Multiple Introductions and Antigenic Mismatch with Vaccines May Contribute to Increased Predominance of G12P[8] Rotaviruses in the United States

Abstract

Rotavirus is the leading global cause of diarrheal mortality for unvaccinated children under 5 years of age. The outer capsid of rotavirus virions consists of VP7 and VP4 proteins, which determine viral G and P types, respectively, and are primary targets of neutralizing antibodies. Successful vaccination depends upon generating broadly protective immune responses following exposure to rotaviruses presenting a limited number of G- and P-type antigens. Vaccine introduction resulted in decreased rotavirus disease burden but also coincided with the emergence of uncommon G and P genotypes, including G12. To gain insight into the recent predominance of G12P[8] rotaviruses in the United States, we evaluated 142 complete rotavirus genome sequences and metadata from 151 clinical specimens collected in Nashville, TN, from 2011 to 2013 through the New Vaccine Surveillance Network. Circulating G12P[8] strains were found to share many segments with other locally circulating strains but to have distinct constellations. Phylogenetic analyses of G12 sequences and their geographic sources provided evidence for multiple separate introductions of G12 segments into Nashville, TN. Antigenic epitopes of VP7 proteins of G12P[8] strains circulating in Nashville, TN, differ markedly from those of vaccine strains. Fully vaccinated children were found to be infected with G12P[8] strains more frequently than with other rotavirus genotypes. Multiple introductions and significant antigenic mismatch may in part explain the recent predominance of G12P[8] strains in the United States and emphasize the need for continued monitoring of rotavirus vaccine efficacy against emerging rotavirus genotypes.IMPORTANCE Rotavirus is an important cause of childhood diarrheal disease worldwide. Two immunodominant proteins of rotavirus, VP7 and VP4, determine G and P genotypes, respectively. Recently, G12P[8] rotaviruses have become increasingly predominant. By analyzing rotavirus genome sequences from stool specimens obtained in Nashville, TN, from 2011 to 2013 and globally circulating rotaviruses, we found evidence of multiple introductions of G12 genes into the area. Based on sequence polymorphisms, VP7 proteins of these viruses are predicted to present themselves to the immune system very differently than those of vaccine strains. Many of the sick children with G12P[8] rotavirus in their diarrheal stools also were fully vaccinated. Our findings emphasize the need for continued monitoring of circulating rotaviruses and the effectiveness of the vaccines against strains with emerging G and P genotypes.

Keywords: G12P[8]; efficacy; genotype; phylogenetics; rotavirus; vaccine.

FIG 1

Phylogenetic relationships among Nashville, TN, rotaviruses, 2005 to 2013. ML trees assembled from nucleotide sequences of four genome segments (VP7, VP4, VP6, and VP1) for all VUMC NVSN rotavirus specimens with completely sequenced genomes are shown. Horizontal branch lengths are drawn to scale and represent substitutions per nucleotide. Internal genotype assignments are indicated on the right, and subgenotype allele assignments for segments other than VP7 are indicated by color. Bootstrap values at nodes defining genotypes or subgenotype alleles are shown as percentages. For a detailed ML tree for each genome segment, see Fig. S1.

FIG 2

Allele-based genome constellations for rotaviruses in Nashville, TN, 2005 to 2013. The bars representing genome segments are colored based on phylogenetic analyses and subgenotype allele assignments, as shown in Fig. 1 and described in the text. Constellations are ordered based on genotype and frequency of detection, which are indicated on the left. The protein encoded by each segment is shown at the top. Allele constellations detected in multiple seasons are indicated by asterisks.

FIG 3

Phylogenetic relationships among globally circulating G12 VP7 rotavirus segments. ML trees assembled from G12 nucleotide sequences of 839 globally circulating rotaviruses. Horizontal branch lengths are drawn to scale and represent substitutions per nucleotide. Lineage (I, II, or III), group (1 or 2), clade (A or B), and monophyletic group or subclade (1 to 10, A1, and B1 to B3) assignments are indicated. Bootstrap values at nodes defining clades are shown as percentages. The same tree is shown in both panels but colored to reveal the continent of origin for each sequence (A) or a Nashville, TN, origin versus other geographic origin (B).

FIG 4

Amino acid variation between VP4 proteins of G12P[8] rotaviruses circulating in Nashville, TN, since 2005 and those of vaccine strains. (Left) Ribbon drawing showing a cutaway view of the rotavirus surface, with VP4 trypsin fragments VP5* (red) and VP8* (purple) labeled (PDB accession no. 4V7Q) (9). VP7 is colored yellow, and VP6 is colored green. (Middle) Front (as in the ribbon drawing) and back (rotated 180°) surface contour views of the enlarged VP8* domain shown in light gray, with known antigenic epitopes colored red (8-1), pink (8-2), purple (8-3), and green (8-4) (PDB no. 1KQR) (50). (Right) Additional surface representations of RRV VP8* showing positions at which all derived P[8] VP4 amino acid sequences from G12P[8] viruses in the VUMC NVSN collection differ from those of all the VP4 components of RV1 (P[8]) and RV5 (P[8] and P[5]) colored cyan.

FIG 5

Amino acid variation between VP7 proteins of rotaviruses circulating in Nashville, TN, since 2005 and those of vaccine strains. (Upper left) Surface representation of a rotavirus virion, with VP4 colored red and VP7 colored yellow (PDB accession no. 4V7Q) (9). The boxed area shows an enlarged RRV VP7 trimer colored light gray, with known antigenic epitopes colored red (7-1A), khaki (7-1b), and purple (7-2) (PDB accession no. 3FMG) (96). Positions at which all derived VP7 amino acid sequences of a particular G type from the VUMC NVSN collection (2005 to 2013) differ from those of the indicated VP7 vaccine component(s) are colored cyan. The word “all” refers to all VP7 components of RV1 (G1) and RV5 (G1, G2, G3, G4, and bovine G6).

FIG 6

Model of vaccination probability based on rotavirus type. Analyses were of data presented in Table 3. The data points indicate the estimated posterior means, with the bars indicating the corresponding 95% HPD intervals, which represent a probabilistic statement of uncertainty about the true probabilities.