Comparison of the genomes of simian, bovine, and human rotaviruses by gel electrophoresis and detection of genomic variation among bovine isolates

A method for the unbiased quantification of reassortment in segmented viruses

Reassortment of segmented viruses can be an important source of genetic diversity underlying viral evolution and emergence. Methods for the quantification of reassortment have been described but are often cumbersome and best suited for the analysis of reassortment between highly divergent parental strains. While it is useful to understand the potential of divergent parents to reassort, outcomes of such heterologous reassortment are driven by differential selection acting on the progeny and are typically strain specific. To quantify reassortment robustly, a system free of differential selection is needed. We have generated such a system for influenza A virus and for mammalian orthoreovirus by constructing well-matched parental viruses carrying small genetic tags. The method utilizes high-resolution melt technology for the identification of reassortant viruses. Ease of sample preparation and data analysis enables streamlined genotyping of a large number of virus clones. The method described here thereby allows quantification of the efficiency of reassortment and can be applied to diverse segmented viruses.

Detection of bovine group a rotavirus using rapid antigen detection kits, rt-PCR and next-generation DNA sequencing

We investigated the sensitivity of human rotavirus rapid antigen detection (RAD) kits, RT-PCR and next-generation DNA sequencing (NGS) for detection of bovine group A rotavirus (RVA). The Dipstick 'Eiken' Rota (Dipstick) showed the highest sensitivity out of the seven RAD kits against all selected strains in limited dilution analyses, which was consistent with the results for equine rotavirus previously reported. RT-PCR had 10⁰-10³-fold higher sensitivity than the Dipstick. NGS using thirteen RT-PCR-negative fecal samples revealed that all samples yielded RVA reads and especially that two of them covered all 11 genome segments. Moreover, mapping reads to reference sequences allowed genotyping. The NGS would be sensitive and useful for analysis of less dependent on specific primers and screening of genotypes.

Geographic differences in sexual reassortment in RNA phage

The genetic structure of natural bacteriophage populations is poorly understood. Recent metagenomic studies suggest that phage biogeography is characterized by frequent migration. Using virus samples mostly isolated in Southern California, we recently showed that very little population structure exists in segmented RNA phage of the Cystoviridae family due to frequent segment reassortment (sexual genetic mixis) between unrelated virus individuals. Here we use a larger genetic dataset to examine the structure of Cystoviridae phage isolated from three geographic locations in Southern New England. We document extensive natural variation in the physical sizes of RNA genome segments for these viruses. In addition, consistent with earlier findings, our phylogenetic analyses and calculations of linkage disequilibrium (LD) show no evidence of within-segment recombination in wild populations. However, in contrast to the prior study, our analysis finds that reassortment of segments between individual phage plays a lesser role among cystoviruses sampled in New England, suggesting that the evolutionary importance of genetic mixis in Cystoviridae phage may vary according to geography. We discuss possible explanations for these conflicting results across the studies, such as differing local ecology and its impact on phage growth, and geographic differences in selection against hybrid phage genotypes.

Genetic Analysis of Orbiviruses by Using RNase T(1) Oligonucleotide Fingerprints

Corresponding double-stranded RNA segments of the related orbiviruses Wallal and Mudjinbarry produced distinctly different RNase T(1) fingerprint patterns. No extensive sequence reiteration was observed between segments of Mudjinbarry virus. Fingerprint analysis of the genome of recombinant orbiviruses confirmed segment reassortment as a mechanism of interchange of genetic information. When temperature-sensitive mutants of each virus were crossed in mixed infection, a consistent pattern of segment reassortment was correlated with generation of the wild-type phenotype. Thus, the temperature-sensitive lesion of group II Wallal serogroup mutants was mapped to segment 1. The group I mutant lesion appears to be located in segment 2.

Concentration of acrylamide in a polyacrylamide gel affects VP4 gene coding assignment of group A equine rotavirus strains with P[12] specificity

BACKGROUND

It is universally acknowledged that genome segment 4 of group A rotavirus, the major etiologic agent of severe diarrhea in infants and neonatal farm animals, encodes outer capsid neutralization and protective antigen VP4.

RESULTS

To determine which genome segment of three group A equine rotavirus strains (H-2, FI-14 and FI-23) with P[12] specificity encodes the VP4, we analyzed dsRNAs of strains H-2, FI-14 and FI-23 as well as their reassortants by polyacrylamide gel electrophoresis (PAGE) at varying concentrations of acrylamide. The relative position of the VP4 gene of the three equine P[12] strains varied (either genome segment 3 or 4) depending upon the concentration of acrylamide. The VP4 gene bearing P[3], P[4], P[6], P[7], P[8] or P[18] specificity did not exhibit this phenomenon when the PAGE running conditions were varied.

CONCLUSIONS

The concentration of acrylamide in a PAGE gel affected VP4 gene coding assignment of equine rotavirus strains bearing P[12] specificity.

Circulating human group A rotavirus genotypes in Malaysia

This study examined the temporal distribution of rotavirus genotypes in Malaysia. Rotaviruses from children with diarrhea admitted to hospitals in 1996 (n = 93) and 2007 (n = 12) in two different regions of Peninsular (West) Malaysia were analyzed for their G and P genotypes using a hemi-nested RT-PCR assay. In the 2007 samples, the dominant strain was G9P[8]. It was identified in 42% of the samples. Different strains all possessing the G1 genotype were identified in the rest of the samples. In contrast, 81% of the samples collected in 1996 were the G1P[8] strain. No strains with G9 genotype were detected in samples collected in 1996.

