Evolution and Taxonomy of Positive-Strand RNA Viruses: Implications of Comparative Analysis of Amino Acid Sequences

References

• Afanasiev B. N., Rupasov V. V., Fedchenko V. I., Dolja V. V., Atabekov J. G., Chernov B. K., Kozlov Yu. V., Bayev A. A. Complete nucleotide sequence of barley stripe mosaic virus RNAs 3,2b, and 4, and possible mechanisms of their interconversions. Dokl. Akad. Nauk SSSR 1986; 290: 724–727
   Google Scholar
• Agranovsky A. A., Boyko V. P., Karasev A. V., Koonin E. V., Dolja V. V. The putative 65K protein of beet yellows closterovirus is a homologue of HSP70 heat shock proteins. J. Mol. Biol. 1991a; 217: 603–610
   Google Scholar
• Agranovsky A. A., Boyko V. P., Karasev A. V., Lunina N. A., Koonin E. V., Dolja V. V. Nucleotide sequence of the 3′-terminal half of beet yellows closterovirus RNA genome: unique arrangement of eight virus genes. J. Gen. Virol. 1991b; 72: 15–23
   Google Scholar
• Agranovsky A. A., Koonin E. V., Boyko V. P., et al. Beet yellows closterovirus: complete genome structure and identification of a leader papain-like thiol protease. Virology 1993, in press
   Google Scholar
• Agrawal D. K., Johnson J. E. Sequence and analysis of the capsid protein of Nudaurelia capensis w virus, an insect virus with T = 4 icosahedral symmetry. Virology 1992; 190: 806–814
   Google Scholar
• Ahlquist P., Dasgupta R., Kaesberg P. Nucleotide sequence of the brome mosaic virus genome and its implications for viral replication. J. Mol. Biol. 1984; 172: 369–383
   PubMed Web of Science ®Google Scholar
• Ahlquist P., Luckow V., Kaesberg P. Complete nucleotide sequence of brome mosaic virus RNA 3. J. Mol. Biol. 1981; 153: 23–38
   PubMed Web of Science ®Google Scholar
• Ahlquist P., Strauss E. G., Rice C. M., Strauss J. H., Haseloff J., Zimmern D. Sindbis virus proteins nsP1 and nsP2 contain homology to nonstructural proteins from several RNA plant viruses. J. Virol. 1985; 53: 536–542
   PubMed Web of Science ®Google Scholar
• Allison R. F., Janda M., Ahlquist P. Sequence of cowpea chlorotic mottle virus RNAs 2 and 3 and evidence of a recombination event during bromovirus evolution. Virology 1989; 172: 321–330
   Google Scholar
• Allison R., Johnson R. E., Dougherty W. G. The nucleotide sequence of the coding region of Tobacco etch virus genomic RNA: evidence for the synthesis of a single polyprotein. Virology 1986; 154: 9–20
   PubMed Web of Science ®Google Scholar
• Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J. Mol. Biol. 1990; 215: 403–410
   PubMed Web of Science ®Google Scholar
• Angenent G. C., Linthorst H. J., van Belkum A. F., Cornelissen B. J., Bol J. F. RNA 2 of tobacco rattle virus strain TCM encodes an unexpected gene. Nucleic Acids Res. 1986; 14: 4673–4682
   PubMedGoogle Scholar
• Argos P., Kamer G., Nicklin M. J., Wimmer E. Similarity in gene organization and homology between proteins of animal picornaviruses and a plant comovirus suggest common ancestry of these virus families. Nucleic Acids Res. 1984; 12: 7251–7267
   PubMedGoogle Scholar
• Bae Y.-S., Eun H.-M., Yoon J.-W. Genomic differences between diabetogenic and nondiabetogenic Encephalomyocarditis virus. Virology 1989; 170: 282–287
   PubMed Web of Science ®Google Scholar
• Bancroft J. B., Rouleau M., Johnston R., Prins L., Mackie G. A. The complete nucleotide sequence of Foxtail mosaic virus RNA. J. Gen. Virol. 1991; 72: 2173–2181
   PubMed Web of Science ®Google Scholar
• Barker R. F., Jarvis N. P., Thompson D. V., Loesch-Fries L. S., Hall T. C. Complete nucleotide sequence of alfalfa mosaic virus RNA3. Nucleic Acids Res. 1983; 11: 2881–2891
   PubMed Web of Science ®Google Scholar
• Bazan J. F., Fletterick R. J. Viral cysteine proteases are homologous to the trypsin-like family of serine protease: structural and functional implications. Proc. Natl. Acad. Sci. U.S.A. 1988; 85: 7872–7876
   PubMed Web of Science ®Google Scholar
• Bazan J. F., Fletterick R. J. Detection of a trypsin-like serine protease domain in flaviviruses and pestiviruses. Virology 1989; 171: 637–639
   PubMed Web of Science ®Google Scholar
• Bazan J. F., Fletterick R. J. Comparative analysis of viral cysteine protease structural models. FEBS Lett. 1989; 249: 5–7
   Google Scholar
• Bazan J. F., Fletterick R. J. Structural and catalytic models of trypsin-like viral proteases. Semin. Virol. 1990; 1: 311–322
   Google Scholar
• Beck D. L., Guilford P. J., Voot D. M., Andersen M. T., Forster R. L. Triple gene block proteins of white clover mosaic potexvirus are required for transport. Virology 1991; 183: 695–702
   Google Scholar
• Benner S. A., Allemann R. K., Ellington A. D., Ge L., Glasfeld A., Leanz G. F., Kruch T., Mac Pherson L. J., Moroney S., Piccirilli J. A., Weinhold E. Natural selection, protein engineering and the last riboorganism: rational model building in biochemistry. Cold Spring Harb. Symp. Quant. Biol. 1987; 52: 53–63
   Google Scholar
• Bernal J. J., Moriones E., Garcia-Arenal F. Evolutionary relationships in the cucumoviruses: nucleotide sequence of tomato aspermy virus RNA 1. J. Gen. Virol. 1991; 72: 2191–2195
   Google Scholar
• Blinov V. M., Donchenko A. P., Gorbalenya A. E. Internal homology of the poliovirus polyprotein primary structure: possible existence of two viral proteinases. Dokl. Akad. Nauk SSSR 1985; 281: 984–987, in Russian
   Google Scholar
• Blinov V. M., Gorbalenya A. E., Donchenko A. P. Sequence similarity between poliovirus cysteine protease P3–7c and cellular serine protease trypsin. Dokl. Akad. Nauk SSSR 1984; 279: 502–505, in Russian
   Google Scholar
• Boursnell M. E., Brown T. D., Foulds I. J., Green P. F., Tomley F. M., Binns M. M. Completion of the sequence of the genome of the coronavirus avian infectious bronchitis virus. J. Gen. Virol. 1987; 68: 57–77
   PubMed Web of Science ®Google Scholar
• Bouzoubaa S., Quillet L., Guilley H., Jonard G., Richards K. Nucleotide sequence of Beet Necrotic Yellow Vein Vims RNA-1. J. Gen. Virol. 1987; 68: 615–626
   Web of Science ®Google Scholar
• Bouzoubaa S., Ziegler V., Beck D., Guilley H., Richards K., Jonard G. Nucleotide sequence of Beet Necrotic Yellow Vein Virus RNA-2. J. Gen. Virol. 1986; 67: 1689–1700
   Web of Science ®Google Scholar
• Boyko V. P., Karasev A. V., Agranovsky A. A., Koonin E. V., Dolja V. V. Coat protein gene duplication in a filamentous RNA virus of plants. Proc. Natl. Acad. Sci. U.S.A. 1992; 89: 9156–9160
   Google Scholar
• Bransom K. L., Weiland J. J., Dreher T. W. Proteolytic maturation of the 206-kDa nonstructural protein encoded by turnip yellow mosaic virus RNA. Virology 1991; 184: 351–358
   Google Scholar
• Brault V., Hibrand L., Candresse T., Le Gall O., Dunez J. Nucleotide sequence and genetic organisation of Hungarian grapevine chrome mosaic nepovirus RNA2. Nucleic Acids Res. 1989; 17: 7809–7819
   Google Scholar
• Brenner S. The molecular evolution of genes and proteins: a tale of two serines. Nature 1988; 334: 528–530
