Sequence analysis of genes encoding structural and nonstructural proteins of a human group B rotavirus detected in Calcutta, India

Nucleotide sequences of RNA segments encoding structural proteins(VP4, VP6, and VP7) and nonstructural proteins(NSP1 and NSP3) of a human group B rotavirus CAL-1, which was detected in Calcutta, India, were determined and their relatedness with cognate genes of other group B rotaviruses was analyzed. The CAL-1 genes showed generally high sequence identities (more than 90%) to those of human group B rotavirus, adult diarrheal rotavirus (ADRV) in China, while identities with bovine, murine, and ovine viruses were considerably lower (58-73%). Among RNA segments analyzed, sequence identity of the VP6 gene was relatively high compared with other gene segments. In the CAL-1 VP7 sequence, many characteristics were shared by ADRV, but not by other animal group B rotaviruses. In contrast, VP4 and NSP3 of CAL-1 were single amino acid and 23 amino acids longer than those of ADRV strain, respectively, due to differences of a few nucleotides. These findings suggested that human group B rotaviruses CAL-1 and ADRV might have originated from a common ancestral virus distinct from animal group B rotaviruses reported so far, while some notable sequence differences indicated the distinct nature of these viruses.

Distribution of aminoglycoside resistance genes in recent clinical isolates of Enterococcus faecalis, Enterococcus faecium and Enterococcus avium

Aminoglycoside modifying enzymes (AMEs) are major factors which confer aminoglycoside resistance on bacteria. Distribution of genes encoding seven AMEs was investigated by multiplex PCR for 279 recent clinical isolates of enterococci derived from a university hospital in Japan. The aac(6')-aph(2"), which is related to high level gentamicin resistance, was detected at higher frequency in Enterococcus faecalis (42.5%) than in Enterococcus faecium (4.3%). Almost half of E. faecalis and E. faecium isolates possessed ant(6)-Ia and aph(3')-IIIa. The profile of AME gene(s) detected most frequently in individual strains of E. faecalis was aac(6')aph(2") + ant(6)-Ia + aph(3')-IIIa, and isolates with this profile showed high level resistance to both gentamicin and streptomycin. In contrast, AME gene profiles of aac(6')-Ii+ ant(6)-Ia+aph(3')-IIIa, followed by aac(6')-Ii alone, were predominant in E. faecium. Only one AME gene profile of ant(6)-Ia+aph(3')-IIIa was found in Enterococcus avium. The ant(4')-Ia and ant(9)-Ia, which have been known to be distributed mostly among Staphylococcus aureus strains, were detected in a few enterococcal strains. An AME gene aph(2")-Ic was not detected in any isolates of the three enterococcal species. These findings indicated a variety of distribution profiles of AME genes among enterococci in our study site.

Genomic rearrangement of the mec regulator region mediated by insertion of IS431 in methicillin-resistant staphylococci

Genomic diversification of the mec regulator region mediated by IS431 was investigated for clinical isolates of methicillin-resistant staphylococci. A single rearranged form of the mecR1 gene due to IS431 insertion was detected in the three staphylococcal species, while another type of mecR1 truncation with IS431 and an IS431 located downstream of mecI were found only in Staphylococcus haemolyticus. Genetic differentiation of IS431 and staphylococcal isolates suggested transmission of mecDNA with IS431-mediated rearrangement among different staphylococcal species.

Analysis on distribution of insertion sequence IS431 in clinical isolates of staphylococci

Distribution of insertion sequence IS431 in clinical isolates of Staphylococcus aureus, Staphylococcus epidermidis, and Staphylococcus haemolyticus was investigated. Except for methicillin susceptible-S. aureus (MSSA), IS431 was detected in all isolates of the three staphylococcal species. In MSSA, only 20% of isolates with distinct coagulase types and genetic types possessed IS431. In a few MSSA isolates, an IS431 variant with internal deletion was found.

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

BACKGROUND

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

OBJECTIVE

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

STUDY DESIGN

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

RESULTS

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

CONCLUSIONS

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

Rearrangement generated in double genes, NSP1 and NSP3, of viable progenies from a human rotavirus strain

We generated rotavirus clones with rearrangement in vitro by serial passages of a human rotavirus strain (IGV-80-3) at high multiplicity of infection and determined nucleotide sequences of the rearranged genes from two distinct rotavirus clones, each of which possesses two rearranged genes: a common rearranged NSP1 gene and NSP3 gene with slightly different migration in polyacrylamide gel electrophoresis. Sequence analysis showed that the rearranged NSP1 and NSP3 genes had similar gene structures: concatemerization in a head to tail orientation and partial duplication of the open reading frame following the termination codon. The rearranged NSP1 gene had a direct repeat, whereas in the rearranged NSP3 gene, no such pattern was found.

