of humans and domestic animals on the ground and probably did not eat invertebrates to complement the diet. Given the lack of evidence of howler health problems, we suggest that the causes of death of the necropsied howlers are the major threats to the long-term conservation of the species at the study periurban landscapes.

Burden is in the eye of the beholder: Sensitivity of yellow fever disease burden estimates to modeling assumptions

Estimates of disease burden are important for setting public health priorities. These estimates involve numerous modeling assumptions, whose uncertainties are not always well described. We developed a framework for estimating the burden of yellow fever in Africa and evaluated its sensitivity to modeling assumptions that are often overlooked. We found that alternative interpretations of serological data resulted in a nearly 20-fold difference in burden estimates (range of central estimates, 8.4 × 10⁴ to 1.5 × 10⁶ deaths in 2021–2030). Uncertainty about the vaccination status of serological study participants was the primary driver of this uncertainty. Even so, statistical uncertainty was even greater than uncertainty due to modeling assumptions, accounting for a total of 87% of variance in burden estimates. Combined with estimates that most infections go unreported (range of 95% credible intervals, 99.65 to 99.99%), our results suggest that yellow fever’s burden will remain highly uncertain without major improvements in surveillance.

Dramatic decline in a titi monkey population after the 2016-2018 sylvatic yellow fever outbreak in Brazil

Platyrrhini are highly vulnerable to the yellow fever (YF) virus. From 2016 to 2018, the Atlantic Forest of southeast Brazil faced its worst sylvatic YF outbreak in about a century, thought to have killed thousands of primates. It is essential to assess the impact of this epidemic on threatened primate assemblages to design effective conservation strategies. In this study, we assessed the impact of the 2016-2018 YF outbreak on a geographically isolated population of Near Threatened black-fronted titi monkeys (Callicebus nigrifrons) in two Atlantic Forest patches of the Santuário do Caraça, MG, Brazil. Extensive preoutbreak monitoring, conducted between 2008 and 2016, revealed that the home range and group sizes of the population remained stable. In 2016, the population size was estimated at 53-57 individuals in 11-12 groups. We conducted monitoring and playback surveys in 2019 and found that the population had decreased by 68% in one forest patch and completely vanished in the other, resulting in a combined decline of 80%. We discuss this severe loss of a previously stable population and conclude that it was highly likely caused by the YF outbreak. The remaining population is at risk of disappearing completely because of its small size and geographic isolation. A systematic population surveys of C. nigrifrons, along other sensible Platyrrhini species, is needed to re-evaluate their current conservation status.

Reemergence of Yellow Fever in Brazil: The Role of Distinct Landscape Fragmentation Thresholds

Yellow Fever Virus (YFV) reemergence in Brazil was followed by human suffering and the loss of biodiversity of neotropical simians on the Atlantic coast. The underlying mechanisms were investigated with special focus on distinct landscape fragmentation thresholds in the affected municipalities. An ecological study in epidemiology is employed to assess the statistical relationship between events of YFV and forest fragmentation in municipal landscapes. Negative binomial regression model showed that highly fragmented forest cover was associated with an 85% increase of events of YFV in humans and simians (RR = 1.85, CI 95% = 1.24–2.75, p=0.003) adjusted by vaccine coverage, population size, and municipality area. Intermediate levels of forest cover combined with higher levels of forest edge densities contribute to the YFV dispersion and the exponential growth of YF cases. Strategies for forest conservation are necessary for the control and prevention of YF and other zoonotic diseases that can spillover from the fragmented forest remains to populated cities of the Brazilian Atlantic coast.

Seasonal and inter-annual drivers of yellow fever transmission in South America

In the last 20 years yellow fever (YF) has seen dramatic changes to its incidence and geographic extent, with the largest outbreaks in South America since 1940 occurring in the previously unaffected South-East Atlantic coast of Brazil in 2016-2019. While habitat fragmentation and land-cover have previously been implicated in zoonotic disease, their role in YF has not yet been examined. We examined the extent to which vegetation, land-cover, climate and host population predicted the numbers of months a location reported YF per year and by each month over the time-period. Two sets of models were assessed, one looking at interannual differences over the study period (2003-2016), and a seasonal model looking at intra-annual differences by month, averaging over the years of the study period. Each was fit using hierarchical negative-binomial regression in an exhaustive model fitting process. Within each set, the best performing models, as measured by the Akaike Information Criterion (AIC), were combined to create ensemble models to describe interannual and seasonal variation in YF. The models reproduced the spatiotemporal heterogeneities in YF transmission with coefficient of determination (R2) values of 0.43 (95% CI 0.41-0.45) for the interannual model and 0.66 (95% CI 0.64-0.67) for the seasonal model. For the interannual model, EVI, land-cover and vegetation heterogeneity were the primary contributors to the variance explained by the model, and for the seasonal model, EVI, day temperature and rainfall amplitude. Our models explain much of the spatiotemporal variation in YF in South America, both seasonally and across the period 2003-2016. Vegetation type (EVI), heterogeneity in vegetation (perhaps a proxy for habitat fragmentation) and land cover explain much of the trends in YF transmission seen. These findings may help understand the recent expansions of the YF endemic zone, as well as to the highly seasonal nature of YF.

