Yellow fever from Angola and Congo: a storm gathers

A historical perspective on arboviruses of public health interest in Southern Africa

Arboviruses are an existing and expanding threat globally, with the potential for causing devastating health and socioeconomic impacts. Mitigating this threat necessitates a One Health approach that integrates vector surveillance, rapid disease detection, and innovative prevention and control measures. In Southern Africa, limited data on the epidemiology of arboviruses, their vectors, and their hosts prevent an effective response. We reviewed the current knowledge on arboviruses in Southern Africa and identified opportunities for further research. A literature search was conducted to identify studies published on arboviruses in 10 tropical and temperate countries of the Southern African Development Community (SADC) from 1900 onward. We identified 280 studies, half (51.1%) originating from South Africa, that described 31 arboviral species, their vectors, and their clinical effects on hosts reported in the region. Arboviral research flourished in the SADC in the mid-20th century but then declined, before reemerging in the last two decades. Recent research consists largely of case reports describing outbreaks. Historical vector surveillance and serosurveys from the mid-20th century suggest that arboviruses are plentiful across Southern Africa, but large gaps remain in the current understanding of arboviral distribution, transmission dynamics, and public health impact.

Identification of potential inhibitors targeting yellow fever virus helicase through ligand and structure-based computational studies

Yellow fever is a flavivirus having plus-sensed RNA which encodes a single polyprotein. Host proteases cut this polyprotein into seven nonstructural proteins including a vital NS3 protein. The present study aims to identify the most effective inhibitor against the helicase (NS3) using different advanced ligand and structure-based computational studies. A set of 300 ligands was selected against helicase by chemical structural similarity model, which are similar to S-adenosyl-l-cysteine using infiniSee. This tool screens billions of compounds through a similarity search from in-built chemical spaces (CHEMriya, Galaxi, KnowledgeSpace and REALSpace). The pharmacophore was designed from ligands in the library that showed same features. According to the sequence of ligands, six compounds (29, 87, 99, 116, 148, and 208) were taken for pharmacophore designing against helicase protein. Subsequently, compounds from the library which showed the best pharmacophore shared-features were docked using FlexX functionality of SeeSAR and their optibrium properties were analyzed. Afterward, their ADME was improved by replacing the unfavorable fragments, which resulted in the generation of new compounds. The selected best compounds (301, 302, 303 and 304) were docked using SeeSAR and their pharmacokinetics and toxicological properties were evaluated using SwissADME. The optimal inhibitor for yellow fever helicase was 2-amino-N-(4-(dimethylamino)thiazol-2-yl)-4-methyloxazole-5-carboxamide (302), which exhibits promising potential for drug development.Communicated by Ramaswamy H. Sarma.

1-Sulfonyl-3-amino-1H-1,2,4-triazoles as Yellow Fever Virus Inhibitors: Synthesis and Structure-Activity Relationship

Yellow fever virus (YFV) transmitted by infected mosquitoes causes an acute viral disease for which there are no approved small-molecule therapeutics. Our recently developed machine learning models for YFV inhibitors led to the selection of a new pyrazolesulfonamide derivative RCB16003 with acceptable in vitro activity. We report that the N-phenyl-1-(phenylsulfonyl)-1H-1,2,4-triazol-3-amine class, which was recently identified as active non-nucleoside reverse transcriptase inhibitors against HIV-1, can also be repositioned as inhibitors of yellow fever virus replication. As compared to other Flaviviridae or Togaviridae family viruses tested, both compounds RCB16003 and RCB16007 demonstrate selectivity for YFV over related viruses, with only RCB16007 showing some inhibition of the West Nile virus (EC50 7.9 μM, CC50 17 μM, SI 2.2). We also describe the absorption, distribution, metabolism, and excretion (ADME) in vitro and pharmacokinetics (PK) for RCB16007 in mice. This compound had previously been shown to not inhibit hERG, and we now describe that it has good metabolic stability in mouse and human liver microsomes, low levels of CYP inhibition, high protein binding, and no indication of efflux in Caco-2 cells. A single-dose oral PK study in mice has a T1/2 of 3.4 h and Cmax of 1190 ng/mL, suggesting good availability and stability. We now propose that the N-phenyl-1-(phenylsulfonyl)-1H-1,2,4-triazol-3-amine class may be prioritized for in vivo efficacy testing against YFV.