   PubMed Web of Science ®Google Scholar
• Bruenn J. Relationships among the positive strand and double-strand RNA viruses as viewed through their RNA-dependent RNA polymerases. Nucleic Acids Res. 1991; 19: 217–226
   Google Scholar
• Bujarski J. J., Kaesberg P. Genetic recombination between RNA components of a multipartite plant virus. Nature 1986; 231: 528–531
   Google Scholar
• Cammisa-Parks H., Cisar L. A., Kane A., Stollar V. The complete nucleotide sequence of cell fusing agent (CFA): homology between the nonstructural proteins encoded by CFA and the nonstructural proteins encoded by arthropod-borne flaviviruses. Virology 1992; 189: 511–524
   Google Scholar
• Candresse T., Morch M. D., Dunez J. Multiple alignment and hierarchical clustering of conserved amino acid sequences in the replication-associated proteins of plant RNA viruses. Res. Virol. 1990; 141: 315–329
   Google Scholar
• Carrington J. C., Hillman B. I., Morris T. J. The genome structure of turnip crinkle virus. Virology 1989; 170: 219–226
   PubMed Web of Science ®Google Scholar
• Carter M. J., Milton I. D., Meanger J., Bennett M. F., Gaskell R. M., Turner P. C. The complete genome sequence of a feline calicivirus. Virology 1992; 190: 443–448
   Google Scholar
• Castle E., Leidner U., Nowak T., Wengler G., Wengler G. Primary structure of the West Nile flavivirus genome region coding for all nonstructural proteins. Virology 1986; 149: 10–26
   PubMed Web of Science ®Google Scholar
• Chambers T. J., Hahn C. S., Galler R., Rice C. M. Flavivirus genome organization, expression, and replication. Annu. Rev. Microbiol. 1990a; 44: 649–688
   PubMed Web of Science ®Google Scholar
• Chambers T. J., Weir R. C., Grakouri A., Mc Court D. W., Bazan J. F., Fletterick R. J., Rice C. M. Evidence that the N-terminal domain of nonstructural protein NS3 from yellow fever virus is a serine proteinase responsible for site-specific cleavages in the viral polyprotein. Proc. Natl. Acad. Sci. U.S.A. 1990b; 87: 8898–8902
   PubMed Web of Science ®Google Scholar
• Chelvanayagam G., Heringa J., Argos P. Anatomy and evolution of proteins displaying the viral capsid jellyroll topology. J. Mol Biol. 1992; 228: 220–241
   Google Scholar
• Choi H.-K., Tong L., Minor W., Dumas P., Boege U., Rossmann M. G., Wengler G. Structure of Sindbis virus core protein reveals a chymotrypsin-like serine proteinase and the organization of the virion. Nature 1991; 354: 37–43
   PubMed Web of Science ®Google Scholar
• Coia G., Parker M. D., Speight G., Byrne M. E., Westaway E. G. Nucleotide and complete amino acid sequences of Kunjin virus: definitive gene order and characteristics of the virus-specific proteins. J. Gen. Virol. 1988; 69: 1–21
   Google Scholar
• Collett M. S., Larson R., Gold C., Strick D., Anderson D. K., Purchio A. F. Molecular cloning and nucleotide sequence of the pestivirus bovine viral diarrhea virus. Virology 1988; 165: 191–199
   PubMed Web of Science ®Google Scholar
• Cornelissen B. J., Brederode F. T., Moormann R. J., Bol J. F. Complete nucleotide sequence of alfalfa mosaic virus RNA 1. Nucleic Acids Res. 1983a; 11: 1253–1265
   PubMed Web of Science ®Google Scholar
• Cornelissen B. J., Brederode F. T., Veeneman G. H., van Boom J. H., Bol J. F. Complete nucleotide sequence of alfalfa mosaic virus RNA 2. Nucleic Acids Res. 1983b; 11: 3019–3025
   PubMed Web of Science ®Google Scholar
• Cornelissen B. J., Janssen H., Bol J. F. Complete nucleotide sequence of tobacco streak virus RNA 3. Nucleic Acids Res. 1984; 12: 2427–2437
   PubMed Web of Science ®Google Scholar
• Coutts R. H., Rigden J. E., Slabas A. R., Lomonossoff G. P., Wise P. J. The complete nucleotide sequence of tobacco necrosis virus strain D. J. Gen. Virol. 1991; 72: 1521–1529
   Google Scholar
• Dasgupta R., Ghosh A., Dasmahapatra B., Guarino L. A., Kaesberg P. Primary and secondary structure of black beetle virus RNA2, the genomic messenger for BBV coat protein precursor. Nucleic Acids Res. 1984; 12: 7215–7223
   Google Scholar
• Dasmahapatra B., Dasgupta R., Ghosh A., Kaesberg P. Structure of the black beetle virus genome and its functional implications. J. Mol. Biol. 1985; 182: 183–189
   Google Scholar
• De Jong W., Ahlquist P. A hybrid plant RNA virus made by transferring the noncapsid movement protein from a rod-shaped to a icosahedral virus is competent for systemic infection. Proc. Nat. Acad. Sci. U.S.A. 1992; 89: 6808–6812
   PubMed Web of Science ®Google Scholar
• Delarue M., Poch O., Tordo N., Moras D., Argos P. An attempt to unify the structure of polymerases. Protein Eng. 1990; 3: 461–467
   PubMedGoogle Scholar
• Demler S. A., de Zoeten G. A. The nucleotide sequence and luteovirus-like nature of RNA 1 of an aphid non-transmissible strain of pea enation mosaic virus. J. Gen. Virol. 1991; 72: 1819–1834
   PubMed Web of Science ®Google Scholar
• Demler S. A., Rucker D. G., de Zoeten G. A. The chimeric nature of the genome of pea enation mosaic virus: the independent replication of RNA 2. J. Gen. Virol. 1993; 74: 1–16
   PubMed Web of Science ®Google Scholar
• den Boon J. A., Snijder E. J., Chirnside E. D., de Vries A. A. F., Horzinek M. C., Spaan W. J. M. Equine arteritis virus is not a togavirus but belongs to the coronavirus-like superfamily. J. Virol. 1991; 65: 2910–2920
   PubMed Web of Science ®Google Scholar
• Ding S.-W., Keese P., Gibbs A. Nucleotide sequence of the Ononis yellow mosaic tymovirus genome. Virology 1989; 172: 555–563
   PubMed Web of Science ®Google Scholar
• Ding S., Keese P., Gibbs A. The nucleotide sequence of the genomic RNA of kennedya yellow mosaic tymovirus-Jervis Bay isolate: relationships with potex- and carlaviruses. J. Gen. Virol. 1990; 71: 925–931
   PubMed Web of Science ®Google Scholar
• Dolja V. V., Boyko V. P., Agranovsky A. A., Koonin E. V. Phylogeny of capsid proteins of rod-shaped and filamentous plant RNA viruses: two families with distinct patterns of sequence and probably structure conservation. Virology 1991; 184: 79–86
   Google Scholar
• Dolja V. V., Carrington J. C. Evolution of positive-strand RNA viruses. Semin. Virol. 1992; 3: 315–326
   Google Scholar
• Dolja V. V., Koonin E. V. Phylogeny of capsid proteins of small icosahedral RNA plant viruses. J. Gen. Virol. 1991; 72: 1481–1486
   Google Scholar
• Domier L. L., Franklin K. M., Shahabuddin M., Hellmann G. M., Overmeyer J. H., Hiremath S. T., Siaw M. F., Lomonossoff G. P., Shaw J. G., Rhoads R. E. The nucleotide sequence of tobacco vein mottling virus RNA. Nucleic Acids Res. 1986; 14: 5417–5430
   PubMed Web of Science ®Google Scholar
• Dominguez G., Wang C.-Y., Frey T. K. Sequence of the rubella virus genome: evidence for genetic rearrangement during togavirus evolution. Virology 1990; 177: 225–238
   Google Scholar
• Domingo E., Martinez-Salas E., Sobrino F., de la Torre J. C., Portela A., Ortin J., Lopez-Galindez C., Perez-Brena P., Villanueva N., Najera R., Vande Pol S., Steinhauer D., De Polo N., Holland J. J. The quasispecies (extremely heterogeneous) nature of viral RNA genome populations: biological relevance — a review. Gene 1985; 40: 1–8
