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J Virol. Sep 2012; 86(17): 9148–9162.
PMCID: PMC3416154
Diversity and Relationships of Cocirculating Modern Human Rotaviruses Revealed Using Large-Scale Comparative Genomics
Sarah M. McDonald,corresponding authora Allison O. McKell,a Christine M. Rippinger,b John K. McAllen,c Asmik Akopov,c Ewen F. Kirkness,c Daniel C. Payne,d Kathryn M. Edwards,e James D. Chappell,ef and John T. Pattonb
aVirginia Tech Carilion Research Institute, Roanoke, Virginia, USA, and the Department of Biomedical Sciences and Pathobiology, Virginia-Maryland Regional College of Veterinary Medicine, Blacksburg, Virginia, USA
bRotavirus Molecular Biology Section, Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
cThe J. Craig Venter Institute, Rockville, Maryland, USA
dCenters for Disease Control and Prevention, Atlanta, Georgia, USA; and Vanderbilt University School of Medicine
eDepartments of Pediatrics
fPathology, Microbiology, and Immunology, Nashville, Tennessee, USA
corresponding authorCorresponding author.
Address correspondence to Sarah M. McDonald, mcdonaldsa/at/
Received May 3, 2012; Accepted June 7, 2012.
Group A rotaviruses (RVs) are 11-segmented, double-stranded RNA viruses and are primary causes of gastroenteritis in young children. Despite their medical relevance, the genetic diversity of modern human RVs is poorly understood, and the impact of vaccine use on circulating strains remains unknown. In this study, we report the complete genome sequence analysis of 58 RVs isolated from children with severe diarrhea and/or vomiting at Vanderbilt University Medical Center (VUMC) in Nashville, TN, during the years spanning community vaccine implementation (2005 to 2009). The RVs analyzed include 36 G1P[8], 18 G3P[8], and 4 G12P[8] Wa-like genogroup 1 strains with VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6 genotype constellations of I1-R1-C1-M1-A1-N1-T1-E1-H1. By constructing phylogenetic trees, we identified 2 to 5 subgenotype alleles for each gene. The results show evidence of intragenogroup gene reassortment among the cocirculating strains. However, several isolates from different seasons maintained identical allele constellations, consistent with the notion that certain RV clades persisted in the community. By comparing the genes of VUMC RVs to those of other archival and contemporary RV strains for which sequences are available, we defined phylogenetic lineages and verified that the diversity of the strains analyzed in this study reflects that seen in other regions of the world. Importantly, the VP4 and VP7 proteins encoded by VUMC RVs and other contemporary strains show amino acid changes in or near neutralization domains, which might reflect antigenic drift of the virus. Thus, this large-scale, comparative genomic study of modern human RVs provides significant insight into how this pathogen evolves during its spread in the community.
Group A rotaviruses (RVs) are important pathogens that cause acute gastroenteritis in infants and young children (11, 27). In developing regions of the world with reduced access to medical care, RV infections lead to the deaths of ~450,000 children each year (50). In industrialized countries, the burden of RV disease is mainly associated with the financial costs of treatment. Specifically, prior to the recent introduction of vaccines in the United States, it was estimated that RV-induced gastroenteritis caused more than 55,000 hospitalizations and 500,000 physician visits each year at a societal cost of ~$1 billion (40, 54). In 2006 and 2008, respectively, the U.S. Advisory Committee on Immunization Practices recommended the live-attenuated vaccines RotaTeq (Merck) and Rotarix (Glaxo-Smith Kline) for the routine immunization of infants (8, 37). RotaTeq is a pentavalent vaccine consisting of five human-bovine RV reassortants, each of which carries a separate human RV VP7 gene (G1, G2, G3, or G4) or a human RV P[8] VP4 gene in the background of the bovine WC3 strain (G6P[5]) (31). In contrast, Rotarix is a monovalent vaccine derived from a human strain (89-12) with G1P[8] specificity (53). Postlicensure studies indicate that both RotaTeq and Rotarix prevent 85 to 100% of severe RV gastroenteritis in developed countries (15). For reasons that remain unclear, the efficacy of the vaccines was found to be lower in developing regions of the world (2, 25, 43, 55). Surveillance networks have been established at various geographical locations (i) to obtain information on the prevalence and types of circulating RV strains, (ii) to determine whether human RVs are changing in the face of vaccine pressures, and (iii) to continue monitoring for the safety and efficacy of RotaTeq and Rotarix (5, 12, 13, 17, 19, 20, 24, 39). Importantly, the viral gene/genome sequences deduced via these epidemiological studies are illuminating the diversity and complex evolutionary dynamics of this common childhood pathogen.
