Prediction of human rotavirus serotype by nucleotide sequence analysis of the VP7 protein gene

Abstract

Human rotavirus field isolates were characterized by direct sequence analysis of the gene encoding the serotype-specific major neutralization protein (VP7). Single-stranded RNA transcripts were prepared from virus particles obtained directly from stool specimens or after two or three passages in MA-104 cells. Two regions of the gene (nucleotides 307 through 351 and 670 through 711) which had previously been shown to contain regions of sequence divergence among rotavirus serotypes were sequenced by the dideoxynucleotide method with two different synthetic oligonucleotide primers. The resulting nucleotide sequences were compared with the corresponding sequences from rotaviruses of known serotype (serotype 1, 2, 3, or 4). A total of 25 field isolates and 10 laboratory strains examined by this method exhibited marked sequence identity in both areas of the gene with the corresponding regions of 1 of the 4 reference strains. In addition, the predicted serotype from the sequence analysis correlated in each case with the serotype determined when the rotaviruses were examined by plaque reduction neutralization or reactivity with serotype-specific monoclonal antibodies. These data suggest that as a result of the high degree of sequence conservation observed among rotaviruses of the same serotype, it is possible to predict the serotype of a rotavirus isolate by direct sequence analysis of its VP7 gene.

Detection of substantial porcine group B rotavirus genetic diversity in the United States, resulting in a modified classification proposal for G genotypes

“…In addition, a correlation between RVB G genotypes based on a 68% nucleotide-cut-off value and G serotypes is unlikely. Although serotyping analyses cannot be performed currently due to the lack of methods to easily adapt RVB strains to cell culture, it is a reasonable assumption that a roughly similar number of amino acid changes (and corresponding nucleotide changes) have to be present into VP7 of RVA and RVB strains before two strains can be considered to belong to the distinct serotype (Green et al, 1988). Since the amino acid residues, which form the epitopes responsible for the serotypes specificity are currently unknown for VP7 of RVB, it is difficult to speculate on the correlation between RVB VP7 serotypes and genotypes, and future serological assays will have to be performed to study these relationships.…”

Molecular characterization of a novel bovine group A rotavirus

“…The present study suggests that Tak2 is a BoRV-A with a novel P genotype specificity, which has not been reported among BoRV-A thus far. RV-As with different G types share <85% aa sequence conservation in the VP7, while strains sharing >90% aa identity are considered to belong to the same G type (Green et al, 1988(Green et al, , 1989Kapikian et al, 2001). Based on sequence and phylogenetic analysis of the partial sequence of the VP7 gene, strain Tak2 could not be assigned to any of the previously established G types.…”

Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes

“…Recently, several groups have determined the nucleotide sequence of the VP7 gene of more than 35 rotavirus strains. Comparison of their deduced amino acid sequences have revealed six discrete divergent regions (A to F) among different serotypes (Green et al, 1987;Green et al, 1988): amino acids 39-50 (region A), 87-101 (region B), 120-130 (region C), 143-152 (region D), 208-221 (region E), and 233-242 (region F). A comparison of these same regions among rotaviruses belonging to the same serotype revealed 91-99% homology (Green et al, 1987 ).…”