Genome analysis and phylogenetic relationships between east, central and west African isolates of Yellow fever virus

Lindern, Jana J. von; Aroner, Sarah A.; Barrett, Nicholas D.; Wicker, Jason A.; Davis, C. Todd; Barrett, Alan D.T.

doi:10.1099/vir.0.81236-0

Cited by 33 publications

(31 citation statements)

References 31 publications

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“…The prM/E phylogeny supports the major genotype and subclade distinctions observed previously in phylogenies based on full genome sequences [22], the complete E gene [9], and the 3′ non-coding region [23] . Four key observations can be drawn from the structure of the YFV phylogeny.…”

Section: Resultssupporting

confidence: 81%

Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas

2007

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Yellow fever virus (YFV) remains the cause of severe morbidity and mortality in South America and Africa. To determine the evolutionary history of this important reemerging pathogen, we performed a phylogenetic analysis of the largest YFV data set compiled to date, representing the prM/E gene region from 133 viral isolates sampled from 22 countries over a period of 76 years. We estimate that the currently circulating strains of YFV arose in Africa within the last 1,500 years and emerged in the Americas following the slave trade approximately 300–400 years ago. These viruses then spread westwards across the continent and persist there to this day in the jungles of South America. We therefore illustrate how gene sequence data can be used to test hypotheses of viral dispersal and demographics, and document the role of human migration in the spread of infectious disease.

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Section: Resultssupporting

confidence: 81%

Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas

2007

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“…The results indicated that the CNYF01/2016 sequence was most closely related to the YFV strain Angola71 (GenBank NO AY968064), which was isolated in Angola in 1971 13 and the complete genomic sequence was reported in 2006. 14 Both strain CNYF01/2016 from the imported case from Angola in 2016 and strain Angola71 from 1971 shared the same Angola genotype.…”

Section: Resultsmentioning

confidence: 99%

A fatal yellow fever virus infection in China: description and lessons

Chen

Liu

et al. 2016

Emerging Microbes & Infections

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Yellow fever (YF) is a viral disease endemic to the tropical regions of Africa and South America. An outbreak of YF has been occurring in Angola, since the beginning of 2016. In March 2016, a 32-year-old Chinese man who returned from Angola was hospitalized and diagnosed with the first case of imported YF in China. Clinical observations, blood viral RNA detection, serological testing and treatments for the patient were performed daily. The virus was isolated in Vero cells, and the complete viral genome was sequenced and analyzed using the next-generation genomic sequencing platform. The patient presented with hemorrhagic fever, jaundice and oliguria at day 3 after onset, which rapidly progressed to multisystem organ failure with extremely elevated liver, pancreatic and myocardial enzymes. The patient died despite the intensive supportive treatments that were performed. A liver biopsy showed severe and multilobular necrosis. Viral RNA was detectable throughout the clinical course of the disease. Whole-genomic sequence analysis revealed that the virus belongs to the Angola71 genotype. Although the virus has been circulating in Angola for 45 years, only 14 amino-acid substitutions and no amino-acid changes were observed in the membrane and envelope proteins compared with the virus collected in 1971. The presence of this imported YF case in China indicated that with the increase in business travel among countries, YF outbreaks in Africa can lead to the international spread of the disease. The production and use of YF vaccines is, therefore, an urgent issue.

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“…A neighbor-joining analysis of African YFV strains, provided evidence for the presence of 5 prototype lineages in circulation in the continent, West Africa I, West Africa II, East Africa, East/Central Africa, and Angola [12]. Subsequent analysis using full-length YFV sequences provided confirmatory evidence for the putative geographic structure [13].…”

Section: Introductionmentioning

confidence: 88%

Phylogeographic Reconstruction of African Yellow Fever Virus Isolates Indicates Recent Simultaneous Dispersal into East and West Africa

Beck

Guzmán

et al. 2013

PLoS Negl Trop Dis

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Yellow fever virus (YFV) is a mosquito-borne flavivirus that is a major public health problem in tropical areas of Africa and South America. There have been detailed studies on YFV ecology in West Africa and South America, but current understanding of YFV circulation on the African continent is incomplete. This inadequacy is especially notable for East and Central Africa, for which the unpredictability of human outbreaks is compounded by limitations in both historical and present surveillance efforts. Sparse availability of nucleotide sequence data makes it difficult to investigate the dispersal of YFV in these regions of the continent. To remedy this, we constructed Bayesian phylogenetic and geographic analyses utilizing 49 partial genomic sequences to infer the structure of YFV divergence across the known range of the virus on the African continent. Relaxed clock analysis demonstrated evidence for simultaneous divergence of YFV into east and west lineages, a finding that differs from previous hypotheses of YFV dispersal from reservoirs located on edges of the endemic range. Using discrete and continuous geographic diffusion models, we provide detailed structure of YFV lineage diversity. Significant transition links between extant East and West African lineages are presented, implying connection between areas of known sylvatic cycling. The results of demographic modeling reinforce the existence of a stably maintained population of YFV with spillover events into human populations occurring periodically. Geographically distinct foci of circulation are reconstructed, which have significant implications for studies of YFV ecology and emergence of human disease. We propose further incorporation of Bayesian phylogeography into formal GIS analyses to augment studies of arboviral disease.

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Genome analysis and phylogenetic relationships between east, central and west African isolates of Yellow fever virus

Cited by 33 publications

References 31 publications

Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas

Out of Africa: A Molecular Perspective on the Introduction of Yellow Fever Virus into the Americas

A fatal yellow fever virus infection in China: description and lessons

Phylogeographic Reconstruction of African Yellow Fever Virus Isolates Indicates Recent Simultaneous Dispersal into East and West Africa

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