Expression of the major inner capsid protein of the group B rotavirus ADRV: primary characterization of genome segment 5

Full genome analysis of group B rotaviruses from western India: genetic relatedness and evolution

To date, full-genome sequences of only seven human group B rotavirus (RVBs) strains have been described. Such data on more RVBs are necessary to establish the evolutionary relationship and ecological features of RVBs from different geographical regions. The present study was aimed at determining the full-length sequences of all 11 genes of 13 human RVB strains detected during 1995-2010 in sporadic and outbreak cases of acute gastroenteritis from four different cities of western India. This study also included estimation of evolutionary rates and site-specific selection pressure analysis for all gene segments. Nucleotide/deduced amino acid sequence analyses of structural and non-structural genes showed 95.1-99.8/94.1-100 % identity with the counterparts of RVB strains isolated in India, Bangladesh and Myanmar. Phylogenetic analyses of all gene segments revealed formation of a monophyletic clade of the western Indian RVB strains, reflecting their highly conserved nature. All gene segments were also found to be under negative/purifying selection pressure. These data suggest that RVB is circulating in the natural host as a series of stable viral clones. Estimates of rates of nucleotide substitution in all RVBs ranged from 1.36-4.78×10(-3) substitutions per site per year. The rate for human RVB VP7 and NSP2 genes were comparable, respectively, with the evolution kinetics of genotype G9/G12 and N1 group A rotavirus strains. The time of the most recent common ancestor of the extant human RVBs was estimated to be during 1915-1974. Evolutionary and genetic analyses carried out in this study provide data that is useful for the elucidation of evolutionary relationship/timescale, stasis or dynamics existing in the RVB population.

Molecular characterization of a novel adult diarrhoea rotavirus strain J19 isolated in China and its significance for the evolution and origin of group B rotaviruses

The complete genome of a novel adult diarrhoea rotavirus strain J19 was cloned and sequenced using an improved single-primer sequence-independent method. The complete genome is 17,961 bp and is AU-rich (66.49 %). Northern blot analysis and genomic sequence analysis indicated that segments 1-11 encode 11 viral proteins, respectively. Protein alignments with the corresponding proteins of J19 with B219, and groups A, B and C rotaviruses, produced higher per cent sequence identities to B219. Among groups A, B and C rotaviruses, 10 proteins from group B rotaviruses exhibited slightly higher amino acid sequence identity to the J19 proteins, but proteins of J19 showed low amino acid sequence identity with groups A and C rotaviruses. Construction of unrooted phylogenetic trees using a set of known proteins and representatives of three known rotavirus groups revealed that six structural proteins were positioned close to B219 and the basal nodes of groups A, B and C lineages, although with a preferred association with group B lineages. Phylogenetic analysis of the five non-structural proteins showed a similar trend. The results of the serological analysis, protein sequence analysis and phylogenetic analysis suggested that J19 would be a novel rotavirus strain with great significance to the evolution and origin of group B rotaviruses.

Molecular characterization of the major capsid protein VP6 of bovine group B rotavirus and its use in seroepidemiology

The major inner capsid protein (VP6) gene of the bovine group B rotavirus (GBR) Nemuro strain is 1269 nt in length and contains one open reading frame encoding 391 aa. Nucleotide and amino acid sequence identities of the Nemuro VP6 gene compared with the published corresponding human and rodent GBR genes were respectively 66–67 and 70–72 %, which are notably lower than those between human and rodent viruses (72–73 and 83–84 %, respectively). Overall identities of VP6 genes among GBRs were substantially lower than those among both group A rotaviruses (GARs) and group C rotaviruses (GCRs) derived from different species of mammals. These results demonstrate that bovine GBR is remarkably distinct from other GBRs and that GBRs from different species may have had a longer period of divergence than GARs and GCRs. Recombinant VP6 was generated with a baculovirus expression system and used for an ELISA to detect GBR antibodies. All 13 paired sera from adult cows with GBR-induced diarrhoea in the field showed antibody responses in the ELISA. In serological surveys of GBR infection using the ELISA, 47 % of cattle sera were positive for GBR antibodies, with a higher antibody prevalence in adults than in young cattle. In pigs, a high prevalence of GBR antibodies (97 %) was detected in sera from sows. These results suggest that GBR infection is common in cattle and pigs, notwithstanding the scarcity of reports of GBR detection in these species to date.