   PubMed Web of Science ®Google Scholar
• Doolittle R. F. URFs and ORFs. A primer on how to analyze derived amino acid sequences. University Science Books, Mill Valley, CA 1986
   Google Scholar
• Molecular evolution, Meth. Enzymol, R. F. Doolittle, 1990; 183
   Google Scholar
• Dougherty W. G., Carrington J. C. Expression and function of potyviral gene products. Annu. Rev. Phytopathol. 1988; 26: 123–143
   Web of Science ®Google Scholar
• Dzianott A. M., Bujarski J. J. The nucleotide sequence and genome organization of the RNA-1 segment in two bromoviruses: broad bean bottle virus and cowpea chlorotic mottle virus. Virology 1991; 185: 553–562
   Google Scholar
• Earle J. A., Skuce R. A., Fleming C. S., Hoey E. M., Martin S. J. The complete nucleotide sequence of a bovine enterovirus. J. Gen. Virol. 1988; 69: 253–263
   Google Scholar
• Esteban L., Rodriguez-Cousino N., Esteban R. T double-stranded RNA (dsRNA) sequence reveals that T and W dsRNAs form a new RNA family in Saccharomyces cerevisiae. J. Biol. Chem. 1992; 267: 10874–10881
   Google Scholar
• Faragher S. G., Meek A. D., Rice C. M., Dalgarno L. Genome sequences of a mouse-avirulent and a mouse-virulent strain of Ross River virus. Virology 1988; 163: 509–526
   Google Scholar
• Felsenstein J. PHYLIP — Phylogeny inference package (Version 3.2). Cladistics 1989; 5: 164–166
   Google Scholar
• Fiers W., Contreras R., Duerinck F., Haegeman G., Iserentant D., Merregaert J., Jou W. M., Molemans F., Raeymaekers A., Van den Berghe A., Volckaert G., Ysebaert M. Complete nucleotide sequence of bacteriophage ms2 rna: primary and secondary structure of the replicase gene. Nature 1976; 260: 500–507
   PubMed Web of Science ®Google Scholar
• Fitch W. M., Margoliash E. Construction of phylogenetic trees. Science 1967; 155: 279–284
   PubMed Web of Science ®Google Scholar
• Forss S., Strebel K., Beck E., Schaller H. Nucleotide sequence and genome organization of foot-and-mouth disease virus. Nucleic Acids Res. 1984; 12: 6587–6601
   PubMedGoogle Scholar
• Forster R. L., Bevan M. W., Harbison S.-A., Gardner R. C. The complete nucleotide sequence of the potexvirus white clover mosaic virus. Nucleic Acids Res. 1988; 16: 291–303
   PubMed Web of Science ®Google Scholar
• Classification and nomenclature of viruses. Fifth report of the International Committee on Taxonomy of Viruses, Archives of Virologyy, R. I. B. Francki, C. M. Fauquet, D. L. Knudson, F. Brown, 1991; 1, Suppl. 2
   Google Scholar
• Franssen H., Leunissen J., Goldbach R., Lomonosoff G. P., Zimmern D. Homologous sequences in nonstructural proteins from cowpea mosaic virus and picornaviruses. EMBO J. 1984; 3: 855–861
   PubMed Web of Science ®Google Scholar
• Geigenmuller-Gnirke U., Weiss B., Wright R., Schlesinger S. Complementation between Sindbis viral RNAs produces infectious particles with a bipartite genome. Proc. Natl. Acad. Sci. U.S.A. 1991; 88: 3253–3257
   Google Scholar
• German S., Candresse T., Lanneau M., Huet J. C., Pernolet J. C., Dunez J. Nucleotide sequence and genomic organization of apple chlorotic leaf spot virus. Virology 1990; 178: 104–112
   Google Scholar
• Gibbs A. A molecular evolution of viruses: “trees,” “clocks,” and “modules”. J. Cell. Sci. (Suppl.) 1987; 7: 319–337
   PubMedGoogle Scholar
• Gilbert W. The RNA world. Nature 1986; 319: 618
   PubMed Web of Science ®Google Scholar
• Gilmer D., Bouzoubaa S., Guilley H., Richards K., Jonard G. Efficient cell-to-cell movement of beet necrotic yellow vein virus requires 3′ proximal genes located on RNA 2. Virology 1992; 189: 40–47
   Google Scholar
• Godeny E. K., Chen L., Kumar S., Methven S. L., Koonin E. V., Brinton M. A. Complete genome sequence and phylogenetic analysis of the lactate dehydrogenase-elevating virus (LDV). Virology 1993; 194: 585–596
   Google Scholar
• Goelet P., Lomonossoff G. P., Butler P. J., Akam M. E., Gait M. J., Karn J. Nucleotide sequence of tobacco mosaic virus RNA. Proc. Natl. Acad. Sci. U.S.A. 1982; 79: 5818–5822
   PubMed Web of Science ®Google Scholar
• Goldbach R. Molecular evolution of plant RNA viruses. Annu. Rev. Phytopathol. 1986; 24: 289–310
   Web of Science ®Google Scholar
• Goldbach R. Genome similarities between plant and animal RNA viruses. Microbiol. Sci. 1987; 4: 197–202
   PubMedGoogle Scholar
• Goldbach R., Le Gall O., Wellink J. Alphalike viruses in plants. Semin. Virol. 1991; 2: 19–25
   Google Scholar
• Goldbach R., Wellink J. Evolution of plusstrand RNA viruses. Intervirology 1988; 29: 260–268
   PubMed Web of Science ®Google Scholar
• Gorbalenya A. E. Host-related sequences in RNA viral genomes. Semin. Virol. 1992; 3: 359–371
   Google Scholar
• Gorbalenya A. E., Blinov V. M., Koonin E. V. Prediction of nucleotide-binding properties of virus proteins from their amino acid sequences. Molek, Genetika 1985; 11: 30–36, in Russian
   Google Scholar
• Gorbalenya A. E., Blinov V. M., Donchenko A. P. Poliovirus-encoded proteinase 3C: a possible evolutionary link between cellular serine and cysteine proteinase families. FEBS Lett. 1986; 194: 253–257
   PubMed Web of Science ®Google Scholar
• Gorbalenya A. E., Koonin E. V. Virus proteins containing the purine nucleotide-binding proteins. Nucleic Acids Res. 1989; 17: 8413–8440
   PubMed Web of Science ®Google Scholar
• Gorbalenya A. E., Koonin E. V. Comparative analysis of the amino acid sequences of the key enzymes of the replication and expression of positivestrand RNA viruses. Validity of the approach and functional and evolutionary implications. Sov. Sci. Rev. D. Physicochem. Biol. 1993a; 11: 1–89
   Google Scholar
• Gorbalenya A. E., Koonin E. V. Helicases. Amino acid sequence comparisons and beyond. Curr. Opin. Struct. Biol. 1993b, in press
   Google Scholar
• Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. A conserved NTP-motif in putative helicases. Nature 1988a; 333: 22
   PubMed Web of Science ®Google Scholar
• Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. A novel superfamily of nucleoside triphosphate-binding motif-containing proteins which are probably involved in duplex unwinding in DNA and RNA replication and recombination. FEBS Lett. 1988b; 239: 16–24
   Google Scholar
• Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. Coronavirus genome: tentative functional mapping of the non-structural polyprotein by theoretical analysis of the amino acid sequence. Nucleic Acids Res. 1989a; 17: 4456–4469
   Google Scholar
• Gorbalenya A. E., Koonin E. V., Donchenko A. P., Blinov V. M. Two related superfamilies of putative helicases involved in replication, recombination, repair and expression of DNA and RNA genomes. Nucleic Acids Res. 1989b; 17: 4713–4730
   PubMed Web of Science ®Google Scholar
• Gorbalenya A. E., Donchenko A. P., Koonin E. V., Blinov V. M. N-terminal domains of putative helicase of flavi- and pestiviruses may be serine proteases. Nucleic Acids Res. 1989c; 17: 3889–3897
