Evolutionary and ecological factors underlying the tempo and distribution of yellow fever virus activity

A proposed One Health approach to control yellow fever outbreaks in Uganda

Yellow Fever (YF) is an acute viral hemorrhagic disease. Uganda is located within the Africa YF belt. Between 2019 and 2022, the Ugandan Health Authorities reported at least one outbreak of YF annually with an estimated 892 suspected cases, on average per year. The persistent recurrence of this disease raises significant concerns about the efficacy of current response strategies and prevention approaches. YF has been recognized as a One Health issue due to its interrelatedness with the animal and environmental domains. Monkeys have been recognized as the virus primary reservoir. The YF virus is transmitted through bites of infected Aedes or Haemagogus species mosquitoes between monkeys and humans. Human activities, monkey health, and environmental health issues (e.g., climate change and land use) impact YF incidence in Uganda. Additionally, disease control programs for other tropical diseases, such as mosquitoes control programs for malaria, impact YF incidence.This review adopts the One Health approach to highlight the limitations in the existing segmented YF control and prevention strategies in Uganda, including the limited health sector surveillance, the geographically localized outbreak response efforts, the lack of a comprehensive vaccination program, the limited collaboration and communication among relevant national and international agencies, and the inadequate vector control practices. Through a One Health approach, we propose establishing a YF elimination taskforce. This taskforce would oversee coordination of YF elimination initiatives, including implementing a comprehensive surveillance system, conducting mass YF vaccination campaigns, integrating mosquito management strategies, and enhancing risk communication. It is anticipated that adopting the One Health approach will reduce the risk of YF incidence and outbreaks.

Using phylogeographic link-prediction in primates to prioritize human parasite screening

Objectives

The ongoing risk of emerging infectious disease has renewed calls for understanding the origins of zoonoses and identifying future zoonotic disease threats. Given their close phylogenetic relatedness and geographic overlap with humans, non-human primates (NHPs) have been the source of many infectious diseases throughout human evolution. NHPs harbor diverse parasites, with some infecting only a single host species while others infect species from multiple families.

Materials and Methods

We applied a novel link-prediction method to predict undocumented instances of parasite sharing between humans and NHPs. Our model makes predictions based on phylogenetic distances and geographic overlap among NHPs and humans in six countries with high NHP diversity: Columbia, Brazil, Democratic Republic of Congo, Madagascar, China and Indonesia.

Results

Of the 899 human parasites documented in the Global Infectious Diseases and Epidemiology Network (GIDEON) database for these countries, 12% were shared with at least one other NHP species. The link prediction model identified an additional 54 parasites that are likely to infect humans but were not reported in GIDEON. These parasites were mostly host generalists, yet their phylogenetic host breadth varied substantially.

Discussion

As human activities and populations encroach on NHP habitats, opportunities for parasite sharing between human and non-human primates will continue to increase. Our study identifies specific infectious organisms to monitor in countries with high NHP diversity, while the comparative analysis of host generalism, parasite taxonomy, and transmission mode provides insights to types of parasites that represent high zoonotic risk.

Rifapentine is an entry and replication inhibitor against yellow fever virus both in vitro and in vivo

Yellow fever virus (YFV) infection is a major public concern that threatens a large population in South America and Africa. No specific anti-YFV drugs are available till now. Here, we report that rifapentine is a potent YFV inhibitor in various cell lines by high-throughput drugs screening, acting at both cell entry and replication steps. Kinetic test and binding assay suggest that rifapentine interferes the viral attachment to the target cells. The application of YFV replicon and surface plasmon resonance assay indicates that rifapentine suppresses viral replication by binding to the RNA-dependent RNA polymerase (RdRp) domain of viral nonstructural protein NS5. Further molecular docking suggests that it might interact with the active centre of RdRp. Rifapentine significantly improves the survival rate, alleviates clinical signs, and reduces virus load and injury in targeted organs both in YFV-infected type I interferon receptor knockout A129^−/− and wild-type C57 mice. The antiviral effect in vivo is robust during both prophylactic intervention and therapeutic treatment, and the activity is superior to sofosbuvir, a previously reported YFV inhibitor in mice. Our data show that rifapentine may serve as an effective anti-YFV agent, providing promising prospects in the development of YFV pharmacotherapy.