Spatial modeling could not differentiate early SARS-CoV-2 cases from the distribution of humans on the basis of climate in the United States

The SARS-CoV-2 coronavirus is wreaking havoc globally, yet, as a novel pathogen, knowledge of its biology is still emerging. Climate and seasonality influence the distributions of many diseases, and studies suggest at least some link between SARS-CoV-2 and weather. One such study, building species distribution models (SDMs), predicted SARS-CoV-2 risk may remain concentrated in the Northern Hemisphere, shifting northward in summer months. Others have highlighted issues with SARS-CoV-2 SDMs, notably: the primary niche of the virus is the host it infects, climate may be a weak distributional predictor, global prevalence data have issues, and the virus is not in population equilibrium. While these issues should be considered, we believe climate's relationship with SARS-CoV-2 is still worth exploring, as it may have some impact on the distribution of cases. To further examine if there is a link to climate, we build model projections with raw SARS-CoV-2 case data and population-scaled case data in the USA. The case data were from across March 2020, before large travel restrictions and public health policies were impacting cases across the country. We show that SDMs built from population-scaled case data cannot be distinguished from control models (built from raw human population data), while SDMs built on raw case data fail to predict the known distribution of cases in the U.S. from March. The population-scaled analyses indicate that climate did not play a central role in early U.S. viral distribution and that human population density was likely the primary driver. We do find slightly more population-scaled viral cases in cooler areas. Ultimately, the temporal and geographic constraints on this study mean that we cannot rule out climate as a partial driver of the SARS-CoV-2 distribution. Climate's role on SARS-CoV-2 should continue to be cautiously examined, but at this time we should assume that SARS-CoV-2 will continue to spread anywhere in the U.S. where governmental policy does not prevent spread.

Spatial epidemiology of yellow fever: Identification of determinants of the 2016-2018 epidemics and at-risk areas in Brazil

Optimise control strategies of infectious diseases, identify factors that favour the circulation of pathogens, and propose risk maps are crucial challenges for global health. Ecological niche modelling, once relying on an adequate framework and environmental descriptors can be a helpful tool for such purposes. Despite the existence of a vaccine, yellow fever (YF) is still a public health issue. Brazil faced massive sylvatic YF outbreaks from the end of 2016 up to mid-2018, but cases in human and non-human primates have been recorded until the beginning of 2020. Here we used both human and monkey confirmed YF cases from two epidemic periods (2016/2017 and 2017/2018) to describe the spatial distribution of the cases and explore how biotic and abiotic factors drive their occurrence. The distribution of YF cases largely overlaps for humans and monkeys, and a contraction of the spatial extent associated with a southward displacement is observed during the second period of the epidemics. More contributive variables to the spatiotemporal heterogeneity of cases were related to biotic factors (mammal richness), abiotic factors (temperature and precipitation), and some human-related variables (population density, human footprint, and human vaccination coverage). Both projections of the most favourable conditions showed similar trends with a contraction of the more at-risk areas. Once extrapolated at a large scale, the Amazon basin remains at lower risk, although surrounding forest regions and notably the North-West region, would face a higher risk. Spatial projections of infectious diseases often relied on climatic variables only; here for both models, we instead highlighted the importance of considering local biotic conditions, hosts vulnerability, social and epidemiological factors to run the spatial risk analysis correctly: all YF cases occurring later on, in 2019 and 2020, were observed in the predicted at-risk areas.

Positively selected variants in functionally important regions of TLR7 in Alouatta guariba clamitans with yellow fever virus exposure in Northern Argentina

BACKGROUND

In 2007-2009, a major yellow fever virus (YFV) outbreak in Northern Argentina decimated the local howler monkey (Alouatta) population.

AIMS

To evaluate whether the surviving howler monkeys possess advantageous genetic variants inherited from monkeys alive prior to the YFV outbreak, we explored the relationship between Toll-like receptor (TLR) 7 and TLR8 gene variation and YFV susceptibility.

METHODS

We used samples from Alouatta individuals in Misiones, Argentina alive before the YFV outbreak, individuals that died during the outbreak, and individuals that survived the outbreak and are alive today. We measured genetic divergence between Alouatta YFV exposure groups and evaluated Alouatta-specific substitutions for functional consequences.

