Rotavirus YM gene 4: analysis of its deduced amino acid sequence and prediction of the secondary structure of the VP4 protein

Early Steps in Rotavirus Cell Entry

Rotaviruses, the leading cause of severe dehydrating diarrhea in infants and young children worldwide, are non-enveloped viruses formed by three concentric layers of protein that enclose a genome of double-stranded RNA. These viruses have a specific cell tropism in vivo, infecting primarily the mature enterocytes of the villi of the small intestine. It has been found that rotavirus cell entry is a complex multistep process, in which different domains of the rotavirus surface proteins interact sequentially with different cell surface molecules, which act as attachment and entry receptors. These recently described molecules include integrins (alpha2beta1, alphavbeta3, and alphaxbeta2) and a heat shock protein (hsc70), and have been found to be associated with cell membrane lipid microdomains. The requirement for several cell molecules, which might need to be present and organized in a precise fashion, could explain the cell and tissue tropism of these viruses. This review focuses on recent data describing the interactions between the virus and its receptors, the role of lipid microdomains in rotavirus infection, and the possible mechanism of rotavirus cell entry.

Rotaviruses interact with alpha4beta7 and alpha4beta1 integrins by binding the same integrin domains as natural ligands

Group A rotaviruses are major intestinal pathogens that express potential alpha4beta1 and alpha4beta7 integrin ligand sequences Leu-Asp-Val and Leu-Asp-Ile in their outer capsid protein VP7, and Ile-Asp-Ala in their spike protein VP4. Monkey rotavirus SA11 can use recombinant alpha4beta1 as a cellular receptor. In this study a new potential alpha4beta1, alpha4beta7 and alpha9beta1 integrin ligand sequence, Tyr-Gly-Leu, was identified in VP4. It was shown that several human and monkey rotaviruses bound alpha4beta1 and alpha4beta7, but not alpha9beta1. Binding to alpha4beta1 mediated the infectivity and growth of monkey rotaviruses, and binding to alpha4beta7 mediated their infectivity. A porcine rotavirus interacted with alpha4 integrins at a post-binding stage to facilitate infection. Activation of alpha4beta1 increased rotavirus infectivity. Cellular treatment with peptides containing the alpha4 integrin ligand sequences Tyr-Gly-Leu and Ile-Asp-Ala eliminated virus binding to alpha4 integrins and infectivity. In contrast, rotavirus recognition of alpha4 integrins was unaffected by a peptide containing the sequence Leu-Asp-Val or by a mutation in the VP7 Leu-Asp-Val sequence. VP4 involvement in rotavirus recognition of alpha4beta1 was demonstrated with rotavirus reassortants. Swapping and point mutagenesis of alpha4 surface loops showed that rotaviruses required the same alpha4 residues and domains for binding as the natural alpha4 integrin ligands: mucosal addressin cell adhesion molecule-1, fibronectin and vascular cell adhesion molecule-1. Several rotaviruses are able to use alpha4beta7 and alpha4beta1 for cell binding or entry, through the recognition of the same alpha4-subunit domains as natural alpha4 ligands.

Interactions of rotavirus VP4 spike protein with the endosomal protein Rab5 and the prenylated Rab acceptor PRA1

Rotavirus spike protein VP4 is implicated in several important functions, such as cell attachment, penetration, hemagglutination, neutralization, virulence, and host range. It is present at the plasma membrane and colocalizes with the cytoskeleton in infected cells. We looked for cellular partners responsible for the localization of VP4 by two-hybrid screening of a monkey CV1 cell cDNA library. In the screen we isolated repeatedly three cDNAs encoding either two isoforms (a and c) of Rab5 protein or the prenylated Rab acceptor (PRA1). The small GTPase Rab5 is a molecule regulating the vesicular traffic and the motility of early endosomes along microtubules. Rab5 interacts with a large number of effectors, in particular with PRA1. Interactions of VP4 with both partners, Rab5 and PRA1, were confirmed by coimmunoprecipitation from infected- or transfected-cell lysates. Interaction of Rab5 and PRA1 was restricted to free VP4, since neither triple-layered particles nor NSP4-VP4-VP7 heterotrimeric complexes could be coprecipitated. Site-directed and deletion mutants of VP4 were used to map a VP4 domain(s) interacting with Rab5 or PRA1. Of the 10 mutants tested, 2 interacted exclusively with a single partner. In contrast, the domain extending from amino acids 560 to 722 of VP4 is essential for both interactions. These results suggest that Rab5 and PRA1 may be involved in the localization and trafficking of VP4 in infected cells.