RVs maintain their double-stranded RNA (dsRNA) genome as 11 separate segments, which can reassort when a host cell is infected with more than one strain (11, 34). These exchanges, described as genetic shift, have long been hypothesized to play an important role in generating viral diversity, allowing the virus to evolve rapidly in response to selection pressures (14). In addition, the error-prone nature of the viral polymerase leads to the accumulation of point mutations in the viral genome, causing RV strains to drift antigenically (11). However, because only limited numbers of complete genome sequences have been determined for naturally circulating human RVs, the frequency and significance of shift and drift are poorly understood. To aid in studies of RV diversity, a comprehensive classification system was developed that designates a genotype for each of the 11 viral genes (i.e., segments) based on established nucleotide identity cutoff values (28). The acronym Gx-P[x]-Ix-Rx-Cx-Mx-Ax-Nx-Tx-Ex-Hx is used to describe a virus based on segments encoding each viral protein(s) (i.e., VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5/6). This system extends the well-known binomial classification of RVs that is based on the genes encoding outer capsid serotype antigens VP7 (G types) and VP4 (P types) to the other nine internal protein genes (encoding VP1 to VP3, VP6, and NSP1 to NSP5/6) (29).
The complete genome classification approach provided data to support the existence of two dominant human RV genogroups (Wa-like and DS-1-like), originally identified using differential RNA-RNA hybridization (35). Wa-like RVs almost invariably exhibit genotype 1 internal protein genes (i.e., I1-R1-C1-M1-A1-N1-T1-E1-H1) and tend to have G1P[8], G3P[8], G4P[8], and G9P[8] specificities (29). In contrast, DS-1-like RVs that have been fully sequenced are usually G2P[4] strains with genotype 2 internal protein genes (i.e., I2-R2-C2-M2-A2-N2-T2-E2-H2) (29). For the purposes of this paper, we will refer to the Wa-like genogroup as genogroup 1 (GG-1) and the DS-1-like genogroup as genogroup 2 (GG-2). Gene reassortment between GG-1 and GG-2 strains is possible, as evidenced by the isolation of human RVs containing both genotype 1 and genotype 2 genes from children suffering acute gastroenteritis (16, 47, 48). However, based on the available sequence data, intergenogroup reassortants seem to be less prevalent in the human population than pure GG-1 or GG-2 strains (29). It is possible that the genes (or the encoded proteins) of RVs belonging to the same genogroup have coevolved and operate best when kept together (3, 6, 16, 18). In this manner, it hypothesized that human RVs belonging to different genogroups create less fit reassortants which may not emerge in the human population. In contrast, segment exchange between RVs within a genogroup would be expected to occur more readily. Nevertheless, large-scale, complete genome sequence analyses of 62 archival GG-1 human RVs (51 G3P[8] and 11 G4P[8] strains) from Washington, DC, revealed that intragenogroup reassortants were less common than had been anticipated (32, 33). Comparative genomic studies of contemporary strains are needed to ascertain whether these previous results reflect the current status of RV diversity.
In this study, we report the complete genome sequence analysis of 58 GG-1 human RVs (36 G1P[8], 18 G3P[8], and 4 G12P[8] strains) from children seeking medical attention for severe, acute gastroenteritis at Vanderbilt University Medical Center (VUMC) in Nashville, TN, from one prevaccine season (2005 to 2006) and two postvaccine seasons (2006 to 2007 and 2008 to 2009). Complete genome sequence analyses of modern human RVs are expected to enhance our understanding of the diversity and evolution of this important pediatric pathogen.
Sample collection, RNA extraction, and G/P typing.
Fecal specimens were collected from infants and children presenting with acute gastroenteritis at VUMC in Nashville, TN, during the years of 2005 to 2009 as part of the Centers for Disease Control and Prevention's (CDC) New Vaccine Surveillance Network (NVSN), which was approved by the CDC and VUMC institutional review boards. Details of patient enrollment and specimen collection have been previously published (40, 41). Briefly, children <36 months of age and hospitalized with diarrhea (≥3 episodes in 24 h) and/or vomiting (≥1 episode in 24 h), who were residents of Davidson County and who had informed consent from a parent or guardian, were enrolled in the study. Children were ineligible if they had a reported history of noninfectious diarrhea or clinical immunodeficiency. Bulk fecal samples were collected from the children within 7 days of enrollment (usually within 7 days of symptom onset) and tested for evidence of viral antigen using the commercial enzyme immunoassay (EIA) Premier Rotaclone (Meridian Bioscience). Total RNA was extracted from deidentified RV-positive fecal specimens using TRIzol (Invitrogen), and samples were classified into G/P types using reverse transcription-PCR (RT-PCR) and/or nucleotide sequencing (Table 1). Clinical and demographic data relating to the 58 samples analyzed in the current study are shown in Table S1 in the supplemental material.
Table 1
Table 1
RV G/P types collected and sequenced from sick children at Vanderbilt University Medical Center in Nashville, TN (2005 to 2009)
RT-PCR, nucleotide sequencing, and genotyping internal protein genes.
Total RNA extracted from a representative subset of RV-positive fecal specimens (84 samples in total) was sent to the J. Craig Venter Institute (Rockville, MD) for high-throughput, RT-PCR, and Sanger sequencing. As described previously by McDonald et al. (33), oligonucleotide primers were designed every 600 bp along both sense and antisense strands of the viral genome, and M13-forward or M13-reverse tags were added to the 5′ ends of the primers for use in sequencing. Primers for the G1 and G12 VP7 genes were designed based on the consensus of G-type-matched sequences available in public databases (see Table S2 in the supplemental material). Primers for the G3 VP7 gene, as well as the VP1 to VP4, VP6, and NSP1 to NSP5/6 genes, were described in McDonald et al. (33). RT-PCR and sequencing reactions were performed as described previously (32, 33). The genotype of each VUMC RV gene sequence was determined by RotaC assignment ( (26).