Insecticide resistance status of Aedes aegypti in southern and northern Ghana

BACKGROUND

Outbreaks of Aedes-borne arboviral diseases are becoming rampant in Africa. In Ghana, there is no organized arboviral control programme with interventions restricted to mitigate outbreaks. Insecticide application is a crucial part of outbreak responses and future preventative control measures. Thus, knowledge of the resistance status and underlying mechanisms of Aedes populations is required to ensure optimal insecticide choices. The present study assessed the insecticide resistance status of Aedes aegypti populations from southern Ghana (Accra, Tema and Ada Foah) and northern Ghana (Navrongo) respectively.

METHODS

Phenotypic resistance was determined with WHO susceptibility tests using Ae. aegypti collected as larvae and reared into adults. Knockdown resistance (kdr) mutations were detected using allele-specific PCR. Synergist assays were performed with piperonyl butoxide (PBO) to investigate the possible involvement of metabolic mechanisms in resistance phenotypes.

RESULTS

Resistance to DDT was moderate to high across sites (11.3 to 75.8%) and, for the pyrethroids deltamethrin and permethrin, moderate resistance was detected (62.5 to 88.8%). The 1534C kdr and 1016I kdr alleles were common in all sites (0.65 to 1) and may be on a trajectory toward fixation. In addition, a third kdr mutant, V410L, was detected at lower frequencies (0.03 to 0.31). Pre-exposure to PBO significantly increased the susceptibility of Ae. aegypti to deltamethrin and permethrin (P < 0.001). This indicates that in addition to kdr mutants, metabolic enzymes (monooxygenases) may be involved in the resistance phenotypes observed in the Ae. aegypti populations in these sites.

CONCLUSION

Insecticide resistance underpinned by multiple mechanisms in Ae. aegypti indicates the need for surveillance to assist in developing appropriate vector control strategies for arboviral disease control in Ghana.

Evolving dynamics of Aedes-borne diseases in Africa: a cause for concern

Aedes-borne viruses, yellow fever (YF), dengue, Chikungunya and Zika are taking a huge toll on global health as Africa faces re-emergence with potential for massive human catastrophe. Transmission driven by diverse vectors in ecological settings that range from urban to rural and sylvatic habitats with human and nonhuman primate/reservoir activities across such habitats has facilitated virus movement and spillover to susceptible human populations. Approved vaccine exists for YF, although availability for routine and mass vaccination is often constrained. Integrating vector surveillance, understanding disease ecology with rationalised vaccination in high-risk areas (YF) remains important in disease prevention and control. We review trends in disease occurrence in Africa, hinting on gaps in disease detection and management and the prospects for prevention and/or control.

Yellow Fever: Origin, Epidemiology, Preventive Strategies and Future Prospects

Yellow fever (YF) virus still represents a major threat in low resource countries in both South America and Africa despite the presence of an effective vaccine. YF outbreaks are not only due to insufficient vaccine coverage for insufficient vaccine supply, but also to the increase in people without history of vaccination living in endemic areas. Globalization, continuous population growth, urbanization associated with inadequate public health infrastructure, and climate changes constitute important promoting factors for the spread of this virus to tropical and subtropical areas in mosquito-infested regions capable of spreading the disease. In the present review, we focus on the origin of the virus and its transmission, representing two debated topics throughout the nineteenth century, going deeply into the history of YF vaccines until the development of the vaccine still used nowadays. Besides surveillance, we highlight the urgent need of routine immunization and vaccination campaigns associated to diverse and innovative mosquito control technologies in endemic areas for YF virus in order to minimize the risk of new YF outbreaks and the global burden of YF in the future.