Isolation of rotaviruses from turkeys and chickens: demonstration of distinct serotypes and RNA electropherotypes

Six isolates of rotavirus were made from turkeys and two from chickens. Three of these required trypsin treatment for isolation and serial passage in cell cultures. The remainder were isolated without trypsin treatment. Most of these viruses were isolated in chick embryo liver cell cultures from the faeces of birds aged under 1 week. In six of the eight instances, rotavirus isolation was associated with enteric disturbance, characterised by signs such as diarrhoea, poor or abnormal appetite, abnormally fluid or gaseous intestinal contents or increased mortality. Cross immunofluorescence tests showed that while avian and mammalian rotaviruses shared a common group antigen, the avian viruses were more closely related to each other than to the Nebraska calf rotavirus isolate. On the basis of serum neutralisation tests seven of the eight avian rotaviruses were grouped into three serotypes, with two turkey isolates (Ty1 and Ty3) and a chicken (Ch1) virus being the prototype strains. The remaining virus, Ty2, was intermediate in type between Ty1 and Ch1. Analysis of the RNA of these viruses by polyacrylamide gel electrophoresis showed that they could also be grouped into a number of electropherotypes. The isolates which were serologically distinct were also electrophoretically distinct. Similarly the five isolates which belonged to the Ty3 sero-type were electrophoretically identical. Analysis of the serological and electrophoretic differences suggested that RNA segment 5 may code for a type-specific antigen.

Experimental infection of chickens with rotaviruses: clinical and virological findings

Specific-pathogen-free chickens were infected orally with two different isolates (Ch 1 and 132) of chicken rotavirus. Chickens aged 1, 14 and 28 days were equally susceptible to infection. Following infection with either virus, the clinical signs were mild. Coincident with the peak of virus excretion and for a period of 1 to 2 days, infected birds passed increased quantities of caecal droppings. At necropsy, the caeca were abnormally distended with gas and fluid. Immunofluorescence showed that for both viruses the principal site of replication was the mature villous epithelial cell of the small intestine. However, Ch 1 rotavirus grew best in the duodenum while 132 virus favoured the jejunum and ileum. Ch 1 rotavirus and 132 virus were detected by direct electron microscopy in the faeces from 2 to 5 days and 1 to 7 days respectively after infection.

Acrylamide concentration affects the relative position of VP7 gene of serotype G2 strains as determined by polyacrylamide gel electrophoresis

BACKGROUND

During the course of development and characterization of various rotavirus reassortants, we found that the relative position of the gene encoding neutralization and protective antigen VP7 of certain rotavirus strains in a PAGE gel was influenced by the concentration of acrylamide.

OBJECTIVES

We investigated systematically various factors that affected the relative position of the rotavirus VP7 gene in a PAGE gel.

STUDY DESIGN

We analyzed dsRNAs of selected rotavirus strains bearing G1, G2, G3 or G9 specificity by PAGE at varying concentrations of acrylamide.

RESULTS

We demonstrated that the relative position of the VP7 gene of three G2 strains varied depending upon the concentration of acrylamide in a PAGE gel, which occurred not only in a homologous G2 virus gene background but also in a heterologous G3 virus gene background; and the VP7 gene bearing G1, G3, G4 or G9 specificity did not display this phenomenon when the PAGE running conditions were varied.

CONCLUSIONS

The concentration of acrylamide in a PAGE gel was the major factor that influenced the relative position of the VP7 gene of G2 rotavirus strains (i.e., VP7 gene coding assignment by PAGE).

Detection of rare G3P[19] porcine rotavirus strains in Chiang Mai, Thailand, provides evidence for origin of the VP4 genes of Mc323 and Mc345 human rotaviruses

Among 175 fecal specimens collected from diarrheic piglets during a surveillance of porcine rotavirus (PoRV) strains in Chiang Mai, Thailand, 39 (22.3%) were positive for group A rotaviruses. Of these, 33.3% (13 of 39) belonged to G3P[19], which was a rare P genotype seldom reported. Interestingly, their VP4 nucleotide sequences were most closely related to human P[19] strains (Mc323 and Mc345) isolated in 1989 from the same geographical area where these PoRV strains were isolated. These P[19] PoRV strains were also closely related to another human P[19] strain (RMC321), isolated from India in 1990. The VP4 sequence identities with human P[19] were 95.4% to 97.4%, while those to a porcine P[19] strain (4F) were only 87.6 to 89.1%. Phylogenetic analysis of the VP4 gene revealed that PoRV P[19] strains clustered with human P[19] strains in a monophyletic branch separated from strain 4F. Analysis of the VP7 gene confirmed that these strains belonged to the G3 genotype and shared 97.7% to 98.3% nucleotide identities with other G3 PoRV strains circulating in the regions. This close genetic relationship was also reflected in the phylogenetic analysis of their VP7 genes. Altogether, the findings provided peculiar evidence that supported the porcine origin of VP4 genes of Mc323 and Mc345 human rotaviruses.

Isolation of a reovirus from a broiler chicken flock with high early mortality

A reovirus was isolated from a flock of 12,000 broiler chickens which experienced a total mortality of 6.3% up to 35 days. The reovirus produced large syncytia in primary chicken kidney cell cultures with eosinophilic intracytoplasmic inclusion body formation. Infected cells reacted with fluorescein conjugated specific anti-reovirus serum. Negatively strained virions had a double shelled appearance with overall diameter of 65 to 70 nm. The nucleic acid had ten discrete segments with electrophoretic mobilities as would be expected for a reovirus.

Porcine rotavirus strain Gottfried-based human rotavirus candidate vaccines: Construction and characterization

Rotavirus gastroenteritis remains the leading cause of severe diarrheal disease in infants and young children worldwide, and thus, a safe and effective rotavirus vaccine is urgently needed in both developing and developed countries. Various candidate rotavirus vaccines that were developed by us and others have been or are being evaluated in different populations in various parts of the world. We have recently confirmed that a porcine rotavirus Gottfried strain bears a P (VP4) serotype (P2B[6]) closely related to human rotavirus P serotype 2A[6] which is of epidemiologic importance in some regions of the world. Based on the modified Jennerian approach to immunization, we have constructed 11 Gottfried-based single VP7 or VP4 gene substitution reassortant vaccine candidates which could provide: (i) an attenuation phenotype of a porcine rotavirus in humans; and (ii) antigenic coverage for G serotypes 1-6 and 8-10 and P serotype 1A[8], 1B[4] and 2A[6]. In addition, following immunization of guinea pigs with Gottfried VP4, we found low but consistent levels of neutralizing antibodies to VP4 with P1A[8] or P1B[4] specificity, both of which are of global epidemiologic importance. Thus, porcine-based VP7 reassortant rotavirus vaccines may provide an advantage over rhesus- or bovine-based VP7 reassortant vaccines since the VP4s of the latter vaccines do not evoke antibodies capable of neutralizing the viruses bearing P1A[8], P1B[4] or P2A[6] VP4.