Alignments, phylogenetic analyses, and structural predictions.
Nucleotide sequence alignments and phylogenies were generated with Geneious Pro v5.5.2 using the ClustalW and PhyML plugins. The Hasegawa-Kishino-Yano substitution model with gamma-distributed rate variation among sites (HKY+G) was chosen by following Bayesian information criterion ranking of each alignment as implemented in MEGA5.05 (45, 49). Trees were constructed with the open reading frame (ORF) nucleotide sequences, and 1,000 pseudoreplicates were generated for bootstrapping analyses. Subgenotype alleles were defined as tight phylogenetic clusters (containing 2 or more sequences) with strong bootstrap support (>75%) at separating nodes and were confirmed by visual inspection of nucleotide alignments. GenBank accession numbers and genotypes of the previously sequenced RV genes used in the phylogenetic analyses are provided in Tables S3 and S4 in the supplemental material. Amino acid alignments were constructed with Geneious Pro v5.5.2 using the ClustalW plugin with the BLOSUM cost matrix. Structural analysis of NSP2 (PDB number 2R7C; strain SA11), VP7 (PBD number 3FMG; strain RRV), and VP8* (PDB number 2DWR; strain Wa) was performed using the UCSF Chimera molecular modeling system (1, 4, 21, 42).
Nucleotide sequence accession numbers.
The nucleotide sequences determined for the 11 genes of each of the 58 VUMC RVs (638 total sequences) were deposited in GenBank and are listed in Table 2.
Table 2
Table 2
GenBank accession numbers for VUMC RVs sequenced in the current study
Complete genome sequencing of VUMC RVs.
Fecal specimens were collected from children <36 months of age presenting symptoms of gastroenteritis at VUMC in Nashville, TN (3941). A total of 669 specimens were collected over four winter seasons (2005-2006, 2006-2007, 2007-2008, and 2008-2009), spanning the time of RotaTeq introduction in the community (beginning in spring 2006). Of these samples, 165 tested positive for the presence of RV antigen by EIA and then were sent to the CDC for G/P typing using RT-PCR (39). The G/P type distribution of RVs in the fecal specimens was typical of that seen in other regions of the United States during this time, with G1P[8], G2P[4], and G3P[8] being detected most years (Table 1) (17). The globally emerging G9P[8] and G12 strains were also detected, albeit in fewer numbers than the more traditional G/P-type strains (Table 1) (17, 30). Similar to what has been seen in many previous epidemiological studies, the dominant G/P type fluctuated from G1P[8] in 2005 to 2008 to G3P[8] in 2008 to 2009 (7, 17, 44). No correlation was found between G/P type and age, sex, and ethnicity of the child or between G/P type and disease severity (see Table S1 in the supplemental material).
We next determined the complete genome sequences of representative VUMC RVs using an established, semiautomated, RT-PCR and dideoxy-nucleotide Sanger sequencing pipeline at the J. Craig Venter Institute (32, 33). Unfortunately, material was unavailable for the 15 samples collected during the 2007-2008 season; therefore, we were not able to sequence RVs from this season (Table 1). Moreover, the pipeline was designed to preferentially amplify and sequence genotype 1 internal protein genes (32, 33). Consequently, no complete genome sequence information was obtained for the 14 G2P[4] samples from this collection (Table 1). Nonetheless, we were able to deduce the complete genome sequences of RVs in 36 G1P[8]-, 18 G3P[8]-, 2 G12P[8]-, and 2 G12P[6]-typed strains (58 RVs in total) that were collected during the 2005-2006, 2006-2007, and 2008-2009 seasons (Table 1). The entire ORFs and, in some cases, the 5′ and 3′ untranslated regions for all 11 genes of these 58 VUMC RVs were sequenced. Multiple, overlapping reads were generated, and the chromatographs showed little evidence of heterogeneity, indicating that a single RV isolate was dominant in each fecal specimen.
Using the web-based genotyping tool RotaC, we assigned genotypes for each of the 11 genes of the 58 VUMC RVs (26). The G/P types of the viruses were verified, except for those of two strains that were initially typed as P[6] by RT-PCR analysis (Table 1). These two G12P[6] isolates (VU05-06-72 and VU05-06-74) from the 2005-2006 season were actually found to be G12P[8] strains by sequencing and RotaC. The nine other genes of each VUMC RV were classified as genotype 1, confirming that the strains sequenced in this study all belong to GG-1. Aside from their different G-type specificities, the 58 RVs share identical genotype constellations (i.e., Gx-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1).
Subgenotype allele designation for VUMC RV genes.