Biophysical Measurement Strategies for Antiviral Drug Development: Recent Progress in Virus-Mimetic Platforms Down to the Single Particle Level

The rapid growth in the global human population has increased the prevalence of emerging infectious diseases, which poses a major risk to public health. In search of effective clinical solutions, the acquisition of knowledge and understanding of biomolecular processes associated with viral pathogens represents a prerequisite. In this context, biophysical engineering approaches are particularly promising since they can resolve biomolecular interactions systematically by circumventing the complexities associated with experiments involving natural biological systems. The engineering approaches encompass the design and construction of biomimetic platforms that simulate the physiological system. This approach enables us to characterize, measure, and quantitatively analyze biomolecular interactions.In this Account, we summarize biophysical measurements that our group has successfully adopted to develop broad-spectrum antiviral drugs based on the lipid envelope antiviral disruption (LEAD) strategy, targeting the structural integrity of the outer viral membrane to abrogate viral infectivity. We particularly focus on the engineering aspects related to the design and construction of the tethered lipid vesicle platform, which closely mimics the viral membrane. We first outline the development of the LEAD agents screening platform that integrates soft matter design components with biomaterials and surface functionalization strategies to facilitate parallel measurements tracking peptide-induced destabilization of nanoscale, virus-mimicking vesicles with tunable size and composition. Then, we describe how this platform can be effectively employed to gain insights into the membrane curvature dependency of certain peptides. The fundamental knowledge acquired through this systematic process is crucial in the identification and subsequent development of antiviral drug candidates. In particular, we highlight the development of curvature-sensitive α-helical (AH) peptides as a broad-spectrum antiviral agent that has been demonstrated as an effective therapeutic treatment against multiple enveloped viruses. Also, we introduce a tethered cluster of vesicles to mimic clusters of enveloped viruses, exhibiting higher infectivity levels in the biological system. Then, we discuss key considerations, including experimental artifacts, namely dye leakage and imaging-related photobleaching, and corresponding corrective measures to improve the accuracy of quantitative interpretation. With the ongoing development and application of the tethered lipid vesicle platform, there is a compelling opportunity to explore fundamental biointerfacial science and develop a new class of broad-spectrum antiviral agents to prepare for the future membrane-enveloped viral pandemics.

Development of Machine Learning Models and the Discovery of a New Antiviral Compound against Yellow Fever Virus

Yellow fever (YF) is an acute viral hemorrhagic disease transmitted by infected mosquitoes. Large epidemics of YF occur when the virus is introduced into heavily populated areas with high mosquito density and low vaccination coverage. The lack of a specific small molecule drug treatment against YF as well as for homologous infections, such as zika and dengue, highlights the importance of these flaviviruses as a public health concern. With the advancement in computer hardware and bioactivity data availability, new tools based on machine learning methods have been introduced into drug discovery, as a means to utilize the growing high throughput screening (HTS) data generated to reduce costs and increase the speed of drug development. The use of predictive machine learning models using previously published data from HTS campaigns or data available in public databases, can enable the selection of compounds with desirable bioactivity and absorption, distribution, metabolism, and excretion profiles. In this study, we have collated cell-based assay data for yellow fever virus from the literature and public databases. The data were used to build predictive models with several machine learning methods that could prioritize compounds for in vitro testing. Five molecules were prioritized and tested in vitro from which we have identified a new pyrazolesulfonamide derivative with EC₅₀ 3.2 μM and CC₅₀ 24 μM, which represents a new scaffold suitable for hit-to-lead optimization that can expand the available drug discovery candidates for YF.

Insecticide resistance status and mechanisms in Aedes aegypti populations from Senegal

Aedes aegypti is the main epidemic vector of arboviruses in Africa. In Senegal, control activities are mainly limited to mitigation of epidemics, with limited information available for Ae. aegypti populations. A better understanding of the current Ae. aegypti susceptibility status to various insecticides and relevant resistance mechanisms involved is needed for the implementation of effective vector control strategies. The present study focuses on the detection of insecticide resistance and reveals the related mechanisms in Ae. aegypti populations from Senegal.

