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Edited by Peter Palese, Icahn School of Medicine at Mount Sinai, New York, NY, and approved March 27, 2014 (received for review December 30, 2013)
Article Figures & SI
Figures
- Fig. 1.
Transmission EM image of JMTV in (A) infected cells and (B) cell culture supernatant. The viral particles are indicated by the orange arrowheads.
- Fig. 2.
Schematic genome organization and putative proteomic maps of JMTV, showing predicted ORFs (blue boxes), transmembrane regions (yellow boxes), signal peptides (red box), and N-linked glycosylation sites (upward-pointing pink triangles).
- Fig. 3.
ML phylogenetic trees of (A) NS3 and (B) NS5 proteins of JMTV and TCLA within the context of representative flaviviruses. The trees are midpoint-rooted, and all horizontal branches are drawn to a scale of amino acid substitutions per site. The branch and taxon labels of the JMTV–TCLA clade are shaded red. For clarity, bootstrap values are only shown for internal nodes.
- Fig. 4.
ML phylogenetic trees of the four genome segments obtained from nine depooled JMTV samples. The trees are midpoint-rooted, and all horizontal branches are drawn to a scale of nucleotide substitutions per site. Major clade/lineages are shaded with blue, yellow, and red, respectively. Phylogenetic incongruence, suggestive of reassortment, is indicated with colored arrowheads.
Tables
- Table 1.
Homology search results and expression levels of JMTV genome segments in the context of total RNA
Contig Top BLAST and HHblits hits Length, nt* No. of mapped reads Expression level** Total reads, % Non-rRNA reads, % comp194 ANT5, NS5 (TABV) 3,072 980,359 15,956.36 4.44 18.67 comp196 — 2,785 961,719 17,266.05 4.36 18.32 comp197 ANT34, NS3 (TABV) 2,793 767,020 13,731.11 3.48 14.61 comp202 ANT3.1 2,751 459,874 8,358.31 2.08 8.76 Total 11,401 3,168,972 51,696.34 14.37 60.36 ↵* Length (measured in nt) of genomic RNAs determined after cyclization RT-PCR, excluding poly(A) tail.
† Expression level is calculated by using length of mapped reads/length of contig.
Species Location* Mammalian host No. of pools tested No. of positive pools R. microplus 1–7 Cattle 181 114 H. longicornis 1 Dog, goat, cattle 91 50 H. campanulata 8 Dog 24 18 H. flava 7–9 Hedgehog, badger 45 5 I. sinesis 1 Wild goat 1 1 I. granulatus 10 NA 3 1 R. sanguineus 11 NA 3 1 Haemaphysalis hystricis 9 Badger 32 0 Armigeres sp. (mosquito) 1 NK 20 1 Culex sp. (mosquito) 1 NK 31 0 Anopheles sp. (mosquito) 1 NK 5 0 Bos sp. (cattle) 1, 6, 10 NK 145 5 Total — — 481 196 NA, not applicable; NK, not known.
↵* Locations: 1, Wuhan; 2, Shiyan; 3, Shengnongjia; 4, Yichang; 5, Enshi; 6, Jingmen; 7, Xiangfan; 8, Xinzhou; 9, Huanggang; 10, Wenzhou; 11, Ningbo.
Data supplements
Supporting Information
Files in this Data Supplement:
Segmented relative of flavivirus
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