Given that the 58 VUMC RVs belong to GG-1 and have genes with the same genotypes (except VP7), we sought to examine their diversity at the subgenotype level. To do this, we created maximum likelihood phylogenetic trees for each gene of the 58 RVs using the ORF nucleotide sequences (Fig. 1). Similar to our previous analyses of archival GG-1 human RVs from Washington, DC, we defined subgenotype alleles as tight phylogenetic clusters (containing 2 or more sequences) that are separated by nodes with strong bootstrap values (>75%) (32, 33). Because the 58 RVs differed in their G-type specificities, we did not divide the VP7 genes into alleles in this study (Fig. 1A). Instead, the VUMC RV VP7 genes were compared phylogenetically to those of archival, contemporary, and vaccine strains and placed into established subgenotypic lineages (discussed below).
Fig 1
Fig 1
Fig 1
Genetic relationships among the individual genes of the VUMC RVs. The unrooted maximum likelihood trees were constructed using the ORF nucleotide sequences for each gene of each isolate. All horizontal branch lengths are drawn to scale (nucleotide substitutions (more ...)
The phylogenetic analyses identified two to five subgenotype alleles for the VP1 to VP4, VP6, and NSP1 to NSP5/6 genes of the 58 VUMC RVs (Fig. 1B to toK).K). For ease of discussion and visualization, the alleles were each assigned a letter (A, B, C, D, and E) and a corresponding color (red, green, cyan, purple, and orange, respectively). Consistent with our previous study of archival strains, we saw that isolates from different seasons could share nearly identical alleles, while those from the same infectious season could have genetically divergent alleles. Together, the phylogenetic data are most consistent with the notion that the VUMC alleles diverged prior to 2005, and that they remained genetically stable, accumulating minimal point mutations over the collection years (2005 to 2009).
Persistent clades (PCs) of VUMC RVs despite frequent gene reassortment.
The summary of the color-coded allele constellations for each of the VUMC RVs reveals the complex genetic diversity of these GG-1 strains (Fig. 2). RVs with several different allele constellations cocirculated each epidemic season (Fig. 2A). In the 2005-2006 season, nine different clades with distinct allele constellations (8 G1P[8] and 1 G12P[8]) were identified, and in the 2006-2007 season, seven different clades (6 G1P[8] and 1 G3P[8]) were found. The 2008-2009 season was less diverse, with a majority of the viruses belonging to a single, homogeneous G3P[8] major clade. Two G12P[8] allele constellations, represented by VU08-09-6 and VU08-09-39, were also found in the 2008-2009 season. Two isolates (VU08-09-9 and VU8-09-28) of the major G3P[8] clade were from children who received two doses of RotaTeq, and another two isolates (VU08-09-17 and VU08-09-22) were from children vaccinated with all three doses (Fig. 2; also see Table S1 in the supplemental material). Overall, we found no allele-level constellation differences between G3P[8] viruses from vaccinated versus unvaccinated children. However, one G3P[8] isolate (VU09-08-22) from a child who was fully vaccinated with RotaTeq seemed related to the major 2008-2009 clade but contained different NSP1 and NSP3 gene alleles (Fig. 2).
Fig 2
Fig 2
Allele-based gene constellations of the VUMC RVs. The schematic illustrates the color coding of each gene for the VUMC RVs based on the phylogenetic analysis shown in Fig. 1. The VUMC RV isolates are listed to the left of their corresponding allele constellations, (more ...)
This analysis showed that many VUMC RV isolates exhibit genes with the same allele designations. This result is unlike what we described for the archival GG-1 DC RVs and is indicative of gene reassortment among the contemporary VUMC strains (32, 33). However, it is not possible to determine whether these genetic exchanges occurred during or prior to the years of study. Nonetheless, several allele constellations were seen repeatedly, even for viruses isolated in different seasons. For instance, the G3P[8] isolate VU06-07-21 from the 2006-2007 season and the major clade of G3P[8] RVs from the 2008-2009 season contain identical allele constellations (Fig. 2A). These PCs of VUMC RVs can be identified when the color-coded allele constellations of VUMC RVs are ordered according to visual genome similarities rather than date of isolation (Fig. 2B). PC-1, PC-3, PC-4, and PC-5 are each comprised of G1P[8] RVs found during the 2005-2006 and 2006-2007 infectious seasons. PC-2 is represented by the aforementioned single G3P[8] isolate from 2006 to 2007 (VU06-07-21) along with 16 G3P[8] isolates from 2 years later (2008 to 2009). Like G/P-type specificity, we found no correlation between allele constellation and age, sex, or ethnicity of the child or between allele constellation and disease severity (Fig. 2; also see Table S1 in the supplemental material).
Subgenotype 1 alleles of VUMC RVs encode different proteins.