Amplification of various genes of human group B rotavirus from stool specimens by RT-PCR

BACKGROUND

The detection of the human group B rotavirus (HuGBR) CAL strain from India has given us an opportunity to design suitable primers for the detection of HuGBR since CAL is the second HuGBR detected until now, the Chinese Adult Diarrhoea Rotavirus (ADRV) being the first reported human pathogen belonging to this group of viruses. The primers described here may thus be used for the detection of human group B rotaviruses by reverse transcription-PCR (RT-PCR) in a diagnostic laboratory.

OBJECTIVE

To establish a set of primers suitable for the detection of various genes of human group B rotaviruses using a rapid RT-PCR assay.

STUDY DESIGN

Until recently, the Chinese ADRV strain was the only HuGBR strain that had been partially sequenced by cloning various viral genes using vector-specific primers. Consequently, there are very few reports in the literature describing primers that may be used for the detection of HuGBR viruses using RT-PCR in a clinical laboratory. The sequences of various genes from the ADRV strain that had been submitted to the nucleotide sequence database GenBank were analyzed in order to design several putative detection primer pairs for an RT-PCR assay. The rationale was to amplify the cognate genes from five isolates of the HuGBR CAL strain (CAL-1 to CAL-5) that have been detected to date from India. Primers that resulted in a specific product of the expected size from the CAL isolates were used to standardize a protocol for amplifying various genes of the CAL isolates under identical reaction conditions.

RESULTS

Out of several synthetic oligonucleotides designed, 12 were found to be satisfactory for the amplification of gene segments 4, 5, 6, 7, and 9 from the five CAL isolates and are presented here. A set of previously described primers that have been shown to be specific for human group B rotavirus gene segment 8 were also found to amplify the cognate gene from the CAL isolates. All the reactions were carried out using the same thermal cycling conditions.

CONCLUSIONS

The extreme virulence potential of HuGBR has been documented in several epidemics in China. Until recently, the Chinese ADRV strain was the only known HuGBr strain. As there have not been any reports of HuGBR infections outside China, there are no consensus nucleotide sequences available for HuGBR that may be used to validate primers for the detection of HuGBR. Here we report a set of 12 primer sequences that were designed from ADRV sequences and also found to amplify various genes from the different CAL isolates and hence may represent consensus primers suitable for the detection of HuGBR.

Detection of group B rotaviruses in fecal samples from diarrheic calves and adult cows and characterization of their VP7 genes

Groups A, B, and C rotaviruses have been identified in cattle. Group B rotaviruses are associated with sporadic cases of diarrhea in calves and adult cows. From diagnostic submissions to our laboratory, 90 fecal samples from cases of calf diarrhea, 81 fecal samples from cases of adult cow diarrhea (winter dysentery), and 20 fecal samples from case control normal adult cows were tested for group B rotaviruses by polyacrylamide gel electrophoresis (PAGE), and reverse transcription (RT)-PCR (targeting 279 bp of the VP7 gene). In addition, 53 fecal samples from diarrheic adult cows were tested for group B rotaviruses by immune electron microscopy (IEM). By RT-PCR, five samples from calves were group B rotavirus positive (5.6%). Fifteen samples from adult cows with diarrhea were group B rotavirus positive (18.5%), and none of the control fecal samples from normal cows were positive for group B rotaviruses. By PAGE, one calf sample (RT-PCR positive) was group B rotavirus positive (short electropherotype), but none of the adult cow samples were positive for group B rotaviruses. By IEM, 5 (9.4%) of the 53 fecal samples from diarrheic adult cows were group B positive (all were also RT-PCR positive). The VP7 genes of three strains (WD653 from an adult cow and the ATI and Mebus calf strains) were sequenced. The VP7 genes from the three bovine strains showed high (over 90%) nucleotide and deduced amino acid homologies, but lower homologies (48 to 61%) were seen between these genes and the genes from rodent (IDIR) and human (ADRV) group B rotaviruses. Although there were some differences of degree, all inoculated gnotobiotic calves (n = 6) showed abnormal feces between 1 and 3 days after inoculation with each of three strains of group B bovine rotaviruses, and group B rotaviruse, were detected in the feces for up to 2 weeks by RT-PCR but for shorter periods by PAGE or IEM.