   PubMed Web of Science ®Google Scholar
• Gorbalenya A. E., Donchenko A. P., Blinov V. M., Koonin E. V. Cysteine proteases of positive strand RNA viruses and chymotrypsin-like serine proteases. A distinct protein superfamily with a common structural fold. FEBS Lett. 1989d; 243: 103–113
   PubMed Web of Science ®Google Scholar
• Gorbalenya A. E., Koonin E. V., Wolf Yu. I. A new superfamily of putative NTP-binding domains encoded by genomes of small DNA and RNA viruses. FEBS Lett. 1990; 252: 145–148
   Google Scholar
• Gorbalenya A. E., Koonin E. V., Lai M. M.-C. Putative papain-related proteases of positive-strand RNA viruses. FEBS Lett. 1991; 288: 201–205
   Web of Science ®Google Scholar
• Gould A. R., Symons R. H. Cucumber mosaic virus RNA 3: determination of the nucleotide sequence provides the amino acid sequences of protein 3a and viral coat protein. Eur. J. Biochem. 1991; 126: 217–226
   Google Scholar
• Goulden M. G., Lomonossoff G. P., Davies J. W., Wood K. R. The complete nucleotide sequence of PEBV RNA2 reveals the presence of a novel open reading frame and provides insights into the structure of tobraviral subgenomic promoters. Nucleic Acids Res. 1990; 18: 4507–4512
   Google Scholar
• Greif C., Hemmer O., Fritsch C. Nucleotide sequence of tomato black ring virus RNA-1. J. Gen. Virol. 1988; 69: 1517–1529
   Google Scholar
• Grieco F., Burgyan J., Russo M. The nucleotide sequence of Cymbidium ringspot virus RNA. Nucleic Acids Res. 1989; 17: 6383
   PubMed Web of Science ®Google Scholar
• Guilley H., Carrington J. C., Balazs E., Jonard G., Richards K., Morris T. J. Nucleotide sequence and genome organization of carnation mottle virus RNA. Nucleic Acids Res. 1985; 13: 6663–6677
   PubMed Web of Science ®Google Scholar
• Gustafson G., Armour S. L. The complete nucleotide sequence of RNA beta from the type strain of barley stripe mosaic virus. Nucleic Acids Res. 1986; 14: 3895–3909
   PubMed Web of Science ®Google Scholar
• Gustafson G. D., Armour S. L., Gamboa G. C., Burgett S. G., Shepherd J. W. Nucleotide sequence of barley stripe mosaic virus RNA-alpha: RNA-alpha encodes a single polypeptide with homology to proteins from other viruses. Virology 1989; 170: 370–377
   PubMed Web of Science ®Google Scholar
• Gustafson G., Hunter B., Hanau R., Armour S. L., Jackson A. O. Nucleotide sequence and genetic organization of barley stripe mosaic virus RNA-gamma. Virology 1987; 158: 394–406
   PubMed Web of Science ®Google Scholar
• Hahn C. S., Lustig S., Strauss E. G., Strauss J. H. Western equine encephalitis virus is a recombinant virus. Proc. Natl. Acad. Sci. U.S.A. 1988; 85: 5997–6001
   PubMed Web of Science ®Google Scholar
• Hahn C. S., Strauss J. H. Site-directed mutagenesis of the proposed catalytic amino acids of the Sindbis virus capsid protein autoprotease. J. Virol 1990; 64: 3069–3073
   PubMed Web of Science ®Google Scholar
• Hahn C. S., Strauss E. G., Strauss J. H. Sequence analysis of three Sindbis virus mutants temperature-sensitive in the capsid protein autoprotease. Proc. Natl. Acad. Sci. U.S.A. 1985; 82: 4648–4652
   Google Scholar
• Hamilton W. D., Boccara M., Robinson D. J., Baulcombe D. C. The complete nucleotide sequence of Tobacco Rattle Virus RNA-1. J. Gen. Virol. 1987; 68: 2563–2575
   PubMed Web of Science ®Google Scholar
• Hardy W. R., Strauss J. H. Processing of the nonstructural polyproteins of Sindbis virus: nonstructural proteinase is in the C-terminal half of nsP2 and functions both in cis and in trans. J. Virol. 1989; 63: 4653–4664
   PubMed Web of Science ®Google Scholar
• Haseloff J., Goelet P., Zimmern D., Ahlquist P., Dasgupta R., Kaesberg P. Striking similarities in amino acid sequence among nonstructural proteins encoded by RNA viruses that have dissimilar genomic organization. Proc. Natl, Acad. Sci. U.S.A. 1984; 81: 4358–4362
   PubMed Web of Science ®Google Scholar
• Hearne P. Q., Knorr D. A., Hillman B. I., Morris T. J. The complete genome structure and synthesis of infectious RNA from clones of tomato bushy stunt virus. Virology 1990; 177: 141–151
   PubMed Web of Science ®Google Scholar
• Higgins D. G., Bleasby A. J., Fuchs R. CLUSTAL V: improved software for multiple sequence alignment. CABIOS 1992; 8: 189–191
   PubMedGoogle Scholar
• Hiroshima A., Hirose T., Inayama S., Inokuchi Y., Jacobson A. B. Analysis of the complete nucleotide sequence of the group IV RNA coliphage SP. Nucleic Acids Res. 1988; 16: 6205–6221
   Google Scholar
• Hodgman T. C. A new superfamily of replicative proteins. Nature 1988; 333: 22–23, 579 (Erratum
   PubMed Web of Science ®Google Scholar
• Holland J. J., Spindler K., Horodyski F., Grabau E., Nichol S., Van de Pol S. Rapid evolution of RNA genomes. Science 1982; 215: 1577–1585
   PubMed Web of Science ®Google Scholar
• Horiuchi K. Genetic studies of RNA phages, in RNA Phages, N. D. Zinder. Harbor Laboratory, Cold Spring 1975; 29–50
   Google Scholar
• Hyypia T., Horsnell C., Maarone M., Khan M., Kalkkinen N., Auvinen P., Kinnunen L., Stanway G. A distinct picornavirus group identified by sequence analysis. Proc. Natl. Acad. Sci. U.S.A. 1992; 89: 8847–8851
   PubMed Web of Science ®Google Scholar
• Icho T., Wickner R. B. The double-stranded RNA genome of yeast virus L-A encodes its own putative RNA polymerase by fusing two open reading frames. J. Biol. Chem. 1989; 264: 6716–6723
   PubMedGoogle Scholar
• Inokuchi Y., Takahashi R., Hirose T., Inayama S., Jacobson A. B., Hirashima A. The complete nucleotide sequence of the group II RNA coliphage GA. J. Biochem. 1986; 99: 1169–1180
   Google Scholar
• Irie K., Mohan P. M., Sasaguri Y., Putnak R., Padmanabhan R. Sequence analysis of cloned dengue virus type 2 genome (New Guinea-C strain). Gene 1989; 75: 197–211
   Google Scholar
• Jelkmann W., Maiss E., Martin R. R. The nucleotide sequence and genome organization of strawberry mild yellow edge-associated potexvirus. J. Gen. Virol. 1992; 73: 475–479
   PubMed Web of Science ®Google Scholar
• Jenkins O., Booth J. D., Minor P. D., Almond J. W. The complete nucleotide sequence of coxsackievirus B4 and its comparison to other members of the Picornaviridae. J. Gen. Virol. 1987; 68: 1835–1848
   PubMed Web of Science ®Google Scholar
• Jiang B., Monroe S. S., Koonin E. V., et al. RNA sequence of astrovirus: unique genome organization and a putative retrovirus-like ribosomal frameshifting signal directing synthesis of the viral repliease. Proc Natl. Acad. Sci. U.S.A. 1993; 90, in press
   Google Scholar
• Johansen E., Rasmussen O. F., Heide M., Borkhardt B. The complete nucleotide sequence of pea seed-borne mosaic virus RNA. J. Gen. Virol. 1991; 72: 2625–2632
   PubMed Web of Science ®Google Scholar
• Kamer G., Argos P. Primary structural comparison of RNA-dependent polymerases from plant, animal and bacterial viruses. Nucleic Acids Res. 1984; 12: 7269–7282