A porcine G9 rotavirus strain shares neutralization and VP7 phylogenetic sequence lineage 3 characteristics with contemporary human G9 rotavirus strains

Of five globally important VP7 (G) serotypes (G1-4 and 9) of group A rotaviruses (the single most important etiologic agents of infantile diarrhea worldwide), G9 continues to attract considerable attention because of its unique natural history. Serotype G9 rotavirus was isolated from a child with diarrhea first in the United States in 1983 and subsequently in Japan in 1985. Curiously, soon after their detection, G9 rotaviruses were not detected for about a decade in both countries and then reemerged in both countries in the mid-1990s. Unexpectedly, however, such reemerged G9 strains were distinct genetically and molecularly from those isolated in the 1980s. Thus, the origin of the reemerged G9 viruses remains an enigma. Sequence analysis has demonstrated that the G9 rotavirus VP7 gene belongs to one of at least three phylogenetic lineages: lineage 1 (strains isolated in the 1980s in the United States and Japan), lineage 2 (strains first isolated in 1986 and exclusively in India thus far), and lineage 3 (strains that emerged/reemerged in the mid-1990s). Currently, lineage 3 G9 viruses are the most frequently detected G9 strains globally. We characterized a porcine rotavirus (A2 strain) isolated in the United States that was known to belong to the P[7] genotype but had not been serotyped by neutralization. The A2 strain was found to bear serotype G9 and P9 specificities as well as NSP4 [B] and subgroup I characteristics. By VP7-specific neutralization, the porcine G9 strain was more closely related to lineage 3 viruses than to lineage 1 or 2 viruses. Furthermore, by sequence analysis, the A2 VP7 was shown to belong to lineage 3 G9. These findings raise intriguing questions regarding possible explanations for the emergence of variations among the G9 strains.

Emergence of human G9 rotavirus with an exceptionally high frequency in children admitted to hospital with diarrhea in Chiang Mai, Thailand

Among 315 fecal specimens collected from children hospitalized with diarrhea in Chiang Mai, Thailand, in 2000-2001, group A rotavirus was detected in 107 (34.0%). Of these, 98 (91.6%) were G9, 6 (5.6%) were G3 and 3 (2.8%) were G2, respectively. Identification of their P-types demonstrated that 103 (96.3%) were P[8], 3 (2.8%) were P[4], and 1 (0.9%) was P[3] genotypes. Determination of G- and P-type combination revealed that all of G9 isolates were associated with P[8]. G9P[8] was the most predominant genotype and accounted for the majority (91.6%) of rotaviruses detected in this study. Molecular characterization of these G9 isolates demonstrated that all had long electropherotype, 96 of 98 (98.0%) belonged to subgroup II, one belonged to subgroup I and the other one was subgroup unidentifiable. All of G9 isolates possessed NSP4 genetic group B except for one isolate that showed dual genetic group specificities, B and C. The full-length VP7 gene nucleotide sequences among 15 representatives of these G9 strains were found to be highly homologous with percent identities of 99.3%-100%. Comparison with other G9 strains recently isolated showed that their nucleotide sequences were closely related to those of the US strain, US1205 (98.7%-99.0%) and Thai strain, 97CM108 (98.1%-99.0%). Interestingly, they were most closely related to the Japanese strain, 00-SG2509VP7, isolated in the same epidemic season, with percent nucleotide sequence identity of 99.4%-99.8%. The data imply that G9 strains isolated in this study and a G9 strain isolated in Japan in the year 2000 might have descended from the same ancestor.

Rotavirus serotype G9 strains belonging to VP7 gene phylogenetic sequence lineage 1 may be more suitable for serotype G9 vaccine candidates than those belonging to lineage 2 or 3

A safe and effective group A rotavirus vaccine that could prevent severe diarrhea or ameliorate its symptoms in infants and young children is urgently needed in both developing and developed countries. Rotavirus VP7 serotypes G1, G2, G3, and G4 have been well established to be of epidemiologic importance worldwide. Recently, serotype G9 has emerged as the fifth globally common type of rotavirus of clinical importance. Sequence analysis of the VP7 gene of various G9 isolates has demonstrated the existence of at least three phylogenetic lineages. The goal of our study was to determine the relationship of the phylogenetic lineages to the neutralization specificity of various G9 strains. We generated eight single VP7 gene substitution reassortants, each of which bore a single VP7 gene encoding G9 specificity of one of the eight G9 strains (two lineage 1, one lineage 2 and five lineage 3 strains) and the remaining 10 genes of bovine rotavirus strain UK, and two hyperimmune guinea pig antisera to each reassortant, and we then analyzed VP7 neutralization characteristics of the eight G9 strains as well as an additional G9 strain belonging to lineage 1; the nine strains were isolated in five countries. Antisera to lineage 1 viruses neutralized lineage 2 and 3 strains to at least within eightfold of the homotypic lineage viruses. Antisera to lineage 2 virus neutralized lineage 3 viruses to at least twofold of the homotypic lineage 2 virus; however, neutralization of lineage 1 viruses was fourfold (F45 and AU32) to 16- to 64-fold (WI61) less efficient. Antisera to lineage 3 viruses neutralized the lineage 2 strain 16- to 64-fold less efficiently, the lineage 1 strains F45 and AU32 8- to 128-fold less efficiently, and WI61 (prototype G9 strain) 128- to 1024-fold less efficiently than the homotypic lineage 3 viruses. These findings may have important implications for the development of G9 rotavirus vaccine candidates, as the strain with the broadest reactivity (i.e., a prime strain) would certainly be the ideal strain for inclusion in a vaccine.