Detection of bovine group B rotaviruses in feces by polymerase chain reaction

A pair of primers designed from the sequence of genome segment 9 of group B rat rotavirus (IDIR) were employed to amplify genome segment 9 of a group B bovine rotavirus in a polymerase chain reaction (PCR) and to sequence the derived PCR products. A new pair of primers were synthesized from the obtained sequence data and used in a PCR detection assay for group B bovine rotavirus in fecal samples. In addition, another pair of primers were designed to produce a PCR-derived internal probe. This probe was used in a chemiluminescent hybridization to confirm the specificity and to increase the sensitivity of the assay. This assay could detect 0.1 fg of target double-stranded RNA. It was specific to group B bovine rotavirus and did not detect group B rat (IDIR) and porcine rotaviruses, group A bovine (NCDV), simian (SA-11), equine (H-2), porcine (OSU), human (DS-1), deer, and avian rotaviruses, coronavirus, or other enteric organisms tested in this study.

Identification and baculovirus expression of the VP4 protein of the human group B rotavirus ADRV

A complete cDNA copy of the fourth RNA segment of the human group B rotavirus adult diarrheal rotavirus (ADRV) has been cloned into lambda phage and excised into plasmid pSK Bluescript. Gene segment 4 contains 2,303 bases and encodes one long open reading frame beginning at base 16 and terminating at base 2263. The encoded protein contains 749 amino acids, with a calculated molecular mass of 84.4 kDa and a pI of 6.1. Gene 4 cDNA was inserted into a recombinant baculovirus via homologous recombination. The gene 4 polypeptide migrates at 84 kDa when expressed either by a recombinant baculovirus or in vitro in a rabbit reticulocyte lysate. The gene 4 protein is immunoprecipitable by hyperimmune serum to ADRV, human ADRV convalescent-phase serum, a porcine group B rotavirus infection serum, and a monoclonal antibody made to ADRV virion. Guinea pig hyperimmune serum to the baculovirus-expressed ADRV VP4 protein recognizes virus and immunoprecipitates an 84-kDa protein from in vitro translations of total ADRV mRNA. In addition, the gene 4-encoded protein shares significant amino acid identity and similarity with the group A rotavirus VP4 protein. This information, together with our previous identification of an 84-kDa protein present on iodinated intact virion but not EDTA-treated ADRV, suggests that gene 4 encodes the VP4 protein equivalent present on the outer capsid of ADRV. The ADRV VP4 protein is also 58% identical to the IDIR rat group B rotavirus gene segment 3 protein. The substantial differences between these two group B VP4 proteins suggests that they are distantly related and likely to define two different group B rotavirus VP4 serotypes. The baculovirus-expressed VP4 protein should be useful for developing serotyping reagents and tests for human and animal group B rotaviruses as well as for addressing the role of VP4 in ADRV neutralization.

Production and characterization of monoclonal antibodies to porcine group C rotaviruses cross-reactive with group A rotaviruses

Five monoclonal antibodies (MAbs) to porcine group (gp) C rotaviruses (Cowden and Ah strains) reactive with both gp A and C rotaviruses in cell culture immunofluorescence (CCIF) tests were produced and characterized. These MAbs reacted with three strains of gp A and two strains of gp C rotaviruses in a CCIF test and were classified into two groups based on their CCIF titers. The MAbs also reacted to various degrees with cell-culture-propagated porcine gp C rotavirus (Cowden) and bovine gp A rotavirus (NCDV) in an enzyme-linked immunosorbent assay by using the MAbs as capture antibodies. Fecal samples containing human, bovine, and porcine strains of gp A and C rotaviruses were positive when tested using one of the MAbs in this assay. The MAbs recognized VP6 of gp A rotavirus and the VP6 counterpart (41-kDa protein) of gp C rotavirus in a Western blot assay. Results of competitive binding assays on four MAbs indicated that gp A and gp C rotaviruses share three overlapping epitopes within a single antigenic domain. These results suggest that gp A and C rotaviruses share a common antigen located on the VP6 protein, which is recognized by certain MAbs in various serologic assays.

