| (Return to Main) | CONSERVED CIS-ACTING SEQUENCES OF RNA VIRUSES |
Sequences shown here are those of the genomic minus-strand RNA
e.g., Bunyamwera (BUNV); LaCrosse (LACV), snowshoe hare (SSHV), Inkoo, California encephalitis; Pahayokee viruses.
segment
BUNV S 5' end AGUAGUGUGCUCCACC....UGUGGAGUACACUACU 3' end BLCNNS D00353
M -----------A-CGA....-CG-U----------- BLCMA M11852
L -------------UA-....GUA------------- BLCLPA X14383
LACV S ---------------U....A--------------- BLCNCNP K00108
M -----------A-CAA....-UG-U----------- BLCMRP D10370
L -------------UAU....AUA------------- LCU12396 U12396
SSHV S ---------------U....A--------------- SSHS J02390
M -----------A-CAA....-UG-U----------- SSHM K02539
L ..AUA------------- SSHL3 J02391
e.g., Hantaan (HTNV), Sin Nombre (SNV, human pulmonary syndrome hantavirus), Puumala (PUUV), Prospect Hill virus (PHV), Dobrava-Belgrade (DOBV), Andes (AND) viruses.
HTNV S 5' end UAGUAGUAUGCUCC....UUUAGGGAGUCUACUACUA 3' end HANSNC M14626
M --------GA-A--....---GC-------------- BUHANM Y00386
L --------GUA-G-....------------------- BUHANL X55901
SNV S ---------A----....----C-A------------ HPSSSEG L25784 strain NM H10
M --------GA----....C--GC-------------- HPSMSEG L25783 strain NM H10
M --------GA----....CC-GC----CA-------- HPSGPG0 L37903 strain NM R11
L --------------....A-CUC-------------- HPSVRPL L37901 strain NM H10
PUUV S ---------A----....--C-A-------------- PUUSNP X61035
M ---------A----....C--GC-------------- PUUMGP X61034
L --------------....A-CUC-------------- PVLSOTKMO Z66548
PHV S ---------A----....--C-A-------------- PHVSSEG Z49098
M --------GA----....C--GC-------------- PHVMSRNA X55129
DOBV S --------------....------------------- HNVNPSS L41916
M --------GA----....C--GC-------------- HNVDOBMS L33685
AND S --------GA----....C-C-A-------------- AF004660 AF004660
e.g. S segments of BUN and HAN:
BUNV S 5' end AGUAGUGUGCUCCACC.....UGUGGAGUACACUACU 3' end HTNV S U------A------CUA.....-AG-----CU------A
It is likely that the bunyaviruses and the hantaviruses are descended from a common progenitor virus. Their divergence probably occurred before the global spread and divergence of the hantaviruses.
e.g., Nairobi sheep disease virus, Dugbe (DUGV); Crimean-Congo hemorrhagic fever (C-CHFV), Hazara (HAZ); Qalyub viruses.
DUGV S 5' end UCUCAAAGAGAAAUCG.....ACGUUUGUCUUUGAGA 3' end DUGNPAA M25150
M ---------U-GCGU-.....-G--A----------- DUG M94133
L ---------A-UCGUU.....-UUGA----------- DVU15018 U15018
C-CHFV S ---------U-UCGUU.....----G-U--------- CCFSRNA M86625
M .....-A--A-U--------- CHU39455 U39455
HAZV S ---------UAUCGUU.....-U-------------- HAZSRNA M86624
e.g., sandfly fever Sicilian, Rift Valley fever (RVFV; East Africa), Punta Toro (PTV [Ihara, et al., 1984]; Panama), Uukuniemi (UUKV [Simons, et al., 1990]), Toscana (TOSV; Italy)) viruses.
Functional analysis of the Uukuniemi virus terminal sequences: Flick et al. [2002]
RVFV S 5' end ACACAAAGCUCCCUAG.....UAGGGGGUCUUUGUGU 3' end RVFNNSG X53771
M --------AC-GG-GC.....-GCACC---------- RVFMRNA M11157
L --------GCG--C-A.....-U---C-C-------- RVFLRNA X56464
PTV S --------AC---CU-.....-CA---AG--A----- PTPSRNA K02736
M --------AC-GGC-C.....CGU-CC---------- PTPMRNA M11156
UUKV S --------AC--UCCA.....-U--A----------- UUKNNSA M33551
M --------ACA-GG-U.....-UA-CC---------- UUKGPM M17417
L --------UC-G-C-A.....CUU--C---------- UUKLRNAP D10759
TOSV S -----G--A-U--CGU.....CG--A----------- TVSRNA X53794
e.g., rice stripe (RSV) [Kakutani, et al., 1989; Takahashi, et al., 1990], rice grassy stunt (RGSV) [Toriyama, et al., 1998], and maize stripe (MSpV) plant viruses
RGSV 1 5' end ACACAAAGUCUGGACA.....GUCCAGGACUUUGUGU 3' end AB009656 AB009656
2 -------------G--.....-C-------------- AB010376 AB010376
3 -------------G--.....-C-------------- AB010377 AB010377
4 -------------G--.....-C-------------- AB010378 AB010378
5 -------------G--.....-C-------------- AB000403 AB000403
6 -------------G--.....-C-------------- AB000404 AB000404
RSV 1 ----------CA--GG.....UC-UCU----A----- RCSRNAP D31879
2 -------------GU-.....AC-------------- RCSRNA D13176
3 -------------GU-.....AC-------------- RSTRSVAS3 D01094
4 ----------A--G--.....-C--U----------- RCSRNA4 D10979
MSpV 2 -------------GU-.....AC-------------- MSU53224 U53224
3 -------------GU-.....AC-------------- MZSRNA3 M57426
4 ----------A--G--.....-C--U----------- MZSNCPNS4P L13438
5 ----------CUUGGC.....UG---A----A----- MZSNSRNA5P L13446
Tenuivirus is a floating genus, i.e., not yet assigned to any family. The following supports its assignment to Bunyaviridae.