New P serotype of group A human rotavirus closely related to that of a porcine rotavirus

The VP7 and VP4 genes of two human group A rotavirus strains Mc323 and Mc345 with unique serologic and genomic properties, and isolated in Chiang Mai, Thailand, in 1989 [Urasawa et al. (1992) Journal of Infectious Diseases 166:227-234] were further characterized. The nucleotide and deduced amino acid sequences of the VP7 genes allowed the classification of both strains as serotype G9. The VP4 genes of both strains are 2,359 nucleotides in length and encode a protein of 775 amino acids like in most human rotaviruses. A comparison of the VP4 amino acid sequence of strain Mc323 with those of strain Mc345 and 24 human and animal rotaviruses representing 20 distinct VP4 genotypes reported to date showed that VP4 of Mc323 and Mc345 belong to genotype 19 previously reported for porcine rotavirus [Burke et al. (1994) Journal of General Virology 75:2205-2212]. To investigate the serological type (P serotype) of these VP4s, six reassortant viruses each containing a distinct VP4 gene characteristic of human rotaviruses and the VP7 gene of porcine rotavirus strain Gottfried (G4) were prepared, and antisera to these reassortants produced in rabbits. In neutralization tests, the P serotype of Mc323 was clearly differentiated from the five major P serotypes reported previously for human rotaviruses, suggesting that Mc323 and Mc345 represent a new human rotavirus P serotype tentatively called P11.

Distribution of insertion sequence-like element IS1272 and its position relative to methicillin resistance genes in clinically important Staphylococci

The distribution of insertion sequence-like element IS1272 was analyzed for clinical isolates of Staphylococcus aureus, Staphylococcus epidermidis, and Staphylococcus haemolyticus. In each of the staphylococcal species, IS1272 was detected in both methicillin-resistant (MR) and methicillin-susceptible strains of different genetic types. In MR isolates, IS1272 was generally located downstream of the truncated mecR1 gene (DeltamecR1), with an identical junction sequence occurring between DeltamecR1 and IS1272, although insertion of an additional gene sequence in the junction sequence was detected in one S. epidermidis isolate. These findings suggest that the mec element with the rearranged form of mecR1 (DeltamecR1-IS1272) has been transmitted to multiple clones of staphylococci.

Analysis on reassortment of rotavirus NSP1 genes lacking coding region for cysteine-rich zinc finger motif

Rotavirus clones A5-10 and A5-16 isolated from a bovine rotavirus strain A5 possess NSP1 gene which has a point mutation generating a nonsense codon and a 500 base-deletion, respectively. As a result, the two A5 clones encode truncated NSP1 product which lacks cysteine-rich region forming zinc finger motif. In order to analyze reassortment of these mutated NSP1 gene with RNA segments from heterologous strains, we investigated a number of reassortant clones derived from coinfection with either A5-10, A5-16 or a reference strain A5-13 (possessing intact NSP1 gene) and either simian rotavirus SA11 or human rotavirus KU. In coinfection with SA11 and A5-13, selection rates of A5-13 segments in reassortants ranged approximately from 20 to 70% (46% for NSP1 gene). In contrast, in the reassortment between SA11 and A5-10 or between SA11 and A5-16, selection rates of NSP1 gene from A5-10 and A5-16 were only 1% (one clone) and 0%, respectively. In reassortants from crosses KU x A5-clones, selection rate of A5-13 NSP1 gene decreased to 15%, while 11 reassortants with A5-10 NSP1 gene (31%) and one reassortant with A5-16 NSP1 gene (2%) were isolated. Reassortants with A5-10 NSP1 possessed a single gene (segment 9 or 11) from KU in the genetic background of A5-10. One reassortant clone (cl-55) with A5-16 NSP1 gene possessed KU gene segments 3, 4, and 8-11. When single-step growth curves were compared, the reassortant cl-55 showed almost identical growth curve to that of KU, while KU showed a better replication than A5-16. These results indicated that although A5-10 or A5-16 NSP1 gene encoding the truncated NSP1 is selected into reassortants much less efficiently than normal NSP1 gene, the reassortants with the mutated NSP1 gene and RNA segments from heterologous strains normally replicated in cultured cells. Thus, cysteine-rich region of NSP1 was not considered essential for genome segment reassortment with heterologous virus.

