Metagenomic Sequencing Characterizes a Wide Diversity of Viruses in Field Mosquito Samples in Nigeria

Abstract Mosquito vectors are a tremendous public health threat as one in six diseases worldwide is vector-borne transmitted mainly by mosquitoes. In the last couple of years, there have been active Yellow fever virus (YFV) outbreaks in many settings in Nigeria, and nationwide, entomological surveillance has been a significant effort geared towards understanding these outbreaks. In this study, we used a metagenomic sequencing approach to characterize viruses present in vector samples collected during various outbreaks of Yellow fever (YF) in Nigeria between 2017 and 2020. Mosquito samples were grouped into pools of one to fifty mosquitoes, each based on species, sex and location. Twenty-five pools of Aedes spp and one pool of Anopheles spp collected from nine states were sequenced and metagenomic analysis was carried out. We identified a wide diversity of viruses belonging to various families in this sample set. Seven different viruses detected included: Fako virus, Phasi Charoen-like virus, Verdadero virus, Chaq like-virus, Aedes aegypti totivirus, cell fusing agent virus and Tesano Aedes virus. Although there are no reports of these viruses being pathogenic, they are an understudied group in the same families and closely related to known pathogenic arboviruses. Our work shows the revolutionary power of genomics to help detect the presence of viruses in mosquito vectors and unravel their pathogenic potential. This can help develop diagnostics and vaccines to help prevent the diseases caused by these viruses before they cause outbreaks in human populations.

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Prescrição da Vacina Contra a Febre Amarela: Experiência do Centro de Vacinação Internacional do Agrupamento de Centros de Saúde Loures-Odivela

Acta Médica Portuguesa ◽

10.20344/amp.10309 ◽

2018 ◽

Vol 31 (12) ◽

pp. 724

Author(s):

Clarisse Martinho ◽

David Lopes ◽

Luciana Bastos ◽

Hugo Esteves

Keyword(s):

Yellow Fever ◽

Yellow Fever Virus ◽

Health Centre ◽

Travel Medicine ◽

Sub Saharan Africa ◽

World Health ◽

Yellow Fever Vaccine ◽

Travel Destination ◽

Vector Borne ◽

Sub Saharan

Introduction: Yellow fever is a vector-borne disease in sub-Saharan Africa and tropical South America regions which is preventable by an effective and safe vaccine. In some cases, it may cause serious adverse effects and should therefore be prescribed only to individuals at risk of exposure to the yellow fever virus or those traveling to countries requiring proof of vaccination. The aim of this study was to analyze the prescriptions of yellow fever vaccine, based on travel destination and type of referring consultation, according to the international recommendations of the World Health Organization.Material and Methods: The database of the International Vaccination Centre of the International Vaccination Centre of the Loures-Odivelas Health Centre Group was used to analyze data concerning the year of 2016. Travelers who were prescribed and administered the yellow fever vaccine were grouped based on travel destination and type of referring consultation (travelers’ medical consultations or non-specialist consultations).Results: A total of 517 yellow fever vaccines were administered, with the highest proportion in female (53%) and in individuals aged 40 - 49 years (20.7%). One hundred and thirteen (22.6%) of the 499 individuals with known-destinations were travelling to non-endemic/non-epidemic countries and a greater proportion of those were prescribed in non-specialist consultations (27.3%) than in travel medicine consultations (8.8%).Discussion/Conclusion: The highest percentage of yellow fever vaccines that were administered to individuals travelling to non-endemic/non-epidemic countries were prescribed in non-specialist consultations.

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A community-level investigation of the yellow fever virus outbreak in South Omo Zone, South-West Ethiopia, 2012–2014

10.1101/320317 ◽

2018 ◽

Author(s):

Ranya Mulchandani ◽

Fekadu Massebo ◽

Fekadu Bocho ◽

Claire L Jeffries ◽

Thomas Walker ◽

...

Keyword(s):

