Genetic diversity of the VP4 and VP7 genes affects the genotyping of rotaviruses: analysis of Paraguayan strains.
The introduction of different multiplex RT-PCR strategies for the characterization of field rotavirus strains has led to improvements of surveillance systems worldwide. Nevertheless, the failure or incorrect characterization of rotavirus strains by these PCR strategies, mainly due to accumulation of point mutations in the VP4 and VP7 genes, has been reported. In this work, sequence analyses of the VP4 and VP7 genes from Paraguayan G1P[8] and G4P[8] strains revealed that the high degree of similarity with the primers pNCDV and ET10 could lead to the incorrect characterization of these strains as P[1] and G10 types. Moreover, the nucleotide diversity of the VP4 gene at the 1T-1 primer binding site could be one, although not the only, reason of the failure of the P[8] typing. Therefore, the typing methods utilized by surveillance programs should be constantly evaluated and sequencing of atypical strains should become a current practice in order to confirm their real nature.
Espínola
Emilio E
EE
Departamento de Biología Molecular, Instituto de Investigaciones en Ciencias de la Salud, Universidad Nacional de Asunción, Asunción, Paraguay.
Parra
Gabriel I
GI
Russomando
Graciela
G
Arbiza
Juan
J
D000956:Antigens, Viral / Q000235:genetics*; D001483:Base Sequence; D036022:Capsid Proteins / Q000235:genetics*; D014644:Genetic Variation; D005838:Genotype; D006801:Humans; D010239:Paraguay; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D012401:Rotavirus / Q000145:classification* / Q000235:genetics*; D012400:Rotavirus Infections / Q000821:virology
D000956:Antigens, Viral; D036022:Capsid Proteins; D012367:RNA, Viral; C060339:VP4 protein, Rotavirus; C050779:VP7 protein, Rotavirus