Sequence analysis of the NSP4 gene from human rotavirus strains isolated in the United States

Mutation distribution in the NSP4 protein in rotaviruses isolated from Mexican children with moderate to severe gastroenteritis

The NSP4 protein is a multifunctional protein that plays a role in the morphogenesis and pathogenesis of the rotavirus. Although NSP4 is considered an enterotoxin, the relationship between gastroenteritis severity and amino acid variations in NSP4 of the human rotavirus remains unclear. In this study, we analyzed the sequence diversity of NSP4 and the severity of gastroenteritis of children with moderate to severe gastroenteritis. The rotavirus-infected children were hospitalized before the rotavirus vaccine program in Mexico. All children had diarrhea within 1-4 days, 44 (88%) were vomiting and 35 (70%) had fevers. The severity analysis showed that 13 (26%) cases had mild gastroenteritis, 23 (46%) moderate gastroenteritis and 14 (28%) severe. NSP4 phylogenetic analysis showed three clusters within the genotype E1. Sequence analysis revealed similar mutations inside each cluster, and an uncommon variation in residue 144 was found in five of the Mexican NSP4 sequences. Most of the amino acid variations were located in the VP4 and VP6 binding site domains, with no relationship to different grades of gastroenteritis. This finding indicates that severe gastroenteritis caused by the rotavirus appears to be related to diverse viral or cellular factors instead of NSP4 activity as a unique pathogenic factor.

Molecular characterization of the NSP4 gene of human group A rotavirus strains circulating in Tunisia from 2006 to 2008

Non-structural protein 4 (NSP4), encoded by group A rotavirus (RVA) genome segment 10, is a multifunctional protein and the first recognized virus-encoded enterotoxin. Recently, a new classification system for RVAs was proposed and a total of 14 NSP4 genotypes (E1-E14) are currently described. The most common NSP4 genotypes in humans are Wa-like E1 and DS-1-like E2. This report represents the first investigation on the genetic diversity of RVA NSP4 genes in Tunisia from 2006 to 2008. In the present study, the NSP4-encoding genes of human RVA strains with different G/P-genotype combinations were analyzed. NSP4 genes of 261 RVA-positive fecal samples were analyzed using a semi-nested reverse transcriptase-polymerase chain reaction and in addition the NSP4 gene of 46 representative RVA strains were sequenced. Phylogenetic analysis of the Tunisian NSP4 nucleotide sequences revealed the presence of two NSP4 genotypes. Genotype E1 was found to be associated with G1P[8], G3P[6], G3P[8], G4P[6] and G4P[8], whereas genotype E2 was associated with G2P[4], G2P[6] and G6P[9] samples. These results support the hypothesis that P[8] carrying RVA strains usually possess the E1 genotype, whereas P[4] carrying RVA strains usually possess the E2 genotype. P[6] carrying strains were found with both E1 and E2. The unusual G6P[9] strains possessed a E2 genotype with a possible animal origin. These results underline the need for further investigations to assess the validity of NSP4 as a suitable target for epidemiologic surveillance of RVA infections and vaccine development.

Multiple-gene characterization of rotavirus strains: evidence of genetic linkage among the VP7-, VP4-, VP6-, and NSP4-encoding genes

A total of 162 rotavirus strains detected between 1996 and 2006 among individuals with diarrhea in Rio de Janeiro, Brazil, were analyzed by multiple-gene genotyping. Characterization of strains was done by RT-PCR assay for amplification and typing of the VP7-, VP4-, VP6-, and NSP4-encoding genes. Overall, 139 (85.8%) strains belonged to the common group A rotavirus combinations: 67 (41.4%) belonged to genotype G1-P[8]-I1-E1; 18 (11.1%) were G2-P[4]-I2-E2; 11 (6.8%) were G3-P[8]-I1-E1; 12 (7.4%) were G4-P[8]-I1-E1; and 31 (19.1%) were G9-P[8]-I1-E1. Two samples presented mixed genotypes (G1 + G3-P[8]-I1-E1 and G1 + G9-P[9]-I1-E1) and rare combinations, such as G2-P[6]-I2-E2 and G9-P[6]-I2-E2, were detected in six (3.7%) strains. The results suggest a linkage among all four genes. Genotypes G1/G3/G4/G5/G9-P[8] were correlated strongly to I1-E1 genotypes and G2-P[4]/P[6] were correlated to I2-E2 genotypes. Unusual combinations of genes, such as G3-P[9]-I2-E2, G9-P[9]-I1-E2, and G3-P[9]-I3-E3, were observed in 15 (9.3%) strains. The characterization of multiple genes allows a more complete analysis of the rotavirus isolates and provides evidence of natural reassortment of strains.