Continuous Circulation of Yellow Fever among Rural Populations in the Central African Republic

Yellow fever remains a public-health threat in remote regions of Africa. Here, we report the identification and genetic characterisation of one yellow-fever case observed during the investigation of a cluster of nine suspected haemorrhagic fever cases in a village in the Central African Republic. Samples were tested using real-time RT-PCR targeting the main African haemorrhagic fever viruses. Following negative results, we attempted virus isolation on VERO E6 cells and new-born mice and rescreened the samples using rRT-PCR. The whole viral genome was sequenced using an Illumina NovaSeq 6000 sequencer. Yellow-fever virus (YFV) was isolated from one woman who reported farming activities in a forest setting several days before disease onset. Phylogenetic analysis shows that this strain belongs to the East–Central African YFV genotype, with an estimated emergence some 63 years ago. Finally, five unique amino-acid changes are present in the capsid, envelop, NS1A, NS3, and NS4B proteins. More efforts are required to control yellow-fever re-emergence in resource-limited settings.

Biological Characterization of Yellow Fever Viruses Isolated From Non-human Primates in Brazil With Distinct Genomic Landscapes

Since the beginning of the XXI Century, the yellow fever virus (YFV) has been cyclically spreading from the Amazon basin to Brazil’s South and Southeast regions, culminating in an unprecedented outbreak that started in 2016. In this work, we studied four YFV isolated from non-human primates obtained during outbreaks in the states of Rio Grande do Sul in 2008 (PR4408), Goiás (GO05), and Espírito Santo (ES-504) in 2017, and Rio de Janeiro (RJ 155) in 2019. These isolates have genomic differences mainly distributed in non-structural proteins. We compared the isolates’ rates of infection in mammal and mosquito cells and neurovirulence in adult mice. RJ 155 and PR4408 YFV isolates exhibited higher infectivity in mammalian cells and neurovirulence in mice. In mosquito Aag2 cells, GO05 and PR4408 displayed the lowest proliferation rates. These results suggest that RJ 155 and PR4408 YFV isolates carry some genomic markers that increase infectivity in mammal hosts. From this characterization, it is possible to contribute to discovering new molecular markers for the virulence of YFV.

Genotype-specific features reduce the susceptibility of South American yellow fever virus strains to vaccine-induced antibodies

The resurgence of yellow fever in South America has prompted vaccination against the etiologic agent, yellow fever virus (YFV). Current vaccines are based on a live-attenuated YF-17D virus derived from a virulent African isolate. The capacity of these vaccines to induce neutralizing antibodies against the vaccine strain is used as a surrogate for protection. However, the sensitivity of genetically distinct South American strains to vaccine-induced antibodies is unknown. We show that antiviral potency of the polyclonal antibody response in vaccinees is attenuated against an emergent Brazilian strain. This reduction was attributable to amino acid changes at two sites in central domain II of the glycoprotein E, including multiple changes at the domain I-domain II hinge, which are unique to and shared among most South American YFV strains. Our findings call for a reevaluation of current approaches to YFV immunological surveillance in South America and suggest approaches for updating vaccines.

Vaccination and Therapeutics: Responding to the Changing Epidemiology of Yellow Fever

At the turn of the nineteenth century, yellow fever (YF) was considered the most dangerous infectious disease with high case fatality. Subsequent, mass vaccination campaigns coupled with widespread elimination of the YF mosquito vector significantly decreased YF cases and reduced outbreaks to the tropical and subtropical forested regions of Africa and South America. However, recent (2016) large outbreaks in Angola, Democratic Republic of Congo (DRC), and South-Eastern Brazil, where previously had been demarcated as low-risk regions, have highlighted the possibility of a rapidly changing epidemiology and the potential re-emergence of yellow fever virus (YFV). Furthermore, the first-ever importation of YFV into Asia has highlighted the potential fear of YFV emerging as a global threat. In this review, we describe the changing epidemiology of YF outbreaks, and highlight the use of public health policies, therapeutics, and vaccination as tools to help eliminate future YFV outbreaks.

Vaccination and Therapeutics: Responding to the Changing Epidemiology of Yellow Fever

Purpose of Review

At the turn of the nineteenth century, yellow fever (YF) was considered the most dangerous infectious disease with high case fatality. Subsequent, mass vaccination campaigns coupled with widespread elimination of the YF mosquito vector significantly decreased YF cases and reduced outbreaks to the tropical and subtropical forested regions of Africa and South America.

Recent Findings

However, recent (2016) large outbreaks in Angola, Democratic Republic of Congo (DRC), and South-Eastern Brazil, where previously had been demarcated as low-risk regions, have highlighted the possibility of a rapidly changing epidemiology and the potential re-emergence of yellow fever virus (YFV). Furthermore, the first-ever importation of YFV into Asia has highlighted the potential fear of YFV emerging as a global threat.

Summary

In this review, we describe the changing epidemiology of YF outbreaks and highlight the use of public health policies, therapeutics, and vaccination as tools to help eliminate future YFV outbreaks.

