A primer pair for amplifying part of the genome of all potyvirids by RT-PCR

J Virol Methods. 1997 Jan;63(1-2):9-16. doi: 10.1016/s0166-0934(96)02103-9.

Abstract

Sequence analysis was used to design a pair of degenerate oligonucleotide primers that amplified a 1.6-2.1 kbp fragment from the 3' end of the genome (virion protein gene and part of the NIb gene) of 17 species of the Potyviridae ('potyvirids'); 11 potyviruses, 2 bymoviruses, 2 macluraviruses, an ipomovirus and a rymovirus. The 'potyvirid primer 1' hybridizes to the 3' terminal poly-A region of the genome, and 'potyvirid primer 2' to the genomic region encoding the-GNNSGQ-motif of the NIb protein. Database searches showed that the potyvirid 2 primer is specific for potyvirids. Associated analyses indicated that the published amino acid sequence of part of the wheat streak mosaic rymovirus NIb protein is probably incorrect in part.

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • DNA Primers*
  • Genome, Viral*
  • Molecular Sequence Data
  • Polymerase Chain Reaction / methods*
  • Potyvirus / genetics*

Substances

  • DNA Primers