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. 2017 Jun 12;14(1):110.
doi: 10.1186/s12985-017-0777-6.

Complete genome sequence of T'Ho virus, a novel putative flavivirus from the Yucatan Peninsula of Mexico

Thomas Briese  1 , Maria A Loroño-Pino  2 , Julian E Garcia-Rejon  2 , Jose A Farfan-Ale  2 , Carlos Machain-Williams  2 , Karin S Dorman  3 , W Ian Lipkin  1 , Bradley J Blitvich  4
Affiliations

Complete genome sequence of T'Ho virus, a novel putative flavivirus from the Yucatan Peninsula of Mexico

Thomas Briese et al. Virol J. .

Abstract

Background: We previously reported the discovery of a novel, putative flavivirus designated T'Ho virus in Culex quinquefasciatus mosquitoes in the Yucatan Peninsula of Mexico. A 1358-nt region of the NS5 gene was amplified and sequenced but an isolate was not recovered.

Results: The complete genome of T'Ho virus was sequenced using a combination of unbiased high-throughput sequencing, 5' and 3' rapid amplification of cDNA ends, reverse transcription-polymerase chain reaction and Sanger sequencing. The genome contains a single open reading frame of 10,284 nt which is flanked by 5' and 3' untranslated regions of 97 and 556-nt, respectively. Genome sequence alignments revealed that T'Ho virus is most closely related to Rocio virus (67.4% nucleotide identity) and Ilheus virus (65.9%), both of which belong to the Ntaya group, followed by other Ntaya group viruses (58.8-63.3%) and Japanese encephalitis group viruses (62.0-63.7%). Phylogenetic inference is in agreement with these findings.

Conclusions: This study furthers our understanding of flavivirus genetics, phylogeny and diagnostics. Because the two closest known relatives of T'Ho virus are human pathogens, T'Ho virus could be an unrecognized cause of human disease. It is therefore important that future studies investigate the public health significance of this virus.

Keywords: Culex quinquefasciatus; Flavivirus; Genome sequence; High-throughput sequencing; Mexico; T’Ho virus.

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Figures

Fig. 1
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
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