Detection of group- and subgroup-specific antigens of bovine rotaviruses in Bangladesh

The study was carried out to detect group- and subgroup-specific antigens of bovine rotaviruses. Stool specimens, collected from diarrhoeic calves of the Savar Dairy Farm, Bangladesh, were examined by an enzyme-linked immunosorbent assay, using group- and subgroup-specific monoclonal antibodies. Thirty-three specimens showed specificity for group A rotavirus. While subgrouping, 21 group A-positive specimens showed subgroup I specificity. Twelve specimens did not react with either of the subgroup I- and subgroup II-specific monoclonal antibodies.

Analysis of genomic diversity within the Xr-region of the protein A gene in clinical isolates of Staphylococcus aureus

Protein A of Staphylococcus aureus contains a polymorphic Xr-region characterized by a tandem repeat of eight amino acid units. In this study, the diversity of genes encoding the repeat regions and their relatedness among S. aureus strains was analyzed. Ten different protein-A types characterized by repeat numbers 4-13 were identified in a total of 293 clinical isolates. The protein-A type with 10 repeat units (10 repeats) in the Xr-region was most frequently detected in methicillin-resistant S. aureus, whereas the majority of methicillin-susceptible strains were distributed almost evenly into protein-A types with 7-11 repeats. Strains that belonged to a single coagulase type were classified into multiple protein-A types, e.g. strains with the common coagulase types II and VII were differentiated into 7 and 8 protein-A types, respectively. Nucleotide sequence analysis of the Xr-region of 42 representative strains revealed the presence of 37 different genotypes (spa types), which were constituted by a combination of several of 24 different repeat unit genotypes. Based on the similarity in arrangement of repeat unit genotypes, 34 strains with different repeat numbers were classified into 5 genetic clusters (C1-C5). The clusters C1, C2 and C3 consisted exclusively of strains with identical coagulase types II, III, and IV, respectively. These findings suggested that the protein-A gene of S. aureus has evolved from a common ancestral clone in individual clusters independently.

Analysis of human rotavirus G serotype in Bangladesh by enzyme-linked immunosorbent assay and polymerase chain reaction

Distribution of human rotavirus G serotype was investigated by enzyme-linked immunosorbent assay (ELISA) and polymerase chain reaction (PCR) with faecal specimens obtained from children with diarrhoea in Bangladesh. By ELISA, subgroup and G serotype were determined for 59.5% and 28.6% of group A rotavirus-positive specimens respectively. However, of the 120 specimens, the G serotype of which was not determined by ELISA, serotype of the 112 specimens was typed by PCR. In total, G serotype was assigned for 95.2% of all the specimens, showing the highest rate of G4 (41.7%), followed by G1 (23.2%) and G2 (14.9%). Twenty-four specimens showed mixed types, such as G2 with G1, G8 or G9, or G1 with G4. These results indicate that PCR combined with ELISA is highly effective for G serotyping of rotavirus.

Molecular discrimination of enterotoxin C subtype in clinical isolates of Staphylococcus aureus

The subtype of staphylococcal enterotoxin C (SEC) of 33 S. aureus clinical isolates was determined by polymerase chain reaction and direct DNA sequencing of a portion of the SEC gene encoding the SEC subtype-specific region. With the exception of a single strain with the SEC2 gene, all other strains showing different biologic and genetic properties were proved to possess the SEC3 gene.

Detection and characterization of novel rotavirus strains in the United States

We recently established a rotavirus strain surveillance system in the United States to monitor the prevalent G serotypes before and after the anticipated implementation of a vaccination program against rotavirus and to identify the emergence of uncommon strains. In this study, we examined 348 rotavirus strains obtained in 1996 to 1997 from children with diarrhea in 10 U.S. cities. Strains were characterized for P and G types, subgroups, and electropherotypes by using a combination of monoclonal antibody immunoassay, reverse transcription-PCR, and hybridization. The four strains most commonly found worldwide comprised 83% of the isolates (P[8]G1, 66.4%; P[4]G2, 8.3%; P[8]G3, 6.9%; P[8]G4, 1.4%), but 9.2% were unusual strains (P[6]G9, 5.5%; P[8]G9, 1.7%; P[6]G1, 1.4%; and P[4]G1 and P[8]G2, 0. 3% each). Strains not typeable for P or G type accounted for 5.5% of the total, while 2.3% of the strains had more than one G type (mixed infections). All P[6]G9 strains tested had short electropherotypes and subgroup I specificity and were detected in 4 of 10 cities, while P[8]G9 strains had long electropherotypes and subgroup II VP6 antigens. Both sequence analysis of the VP7 open reading frame (about 94 to 95% amino acid identity with the VP7 gene of G9 prototype strain WI61) and binding to a G9-specific monoclonal antibody strongly suggest that U.S. G9 strains belong to serotype G9. The high detection rates of unusual rotaviruses with G9 (7.2%) or P[6] (6.9%) specificity in multiple U.S. cities suggest the emergence of new strains or inadequate diagnosis in the past. The epidemiologic importance of these strains remains to be determined.

