Analysis of human rotavirus G1P[8] strains by RFLP reveals higher genetic drift in the VP7 than the VP4 gene during a 4-year period in Mexico

• Published in: Journal of virological methods 2006-12, Vol.138 (1), p.177-183
• Main Authors: Rodríguez-Castillo, Araceli, Ramírez-González, José Ernesto, Padilla-Noriega, Luis, Barrón, Blanca Lilia
• Format: Article
• Language: English
• Subjects: Antigens, Viral - genetics; Biological and medical sciences; Capsid Proteins - genetics; Child, Preschool; Cluster Analysis; Diarrhea - virology; DNA Fingerprinting; DNA Primers; DNA Restriction Enzymes; Feces - virology; Fundamental and applied biological sciences. Psychology; G1P; Genetic Drift; Genome, Viral; Human rotavirus; Humans; Mexico; Microbiology; Polymorphism, Genetic; Polymorphism, Restriction Fragment Length; Reverse Transcriptase Polymerase Chain Reaction; RFLP; Rotavirus; Rotavirus - classification; Rotavirus - genetics; Rotavirus - isolation & purification; Rotavirus Infections - virology; Techniques used in virology; Virology; VP4; VP7
• ISSN: 0166-0934; 1879-0984
• DOI: 10.1016/j.jviromet.2006.08.013

Several studies have demonstrated that rotaviruses of the G1P[8] genotype are among the most important worldwide. Sequence analysis of G1P[8] strains has revealed high genetic variability of VP4 and VP7 genes. The aim of this study was to investigate by restriction fragment length polymorphism (RFLP) analysis the genetic variability of the VP7 and VP4 genes within rotaviruses of the G1P[8] genotype. A total of 60 rotavirus-positive fecal samples genotyped as G1P[8], were collected from children with acute diarrhea under 5 years of age, between October 1995 and October 1998. The VP7 and VP4 genes were amplified by RT/PCR, using the Beg9/End9 primer pair and the Con3 and Con2 primers, respectively. VP7 amplicons were digested with three restriction enzymes Hae III, Taq I and Rsa I in separate reactions and VP4 amplicons were digested similarly with endonucleases Hinf I, Sau96 I and Rsa I. Analysis of the digested VP7 and VP4 amplicons showed a higher genetic drift for the VP7 gene (18 RFLPs) compared to the VP4 gene (9 RFLPs). The combination of profiles for both VP7 and VP4 amplicons, showed 27 different patterns, none of them similar to the Wa-1 strain. Furthermore, RFLP analysis of these G1P[8] strains, clearly differentiated the viruses into two main clusters, both of them sharing the same restriction pattern for the VP4 gene, and a different one for the VP7 gene.