Sequence analysis and in vitro expression of genes 6 and 11 of an ovine group B rotavirus isolate, KB63: evidence for a non-defective, C-terminally truncated NSP1 and a phosphorylated NSP5

An ovine group B rotavirus (GBR) isolate, KB63, was isolated from faeces of a young goat with diarrhoea in Xinjiang, People's Republic of China. Sequence determination and comparison of genes 6 and 11 with the corresponding sequences of GBR strains ADRV and IDIR showed that they were the cognate genes encoding NSP1 and NSP5, respectively. While the overall identities of nucleotide sequences between these two genes and the corresponding genes of strains ADRV and IDIR were in the range 52.6-57.2%, the identities of deduced amino acid sequences were only 34.9-46.3%. These results demonstrate that the substantial diversity of NSP1 observed among group A rotaviruses (GAR) also exists within GBRs and that a high degree of diversity also exists among NSP5 of GBRs, in contrast to GAR NSP5. The NSP1 gene of KB63 contains three ORFs, whereas the NSP1 genes of other GBR strains contain only two. ORFs 2 and 3 of the KB63 gene may be derived from a single ORF corresponding to ORF2 of other GBR strains by the usage of a stop codon created by an upstream single base deletion and single point mutations. In vitro expression studies showed that ORFs 1 and 2, but not 3, of gene 6 can be translated, suggesting that ORF2 may encode a C-terminally truncated, potentially functional product. It may play a role, together with the product of ORF1, in virus replication, as the virus can be passaged further in kids. Similarly, gene 11 can be translated in vitro. Like its counterpart in GARs, the protein encoded by gene 11 was shown to be phosphorylated in vitro.

Genetics of the rotaviruses

Genetic analyses have contributed significantly to our understanding of the biology of the rotaviruses. The distinguishing feature of the virus is a genome consisting of 11 segments of double-stranded RNA. The segmented nature of the genome allows reassortment of genome segments during mixed infections, which is the major distinguishing feature of rotavirus genetics. Reassortment has been a powerful tool for mapping viral mutations and other determinants of biological phenotypes to specific genome segments. However, more detailed genetic analysis of rotaviruses is currently limited by the inability to perform reverse genetics. Development of a reverse genetic system will facilitate analysis of the molecular mechanisms involved in various genetic, biochemical, and biological phenomena of the virus.

G3P2 rotaviruses causing diarrhoeal disease in neonates differ in VP4, VP7 and NSP4 sequence from G3P2 strains causing asymptomatic neonatal infection

During longitudinal epidemiological studies of rotavirus infections in children in Melbourne, Australia human G3P2 rotavirus strains causing asymptomatic or symptomatic infections have been identified. Eleven strains (AS strains) associated with asymptomatic infection of newborn babies from 1974-1984, and five strains (S strains) associated with symptomatic infection of newborn babies (4) or a 22 week old infant (1) during 1980-1986 were studied. The entire nucleotide sequences of genes coding for VP4, VP7, NSP4 and VP6 were derived for representative AS and S strains. The nucleotide sequences of neutralization epitope regions present on the outer capsid proteins VP4 and VP7 (regions C and F) showed extensive conservation of nucleotide and deduced amino acid sequence in all strains. Minor variations were observed over the 12 year period in VP7 epitope regions A and B in some strains. Specific conserved amino acids differences between the asymptomatic and symptomatic strains were observed in the genes encoding VP4 at aa133 and 303 (asparagine or threonine) and 380 (serine or isoleucine), VP7 at aa27 (threonine or isoleucine), aa29 (isoleucine or threonine), aa42 (valine or alanine) and aa238 (asparagine or aspartic acid/serine) and NSP4 at aa135 (isoleucine or valine). No amino acid changes were identified in gene 6. The observed amino acid differences occurred in proteins that have been implicated in virulence, and correlate with differences in clinical symptoms of infants infected with these strains. These results permit speculation about the genetic basis for virulence of human strains.

Development of rotavirus molecular epidemiology: electropherotyping

Early in the era of rotavirology it was realized that the characteristic patterns of bands produced in polyacrylamide gels following electrophoresis of genomic dsRNA were useful for checking the identity of rotavirus isolates. However it was Romilio Espejo who first proposed the use of this technique for epidemiology, although most others did not take the suggestion seriously because the technique was then rather specialized and RNA staining methods were not very sensitive. Using samples collected by Ruth Bishop in Melbourne following the original identification of human rotaviruses, Sue Rodger recorded the "electropherotypes" of all samples available to 1979 and painstakingly compared them, side by side (since minor variations in conditions, especially temperature, alter the relative migration distances of dsRNA bands). These efforts produced the first longitudinal, extensive study of human rotavirus strain variation. Since then, technical improvements have greatly increased the sensitivity of the procedures, and electropherotyping has been recognized as a powerful and economical method for epidemiological studies of rotaviruses.

Rotavirus serotypes and electropherotypes in Finland from 1986 to 1990

Four epidemic seasons of rotaviruses were studied in Helsinki during 1986-1990. This is the first Scandinavian study, where both electropherotypes and serotypes are determined. Out of 5316 fecal specimens 769 (14.5%) rotavirus positive samples were detected by electron microscopy. Of these, 645 isolates (83.9%) gave a clear RNA pattern in gel electrophoresis and they clustered into 87 electropherotypes. An illustrative number of isolates representing each electropherotype (= E-type) was serotyped using VP7 protein-specific monoclonal antibodies for serotypes G1-G4 and without exceptions, within one E-type only a single serotype specificity was found. After establishment of the serotype of each E-type, the distribution of serotypes was scored as 61.2%, 2.0%, 0.5% and 29.8% for G1-G4, respectively; 6.5% remained untypable. Two seasons had one predominant E-type (Season 1, 1986-87, and Season 3, 1988-89, 84.2% and 80.6% of rotavirus positive samples, respectively). Both were followed by a season with no predominant E-type, but several minor E-types. Altogether, 5 short E-types (13/645 samples) with serotype G2 specificity were found, most of them occurring in Season 2. Only 2 E-types (3 samples) belonged to serotype G3. Group C rotavirus was found in 8 specimens. In this study a shift in serotypes, from G1 to G4, was observed in Finland in 1988/89; a similar shift was reported in many European countries at that time.