Molecular biology of rotavirus cell entry

Rotaviruses, the leading cause of severe dehydrating diarrhea in infants and young children worldwide, are non-enveloped viruses formed by three concentric layers of protein that enclose a genome of double-stranded RNA. The entry of rotaviruses into epithelial cells appears to be a multistep process during which at least three contacts between the virus and cell receptors occur. Different rotavirus strains display different requirements to infect cells. Some strains depend on the presence of sialic acid on the cell surface; however, interaction with a sialic acid-containing receptor does not seem to be essential, because variants that no longer need sialic acid to infect the cells can be isolated from sialic acid-dependent strains. Comparative characterization of the sialic acid-dependent rotavirus strain RRV, its neuraminidase-resistant variant nar3, and the human rotavirus strain Wa have allowed to show that alpha2beta1 integrin is used by nar3 as its primary cell attachment site, and by RRV in a second interaction subsequent to its initial contact with a sialic acid-containing cell receptor. These first two interactions are mediated by the virus spike protein VP4. After attaching to the cell, all three strains interact with integrin alphaVbeta3 and protein hsc70, interactions perhaps important for the virus to penetrate into the cell's interior. The cell molecules proposed to serve as rotavirus receptors have been found associated with cholesterol and glycosphingolipid-enriched lipid microdomains, and disorganization of these domains greatly inhibits rotavirus infectivity. We propose that the functional rotavirus receptor is a complex of several cell molecules most likely immersed in plasma membrane lipid microdomains.

Localization of membrane permeabilization and receptor binding sites on the VP4 hemagglutinin of rotavirus: implications for cell entry

The surface of rotavirus is decorated with 60 spike-like projections, each composed of a dimer of VP4, the viral hemagglutinin. Trypsin cleavage of VP4 generates two fragments, VP8*, which binds sialic acid (SA), and VP5*, containing an integrin binding motif and a hydrophobic region that permeabilizes membranes and is homologous to fusion domains. Although the mechanism for cell entry by this non-enveloped virus is unclear, it is known that trypsin cleavage enhances viral infectivity and facilitates viral entry. We used electron cryo-microscopy and difference map analysis to localize the binding sites for two neutralizing monoclonal antibodies, 7A12 and 2G4, which are directed against the SA-binding site within VP8* and the membrane permeabilization domain within VP5*, respectively. Fab 7A12 binds at the tips of the dimeric heads of VP4, and 2G4 binds in the cleft between the two heads of the spike. When these binding results are combined with secondary structure analysis, we predict that the VP4 heads are composed primarily of beta-sheets in VP8* and that VP5* forms the body and base primarily in beta-structure and alpha-helical conformations, respectively. Based on these results and those of others, a model is proposed for cell entry in which VP8* and VP5* mediate receptor binding and membrane permeabilization, and uncoating occurs during transfer across the lipid bilayer, thereby generating the transcriptionally active particle.

Avian-to-mammal transmission of an avian rotavirus: analysis of its pathogenicity in a heterologous mouse model

It has been suggested that group A avian rotaviruses can be transmitted to mammals, but there is no direct evidence that such viruses induce disease in mammals. Suckling mice were orally inoculated with two avian rotaviruses. A pigeon rotavirus, PO-13, was found to induce diarrhea, but a turkey rotavirus, Ty-3, did not. The diarrhea induced by PO-13 was dependent on the age of the mouse. In histopathological examinations, antigens of PO-13 were sporadically detected in absorptive cells in the ileum, and lesions were observed as ballooning degenerations of absorptive cells in a region from the duodenum to the ileum. However, the rotavirus antigen was not detected in the majority of these degenerative cells. These results indicated that PO-13 could infect and induce diarrhea in suckling mice. This is the first evidence of an avian rotavirus being experimentally transmissible to a mammal.

