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

¹ Department of Pathology, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-0609, USA
² University of California at Berkeley, Berkeley, CA 94720, USA
³ School of Natural Sciences, University of Texas, Austin, TX 78712, USA
⁴ Department of Microbiology and Immunology, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-0609, USA
⁵ Sealy Center for Vaccine Development and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch at Galveston, 301 University Blvd, Galveston, TX 77555-0609, USA

Correspondence
Alan D. T. Barrett
abarrett{at}utmb.edu

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.

Supplementary tables are available in JGV Online.