Yellow Fever: Integrating Current Knowledge with Technological Innovations to Identify Strategies for Controlling a Re-Emerging Virus

Yellow fever virus (YFV) represents a re-emerging zoonotic pathogen, transmitted by mosquito vectors to humans from primate reservoirs. Sporadic outbreaks of YFV occur in endemic tropical regions, causing a viral hemorrhagic fever (VHF) associated with high mortality rates. Despite a highly effective vaccine, no antiviral treatments currently exist. Therefore, YFV represents a neglected tropical disease and is chronically understudied, with many aspects of YFV biology incompletely defined including host range, host–virus interactions and correlates of host immunity and pathogenicity. In this article, we review the current state of YFV research, focusing on the viral lifecycle, host responses to infection, species tropism and the success and associated limitations of the YFV-17D vaccine. In addition, we highlight the current lack of available treatments and use publicly available sequence and structural data to assess global patterns of YFV sequence diversity and identify potential drug targets. Finally, we discuss how technological advances, including real-time epidemiological monitoring of outbreaks using next-generation sequencing and CRISPR/Cas9 modification of vector species, could be utilized in future battles against this re-emerging pathogen which continues to cause devastating disease.

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.

Inactivation of yellow fever virus in plasma after treatment with methylene blue and visible light and in platelet concentrates following treatment with ultraviolet C light

BACKGROUND

Yellow fever virus (YFV) is endemic to tropical and subtropical areas in South America and Africa, and is currently a major public health threat in Brazil. Transfusion transmission of the yellow fever vaccine virus has been demonstrated, which is indicative of the potential for viral transfusion transmission. An approach to manage the potential YFV transfusion transmission risk is the use of pathogen inactivation (PI) technology systems, such as THERAFLEX MB-Plasma and THERAFLEX UV-Platelets (Macopharma). We aimed to investigate the efficacy of these PI technology systems to inactivate YFV in plasma or platelet concentrates (PCs).

STUDY DESIGN AND METHODS

YFV spiked plasma units were treated using THERAFLEX MB-Plasma system (visible light doses: 20, 40, 60, and 120 [standard] J/cm2 ) in the presence of methylene blue (approx. 0.8 μmol/L) and spiked PCs were treated using THERAFLEX UV-Platelets system (ultraviolet C doses: 0.05, 0.10, 0.15, and 0.20 [standard] J/cm2 ). Samples were taken before the first and after each illumination dose and tested for residual virus using a modified plaque assay.

RESULTS

YFV infectivity was reduced by an average of 4.77 log or greater in plasma treated with the THERAFLEX MB-Plasma system and by 4.8 log or greater in PCs treated with THERAFLEX UV-Platelets system.

CONCLUSIONS

Our study suggests the THERAFLEX MB-Plasma and the THERAFLEX UV-Platelets systems can efficiently inactivate YFV in plasma or PCs to a similar degree as that for other arboviruses. Given the reduction levels observed in this study, these PI technology systems could be an effective option for managing YFV transfusion-transmission risk in plasma and PCs.

Distinct YFV Lineages Co-circulated in the Central-Western and Southeastern Brazilian Regions From 2015 to 2018

The current outbreak of yellow fever virus (YFV) that is afflicting Brazil since the end of 2016 probably originated from a re-introduction of YFV from endemic areas into the non-endemic Southeastern Brazil. However, the lack of genomic sequences from endemic regions hinders the tracking of YFV's dissemination routes. We assessed the origin and spread of the ongoing YFV Brazilian outbreak analyzing a new set of YFV strains infecting humans, non-human primates (NHPs) and mosquitoes sampled across five Brazilian states from endemic and non-endemic regions between 2015 and 2018. We found two YFV sub-clade 1E lineages circulating in NHP from Goiás state (GO), resulting from independent viral introductions into the Araguaia tributary river basin: while one strain from 2017 clustered intermingled with Venezuelan YFV strains from 2000, the other YFV strains sampled in 2015 and 2017 clustered with sequences of the current YFV outbreak in the Brazilian Southeastern region (named YFV2015-2018 lineage), displaying the same molecular signature associated to the current YFV outbreak. After its introduction in GO at around mid-2014, the YFV2015-2018 lineage followed two paths of dissemination outside GO, originating two major YFV sub-lineages: (1) the YFVMG/ES/RJ sub-lineage spread sequentially from the eastern area of Minas Gerais state to Espírito Santo and then to Rio de Janeiro states, following the Southeast Atlantic basin; (2) the YFVMG/SP sub-lineage spread from the southwestern area of Minas Gerais to the metropolitan region of São Paulo state, following the Paraná basin. These results indicate the ongoing YFV outbreak in Southeastern Brazil originated from a dissemination event from GO almost 2 years before its recognition at the end of 2016. From GO this lineage was introduced in Minas Gerais state at least two times, originating two sub-lineages that followed different routes toward densely populated areas. The spread of YFV outside endemic regions for at least 4 years stresses the imperative importance of the continuous monitoring of YFV to aid decision-making for effective control policies aiming the increase of vaccination coverage to avoid the YFV transmission in densely populated urban centers.