Bioassays were performed on Ae. aegypti adults from nine Senegalese localities (Matam, Louga, Barkedji, Ziguinchor, Mbour, Fatick, Dakar, Kédougou and Touba). Mosquitoes were exposed to four classes of insecticides using the standard WHO protocols. Resistance mechanisms were investigated by genotyping for pyrethroid target site resistance mutations (V1016G, V1016I, F1534C and S989P) and measuring gene expression levels of key detoxification genes (CYP6BB2, CYP9J26, CYP9J28, CYP9J32, CYP9M6, CCEae3a and GSTD4).

All collected populations were resistant to DDT and carbamates except for the ones in Matam (Northern region). Resistance to permethrin was uniformly detected in mosquitoes from all areas. Except for Barkédji and Touba, all populations were characterized by a susceptibility to 0.75% Permethrin. Susceptibility to type II pyrethroids was detected only in the Southern regions (Kédougou and Ziguinchor). All mosquito populations were susceptible to 5% Malathion, but only Kédougou and Matam mosquitoes were susceptible to 0.8% Malathion. All populations were resistant to 0.05% Pirimiphos-methyl, whereas those from Louga, Mbour and Barkédji, also exhibited resistance to 1% Fenitrothion. None of the known target site pyrethroid resistance mutations was present in the mosquito samples included in the genotyping analysis (performed in > 1500 samples). In contrast, a remarkably high (20-70-fold) overexpression of major detoxification genes was observed, suggesting that insecticide resistance is mostly mediated through metabolic mechanisms. These data provide important evidence to support dengue vector control in Senegal.

In Senegal, as in most African countries, the arbovirus epidemics control policy relies on the control of the main vector Ae. aegypti though insecticide applications. Vector control strategies have been largely adopted without information on the vector populations’ insecticide resistance mechanisms. We profiled here the resistance status of nine Ae. aegypti populations from Senegal to four classes of insecticides and their related mechanisms. Our findings revealed high resistance to carbamates, a relative susceptibility of southern populations to pyrethroids and a variable efficacy of organophosphates. Resistance to pyrethroids was driven by a significant overexpression of detoxification genes linked to insecticide metabolism. Our results contribute towards a more targeted and efficient control of Ae. aegypti populations and thus of arbovirus epidemics in Senegal.

Laboratory capacity assessments in 25 African countries at high risk of yellow fever, August-December 2018

Introduction

accurate and timely laboratory diagnosis of yellow fever (YF) is critical to the Eliminate Yellow Fever Epidemics (EYE) strategy. Gavi, the Vaccine Alliance recognized the need to support and build capacity in the national and regional laboratories in the Global YF Laboratory Network (GYFLN) as part of this strategy.

Methods

to better understand current capacity, gaps and needs of the GYFLN laboratories in Africa, assessments were carried out in national and regional reference laboratories in the 25 African countries at high risk for YF outbreaks that were eligible for new financial support from Gavi.

Results

the assessments found that the GYFLN in Africa has high capacity but 21% of specimens were not tested due to lack of testing kits or reagents and approximately 50% of presumptive YF cases were not confirmed at the regional reference laboratory due to problems with shipping.

Conclusion

the laboratory assessments helped to document the baseline capacities of these laboratories prior to Gavi funding to support strengthening YF laboratories.

Multiplex-RT-PCR-ELISA panel for detecting mosquito-borne pathogens: Plasmodium sp. preserved and eluted from dried blood spots on sample cards

BACKGROUND

Children are the most vulnerable group affected by malaria and other tropical, vector-borne diseases in low-resource countries. Infants presenting with acute onset fever represent a major sector of outpatient care in the Lake Victoria region. Misclassification and overuse of antibiotics and anti-malarial medications are consistent problems. Identifying the prevalent mosquito-borne pathogens in the region will reduce the prescription of non-indicated medicines.

