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

John Paul Mutebi, René C A Rijnbrand, Heiman Wang, Kate D. Ryman, Eryu Wang, Lynda D. Fulop, Rick Titball, Alan Barrett

Research output: Contribution to journalArticle

39 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)9652-9665
Number of pages14
JournalJournal of Virology
Volume78
Issue number18
DOIs
StatePublished - Sep 2004

Fingerprint

Yellow fever virus
Flavivirus
Molecular Evolution
genetic relationships
Genotype
genotype
Yellow Fever
nucleotide sequences
Angola
viral morphology
Flaviviridae
Viral Structures
Sequence Analysis
cell culture
Vaccines
Cell Culture Techniques
nucleotides
vaccines
stems
prediction

ASJC Scopus subject areas

  • Immunology

Cite this

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. / Mutebi, John Paul; Rijnbrand, René C A; Wang, Heiman; Ryman, Kate D.; Wang, Eryu; Fulop, Lynda D.; Titball, Rick; Barrett, Alan.

In: Journal of Virology, Vol. 78, No. 18, 09.2004, p. 9652-9665.

Research output: Contribution to journalArticle

Mutebi, John Paul ; Rijnbrand, René C A ; Wang, Heiman ; Ryman, Kate D. ; Wang, Eryu ; Fulop, Lynda D. ; Titball, Rick ; Barrett, Alan. / 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. In: Journal of Virology. 2004 ; Vol. 78, No. 18. pp. 9652-9665.
@article{83a6840ecaec422baccc849c0c938942,
title = "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",
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.",
author = "Mutebi, {John Paul} and Rijnbrand, {Ren{\'e} C A} and Heiman Wang and Ryman, {Kate D.} and Eryu Wang and Fulop, {Lynda D.} and Rick Titball and Alan Barrett",
year = "2004",
month = "9",
doi = "10.1128/JVI.78.18.9652-9665.2004",
language = "English (US)",
volume = "78",
pages = "9652--9665",
journal = "Journal of Virology",
issn = "0022-538X",
publisher = "American Society for Microbiology",
number = "18",

}

TY - JOUR

T1 - 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

AU - Mutebi, John Paul

AU - Rijnbrand, René C A

AU - Wang, Heiman

AU - Ryman, Kate D.

AU - Wang, Eryu

AU - Fulop, Lynda D.

AU - Titball, Rick

AU - Barrett, Alan

PY - 2004/9

Y1 - 2004/9

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=4444243327&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=4444243327&partnerID=8YFLogxK

U2 - 10.1128/JVI.78.18.9652-9665.2004

DO - 10.1128/JVI.78.18.9652-9665.2004

M3 - Article

C2 - 15331698

AN - SCOPUS:4444243327

VL - 78

SP - 9652

EP - 9665

JO - Journal of Virology

JF - Journal of Virology

SN - 0022-538X

IS - 18

ER -