Amino Acid Sequence Homology of Coat Proteins as a Basis for Identification and Classification of the Potyvirus Group

Abstract

SUMMARYAnalysis of the 136 possible pairings of the coat protein amino acid sequences from 17 strains of eight distinct potyviruses revealed a bimodal distribution of sequence homology. Distinct members of the group exhibited sequence homologies ranging from 38 to 71 ~ (average 54%) with major differences in the length and sequence of their N termini and high sequence homology in the C-terminal half of the coat proteins. In contrast strains of individual viruses exhibited sequence homologies of 90 to 99% (average 95 9/o) and had very similar N-terminal sequences. These findings cast doubt on the currently held 'continuum' hypothesis proposed to explain the unsatisfactory taxonomy of the potyvirus group. The coat protein sequence data, in combination with information on the nature of the potyvirus particle assembly, can be used to develop rationally designed, simple serological techniques that appear to be more useful and more easily applied than those properties previously used for potyvirus identification and classification.

No recombination detected in artificial potyvirus mixed infections and between potyvirus derived transgenes and heterologous challenging potyviruses

“…The comparison of PPV-SK68 and PVY-H showed two conserved regions in the genomic 3 -part (NIb, CP) consisting of 28 and 29 nt stretches with similarities of 96% and 93%, respectively. The observed similarities corresponded with the alignment data of Shukla and Ward (1988). Bujarski and Nagy (1996) showed for Brome mosaic virus that sequence similarities of at least 15 nt between RNA2 and RNA3 were sufficient to promote efficient RNA2/RNA3 recombination, while sequence identities of nine or fewer nucleotides reduced the level of detectable recombinants.…”

Sequence polymorphism in the 5'NTR and in the P1 coding region of potato virus Y genomic RNA

“…Due to its large size, the taxonomy of this group was not resolved until sequence data, and particularly capsid sequence data, clarified the classification. There is a bimodal distribution of coat protein sequence similarity, with known distinct potyviruses ranging in sequence similarity between 38-71% and known strains of given viruses ranging between 90-99% (Shukla & Ward, 1988). D. D. Shukla and coworkers have shown that comparative sequence analysis 0001-2803 © 1995 SGM of whole coat protein sequences can produce plausible phylogenetic trees of potyviruses (Rybicki & Shukla, 1992).…”

The Use of 3' Non-coding Nucleotide Sequences in the Taxonomy of Potyviruses: Application to Watermelon Mosaic Virus 2 and Soybean Mosaic Virus-N

“…We have shown recently that coat protein sequence data can be used to discriminate between distinct viruses and strains (Shukla & Ward, 1988). Distinct potyviruses have coat protein sequence identities of 38 to 71 ~o compared to 90 to 99~ for related strains (see Shukla & Ward, 1989a, for review).…”