Having observed the intragenotypic diversity of the VUMC RV genes at the nucleotide level, we next performed amino acid alignments to determine whether the alleles (A to E) encode different VP1 to VP4, VP6, and NSP1 to NSP5/6 proteins (data not shown). The results indicate that, in general, the proteins are different, with 1 to 78 allele-specific amino acid changes. The intermediate capsid protein of the virion (VP6) was the most highly conserved for the VUMC RVs, showing less than five allele-specific amino acid changes in all pairwise comparisons (Fig. 3A). In contrast, the innate immune antagonist (NSP1) was the most variable protein, with 19 to 78 amino acid differences between proteins encoded by different alleles (Fig. 3A). From this amino acid analysis, it became apparent that some gene alleles encode more similar proteins than do others. For instance, the viral RNA-dependent RNA polymerase encoded by the VP1 A allele (red) differs by only 2 amino acids from those encoded by either the B allele (green) or the C allele (cyan) (Fig. 3A). However, VP1 differs by 10 to 12 amino acids in alleles A and D (red versus purple), B and D (green versus purple), or C and D (cyan versus purple). For the VP4 spike attachment protein and P-type antigen, we found that proteins encoded by the D allele (purple) were much more divergent than the others, showing 35 unique differences. Thirteen of the 35 allele D (purple)-specific changes lie within VP8*, the distal cleavage fragment of spike protein (Fig. 3B) (4, 10). Seven of these VP8* changes (T78N, D113T, N120M, N125S, R131S, G146S, D150E, and N190S) are located within antibody neutralization domains (8-1, 8-2, 8-3, and 8-4) (Fig. 3B) (23). Thus, the exchange of a VP4 D allele (purple) for a VP4 A, B, or C allele (red, green, or cyan, respectively) via gene reassortment could result in an antigenically distinct virus. We hypothesize that gene constellations at both the genotype level and allele level are influenced, at least in part, by the coevolution of viral proteins that must interact during the replication cycle (16, 33). In this manner, exchange of genes encoding nearly identical proteins would be evolutionarily neutral in terms of viral fitness. In contrast, nonconservative protein exchanges might result in suboptimal protein interactions during replication for which the virus could compensate by also exchanging the interacting protein via gene reassortment.
Fig 3
Fig 3
VUMC RV gene alleles encode divergent proteins. (A) Allele-specific amino acid changes. The table illustrates the number of amino acid changes between different alleles in pairwise combinations. This analysis is meant to determine how many amino acids (more ...)
To gain a better understanding of whether the VUMC RVs exchanged genes encoding relatively conservative versus nonconservative proteins, we analyzed three sets of putative multiallele G1P[8] reassortants from the 2005-2006 and 2006-2007 seasons (Fig. 3C). The viruses within each set showed identical allele constellations, with the exception of 2 to 3 genes, which we predict were reassorted. Set 1 RVs likely made two allele exchanges (VP4 and NSP4), each of which resulted in few amino acid changes in the encoded proteins. Set 2 viruses exchanged fairly conservative VP3 and NSP3 proteins (changing 9 or 3 amino acids, respectively) but also exchanged relatively nonconservative NSP1 proteins (78 amino acid changes). NSP1 is not expected to interact with other viral proteins, so such a dramatic swap might also be considered neutral as related to viral protein coevolution. Set 3 viruses exchanged alleles encoding NSP2 and NSP5, resulting in a significant number of changes for these proteins considering their small sizes (15/317 and 9/197 amino acids, respectively). NSP2-NSP5 interactions play important roles during RV genome replication and core assembly (38). Nine of 15 amino acid changes between NSP2 proteins encoded by alleles B (green) and C (cyan) are surface exposed on the high-resolution structure of the octamer, and five of them (Q56P, R58K, A249V, I282L, and I284V) map to the tetramer-tetramer groove, which is a site of NSP5 binding (Fig. 3C) (21, 23). The nine changes in NSP5 (S37N, V41I, S43P, L108M, N121S, I126V, D131N, and R187Q) are generally spread throughout the linear amino acid sequence (data not shown). While no atomic structure of NSP5 exists, a region of the protein encompassing residues 66 to 188 has been shown to bind within the NSP2 groove (23). It is speculated that viruses in set 3 kept specific NSP2-NSP5 gene sets due to the important interactions among these proteins.
Comparison of VUMC RV VP1 to VP3, VP6, and NSP1 to NSP5/6 genes and proteins to those of other strains.
We next sought to determine how similar the protein gene alleles A to E of VUMC RVs are to those of other human and animals strains, particularly to those of archival and contemporary GG-1 viruses. Therefore, we constructed maximum likelihood phylogenetic trees for VP1 to VP3, VP6, and NSP1 to NSP5/6 using the ORF sequences of representative GG-1 strains for which complete genome sequences exist in GenBank (Fig. 4; also see Table S3 in the supplemental material). The results show that, in general, the VUMC RV alleles A to E group with those of other contemporary strains (isolated during 2002 to 2010) from various regions of the world, including 6361 and 061060 (India), BE00036 and BE00029 (Belgium), Dhaka16-03 and Matlab36-02 (Bangladesh), GER126-08 and GER172-08 (Germany), 2008747332 and 2008747336 (United States), and CK00005 and CK00034 (Australia) (Fig. 4; also see Table S3). The VP1 to VP3, VP6, NSP1, and NSP5/6 genes of contemporary human RVs are found in one or two putative clusters and are distinct from the genotype 1 genes of animal strains (e.g., YM, OSU, A253, etc.) (Fig. 4). One cluster seems to share evolutionary relationships with the genes of the GG-1 neonatal strain ST3 (G4P[6]), whereas another cluster contains genes more closely related to those of the classic GG-1 prototype strain Wa (G1P[8]) (Fig. 4). To date, there is no evidence of modern VP2 or VP6 genes in the Wa cluster. For NSP2, NSP3, and NSP4, the bootstrap values were too low to clearly resolve any specific clusters of human RV genotype 1 genes (Fig. 4F to toH).H). However, the NSP2 C allele (cyan), which is represented by VU05-06-16, seems more divergent than any of the modern RV genes and grouped closely with the NSP2 genes of several archival DC RVs (DC827, DC2241, and DC2102) in the phylogenetic tree (Fig. 4F).