Serological and genomic characterization of human rotaviruses detected in China

A total of 1,385 stool specimens were collected from children with diarrhea at two hospitals in Wuhan, Hubei Province, China, in 1994 and 1995, and screened for rotavirus by polyacrylamide gel electrophoresis of viral RNA. Group A rotavirus was detected with high frequency; 56.5% (87/154) and 40.8% (502/1,231) of the specimens collected in 1994 and 1995, respectively, were positive for rotavirus. Assignment of G serotype and P type (VP4 genotype) of group A rotavirus by ELISA with monoclonal antibodies and/or PCR, respectively, showed that strains of G2-P[4] and G1-P[8] specificity were predominant in 1994 and in 1995, respectively. In contrast, a single strain was found to have a P[9] type specificity, and no G4 strain was detected. Unusual combinations of RNA pattern-subgroup-G serotype-P type, such as long pattern-subgroup I-G1-P[8], short pattern-subgroup II-G3-P[4] and short pattern-subgroup I-G1-P[4], were detected in four specimens. Nucleotide sequences of the VP8* and/or NSP5 genes from two Chinese P[8] strains 470 and 582 and one Chinese P[9] strain 512 as well as five Japanese P[9] strains (K8, AU1, M318, 0264, and 0265) were determined and compared with the published sequences of the corresponding gene. In the phylogenetic tree of VP8* sequences of P[9] strains, which formed two clusters each having strain K8 or AU-1 as the representative strain, the Chinese P[9] strain was found in the cluster represented by AU-1, although it was most distantly related to other strains. While NSP5 sequences of human strains with P[9] specificity were related to simian and bovine strains, that of Chinese P[8] strains was most closely related to those of porcine strains. A single group C rotavirus (No. 208) was detected. Nucleotide sequences of its VP4, VP6, VP7, and NSP4 genes were very similar to those of group C human rotaviruses detected worldwide.

Preferential selection of heterologous G3-VP7 gene in the genetic background of simian rotavirus SA11 detected by using a homotypic single-VP7 gene-substitution reassortant

Introduction of segmented genomes into virion is an important process in viral replication of rotavirus. We previously studied the assortment of the VP7 gene segment (encoding outer capsid protein VP7) in the genetic background of simian rotavirus SA11 (G serotype 3, G3) and found the preferential selection of homologous G3 VP7 gene over VP7 gene of heterologous G serotype (G1, G2 or G4). In the present study, in order to clarify whether or not VP7 gene derived from different G3 rotavirus (heterologous G3-VP7 gene) is also preferentially selected in the SA11 background, a single-VP7 gene-substitution reassortant was prepared from SA11 through multiple steps of coinfection with rotaviruses in vitro. The isolated reassortant, SNR1, possessed VP7 gene derived from canine G3 rotavirus K9 and all other gene segments of SA11 origin, and showed an identical growth characteristic to that of SA11. Amino acid sequence of K9 VP7 gene showed a high degree of identity (93.6%) to SA11 VP7 gene. In analysis by mixed infection and multiple passages of SNR1 and a single VP7 gene (with G1, G2 or G4 specificity) reassortant in the SA11 background, the G3-VP7 gene became predominant at early passage numbers. However, in mixed infection with SA11 and SNR1, homologous G3-VP7 gene (SA11-VP7 gene) was preferentially selected into progenies over heterologous one (K9-VP7 gene). These results together with our previous findings suggested that G3-VP7 gene, irrespective of origin of species, was functionally adapted to the genetic background of SA11, although the homologous gene had a better fit with other SA11 genes than did heterologous one, providing suggestions for efficaciousness of multivalent reassortant rotavirus vaccine.

Analysis of diversity of mutations in the mecI gene and mecA promoter/operator region of methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis

Genomic diversity of mutation in the mecI gene or mecA promoter/operator region was analyzed for clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus epidermidis (MRSE). In most MRSA strains, a single base substitution was detected in either the mecI (three different positions) or the mecA promoter (two different positions), while a 28-base deletion in mecI was found in one strain. In contrast, no mutation was detected in these gene sequences of MRSE strains.