Yellow Fever ◽

Yellow Fever Virus ◽

Mosquito Species ◽

Breeding Site ◽

Fever Virus ◽

Entomological Surveillance ◽

Breeding Sites ◽

South Omo ◽

South West Ethiopia ◽

Aedes Simpsoni

AbstractBackgroundA yellow fever (YF) outbreak occurred in South Omo Zone, Ethiopia in 2012-2014. This study aimed to analyse historical epidemiological data, to assess the risk for future YF outbreaks through entomological surveillance, including mosquito species identification and molecular screening for arboviruses, and finally to determine the knowledge, attitudes and current preventative practices within the affected communities.Methodology/Principal FindingsFrom October 2012 to March 2014, 165 cases and 62 deaths were reported, principally in rural areas of South Ari region (83.6%), south-west Ethiopia. The majority of patients were 15-44 years old (74.5%) and most case deaths were males (76%). Between June and August 2017, 688 containers were sampled from across 177 households to identify key breeding sites forAedesmosquitoes.Ensete ventricosum(“false banana”) was identified as the primary natural breeding site, and clay pots outside the home as the most productive artificial breeding site. Entomological risk indices from the majority of sites were classified as “high risk” for future outbreaks under current World Health Organization criteria. Adult trapping resulted in the identification of members of theAedes simpsonicomplex in and around households. Screening of adult females revealed no detection of yellow fever virus (YFV) or other arboviruses. 88% of 177 participants had heard of YF, however many participants easily confused transmission and symptoms of YF with malaria, which is also endemic in the area.Conclusions/SignificanceStudy results emphasise the need for further entomological studies to improve our understanding of local vector species and transmission dynamics. Disease surveillance systems and in-country laboratory capacity also need to be strengthened to facilitate more rapid responses to future YF outbreaks.Author SummaryDespite the availability of a highly effective vaccine, yellow fever virus (YFV) remains an important public health problem across Africa and South America due to its high case-fatality rate. This study aimed to assess and reduce the risk for future outbreaks. During this study, historical data analysis was conducted to understand the epidemiology of the recent outbreak in 2012-2014. Entomological surveillance was also carried out, including both mosquito species identification and molecular screening for arboviruses, as well as a household survey to understand the knowledge and attitudes towards yellow fever (YF) within the affected areas and to assess community-level practices for YF prevention. We found a high abundance ofAedes simpsonicomplex in the context of low vaccination coverage. Community knowledge and practice levels were low for reducing potential breeding sites, highlighting the need for increased dissemination of information to community members on how to reduce their risk of exposure to mosquito vectors of arboviruses.

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Re-emergence of yellow fever in the neotropics — quo vadis?

Emerging Topics in Life Sciences ◽

10.1042/etls20200187 ◽

2020 ◽

Vol 4 (4) ◽

pp. 411-422

Author(s):

Livia Sacchetto ◽

Betania P. Drumond ◽

Barbara A. Han ◽

Mauricio L. Nogueira ◽

Nikos Vasilakis

Keyword(s):

Yellow Fever ◽

Amazon Basin ◽

Yellow Fever Virus ◽

Animal Health ◽

Anthropogenic Factors ◽

Human Populations ◽

Sylvatic Cycle ◽

Tropical Regions ◽

Transmission Cycle ◽

Quo Vadis

Yellow fever virus (YFV) is the etiological agent of yellow fever (YF), an acute hemorrhagic vector-borne disease with a significant impact on public health, is endemic across tropical regions in Africa and South America. The virus is maintained in two ecologically and evolutionary distinct transmission cycles: an enzootic, sylvatic cycle, where the virus circulates between arboreal Aedes species mosquitoes and non-human primates, and a human or urban cycle, between humans and anthropophilic Aedes aegypti mosquitoes. While the urban transmission cycle has been eradicated by a highly efficacious licensed vaccine, the enzootic transmission cycle is not amenable to control interventions, leading to recurrent epizootics and spillover outbreaks into human populations. The nature of YF transmission dynamics is multifactorial and encompasses a complex system of biotic, abiotic, and anthropogenic factors rendering predictions of emergence highly speculative. The recent outbreaks in Africa and Brazil clearly remind us of the significant impact YF emergence events pose on human and animal health. The magnitude of the Brazilian outbreak and spillover in densely populated areas outside the recommended vaccination coverage areas raised the specter of human — to — human transmission and re-establishment of enzootic cycles outside the Amazon basin. Herein, we review the factors that influence the re-emergence potential of YFV in the neotropics and offer insights for a constellation of coordinated approaches to better predict and control future YF emergence events.

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Yellow fever virus susceptibility of two mosquito vectors from Kenya, East Africa

Transactions of the Royal Society of Tropical Medicine and Hygiene ◽

10.1016/j.trstmh.2012.02.007 ◽

2012 ◽

Vol 106 (6) ◽

pp. 387-389 ◽

Cited By ~ 12

Author(s):

Brett R. Ellis ◽

Rosemary C. Sang ◽

Kate McElroy Horne ◽

Stephen Higgs ◽

Dawn M. Wesson

Keyword(s):

East Africa ◽

Yellow Fever ◽

Yellow Fever Virus ◽

Fever Virus ◽

Mosquito Vectors ◽

Virus Susceptibility

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Surveillance for Yellow Fever Virus in Non-Human Primates in Southern Brazil, 2001–2011: A Tool for Prioritizing Human Populations for Vaccination

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0002741 ◽

2014 ◽

Vol 8 (3) ◽

pp. e2741 ◽

Cited By ~ 38

Author(s):

Marco A. B. Almeida ◽

Jader da C. Cardoso ◽

Edmilson dos Santos ◽

Daltro F. da Fonseca ◽

Laura L. Cruz ◽

...