Proteolysis of monomeric recombinant rotavirus VP4 yields an oligomeric VP5* core

Rotavirus particles are activated for cell entry by trypsin cleavage of the outer capsid spike protein, VP4, into a hemagglutinin, VP8*, and a membrane penetration protein, VP5*. We have purified rhesus rotavirus VP4, expressed in baculovirus-infected insect cells. Purified VP4 is a soluble, elongated monomer, as determined by analytical ultracentrifugation. Trypsin cleaves purified VP4 at a number of sites that are protected on the virion and yields a heterogeneous group of protease-resistant cores of VP5*. The most abundant tryptic VP5* core is trimmed past the N terminus associated with activation for virus entry into cells. Sequential digestion of purified VP4 with chymotrypsin and trypsin generates homogeneous VP8* and VP5* cores (VP8CT and VP5CT, respectively), which have the authentic trypsin cleavages in the activation region. VP8CT is a soluble monomer composed primarily of beta-sheets. VP5CT forms sodium dodecyl sulfate-resistant dimers. These results suggest that trypsinization of rotavirus particles triggers a rearrangement in the VP5* region of VP4 to yield the dimeric spikes observed in icosahedral image reconstructions from electron cryomicroscopy of trypsinized rotavirus virions. The solubility of VP5CT and of trypsinized rotavirus particles suggests that the trypsin-triggered conformational change primes VP4 for a subsequent rearrangement that accomplishes membrane penetration. The domains of VP4 defined by protease analysis contain all mapped neutralizing epitopes, sialic acid binding residues, the heptad repeat region, and the membrane permeabilization region. This biochemical analysis of VP4 provides sequence-specific structural information that complements electron cryomicroscopy data and defines targets and strategies for atomic-resolution structural studies.

Rotavirus capsid protein VP5* permeabilizes membranes

Proteolytic cleavage of the VP4 outer capsid spike protein into VP8* and VP5* proteins is required for rotavirus infectivity and for rotavirus-induced membrane permeability. In this study we addressed the function of the VP5* cleavage fragment in permeabilizing membranes. Expressed VP5* and truncated VP5* proteins were purified by nickel affinity chromatography and assayed for their ability to permeabilize large unilamellar vesicles (LUVs) preloaded with carboxyfluorescein (CF). VP5* and VP5* truncations, but not VP4 or VP8*, permeabilized LUVs as measured by fluorescence dequenching of released CF. Similar to virus-induced CF release, VP5*-induced CF release was concentration and temperature dependent, with a pH optimum of 7.35 at 37 degrees C, but independent of the presence of divalent cations or cholesterol. VP5*-induced permeability was completely inhibited by VP5*-specific neutralizing monoclonal antibodies (2G4, M2, or M7) which recognize conformational epitopes on VP5* but was not inhibited by VP8*-specific neutralizing antibodies. In addition, N-terminal and C-terminal VP5* truncations including residues 265 to 474 are capable of permeabilizing LUVs. These findings demonstrate that VP5* permeabilizes membranes in the absence of other rotavirus proteins and that membrane-permeabilizing VP5* truncations contain the putative fusion region within predicted virion surface domains. The ability of recombinant expressed VP5* to permeabilize membranes should permit us to functionally define requirements for VP5*-membrane interactions. These findings indicate that VP5* is a specific membrane-permeabilizing capsid protein which is likely to play a role in the cellular entry of rotaviruses.

Viral factors determining rotavirus pathogenicity

The pathogenicity of rotaviruses depends on multiple viral and host factors. Evidence is presented for the involvement of a number of viral genes (coding for structural and non-structural proteins) in the ability of the virus to cause diarrhoea. Different genes are important in different rotavirus--host systems suggesting that there is no single viral pathogenicity factor.

Functional and structural analysis of the sialic acid-binding domain of rotaviruses