Pluripotency of Wolbachia against Arboviruses: the case of yellow fever

Background: Yellow fever outbreaks have re-emerged in Brazil during 2016-18, with mortality rates up to 30%. Although urban transmission has not been reported since 1942, the risk of re-urbanization of yellow fever is significant, as Aedes aegypti is present in most tropical and sub-tropical cities in the World and still remains the main vector of urban YFV. Although the YFV vaccine is safe and effective, it does not always reach populations at greatest risk of infection and there is an acknowledged global shortage of vaccine supply. The introgression of Wolbachia bacteria into Ae. aegypti mosquito populations is being trialed in several countries ( www.worldmosquito.org) as a biocontrol method against dengue, Zika and chikungunya. Here, we studied the ability of Wolbachia to reduce the transmission potential of Ae. aegypti mosquitoes for Yellow fever virus (YFV). Methods: Two recently isolated YFV (primate and human) were used to challenge field-derived wild-type and Wolbachia-infected ( wMel +) Ae. aegypti mosquitoes. The YFV infection status was followed for 7, 14 and 21 days post-oral feeding (dpf). The YFV transmission potential of mosquitoes was evaluated via nano-injection of saliva into uninfected mosquitoes or by inoculation in mice. Results: We found that Wolbachia was able to significantly reduce the prevalence of mosquitoes with YFV infected heads and thoraces for both viral isolates. Furthermore, analyses of mosquito saliva, through indirect injection into naïve mosquitoes or via interferon-deficient mouse model, indicated Wolbachia was associated with profound reduction in the YFV transmission potential of mosquitoes (14dpf). Conclusions: Our results suggest that Wolbachia introgression could be used as a complementary strategy for prevention of urban yellow fever transmission, along with the human vaccination program.

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

Mapping yellow fever (YF) risk is often based on place of infection of human cases, whereas the circulation between nonhuman primates (NHP) and vectors is neglected. In 2008/2009, YF devastated NHP at the southern limit of the disease in the Americas. In view of the recent expansion of YF in Brazil, we modeled the environmental suitability for YF with data from 2008/2009 epizootic, the distribution of NHP (Alouatta spp.), and the mosquito (Haemagogus leucocelaenus) using the maximum entropy algorithm (Maxent) to define risk areas for YF and their main environmental predictors. We evaluated points of occurrence of YF based on dates of confirmed deaths of NHP in three periods, from October 2008 to: December 2008, March 2009, and June 2009. Variables with greatest influence on suitability for YF were seasonality in water vapor pressure (36%), distribution of NHP (32%), maximum wind speed (11%), annual mean rainfall (7%), and maximum temperature in the warmest month (5%). Models of early periods of the epizootic identified suitability for YF in localities that recorded NHP deaths only months later, demonstrating usefulness of the approach for predicting the disease spread. Our data supported influence of rainfall, air humidity, and ambient temperature on the distribution of epizootics. Wind was highlighted as a predicting variable, probably due to its influence on the dispersal of vectors infected with YF in fragmented landscapes. Further studies on the role of wind are necessary to improve our understanding of the occurrence of YF and other arboviruses and their dispersal in the landscape.

Pluripotency of Wolbachia against Arbovirus: the case of yellow fever

Background: Yellow fever outbreaks have re-emerged in Brazil during 2016-18, with mortality rates up to 30%. Although urban transmission has not been reported since 1942, the risk of re-urbanization of yellow fever is significant, as Aedes aegypti is present in most tropical and sub-tropical cities in the World and used to be the main vector in the past. The introgression of Wolbachia bacteria into Ae. aegypti mosquito populations is being trialed in several countries (www.worldmosquito.org)as a biocontrol method against dengue, Zika and chikungunya. Here, we studied the ability of Wolbachia to reduce the transmission potential of Ae. aegypti mosquitoes for yellow fever virus (YFV). Methods: Two recently isolated YFV (primate and human) were used to challenge field-derived wild-type and Wolbachia-infected (wMel +) Ae. aegypti mosquitoes. The YFV infection status was followed for 7, 14 and 21 days post-oral feeding (dpf). The YFV transmission potential of mosquitoes was evaluated via nano-injection of saliva into uninfected mosquitoes or by inoculation in mice. Results: We found that Wolbachia was able to significantly reduce the prevalence of mosquitoes with YFV infected heads and thoraces for both viral isolates. Furthermore, analyses of mosquito saliva, through indirect injection into naïve mosquitoes or via interferon-deficient mouse model, indicated Wolbachia was associated with profound reduction in the YFV transmission potential of mosquitoes (14dpf). Conclusions: Our results suggest that Wolbachia introgression could be used as a complementary strategy for prevention of urban yellow fever transmission, along with the human vaccination program.