METHODS

The literature was reviewed focusing on the mosquito-borne pathogens most prevalent in sub-Saharan Africa. Accordingly, an assay comprised of a multiplex-reverse transcriptase-polymerase chain reaction and an enzyme-linked immunosorbent assay (multiplex-RT-PCR-ELISA) was designed and validated in its ability to identify and differentiate nine human mosquito-borne pathogens including eight arboviruses and Plasmodium sp., the aetiologic agents of malaria. Blood samples obtained from 132 children suspected of having malaria were spotted and preserved on Whatman^® 903 protein sample cards. Multiplex-RT-PCR-ELISA analysis was assessed and compared to results obtained by blood smear microscopy and the malaria rapid diagnostic test (RDT).

RESULTS

Nine out of nine pathogens were amplified specifically by the multiplex-RT-PCR-ELISA panel. Twenty-seven out of 132 paediatric patients presenting with acute fever were infected with Plasmodium sp., confirmed by multiplex-RT-PCR. The results of blood smear microscopy were only 40% sensitive and 92.8% specific. The malaria RDT, on the other hand, detected acute Plasmodium infections with 96.3% sensitivity and 98.1% specificity. The preservation of Plasmodium sp. in clinical sera and whole blood samples spotted on sample cards was evaluated. The duration of successful, sample card storage was 186 to 312 days.

CONCLUSIONS

Reliable, easy-to-use point of care diagnostic tests are a powerful alternative to laboratory-dependent gold standard tests. The multiplex-RT-PCR-ELISA amplified and identified nine vector-borne pathogens including Plasmodium sp. with great accuracy. Translation of improved diagnostic approaches, i.e., multiplex-RT-PCR-ELISA, into effective treatment options promises to reduce childhood mortality and non-indicated prescriptions.

TMEM41B Is a Pan-flavivirus Host Factor

Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection, we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results, we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms present at nearly 20% in East Asian populations reduce flavivirus infection. Based on our mechanistic studies, we propose that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.

Morphology and taxonomic status of Aedes aegypti populations across Senegal

Aedes aegypti is the primary vector of dengue, Zika, yellow fever and chikungunya viruses to humans. In Africa, two subspecies, Ae. aegypti aegypti (Aaa) and Ae. aegypti formosus (Aaf) have been described. Until very recently, it was considered that the two forms were sympatric in East Africa and that only Aaf was present in Central and West Africa. However, recent data suggests that Aaa was also common in Senegal without any clear evidence of genetic differences with Aaf. This study was carried out in different Ae. aegypti populations from Senegal to better clarify their taxonomic status. The larvae, pupae and eggs were collected between July and September 2018 and reared individually to adult stage. For each population, F1 progeny from eggs laid by a single female F0 were reared as sibling samples. The number of pale scales on the first abdominal tergite (T1) and the basal part of the second tergite (T2) were counted. Individuals with no pale scale on T1 were classified as Aaf while those with at least one pale scale on this tergite were classified as Aaa. The morphological variations within families of Aaf were studied across 4 generations. In total, 2400 individuals constituting 240 families were identified, of which 42.5% were heterogeneous (families with both forms). Multivariate statistical analysis of variance including T1 and T2 data together showed that populations were significantly different from each other. Statistical analysis of T1 alone showed a similarity between populations from the southeast while variations were observed within northwest population. The analysis of family composition across generations showed the presence of Aaa and Aaf forms in each generation. The classification of Ae. aegypti into two subspecies is invalid in Senegal. Populations exhibit morphological polymorphism at the intra-family level that could have biological and epidemiological impacts.

TMEM41B is a pan-flavivirus host factor

Flaviviruses pose a constant threat to human health. These RNA viruses are transmitted by the bite of infected mosquitoes and ticks and regularly cause outbreaks. To identify host factors required for flavivirus infection we performed full-genome loss of function CRISPR-Cas9 screens. Based on these results we focused our efforts on characterizing the roles that TMEM41B and VMP1 play in the virus replication cycle. Our mechanistic studies on TMEM41B revealed that all members of the Flaviviridae family that we tested require TMEM41B. We tested 12 additional virus families and found that SARS-CoV-2 of the Coronaviridae also required TMEM41B for infection. Remarkably, single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection. Based on our mechanistic studies we hypothesize that TMEM41B is recruited to flavivirus RNA replication complexes to facilitate membrane curvature, which creates a protected environment for viral genome replication.