e.g. S segment of RVFV, DUGV, and segment 1 of RGSV:
RVFV S 5' end ACACAAAGCUCCCUAG.....UAGGGGGUCUUUGUGU 3' end DUGV S U-U-----AGAAA-C-.....AC-UUU-------A-A RGSV 1 --------UCUGGACA.....GUCCA--A--------
It is likely that the Phleboviruses, Tenuiviruses, and the Nairoviruses are descended from a common progenitor. The cis-acting sequences of this group have no resemblance to that of the Bunyavirus-Hantavirus group. The Bunyaviridae family is therefor likely to have undergone at least two major divergence events, first to separate out the two groups, then to separate out the genera in each group. Finally, the species in each genus diverged to give the contemporary viruses.
e.g., tomato spotted wilt (TSWV), impatiens necrotic spot (INSV), peanut bud necrosis (PBNV), peanut yellow spot (PYSV), watermelon silver mottle (WSMV) plant viruses.
segment
TSWV L 5' end AGAGCAAUCAGGUACAACUA...CGUUGUUACCUGAUUGCUCU 3' end TSWLRPOLM D10066 D01230
M -----------UGCAUCAG-...UUG-U-GCA----------- S48091 S48091
S --------UGU--CAG-A-U...AAAAU-G--AC--------- TSWSRS D00645
INSV L ------------C-------...U------G------------ INSVL X93218
M -----------UGCAUCAA-...UUG-U-GCA----------- IMNGNSM M74904
S --A---C--A-CUAC-AC-...AU-C--G--ACA-------- INSVNSP X66972 S40057
PBNV L ---------GA-C-AC-AAU...UA-----G-AC--------- AF025538 AF025538
M ---------G-UGCGCCAAU...AU-GU-GCA----------- PBU42555 U42555
S ---------G--GCAUCUA-...AU-A-CGC-UC--------- PBU27809 U27809
PYSV S ---------G--GCAU-AA-...AU--U-GC-U---------- AF013994 AF013994
WSMV M ---------G-UGCGCCAAU...AU-GU-GCA----------- WSU75379 U75379
S ---------GA-GCA--UA-...AU-A-CGC-UC--------- WSU78734 U78734
Thanks to Dr. Ralf Dietzgen (Queensland Agricultural Biotechnology Centre) for informing me of the conserved termini of the Tospoviruses.
While the L (polymerase) protein is more closely related to the Bunyaviruses (van Poelwijk et al., 1997), the termini of the Tospoviruses have little resemblance to those of Bunyaviruses:
BUNV S 5' end AGUAGUGUGCUCCACC.....UGUGGAGUACACUACU 3' end TSWV L --AGCAA-CAGGU--A.....GU-ACCUG-UUGCU--
There is a slightly better match between the Tospovirus and Phlebovirus termini. However, this is not statistically significant, as the probability of 4 or more matches in 8 is 11.4%:
RVFV S 5' end ACACAAAGCUCCCUAG.....UAGGGGGUCUUUGUGU 3' end TSWV L -G-GC--U-AGGUACA.....GUUACCUGA--GC-C-
From the perspective of the cis-acting sequences, and barring convergent evolution, the Bunyaviridae family appears to consist of at least three clades: the Bunyavirus-Hantavirus clade, the Phlebovirus-Nairovirus-Tenuivirus clade, and the Tospovirus clade.
e.g., LaCrosse virus S segment:
LAC 5' end AGUAGUGUGCUCCACU GAAUACAUU_____
||||||||:||||||| |||||| || )
3' end UCAUCACAUGAGGUGAACUUAUGAAA-----
| (Return to Main) | Conserved cis-acting sequences of RNA viruses |
| Send suggestions and comments to: huang@borcim.wustl.edu Henry V. Huang Department of Molecular Microbiology, Box 8230 Washington University School of Medicine St. Louis, MO 63110-1093 USA | Tel 314-362-2755 FAX 314-362-1232 | |