   PubMed Web of Science ®Google Scholar
• Kanyuka K., Vishnichenko V., Levay K., Kondrikov D., Ryabov E., Zavriev S. K. Nucleotide sequence of shallot virus X RNA reveals a 5′-proximal cistrons. J. Gen. Virol. 1992; 73: 2553–2560
   Google Scholar
• Karasawa A., Nakaho K., Kakutani T., Minobe Y., Ehara Y. Nucleotide sequence analyses of peanut stunt cucumovirus RNAs 1 and 2. J. Gen. Virol. 1992; 73: 701–707
   Google Scholar
• Karasawa A., Nakaho K., Kakutani T., Minobe Y., Ehara Y. Nucleotide sequence of RNA 3 of peanut stunt cucumovirus. Virology 1991; 185: 464–467
   Google Scholar
• Kashiwazaki S., Minobe Y., Omura T., Hibino H. Nucleotide sequence of barley yellow mosaic virus RNA 1: a close evolutionary relationship wim potyviruses. J. Gen. Virol. 1990; 71: 2781–2790
   Google Scholar
• Kashiwazaki S., Minobe Y., Hibino H. Nucleotide sequence of barley yellow mosaic virus RNA 2. J. Gen. Virol. 1991; 72: 995–999
   Google Scholar
• Kato N., Hijikata M., Ootsuyama Y., Nakagawa M., Ohkoshi S., Sugimura T., Shimotohno K. Molecular cloning of the human hepatitis C virus genome from Japanese patients with non-A, non-B hepatitis. Proc. Natl. Acad. Sci. U.S.A. 1990; 87: 9524–9528
   PubMed Web of Science ®Google Scholar
• Keese P. K., Gibbs A. Origins of genes: “big bang” or continuous creation. Proc. Natl. Acad. Sci. U.S.A. 1992; 89: 9489–9493
   PubMedGoogle Scholar
• Kimura M. The Neutral Theory of Molecular Evolution. University Press, Cambridge 1983
   Google Scholar
• King A. M., McCahon D., Slade W. R., Newman J. W. Recombination in RNA. Cell 1982; 29: 921–928
   PubMedGoogle Scholar
• King L. A., Pullin J. S., Stanway G., Almond J. W., Moore N. F. Cloning of the genome of cricket paralysis virus: Sequence of the 3′ end. Virus Res. 1987; 6: 331–344
   Google Scholar
• Kinney R. M., Tsuchiya K. R., Sneider J. M., Trent D. W. Genetic evidence that epizootic Venezuelan equine encephalitis (VEE) viruses may have evolved from enzootic VEE subtype I-D virus. Virology 1992; 191: 569–580
   Google Scholar
• Koonin E. V. The phytogeny of RNA-dependent RNA polymerases of positive-strand RNA viruses. J. Gen. Virol. 1991a; 72: 2197–2206
   PubMed Web of Science ®Google Scholar
• Koonin E. V. Similarities in RNA helicases. Nature 1991b; 352: 290
   PubMed Web of Science ®Google Scholar
• Koonin E. V. Evolution of double-stranded RNA viruses: a case for polyphyletic origin from different groups of positive-stranded RN A viruses. Semin. Virol. 1992a; 3: 327–339
   Google Scholar
• Koonin E. V. A new group of putative helicases. Trends Biochem. Sci. 1992b; 17: 496–497
   Google Scholar
• Koonin E. V. Computer-assisted identification of a putative methyltransferase domain in NS5 protein of flaviviruses and lambda2 protein of reovirus. J. Gen. Virol. 1993; 73: 733–740
   Google Scholar
• Koonin E. V., Mushegian A. R., Ryabov E. V., Dolja V. V. Diverse groups of plant RNA and DNA viruses share related movement proteins that may possess chaperone-like activity. J. Gen. Virol. 1991a; 72: 2895–2903
   PubMed Web of Science ®Google Scholar
• Koonin E. V., Choi G., Nuss D. L., Shapira R., Carrington J. C. Common ancestry for a chestnut blight hypovirulence-associated dsRNA virus and a group of positive-strand RNA plant viruses: evidence for evolution by genome rearrangement. Proc. Natl. Acad. Sci. U.S.A. 1991b; 88: 10647–10651
   PubMedGoogle Scholar
• Koonin E. V., Chumakov K. M., Gorbalenya A. E. Tentative identification of the RNA-dependent RNA polymerases of dsRNA viruses. FEBS Lett. 1989; 252: 42–46
   Google Scholar
• Koonin E. V., Gorbalenya A. E. Evolution of RNA genomes: Does the high mutation rate necessitate high rate of evolution of viral proteins. J. Molec. Evol. 1989; 28: 524–527
   Google Scholar
• Koonin E. V., Gorbalenya A. E. An insect picornavirus may have genome organization similar to that of caliciviruses. FEBS Lett. 1992; 297: 81–86
   PubMed Web of Science ®Google Scholar
• Koonin E. V., Gorbalenya A. E., Chumakov K. M., Donchenko A. P., Blinov V. M. Evolution of RNA-dependent RNA polymerases of positive-strand RNA viruses. Molek. Genetika 1987; 7: 27–39, in Russian
   Google Scholar
• Koonin E. V., Gorbalenya A. E., Purdy M. A., Rozanov M. N., Reyes G. R., Bradley D. W. Computer-assisted assignment of functional domains in the non-structural polyprotein of hepatitis E virus: delineation of an additional group of positive-strand RNA plant and animal viruses. Proc. Natl. Acad. Sci. U.S.A. 1992; 89: 8259–8263
   PubMed Web of Science ®Google Scholar
• Kraev A. S., Morozov S. Y., Lukasheva L. I., Rozanov M. N., Chernov B. K., Simonova M. L., Golova Y. B., Belzhelarskaya S. N., Pozmogova G. E., Skryabin K. S., Atabekov I. G. Primary structure and organization of the genome of potato X-virus. Dokl. Akad. Nauk. SSSR 1988; 300: 711–716
   Google Scholar
• Lai M. M. C. Coronavirus: organization, replication, and expression of genome. Annu. Rev. Microbiol. 1990; 44: 303–333
   PubMedGoogle Scholar
• Lai M. M. C. RNA recombination in animal and plant viruses. Microbiol. Rev. 1992; 56: 61–79
   PubMedGoogle Scholar
• Lain S., Riechmann J. L., Martin M. T., Garcia J. A. Homologous potyvirus and flavivirus proteins belonging to a superfamily of helicase-like proteins. Gene 1989; 82: 357–362
   PubMed Web of Science ®Google Scholar
• Lain S., Riechmann J. L., Garcia J. A. RNA Helicase: a novel activity associated with a protein encoded by a positive strand RNA virus. Nucleic Acids Res. 1990; 18: 7003–7006
   PubMed Web of Science ®Google Scholar
• Lain S., Martin M. T., Riechmann J. L., Garcia J. A. Novel catalytic activity associated with positive-strand RNA virus infection: nucleic acid-stimulated ATPase activity of the Plum Pox potyvirus helicase-like protein. J. Virol. 1991; 65: 1–6
   PubMed Web of Science ®Google Scholar
• Lambden P. R., Caul O., Ashley C., Clarke I. N. Sequence and genome organization of a human Small Round Structured (NorwaLk-like) virus. Science 1993; 259: 516–519
   PubMedGoogle Scholar
• Lee C.-J., Shieh C.-K., Gorbalenya A. E., Koonin E. V., La Monica N., Tuler J., Bagdzhadzhyan A., Lai M. M. C. The complete sequence (22 kb) of murine coronavirus gene 1 encoding the putative proteases and RNA polymerase. Virology 1991; 180: 567–582
   PubMed Web of Science ®Google Scholar
• Le Gall O., Candresse T., Brault V., Dunez J. Nucleotide sequence of Hungerian grapevine chrome mosaic nepovirus RNA1. Nucleic Acids Res. 1989; 17: 7795–7807
   Google Scholar
• Levinson R. S., Strauss J. H., Strauss E. G. Complete sequence of the genomic RNA of O'Nyongnyong virus and its use in the construction of alphavirus phylogenetic trees. Virology 1990; 175: 110–123
   Google Scholar
• Linthorst H. J., Huisman M. J., Asjes C. J., Bol J. F. Nucleotide sequence of narcissus mosaic virus RNA. J. Gen. Virol. 1989; 70: 267–276
   Google Scholar
• Lommel S. A., Weston-Fina M., Xiong Z., Lomonossoff G. P. The nucleotide sequence and gene organization of red clover necrotic mosaic virus RNA-2. Nucleic Acids Res. 1988; 16: 8587–8602
