Epidemiology and evolution of rotaviruses and noroviruses from an archival WHO Global Study in Children (1976-79) with implications for vaccine design

Abstract

Prompted by the discovery of new gastrointestinal viruses, the NIH, NIAID and WHO investigated the etiology of acute diarrhea that occurred from 1976-1979 in a global cohort of infants and young children. Rotaviruses were found to be major pathogens worldwide, whereas the Norwalk virus could not be detected using a radioimmunoassay. The aim of this study is to re-evaluate the role and diversity of rotaviruses and noroviruses in the original cohort using more sensitive current technologies. Stools collected from Asia, Africa, and South America (n = 485) were evaluated for viral genotypes by RT-PCR and sequencing. Rotaviruses were detected in 28.9% and noroviruses in 9.7% of the specimens, with G1 rotaviruses and GII noroviruses accounting for the majority of each respective virus. Various strains in this study predated the currently assigned dates of discovery for their particular genotype, and in addition, two noroviruses (KL45 and T091) could not be assigned to current genotypes. Phylogenetic analyses demonstrated a relative constancy in circulating rotavirus genotypes over time, with several genotypes from this study becoming established in the current repertoire of viral species. Similarly, GII noroviruses have maintained dominance, with GII.4 noroviruses continuing as a predominant genotype over time. Taken together, the complex molecular epidemiology of rotaviruses and noroviruses circulating in the 1970's is consistent with current patterns, an important consideration in the design of multivalent vaccines to control these viruses.

Figure 1. Map of the relative frequencies of rotaviruses and noroviruses detected in each region of this study.

Figure 2. Overall distribution of rotavirus and norovirus genotypes detected in this study.

Figure 3. Phylogenetic analyses of partial VP7 capsid nucleotide sequences from rotaviruses.

Bootstrap values are shown as percent values for major nodes, and large clusters are collapsed. Black stars indicate sequences obtained from this study. (a) Inferred phylogeny for G9 rotaviruses as determined by a maximum likelihood phylogenetic analysis, including previously defined lineages. Bold brackets indicate consistently defined lineages I, II, and III. Subclusters within lineage III, described by Matthijnssens et al., are indicated in italics, and lineages IV, V, and VI, described by Martinez-Laso et al., are also listed. Strains Hu/RV/G2275/USA/1980/G9 and Hu/RV/DC706/USA/1980/G9 are of indeterminate lineage. (b) Inferred phylogeny for G5 rotaviruses as determined by a maximum likelihood phylogenetic analysis, including previously defined lineages.

Figure 4. Maximum likelihood phylogenetic analysis of full-length VP1 capsid nucleotide sequences from noroviruses.

Bootstrap values are shown as percent values for major nodes. Black stars indicate sequences obtained from this study. Bold brackets indicate genotypes with representatives from this study, and genotypes without representatives from this study are collapsed. Animal sequences representing additional genogroups GIII and GV are also provided.

Figure 5. Maximum likelihood phylogenetic analysis of full-length VP1 capsid nucleotide sequences from all GII.4 variant clusters (n = 162 sequences).

Variant clusters described by Zheng et al. are indicated in italics along with their associated years of specimen collection. A new cluster was defined (“08–10”), which contains strains obtained from the United States, Australia, Europe, Asia, and Africa. Percent nucleotide and amino acid distances are provided in an inlaid table. These distances were determined from a multiple sequence alignment containing all known GII.4 nucleotide sequences available in GenBank as of April 2012 (n = 663 sequences). An average intragroup distance was calculated for all GII.4 sequences, excluding the unique genogroup GII variants KL45 and T091.

Figure 6. Maximum likelihood phylogenetic analysis of partial VP1 capsid sequences from GIV noroviruses.

Bootstrap values are shown as percent values for major nodes. A black star indicates the sequence obtained from this study.