Keyword(s):

Yellow Fever ◽

Yellow Fever Virus ◽

Fever Virus ◽

Human Populations ◽

Southern Brazil

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Spatial distribution of arboviral mosquito vectors (Diptera, Culicidae) in Vale do Ribeira in the South-eastern Brazilian Atlantic Forest

Cadernos de Saúde Pública ◽

10.1590/s0102-311x2012000200003 ◽

2012 ◽

Vol 28 (2) ◽

pp. 229-238 ◽

Cited By ~ 8

Author(s):

Gabriel Zorello Laporta ◽

Milton Cezar Ribeiro ◽

Daniel Garkauskas Ramos ◽

Maria Anice Mureb Sallum

Keyword(s):

Spatial Distribution ◽

Atlantic Forest ◽

Yellow Fever Virus ◽

The State ◽

Mosquito Vectors ◽

Rio Grande Do Sul ◽

Entomological Surveillance ◽

Hemorrhagic Fevers ◽

Vast Area ◽

Southeastern Atlantic

Mosquitoes are vectors of arboviruses that can cause encephalitis and hemorrhagic fevers in humans. Aedes serratus (Theobald), Aedes scapularis (Rondani) and Psorophora ferox (Von Humboldt) are potential vectors of arboviruses and are abundant in Vale do Ribeira, located in the Atlantic Forest in the southeast of the State of São Paulo, Brazil. The objective of this study was to predict the spatial distribution of these mosquitoes and estimate the risk of human exposure to mosquito bites. Results of the analyses show that humans are highly exposed to bites in the municipalities of Cananéia, Iguape and Ilha Comprida. In these localities the incidence of Rocio encephalitis was 2% in the 1970s. Furthermore, Ae. serratus, a recently implicated vector of yellow fever virus in the State of Rio Grande do Sul, should be a target for the entomological surveillance in the southeastern Atlantic Forest. Considering the continental dimensions of Brazil and the inherent difficulties in sampling its vast area, the habitat suitability method used in the study can be an important tool for predicting the distribution of vectors of pathogens.

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Dengue and Zika virus 5’-UTRs harbor IRES functions

10.1101/557942 ◽

2019 ◽

Author(s):

Yutong Song ◽

JoAnn Mugavero ◽

Charles B. Stauft ◽

Eckard Wimmer

Keyword(s):

Yellow Fever ◽

Zika Virus ◽

Yellow Fever Virus ◽

Fever Virus ◽

Human Populations ◽

Human Pathogens ◽

West Nile Fever ◽

West Nile ◽

Ribosomal Entry ◽

Dependent Mechanism

AbstractMembers ofFlavivirus, a genus ofFlaviviridae, encompass numerous enveloped plus strand RNA viruses, of which globally dengue virus (DENV) is the leading cause of serious arthropod-borne disease. The genomes of DENV, just as those of yellow fever virus (YFV), West Nile fever virus (WNV), or Zika virus (ZIKV), control their translation by a 5’-terminal capping group. Three other genera of Flaviviridae are remarkable because their viruses use internal ribosomal entry sites (IRESs) to control translation and they are not arthropod transmitted. In 2006 E. Harris’ group published work suggesting that DENV RNA does not stringently need a cap for translation. They proposed that instead DENV translation is controlled by an interplay between 5’ and 3’ termini. Here we present evidence that the DENV or ZIKV 5’-untranslated regions (5’-UTRs) alone have IRES competence. This conclusion is based, first, on the observation that uncapped mono-cistronic mRNAs 5’ terminated with the DENV or ZIKV 5’-UTRs can efficiently direct translation of a reporter gene in BHK and C6/36 cells; second, that either 5’-UTR placed between two reporter genes can efficiently induce expression of the downstream gene in BHK but not in C6/36 cells. These experiments followed observations that uncapped DENV/ZIKV genomic transcripts, 5’ terminated with pppAN… or GpppAN…, can initiate infections of mammalian (BHK) or mosquito (C6/36) cells. IRES competence of the 5’-UTRs of DENV/ZIKV raises many open questions regarding the biology and control, as well as the evolution, of insect-borne flaviviruses.ImportanceMembers of the genusFlavivirusofFlaviviridaeare important human pathogens of great concern because they cause serious diseases, sometimes death, in human populations living in tropical, subtropical (dengue, DENV; Zika, ZIKV; yellow fever virus), or moderate climates (West Nile virus). Flaviviruses are known to control their translation by a cap-dependent mechanism. We have observed, however, that the uncapped genomes of DENV or ZIKV can initiate infection of mammalian and insect cells. We provide evidence that the short 5’ untranslated region (5’-UTR) of DENV or ZIKV genomes can fulfill the function of an internal ribosomal entry site (IRES). This strategy frees these organisms from the cap-dependent mechanism of gene expression at an as yet unknown stage of proliferation. The data raise new questions about the biology and evolution of flaviviruses, possibly leading to new controls of flavivirus disease.