   Google Scholar
• Lomonossoff G. P., Shanks M. The nucleotide sequence of cowpea mosaic virus B RNA. EMBO J. 1983; 2: 2253–2258
   Google Scholar
• Mac Farlane S. A., Taylor S. C., King D. I., Hughes G., Davies J. W. Pea early browning virus RNA1 encodes four polypeptides including a putative zinc finger protein. Nucleic Acids Res. 1989; 17: 2245–2252
   Google Scholar
• Maiss E., Timpe U., Brisske A., Jelkmann W., Casper R., Himmler G., Mattanovich D., Katinger H. W. The complete nucleotide sequence of plum pox virus RNA. J. Gen. Virol. 1989; 70: 513–524
   PubMed Web of Science ®Google Scholar
• Martin R. R., Keese P. K., Young M. G., Waterhouse P. M., Gerlach W. L. Evolution and molecular biology of luteoviruses. Annu. Rev. Phytopathol. 1990; 28: 341–363
   Web of Science ®Google Scholar
• Matthews R. E. F. Virus taxonomy for the non-virologist. Annu. Rev. Microbiol. 1985; 39: 451–474
   Google Scholar
• Meshi T., Ohno T., Iba H., Okada Y. Nucleotide sequence of a cloned cDNA copy of TMV (cowpea strain) RNA, including the assembly origin, the coat protein cistron, and the 3′ non-coding region. Mol. Gen. Genet. 1981; 184: 20–25
   PubMedGoogle Scholar
• Meulenberg J. J., Hulst M. M., de Meijer E. J., Moonen P. L., den Besten A., de Kluyver E. P., Wensvoort G., Moorman R. J. Lelystad Virus, the causative agent of porcine epidemic abortion and respiratory syndrome (PEARS), is related to LDV and EAV. Virology 1993; 192: 62–72
   PubMed Web of Science ®Google Scholar
• Meyer M., Hemmer O., Mayo M. A., Fritsch C. The nucleotide sequence of tomato black ring virus RNA-2. J. Gen. Virol. 1986; 67: 1257–1271
   Web of Science ®Google Scholar
• Meyers G., Tautz N., Dubovi E. J., Thiel H.-J. Viral pathogenicity correlated with integration of ubiquitin-coding sequences. Virology 1991; 180: 602–616
   PubMedGoogle Scholar
• Meyers G., Ruemenapf T., Thiel H.-J. Molecular cloning and nucleotide sequence of the genome of hog cholera virus. Virology 1989; 171: 555–567
   Google Scholar
• Meyers G., Wirblich C., Thiel H.-J. Rabbit hemorrhagic disease virus — molecular cloning and nucleotide sequencing of a Calicivirus genome. Virology 1991; 184: 664–676
   Google Scholar
• Mi S., Durbin R., Huang H. V., Rice C. M., Stollar V. Association of the Sindbis virus RNA methyltransferase activity with the nonstructural protein nsP1. Virology 1989; 170: 385–391
   PubMed Web of Science ®Google Scholar
• Mi S., Stollar V. Expression of Sindbis virus nsP1 and methyltransferase activity in. Escherichia coli, Virology 1991; 178: 429–434
   Google Scholar
• Miller W. A., Waterhouse P. M., Gerlach W. L. Sequence and organization of barley yellow dwarf virus genomic RNA. Nucleic Acids Res. 1988; 16: 6097–6111
   PubMed Web of Science ®Google Scholar
• Mirzayan C., Wimmer E. Genetic and biochemical characterization of poliovirus polypeptide 2C, Abstracts of the 3rd International Symposium on Positive Strand RNA Viruses. Clearwater, FL September 19–24, 1992a; P4–28, Abstract
   Google Scholar
• Mirzayan C., Wimmer E. Genetic analysis of an NTP-binding motif in poliovirus polypeptide 2C. Virology 1992b; 189: 547–555
   Google Scholar
• Molla A., Jang S. K., Paul A. V., Reuer Q., Wimmer E. Cardioviral internal ribosomal entry site is functional in a genetically engineered dicistronic poliovirus. Nature 1992; 356: 255–257
   PubMed Web of Science ®Google Scholar
• Morch M. D., Boyer J. C., Haenni A. L. Overlapping open reading frames revealed by complete nucleotide sequencing of turnip yellow mosaic virus genomic RNA. Nucleic Acids Res. 1988; 16: 6157–6173
   Google Scholar
• Morch M. D., Drugeon G., Szafranski P., Haenni A. L. Proteolytic origin of the 150-kilodalton protein encoded by tumip yellow mosaic virus genomic RNA. J. Virol. 1989; 63: 5153–5158
   Google Scholar
• Moriones E., Roossinck M. J., Garcia-Arenal F. Nucleotide sequence of tomato aspermy virus RNA 2. J. Gen. Virol. 1991; 72: 779–783
   Google Scholar
• Yu Morozov S., Dolja V. V., Atabekov J. G. Probable reassortment of genomic elements among elongated RNA-containing plant viruses. J. Mol. Evol. 1989; 29: 52–62
   Google Scholar
• Yu Morozov S., Rupasov V. V. On the possibility of a common origin of the genes encoding the RNA polymerases of bacterial, plant, and animal positive-strand RNA viruses. Biol. Nauki 1985; 10: 19–24, in Russian
   Google Scholar
• Mushegian A. R., Koonin E. V. Movement proteins of plant viruses: sequence motifs, protein families, and evolutionary pathways. Arch. Virol., in press
   Google Scholar
• Najarian R., Caput D., Gee W., Potter S. J., Renard A., Merryweather J., Van Nest G., Dina D. Primary structure and gene organization of human hepatitis A virus. Proc. Natl. Acad. Sci. U.S.A. 1985; 82: 2627–2631
   PubMed Web of Science ®Google Scholar
• Natsuaki T., Mayo M. A., Jolly C. A., Murant A. F. Nucleotide sequence of raspberry bushy dwarf virus RNA-2: a bicistronic component of a bipartite genome. J. Gen. Virol. 1991; 72: 2183–2189
   Google Scholar
• Nitayaphan S., Grant J. A., Chang G.-J. J., Trent D. W. Nucleotide sequence of the virulent SA-14 strain of Japanese encephalitis virus and its attenuated vaccine derivative. Virology 1990; 177: 541–552
   PubMed Web of Science ®Google Scholar
• Oh C.-S., Carrington J. C. Identification of essential residues in potyvirus proteinase HC-Pro by site-directed mutagenesis. Virology 1989; 173: 692–699
   PubMed Web of Science ®Google Scholar
• Ohno S. Evolution by Gene Duplication. Springer 1970
   Google Scholar
• O'Reilly D. R., Thomas C. J., Coutts R. H. Tomato aspermy virus has an evolutionary relationship with other tripartite RNA plant viruses. J. Gen. Virol. 1991; 72: 1–7
   Google Scholar
• Osorio-Keese M. E., Keese P., Gibbs A. Nucleotide sequence of the genome of eggplant mosaic tymovirus. Virology 1989; 172: 547–554
   Google Scholar
• Palmenberg A. C. Sequence alignments of picomaviral capsid proteins. Molecular Aspects of Picornavirus Infection and Detection, B. L. Semler, E. Ehrenfeld, 1989; 211–230
   Google Scholar
• Petty I. T., French R., Jones R. W., Jackson A. O. Identification of barley stripe mosaic virus genes involved in viral RNA replication and systemic movement. EMBO J. 1990; 9: 3453–3457
   PubMed Web of Science ®Google Scholar
• Pevear D. C., Borkowski J., Calenoff M., Oh C. K., Ostrawski B., Lipton H. L. Insights into Theiler's virus neurovirulence based on a genomic comparison of the neurovirulent GDVII and less virulent BeAn strains. Virology 1988; 165: 1–12
   Google Scholar
• Pletnev A. G., Yamschikov V. F., Blinov V. M. Nucleotide sequence of the genome and complete amino acid sequence of the polyprotein of tick-borne encephalitis virus. Virology 1989; 174: 250–263
   Google Scholar
• Poch O., Sauvageut I., Delarue M., Tordo N. Identification of four conserved motifs among the RNA-dependent polymerase encoding elements. EMBO J. 1989; 8: 3867–3874