Molecular epidemiology of human rotaviruses in Manipur: genome analysis of rotaviruses of long electropherotype and subgroup I

In 1987/88 a winter outbreak of infantile gastroenteritis occurred in Manipur, India which was mainly due to rotaviruses of long electropherotype and subgroup (SG) I. The VP7 gene of one of these viruses (M48) has been cloned and sequenced. It was found to be very closely related to the VP7 genes of the G2 serotype human rotaviruses RV-5 and S2. Follow-up epidemiology of this event in Manipur during 1989-1992 yielded mainly rotaviruses of more conventional characteristics (94 isolates of SG II and long electropherotype, and 90 isolates of SG I and short electropherotype), but also 6 isolates of SG I with long electropherotype, indicating that these viruses continue to circulate in the Manipur community. One isolate of short electropherotype was of subgroup II, and one long electropherotype isolate reacted with the group A but not with either the subgroup I or subgroup II monoclonal antibodies.

Rearrangement of the VP6 gene of a group A rotavirus in combination with a point mutation affecting trimer stability

A group A rotavirus isolated from a lamb with diarrhea in Qinhai province, China, was serially passaged in fetal calf kidney cells. In passage 96, rearrangements of RNA segments 5 and 6 of the viral genome were found. Here we report the nucleotide and predicted amino acid sequences of normal and rearranged RNA 6, coding for the major inner capsid protein VP6. In comparison with the normal gene (N6), the rearranged RNA 6 (R6) contained the normal open reading frame followed by a 473-nucleotide (nt) duplication of the gene beginning 23 nt after the termination codon. The duplicated region starts at nt 768 and runs through to the 3' end of the gene. In accordance with the nucleotide sequence of the rearranged RNA 6, a normal-length VP6 product was found in cells infected with the mutant. However, a single-amino-acid change from proline to glutamine at position 309 slightly affected the electrophoretic mobility of the VP6 monomer of the R6 mutant and reduced the stability of VP6 trimers on gels and at low pH values compared with the normal gene product. The degree of relatedness of VP6 of the Chinese lamb rotavirus Lp14 to those of other group A rotaviruses was determined.

Rotavirus vaccines and vaccination potential

The development of a successful rotavirus vaccine is a complex problem. Our review of rotavirus vaccine development shows that many challenges remain, and priorities for future studies need to be established. For example, the evaluation of administration of a vaccine with OPV or breast milk might receive less emphasis until a vaccine is made that shows clear efficacy against all virus serotypes. Samples remaining from previous trials should be analyzed to determine epitope-specific serum and coproantibody responses to clarify why only some trials were successful. Detailed evaluation of the antigenic properties of the viruses circulating and causing illness in vaccinated children also should be performed for comparisons with the vaccine strains. In future trials, sample collection should include monitoring for asymptomatic infections and cellular immune responses should be analyzed. The diversity of rotavirus serotype distribution must be monitored before, during, and after a trial in the study population and placebo recipients must be matched carefully to vaccine recipients. Epidemiologic and molecular studies should be expanded to document, or disprove, the possibility of animal to human rotavirus transmission, because, if this occurs, vaccine protection may be more difficult in those areas of the world where cohabitation with animals occurs. We also need to have an accurate assessment of the rate of protection that follows natural infections. Is it realistic to try to achieve 90% protective efficacy with a vaccine if natural infections with these enteric pathogens only provide 60% or 70% protection? Subunit vaccines should be considered to be part of vaccine strategies, especially if maternal antibody interferes with the take of live vaccines. The constraints on development of new vaccines are not likely to come from molecular biology. The challenge remains whether the biology and immunology of rotavirus infections can be understood and exploited to permit effective vaccination. Recent advances in developing small animal models for evaluation of vaccine efficacy should facilitate future vaccine development and understanding of the protective immune response(s) (Ward et al. 1990b; Conner et al. 1993).

Molecular epidemiology and subgroup analysis of bovine group A rotaviruses associated with diarrhea in South African calves

Rotavirus-positive specimens were recovered from 143 Afrikander calves on two farms in the northeastern Cape of South Africa during late 1988 and 1989. The rotavirus strains were analyzed by polyacrylamide gel electrophoresis of the RNA genome, and four rotavirus RNA electrophoretypes, each with a long profile, were identified. A distinct RNA profile was identified on the farms during 1988, but by early 1989, two patterns existed, one unique to each farm. Over the next 8 months a new electrophoretic pattern emerged on one farm, whereas the pattern on the other farm remained unchanged. The rotavirus subgroup I antigen was detected in all specimens examined with subgroup-specific monoclonal antibodies. Non-group A rotaviruses were not identified by RNA genome analysis of 82 specimens from calves with diarrhea negative for group A rotaviruses by an enzyme-linked immunosorbent assay.

A family outbreak of gastroenteritis caused by group C rotavirus

A family outbreak of gastroenteritis caused by group C rotavirus is described. All five members of the family, with children between 8 and 15 years of age, fell ill with diarrhea. The diagnosis was initially based on the detection of rotavirus RNA showing a typical group C profile in gel electrophoresis in stool samples, and it was serologically verified from patient sera using a cell culture adapted porcine group C rotavirus as a source of standard antigen. All collected serum samples from the family contained IgM and/or IgG class antibodies to group C rotavirus measurable by immunofluorescence antibody test (IFAT). Group C rotavirus specific IgM class antibodies were present in the early serum samples in 3/4 patients. A roller tube neutralization test (NT) was established to demonstrate neutralizing antibodies to porcine group C rotavirus in human sera. These methods can be used to detect serologically group C rotavirus infections.

