Multiple-gene characterization of rotavirus strains: evidence of genetic linkage among the VP7-, VP4-, VP6-, and NSP4-encoding genes.
A total of 162 rotavirus strains detected between 1996 and 2006 among individuals with diarrhea in Rio de Janeiro, Brazil, were analyzed by multiple-gene genotyping. Characterization of strains was done by RT-PCR assay for amplification and typing of the VP7-, VP4-, VP6-, and NSP4-encoding genes. Overall, 139 (85.8%) strains belonged to the common group A rotavirus combinations: 67 (41.4%) belonged to genotype G1-P[8]-I1-E1; 18 (11.1%) were G2-P[4]-I2-E2; 11 (6.8%) were G3-P[8]-I1-E1; 12 (7.4%) were G4-P[8]-I1-E1; and 31 (19.1%) were G9-P[8]-I1-E1. Two samples presented mixed genotypes (G1 + G3-P[8]-I1-E1 and G1 + G9-P[9]-I1-E1) and rare combinations, such as G2-P[6]-I2-E2 and G9-P[6]-I2-E2, were detected in six (3.7%) strains. The results suggest a linkage among all four genes. Genotypes G1/G3/G4/G5/G9-P[8] were correlated strongly to I1-E1 genotypes and G2-P[4]/P[6] were correlated to I2-E2 genotypes. Unusual combinations of genes, such as G3-P[9]-I2-E2, G9-P[9]-I1-E2, and G3-P[9]-I3-E3, were observed in 15 (9.3%) strains. The characterization of multiple genes allows a more complete analysis of the rotavirus isolates and provides evidence of natural reassortment of strains.
Benati
Fabrício José
FJ
Microbiology Institute, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil.
Maranhão
Adriana G
AG
Lima
Rodrigo S
RS
da Silva
Raquel Cirlene
RC
Santos
Norma
N
D000956:Antigens, Viral / Q000235:genetics*; D001938:Brazil; D036022:Capsid Proteins / Q000235:genetics*; D002675:Child, Preschool; D016000:Cluster Analysis; D003967:Diarrhea / Q000821:virology; D008040:Genetic Linkage; D005838:Genotype; D006023:Glycoproteins / Q000235:genetics*; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D012367:RNA, Viral / Q000235:genetics; D011995:Recombination, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012401:Rotavirus / Q000235:genetics*; D012400:Rotavirus Infections / Q000821:virology; D017422:Sequence Analysis, DNA; 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; C060339:VP4 protein, Rotavirus; C061332:VP6 protein, Rotavirus; C050779:VP7 protein, Rotavirus; D017361:Viral Nonstructural Proteins