   PubMed Web of Science ®Google Scholar
• Preugshat F., Yao C.-W., Strauss J. H. In vitro processing of Dengue virus type 2 nonstructural proteins NS2A, NS2B, and NS3. J. Virol. 1990; 64: 4364–4374
   Google Scholar
• Racaniello V. R., Baltimore D. Molecular cloning of poliovirus cDNA and determination of the complete nucleotide sequence of the viral genome. Proc. Natl. Acad. Sci. U.S.A. 1981; 78: 4887–4891
   PubMed Web of Science ®Google Scholar
• Rao A. L. N., Sullivan B. R., Hall T. C. Use of Chenopodium hybridum facilitates isolation of BMV RNA recombinants. J. Gen. Virol. 1990; 71: 1403–1407
   PubMed Web of Science ®Google Scholar
• Rezaian M. A., Williams R. H., Gordon K. H., Gould A. R., Symons R. H. Nucleotide sequence of cucumber-mosaic-virus RNA 2 reveals a translation product significantly homologous to corresponding proteins of other viruses. Eur. J. Biochem. 1984; 143: 277–284
   PubMedGoogle Scholar
• Rezaian M. A., Williams R. H., Symons R. H. Nucleotide sequence of cucumber mosaic virus RNA 1: presence of a sequence complementary to part of the viral satellite RNA and homologies with other viral RNAs. Eur. J. Biochem. 1985; 150: 331–339
   PubMedGoogle Scholar
• Rice C. M., Lenches E. M., Eddy S. R., Shin S. J., Sheets R. L., Strauss J. H. Nucleotide sequence of yellow fever virus: implications for flavivirus gene expression and evolution. Science 1985; 229: 726–733
   PubMed Web of Science ®Google Scholar
• Ritzenthaler C., Viry M., Pinck M., Fuchs M., Pinck L. Complete nucleotide sequence and genetic organization of grapevine fanleaf nepovirus RNA1. J. Gen. Virol. 1993, in press
   Google Scholar
• Riviere C. J., Rochon D. M. Nucleotide sequence and genomic organization of melon necrotic spot virus. J. Gen. Virol. 1990; 71: 1887–1896
   PubMed Web of Science ®Google Scholar
• Robaglia C., Durand-Tardif M., Tronchet M., Boudazin G., Astier-Manifacier S., Casse-Delbart F. Nucleotide sequence of potato virus Y (N strain) genomic RNA. J. Gen. Virol. 1989; 70: 935–947
   PubMed Web of Science ®Google Scholar
• Rochon D. M., Tremaine J. H. Complete nucleotide sequence of the cucumber necrosis virus genome. Virology 1989; 169: 251–259
   PubMed Web of Science ®Google Scholar
• Rodriguez-Cousino N., Esteban L. M., Esteban R. Molecular cloning and characterization of W double-stranded RNA, a linear molecule present in Saccharomyces cerevisiae. Identification of its single-stranded RNA form as 20 S RNA. J. Biol. Chem. 1991; 266: 12772–12778
   PubMedGoogle Scholar
• Romero J., Dzianott A. M., Bujarski J. J. The nucleotide sequence and genome organization of the RNA2 and RNA3 segments in broad bean mottle virus. Virology 1992; 187: 671–681
   Google Scholar
• Rossmann M. G., Johnson J. E. Icosahedral RNA virus structure. Annu. Rev. Biochem. 1989; 58: 533–573
   PubMed Web of Science ®Google Scholar
• Rozanov M. N., Drugeon G., Seron K., Haenni A.-L. Papain-related proteinase of turnip yellow mosaic virus. Abstract Book, NATO Advanced Study Institute and EEC Course on the Regulation of Gene Expression by Animal Viruses. Mallorca, Spain May 30-June 8, 1992a, Abstract S16
   Google Scholar
• Rozanov M. N., Koonin E. V., Gorbalenya A. E. Conservation of the putative methyltransferase domain: a hallmark of the “Sindbis-like” supergroup of positive-strand RNA viruses. J. Gen. Virol. 1992; 73: 2129–2134
   PubMed Web of Science ®Google Scholar
• Rozanov M. N., Yu Morozov S., Skryabin K. G. Unexpected close relationship between the large non-virion proteins of filamentous potexviruses and spherical tymoviruses. Virus Genes 1990; 3: 373–379
   Google Scholar
• Saitou N., Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 1987; 4: 406–425
   PubMed Web of Science ®Google Scholar
• Sankar S., Porter A. G. Point mutations which drastically affect the polymerization activity of encephalomyocarditis virus RNA-dependent RNA polymerase correspond to the active site of Escherichia coli DNA polymerase. I. J. Biol. Chem. 1992; 267: 10168–10176
   PubMed Web of Science ®Google Scholar
• Sekiya M. E., Lawrence S. D., McCaffery M., Cline K. Molecular cloning and nucleotide sequencing of the coat protein of citrus tristeza virus. J. Gen. Virol 1991; 72: 1013–1020
   Google Scholar
• Selling B. H., Allison R. F., Kaesberg P. Genomic RNA of an insect virus directs synthesis of infectious virions in plants. Proc. Natl. Acad. Sci. U.S.A. 1990; 87: 434–438
   Google Scholar
• Serghini M. A., Fuchs M., Pinck M., Reinbolt J., Walter B., Pinck L. RNA2 of Grapevine Fanleaf Virus: sequence analysis and coat protein cistron location. J. Gen. Virol. 1990; 71: 1433–1441
   Google Scholar
• Shanks M., Stanley J., Lomonossoff G. P. The primary structure of Red clover mottle virus middle component RNA. Virology 1986; 155: 697–706
   Google Scholar
• Shanks M., Lomonossoff G. P. The nucleotide sequence of red clover mottle virus bottom component RNA. J. Gen. Virol. 1992; 73: 2473–2477
   Google Scholar
• Shapira R., Choi G. H., Nuss D. L. Virus-like genetic organization and expression strategy for a double-stranded RNA genetic element associated with biological control of chestnut blight. EMBO J. 1991; 10: 731–739
   PubMed Web of Science ®Google Scholar
• Shen P., Kaniewska M., Smith C., Beachy R. N. Nucleotide sequence and genomic organization of rice tungro spherical virus. Virology 1993; 193: 621–630
   Google Scholar
• Shirako Y., Wilson T. M. A. Complete nucleotide sequence and organization of the bipartite RNA genome of soil-borne wheat mosaic virus. Virology 1993; 195: 16–32
   Google Scholar
• Simpson G. G. Tempo and Mode in Evolution. Columbia University Press, New York 1944
   Google Scholar
• Sit T. L., Abouhaidar M. G., Holy S. Nucleotide sequence of papaya mosaic virus RNA. J. Gen. Virol. 1989; 70: 2325–2331
   Google Scholar
• Skern T., Sommergruber W., Blaas D., Gruendler P., Fraundorfer F., Pieler C., Fogy I., Kuechler E. Human rhinovirus 2: complete sequence and proteolytic processing signals in the capsid protein region. Nucleic Acids Res. 1985; 13: 2111–2126
   Web of Science ®Google Scholar
• Sneath P., Sokal R. Principles of Numerical Taxonomy. Freeman, San Francisco 1973
   Google Scholar
• Snijder E. J., den Boon J. A., Bredenbeek P. J., Horzinek M. C., Rijnbrand R., Spaan W. J. M. The carboxyl-terminal part of the putative Berne virus polymerase is expressed by ribosomal frameshifting and contains sequence motifs which indicate that toro-and coronaviruses are evolutionarily related. Nucleic Acids Res. 1990; 18: 4535–4542
   PubMedGoogle Scholar
• Sogin M. L. Early evolution and the origin of eukaryotes. Curr. Opin. Genet. Dev. 1991; 1: 457–463
   Google Scholar
• Stanway G. Structure, function and evolution of pi-cornaviruses. J. Gen. Virol. 1990; 71: 2483–2501
   PubMedGoogle Scholar
• Stanway G., Hughes P. J., Mountford R. C., Minor P. D., Almond J. W. The complete nucleotide sequence of a common cold virus: human rhinovirus 14. Nucleic Acids Res. 1984; 12: 7859–7875