RESULTS

We did not find different allele frequencies in the post-YFV exposure Alouatta group compared to the pre-exposure group. We identified three nonsynonymous variants in TLR7 in Alouatta guariba clamitans. Two of these substitutions are under positive selection in functionally important regions of the gene.

DISCUSSION AND CONCLUSIONS

Our results did not indicate that surviving howler monkey spossess advantageous genetic variants at greater frequency than those alive before the YFV outbreak. However, the positively selected unique coding differences in A. guariba clamitans are in the region important in pathogen detection which may affect YFV resistance. Morework is necessary to fully explore this hypothesis.

Eliminating yellow fever epidemics in Africa: Vaccine demand forecast and impact modelling

BACKGROUND

To counter the increasing global risk of Yellow fever (YF), the World Health Organisation initiated the Eliminate Yellow fever Epidemics (EYE) strategy. Estimating YF burden, as well as vaccine impact, while accounting for the features of urban YF transmission such as indirect benefits of vaccination, is key to informing this strategy.

METHODS AND FINDINGS

We developed two model variants to estimate YF burden in sub-Saharan Africa, assuming all infections stem from either the sylvatic or the urban cycle of the disease. Both relied on an ecological niche model fitted to the local presence of any YF reported event in 34 African countries. We calibrated under-reporting using independent estimates of transmission intensity provided by 12 serological surveys performed in 11 countries. We calculated local numbers of YF infections, deaths and disability-adjusted life years (DALYs) lost based on estimated transmission intensity while accounting for time-varying vaccination coverage. We estimated vaccine demand and impact of future preventive mass vaccination campaigns (PMVCs) according to various vaccination scenarios. Vaccination activities conducted in Africa between 2005 and 2017 were estimated to prevent from 3.3 (95% CI 1.2-7.7) to 6.1 (95% CI 2.4-13.2) millions of deaths over the lifetime of vaccinees, representing extreme scenarios of none or maximal herd effects, respectively. By prioritizing provinces based on the risk of urban YF transmission in future PMVCs, an average of 37.7 million annual doses for PMVCs over eight years would avert an estimated 9,900,000 (95% CI 7,000,000-13,400,000) infections and 480,000 (180,000-1,140,000) deaths over the lifetime of vaccinees, corresponding to 1.7 (0.7-4.1) deaths averted per 1,000 vaccine doses.

CONCLUSIONS

By estimating YF burden and vaccine impact over a range of spatial and temporal scales, while accounting for the specificity of urban transmission, our model can be used to inform the current EYE strategy.

Howler monkey tolerance to habitat shrinking: Lifetime warranty or death sentence?

Habitat loss and fragmentation are major threats to the conservation of nonhuman primates. Given that species differ in their responses to fragmented landscapes, identifying the factors that enable them to cope with altered environments or that cause their extirpation is critical to design conservation management strategies. Howler monkeys (Alouatta spp.) are good models for studying the strategies of tolerant arboreal taxa and how they cope with spatial restriction, because they live in habitats ranging from vast pristine forests to small disturbed fragments and orchards. While some aspects of their ecology and behavior are conserved, others vary in predictable ways in response to habitat shrinking and decreasing resource availability. We argue that the ability of individual howler monkeys to inhabit low-quality environments does not guarantee the long-term persistence of the small populations that live under these conditions. Their local extirpation explains why few forest fragments below a given area threshold are frequently inhabited in landscapes where recolonization and gene flow are compromised by long isolation distances or less permeable matrices. In sum, howlers' ability to cope with habitat restriction at the individual level in the short-term may mask the inevitable fate of isolated populations, thereby compromising the persistence of the species at a regional scale in the long-term if howlers' need for protection in large forests is undervalued.

Yellow fever in Brazil threatens successful recovery of endangered golden lion tamarins

The golden lion tamarin is an endangered primate endemic to Brazil's Atlantic Forest. Centuries of deforestation reduced numbers to a few hundred individuals in isolated forest fragments 80 km from Rio de Janeiro city. Intensive conservation action including reintroduction of zoo-born tamarins into forest fragments 1984-2000, increased numbers to about 3,700 in 2014. Beginning in November 2016, southeastern Brazil experienced the most severe yellow fever epidemic/epizootic in the country in 80 years. In May 2018, we documented the first death of a golden lion tamarin due to yellow fever. We re-evaluated population sizes and compared them to results of a census completed in 2014. Tamarin numbers declined 32%, with ca. 2,516 individuals remaining in situ. Tamarin losses were significantly greater in forest fragments that were larger, had less forest edge and had better forest connectivity, factors that may favor the mosquito vectors of yellow fever. The future of golden lion tamarins depends on the extent of additional mortality, whether some tamarins survive the disease and acquire immunity, and the potential development of a vaccine to protect the species against yellow fever.