Molecular epidemiology of dengue, yellow fever, Zika and Chikungunya arboviruses: An update

Arboviruses are a group of viruses transmitted by arthropods. They are characterized by a wide geographic distribution, which is associated with the presence of the vector, and cause asymptomatic infections or febrile diseases in humans in both enzootic and urban cycles. Recent reports of human infections caused by viruses such as dengue, Zika, and chikungunya have raised concern regarding public health, and have led to the re-evaluation of surveillance mechanisms and measures to control the transmission of these arboviruses. Viruses such as Mayaro and Usutu are not currently responsible for a high number of symptomatic infections in humans, but should remain under epidemiological surveillance to avoid the emergence of new epidemics, as happened with Zika virus, that are associated with new or more severe symptoms. Additionally, significant variation has been observed in these viruses, giving rise to different lineages. Until recently, the emergence of new lineages has primarily been related to geographical distribution and dispersion, allowing us to ascertain the possible origins and direction of expansion of each virus type, and to make predictions regarding regions where active infections in humans are likely to occur. Therefore, this review is focused on untangling the molecular epidemiology of Dengue, Yellow fever, Zika and Chikungunya due to their recent epidemics in Latinamerica but provides an update on the geographical distribution globally of these viral variants, and outlines the need for further understanding of the genotypes/lineages assignment.

Detection and Molecular Characterization of Yellow Fever Virus, 2017, Brazil

At the end of 2016, Brazil experienced an unprecedented yellow fever (YF) outbreak. Clinical, molecular and ecological aspects of human and non-human primate (NHP) samples collected at the beginning of the outbreak are described in this study. Spatial distribution analyses demonstrated a strong overlap between human and NHP cases. Through molecular analyses, we showed that the outbreak had a sylvatic origin, caused by the South American genotype 1 YFV, which has already been shown to circulate in Brazil. As expected, the clusters of cases were identified in regions with a low vaccination coverage. Our findings highlight the importance of the synchronization of animal surveillance and health services to identify emerging YF cases, thereby promoting a better response to the vulnerable population.

Yellow fever in Africa and the Americas: a historical and epidemiological perspective

Yellow fever was transported during the slave trade in the 15th and 16th centuries from Africa to the Americas where the virus encountered favorable ecological conditions that allowed creation of a sustainable sylvatic cycle. Despite effective vector control and immunization programs for nearly a century, yellow fever epidemics reemerged in many Latin American countries, particularly Brazil. The emergence or reemergence of vector-borne diseases encompasses many intricate factors. Yellow fever outbreaks occur if at least three conditions are fulfilled: the introduction of the virus into a non-immune human community, presence of competent and anthropophilic vectors and insufficiency of prevention and/or adequate management of the growing outbreak. On the other hand, two weapons are available to constrain yellow fever: vector control and immunization. In contrast, yellow fever is absent from Asia and the Pacific despite the presence of the vector and the susceptibility of human populations to the virus. Based on a review of the global history of yellow fever and its epidemiology, the authors deliver some recommendations for improving the prevention of epidemics.

What Does the Future Hold for Yellow Fever Virus? (II)

As revealed by the recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America, YFV control measures need urgent rethinking. Over the last decade, most reported outbreaks occurred in, or eventually reached, areas with low vaccination coverage but that are suitable for virus transmission, with an unprecedented risk of expansion to densely populated territories in Africa, South America and Asia. As reflected in the World Health Organization's initiative launched in 2017, it is high time to strengthen epidemiological surveillance to monitor accurately viral dissemination, and redefine vaccination recommendation areas. Vector-control and immunisation measures need to be adapted and vaccine manufacturing must be reconciled with an increasing demand. We will have to face more yellow fever (YF) cases in the upcoming years. Hence, improving disease management through the development of efficient treatments will prove most beneficial. Undoubtedly, these developments will require in-depth descriptions of YFV biology at molecular, physiological and ecological levels. This second section of a two-part review describes the current state of knowledge and gaps regarding the molecular biology of YFV, along with an overview of the tools that can be used to manage the disease at the individual, local and global levels.

Untold stories of the Zika virus epidemic in Brazil

The Zika virus infection outbreak in Brazil in 2014 to 2015 resulted in the identification of previously unknown consequences of the disease, including the notorious microcephaly among many defects in fetuses born to women infected during pregnancy. A number of individuals were involved in this remarkable discovery, from the detection of viral circulation in the country to the studies on the causal link with congenital abnormalities and the provision of awareness and social support to families affected by the disease. In this article, we review the background to this experience, describing aspects of the epidemiology, medical research, and scientific response to the Zika virus outbreak in Brazil.