Survey of human group C rotaviruses in Japan during the winter of 1992 to 1993

Fecal specimens from patients with acute diarrhea were collected from 10 prefectures in Japan over a 6-month period (November 1992 to April 1993), and the specimens that were negative for human group A rotaviruses were screened for the presence of human group C rotaviruses (CHRVs) by the reverse passive hemagglutination test. Of 784 specimens examined, 53 samples (6.8%) that were collected in 7 of 10 prefectures were positive for CHRV, indicating that CHRVs are widely distributed across Japan. Most of the CHRV isolates were detected in March and April, and CHRVs mainly prevailed in children ages 3 to 8 years. The genome electropherotypes of eight strains isolated in five individual prefectures were surprisingly similar to each other and were different from those of CHRV strains isolated to date. The outer capsid glycoprotein (VP7) gene homologies of the isolates retrieved in 1993 were subsequently analyzed by the dot blot hybridization method. As a result, the VP7 genes of the isolates revealed very high levels of homology not only with each other but also with the VP7 gene of the OK118 strain isolated in 1988. These results suggest that a large-scale outbreak of CHRV occurred during the winter of 1992 and 1993 in Japan.

Outbreaks of nosocomial rotavirus gastro-enteritis in a paediatric ward

Faecal samples were collected from patients with gastro-enteritis during two winter seasons on a paediatric ward. Three outbreaks of nosocomial rotavirus gastro-enteritis were identified by latex agglutination and the virus strains were characterized by polyacrylamide gel electrophoresis of the genome nucleic acid and by subgrouping and serotyping enzyme-linked immunosorbent assays (ELISA). One outbreak was caused by serotype 1 rotavirus, one by serotype 2 and the remaining outbreak was caused by a mixture of serotypes 1 and 4. Identical electrophoretic patterns of the rotavirus genome in each outbreak combined with the ELISA results indicate that these three outbreaks were hospital-acquired cases. The index cases in the three outbreaks were community-acquired and one of two index cases in the second outbreak was hospital-acquired. On each occasion, susceptible roommates were easily infected from the index cases and then cross-infection occurred in the paediatric ward. Possible vehicles were the medical staff, especially doctors, parents of infected patients and infected patients who were moved to other rooms. One patient who had been treated with a series of antitumour therapies excreted rotaviruses in faeces for a long time period and probably played a role as a source of the outbreak. Moreover, some patients still excreted rotaviruses in their normal stool 1 week after recovery from gastro-enteritis. These findings indicate that continual examination of stool samples for rotaviruses until they are negative may be important to prevent the spread of rotavirus infection.

CONCLUSION

Nucleic acid analysis and serotyping ELISA are useful tools for analyzing nosocomial rotavirus gastro-enteritis and important to prevent the spread of rotavirus infection in institutions.

Sequence analysis of normal and rearranged NSP5 genes from human rotavirus strains isolated in nature: implications for the occurrence of the rearrangement at the step of plus strand synthesis

We determined the nucleotide sequences of normal and rearranged NSP5 genes from the human rotavirus strains (Mc323 and Mc345, respectively) which had previously been isolated from Thai infants with diarrhea in the same epidemic season. While the two strains shared G serotype 9 specificity and subgroup I specificity and they showed a high level of overall genomic relatedness to each other, they exhibited different RNA profiles; a long pattern for Mc323 and a super-short pattern for Mc345. Their NSP5 sequences were more closely related to those of porcine rotaviruses than to those of human rotaviruses. Mc345 NSP5 gene was shown to have concatemerization. In a head-to-tail orientation resulting in its length being 1182 bp, as compared with the Mc323 NSP5 sequence which was 664 bp in length. Sequence analysis suggested that the rearrangement found in the strain Mc345 occurred at the step of plus strand synthesis.