Terminal sequence conservation among the genomic segments of a group B rotavirus (IDIR strain)

Terminal nucleic acid sequences were determined for all 11 segments of the IDIR strain of group B rotavirus. Consensus sequences were defined at both ends of the (+) RNA strands as 5' GGN(A/U)NA(A/U)(A/U)(A/U)---and---(A/U)NA(A/G)N(A/C)(C/A)CC3 '. The 5' and 3' terminal sequences of the (+) strand IDIR RNA were not complementary to one another. The IDIR terminal sequences and those of group A rotaviruses (GAR) were similar in that each of the (+) strands began with "GG" and ended with "CC." Otherwise, the IDIR terminal sequences did not match the consensus sequences that have been reported for the ends of the GAR genomic segments.

Expression of the major capsid protein VP6 of group C rotavirus and synthesis of chimeric single-shelled particles by using recombinant baculoviruses

VP6 of group C (Cowden strain) rotavirus was expressed in the baculovirus system. The recombinant protein, expressed to a high level in insect cells, was purified by ion-exchange chromatography. The purified protein was proven to be trimeric. The effect of pH on the trimer's stability was investigated. Coexpression of VP6 from group A (bovine strain RF) and VP6 from group C in the baculovirus system did not result in the formation of chimeric trimers. Coexpression of VP2 from group A rotavirus (bovine strain RF) and VP6 from group C in the baculovirus system led to the formation of chimeric, empty, single-shelled particles. These results demonstrate conservation in the domains necessary for binding to VP2 in different serogroups of VP6. The locations of the domains involved in trimerization and in the interaction with VP2 are discussed.

Nucleotide sequence of gene 5 encoding the inner capsid protein (VP6) of bovine group C rotavirus: comparison with corresponding genes of group C, A, and B rotaviruses

To further study the molecular characteristics of group (gp) C rotaviruses, we produced, cloned, and sequenced cDNA to gene 5 of the Shintoku strain of bovine gp C rotavirus. The resulting clone was specific for gene 5 and was genetically related to the human and porcine gp C rotaviruses, as demonstrated by Northern blot hybridization analysis. The Shintoku gene 5 is 1352 nucleotides in length and has one open reading frame encoding a polypeptide of 395 amino acids with a predicted molecular mass of 44.5 kDa. Comparative sequence analysis indicated that: (i) the Shintoku gene 5 protein shared 88.4 to 90.6% homology with the VP6 of the human (Bristol and 88-220) and porcine (Cowden) strains of gp C rotaviruses, but only low homology with the VP6 of bovine gp A (RF) and human gp B (ADRV) rotaviruses (41.3 and 16.3%, respectively); (ii) the predicted secondary structure was highly conserved among the gene 5 proteins of the bovine, porcine, and human gp C rotaviruses; and (iii) seven highly conserved regions were identified for the first time in the deduced primary amino acid sequences of gene 5 of gp C and gene 6 of gp A rotaviruses. However, only three of these highly conserved areas were present in the regions of VP6, where the secondary structure was predicted to be similar for the rotavirus strains examined. These three regions may contribute to common epitopes between the two groups of rotaviruses. Our results, in comparison with data for other rotaviruses, indicate that gene 5 of the bovine gp C rotavirus codes for the major inner capsid protein (VP6).

Molecular cloning, sequence analysis, in vitro expression, and immunoprecipitation of the major inner capsid protein of the IDIR strain of group B rotavirus (GBR)

The sixth genomic segment of the infectious diarrhea of infant rats (IDIR) strain of group B rotavirus (GBR) was cloned from double-stranded RNA purified from infected rat feces. Sequence comparison with group A rotaviruses (GAR) and the human ADRV strain of GBR indicated that IDIR gene 6 encoded the major inner capsid protein. The nucleic acid sequences of the two GBR genes were 72.9% conserved, and 83.4% of the amino acids were identical. Sequence substitutions between IDIR and ADRV were more numerous than reported for heterologous GAR strains, indicating that the two GBR strains may have diverged from one another over a longer period of time. Despite the sequence heterogeneity exhibited by the major inner capsid proteins of ADRV and IDIR, hydrophilicity plots of the two gene products were nearly indistinguishable. The GBR hydrophilicity plots displayed little similarity with those of rotavirus groups A or C, indicating substantial differences in the structures of those major inner capsid proteins. In vitro transcription and translation of IDIR gene 6 yielded a polypeptide product consistent in size with that predicted from the deduced amino acid sequence and the virion major inner capsid protein. The IDIR 6 polypeptide was immunoprecipitated by antisera directed against IDIR as well as antisera directed against ADRV and a heterologous bovine strain of GBR. No immunoprecipitation was observed with control sera or antisera directed against GAR. These results confirmed that group-specific epitopes were displayed by the major inner capsid protein encoded by IDIR gene 6. Reactivity with heterologous GBR antisera also indicated that the IDIR gene 6 product may prove useful as a standard reagent in immunoassays for the detection of GBR.