The infectivity of most animal rotaviruses is dependent on the interaction of the virus spike protein VP4 with a sialic acid (SA)-containing cell receptor, and the SA-binding domain of this protein has been mapped between amino acids 93 and 208 of its trypsin cleavage fragment VP8. To identify which residues in this region are essential for the SA-binding activity, we performed alanine mutagenesis of the rotavirus RRV VP8 expressed in bacteria as a fusion polypeptide with glutathione S-transferase. Tyrosines were primarily targeted since tyrosine has been involved in the interaction of other viral hemagglutinins with SA. Of the 15 substitutions carried out, 10 abolished the SA-dependent hemagglutination activity of the protein, as well as its ability to bind to glycophorin A in a solid-phase assay. However, only alanine substitutions for tyrosines 155 and 188 and for serine 190 did not affect the overall conformation of the protein, as judged by their interaction with a panel of conformationally sensitive neutralizing VP8 monoclonal antibodies (MAbs). These findings suggest that these three amino acids play an essential role in the SA-binding activity of the protein, presumably by interacting directly with the SA molecule. The predicted secondary structure of VP8 suggests that it is organized as 11 beta-strands separated by loops; in this model, Tyr-155 maps to loop 7 while Tyr-188 and Ser-190 map to loop 9. The close proximity of these two loops is also supported by previous results from competition experiments with neutralizing MAbs directed at RRV VP8.

A hypothesis about the mechanism of assembly of double-shelled rotavirus particles

During double-shelled (ds) particle assembly, subviral particles [possibly single-shelled (ss) particles] acquire the outer capsid protein during their transport across the endoplasmic reticulum (ER) membrane by an exocytosis-like process, probably by a fusion-like mechanism. Fine reticular material is observed around the junction area between virus particles and the ER membrane on the cytoplasmic side of projecting ss particles, suggesting this is the site of assembly of ds particles. It is assumed that the reticular material may correspond to the hetero-oligometric complexes consisting of the non-structural glycoprotein NSP4, the structural proteins VP4 and VP7, and that both VP7 and VP4 may fold onto ss particles as a complex. On the other hand, the budding process simply serves as a vehicle to transport ss particles from the cytoplasm to the ER lumen. Thus, it is assumed that the production of protein complexes may be indispensable for virion assembly, in which NSP4 regulates VP4 folding as an ER chaperone and also the exocytosis-like or fusion-like transport systems through the ER membrane.

Rotavirus-induced fusion from without in tissue culture cells

We present the first evidence of fusion from without induced in tissue culture cells by a nonenveloped virus. Electron micrographs of two strains of rotavirus, bovine rotavirus C486 and rhesus rotavirus, show that virally mediated cell-cell fusion occurs within 1 h postinfection. Trypsin activation is necessary for rotavirus to mediate cell-cell fusion. The extent of fusion is relative to the amount of virus used, and maximum fusion occurs between pHs 6.5 and 7.5. Fusion does not require virus-induced protein synthesis, as virus from both an empty capsid preparation and from an EDTA-treated preparation, which is noninfectious, can induce fusion. Incubation of rotavirus with neutralizing and nonneutralizing monoclonal antibodies before addition to cells indicates that viral protein 4 (VP4; in the form of VP5* and VP8*) and VP7 are involved in fusion. Light and electron micrographs document this fusion, including the formation of pores or channels between adjacent fused cells. These data support direct membrane penetration as a possible route of infection. Moreover, the assay should be useful in determining the mechanisms of cell entry by rotavirus.

Mapping the hemagglutination domain of rotaviruses

Most strains of animal rotaviruses are able to agglutinate erythrocytes, and the surface protein VP4 is the virus hemagglutinin. To map the hemagglutination domain on VP4 while preserving the conformation of the protein, we constructed full-length chimeras between the VP4 genes of hemagglutinating (YM) and nonhemagglutinating (KU) rotavirus strains. The parental and chimeric genes were expressed in insect cells, and the recombinant VP4 proteins were evaluated for their capacity to agglutinate human type O erythrocytes. Three chimeric genes, encoding amino acids 1 to 208 (QKU), 93 to 208 (QC), and 93 to 776 (QYM) of the YM VP4 protein in a KU VP4 background, were constructed. YM VP4 and chimeras QKU and QC were shown to specifically hemagglutinate, indicating that the region between amino acids 93 and 208 of YM VP4 is sufficient to determine the hemagglutination activity of the protein.