Genomic diversity of mec regulator genes in methicillin-resistant Staphylococcus aureus and Staphylococcus epidermidis

Low-affinity penicillin-binding protein PBP-2a encoded by mecA is closely related to methicillin resistance in staphylococci, and expression of PBP-2a is controlled by regulator elements encoded by mecR1 and mecI which are located adjacent to mecA on the chromosome. Deletion or mutation which occurred in mec regulator gene is considered to be associated with constitutive production of PBP-2a. The distribution of the mec regulator genes in 176 strains of Staphylococcus aureus and 33 strains of S. epidermidis isolated from a single hospital was studied by polymerase chain reaction amplification. Most clinical isolates of methicillin-resistant S. aureus (MRSA) (94.3%) and S. epidermidis (MRSE) (83.9%) possessed both mecI and mecR1 genes (type I), whereas no mec regulator genes were detected in mecA-negative isolates. In contrast, 7 MRSA and 5 MRSE isolates were found to have incomplete regulator genes, and they were classified into three groups; strains which lacked only mecI gene (type II), strains which lacked mecI and 3'-end of mecR1 gene (type III), and strains which lacked both regulator genes (type IV). Analysis of mecI gene from all the strains having mecI by restriction fragment length polymorphism after Mse I digestion indicated that three MRSA strains possessed one of the known point mutations identified previously. These findings indicated the predominance of a single type of MRSA possessing both mecI and mecR1 in the study period and also suggested a high genomic diversity in mec regulator region of staphylococci.

Selection of rotavirus VP7 gene in the genetic background of simian rotavirus SA11: implications for rotavirus reassortant vaccine development

We previously reported that the VP7 gene from simian rotavirus SA11 with G-serotype 3(G3-VP7 gene) was preferentially selected in the genetic background of SA11 compared with the G1- or G2-VP7 gene. In the present study, selection of the G4-VP7 gene in competition with G1-, G2- or G3-VP7 gene in the SA11 background was analyzed through mixed infection experiments using SA11 and SA11-human rotavirus single-VP7 gene-substitution reassortants with G-serotypes 1, 2, and 4 (G1-, G2- and G4-reassortant). In virus clones from coinfection of SA11 and G4-reassortant, the frequency of G4 virus decreased to 7% at the 3rd passage and the G4 virus disappeared at the 10th passage, whereas the majority of the clones possessed G3 specificity. However, the predominance of either of the viruses coinfected was not observed in the mixed infection with G4-reassortant and G1- or G2-reassortant. Although growth kinetics of SA11 and G4-reassortant was similar, G4-reassortant showed significantly smaller plaque size than SA11, G1- and G2-reassortant did. These results indicated that the G3-VP7 gene from SA11 might be preferentially selected in the SA11 genetic background compared with the G4-VP7 gene, and suggested that the introduction of a single G4-VP7 gene may affect growth characteristics of recipient virus SA11. These results together with our previous findings suggested the significance of genetic compatibility between recipient viral genes and foreign VP7 gene in the development of multivalent reassortant rotavirus vaccines.

G (VP7) serotype-dependent preferential VP7 gene selection detected in the genetic background of simian rotavirus SA11

We previously found the preferential selection of VP7 gene from a parent rotavirus strain SA11 with G serotype 3 (G3) in the sequential passages after mixed infection of simian rotavirus SA11 and SA11-human rotavirus single-VP7 gene-substitution reassortants with G1, G2, or G4 specificity. However, it has not been known whether or not VP7 genes derived from other strains with G3 specificity (G3-VP7 gene) are preferentially selected in the genetic background of SA11. To address this question, mixed infections followed by multiple passages were performed with a reassortant SA11-L2/KU-R1 (SKR1) (which possesses VP7 gene derived from G1 human rotavirus KU and other 10 genes of SA11 origin) and one of the five G3-rotaviruses, RRV, K9, YO, AK35, and S3. After the 10th passage, selection rates of SA11-L2/KU-R1 gene 9 (G1-VP7 gene) and gene 5 (NSP1 gene) reduced considerably (0 to 20.4%) in the clones obtained from all the coinfection experiments, while all or some of other segments were preferentially selected from SKR1 depending on the pairs of coinfection. When viral growth kinetics was examined, SKR1 exhibited better growth and reached a higher titer than any G3 viruses. Although the generated reassortants with VP7 gene and NSP1 gene derived from G3 viruses showed almost similar growth kinetics to that of SKR1 during the first 20 h of replication, the titers of these reassortants were higher than that of SKR1 after 36 h postinfection. The results obtained in this study suggested that G3-VP7 gene is functionally more adapted to the genetic background of SA11.

