Characterization of novel VP7, VP4, and VP6 genotypes of a previously untypeable group A rotavirus

Abstract

Rotavirus is the most common cause of acute gastroenteritis among infants and young children throughout the world, but rotavirus cases in developing countries account for nearly all of the ∼600,000 annual deaths. We studied the epidemiology of rotavirus in 22 rural communities in northern coastal Ecuador over a five-year period. From 250 rotavirus positive stool specimens, the percentage that could not be RT-PCR genotyped for VP4 and VP7 was 77% and 63%, respectively. The possibility of sample degradation was considered but discounted after an experimental examination of rotavirus stability and EM visualization of rotavirus-like particles in several untypeable samples. Finally, alternate primers were used to amplify Ecu534, a sample that was untypeable using most published VP4 and VP7 primers. Characterization of the VP7, VP4, and VP6 full gene segments revealed novel genotypes and nucleotide mismatches with most published primer sequences. When considered with other findings, our results suggest that primer mismatch may be a widespread cause of genotyping failure, and might be particularly problematic in countries with greater rotavirus diversity. The novel sequences described in this study have been given GenBank accession numbers EU805775 (VP7), EU805773 (VP4), EU805774 (VP6) and the RCWG has assigned them novel genotypes G20P[28]I13, respectively.

Rotavirus genotypes co-circulating in Europe between 2006 and 2009 as determined by EuroRotaNet, a pan-European collaborative strain surveillance network

“…5% of strains were of this genotype. Over the three seasons, and in the majority of countries, the number of G1P [8] strains rose in the second season and fell in the third. The highest incidences of infection with G2P [4] strains in any season were in Belgium, Bulgaria and Greece where this genotype was found in >30 % of the strains.…”

“…G1P [8] strains were most prevalent in the 2007/2008 season with the exception of Lithuania where only 5 . 5% of strains were of this genotype.…”

“…The total number of rotavirus-positive samples in- as multiple infections of G1, G2, G3, G4, G6, G8, G9, G10, G12 and P [3], P [4], P [6], P [8], P [9], P [10], P [11], P [14] genotypes (Table 2). …”

“…The system differentiates G-types (VP7-specific, G for glycoprotein) and P-types (VP4-specific, P for protease-sensitive protein). To date, 23 different G-types and 31 P-types have been described [5][6][7][8][9], indicating extensive genomic diversity within group A rotaviruses.…”

Distribution of rotavirus VP7 and VP4 genotypes circulating in Tunisia from 2009 to 2014: Emergence of the genotype G12

“…In human RVAs, 6 G-genotypes (G1-4, G9 and G12) and 3 P genotypes (P[4], P [6] and P[8]) are commonly associated with human infections (Santos & Hoshino, 2005). In addition, several G-genotypes (G5, G6, G8, G10, G11 and G20) and Pgenotypes (Ben Hadj Fredj et al, 2013b;Gautam et al, 2015;Gentsch et al, 2005;Santos & Hoshino, 2005;Solberg et al, 2009;Tacharoenmuang et al, 2015). At least 73 G/P-genotype combinations of RVAs infecting humans have been described (Matthijnssens et al, 2009 (B anyai et al, 2012;Gómez et al, 2014;Matthijnssens et al, 2010;Rahman et al, 2007;Santos & Hoshino, 2005;Stupka et al, 2012).…”