Localization of rotavirus VP4 neutralization epitopes involved in antibody-induced conformational changes of virus structure

We previously characterized three neutralization-positive epitopes (NP1 [1a and 1b], NP2, and NP3) and three neutralization-negative epitopes on the simian rotavirus SA11 VP4 with 13 monoclonal antibodies (MAbs). Conformational changes occurred as a result of the binding of NP1 MAbs to the SA11 spike VP4, and enhanced binding of all neutralization-negative MAbs was observed when NP1 MAbs bound VP4 in a competitive MAb capture enzyme-linked immunosorbent assay. To further understand the structure and function of VP4, we have continued studies with these MAbs. Electron microscopic and sucrose gradient analyses of SA11-MAb complexes showed that triple-layered viral particles disassembled following treatment with NP1b MAbs 10G6 and 7G6 but not following treatment with NP1a MAb 9F6, NP2 MAb 2G4, and NP3 MAb 23. Virus infectivity was reduced approximately 3 to 5 logs by the NP1b MAbs. These results suggest that NP1b MAb neutralization occurs by a novel mechanism. We selected four neutralization escape mutants of SA11 with these VP4 MAbs and characterized them by using plaque reduction neutralization assays, hemagglutination inhibition assays, and an antigen capture enzyme-linked immunosorbent assay. These analyses support the previous assignment of the NP1a, NP1b, NP2, and NP3 MAbs into separate epitopes and confirmed that the viruses were truly neutralization escape mutants. Nucleotide sequence analyses found 1 amino acid (aa) substitution in VP8* of VP4 at (i) aa 136 for NP1a MAb mutant 9F6R, (ii) aa 180 and 183 for NP1b MAb mutants 7G6R and 10G6R, respectively, and (iii) aa 194 for NP3 MAb mutant 23R. The NP1b MAb mutants showed an unexpected enhanced binding with heterologous nonneutralization MAb to VP7 compared with parental SA11 and the other mutants. Taken together, these results suggest that the NP1b epitope is a critical site for VP4 and VP7 interactions and for virus stability.

Serotypic differentiation of rotaviruses in field samples from diarrheic pigs by using nucleic acid probes specific for porcine VP4 and human and porcine VP7 genes

Of 216 fecal and intestinal samples collected from nursing or weaned diarrheic pigs in the United States and Canada, 57 were identified as group A rotavirus positive by RNA electrophoresis and silver staining. Fifty-seven and 52 rotavirus-positive samples were analyzed by hybridization with Gottfried and OSU PCR-derived gene 9 and 4 probes, respectively. Only 17 samples were identified with either homologous VP4 (P)- or VP7 (G)-coding genes or both. One rotavirus identified as G4 and P7 was similar to the previously characterized interserotype rotavirus, SB-1A. Additional hybridization analyses were performed with PCR-derived probes prepared from gene 9 cDNA of the human rotaviruses Wa (G1), DS-1 (G2), and P (G3) and of the porcine rotavirus YM (G11). Eleven of 52 samples collected and analyzed from swine in Ohio, California, and Nebraska were identified as G11. No samples with G1-, G2-, or G3-type specificities were detected among the 25 of 57 rotavirus-positive samples analyzed with human rotavirus-derived probes. Further investigations with a PCR-derived gene 4 probe prepared from porcine rotavirus YM revealed hybridization specificities similar to those of the OSU gene 4 probe.

Binding to sialic acids is not an essential step for the entry of animal rotaviruses to epithelial cells in culture

The infection of target cells by animal rotaviruses requires the presence of sialic acids on the cell surface. Treatment of the cells with neuraminidases or incubation of the viruses with some sialoglycoproteins, such as glycophorin A, greatly reduces virus binding, with the consequent reduction of viral infectivity. In this work, we report the isolation of animal rotavirus variants whose infectivity is no longer dependent on the presence of sialic acids on the cell surface. In addition, although these variants bind to glycophorin A as efficiently as the wild-type virus, this interaction no longer inhibit viral infectivity. These observations indicate that the initial interaction of the mutants with the cell occurs at a site different from the sialic acid-binding site located on VP8, the smaller trypsin cleavage product of VP4. Reassortant analysis showed that the mutant phenotype segregates with the VP4 gene. Neutralizing monoclonal antibodies directed to VP4 and VP7 were tested for their ability to neutralize the variants. Antibodies to VP7 and VP5, the larger trypsin cleavage product of VP4, neutralized the mutants as efficiently as the wild-type virus. In contrast, although antibodies to VP8 were able to bind to the mutants, they showed little or no neutralizing activity. The implications of these findings in rotavirus attachment to and penetration of epithelial cells in culture are discussed.