Fig 4
Fig 4
Fig 4
Comparison of VUMC RV VP1 to VP3, VP6, and NSP1 to NSP5/6 genes and proteins to those of other strains. The maximum likelihood trees were constructed using the ORF nucleotide sequences for representative human and animals strains (listed by common names). (more ...)
Together, the analyses shown in Fig. 3 and and44 reveal that the VUMC RV alleles found to encode divergent proteins may actually belong to different phylogenetic clusters (i.e., Wa cluster versus ST3 cluster). For example, VP3 alleles B and D (green and purple, respectively) both belong to the Wa cluster and show only 9 amino acid changes between them (Fig. 3A and and4).4). However, VP3 allele B (green; Wa cluster) versus A, C, or D (red, cyan, or orange; ST3 cluster) exhibits 25 to 29 amino acid changes. This result expands our allele-based analysis of gene reassortment and suggests that the exchange of gene alleles belonging to the same evolutionary cluster occurs more readily than the exchange of gene alleles belonging to different clusters because they alter similar proteins.
Comparison of VUMC RV VP7 and VP4 genes and proteins to those of other strains.
Since the 58 VUMC RVs were of various G-type specificities, we did not define subgenotype alleles for the VP7 genes. Nonetheless, we did seek to determine how similar the VP7 genes and proteins of these contemporary Nashville strains were to each other and to those of other modern, archival, and vaccine strains. This analysis is important, as anti-VP7 neutralizing antibodies are thought to play a critical role in vaccine-mediated immunological protection against RV disease. To determine the genetic relationships of VUMC RV VP7 genes to other strains, we first constructed maximum likelihood phylogenetic trees using the ORF sequences of representative G1, G3, or G12 RVs (Fig. 5A to toC)C) (see Table S4). For the 36 VUMC strains with G1 specificity, the VP7 sequences cluster along with those of other contemporary strains in well-characterized lineage 1 or 2, and all of them are distinct from VP7 genes in lineages 3 (strains D and Wa) and 4 (strains K54, 421, and Kor-64) (Fig. 5A) (31). The VP7 gene of the Rotarix vaccine clusters phylogenetically with those of many modern G1 strains of lineage 1. The VP7 gene of the G1 component strain of the RotaTeq vaccine, on the other hand, is more divergent from those of contemporary strains and is found in lineage 3, consistent with what has been described previously (31).
Fig 5
Fig 5
Comparison of VUMC RV VP7 and VP4 genes and proteins to those of other strains. The maximum likelihood trees were constructed using the VP7 ORF nucleotide sequences and are outgroup rooted to the most recent common ancestor. All horizontal branch lengths (more ...)
This analysis revealed that the G1 VP7 genes belonging to both lineage 1 (19 VUMC RVs) and lineage 2 (17 VUMC RVs) were found to cocirculate in Nashville in 2005 to 2006. These lineages correspond to two phylogenetic clusters observed in the trees created using only VUMC RV VP7 gene sequences and could represent distinct subgenotype G1 alleles (Fig. 1A). By creating amino acid sequence alignments, we found that proteins encoded by G1 VP7 lineage 1 and 2 genes differ at nine positions (S37F, R49K, I55L, L57I, A66V, A68S, N94S, S123N, M217T, T281I, and K291R) (data not shown). When mapped onto the structure of the VP7 trimer, four amino acid changes (N94S, S123N, M217T, and K291R) are found in or near VP7 neutralization domains 7-1A, 7-1B, and 7-2 (Fig. 5A, inset) (1, 33). The G1 VP7 proteins of both RotaTeq and Rotarix match those encoded by lineage 1 genes at each of these four sites. A recent analysis of the G1 VP7 proteins of contemporary Belgium strains versus those in RotaTeq and Rotarix also identified these four residues (56). This result suggests that G1 lineage 2 VP7 proteins are antigenically distinct from those of the G1 lineage 1 proteins as well as those of the current vaccine strains.