Yellow Fever: Factors Associated with Death in a Hospital of Reference in Infectious Diseases, São Paulo, Brazil, 2018

Faced with the reemergence of yellow fever (YF) in the metropolitan region of São Paulo, Brazil, we developed a retrospective study to describe the cases of YF attended at the Institute of Infectology Emilio Ribas from January to March 2018 and analyze the factors associated with death, from the information obtained in the hospital epidemiological investigation. A total of 72 cases of sylvatic YF were confirmed, with 21 deaths (29.2% lethality rate). Cases were concentrated in males (80.6%) and in the age group of 30 to 59 years (56.9%). Two logistic regression models were performed, with continuous variables adjusted for the time between onset of symptoms and hospitalization. The first model indicated age (odds ratiosadjusted [ORadj]: 1.038; CI 95%: 1.008-1.212), aspartate aminotransferase (AST) (ORadj: 1.038; CI 95%: 1.005-1.072), and creatinine (ORadj: 2.343; CI 95%: 1.205-4.553) were independent factors associated with mortality. The second model indicated age (ORadj: 1.136; CI 95%: 1.013-1.275), alanine aminotransferase (ALT) (ORadj: 1.118; CI 95%: 1.018-1.228), and creatinine (ORadj: 2.835; CI 95%: 1.352-5,941). The risk of death in the model with continuous variables was calculated from the increase of 1 year (age), 1 mg/dL (creatinine), and 100 U/L for AST and ALT. Another logistic regression analysis with dichotomous variables indicated AST > 1,841 IU/L (ORadj: 12.92; CI 95%: 1.50-111.37) and creatinine > 1.2 mg/dL (ORadj: 81.47; CI 95%: 11.33-585.71) as independent factors associated with death. These results may contribute to the appropriate clinical management of patients with YF in health-care services and improve the response to outbreaks and public health emergencies.

Southern extension of the geographic range of black-and-gold howler monkeys (Alouatta caraya)

The black-and-gold howler monkey (Alouatta caraya) is widely distributed in Brazil, Bolivia, Paraguay, and northeastern Argentina. Despite this wide distribution, it is locally threatened in some parts of its southern range by forest loss and fragmentation, and yellow fever outbreaks. We present 14 new localities of A. caraya occurrence in the Pampa biome of southern Brazil, extending its range southwards by approximately 100 km.

Combination of surveillance tools reveals that Yellow Fever virus can remain in the same Atlantic Forest area at least for three transmission seasons

BACKGROUND

In Brazil, the Yellow Fever virus (YFV) is endemic in the Amazon, from where it eventually expands into epidemic waves. Coastal south-eastern (SE) Brazil, which has been a YFV-free region for eight decades, has reported a severe sylvatic outbreak since 2016. The virus spread from the north toward the south of the Rio de Janeiro (RJ) state, causing 307 human cases with 105 deaths during the 2016-2017 and 2017-2018 transmission seasons. It is unclear, however, whether the YFV would persist in the coastal Atlantic Forest of RJ during subsequent transmission seasons.

OBJECTIVES

To conduct a real-time surveillance and assess the potential persistence of YFV in the coastal Atlantic Forest of RJ during the 2018-2019 transmission season.

METHODS

We combined epizootic surveillance with fast diagnostic and molecular, phylogenetic, and evolutionary analyses.

FINDINGS

Using this integrative strategy, we detected the first evidence of YFV re-emergence in the third transmission season (2018-2019) in a dying howler monkey from the central region of the RJ state. The YFV detected in 2019 has the molecular signature associated with the current SE YFV outbreak and exhibited a close phylogenetic relationship with the YFV lineage that circulated in the same Atlantic Forest fragment during the past seasons. This lineage circulated along the coastal side of the Serra do Mar mountain chain, and its evolution seems to be mainly driven by genetic drift. The potential bridge vector Aedes albopictus was found probing on the recently dead howler monkey in the forest edge, very close to urban areas.

MAIN CONCLUSIONS

Collectively, our data revealed that YFV transmission persisted at the same Atlantic Forest area for at least three consecutive transmission seasons without the need of new introductions. Our real-time surveillance strategy permitted health authorities to take preventive actions within 48 h after the detection of the sick non-human primate. The local virus persistence and the proximity of the epizootic forest to urban areas reinforces the concern with regards to the risk of re-urbanisation and seasonal re-emergence of YFV, stressing the need for continuous effective surveillance and high vaccination coverage in the SE region, particularly in RJ, an important tourist location.