Nucleotide mismatches between the VP7 gene and the primer are associated with genotyping failure of a specific lineage from G1 rotavirus strains

Gabriel I Parra,Emilio E Espinola

doi:10.1186/1743-422x-3-35

Abstract

In recent years it was reported that the accumulation of point mutations in VP4 and VP7 genes of rotavirus strains was the main cause of the failure of the G or P-typing. Failures in the correct genotyping of G1, G2, G8, G9 and G10 rotavirus strains were reported in the most commonly used reverse transcription (RT)-PCR strategies. Collecting VP7 gene sequences of G1 rotavirus strains from databases we found that 74 (61.2 %) out of 121 G1 strains from lineage I showed the four specific mismatches at the 5' end of the 9T1-1 primer, previously associated with the failure of G1-typing. Thus, a great percentage of the G1 strains from lineage I worldwide reported could not have been typed if the Das's RT-PCR strategy were used. This analysis shows that the failure on the detection of the G1 strains could be due to the diversification of rotavirus strains in phylogenetic lineages. Therefore, the use of different RT-PCR strategies with different primer binding locations on the VP7 gene or new typing methodologies -like microarrays procedures- could be a better option to avoid the failure of the G-typing of rotavirus strains detected during surveillance programs.

Highlights

Causing more than 450,000 deaths per year, group A rotaviruses are the most important cause of acute diarrhea in children throughout the world [1]
In order to evaluate the vaccine efficiency, the surveillance programs should detect the diversity of rotavirus strains before, during and after the introduction of a rotavirus vaccine [14]
In a recent paper published by Rahman et al [19], it was reported the failure of the Das's reverse transcription (RT)-PCR strategy to detect most (75%) of the G1 human rotavirus isolated in Bangladesh during the surveillance in 2002

Summary

Introduction

Causing more than 450,000 deaths per year, group A rotaviruses are the most important cause of acute diarrhea in children throughout the world [1]. In a recent paper published by Rahman et al [19], it was reported the failure of the Das's RT-PCR strategy to detect most (75%) of the G1 human rotavirus isolated in Bangladesh during the surveillance in 2002. They argue that this failure was due to four mismatches found at the 5' end of the primer binding site.

Results

Conclusion