Identification of potyviruses using the polymerase chain reaction with degenerate primers

J Gen Virol. 1991 Jul:72 ( Pt 7):1531-41. doi: 10.1099/0022-1317-72-7-1531.

Abstract

Local areas of conserved amino acid sequence in the replicase and coat proteins of potyviruses were used to select nucleotide sequences for use in the construction of sets of degenerate oligonucleotide primers for amplification of DNA fragments on potyvirus-specific templates in a combined assay of reverse transcription and the polymerase chain reaction (RT-PCR). Sequences selected for the construction of degenerate primers included the coat protein gene sequence of tulip breaking virus from lily, which is reported in this paper. It is shown that the degenerate primers support potyvirus-specific amplification, but do not support amplification on carlavirus and potexvirus templates. A panel consisting of definite and prospective members of the potyvirus group occurring in bulbous crops was subjected to the degenerate primer RT-PCR assay; amplified fragments were used in cross-hybridization experiments and restriction fragment length polymorphism analysis to detect relationships among these potyviruses. A partially characterized virus isolated from Gloriosa rothschildiana was positively identified as a potyvirus by specific amplification and subsequent sequence analysis of an amplified DNA fragment.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Blotting, Southern
  • Capsid / chemistry*
  • Capsid / genetics
  • Cloning, Molecular
  • DNA Probes
  • DNA, Viral / chemistry
  • Electrophoresis, Agar Gel
  • Gene Amplification
  • Gene Library
  • Molecular Sequence Data
  • Nucleic Acid Hybridization
  • Open Reading Frames
  • Plant Viruses / classification
  • Plant Viruses / genetics
  • Plant Viruses / isolation & purification*
  • Polymerase Chain Reaction*
  • Polymorphism, Restriction Fragment Length
  • RNA, Viral / chemistry
  • RNA-Dependent RNA Polymerase / chemistry*
  • RNA-Dependent RNA Polymerase / genetics
  • Templates, Genetic
  • Transcription, Genetic

Substances

  • DNA Probes
  • DNA, Viral
  • RNA, Viral
  • RNA-Dependent RNA Polymerase