Exploratory re-encoding of yellow fever virus genome: new insights for the design of live-attenuated viruses

Virus attenuation by genome re-encoding is a pioneering approach for generating effective live-attenuated vaccine candidates. Its core principle is to introduce a large number of synonymous substitutions into the viral genome to produce stable attenuation of the targeted virus. Introduction of large numbers of mutations has also been shown to maintain stability of the attenuated phenotype by lowering the risk of reversion and recombination of re-encoded genomes. Identifying mutations with low fitness cost is pivotal as this increases the number that can be introduced and generates more stable and attenuated viruses. Here, we sought to identify mutations with low deleterious impact on the in vivo replication and virulence of yellow fever virus (YFV). Following comparative bioinformatic analyses of flaviviral genomes, we categorised synonymous transition mutations according to their impact on CpG/UpA composition and secondary RNA structures. We then designed seventeen re-encoded viruses with 100–400 synonymous mutations in the NS2A-to-NS4B coding region of YFV Asibi and Ap7M (hamster-adapted) genomes. Each virus contained a panel of synonymous mutations designed according to the above categorisation criteria. The replication and fitness characteristics of parent and re-encoded viruses were compared in vitro using cell culture competition experiments. In vivo laboratory hamster models were also used to compare relative virulence and immunogenicity characteristics. Most of the re-encoded strains showed no decrease in replicative fitness in vitro. However, they showed reduced virulence and, in some instances, decreased replicative fitness in vivo. Importantly, the most attenuated of the re-encoded strains induced robust, protective immunity in hamsters following challenge with Ap7M, a virulent virus. Overall, the introduction of transitions with no or a marginal increase in the number of CpG/UpA dinucleotides had the mildest impact on YFV replication and virulence in vivo. Thus, this strategy can be incorporated in procedures for the finely tuned creation of substantially re-encoded viral genomes.

What Does the Future Hold for Yellow Fever Virus? (I)

The recent resurgence of yellow fever virus (YFV) activity in the tropical regions of Africa and South America has sparked renewed interest in this infamous arboviral disease. Yellow fever virus had been a human plague for centuries prior to the identification of its urban transmission vector, the Aedes (Stegomyia) aegypti (Linnaeus) mosquito species, and the development of an efficient live-attenuated vaccine, the YF-17D strain. The combination of vector-control measures and vaccination campaigns drastically reduced YFV incidence in humans on many occasions, but the virus never ceased to circulate in the forest, through its sylvatic invertebrate vector(s) and vertebrate host(s). Outbreaks recently reported in Central Africa (2015⁻2016) and Brazil (since late 2016), reached considerable proportions in terms of spatial distribution and total numbers of cases, with multiple exports, including to China. In turn, questions about the likeliness of occurrence of large urban YFV outbreaks in the Americas or of a successful import of YFV to Asia are currently resurfacing. This two-part review describes the current state of knowledge and gaps regarding the molecular biology and transmission dynamics of YFV, along with an overview of the tools that can be used to manage the disease at individual, local and global levels.

Molecular determinants of Yellow Fever Virus pathogenicity in Syrian Golden Hamsters: one mutation away from virulence

Yellow fever virus (Flavivirus genus) is an arthropod-borne pathogen, which can infect humans, causing a severe viscerotropic disease with a high mortality rate. Adapted viral strains allow the reproduction of yellow fever disease in hamsters with features similar to the human disease. Here, we used the Infectious Subgenomic Amplicons reverse genetics method to produce an equivalent to the hamster-virulent strain, Yellow Fever Ap7, by introducing a set of four synonymous and six nonsynonymous mutations into a single subgenomic amplicon, derived from the sequence of the Asibi strain. The resulting strain, Yellow Fever Ap7M, induced a disease similar to that described for Ap7 in terms of symptoms, weight evolution, viral loads in the liver and lethality. Using the same methodology, we produced mutant strains derived from either Ap7M or Asibi viruses and investigated the role of each of Ap7M nonsynonymous mutations in its in vivo phenotype. This allowed identifying key components of the virulence mechanism in hamsters. In Ap7M virus, the reversion of either E/Q27H or E/D155A mutations led to an important reduction of both virulence and in vivo replicative fitness. In addition, the introduction of the single D155A Ap7M mutation within the E protein of the Asibi virus was sufficient to drastically modify its phenotype in hamsters toward both a greater replication efficiency and virulence. Finally, inspection of the Asibi strain E protein structure combined to in vivo testing revealed the importance of an exposed α-helix in domain I, containing residues 154 and 155, for Ap7M virulence in hamsters.

