Development of specific nucleic acid probes for the differentiation of porcine rotavirus serotypes

Genetic and antigenic characterization of a serotype G6 human rotavirus isolated in Melbourne, Australia

An unusual rotavirus strain, MG6, was isolated from a 16-month-old child admitted to hospital with acute gastroenteritis. The virus could not be serotyped (G-typed) by enzyme immunoassay using standard reagents specific for common serotypes of human Group A rotaviruses. Nucleotide sequencing of cDNA derived from the gene encoding the outer capsid protein, VP7, and deduction of the VP7 amino acid sequence indicated that this strain belonged to serotype G6, a serotype normally associated with viruses causing disease in cattle. This was confirmed by polymerase chain reaction typing and enzyme immunoassay using a G6-specific monoclonal antibody. The VP4 genotype of MG6 was determined by hybridization of its VP4 cDNA to genomic RNA isolated from standard strains of defined P-types. This analysis, confirmed by deduced amino acid sequence analysis, classified MG6 into the novel genotype P13. MG6, therefore, is related to the previously described G6P13 human strain PA169, isolated in Italy. The emergence of strain MG6, the first human G6 rotavirus identified in Australia, provides further evidence of reassortment between human and animal rotaviruses.

Prevalence of P types among porcine rotaviruses using subgenomic VP4 gene probes

Nucleic acid probes were developed to differentiate VP4 (P) types among porcine rotaviruses. These probes were then used to determine the relative prevalence of P types 6 (Gottfried-like) and 7 (OSU-like) in cultivated rotaviruses and field specimens. The variable regions between bases 205-551 of the VP4 gene of rotavirus strains OSU and Gottfried were amplified by the polymerase chain reaction and radiolabeled with 32P by random primer extension. Radiolabeled probes were tested in a dot blot hybridization assay. The subgenomic probes prepared from VP4 gene detected as little as 5 ng oF rotavirus RNA and were specific for differentiating the two porcine rotavirus P types. The probes were used to determine the P type of several reference rotavirus strains and recently cultivated porcine rotavirus strains. Eight of the 10 cultivated, previously untyped, rotaviruses isolates tested were of P type 7 (OSU-like). Two rotavirus strains neither reacted with OSU nor with the Gottfried probe, therefore, their P type could not be determined. Seventeen out of the 26 rotavirus (65.4%) field samples tested had a P type 6 (Gottfried-like) whereas 5 out of 26 (19.2%) had a P type 7 (OSU-like). Four of the 26 samples (15.4%) reacted neither with the OSU nor with the Gottfried probe and possibly represent previously unrecognized P types in swine. Data in this study suggests that (1) rotaviruses with P type 7 are most common among the cultivated rotaviruses, (2) rotaviruses with P type 6 are the most abundant type of rotavirus in natural infections and (3) rotaviruses with additional P types are also associated with diarrheic swine.

Immunogens of rotaviruses

Rotaviruses cause gastroenteritis in neonates of many animal species including cattle, swine, horses, dogs, cats, chickens and turkeys. Rotavirions are nonenveloped, are about 75 nm in diameter, have a double capsid, and contain 11 double-stranded RNA segments as their genome. Several antigenically distinct groups of rotaviruses have been identified and have been alphabetically designated as A through G. Group A rotaviruses were the first group of rotaviruses isolated and are the most commonly detected rotaviruses in diarrheic animals. Group A rotaviruses have two surface proteins, VP4 and VP7, both of which are important in serotype determination and in inducing neutralizing antibodies and protective immunity. Multiple serotypes of group A rotavirus based on glycoprotein VP7 (designated as G types) and based on VP4 (P types) have been identified. The immune response to rotaviruses is essentially serotype specific, however, cross-reactive or heterotypic epitopes have also been identified. Currently acceptable methods for immunogen quantitation include the induction of neutralizing antibody in host or laboratory animals. The in vivo efficacy of vaccines against rotavirus-associated gastroenteritis remains the standard method against which in vitro methods must be compared. Several animal models have been developed which could potentially be used in evaluating the efficacy of candidate vaccines. Monoclonal antibodies to rotavirus immunogens are also currently available and serve as valuable reagents for in vitro quantitation of rotaviral immunogens.

Development of cDNA probes for typing group A bovine rotaviruses on the basis of VP4 specificity

Dot and Northern (RNA) blot hybridization assays were developed for the P typing of group A bovine rotaviruses (BRV) by using cDNA probes prepared from gene segment 4. The probes were prepared by polymerase chain reaction amplification of hyperdivergent regions (nucleotides 211 to 686) of BRV strain UK, IND, NCDV, and Cr VP4 cDNA by using specific oligonucleotide primers. The probes were P type specific (VP4) and exhibited little or no cross-reactivity with double-stranded RNA from heterologous rotavirus P types. Our studies indicate that at least three P types, as defined by polymerase chain reaction-derived VP4 gene probes from the UK, NCDV, and Cr strains, exist among the seven BRV isolates tested.

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.

Detection and differentiation of bovine group A rotavirus serotypes using polymerase chain reaction-generated probes to the VP7 gene

Dot and Northern blot hybridization assays were developed to detect and differentiate group A bovine rotavirus serotypes using radiolabeled serotype 6 (Nebraska calf diarrhea virus [NCDV] and United Kingdom [UK] strains) or serotype 10 (Crocker [Cr] strain) VP7 gene probes. Partial length VP7-specific cDNA encompassing areas of major sequence diversity were generated by the polymerase chain reaction (PCR) using either cloned VP7 genes (NCDV and UK strains) or reverse transcribed mRNA (Cr strain) as templates. Radiolabeled probes prepared from the PCR-generated cDNA were tested at various stringency conditions to optimize the hybridization assays. At high stringency conditions (52 C, 50% formamide, 5 x standard saline citrate), the NCDV, UK, and Cr probes serotypically differentiated bovine rotavirus isolates in RNA samples prepared from cell culture propagated viruses or in fecal specimens from infected gnotobiotic calves. The sensitivity and specificity of NCDV and Cr VP7 probes were characterized in dot blot hybridization assays, and the probes were estimated to detect at least 1 ng of viral RNA. The serotyping results obtained using VP7 probes were similar to those obtained using serologic assays. Further development of these assays may provide a useful means for the rapid detection and differentiation of bovine rotavirus serotypes in fecal samples from calves in the field.

Applications of nucleic acid probes in veterinary infectious diseases

Nucleic acid probe technology is increasingly being used in basic research in veterinary microbiology and in diagnosis of infectious diseases of veterinary importance. This review presents an overview of nucleic acid probe methodology and its applications in veterinary infectious diseases. The major applications of nucleic acid probes include detection of pathogens in clinical samples, especially those organisms which are fastidious and difficult to cultivate, differentiation of virulent from avirulent organisms and vaccine strains from wild type isolates, typing of microorganisms, mapping genes, screening libraries of cloned DNA for specific genes, detection of latently infected or carrier animals, study of mechanisms of pathogenesis, epidemiological studies and food safety.