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

2006 ◽  
Vol 87 (4) ◽  
pp. 895-907 ◽  
Author(s):  
Jana J. von Lindern ◽  
Sarah Aroner ◽  
Nicholas D. Barrett ◽  
Jason A. Wicker ◽  
C. Todd Davis ◽  
...  
Keyword(s):  
Amino Acid ◽  
Yellow Fever ◽  
Genome Analysis ◽  
Yellow Fever Virus ◽  
Prototype Strain ◽  
West African ◽  
Fever Virus ◽  
Full Genome ◽  
Genome Database ◽  
East Central

Yellow fever virus (YFV), a reemerging disease agent in Africa and South America, is the prototype member of the genus Flavivirus. Based on examination of the prM/M, E and 3′ non-coding regions of the YFV genome, previous studies have identified seven genotypes of YFV, including the Angolan, east/central African and east African genotypes, which are highly divergent from the prototype strain Asibi. In this study, full genome analysis was used to expand upon these genetic relationships as well as on the very limited full genome database for YFV. This study was the first to investigate genomic sequences of YFV strains from east and central Africa (Angola71, Uganda48a and Ethiopia61b). All three viruses had genomes of 10 823 nt in length. Compared with the prototype strain Asibi (from west Africa) they were approximately 25 % divergent in nucleotide sequence and 7 % divergent in amino acid sequence. Comparison of multiple flaviviruses in the N-terminal region of NS4B showed that amino acid sequences were variable and that west African strains of YFV had an amino acid deletion at residue 21. Additionally, N-linked glycosylation sites were conserved between viral genotypes, while codon usage varied between strains.

scholarly journals Phylogenetic and Evolutionary Relationships among Yellow Fever Virus Isolates in Africa

2001 ◽  
Vol 75 (15) ◽  
pp. 6999-7008 ◽  
Author(s):  
John-Paul Mutebi ◽  
Heiman Wang ◽  
Li Li ◽  
Juliet E. Bryant ◽  
Alan D. T. Barrett
Keyword(s):  
Amino Acid ◽  
West Africa ◽  
East Africa ◽  
Yellow Fever ◽  
Yellow Fever Virus ◽  
Amino Acid Level ◽  
Central Africa ◽  
The Other ◽  
Genotype I ◽  
East Central

ABSTRACT Previous studies with a limited number of strains have indicated that there are two genotypes of yellow fever (YF) virus in Africa, one in west Africa and the other in east and central Africa. We have examined the prM/M and a portion of the E protein for a panel of 38 wild strains of YF virus from Africa representing different countries and times of isolation. Examination of the strains revealed a more complex genetic relationship than previously reported. Overall, nucleotide substitutions varied from 0 to 25.8% and amino acid substitutions varied from 0 to 9.1%. Phylogenetic analysis using parsimony and neighbor-joining algorithms identified five distinct genotypes: central/east Africa, east Africa, Angola, west Africa I, and west Africa II. Extensive variation within genotypes was observed. Members of west African genotype II and central/east African genotype differed by 2.8% or less, while west Africa genotype I varied up to 6.8% at the nucleotide level. We speculate that the former two genotypes exist in enzootic transmission cycles, while the latter is genetically more heterogeneous due to regular human epidemics. The nucleotide sequence of the Angola genotype diverged from the others by 15.7 to 23.0% but only 0.4 to 5.6% at the amino acid level, suggesting that this genotype most likely diverged from a progenitor YF virus in east/central Africa many years ago, prior to the separation of the other east/central African strains analyzed in this study, and has evolved independently. These data demonstrate that there are multiple genotypes of YF virus in Africa and suggest independent evolution of YF virus in different areas of Africa.

scholarly journals Interaction of Yellow Fever Virus French Neurotropic Vaccine Strain with Monkey Brain: Characterization of Monkey Brain Membrane Receptor Escape Variants

2000 ◽  
Vol 74 (6) ◽  
pp. 2903-2906 ◽  
Author(s):  
Haolin Ni ◽  
Kate D. Ryman ◽  
Heiman Wang ◽  
Mohammad F. Saeed ◽  
Robin Hull ◽  
...  
Keyword(s):  
Amino Acid ◽  
Yellow Fever ◽  
Mouse Brain ◽  
Amino Acid Substitution ◽  
Yellow Fever Virus ◽  
Fever Virus ◽  
Monkey Brain ◽  
Intracerebral Inoculation ◽  
E Protein ◽  
Monkey Liver

