Fig. 1

Unrooted maximum likelihood phylogeny of T'Ho virus and other relevant flaviviruses estimated by RAxML. The support out of 100 bootstraps is indicated on each branch. The branch length of cell fusing agent virus (CFAV; the outgroup) is not shown to scale: the actual estimated branch length is 15.60. Although T’Ho virus clusters with Ntaya and JE group viruses with 88% bootstrap support in this phylogeny and 98% posterior support in the MrBayes tree, the CFAV outgroup splits these two groups in around 50% of neighbor-joining bootstrap trees; there is considerable uncertainty in the deep branches of the phylogeny. Genbank Accession numbers for sequences used in the analysis are as follows: T’Ho virus, EU879061.2; Alfuy virus, AY898809.1; Aroa virus, KF917535.1; Bagaza virus, NC_012534.1; Bussuquara virus, AY632536.4; Cacipacore virus, LN849009.1; Cell fusing agent virus, NC_001564.1; Dengue virus type 1, AY277665.2; Dengue virus type 4, KF041260.1; Dengue virus type 2, U87411.1; Dengue virus type 3, AY099336.1; Iguape virus, AY632538.4; Ilheus virus, NC_009028.2; Israel turkey meningoencephalomyelitis virus, KC734552.1; Japanese encephalitis virus, NC_001437.1; Kokobera virus, NC_009029.2; Koutango virus, EU082200.2; Kunjin virus, KX394383.1; Murray Valley encephalitis virus, AF161266.1; Naranjal virus, KF917538.1; Ntaya virus, NC_018705.3; Rocio virus, AY632542.4; Sepik virus, NC_008719.1; St. Louis encephalitis virus, DQ525916.1; Stratford virus, KM225263.1; Tembusu virus, NC_015843.2; Usutu virus, NC_006551.1; Wesselsbron virus, NC_012735.1; West Nile virus, M12294.2; Yaounde virus, EU082199.2; Yellow fever virus, NC_002031.1 and Zika virus, NC_012532.1