For the VUMC RVs with G3 specificity, the VP7 sequences were found to cluster with those of other contemporary strains within lineage 1 (Fig. 5B) (31). The VP7 gene of the G3 component strain of the RotaTeq vaccine is genetically more divergent from those of modern strains and groups within lineage 2, in agreement with other reports (31, 56). By performing amino acid alignments, we found six residue changes (P66S, E104G, A212T, K238N, D242N, and A278M) between the VP7 of RotaTeq and those of modern strains, including the 18 G3P[8] VUMC RVs (data not shown). Three of the changes (A212T, K238N, and D242N) are located in or near neutralization domains on the trimer structure (7-1A, 7-1B, and 7-2) and might change VP7 antigenicity (Fig. 5B, inset). Changes at positions 212, 238, and 242 were also found in the analysis of G3 VP7 proteins from contemporary Belgium strains versus RotaTeq G3 VP7 (56).
The VP7 sequences of the four VUMC RVs with G12 specificity were found within lineage 3, separate from those of lineage 1 (strain L26) and 2 (strains 10941 and K12) (Fig. 5C) (56). We found that lineage 3 could be further defined into 2 sublineages (3-A and 3-B), both of which contain contemporary human RVs. This observation suggests that lineages 3-A and 3-B diverged prior to the estimated time of G12 introduction to the United States in 1999 to 2000 (56). All four G12 strains sequenced in this study have lineage 3-B VP7 genes. However, there are no amino acid changes that distinguished lineage 3-A from 3-B G12 VP7 proteins (data not shown). Thus, while these genes are divergent at the nucleotide level, they are expected to encode antigenically identical VP7 proteins.
In addition to VP7, the spike attachment protein VP4 also induces neutralizing antibodies during infection and is important for immunological protection against RV disease. Thus, we sought to determine how similar the VP4 genes and proteins of the contemporary VUMC RV strains were to each other and to those of other modern, archival, and vaccine strains. To do this, we constructed maximum likelihood phylogenetic trees using the VP4 ORF sequences of representative P[8] RVs (Fig. 5D) (see Table S4). The results show that the VP4 genes of contemporary RVs cluster into two known phylogenetic lineages, 1 and 3; RVs with both lineage 1 (8 VUMC RVs) and lineage 3 (50 VUMC RVs) genes cocirculated in Nashville in 2005-2006 and 2006-2007 seasons (31). Lineage 1 is comprised mainly of the VP4 genes from archival DC RVs DC2262, DC2241, and DC2102 and the prototypic laboratory strains Hochi, Odelia, D, and Wa. However, the VP4 genes of VUMC RVs designated allele D (purple), and from other contemporary strains for which sequences are available in GenBank, form a cluster within lineage 1. These other allele D-like sequences are from human RV isolated after 2006 in the United States (strains 20007744509 and 2008747288), Belgium (strain BE00010), and Australia (strains CK00005 and CK00034). The VP4 gene of Rotarix is also lineage 1 and is closely related to this contemporary allele D-like cluster (56).
The VP4 gene of the P[8] component strain of the RotaTeq vaccine, considered lineage 2, is genetically more divergent from modern strains, in agreement with a previously published report (31). At the protein level, the RotaTeq P[8] VP4 protein is different from those encoded by the contemporary lineage 1 and 3 genes. Specifically, there are 40 amino acid differences between the P[8] VP4 protein of RotaTeq and the P[8] VP4 protein of contemporary lineage 1 strains (i.e., those encoded by allele D-like genes) (data not shown). The VP4 proteins of RotaTeq and contemporary lineage 3 strains are more similar but still show 28 amino acid changes when aligned to each other (data not shown). We found three amino acid residues (I78, T120, and K163) of RotaTeq VP4 that (i) differ from nearly every modern P[8] strain (i.e., isolated since 2000) for which sequences are available and (ii) are located in or near neutralization domain 8-1, 8-3, or 8-4 of VP8*, the distal cleavage product of trypsin-activated VP4 (Fig. 5D, inset). The location of these three residues suggests that they influence the antigenicity of VP4.
RV is a ubiquitous pediatric pathogen, infecting nearly every unvaccinated child by age 5 (27). Despite their medical significance, the genetic diversity of human RVs is not yet fully known, mainly due to the lack of complete genome sequences. In this study, we deduced the sequences of 58 human RVs isolated as part of active, prospective surveillance for community-acquired gastroenteritis at VUMC in Nashville, TN. The viruses are contemporary strains from the years 2005 to 2009, and they represent G/P types that are dominant in many regions of the world today. The years of sample collection spanned the widespread implementation of RotaTeq vaccination in the Nashville community (40, 41). We found that VUMC RVs circulating in the prevaccine season (i.e., the 2005-2006 season) were different from those circulating 2 to 3 years following community RotaTeq implementation (i.e., the 2008-2009 season). Specifically, in the 2005-2006 season, a heterogeneous mix of G1P[8] RVs, with various allele constellations and antigenically distinct VP7 and VP4 proteins, cocirculated in Nashville, TN. In contrast, the 2008-2009 season was marked by a single genetically and antigenically homogeneous G3P[8] RV clade. The 2006-2007 season, while technically considered postvaccine, had only an ~36% community vaccine compliance rate (40). The RV strains appearing in the 2006-2007 season are more similar to those found in the 2005-2006 season. While it is tempting to speculate that the differences in VUMC RVs from 2005-2006 and 2006-2007 seasons versus the 2008-2009 season is attributable to RotaTeq introduction, they might instead just reflect the well-documented, albeit poorly understood, seasonal fluctuation of RV G/P types (7, 17, 44). It is important to note that the majority of VUMC RVs were isolated from children who themselves did not receive any RV vaccine (Fig. 2; also see Table S1 in the supplemental material). However, two G3P[8] RV isolates (VU08-09-9 and VU8-09-28) were from children who received two doses of RotaTeq, and two G3P[8] RV isolates (VU08-09-17 and VU08-09-22) were from children vaccinated with all three doses (see Table S1). Overall, we found no VP7 or VP4 amino acid changes between G3 viruses from vaccinated and unvaccinated children. In fact, full-genome inspection of these isolates did not reveal any appreciable differences from RVs found in vaccinated versus unvaccinated children. The reason for the lack of protection against RV disease for these vaccinated children is not known, but immunologically driven evasion mechanisms do not appear to be at work.