Molecular and serological analyses of two bovine rotaviruses (B-11 and B-60) causing calf scours in Australia

Fecal specimens from 78 calves involved in outbreaks of calf diarrhea which occurred in three farms in Victoria, Australia, in 1988 were analyzed for rotaviruses. Thirty-eight samples were positive for group A virus antigen by enzyme-linked immunosorbent assay, and 20 of these contained viral double-stranded RNAs that could be detected by polyacrylamide gel electrophoresis. Two major electropherotypes could be observed, and a representative isolate of each electropherotype (isolates B-11 and B-60) was successfully adapted to grow in MA104 cells. Sequencing of the VP7 genes directly from RNA transcripts of fecal and cell culture-adapted viruses demonstrated that no base changes occurred in this gene upon adaptation to growth in MA104 cells. Sequencing also revealed that the VP7 protein of B-60 was closely related to G serotype 6 (G6) strains, whereas the B-11 sequence was significantly different from all previously published sequences except the recently reported VP7 sequences of bovine isolates 61A and B223, particularly across the antigenic regions A, B, and C. The other strains most closely related to B-11 by VP7 amino acid sequence analysis were G4 porcine strains BMI-1 and BEN-144 and G8 human strain 69M. Serotyping of B-11 and B-60 gave results that were in good agreement with the sequencing data. Hyperimmune typing sera clearly identified B-60 as a member of G6, whereas the B-11 strain reacted to moderate titers only with antisera to some G10 strains. Antiserum raised against B-11 neutralized some strains of G10 cross-reacted with porcine G4 type isolates BMI-1 and BEN-144 but not with other G4 strains or with rotaviruses of other mammalian G serotypes. Northern blot hybridization showed that B-11 was closely related to the recently reported bovine G10 strain B223, and they both possessed a similar segment 4 that was different from that of either UK bovine or NCDV rotavirus.

Isolation, characterization, and serial propagation of a bovine group C rotavirus in a monkey kidney cell line (MA104)

A virus (designated the Shintoku strain) which was morphologically indistinguishable from group A rotaviruses was detected in the feces of adult cows with diarrhea in Japan. The virus contained 11 segments of double-stranded RNA and had an electrophoretic migration pattern in polyacrylamide gels similar to that of other group C rotaviruses (4-3-2-2). Feces containing the bovine virus reacted with antiserum to porcine group C rotavirus (Cowden strain) but not group A or B rotaviruses in immunoelectron microscopy. The virus was adapted to serial propagation in roller tube cultures of a rhesus monkey kidney cell line (MA104) by using high concentrations of trypsin. Evidence for viral replication in MA104 cell cultures was demonstrated by immunoelectron microscopy and indirect immunofluorescence by using antiserum to porcine group C rotavirus and by electrophoretic analysis of extracted viral double-stranded RNA. A significant antibody response against the isolate was detected in convalescent-phase sera of cows which excreted the virus: no increased antibody response to bovine group A rotavirus was observed. To our knowledge, this is the first isolation of a group C rotavirus from cattle.

Molecular epidemiology of rotaviruses associated with pediatric diarrhea in Bangkok, Thailand

Rotavirus diarrhea in 453 pediatric patients (29.8% of 1,518) was studied in greater Bangkok during 1985 to 1987. The disease persisted all year, increasing in incidence from August to January (30 to 50%). Polyacrylamide gel electrophoresis of rotavirus RNA from these patients and from an additional 46 patients of a 1982 to 1983 epidemic revealed 26 electropherotypes, 4 with short (S) and 22 with long (L) RNA profiles. Of the analyzed specimens, 85.5% were L forms. Only one or a few electropherotypes predominated in each epidemic, whereas others appeared sporadically at low frequencies. Shifts in the predominant electropherotypes were observed in every epidemic. Of these, 126 strains were tested for subgroup and serotype by monoclonal antibody enzyme immunoassay. Serotype 4 prevailed from 1982 to 1983, while serotype 1 was encountered more frequently than serotypes 2 and 4 from 1985 to 1987. A complete correlation was found between the electrophoretic migration of segments 10 and 11 and the serologically defined subgroup specificity. Distinct electropherotypes occurred within the same serotype, and strains with the identical electropherotype always showed the same serotype specificity. No specific electropherotype or serotype correlated with patient age. In this study, atypical rotaviruses and mixed infections with different rotaviruses were identified.

Rotavirus excretion by village pigs in Papua New Guinea

Cohort studies were conducted on 29 pigs from 3 villages in the Highlands of Papua New Guinea. Animals ranged in age from 9 d to 5 m old. Three hundred and twenty nine faecal samples were collected from individual pigs followed over 3 to 6 w periods, and were examined for group A rotavirus antigen by ELISA, and rotaviral genomic RNA by polyacrylamide gel electrophoresis (PAGE). Electron microscopy was also conducted on selected samples. Group A rotavirus was detected in the faeces of 16 pigs with infected individuals coming from all villages. Non-group A rotavirus resembling group C was found in faeces from pigs from 2 villages. All of the group A rotaviruses examined had the same electrophoretype and this was distinct from that of the common type infecting humans in the area at the time of the study. None of the group A positive samples reacted with monoclonal antisera specific for human group A rotaviruses of serotypes 1, 2, 3, 4, or 8. The non-group A rotaviruses also all had identical electrophoretypes. In contrast to previous findings in intensive piggeries, rotavirus infection did not occur in all young pigs and was not limited to young animals under 2 m of age. Infected pigs varied in age from 12 days to 20 weeks of age. This pattern of infection was attributed to the non-intensive husbandry situations in the villages, with less opportunity for transmission to occur than in intensive piggeries.

Incidence, clinical features and epidemiology of rotavirus gastro-enteritis in hospitalized children

Two hundred and eighteen patients with acute gastro-enteritis (GE) and 67 controls (patients admitted during the period of study for illness other than (GE) were included in this study. Their stool samples were subjected to the following tests to detect the presence of rotavirus: enzyme-linked immunosorbent assay (ELISA), latex agglutination and electron microscopy. Samples positive by any one or more of the above methods were considered positive for rotavirus and were subjected to polyacrylamide gel electrophoresis of viral RNA. Rotavirus was detected in 59 (27.1%) of the 218 GE samples and four (6%) of the control samples. ELISA was the most sensitive test and could detect viral antigen long after the other methods failed to do so.