Genetic variation ofNSP1 andNSP4 genes among serotype G9 rotaviruses causing hospitalization of children in Melbourne, Australia, 1997–2002

Serotype G9 rotaviruses have emerged as one of the leading causes of gastroenteritis in children worldwide. We examined 29 representative G9 rotavirus isolates from a 6-year collection (1997-2002) and determined the level of variation in genes encoding non-structural proteins, NSP1 and NSP4. Northern hybridization analysis with a whole genome probe derived from the prototype G9 strain, F45, revealed that the NSP1 gene (gene 5) of two isolates (R1 and R14) did not exhibit significant homology. Complementary DNA probes of R1 and R14 genes 5 were used in Northern blot hybridization and indicated the presence of at least two gene 5 alleles among Melbourne G9 rotaviruses. Nucleotide sequence analysis revealed that isolates carrying the R14 gene 5 shared 94-98% sequence identities with one another, while sequence identity to R1 was 78%. Surprisingly, R1 displayed 96% nucleotide identity with the prototype serotype G1 strain, Wa. The detection of different alleles of NSP1 genes prompted us to investigate the level of variation in another non-structural protein, NSP4, a multifunctional protein and the first viral-encoded enterotoxin. Phylogenetic analysis indicated that while all isolates clustered into one group containing the Wa NSP4 allele (genotype 1), isolate R1 was most closely related to Wa. This study reveals new information about the diversity of non-structural proteins of G9 rotaviruses.

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A human vaccine strain of lamb rotavirus (Chinese) NSP4 gene: complete nucleotide sequence and phylogenetic analyses

A lamb strain of rotavirus has recently been licensed for use in China as a live vaccine to prevent rotavirus diarrhea in children. As rotavirus NSP4, especially the cytotoxic domain alone is considered to be associated with diarrhea, we sequenced gene segment 10, which encodes NSP4, of lamb rotavirus. Comparative analyses was performed to identify differences from human rotavirus strains, that might be associated with attenuation, and to ascertain whether the lamb rotavirus gene fits among the NSP4 of other sequenced rotavirus strains. Our comparative nucleotide sequence analysis suggests its close identity (91.17% homology) with that of group-A equine rotavirus (strain HI23). Multiple alignment of the deduced amino acid sequence of lamb NSP4 with that of other group A rotaviruses demonstrated homology ranging from 63.42% with that of porcine YM strain to 93.71% with equine HI23 strain of rotavirus. A group A-specific NSP4 monoclonal antibody recognized the glycosylated and unglycosylated forms of the protein from virus-infected lysates, suggesting a well-conserved group-specificity of the lamb NSP4. Phylogenetic analysis of the lamb rotavirus gene, with 60 other NSP4 gene sequences of human and animal rotavirus strains, demonstrated that the lamb rotavirus strain belongs to genotype A. Comparative analysis also revealed that although it is a vaccine strain, the NSP4 cytotoxic domain of lamb strain demonstrated an overall amino acid conservation similar to that of other strains, whose NSP4 alone causes diarrhea in animal models. These results taken together with our previous observations clearly reaffirm the idea that the attenuation phenotype of rotaviruses does not involve NSP4 cytotoxic domain, perhaps due to the suppression of NSP4 cytotoxic activity by other rotaviral proteins.

Evidence for genetic linkage between the gene segments encoding NSP4 and VP6 proteins in common and reassortant human rotavirus strains

NSP4-encoding genes of 78 human rotavirus strains of common or reassortant genotypes were characterized by reverse transcription-PCR followed by sequencing and phylogenetic analysis. It was found that all the human strains characterized clustered into only two of the five known NSP4 genotypes. Linkage between NSP4 genotypes and VP6 subgroups was 100%, NSP4 genotype A being linked to VP6 of subgroup I (SGI) and NSP4 of genotype B being linked to VP6 of SGII. The diversity among the NSP4- and VP6-encoding genes was significantly less than that among the VP7 and VP4 genes in cocirculating human rotavirus strains. Whereas G and P types appear to be shared among different animal species and humans, the NSP4- and VP6-encoding genes appear to segregate according to their host of origin, suggesting that these two proteins may be host restriction determinants. The NSP4-VP6 association may be structurally determined during rotavirus replication (morphogenesis).

