Detection and classification of allexiviruses from garlic in China.
Degenerate primers for RT-PCR were designed and used to amplify genome fragments ( c. 750 nt in the coat protein-ORF6 region) of allexiviruses from a total of 28 garlic samples from 24 provinces in China. Many samples contained more than one distinct sequence. A total of 60 different sequences were obtained. Phylogenetic analysis and two-way comparisons were used to assess the status of the sequences and to re-examine the criteria for distinguishing species within the genus. Most of the sequences could be allocated to either Garlic virus D or Garlic virus X on the basis of sequence similarity but some appeared to be intermediate between existing species. There were no sequences of Garlic virus C or Shallot virus X. A comparison with the related genera Carlavirus, Foveavirus and Potexvirus suggests that the published allexivirus species demarcation criteria may have been drawn too tightly and should be re-examined.
Chen
J
J
Virology and Biotechnology Department, Zhejiang Academy of Agricultural Sciences, Hangzhou, P.R., China. jchen1@netease.com
Zheng
H-Y
HY
Antoniw
J F
JF
Adams
M J
MJ
Chen
J-P
JP
Lin
L
L
D002681:China; D017931:DNA Primers; D018076:DNA, Complementary / Q000235:genetics; D005737:Garlic / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D010935:Plant Diseases / Q000821:virology; D010942:Plant Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D012328:RNA Viruses / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D017422:Sequence Analysis, DNA
D017931:DNA Primers; D018076:DNA, Complementary