The complete genome sequence analysis of the 58 VUMC RVs revealed that they belong in GG-1, and none contained genotype 2 or animal RV-like genes. Still, a major limitation of this study is in the design of primers to preferentially amplify genotype 1 genes during RT-PCR and sequencing via the established, semiautomated pipeline at the J. Craig Venter Institute. Future studies will rely on sequence-independent amplification and sequencing approaches to address the frequency of gene reassortment between GG-1 and GG-2 strains (22, 46). Nonetheless, the fact that all 58 VUMC RVs were GG-1, with genotype 1 internal protein genes, afforded us the unique opportunity to analyze modern RV diversity at the subgenotype level. As was done in our previous analyses of archival GG-1 RVs from Washington, DC, we used phylogenetic trees to designate each gene of each VUMC RV (except VP7) into alleles (32, 33). By plotting the allele constellations of the VUMC isolates, it became clear that genetic exchange occurred among these strains. However, we note that, given our level of analysis, it is not possible to determine whether such exchanges occurred during (rather than prior to) 2005 to 2009. Interestingly, we found that some allele constellations persisted over a 1- to 3-year time span, despite the observation that gene reassortment was possible for other cocirculating strains. Why these RV PCs continued to circulate in Nashville, nearly unchanged, over time is a fascinating question. One hypothesis is that specific combinations of alleles were advantageous to the viruses and provided selective pressure(s) against gene reassortment. The basis for preferred gene sets might be related to the interactions of the encoded viral proteins during replication. In this manner, we expect more closely related genes, such as those belonging to the same phylogenetic lineage, to be reassorted more freely. Future experiments in our laboratories will use reverse-genetic and biochemical approaches to test the hypothesis that certain alleles encode proteins that interact preferentially (51). We cannot exclude the alternative explanation that the PCs were maintained simply due to lack of gene reassortment opportunities. Specifically, instead of children being inoculated with a heterogeneous mix of GG-1 viruses (i.e., with several different allele constellations), they might have been infected with a single strain. As such, the lack of intrahost RV diversity would abrogate the chance for gene reassortment as analyzed at the allele level. Future deep-sequencing studies will elucidate the quasi-species dynamics of RVs within a single host, in addition to revealing reassortment frequencies.
In this study, we also analyzed the genetic and antigenic similarities among these 58 modern VUMC RVs and compared their VP7 and VP4 genes/proteins to those of other strains. We found that G1, G3, and P[8] RVs can encode different types of VP7 and/or VP4, which show changes in regions involved in neutralizing antibody binding. The VP7 and VP4 proteins of VUMC RVs and other modern strains also differ from those of the currently available vaccines, RotaTeq and Rotarix, a result consistent with recent findings by Zeller et al. (56). It is conceivable that amino acid differences between vaccine strains and currently circulating RVs could set the stage for the emergence of vaccine-resistant variants. However, immunological protection against RV is thought to be both homotypic (the same G/P type) as well as heterotypic (different G/P types) (9, 52). For example, Rotarix, which only contains the G1 and P[8] antigens, has proven effective at preventing moderate to severe gastroenteritis against non-G1P[8] strains (36). Still, given the evolutionary potential for RVs to rapidly adapt through gene reassortment and the accumulation of point mutations, ongoing genetic surveillance of strains is imperative. The complete genome sequences of human RVs circulating in a defined region during or just prior to widespread vaccination will provide a baseline for monitoring changes in the viral landscape that could affect vaccine performance over time.
Supplementary Material
Supplemental material
We thank Elizabeth Teel, Mike Bowen, and Jon Gentsch (Centers for Disease Control and Prevention) for scientific support in the collection and typing of fecal specimens and for editorial suggestions on the manuscript. We also acknowledge David Spiro for assistance in the initial development of the sequencing pipeline at the J. Craig Venter Institute.
S.M.M. and A.O.M. were supported by the Virginia Tech Carilion Research Institute. J.T.P. and C.M.R. were supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health. This project was also supported in part by a contract from the Centers for Disease Control and Prevention (contract no. 1U01IP00022) and by federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services (contract no. HHSN272200900007C).
Published ahead of print 13 June 2012
Supplemental material for this article may be found at
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