Analysis of genetic diversity in the VP1 unique region gene of human parvovirus B19 using the mismatch detection method and direct nucleotide sequencing.
To assess the prevalent genetic types of human parvovirus B19 strains derived from various sources and their relation to particular clinical symptoms, the genetic diversity in the VP1 unique region, which is important for the neutralizing response to human parvovirus B19, was examined by the mismatch detection method using the Non-isotopic RNase Cleavage Assay (NIRCA) and direct nucleotide sequencing. Twenty three samples obtained between 1986 and 1997 were examined. Three electrophoresis patterns were observed with NIRCA. The nucleotide sequence showed that there were 14 nucleotide changes and 4 amino acid substitutions in comparison with Au strains employed as a standard strain. The nucleotide variability of all samples ranged from 0.3 to 2.7% and the amino acid variability ranged from 1.0 to 3.0%. They were classified into three types according to NIRCA. Types 1 and 3 had similar sequences, but the type 2 sequence was quite different. Although there were some nucleotide variations in the same NIRCA type, these were silent. However, there was no relationship between the clinical features and NIRCA types or between clinical features and the nucleotide sequence. All samples obtained before 1987 were NIRCA type 2. On the other hand, 19 of 20 samples obtained after 1989 were NIRCA type 1. The other sample obtained in 1992 was type 3. The results suggest that the B19 strain of type 2 disappeared by 1988 and changed to other B19 strains such as type 1 and type 3 after 1988, indicating a correlation between genome type and prevalence. NIRCA is a convenient method for screening mutations due to its simplicity and quickness.
Haseyama
K
K
Department of Pediatrics, Sapporo Medical University School of Medicine, Japan. haseyama@serpent.cc.sapmed.ac.jp
Kudoh
T
T
Yoto
Y
Y
Suzuki
N
N
Chiba
S
S
D000293:Adolescent; D019943:Amino Acid Substitution; D020137:Base Pair Mismatch; D001483:Base Sequence; D002213:Capsid / Q000235:genetics*; D036022:Capsid Proteins; D002648:Child; D002675:Child, Preschool; D005260:Female; D005814:Genes, Viral; D014644:Genetic Variation; D006801:Humans; D008297:Male; D009154:Mutation; D010322:Parvoviridae Infections / Q000821:virology*; D016732:Parvovirus B19, Human / Q000235:genetics*; D016133:Polymerase Chain Reaction
D036022:Capsid Proteins; C095547:capsid protein VP1, parvovirus B19