Genomic and structural features of the yellow fever virus from the 2016-2017 Brazilian outbreak

Southeastern Brazil has been suffering a rapid expansion of a severe sylvatic yellow fever virus (YFV) outbreak since late 2016, which has reached one of the most populated zones in Brazil and South America, heretofore a yellow fever-free zone for more than 70 years. In the current study, we describe the complete genome of 12 YFV samples from mosquitoes, humans and non-human primates from the Brazilian 2017 epidemic. All of the YFV sequences belong to the modern lineage (sub-lineage 1E) of South American genotype I, having been circulating for several months prior to the December 2016 detection. Our data confirm that viral strains associated with the most severe YF epidemic in South America in the last 70 years display unique amino acid substitutions that are mainly located in highly conserved positions in non-structural proteins. Our data also corroborate that YFV has spread southward into Rio de Janeiro state following two main sylvatic dispersion routes that converged at the border of the great metropolitan area comprising nearly 12 million unvaccinated inhabitants. Our original results can help public health authorities to guide the surveillance, prophylaxis and control measures required to face such a severe epidemiological problem. Finally, it will also inspire other workers to further investigate the epidemiological and biological significance of the amino acid polymorphisms detected in the Brazilian 2017 YFV strains.

Phylodynamics of Yellow Fever Virus in the Americas: new insights into the origin of the 2017 Brazilian outbreak

Yellow fever virus (YFV) strains circulating in the Americas belong to two distinct genotypes (I and II) that have diversified into several concurrent enzootic lineages. Since 1999, YFV genotype I has spread outside endemic regions and its recent (2017) reemergence in non-endemic Southeastern Brazilian states fuels one of the largest epizootic of jungle Yellow Fever registered in the country. To better understand this phenomenon, we reconstructed the phylodynamics of YFV American genotypes using sequences from nine countries sampled along 60 years, including strains from Brazilian 2017 outbreak. Our analyses reveals that YFV genotypes I and II follow roughly similar evolutionary and demographic dynamics until the early 1990s, when a dramatic change in the diversification process of the genotype I occurred associated with the emergence and dissemination of a new lineage (here called modern). Trinidad and Tobago was the most likely source of the YFV modern-lineage that spread to Brazil and Venezuela around the late 1980s, where it replaced all lineages previously circulating. The modern-lineage caused all major YFV outbreaks detected in non-endemic South American regions since 2000, including the 2017 Brazilian outbreak, and its dissemination was coupled to the accumulation of several amino acid substitutions particularly within non-structural viral proteins.

Adaptive Diversification Between Yellow Fever Virus West African and South American Lineages: A Genome-Wide Study

Yellow fever virus (YFV) has emerged as the causative agent of a vector-borne disease with devastating mortality in the tropics of Africa and the Americas. YFV phylogenies indicate that the isolates collected from West Africa, East and Central Africa, and South America cluster into different lineages and the virus spread into the Americas from Africa. To determine the nature of genetic variation accompanying the intercontinental epidemic, we performed a genome-wide evolutionary study on the West African and South American lineages of YFV. Our results reveal that adaptive genetic diversification has occurred on viral nonstructural protein 5 (NS5), which is crucially required for viral genome replication, in the early epidemic phase of these currently circulating lineages. Furthermore, major amino acid changes relevant to the adaptive diversification generally cluster in different structural regions of NS5 in a lineage-specific manner. These results suggest that YFV has experienced adaptive diversification in the epidemic spread between the continents and shed insights into the genetic determinants of such diversification, which might be beneficial for understanding the emergence and re-emergence of yellow fever as an important global public health issue.

Yellow fever cases in Asia: primed for an epidemic

There is currently an emerging outbreak of yellow fever in Angola. Cases in infected travellers have been reported in a number of other African countries, as well as in China, representing the first ever documented cases of yellow fever in Asia. There is a large Chinese workforce in Angola, many of whom may be unvaccinated, increasing the risk of ongoing importation of yellow fever into Asia via busy commercial airline routes. Large parts of the region are hyperendemic for the related Flavivirus dengue and are widely infested by Aedes aegypti, the primary mosquito vector of urban yellow fever transmission. The combination of sustained introduction of viraemic travellers, an ecology conducive to local transmission, and an unimmunized population raises the possibility of a yellow fever epidemic in Asia. This represents a major global health threat, particularly in the context of a depleted emergency vaccine stockpile and untested surveillance systems in the region. In this review, the potential for a yellow fever outbreak in Asia is discussed with reference to the ecological and historical forces that have shaped global yellow fever epidemiology. The limitations of surveillance and vector control in the region are highlighted, and priorities for outbreak preparedness and response are suggested.

Geographical distribution of the red howler monkey (Alouatta seniculus) and yellow fever in Colombia

INTRODUCTION

Colombia is a country with an important diversity of non-human primates, of which the red howler monkey (Alouatta seniculus) stands out because of its distribution and the role it plays in the occurrence of yellow fever. 