Cloning of noncultivatable human rotavirus by single primer amplification

A novel, sequence-independent strategy has been developed for the amplification of full-length cDNA copies of the genes of double-stranded RNA (dsRNA) viruses. Using human (Bristol) group C rotavirus as an example, a single amino-linked modified oligonucleotide (primer 1) was ligated to either end of each dsRNA genome segment by using T4 RNA ligase. Following reverse transcription, annealing, and repair of cDNA strands, amplification of the viral dsRNA genome was accomplished by polymerase chain reaction using a single complementary oligonucleotide (primer 2). Northern (RNA) hybridization of cDNA to virus dsRNA indicated that it was possible to generate cDNA representing the complete genome from very small clinical samples. This technique was used to determine the complete nucleotide sequence (728 bp) and coding assignment of gene 10, which revealed an open reading frame of 212 amino acids with limited homology to NS26 from human group A rotavirus. In contrast to previous tailing methods, the addition of one defined primer allowed unequivocal identification of terminal nucleotides and should be generally applicable to viruses with segmented dsRNA genomes and especially for analysis of clinical samples, for which very limited quantities of biological material are available.

Coding assignments of the genome of adult diarrhea rotavirus

Adult diarrhea rotavirus (ADRV) has caused epidemics of diarrhea in China since 1982 and remains the only group B rotavirus associated with widespread disease in humans. We recently characterized the proteins of ADRV and have now proceeded to identify the gene segments encoding each protein. Viral RNA transcripts were synthesized in vitro with the endogenous viral RNA polymerase and separated by electrophoresis in agarose. The individual transcripts were translated in a cell-free system using nuclease-treated rabbit reticulocyte lysates. The translation products were compared with polypeptides found in purified virus and were characterized by SDS-PAGE, immunoprecipitation, and Western blot analysis using antisera to double- and single-shelled virions, virus cores, and monoclonal antibodies. Furthermore, individual RNA transcripts were hybridized to total dsRNA to determine their genomic origin. Based on this analysis, the core polypeptides VP1, VP2 and VP3 are encoded by segments 1, 2, and 3, respectively. The main polypeptides in the inner capsid, VP6, and the outer capsid, VP4 and VP7, are encoded by segments 6, 4, and 8 respectively. Segments 5, 7, and 9 code for 60, 45, and 30 kDa nonstructural polypeptides. Two other nonstructural polypeptides (24 and 25 kDa) are derived from gene segment 11. Gene segment 10 codes for a 26 kDa polypeptide that is precipitated with serum to ADRV and may be a structural protein VP9. With this exception, gene coding assignments of ADRV are comparable to those of the group A rotaviruses. Our results have clear implications for further work in cloning, sequencing, and expression genes of ADRV and can provide direction towards understanding the origin and the evolution of this virus.

In vitro transcription and translation of group B rotavirus strain IDIR gene 8 and immunoprecipitation by human sera

Group B rotaviruses (GBRs) are associated with episodes of acute diarrhea in humans and a variety of animal species. To date, these agents have not been well adapted to growth in tissue culture, and evaluation of human sera for antibodies directed against GBRs has been hindered by the inability to obtain standardized and highly purified preparations of GBR antigens. In order to evaluate the reactivities of antisera with a highly specific antigen, we prepared a full-length cDNA clone of gene 8 of the IDIR strain of GBR. This clone was transcribed with T7 RNA polymerase, and the resulting RNA was translated in vitro with rabbit erythrocyte lysates. The polypeptide expressed from IDIR gene 8 was specifically precipitated by antibody directed against IDIR but not by antibody directed against ADRV (adult diarrhea rotavirus) or bovine strains of GBR. Subsequent immunoprecipitation reactions confirmed the presence of anti-IDIR antibodies among the U.S. population. Of 129 human serum specimens, 3 specifically immunoprecipitated the IDIR gene 8 polypeptide.