The Yellow Fever Virus Automated Phylogenetic Typing Tool: introduction.
Yellow fever causes 200,000 infections and 30,000 deaths every year, with nearly 90% of these occurring in Africa. Nearly a billion people live in an area of the world where the disease is common. It is common in tropical areas of South America and Africa, but not in Asia.
The definition of a Yellow Fever genotype is based on the identification of well defined phylogenetic clusters that its origin has been associated to a given geographic region.
We have carefully analysed all of YFV whole genomes and reviewed in the literature in order to represent the diversity of each phylotype. In addition, we performed extensive testing to be sure that our reference strains accurately classify other sequences.
We include 4 genotypes
South American Genotype I (blue)
▸ JF912190, JF912187, JF912188, JF912189, JF912180, JF912182, JF912185, JF912179, JF912184, JF912183 and JF912186.
South American Genotype II (red)
▸ TVP17388 and JF912181.
East African Genotype (green)
▸ AY968064, AY968065, DQ235229 and JN620362.
West African Genotype (orange)
▸ AF094612, JX898871, JX898872, AY640589, JX898875, JX898874, JX898873, AY572535, AY603338, JX898868, JX898870, JX898876, JX898878, JX898880, X898877, JX898869 and YFU54798.
Fig. 1. Yellow fever virus maximum likelihood phylogenetic tree of (A) WGS and (B) E gene.
Blue cluster - South American Genotype I; Red cluster - South American Genotype II; Green cluster - East African Genotype; Orange cluster - West African Genotype.