OBJECTIVE

To describe the geographic co-occurrence of Alouatta seniculus and the reported presence of yellow fever. 

MATERIALS AND METHODS

We conducted a descriptive study. The reported presence of yellow fever in Colombia was obtained from the reports and bulletins issued by the Instituto Nacional de Salud, and the study by Segura, et al. (2013). The occurrence of A. seniculus was determined based on the data from the Global Biodiversity Information Facility and the Colombian Biodiversity Information System. A map of the occurrence was developed using the DIVA-GIS program, and the ecological niche model under current conditions was created with the Maxent program. 

RESULTS

The departments with the highest occurrence of A. seniculus were Antioquia, Meta and Casanare; 69.5% of the departments with reported history of yellow fever had co-occurrence with A. seniculus. The ecological niche model showed that Antioquia, Bolívar, La Guajira, Magdalena, Meta, Santander, Norte de Santander and Vichada had geographical portions with a probability rate nearing to 0.9 (90%). 

CONCLUSIONS

In 69.5% of the departments with a history of yellow fever there was co-occurrence with A. seniculus, which is relevant because non-human primates play a well-known role as natural reservoirs of the virus, and they might contribute to the occurrence of the yellow fever, which makes them very useful as sentinels.

Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales

Determining the time scale of virus evolution is central to understanding their origins and emergence. The phylogenetic methods commonly used for this purpose can be misleading if the substitution model makes incorrect assumptions about the data. Empirical studies consider a pool of models and select that with the highest statistical fit. However, this does not allow the rejection of all models, even if they poorly describe the data. An alternative is to use model adequacy methods that evaluate the ability of a model to predict hypothetical future observations. This can be done by comparing the empirical data with data generated under the model in question. We conducted simulations to evaluate the sensitivity of such methods with nucleotide, amino acid, and codon data. These effectively detected underparameterized models, but failed to detect mutational saturation and some instances of nonstationary base composition, which can lead to biases in estimates of tree topology and length. To test the applicability of these methods with real data, we analyzed nucleotide and amino acid data sets from the genus Flavivirus of RNA viruses. In most cases these models were inadequate, with the exception of a data set of relatively closely related sequences of Dengue virus, for which the GTR+Γ nucleotide and LG+Γ amino acid substitution models were adequate. Our results partly explain the lack of consensus over estimates of the long-term evolutionary time scale of these viruses, and indicate that assessing the adequacy of substitution models should be routinely used to determine whether estimates are reliable.

Yellow fever virus: genetic and phenotypic diversity and implications for detection, prevention and therapy

Yellow fever virus (YFV) is the prototypical hemorrhagic fever virus, yet our understanding of its phenotypic diversity and any molecular basis for observed differences in disease severity and epidemiology is lacking, when compared to other arthropod-borne and haemorrhagic fever viruses. This is, in part, due to the availability of safe and effective vaccines resulting in basic YFV research taking a back seat to those viruses for which no effective vaccine occurs. However, regular outbreaks occur in endemic areas, and the spread of the virus to new, previously unaffected, areas is possible. Analysis of isolates from endemic areas reveals a strong geographic association for major genotypes, and recent epidemics have demonstrated the emergence of novel sequence variants. This review aims to outline the current understanding of YFV genetic and phenotypic diversity and its sources, as well as the available animal models for characterizing these differences in vivo. The consequences of genetic diversity for detection and diagnosis of yellow fever and development of new vaccines and therapeutics are discussed.

A game of numbers: the stoichiometry of antibody-mediated neutralization of flavivirus infection

The humoral response contributes to the protection against viral pathogens. Although antibodies have the potential to inhibit viral infections via several mechanisms, an ability to neutralize viruses directly may be particularly important. Neutralizing antibody titers are commonly used as predictors of protection from infection, especially in the context of vaccine responses and immunity. Despite the simplicity of the concept, how antibody binding results in virus inactivation is incompletely understood despite decades of research. Flaviviruses have been an attractive system in which to seek a structural and quantitative understanding of how antibody interactions with virions modulate infection because of the contribution of antibodies to both protection and pathogenesis. This review will present a stoichiometric model of antibody-mediated neutralization of flaviviruses and discuss how these concepts can inform the development of vaccines and antibody-based therapeutics.

Flavivirus-mosquito interactions

The Flavivirus genus is in the family Flaviviridae and is comprised of more than 70 viruses. These viruses have a broad geographic range, circulating on every continent except Antarctica. Mosquito-borne flaviviruses, such as yellow fever virus, dengue virus serotypes 1-4, Japanese encephalitis virus, and West Nile virus are responsible for significant human morbidity and mortality in affected regions. This review focuses on what is known about flavivirus-mosquito interactions and presents key data collected from the field and laboratory-based molecular and ultrastructural evaluations.