HIGHLIGHTS

TMEM41B and VMP1 are required for both autophagy and flavivirus infection, however, autophagy is not required for flavivirus infection.TMEM41B associates with viral proteins and likely facilitates membrane remodeling to establish viral RNA replication complexes.TMEM41B single nucleotide polymorphisms (SNPs) present at nearly twenty percent in East Asian populations reduce flavivirus infection.TMEM41B-deficient cells display an exaggerated innate immune response upon high multiplicity flavivirus infection.

An analysis of International Health Regulations Emergency Committees and Public Health Emergency of International Concern Designations

INTRODUCTION

Nine events have been assessed for potential declaration of a Public Health Emergency of International Concern (PHEIC). A PHEIC is defined as an extraordinary event that constitutes a public health risk to other states through international spread and requires a coordinated international response. The WHO Director-General convenes Emergency Committees (ECs) to provide their advice on whether an event constitutes a PHEIC. The EC rationales have been criticised for being non-transparent and contradictory to the International Health Regulations (IHR). This first comprehensive analysis of EC rationale provides recommendations to increase clarity of EC decisions which will strengthen the IHR and WHO's legitimacy in future outbreaks.

METHODS

66 EC statements were reviewed from nine public health outbreaks of influenza A, Middle East respiratory syndrome coronavirus, polio, Ebola virus disease, Zika, yellow fever and coronavirus disease-2019. Statements were analysed to determine which of the three IHR criteria were noted as contributing towards the EC's justification on whether to declare a PHEIC and what language was used to explain the decision.

RESULTS

Interpretation of the criteria were often vague and applied inconsistently. ECs often failed to describe and justify which criteria had been satisfied.

DISCUSSION

Guidelines must be developed for the standardised interpretation of IHR core criteria. The ECs must clearly identify and justify which criteria have contributed to their rationale for or against PHEIC declaration.

CONCLUSION

Striving for more consistency and transparency in EC justifications would benefit future deliberations and provide more understanding and support for the process.

The V410L knockdown resistance mutation occurs in island and continental populations of Aedes aegypti in West and Central Africa

The extensive use of insecticides for vector control has led to the development of insecticide resistance in Aedes aegypti populations on a global scale, which has significantly compromised control actions. Insecticide resistance, and its underlying mechanisms, has been investigated in several countries, mostly in South American and Asian countries. In Africa, however, studies reporting insecticide resistance are rare and data on resistance mechanisms, notably knockdown resistance (kdr) mutations, is scarce. In this study, the recently described V410L kdr mutation is reported for the first time in old world Ae. aegypti populations, namely from Angola and Madeira island. Two additional kdr mutations, V1016I and F1534C, are also reported for the first time in populations from Angola and Cape Verde. Significant associations with the resistance phenotype were found for both V410L and V1016I individually as well as for tri-locus genotypes in the Angolan population. However, no association was found in Madeira island, probably due to the presence of a complex pattern of multiple insecticide resistance mechanisms in the local Ae. aegypti population. These results suggest that populations carrying the same kdr mutations may respond differently to the same insecticide, stressing the need for complementary studies when assessing the impact of kdr resistance mechanisms in the outcome of insecticide-based control strategies.

A Systematic Review: Is Aedes albopictus an Efficient Bridge Vector for Zoonotic Arboviruses?

Mosquito-borne arboviruses are increasing due to human disturbances of natural ecosystems and globalization of trade and travel. These anthropic changes may affect mosquito communities by modulating ecological traits that influence the “spill-over” dynamics of zoonotic pathogens, especially at the interface between natural and human environments. Particularly, the global invasion of Aedes albopictus is observed not only across urban and peri-urban settings, but also in newly invaded areas in natural settings. This could foster the interaction of Ae. albopictus with wildlife, including local reservoirs of enzootic arboviruses, with implications for the potential zoonotic transfer of pathogens. To evaluate the potential of Ae. albopictus as a bridge vector of arboviruses between wildlife and humans, we performed a bibliographic search and analysis focusing on three components: (1) The capacity of Ae. albopictus to exploit natural larval breeding sites, (2) the blood-feeding behaviour of Ae. albopictus, and (3) Ae. albopictus’ vector competence for arboviruses. Our analysis confirms the potential of Ae. albopictus as a bridge vector based on its colonization of natural breeding sites in newly invaded areas, its opportunistic feeding behaviour together with the preference for human blood, and the competence to transmit 14 arboviruses.