   PubMed Web of Science ®Google Scholar
• Steinhauer D., Holland J. J. Rapid evolution of RNA viruses. Annu. Rev. Biochem. 1987; 41: 409–433
   Google Scholar
• Strauss J. H. Viral proteases. Sem. Virol. 1990; 1(No. 1)
   Google Scholar
• Strauss E. G., Rice C. M., Strauss J. H. Complete nucleotide sequence of the genomic RNA of Sindbis virus. Virology 1984; 133: 92–110
   PubMed Web of Science ®Google Scholar
• Strauss J. H., Strauss E. G. Evolution of RNA viruses. Annu. Rev. Microbiol. 1988; 42: 657–683
   PubMedGoogle Scholar
• Strauss E. G., Strauss J. H., Levine A. J. Virus evolution, in Fundamental Virology, B. N. Fields, D. M. Knipe. Raveri Press, New York 1991; 167–190
   Google Scholar
• Stuart K. D., Weeks R., Guilbride L., Myler P. J. Molecular organization of Leishmania RNA virus 1. Proc. Natl. Acad. Sci. U.S.A. 1992; 89: 8596–8590
   PubMed Web of Science ®Google Scholar
• Takkinen K. Complete nucleotide sequence of the nonstructural protein genes of Semliki Forest virus. Nucleic Acids Res. 1986; 14: 5667–5682
   PubMed Web of Science ®Google Scholar
• Tam A. W., Smith M. M., Guerra M. E., Huang C.-C., Bradley D. W., Fry K. E., Reyes G. R. Hepatitis E virus (HEV): molecular cloning and sequencing of the full-length viral genome. Virology 1991; 185: 120–131
   PubMed Web of Science ®Google Scholar
• Teterina N. L., Kean K. M., Gorbalenya A. E., Agol V. I., Girard M. Analysis of the functional significance of amino acid residues in the putative NTP-binding pattern of the poliovirus 2C protein. J. Gen. Virol. 1992; 73: 1977–1986
   Google Scholar
• Tolskaya E. A., Romanova L. A., Kolesnikova M. S., Agol V. I. Intertypic recombination in poliovirus: genetic and biochemical studies. Virology 1983; 124: 121–132
   Google Scholar
• Tsarev S. A., Emerson S. U., Balayan M. S., Ticehurst J. R., Purcell R. H. Simian hepatitis a virus (HAV) strain AGM-27: comparison of genome structure and growth in cell culture with other HAV strains. J. Gen. Virol. 1991; 72: 1677–1683
   Google Scholar
• Turnbull-Ross A. D., Reavy B., Mayo M. A., Murant A. F. The nucleotide sequence of parsnip yellow fleck virus: a plant picorna-like virus. J. Gen. Virol. 1992; 73: 3203–3211
   Google Scholar
• Valegard K., Liljas L., Fridborg K., Unge T. The three-dimensional structure of the bacterial virus MS2. Nature 1990; 345: 36–41
   PubMed Web of Science ®Google Scholar
• Vance V. B., Moore D., Turpen T. H., Bracker A., Hollowed V. C. The complete nucleotide sequence of pepper mottle virus genomic RNA: comparison of the encoded polyprotein with those of other sequenced potyviruses. Virology 1992; 191: 19–30
   PubMed Web of Science ®Google Scholar
• Van der Wilk F., Huisman M. J., Cornelissen B. J., Huttinga H., Goldbach R. W. Nucleotide sequence and organization of potato leafroll virus genomic RNA. FEBS Lett. 1989; 245: 51–56
   PubMed Web of Science ®Google Scholar
• van Wezenbeck P., Verver J., Harmsen J., Vos P., van Kammen A. Primary structure and gene organization of the middle-component RNA of cowpea mosaic virus. EMBO J. 1983; 2: 941–946
   Google Scholar
• Vartapetian A. B., Bogdanov A. A. Proteins covalently linked to the viral genome. Prog. Nucl. Acids Res. Molec. Biol. 1987; 34: 209–251
   Google Scholar
• Veidt I., Lot H., Leiser R. M., Scheidecker D., Guilley H., Richards K., Jonard G. Nucleotide sequence of beet western yellows virus RNA. Nucleic Acids Res. 1988; 16: 9917–9932
   PubMedGoogle Scholar
• Verchot J., Koonin E. V., Carrington J. C. The 35-kDa protein from the N-terminus of the potyviral polyprotein functions as a third virus-encoded proteinase. Virology 1991; 185: 527–535
   PubMed Web of Science ®Google Scholar
• Verchot J., Herndon K. L., Carrington J. C. Mutational analysis of the tobacco etch potyviral 35-kDa proteinase: identification of essential residues and requirements for autoproteolysis. Virology 1992; 190: 298–306
   Google Scholar
• Vincent J. R., Lister R. M., Larkins B. A. Nucleotide sequence analysis and genomic organization of the NY-RPV isolate of barley yellow dwarf virus. J. Gen. Virol. 1991; 72: 2347–2355
   PubMedGoogle Scholar
• Volchkov V. E., Volchkova V. A., Netesov S. V. Complete nucleotide sequence of the genomic RNA of eastern equine encephalomyelitis virus. Molek. Genetika 1991; 5: 8–15
   Google Scholar
• Von Heijne G. Sequence Analysis in Molecular Biology. Treasure Trove or Trivial Pursuit. Academic Press. 1987
   Google Scholar
• Walker J. E., Saraste M., Runswick M. J., Gay N. J. Distantly Related Sequences in the a-and b-Subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J. 1982; 1: 945–951
   PubMed Web of Science ®Google Scholar
• Warrener P., Tamura J., Colett M. S. RNA-stimulated NTPase activity associated with yellow fever virus NS3 protein expressed in bacteria. J. Virol. 1993; 67: 989–996
   PubMedGoogle Scholar
• Wengler G., Czaya G., Farber P. M., Hegemann J. H. In vitro synthesis of West Nile virus proteins indicates that the aminoterminal segment of the NS3 protein contains the active centre of the protease which cleaves the viral polyprotein after multiple basic amino acids. J. Gen. Virol. 1991; 72: 851–858
   Google Scholar
• Wengler G., Wengler G. The carboxy-terminal part of the NS3 protein of the West Nile flavivirus can be isolated as a soluble protein after proteolytic cleavage and represents an RNA-stimulated NTPase. Virology 1991; 184: 707–715
   PubMed Web of Science ®Google Scholar
• Wiskerchen M., Collett M. Pestivirus gene expression: protein p80 of bovine viral diarrhea virus is a proteinase involved in polyprotein processing. Virology 1991; 184: 341–350
   Google Scholar
• Wu S., Rinehart C. A., Kaesberg P. Sequence and organization of Southern Bean mosaic virus genomic RNA. Virology 1987; 161: 73–80
   PubMed Web of Science ®Google Scholar
• Xiong Y., Eickbusch T. H. Origin and evolution of retroelements based upon their reverse transcriptase sequences. EMBO J. 1990; 9: 3353–3362
   PubMed Web of Science ®Google Scholar
• Xiong Z., Lommel S. A. The complete nucleotide sequence and genome organization of red clover necrotic mosaic virus RNA 1. Virology 1989; 171: 543–554
   PubMed Web of Science ®Google Scholar
• Yoshikawa N., Sasaki E., Kato M., Takahashi T. The nucleotide sequence of apple stem grooving capillovirus genome. Virology 1992; 191: 98–105
   PubMed Web of Science ®Google Scholar
• Zavriev S. K., Kanyuka K. V., Levay K. E. The genome organization of potato virus M RNA. J. Gen. Virol. 1991; 72: 9–14
   Google Scholar
• Ziegler A., Natsuaki T., Mayo M. A., Jolly C. A., Murant A. F. The nucleotide sequence of RNA-1 of raspberry bushy dwarf virus. J. Gen. Virol. 1992; 73: 3213–3218
   Google Scholar
• Zimmern D. Evolution of RNA viruses, in RNA Genetics, J. J. Holland, E. Domingo, P. Ahlquist. CRC Press, Boca Raton, FL 1988; 211–240
   Google Scholar