Nondefective rotavirus mutants with an NSP1 gene which has a deletion of 500 nucleotides, including a cysteine-rich zinc finger motif-encoding region (nucleotides 156 to 248), or which has a nonsense codon at nucleotides 153-155

We isolated two nondefective bovine rotavirus mutants (A5-10 and A5-16 clones) which have nonsense mutations in the early portion of the open reading frame of the NSP1 gene. In the NSP1 gene (1,587 bases long) of A5-10, a nonsense codon is present at nucleotides 153 to 155 just upstream of the coding region (nucleotides 156 to 230) of a cysteine-rich Zn finger motif. A5-16 gene 5 (1,087 bases long) was found to have a large deletion of 500 bases corresponding to nucleotides 142 to 641 of a parent A5-10 NSP1 gene and to have a nonsense codon at nucleotides 183 to 185, which resulted from the deletion. Expression of gene 5-specific NSP1 could not be detected in MA-104 cells infected with the A5-10 or A5-16 clone or in an in vitro translation system using the plasmids with gene 5 cDNA from A5-10 or A5-16. Nevertheless, both A5-10 and A5-16 replicated well in cultured cells, although the plaque size of A5-16 was extremely small.

Superantigen as a modifying factor in HIV infection

Superantigen is characterized as a potent stimulator of T cells through its unique interaction with major histocompatibility complex class II molecule and the V beta chain of T cell receptor. It has been reported that symptoms in several infectious diseases are associated with superantigen activity, i.e., abnormal reaction due to excess activation of T cells. However, the implications of superantigen in human immunodeficiency virus (HIV) infections have not been well elucidated. In this article, we review the possible mechanisms by which superantigens may modify HIV infections. In conclusion, superantigen is considered to be a factor that aggravates the immunodeficient state in HIV-infected patients through activation of HIV expression in infected T cells and monocytes, and facilitation of CD4 T cell depletion. Since exogenous superantigen is most likely to be provided by microbial infections such as Staphylococcus aureus infection, countermeasures against these complicating infections may be important to avert the detrimental impact of superantigens.

Serological and genomic characterization of porcine rotaviruses in Thailand: detection of a G10 porcine rotavirus

A total of 557 fecal specimens collected from piglets with diarrhea in Thailand were examined for rotavirus RNA by polyacrylamide gel electrophoresis. Twenty-three, one, and two samples were positive for group A, group B, and group C rotaviruses, respectively. Two samples exhibited two segments found in picobirnavirus RNA. RNA electropherotyping of 23 group A rotaviruses showed that they were classified into five patterns. By serotyping by enzyme-linked immunosorbent assay and PCR, viruses in 3 and 14 specimens were found to be serotype G3 and serotype G10, respectively. For one specimen, containing a serotype G10 virus (strain P343), virus was isolated in MA-104 cells, and the nucleotide sequences of the VP7 and VP4 genes were determined. Comparative sequence analysis and cross-neutralization tests showed that strain P343 has B223-like G10 and UK-like P7 serotype (or VP4 genotype 5) specificities. Rotaviruses having such antigenic specificities have not been detected in piglets. Thus, the interspecies transmission of rotaviruses between cows and pigs was suggested.

Effect of MDP-Lys(L18) as a mucosal immunoadjuvant on protection of mucosal infections by Sendai virus and rotavirus

To examine the effect of MDP-Lys(L18), a derivative of muramyl dipeptide (MDP), as a mucosal immunoadjuvant, we investigated its activity to augment host resistance against mucosal infections by Sendai virus and rotavirus in mice. In an experimental infection model using suckling mice (10-day-old) inoculated perorally (p.o.) with 1.5 x 10(6) p.f.u. mouse-1 of rotavirus strain SA11, intrarectal (i.r.) as well as p.o. administration of MDP-Lys(L18) (50 micrograms mouse-1) prior to virus infection markedly reduced rotavirus-induced diarrhea. Furthermore, when MDP-Lys(L18) was administered p.o. (1 mg mouse-1), i.r. (300 micrograms mouse-1) or intranasally (i.n., 100 micrograms mouse-1) various days before Sendai virus infection (2.6 x 10(4) HAD mouse-1), all the mucosal administration of MDP-Lys(L18) significantly protected a lethal infection of Sendai virus, showing a dose-dependent manner. However, the efficacy of MDP-Lys(L18) to induce the prophylactic activity against the viruses somewhat varied according to the administration route and timing. In time course analysis of virus isolation in vivo, the mice administered with MDP-Lys(L18) exhibited a significant reduction of both viruses in the lungs for Sendai virus and in the bowels for rotavirus. These results suggest that MDP-Lys(L18) is a potent mucosal immunoadjuvant to enhance nonspecific host resistance against two mucosal infectious viruses, Sendai virus and rotavirus.