Detailed computational analysis of a comprehensive set of group A rotavirus NSP4 proteins

Rotavirus infection causes diarrhea to humans, animals and birds. The NSP4 protein of Group A rotavirus has been recognized as a viral enterotoxin. This single protein plays important roles in viral pathogenesis and morphogenesis. Domains involved in structure and biologic functions have been proposed mainly based on the SA11 strain, a prototype of group A rotavirus. NSP4 has been classified into different genotypes based on sequence homology. These analyses are based on representative strains selected but not comprehensive. In this paper, we collected all NSP4 sequences in the GenBank and performed a detailed computational analysis. Our analysis of 176 NSP4 proteins in Groups A, B and C rotaviruses confirms that the recently published avian NSP4 sequences belong to a new genotype (Mori Y., Borgan M.A., Ito N., Sugiyama M. and Minamoto N., Virus Res 89, 145-151, 2002), besides the four known NSP4 genotypes of Group A mammalian rotaviruses. Significant differences were discovered in the physicochemical properties between the avian and mammalian NSP4 proteins. In particular, lack of a highly probable coiled-coil region in the avian sequences implies a diversion of the NSP4 quaternary structure from the latter, although the secondary and tertiary structures may be similar. Fourteen amino acids are found absolutely conserved in the Group A NSP4 sequences, regardless of genotype. Of the conserved residues, two are glycosylation sites, one is in the middle of the transmembrane segment, seven span the VP4 binding domain, and five are clustered in the middle of the toxic peptide region, indicating the functional importance of the conservation.

Molecular characterization of serotype G9 rotavirus strains from a global collection

Between 1992 and 1998, serotype G9 human rotavirus (RV) strains have been detected in 10 countries, including Thailand, India, Brazil, Bangladesh, Malawi, Italy, France, the United States, the United Kingdom, and Australia, suggesting the possible emergence of the fifth common serotype worldwide. Unlike the previously characterized reference G9 strains (i.e., WI61 and F45), the recent G9 isolates had a variety of gene combinations, raising questions concerning their origin and evolution. To identify the progenitor strain and examine the on-going evolution of the recent G9 strains, we characterized by genetic and antigenic analyses 16 isolates obtained from children with diarrhea in India, Bangladesh, the United States, and Malawi. Specifically, we sequenced their VP7 and NSP4 genes and compared the nucleotide (nt) and deduced amino acid sequences with the reference G9 strains. To identify reassortment, we examined the products of five gene segments; VP4, VP7, and NSP4 genotypes (genes 4, 9, and 10); subgroups (gene 6); electropherotypes (gene 11); and the genogroup profiles of all of the recent G9 isolates. Sequence analysis of the VP7 gene indicated that the recent U.S. P[6],G9 strains were closely related to the Malawian G9 strains (>99% nt identity) but distinct from G9 strains of India ( approximately 97% nt identity), Bangladesh ( approximately 98% nt identity), and the reference strains ( approximately 97% nt identity). Phylogenetic analysis identified a single cluster for the U.S. P[6],G9 strains that may have common progenitors with Malawian P[6],G9 strains whereas separate lineages were defined for the Indian, Bangladeshi, and reference G9 strains. Northern hybridization results indicated that all 11 gene segments of the Malawian P[6],G9 strains hybridized with a probe derived from a U.S. strain of the same genotype and may have the same progenitor, different from the Indian G9 strains, whereas the Bangladesh strains may have evolved from the U.S. G9 progenitors. Overall, our findings suggest that much greater diversity among the newly identified G9 strains has been generated by reassortment between gene segments than through the accumulation of mutations in a single gene.

A functional NSP4 enterotoxin peptide secreted from rotavirus-infected cells

Previous studies have shown that the nonstructural glycoprotein NSP4 plays a role in rotavirus pathogenesis by functioning as an enterotoxin. One prediction of the mechanism of action of this enterotoxin was that it is secreted from virus-infected cells. In this study, the media of cultured (i) insect cells infected with a recombinant baculovirus expressing NSP4, (ii) monkey kidney (MA104) cells infected with the simian (SA11) or porcine attenuated (OSU-a) rotavirus, and (iii) human intestinal (HT29) cells infected with SA11 were examined to determine if NSP4 was detectable. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis-Western blotting, immunoprecipitation and N-terminal amino acid sequencing identified, in the early media from virus-infected cells, a secreted, cleavage product of NSP4 with an apparent molecular weight of 7,000 that represented amino acids 112 to 175 (NSP4 aa112-175). The secretion of NSP4 aa112-175 was not affected by treatment of cells with brefeldin A but was abolished by treatment with nocodazole and cytochalasin D, indicating that secretion of this protein occurs via a nonclassical, Golgi apparatus-independent mechanism that utilizes the microtubule and actin microfilament network. A partial gene fragment coding for NSP4 aa112-175 was cloned and expressed using the baculovirus-insect cell system. Purified NSP4 aa112-175 increased intracellular calcium mobilization in intestinal cells when added exogenously, and in insect cells when expressed endogenously, similarly to full-length NSP4. NSP4 aa112-175 caused diarrhea in neonatal mice, as did full-length NSP4. These results indicate that NSP4 aa112-175 is a functional NSP4 enterotoxin peptide secreted from rotavirus-infected cells.