Disease Resurgence, Production Capability Issues and Safety Concerns in the Context of an Aging Population: Is There a Need for a New Yellow Fever Vaccine?

Yellow fever is a potentially fatal, mosquito-borne viral disease that appears to be experiencing a resurgence in endemic areas in Africa and South America and spreading to non-endemic areas despite an effective vaccine. This trend has increased the level of concern about the disease and the potential for importation to areas in Asia with ecological conditions that can sustain yellow fever virus transmission. In this article, we provide a broad overview of yellow fever burden of disease, natural history, treatment, vaccine, prevention and control initiatives, and vaccine and therapeutic agent development efforts.

Identification of Protective CD8 T Cell Responses in a Mouse Model of Zika Virus Infection

Many flaviviruses including dengue (DENV), and Zika (ZIKV) have attracted significant attention in the past few years. As many flaviviruses are spread by arthropods, most of the world's population is at risk of encountering a flavivirus, and infection with these viruses has created a significant disease burden worldwide. Vaccination against flaviviruses is thought to be one of the most promising avenues for reducing the disease burden associated with these viruses. The optimism surrounding a vaccine approach is supported by the highly successful vaccines for yellow fever and Japanese encephalitis. Central to the development of new successful vaccines is the understanding of the correlates of protection that will be necessary to engineer into new vaccines. To aid in this endeavor we have directed our efforts to identify correlates of protection that will reduce the disease burden associated with ZIKV and DENV. Within this study we have identified a novel murine ZIKV specific CD8⁺ T cell epitope, and shown that the ZIKV epitope specific CD8⁺ T cell response has a distinct immunodominance hierarchy present during acute infection and is detectible as part of the memory T cell responses. Our studies confirm that ZIKV-specific CD8⁺ T cells are an important correlate of protection for ZIKV and demonstrate that both naïve and ZIKV immune CD8⁺ T cells are sufficient for protection against a lethal ZIKV infection. Overall this study adds to the body of literature demonstrating a role for CD8⁺ T cells in controlling flavivirus infection.

Lipase and factor V (but not viral load) are prognostic factors for the evolution of severe yellow fever cases

BACKGROUND

Despite a highly efficacious vaccine, yellow fever (YF) is still a major threat in developing countries and a cause of outbreaks. In 2018, the Brazilian state of São Paulo witnessed a new YF outbreak in areas where the virus has not been detected before.

OBJECTIVE

The aim is to describe the clinical and laboratorial characteristics of severe cases of YF, evaluate viral to determine markers associated with fatal outcome.

METHODS

Acute severe YF cases (n = 62) were admitted to the Intensive Care Unit of a reference hospital and submitted to routine laboratorial evaluation on admission. YFV-RNA was detected in serum and urine by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and then sequenced. Patients were classified in two groups: survival or death.

FINDINGS

In the univariate analysis the following variables were associated with outcome: alanin aminotransferase (ALT), aspartat aminotransferase (AST), AST/ALT ratio, total bilirubin (TB), chronic kidney disease epidemiology collaboration (CKD-EPI), ammonia, lipase, factor V, international normalised ratio (INR), lactate and bicarbonate. Logistic regression model showed two independent variables associated with death: lipase [odds ratio (OR) 1.018, 95% confidence interval (CI) 1.007 to 1.030, p = 0.002], and factor V (OR -0.955, 95% CI 0.929 to 0.982, p = 0.001). The estimated lipase and factor V cut-off values that maximised sensitivity and specificity for death prediction were 147.5 U/L [area under the curve (AUC) = 0.879], and 56.5% (AUC = 0.913).

