Determination of human rotavirus VP6 genogroups I and II by reverse transcription-PCR.
Based on nucleotide sequence and phylogenetic analysis of the partial VP6 genes, group A rotaviruses can be mainly differentiated into two genogroups. In this study, a method employing reverse transcription-PCR (RT-PCR) and degenerate primers was established to assign the VP6 genogroup. VP6 genogroup I and genogroup II could be determined according to the sizes of the amplicons: 380 and 780 bp, respectively. The VP6 genogroup of human reference strains of G1 to G4 and G9 types and RotaTeq vaccine strains could be properly assigned by RT-PCR. Eighty rotavirus-positive fecal samples were subjected to enzyme-linked immunosorbent assay (ELISA), RT-PCR, and sequencing of the partial VP6 gene for subgroup and genogroup determination. The results correlated well among these three methods, except for seven samples whose subgroups could not be determined by ELISA. VP6 genogroups of another 150 rotavirus strains recovered between 1981 and 2005 were determined by RT-PCR and sequencing, and the same results were obtained by these two methods. Furthermore, an additional 524 rotavirus-positive fecal samples were tested by RT-PCR, and the VP6 genogroups could be easily determined. The RT-PCR assay developed here provided a reliable and convenient method for assigning the VP6 genogroups of human rotaviruses with a wide range of genetic variation.
Lin
Yi-Pei
YP
Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, No. 1, Chang-Te St., Taipei 100, Taiwan.
Kao
Chuan-Liang
CL
Chang
Sui-Yuan
SY
Taniguchi
Koki
K
Hung
Pei-Yung
PY
Lin
Hsueh-Ching
HC
Huang
Li-Min
LM
Huang
Hsueh-Hung
HH
Yang
Jyh-Yuan
JY
Lee
Chun-Nan
CN
D000956:Antigens, Viral / Q000235:genetics*; D036022:Capsid Proteins / Q000235:genetics*; D005243:Feces / Q000821:virology; D005838:Genotype; D006023:Glycoproteins / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction / Q000379:methods*; D012401:Rotavirus / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D012400:Rotavirus Infections / Q000821:virology; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D014118:Toxins, Biological / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000235:genetics
D000956:Antigens, Viral; D036022:Capsid Proteins; D006023:Glycoproteins; C081369:NS28 protein, rotavirus; D012367:RNA, Viral; D014118:Toxins, Biological; C061332:VP6 protein, Rotavirus; D017361:Viral Nonstructural Proteins