Intra-genotypic diversity of archival G4P[8] human rotaviruses from Washington, DC

Abstract

Group A human rotaviruses (RVs) remain the most frequently detected viral agents associated with acute gastroenteritis in infants and young children. Despite their medical importance, relatively few complete genome sequences have been determined for commonly circulating G/P-type strains (i.e., G1P[8], G2P[4], G3P[8], G4P[8], and G9P[8]). In the current study, we sequenced the genomes of 11 G4P[8] isolates from stool specimens that were collected in Washington, DC during the years of 1974-1991. We found that the VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6-encoding genes of all 11 G4P[8] RVs have the genotypes of G4-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1. By constructing phylogenetic trees for each gene, extensive intra-genotypic diversity was revealed among the G4P[8] RVs, and new sub-genotype gene alleles were identified. Several of these alleles are nearly identical to those of G3P[8] isolates previously sequenced from this same Washington, DC collection, strongly suggesting that the RVs underwent gene reassortment. On the other hand, we observed that some G4P[8] RVs exhibit completely different allele-based genome constellations, despite being collected during the same epidemic season; there was no evidence of gene reassortment between these strains. This observation extends our previous findings and supports the notion that stable, genetically-distinct clades of human RVs with the same G/P-type can co-circulate in a community. Interestingly, the sub-genotype gene alleles found in some of the DC RVs share a close evolutionary relationship with genes of more contemporary human strains. Thus, archival human RVs sequenced in this study might represent evolutionary precursors to modern-day strains.

Fig. 1

Genetic relationships among the genes of G3P[8] and G4P[8] RVs from an archival Washington, DC stool collection. The neighbor-joining phylogenetic trees were generated for each gene using the ORF nucleotide sequences. The trees are mid-group rooted for purposes of clarity, horizontal branch lengths are drawn to scale (nucleotide substitutions per base), and bootstrap values are shown as percentages for key nodes. Strain names are listed followed parenthetically by the year of specimen collection. Colored boxes indicate the genotype 1 allele designation (red, orange, green, cyan, navy, or brown). The archival G4P[8] RVs sequenced in this study are highlighted in yellow.

Fig. 1

Genetic relationships among the genes of G3P[8] and G4P[8] RVs from an archival Washington, DC stool collection. The neighbor-joining phylogenetic trees were generated for each gene using the ORF nucleotide sequences. The trees are mid-group rooted for purposes of clarity, horizontal branch lengths are drawn to scale (nucleotide substitutions per base), and bootstrap values are shown as percentages for key nodes. Strain names are listed followed parenthetically by the year of specimen collection. Colored boxes indicate the genotype 1 allele designation (red, orange, green, cyan, navy, or brown). The archival G4P[8] RVs sequenced in this study are highlighted in yellow.

Fig. 2

Allele-based genome constellations of the G3P[8] and G4P[8] RVs. The schematic illustrates the color-coding of each gene based on the phylogenetic trees shown in Fig. 1. The strain name and year of isolation are listed to the left of the corresponding genome constellation (excluding the VP7 gene), and the protein encoded by each gene is listed at the top. The G4P[8] RVs sequenced in this study are highlighted in yellow, and those of the same clade are indicated with brackets.

Fig. 3

Genetic relationships of DC RV genes to those of other human and animal strains. The neighbor-joining phylogenetic trees were generated for each gene using the ORF nucleotide sequences. Horizontal branch lengths are drawn to scale (nucleotide substitutions per base), and bootstrap values are shown as percentages for key nodes. Strain names are listed followed parenthetically by host species: human (hu), porcine (po), and bovine (bo). The VP7 tree (A) is mid-group rooted and the VP1-VP4, VP6, and NSP1-NSP5/6 trees (B-K) are outgroup rooted to strain DS-1. Colored dots indicate the allele designation of the DC RV gene according to Fig.1. The archival G4P[8] RVs sequenced in this study are highlighted in yellow. Asterisks (*) indicate human RVs isolated during the years of 2002-2010.

Fig. 3

Genetic relationships of DC RV genes to those of other human and animal strains. The neighbor-joining phylogenetic trees were generated for each gene using the ORF nucleotide sequences. Horizontal branch lengths are drawn to scale (nucleotide substitutions per base), and bootstrap values are shown as percentages for key nodes. Strain names are listed followed parenthetically by host species: human (hu), porcine (po), and bovine (bo). The VP7 tree (A) is mid-group rooted and the VP1-VP4, VP6, and NSP1-NSP5/6 trees (B-K) are outgroup rooted to strain DS-1. Colored dots indicate the allele designation of the DC RV gene according to Fig.1. The archival G4P[8] RVs sequenced in this study are highlighted in yellow. Asterisks (*) indicate human RVs isolated during the years of 2002-2010.