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Flaviviruses – new human pathogens

Postępy Higieny i Medycyny Doświadczalnej ◽

10.5604/01.3001.0011.6683 ◽

2018 ◽

Vol 72 ◽

pp. 184-191

Author(s):

Martyna Biała ◽

Bartosz Jerczak ◽

Małgorzata Inglot ◽

Brygida Knysz

Keyword(s):

Yellow Fever ◽

Yellow Fever Virus ◽

Clinical Manifestations ◽

Health Impact ◽

Human Populations ◽

Human Pathogens ◽

Tick Borne Encephalitis ◽

Animal Pathogens ◽

The Family ◽

Significant Public Health

The family Flaviviridae includes arthropod-borne viruses that are transmitted to vertebrates by infected mosquitoes and ticks. There are over a 100 species in this family, most of which are animal pathogens, although it cannot be excluded that some animal flaviviruses will also cause human disease. The family name is due to the discovery of the yellow fever virus and is derived from the Latin word flavus, meaning yellow. Several human-pathogenic flaviviruses have a significant public health impact in different parts of the world and the potential of emerging in previously non-endemic regions. The medically important flaviviruses include among others: dengue, Zika, yellow fever, tick‐borne encephalitis (TBE) and West Nile viruses. Diseases that are caused by these viruses include a spectrum of illnesses ranging from asymptomatic infections to severe and fatal disease. Although the characteristics of these viruses are well defined, they are still unpredictable with increases in disease severity, unusual clinical manifestations, unexpected methods of transmission, long-term persistence, and the discovery of new species. This review compares the epidemiological and clinical features of the medically important flaviviruses and considers the effect of human activity on their evolution and dispersal. Climate change, urbanization and increasing ease of travel have created opportunities for the vector to spread and expand into new human populations. The combination of these factors makes it possible for the family Flaviviridae to change and emerge quickly as a new, potential human pathogen.

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

PLoS Neglected Tropical Diseases ◽

10.1371/journal.pntd.0010019 ◽

2022 ◽

Vol 16 (1) ◽

pp. e0010019

Author(s):

Sabrina L. Li ◽

André L. Acosta ◽

Sarah C. Hill ◽

Oliver J. Brady ◽

Marco A. B. de Almeida ◽

...

Keyword(s):

Yellow Fever ◽

Yellow Fever Virus ◽

Boosted Regression Trees ◽

Transmission Risk ◽

Infected Mosquito ◽

Effective Vaccine ◽

Human Populations ◽

Vector Surveillance ◽

Transmission Cycle ◽

Environmental Suitability

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 1x1 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.

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Oviposition behavior of wild yellow fever vector mosquitoes (Diptera: Culicidae) in an Atlantic Forest fragment, Rio de Janeiro state, Brazil

Scientific Reports ◽

10.1038/s41598-021-85752-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Shayenne Olsson Freitas Silva ◽

Cecilia Ferreira de Mello ◽

Ronaldo Figueiró ◽

Tatiana Docile ◽

Michele Serdeiro ◽

...

Keyword(s):

Atlantic Forest ◽

Yellow Fever ◽

Rio De Janeiro ◽

Yellow Fever Virus ◽

Diversity Index ◽

Oviposition Behavior ◽

Abiotic Factors ◽

Ground Level ◽

Mosquito Vectors ◽

Janeiro State

AbstractAlthough there are many studies on the control of mosquito vectors of the yellow fever virus (YFV) in tropical forests, there are still few ecological studies regarding abiotic factors effect on these mosquitoes. Here we characterize these effects on oviposition behavior, abundance, and diversity of mosquito vectors of YFV. The study was conducted in Córrego da Luz Municipal Park, in Casimiro de Abreu, Rio de Janeiro state, Brazil, from July 2018 to December 2019. Ovitraps were placed at ground level and 3 m high. The data were tested for normality using the Shapiro–Wilk test, followed by an independent sample analysis, the Mann–Whitney test. The Shannon Diversity Index was used to evaluate the abundance of mosquitos' eggs collected at both ground level and 3 m high. We highlight the presence of Haemagogus janthinomys and Hg. leucocelaenus, primary YFV vectors in forest areas. The abundance of Hg. leucocelaenus (63%), Hg. janthinomys (75%), and Aedes terrens (58%) was higher at the height of 3 m, while Ae. albopictus (52%) was higher at ground level. Aedes albopictus was positively correlated with temperature. Culicidae monitoring is essential for assessing the YFV transmission cycle in Atlantic forest fragments.

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