ABSTRACT Binding of yellow fever virus wild-type strains Asibi and French viscerotropic virus and vaccine strains 17D and FNV to monkey brain and monkey liver cell membrane receptor preparations (MRPs) was investigated. Only FNV bound to monkey brain MRPs, while French viscerotropic virus, Asibi, and FNV all bound to monkey liver MRPs. Four monkey brain and two mouse brain MRP escape (MRPR) variants of FNV were selected at pH 7.6 and 6.0. Three monkey brain MRPR variants selected at pH 7.6 each had only one amino acid substitution in the envelope (E) protein in domain II (E-237, E-260, or E274) and were significantly attenuated in mice following intracerebral inoculation. Two of the variants were tested in monkeys and retained parental neurotropism following intracerebral inoculation at the dose tested. We speculate that this region of domain II is involved in binding of FNV E protein to monkey brain and is, in part, responsible for the enhanced neurotropism of FNV for monkeys. A monkey brain MRPR variant selected at pH 6.0 and two mouse brain MRPR variants selected at pH 7.6 were less attenuated in mice, and each had an amino acid substitution in the transmembrane region of the E protein (E-457 or E-458).

scholarly journals Genetic Relationships and Evolution of Genotypes of Yellow Fever Virus and Other Members of the Yellow Fever Virus Group within the Flavivirus Genus Based on the 3′ Noncoding Region

2004 ◽  
Vol 78 (18) ◽  
pp. 9652-9665 ◽  
Author(s):  
John-Paul Mutebi ◽  
René C. A. Rijnbrand ◽  
Heiman Wang ◽  
Kate D. Ryman ◽  
Eryu Wang ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Yellow Fever ◽  
Yellow Fever Virus ◽  
Genetic Relationships ◽  
West African ◽  
Fever Virus ◽  
Genetic Group ◽  
Noncoding Region ◽  
South American ◽  
Sequence Elements

ABSTRACT Genetic relationships among flaviviruses within the yellow fever (YF) virus genetic group were investigated by comparing nucleotide sequences of the 3′ noncoding region (3′NCR). Size heterogeneity was observed between members and even among strains of the same viral species. Size variation between YF strains was due to duplications and/or deletions of repeated nucleotide sequence elements (RYF). West African genotypes had three copies of the RYF (RYF1, RYF2, and RYF3); the Angola and the East and Central African genotypes had two copies (RYF1 and RYF3); and South American genotypes had only a single copy (RYF3). Nucleotide sequence analyses suggest a deletion within the 3′NCR of South American genotypes, including RYF1 and RYF2. Based on studies with the French neurotropic vaccine strain, passage of a YF virus strain in cell culture can result in deletion of RYF1 and RYF2. Taken together, these observations suggest that South American genotypes of YF virus evolved from West African genotypes and that the South American genotypes lost RYF1 and RYF2, possibly in a single event. Repeated sequence elements were found within the 3′NCR of other members of the YF virus genetic group, suggesting that it is probably characteristic for members of the YF virus genetic group. A core sequence of 15 nucleotides, containing two stem-loops, was found within the 3′NCR of all members of the YF genetic group and may represent the progenitor repeat sequence. Secondary structure predictions of the 3′NCR showed very similar structures for viruses that were closely related phylogenetically.

scholarly journals Genome analysis of yellow fever virus of the ongoing outbreak in Brazil reveals polymorphisms

2017 ◽  
Vol 112 (6) ◽  
pp. 447-451 ◽  
Author(s):  
Myrna C Bonaldo ◽  
Mariela Martínez Gómez ◽  
Alexandre AC dos Santos ◽  
Filipe Vieira Santos de Abreu ◽  
Anielly Ferreira-de-Brito ◽  
...  
Keyword(s):  
Yellow Fever ◽  
Genome Analysis ◽  
Yellow Fever Virus ◽  
Fever Virus

scholarly journals Genomic and structural features of the Yellow Fever virus from the 2016-2017 Brazilian outbreak

2017 ◽  
Author(s):  
Mariela Martínez Gómez ◽  
Filipe Vieira Santos de Abreu ◽  
Alexandre Araujo Cunha dos Santos ◽  
Iasmim Silva de Mello ◽  
Marta Pereira Santos ◽  
...  
Keyword(s):  
Amino Acid ◽  
Yellow Fever ◽  
Yellow Fever Virus ◽  
Viral Proteins ◽  
Structural Features ◽  
Fever Virus ◽  
Viral Fitness ◽  
And Function ◽  
Enzyme Structure And Function ◽  
Unique Amino Acid

ABSTRACTBrazil has been suffering a severe sylvatic epidemic of yellow fever virus (YFV) since late 2016. Analysis of full-length YFV genomes from all hosts involved in the Brazilian 2017 outbreak reveals that they belong to sub-lineage 1E within modern-lineage, but display several unique amino acid substitutions in highly conserved positions at NS3 and NS5 viral proteins. Evolutionary analyses indicate that YFV carrying that set of amino acid substitution circulates in the Southern Brazilian region for several months before being detected in December 2016. Structural and selection analyses support that some of these substitutions were under positive selection and could impact enzyme structure and function. Altogether, this evidence demonstrated that the current Brazilian YFV carries unique amino acid signatures in the non-structural proteins and support the hypothesis that those substitutions may be affecting the viral fitness and transmissibility.

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