Bunyaviridae

Single-stranded ambisense, segmented RNA genome: small (S), medium (M) and large (L) segments

Sequences shown here are those of the genomic minus-strand RNA

Conserved terminal sequences of S, M, and L genomic RNAs

Orthobunyavirus

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

Hantavirus

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

Note similarity of termini of Bunyaviruses and Hantaviruses

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.

Nairovirus

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

Phlebovirus

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

Tenuivirus

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.

Note similarity of termini of Phleboviruses, Nairoviruses and Tenuiviruses

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.

Tospovirus

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.

 

5' and 3' ends are invert repeats that can potentially form panhandle structures

e.g., LaCrosse virus S segment:

LAC     5' end AGUAGUGUGCUCCACU GAAUACAUU_____
               ||||||||:||||||| |||||| ||     )
        3' end UCAUCACAUGAGGUGAACUUAUGAAA-----