Background
Methods
High-throughput sequencing
5′ and 3′ rapid amplification of cDNA ends
Nucleotide and amino acid sequence alignments
Phylogenetic analysis
Results
Genomic organization and BLAST analysis
Gene/genetic region | Size (nt) | Genome position | Protein size (aa) | Polyprotein position |
---|---|---|---|---|
5′ UTR | 97 | 1–97 | - | - |
C | 357 | 98–454 | 119 | 1–119 |
VirC | 306 | 98–403 | 102 | 1–102 |
AnchC | 51 | 404–454 | 17 | 103–199 |
prM | 501 | 455–955 | 167 | 120–286 |
pr | 276 | 455–730 | 92 | 120–211 |
M | 225 | 731–955 | 75 | 212–286 |
E | 1503 | 956–2458 | 501 | 287–787 |
NS1 | 1059 | 2459–3517 | 353 | 788–1141 |
NS2A | 678 | 3518–4195 | 226 | 1142–1367 |
NS2B | 393 | 4196–4588 | 131 | 1368–1498 |
NS3 | 1857 | 4589–6445 | 619 | 1499–2117 |
NS4A | 378 | 6446–6823 | 126 | 2118–2243 |
2 K | 69 | 6824–6892 | 23 | 2244–2266 |
NS4B | 771 | 6893–7663 | 257 | 2267–2523 |
NS5 | 2718 | 7664–10,381 | 905 | 2524–3428 |
3′ UTR | 556 | 10,382–10,937 | - | - |
Virus | % nucleotide identity (genome) | % nucleotide identity (ORF) | % amino acid identity (polyprotein) |
---|---|---|---|
Ntaya group viruses | |||
Bagaza virus | 62.6 | 63.5 | 66.0 |
Ilheus virus | 65.9 | 65.8 | 70.6 |
1Rocio virus | 67.4 | 67.3 | 72.2 |
Israel turkey meningoencephalitis virus | 63.3 | 64.0 | 66.3 |
Ntaya virus | 62.9 | 63.6 | 65.2 |
Tembusu virus | 63.0 | 63.4 | 65.3 |
Zika virus | 58.8 | 59.4 | 57.1 |
Japanese encephalitis group viruses | |||
Cacipacore virus | n/a | 62.5 | 63.2 |
Japanese encephalitis virus | 63.5 | 63.8 | 64.7 |
Koutango virus | n/a | 63.4 | 64.0 |
Murray Valley encephalitis virus | 62.8 | 63.3 | 64.4 |
2Alfuy virus | 62.3 | 62.6 | 64.1 |
St. Louis encephalitis virus | 63.7 | 64.1 | 66.3 |
Usutu virus | 63.1 | 63.4 | 64.3 |
West Nile virus | 62.8 | 63.4 | 64.5 |
3Kunjin virus | 62.0 | 62.8 | 64.5 |
Yaounde virus | n/a | 63.8 | 65.5 |
Other flaviviruses | |||
Cell fusing agent virus | 42.1 | 42.0 | 29.2 |
Dengue virus type-2 | 56.4 | 56.9 | 51.7 |
Modoc virus | 50.2 | 48.1 | 38.4 |
Tick-borne encephalitis virus | 48.5 | 49.1 | 41.9 |
Yellow fever virus | 53.4 | 53.7 | 45.8 |
Organization of the polyprotein
Virus | Junction | |||||
---|---|---|---|---|---|---|
1VirC/Anch |
2C/prM |
3pr/M |
2prM/E |
2E/NS1 |
4NS1/NS2A | |
T’Ho virus | KNNKR↓GMTTT | ATTMA↓ARLSS | RRGRR↓SINIA | VPAYS↓LNCLG | MNVHA↓DTGCV | SMVVA↓GHGSS |
ROCV | RKAKR↓GNGSV | TGSMA↓LRLGT | RRGRR↓SVNIP | APAYS↓INCLG | MNVHA↓DTGCA | SKVTA↓GTGND |
ILHV | KEKKK↓SFSTA | TAVAG↓LKISS | RRGRR↓AINIP | APAYS↓LNCLG | VNVHA↓DTGCA | SKVSA↓GNGQT |
BAGV | GKKKR↓GGTTV | GVAQA↓IKIGS | RRSRR↓SITVH | APAYS↓FNCLG | TNVHA↓DTGCA | SRVTA↓YDGAG |
WNV |
KQKKR↓GGTAG |
ACAGA↓VTLSN
| RRSRR↓SLTVQ
| APAYS↓FNCLG
|
VNVHA↓DTGCA | SRVNA↓YNADM |
1NS2A/NS2B |
1NS2B/NS3 |
1NS3/NS4A |
1NS4A/2K |
22K/NS4B |
1NS4B/NS5 | |
T’Ho virus | GMTRR↓GWPAS | RLQKR↓GGVLW | AAGKR↓SASAI | PEKQR↓SQTDN | SAVSA↓NEMGW | PKVKR↓GGGTG |
ROCV | CATKR↓GWPAS | KIHKR↓GGVLW | AAGKR↓SAGSM | PEKQR↓SQTDN | SAVSA↓NEMGW | PKVKR↓GGIAA |
ILHV | SLGKR↓GWPAS | KIHKR↓GGVMW | AAGKR↓SAGSV | PEKQR↓SQTDN | GAVSA↓NEMGW | PKLKR↓GGGSA |
BAGV | PSNRR↓GWPVS | HSPKR↓SGAIW | ACGKR↓SAIGV | PEKQR↓SQTDS | GTVAS↓NEMGW | GSMRR↓GGGKG |
WNV | PNRKR↓GWPAT | QYTKR↓GGVLW | ASGKR↓SQIGL | PEKQR↓SQTDN | GAVAA↓NEMGW | PGLKR↓GGAKG |