Volume 19, Number 8—August 2013
Rotavirus G9P in 3 Countries in Latin America, 2009–2010
To the Editor: Group A rotaviruses are the most common viral cause of acute gastroenteritis in young children. The most frequently detected group A rotavirus genotype combinations include G1P, G2P, G3P, G4P, and G9P. The G9 genotype has been associated with multiple P types, including P, P, and P, although genotype G9P is predominant (1).
In Latin America, a large number of unusual G-P combinations have been reported, and among these is the rare G9P genotype, which was identified in Brazil in the 1990s (2), and later reported infrequently elsewhere in Latin America (3). In 2010, cases of group A rotavirus gastroenteritis associated with genotype G9P were reported in Mexico (4). Increases in the incidence of group A rotavirus gastroenteritis were reported in 2010 in Mexico and Guatemala and in 2009 in Honduras (http://new.paho.org/hq/dmdocuments/2010/Epi_Alerts_2010_mar_5_rotavirus.pdf).
In response to these reports of increased group A rotavirus disease, fecal samples collected in Chiapas State, Mexico (in 2010, 30% of the cases in Mexico were from Chiapas), Guatemala, and Honduras in 2009–2010 that were positive by enzyme immunoassay were sent to the US Centers for Disease Control and Prevention (Atlanta, GA, USA) for characterization. Viral protein 4 (VP4) (P) and VP7 (G) genotyping, nucleotide sequencing, and genotype identification were performed by using consensus and genotype-specific oligonucleotide primers (5), and sequences were subjected to phylogenetic analyses. VP6 and nonstructural protein 4 (NSP4) genes of selected samples were also sequenced.
For 26 samples from Mexico, G9 accounted for ≈90% of all the G types; all samples had mixed P types. Approximately 80% of samples were genotype G9P[4,8]; genotypes G3P[4,8], G3,9P[4,8], and G9P[4,9] accounted for the remaining samples. We hypothesize that the G9P[4,8] genotype was the result of mixed G9P and G9P infections by strains with homologous G9 VP7 genes. For 41 samples from Guatemala, G9P accounted for 66%, followed by G9P (32%), and G3,9P[4,8] (2%). For 50 samples from Honduras, 50% were G1P and 36% were G9P. G3P, G1,3P, and G4P comprised the remaining samples.
Results showed an increase in prevalence of the rare G9P strain, which was the predominant strain in Guatemala and Mexico, and the second most predominant strain in Honduras, after G1P. Group A rotavirus genotypes G1P and G3P have been reported to be predominant in Mexico (4). G1P and G2P were associated with most group A rotavirus infections in Guatemala (6,7) and G2P predominated in Honduras (7). G9P has not been reported in Guatemala or Honduras. In Mexico, the outbreak might have originated from a common source, such as untreated drinking water (http://new.paho.org/hq/dmdocuments/2010/Epi_Alerts_2010_mar_5_rotavirus.pdf).
Phylogenetic analysis of G9 gene sequences from the 3 countries showed that they clustered in a sublineage and were closest to G9P strains circulating globally (Figure, Appendix, panel A). VP4 genes from the 3 countries also clustered within a sublineage of a clade containing global strains (Figure, Appendix, panel B). VP6 sequences clustered within a sublineage of the I2 genotype clade (Figure, Appendix, panel C). NSP4 gene sequences clustered within a sublineage of the E6 genotype clade, which they shared with group A rotavirus strains from India and Bangladesh (Figure, Appendix, panel D).
The high degree of genetic similarity among these strains in all 4 genes (99.6%–100%), as demonstrated in this study, suggests that strains from all 3 countries had a common origin. In regions of overlapping sequence, VP4 gene sequences from this study shared 98.3%–100% identity (408 bases) with G9P strains from Mexico (GenBank accession nos. JN180414–JN180451), and VP7 gene sequences shared 97.9%–98.9% identity (97 bases) (GenBank accession nos. JN180376–JN180413).
Rahman et al. have hypothesized that the G9P genotype combination was formed by reassortment between more frequently occurring strains (e.g., G2P and G9P strains) (8). Potential parental strains have been circulating at high levels in Latin America for ≈30 years. During this period, G9 and P accounted for 15% and 22% of all G and P types, respectively, in Latin America and the Caribbean (3). Only 0.4% of strains were G9P during this period, which suggests that the markedly increased prevalence of this genotype in 2009–2010 was the result of a dramatic event, such as genetic reassortment.
Previous studies of G9P strains examined only VP4 and VP7 genes and had not characterized VP6 and NSP4 genes of these strains. The presence of an NSP4 genotype E6 gene within these viruses was surprising. The NSP4 E6 genotype has been described in only 5 strains, all of which were from human cases of infection in Bangladesh or India (9,10) and were associated with VP4 genotype P and VP7 genotypes G8 or G12. The complete global distribution of this NSP4 genotype remains to be determined.
Although many factors account for increased reports of group A rotavirus gastroenteritis observed in Mexico, Guatemala, and Honduras in 2009–2010, our data suggest emergence of the previously rare G9P group A rotavirus genotype in these countries. Whether the G9P genotype becomes the common strain in Latin America or elsewhere remains to be determined.
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1Current affiliation: University of Ghana, Legon, Ghana.