Priming for rotavirus neutralizing antibodies by a VP4 protein-derived synthetic peptide

In the rotavirus SA11 surface protein VP4, the trypsin cleavage sites associated with the enhancement of infectivity are flanked by two amino acid regions that are highly conserved among different rotaviruses. We have tested the ability of synthetic peptides that mimic these two regions to induce and prime for a rotavirus neutralizing antibody response in mice. After the peptide immunization schedule, both peptides induced peptide antibodies, but neither was able to induce virus antibodies, as measured by an enzyme-linked immunosorbent assay or a neutralization assay. However, when the peptide-inoculated mice were subsequently injected with intact SA11 virus, a rapid and high neutralizing antibody response was observed in mice that had previously received the peptide comprising amino acids 220 to 233 of the VP4 protein. This neutralizing activity was serotype specific; however, this peptide was also able to efficiently prime the immune system of mice for a neutralizing antibody response to the heterotypic rotavirus ST3 when the ST3 virus was used for the secondary inoculation.

Rotavirus gene structure and function

Knowledge of the structure and function of the genes and proteins of the rotaviruses has expanded rapidly. Information obtained in the last 5 years has revealed unexpected and unique molecular properties of rotavirus proteins of general interest to virologists, biochemists, and cell biologists. Rotaviruses share some features of replication with reoviruses, yet antigenic and molecular properties of the outer capsid proteins, VP4 (a protein whose cleavage is required for infectivity, possibly by mediating fusion with the cell membrane) and VP7 (a glycoprotein), show more similarities with those of other viruses such as the orthomyxoviruses, paramyxoviruses, and alphaviruses. Rotavirus morphogenesis is a unique process, during which immature subviral particles bud through the membrane of the endoplasmic reticulum (ER). During this process, transiently enveloped particles form, the outer capsid proteins are assembled onto particles, and mature particles accumulate in the lumen of the ER. Two ER-specific viral glycoproteins are involved in virus maturation, and these glycoproteins have been shown to be useful models for studying protein targeting and retention in the ER and for studying mechanisms of virus budding. New ideas and approaches to understanding how each gene functions to replicate and assemble the segmented viral genome have emerged from knowledge of the primary structure of rotavirus genes and their proteins and from knowledge of the properties of domains on individual proteins. Localization of type-specific and cross-reactive neutralizing epitopes on the outer capsid proteins is becoming increasingly useful in dissecting the protective immune response, including evaluation of vaccine trials, with the practical possibility of enhancing the production of new, more effective vaccines. Finally, future analyses with recently characterized immunologic and gene probes and new animal models can be expected to provide a basic understanding of what regulates the primary interactions of these viruses with the gastrointestinal tract and the subsequent responses of infected hosts.

Comparative sequence analysis of VP7 genes from five Australian porcine rotaviruses

The genes coding for the rotavirus major neutralizing protein, VP7, from 5 Australian porcine rotaviruses representing glycoprotein (i.e. VP7 or G) serotypes 3, 4, and 5, were sequenced. The genes were each 1,062 nucleotides long with two long open reading frames for proteins of either 326 or 297 amino acids and containing only one potential glycosylation site at amino acid position 69. When compared to the corresponding genes of human viruses, the porcine genes showed very high nucleotide and deduced amino acid homology. Sequence comparison also revealed that Australian porcine rotaviruses of G serotype 4 and 5 were similar to the corresponding porcine strains found in the U.S.A. and U.K., while G serotype 3 and 4 porcine rotaviruses were closely related to human G serotype 3 strain, RV-3 and serotype 4 strain, ST-3, respectively. These Australian rotavirus VP7 sequences were found to correlate with serological data we reported previously.

Molecular epidemiology and subgroup determination of bovine group A rotaviruses associated with diarrhea in dairy and beef calves

The genome electropherotyping technique was used to examine group A rotaviral infections of diarrheic calves ranging from 1 to 85 days of age in 2 beef and 27 dairy herds. Coelectrophoresis studies demonstrated 38 distinct bovine group A rotavirus genome electropherotypes; all were long genome electropherotypes, and none had extra segments or unusual segment rearrangements. Genome electropherotypes in fecal specimens from diarrheic calves previously inoculated orally with a commercial, modified-live group A rotavirus vaccine differed from the vaccine genome electropherotype. Generally, when fecal specimens for genome electropherotyping were collected from two or more different calves within the same herd over a relatively short time, only one genome electropherotype was detected within a given herd. Different genome electropherotypes were detected in the same herd, however, when fecal specimens were obtained from different diarrheic calves over longer intervals (6 months or more). Twenty-three group A rotavirus strains with distinct genome electropherotypes, from diarrheic calves in 22 herds, were isolated and plaque purified in cell culture, and all were subgroup 1 group A rotaviruses. Non-group A rotavirus genome electropherotypes were not detected in 131 fecal specimens, negative for group A rotavirus, collected from diarrheic calves in 17 dairy herds.

Molecular and antigenic characterization of porcine rotavirus YM, a possible new rotavirus serotype

In 1983, we isolated a porcine rotavirus (strain YM) that was prevalent in several regions of Mexico, as judged by the frequency of its characteristic electropherotype. By a focus reduction neutralization test, rotavirus YM was clearly distinguished from prototype rotavirus strains belonging to serotypes 1 (Wa), 2 (S2), 3 (SA11), 4 (ST3), 5 (OSU), and 6 (NCDV). Minor, one-way cross-neutralization (1 to 5%) was observed when antisera to the various rotavirus strains were incubated with rotavirus YM. In addition, the YM virus was not neutralized by neutralizing monoclonal antibodies with specificity to serotypes 1, 2, 3, and 5. The subgroup of the virus was determined to be I by enzyme-linked immunosorbent assay. To characterize the serotype-specific glycoprotein of the virus at the molecular level, we cloned and sequenced the gene coding for VP7. Comparison of the deduced amino acid sequence with reported homologous sequences from human and animal rotavirus strains belonging to six different serotypes further supported the distinct immunological identity of the YM VP7 protein.

Atypical rotaviruses in Australian pigs

Atypical rotaviruses of two different electropherotypes were identified by PAGE in 16 out of 237 (5.3%) diarrhoeic faecal samples from piglets. A cDNA probe derived from a group B rotavirus hybridized strongly to two samples (of 3 tested) with electropherotypes suggestive of groups B or E, identifying them as group B. The electropherotype(s) of seven samples were typical of group C. By immunofluorescence, antibodies to group B, C, and E rotaviruses have been detected in sera from Australian sows, so it appears that atypical rotaviruses belonging to three different groups occur in pigs in this country.