Location of intrachain disulfide bonds in the VP5* and VP8* trypsin cleavage fragments of the rhesus rotavirus spike protein VP4

Because the rotavirus spike protein VP4 contains conserved Cys residues at positions 216, 318, 380, and 774 and, for many animal rotaviruses, also at position 203, we sought to determine whether disulfide bonds were structural elements of VP4. Electrophoretic analysis of untreated and trypsin-treated rhesus rotavirus (RRV) and simain rotavirus SA11 in the presence and absence of the reducing agent dithioerythritol revealed that VP4 and its cleavage fragments VP5* and VP8* possessed intrachain disulfide bonds. Given that the VP8* fragments of RRV and SA11 contain only two Cys residues, those at positions 203 and 216, these data indicated that these two residues were covalently linked. Electrophoretic examination of truncated species of VP4 and VP4 containing Cys-->Ser mutations synthesized in reticulocyte lysates provided additional evidence that Cys-203 and Cys-216 in VP8* of RRV were linked by a disulfide bridge. VP5* expressed in vitro was able to form a disulfide bond analogous to that in the VP5* fragment of trypsin-treated RRV. Analysis of a Cys-774-->Ser mutant of VP5* showed that, while it was able to form a disulfide bond, a Cys-318-->Ser mutant of VP5* was not. These results indicated that the VP4 component of all rotaviruses, except B223, contains a disulfide bond that links Cys-318 and Cys-380 in the VP5* region of the protein. This bond is located between the trypsin cleavage site and the putative fusion domain of VP4. Because human rotaviruses lack Cys-203 and, hence, unlike many animal rotaviruses cannot possess a disulfide bond in VP8*, it is apparent that VP4 is structurally variable in nature, with human rotaviruses generally containing one disulfide linkage and animal rotaviruses generally containing two such linkages. Considered with the results of anti-VP4 antibody mapping studies, the data suggest that the disulfide bond in VP5* exists within the 2G4 epitope and may be located at the distal end of the VP4 spike on rotavirus particles.

Reactivity of anti-human rotavirus VP4 neutralizing monoclonal antibodies with animal rotaviruses and with unusual human rotaviruses having different P and G serotypes

The reactivity of five anti-human rotavirus VP4 neutralizing monoclonal antibodies (N-mAb) with 20 animal rotavirus strains and three unusual human rotavirus (HRV) strains was investigated. Five N-mAb prepared previously by the immunization of mice with HRV were employed in this study. They were found to neutralize HRV belonging to P types 4, 6 and 8, which were designated according to P (or VP4) type nomenclature proposed by Estes and Cohen (1989). A porcine rotavirus strain Gottfried was reactive with four of the five mAb both in neutralization tests and in ELISA. However, no other animal rotaviruses were neutralized by any of the mAb. Fourteen animal strains were reactive with only one or two mAb in ELISA, and five animal strains were inactive with all. These results indicate that neutralization epitopes on VP4 are serologically considerably different between HRV (except for unusual Indonesian strains 57M and 69M) and animal rotaviruses (except for porcine rotavirus strain Gottfried).

Amino acid sequence analysis of bovine rotavirus B223 reveals a unique outer capsid protein VP4 and confirms a third bovine VP4 type

The nucleotide and deduced amino acid sequence of the gene 4 of bovine rotavirus strain B223 is described. The open reading frame is predicted to encode a VP4 of 772 amino acids, shorter than described for any other rotavirus strain sequenced to date. B223 VP4 shows 70 to 73% similarity to other rotavirus VP4 proteins, demonstrating the presence of a unique VP4 type, and confirming a third VP4 allele in the bovine rotavirus population. Multiple sequence alignment with several other rotavirus strains created gaps in the sequence to account for a shorter VP4. The alignment shows a two contiguous amino acid deletions within the trypsin cleavage region of B223 VP4. Comparisons of two regions flanking the trypsin cleavage site, (aa 224 to 235, and aa 257 to 271) which show high homologies between strains, demonstrate that the region 5' to the trypsin cut site has a low homology (66%) to other rotavirus strains, although the region 3' to the trypsin cleavage site shows high homologies (86 to 93%) with other rotavirus strains. The lack of a conserved proline residue within the 5' flanking region suggests a possible altered local conformation of this site in B223 VP4. A second gap inserted into the VP4 of B223 on multiple sequence alignment is a three contiguous amino acid deletion at position 613-615 in the VP5* subunit. Previously defined biologic properties of this strain in relation to the determination of the amino acid composition of VP4 are discussed.

