RNA-dependent RNA polymerase gene sequence from foot-and-mouth disease virus in Hong Kong

Biochem Biophys Res Commun. 2003 Sep 5;308(4):899-905. doi: 10.1016/s0006-291x(03)01511-0.

Abstract

A foot-and-mouth disease virus (FMDV, HKN/2002) was isolated in Hong Kong in 2002. The nucleotide sequence of the 3D(pol) gene encoding the viral RNA-dependent RNA polymerase was determined and compared with that of the same gene from other FMDVs. The 3D(pol) gene was 1410 nucleotides in length encoding a protein of 470 amino acid residues. Sequence comparisons indicated that HKN/2002 belonged to serotype O. An evolutionary tree based on the 3D(pol) sequences of 20 FMDV isolates revealed that the nucleotide sequence of the HKN/2002 3D(pol) gene was most similar to those of isolates found in Taiwan in 1997, suggesting that they share a common ancestor. The amino acid sequence of the HKN/2002 3D(pol) gene was determined and aligned with those of representative isolates from seven other Picornaviridae genera. Eight highly conserved regions were detected, indicating a conserved functional relevance for these motifs. Alignment of 20 FMDV 3D(pol) amino acid sequences revealed a hypermutation region near the N-terminus that may help the virus evade host immune systems.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Base Sequence
  • Cloning, Molecular
  • Conserved Sequence
  • DNA-Directed RNA Polymerases / chemistry
  • Foot-and-Mouth Disease Virus / enzymology*
  • Foot-and-Mouth Disease Virus / genetics*
  • Genetic Variation
  • Hong Kong
  • Models, Genetic
  • Molecular Sequence Data
  • Mutation
  • Phylogeny
  • Protein Structure, Tertiary
  • RNA, Viral*
  • RNA-Dependent RNA Polymerase / genetics*
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sequence Analysis, DNA
  • Sequence Homology, Amino Acid

Substances

  • RNA, Viral
  • RNA-Dependent RNA Polymerase
  • DNA-Directed RNA Polymerases