MAIN CONCLUSIONS

YF acute severe cases show a generalised involvement of different organs (liver, spleen, heart, kidneys, intestines and pancreas), and different parameters were related to outcome. Factor V and lipase are independent variables associated with death, reinforcing the importance of hemorrhagic events due to fulminant liver failure and pointing to pancreatitis as a relevant event in the outcome of the disease.

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.

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.

Yellow Fever Virus: Knowledge Gaps Impeding the Fight Against an Old Foe

Yellow fever (YF) was one of the most dangerous infectious diseases of the 18th and 19th centuries, resulting in mass casualties in Africa and the Americas. The etiologic agent is yellow fever virus (YFV), and its live-attenuated form, YFV-17D, remains one of the most potent vaccines ever developed. During the first half of the 20th century, vaccination combined with mosquito control eradicated YFV transmission in urban areas. However, the recent 2016-2018 outbreaks in areas with historically low or no YFV activity have raised serious concerns for an estimated 400-500 million unvaccinated people who now live in at-risk areas. Once a forgotten disease, we highlight here that YF still represents a very real threat to human health and economies. As many gaps remain in our understanding of how YFV interacts with the human host and causes disease, there is an urgent need to address these knowledge gaps and propel YFV research forward.

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.

Geographic patterns and environmental factors associated with human yellow fever presence in the Americas

Background

In the Americas, yellow fever virus transmission is a latent threat due to the proximity between urban and wild environments. Although yellow fever has nearly vanished from North and Central America, there are still 13 countries in the Americas considered endemic by the World Health Organization. Human cases usually occur as a result of the exposure to sylvatic yellow fever in tropical forested environments; but urban outbreaks reported during the last decade demonstrate that the risk in this environment still exists. The objective of this study was to identify spatial patterns and the relationship between key geographic and environmental factors with the distribution of yellow fever human cases in the Americas.

Methodology/Principal findings

An ecological study was carried out to analyze yellow fever human cases reported to the Pan American Health Organization from 2000 to 2014, aggregated by second administrative level subdivisions (counties). Presence of yellow fever by county was used as the outcome variable and eight geo-environmental factors were used as independent variables. Spatial analysis was performed to identify and examine natural settings per county. Subsequently, a multivariable logistic regression model was built. During the study period, 1,164 cases were reported in eight out of the 13 endemic countries. Nearly 83.8% of these cases were concentrated in three countries: Peru (37.4%), Brazil (28.1%) and Colombia (18.4%); and distributed in 57 states/provinces, specifically in 286 counties (3.4% of total counties). Yellow fever presence was significantly associated with altitude, rain, diversity of non-human primate hosts and temperature. A positive spatial autocorrelation revealed a clustered geographic pattern in 138/286 yellow fever positive counties (48.3%).

Conclusions/Significance

A clustered geographic pattern of yellow fever was identified mostly along the Andes eastern foothills. This risk map could support health policies in endemic countries. Geo-environmental factors associated with presence of yellow fever could help predict and adjust the limits of other risk areas of epidemiological concern.

Yellow fever (YF) is a zoonotic disease caused by yellow fever virus (YFV), which is transmitted to humans through the bite of an infected mosquito. Sylvatic and urban cycles have been present in different periods, but currently most cases result from human exposure to jungle or forested environments. The World Health Organization considers 13 countries endemic for YFV in the Americas. The objective of this study was to identify spatial patterns and the relationship between key geographic and environmental factors with the distribution of YF human cases in the Americas. Cases of YF from 2000 to 2014 aggregated by county and eight geo-environmental factors were studied via spatial and statistical analysis. A total of 1,164 cases were reported in this time period, with the majority of them located in Peru, Brazil and Colombia. Yellow fever presence was associated with rain, altitude, diversity of non-human primate hosts and temperature. A large clustered geographic pattern of YF cases was identified along the Andes eastern foothills. Although YF cases can be seen as rare events, the results of this study demonstrate that YF human cases in the Americas are geographically concentrated and are not happening at random, even within areas known to be at risk. Determining the geo-environmental factors related to YFV is essential to delineate risk areas and to consequently improve resource allocation and prevent human cases.