A novel method for pestivirus genotyping based on palindromic nucleotide substitutions in the 5′-untranslated region

被引:41
作者
Harasawa, R [1 ]
Giangaspero, M
机构
[1] Univ Tokyo, Fac Med, Anim Ctr Biomed Res, Bunkyo Ku, Tokyo 113, Japan
[2] Univ Milan, Fac Vet Med, Special Pathol & Vet Med Clin Inst, I-20133 Milan, Italy
关键词
genotyping; palindromic sequence; pestivirus; secondary structure; untranslated region;
D O I
10.1016/S0166-0934(97)00180-8
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
A simple and practical method was developed for pestivirus genotyping based on analysis of the secondary structures in the 5'-untranslated region (UTR). Three stable stem-loop structures, V1, V2 and V3, predicted by computer in the 5'-UTR, included strictly conserved consensus base-pairings which are shared by all the genotypes of pestivirus or are characteristic to each genotype of pestivirus. On the basis of the palindromic nucleotide substitution at the secondary structural level, six genotypes have been identified among pestivirus strains, irrespective of the cytopathic and non-cytopathic biotypes. They are genotypes Ia, Ib, Ic and II in bovine viral diarrhea virus, genotype III in border disease virus, and genotype IV in classical swine fever virus. The stable stem-loop structures, which were maintained by palindromic nucleotide substitutions in the stem region, may represent references for the classification and identification of pestivirus species and/or genotypes. (C) 1998 Elsevier Science B.V, All rights reserved.
引用
收藏
页码:225 / 230
页数:6
相关论文
共 29 条
[1]   FURTHER CHARACTERIZATION OF BORDER DISEASE VIRUS ISOLATES - EVIDENCE FOR THE PRESENCE OF MORE THAN 3 SPECIES WITHIN THE GENUS PESTIVIRUS [J].
BECHER, P ;
KONIG, M ;
PATON, DJ ;
THIEL, HJ .
VIROLOGY, 1995, 209 (01) :200-206
[2]   SECONDARY STRUCTURE OF THE 5' NONTRANSLATED REGIONS OF HEPATITIS-C VIRUS AND PESTIVIRUS GENOMIC RNAS [J].
BROWN, EA ;
ZHANG, HC ;
PING, LH ;
LEMON, SM .
NUCLEIC ACIDS RESEARCH, 1992, 20 (19) :5041-5045
[3]  
BROWNLIE J, 1997, P 3 ESVV S PEST INF, P188
[4]  
DEMOERLOOZE L, 1993, J GEN VIROL, V74, P1433, DOI 10.1099/0022-1317-74-7-1433
[5]   5' AND 3' UNTRANSLATED REGIONS OF PESTIVIRUS GENOME - PRIMARY AND SECONDARY STRUCTURE ANALYSES [J].
DENG, RT ;
BROCK, KV .
NUCLEIC ACIDS RESEARCH, 1993, 21 (08) :1949-1957
[6]   A COMPREHENSIVE SET OF SEQUENCE-ANALYSIS PROGRAMS FOR THE VAX [J].
DEVEREUX, J ;
HAEBERLI, P ;
SMITHIES, O .
NUCLEIC ACIDS RESEARCH, 1984, 12 (01) :387-395
[7]   COMPARATIVE-STUDIES OF BORDER DISEASE AND CLOSELY-RELATED VIRUS-INFECTIONS IN EXPERIMENTAL PIGS AND SHEEP [J].
EDWARDS, S ;
ROEHE, PM ;
IBATA, G .
BRITISH VETERINARY JOURNAL, 1995, 151 (02) :181-187
[8]   IMPROVED FREE-ENERGY PARAMETERS FOR PREDICTIONS OF RNA DUPLEX STABILITY [J].
FREIER, SM ;
KIERZEK, R ;
JAEGER, JA ;
SUGIMOTO, N ;
CARUTHERS, MH ;
NEILSON, T ;
TURNER, DH .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1986, 83 (24) :9373-9377
[9]  
Giangaspero M, 1993, Arch Virol Suppl, V7, P53
[10]  
Harasawa R, 1996, ACTA VIROL, V40, P49