Characterization of full-length and polymerase chain reaction-derived partial-length Gottfried and OSU gene 4 probes for serotypic differentiation of porcine rotaviruses

To determine the VP4 (P type) specificity of porcine rotaviruses, full- and partial-length gene 4 probes were produced from cloned Gottfried and OSU porcine rotavirus genomic segment 4 cDNAs. The gene 4 segments from the prototype Gottfried (VP7 serotype 4) and OSU (VP7 serotype 5) porcine rotavirus strains were selected for study because of their distinct P types and the occurrence of rotaviruses with similar serotypes among swine. Partial-length gene 4 cDNAs were produced and amplified by the polymerase chain reaction (PCR) and encompassed portions of the variable region (nucleotides 211 to 612) of VP8 encoded by genomic segment 4. The hybridization stringency conditions necessary for optimal probe specificity and sensitivity were determined by dot or Northern (RNA) blot hybridizations against a diverse group of human and animal rotaviruses of heterologous group A serotypes and against representative group B and C porcine rotaviruses. The PCR-derived gene 4 probes were more specific than the full-length gene 4 probes but demonstrated equivalent sensitivity. The Gottfried PCR-derived probe hybridized with Gottfried, SB2, SB3, and SB5 G serotype 4 porcine rotaviruses. The OSU PCR-derived probe hybridized with OSU, EE, A580, and SB-1A porcine rotaviruses and equine H1 rotavirus. Results of the hybridization reactions of the PCR-derived gene 4 probes with selected porcine rotavirus strains agreed with previous serological or genetic analyses, indicating their suitability as diagnostic reagents.

A liquid-hybridization method for typing the Vp4 and Vp7 genes of bovine rotaviruses

A simple liquid-hybridization assay was developed which allows assessment of the degree of hybridization between the two serotype-determining genes of the bovine rotavirus strain UK and the homologous genes of the isolate under test. 32P-labelled transcription probes were produced from cloned complementary DNA (cDNA) copies of UK gene segments 4 and 8 and hybridized to double stranded RNA (dsRNA) extracted from rotavirus-positive field samples. Subsequent treatment with ribonuclease A (RNase A), separation of the RNase A-resistant hybrid fragments by polyacrylamide gel electrophoresis (PAGE) and autoradiography yielded a specific, reproducible banding pattern for each isolate. A total of 74 field samples was tested by both the hybridization assay and by an enzyme-linked immunosorbent assay (ELISA) using serotype-specific monoclonal antibodies (Mabs). The results obtained were in excellent agreement and confirmed that serotype G6 rotaviruses predominated. Hybridization of these G6 viruses with the gene 4 probe suggested that viruses with Vp4s related to that of UK rotavirus are also common. The hybridization assay was more sensitive than the ELISA.

Sequences of the four larger proteins of a porcine group C rotavirus and comparison with the equivalent group A rotavirus proteins

The sequences of the four larger proteins of rotavirus group C (Cowden strain) are presented and compared with the sequences of the corresponding group A proteins. They exhibit a significant level of homology, allowing gene coding assignment for the group C rotavirus. The coding strategy of the group C virus RNA segment is the same as that for the group A large segments as one long open reading frame is present in each segment. The genome segment 1 encodes the structural protein VP1 which presents the RNA-dependent RNA polymerase consensus motifs. The VP1 protein is the most highly conserved between the rotaviruses of groups A and C. The genome segment 2 encodes the VP2 protein. The deduced protein sequence does not present the putative leucine zippers identified in the group A protein but its amino terminal is hydrophilic and highly charged as previously noted for the group A protein. The genome segment 3 encodes for a protein homologous to the group A outer capsid protein VP4. As observed among the various group A sequences, the amino terminal is the region presenting the fewest similarities. A cleavage region and a putative fusion motif similar to those present in the group A viruses have been identified. For this protein the comparison has been extended to the IDIRV [corrected] VP3 previously sequenced and indicates that groups A and C VP4 proteins are much more related to each other than to the group B equivalent. The genome segment 4 encodes for a protein showing an approximate 40% sequence identity to the minor core protein, VP3, of the group A rotavirus. This remarkable conservation of primary structures argues for severe functional constraint on the evolution of these proteins.