New porcine rotavirus serotype antigenically related to human rotavirus serotype 3

Serotyping of porcine rotaviruses isolated in MA104 cells from Australian piglets with diarrhea showed that two strains belonged to serotype 3 and one strain was antigenically similar to the OSU strain of porcine rotavirus (serotype 5). In addition, neutralizing antibodies to human rotavirus serotype 4 (ST-3 strain) were detected in serum samples from sows in one area, and so it seems probable that porcine rotaviruses of at least three serotypes occur in Australia.

Polyacrylamide gel electrophoresis and silver staining for detection of rotavirus in stools from diarrheic patients in Thailand

Detection of rotavirus by polyacrylamide gel electrophoresis in combination with silver staining and by enzyme-linked immunosorbent assay showed 96.7% identical results in tests with 1,304 stool specimens from diarrheic patients. The polyacrylamide gel electrophoresis method can be modified to reduce cost and working time. Phenol extraction of stools, however, is essential in maintaining the sensitivity of the method.

Serologic characteristics of a human rotavirus isolate, AU-1, which has a "long" RNA pattern and subgroup I specificity

An unusual human rotavirus (HRV) isolate, designated AU-1, has a "long" RNA electrophoretic pattern and subgroup I specificity, in contrast to properties common to HRVs previously isolated. Hemagglutination activity of the AU-1 strain was demonstrated using erythrocytes of 1-day-old chicken. Neutralization assays revealed that the AU-1 strain was crossneutralized by hyperimmune antisera against the MO strain (serotype 3). However, antiserum directed against a reassortant in which the gene for Vp7 was replaced by the corresponding AU-1 gene neutralized the AU-1 strain to a significantly higher titer than the MO strain.

Variation in neutralization epitopes of human rotaviruses in relation to genomic RNA polymorphism

Fecal rotaviruses collected from October 1983 to September 1984 from outpatients and inpatients attending the Royal Children's Hospital, Melbourne, Australia, with acute gastroenteritis were serotyped by enzyme immunoassay using rotavirus-neutralizing mouse monoclonal antibodies specific for serotypes 1 to 4. Application of three different serotype 1-neutralizing antibodies indicated variations in neutralization epitopes between serotype 1 rotaviruses on the major outer capsid glycoprotein, including a site shared with serotype 3 rotaviruses. The three different binding patterns observed were termed "monotypes." Comparison of monotype and serotype with genomic RNA profiles generated by gel electrophoresis of ds viral RNA indicated that each RNA electropherotype corresponded to only one monotype (1a, 1b, 1c) or serotype (3, 4). However, serotypes 1 (a and c) and 4 contained multiple electropherotypes. Greater numbers of RNA segment variations, including alteration in mobility of gene segments 7, 8, and 9, were evident between rotaviruses of different serotype or monotype than within those groups. Within limits of time and location, rotavirus neutralization epitope variations appear to correlate with RNA polymorphism. Where rotavirus epidemiology has been analyzed by year using RNA electropherotypes, only limited numbers of each RNA pattern need to be serotyped to ascertain the major serotypes in circulation.

Characterisation of rotavirus isolates from sub-clinically infected calves by genome profile analysis

Rotaviruses isolated from 43 sub-clinically infected calves from a single farm were analysed by genome profile analysis. The isolates showed genomic variation and eight different profiles were observed, including one which was atypical for Group A rotaviruses. The 3' terminal labelling method for the analysis of genome profiles used in this study required only 1 ng of viral RNA, an increase of 1000-fold in sensitivity over ethidium bromide staining for detecting all rotavirus genome segments. However, dual infections involving two rotaviruses with distinct profiles could not be detected if the concentrations of the viruses differed by greater than 10-fold.

Conservation in rotaviruses of the protein region containing the two sites associated with trypsin enhancement of infectivity

The primary structure of the region in the outer layer protein VP3, containing the two sites associated with trypsin enhancement of infectivity of rotavirus was found to be greatly conserved in cultivable human rotavirus serotypes 1 (Wa), 2 (DS1), and 3 (P) and in four human rotaviruses directly purified from feces. Significant differences with this conserved sequence were found in human rotavirus serotype 4 (ST3), isolated from an asymptomatic neonate, and in seven animal rotaviruses. However, the two trypsin cleavage sites were conserved in every rotavirus VP3 sequence analyzed.

Epidemiologic and genomic study of rotavirus strains infecting young children and calves in the same rural environment

The epidemiological profile of rotavirus infection in young calves and young children form the same rural environment in France was studied during autumn-winter 1983-1984. Viruses were isolated from calves on each farm and were identified by their electropherotype for 8 out of the 9 farms under study. Among 13 children regularly checked on 9 farms for 25 weeks, 7 were found to be rotavirus positive. Nevertheless, no transfer of virus between child and bovine was documented by the electropherotype migration. In the case of the calves, the predominance of the Ib IIa IIIe IVa electropherotype at 5 of the 9 farms is similar to the epidemiological situation observed among newborn in some maternity wards.

Isolation of two lapine rotaviruses: characterization of their subgroup, serotype and RNA electropherotypes

Rotaviruses were detected by an ELISA test in stool specimens from diarrheic rabbits in two commercial rabbitries and cultured in MA 104 cells. Their identity was confirmed by electron microscopy and indirect immunofluorescence. They were found to belong to subgroup I by testing with monoclonal antibodies and to serotype 3 by neutralization with homologous and heterologous antisera. Although both viruses were neutralized by antiserum to human serotype 3 the ALA rabbit rotavirus was minimally neutralized by antiserum to the C11 rabbit rotavirus. Electrophoresis of viral RNA revealed 11 segments characteristic of rotavirus, however both rabbit rotaviruses had unusual electropherotypes. They differed from each other with greatly reduced mobility of the tenth segment in one virus and the eleventh segment in the other virus.