The distribution of G and P types within isolates of bovine rotavirus in Japan

Various combinations of G type and P type were observed in 76 bovine rotavirus (BRV) strains isolated from 235 diarrheal calves in three prefectures of Japan in 1992-1994. The most prevalent combination was G6:P5 (46/76, 60.5%), followed by G10:P11 (13/76, 17.1%), G6:P11 (7/76, 9.2%) and G10:P5 (5/76, 6.6%). No G6:P1 strain of BRV was recognized from the isolates in the present study, though this type of BRV is well known as a suitable vaccine strain against BRV infection.

Structure and function of rotavirus NSP1

Studies on the structure and function of the nonstructural proteins (NSP1-NSP5) of rotaviruses are important for dissection of the morphogenesis and replication processes of rotavirus. Above all, NSP1, the product of gene 5, has several interesting features, such as extreme sequence diversity, a highly conserved cysteine-rich region, RNA-binding activity, accumulation on the cytoskeleton, and non-random segregation in reassortment. Recently, comparable NSP1 sequence analysis has been performed on a number of rotavirus strains from various species. Furthermore, characterization of mutants with rearranged NSP1 genes has helped to elucidate the structure-function interaction of NSP1. We isolated and characterized two interesting mutants which have a large deletion including the cysteine-rich region or a nonsense codon at the early portion in the open reading frame (ORF) of the NSP1 gene. In this report, we summarize the structure and function of NSP1.

Analysis of methicillin-resistant and methicillin-susceptible Staphylococcus aureus by a molecular typing method based on coagulase gene polymorphisms

A molecular typing method for Staphylococcus aureus based on coagulase gene polymorphisms (coagulase gene typing) was evaluated by examining a total of 240 isolates which comprised 210 methicillin-resistant S. aureus (MRSA) and 30 methicillin-susceptible S. aureus (MSSA) collected from a single hospital. By AluI restriction enzyme digestion of the PCR-amplified 3'-end region of the coagulase gene including 81-bp repeated units, the MRSA and MSSA isolates examined were divided into 6 and 12 restriction fragment length polymorphism (RFLP) patterns, respectively, whereas five patterns were commonly detected in MRSA and MSSA. MRSA isolates that showed a particular RFLP pattern were considered to be predominant in the hospital. Coagulase typing with type-specific antisera was also performed for all S. aureus isolates for comparison. Coagulase types II and VII were most frequently detected and included isolates with four and five different AluI RFLP patterns, respectively, whereas each of the other coagulase types corresponded to a single RFLP pattern. These results indicated that RFLP typing was more discriminatory than serological typing, for typing S. aureus and demonstrated its utility in epidemiologic investigation of S. aureus infection in hospitals.

Preferential selection of specific rotavirus gene segments in coinfection and multiple passages with reassortant viruses and their parental strain

We previously reported non-random selections of human rotavirus (HRV) Wa genes 2 and 5 in reassortant formation between HRV strains Wa and HN126 under selection pressure with neutralizing monoclonal antibodies. In order to study whether or not these genes are preferentially selected in the genetic background of a parental strain HN126 in vitro without selection pressures, coinfection and multiple passage experiments were performed between HN126 and one of three reassortants, C1, C1T and C1F; C1 possessed genes 2 and 5 derived from Wa and the other genes derived from HN126, while C1T and C1F were single gene reassortants having Wa gene 2 or Wa gene 5 in the genetic background of HN126, respectively. When MA-104 cells were coinfected with the same infectious units of HN126 and C1, Wa genes 2 and 5 of reassortant C1 became predominant within 10 repeated passages, although Wa gene 5 was selected more preferably than Wa gene 2. Similar results were obtained under different experimental conditions in which different doses of parental strains or different type of cells were used. Also, in coinfections of MA-104 cells with HN126 and C1T, or HN126 and C1F, Wa gene 2 or Wa gene 5 became predominant at the sixth passage. Analysis of viral growth curves indicated that two reassortants, C1 and C1F, replicated to a titre higher than HN126, while no difference in viral growth was observed between C1T and HN126. These results indicated that in the genetic background of HN126, Wa gene 5 might provide viruses with a growth advantage compared with its HN126 counterpart, while Wa gene 2 might be preferentially selected into reassortant clones through its greater functional capacity for assortment during viral replication.

Persistence of a single electropherotype and serotype (G6P5) of bovine rotavirus in calves on a closed dairy farm from 1990 to 1993

A virologic survey was conducted on calves with diarrhea associated with bovine rotavirus (BRV) on a closed dairy farm. The BRV was detected from 32 of 219 (14.6%) fecal specimens repeatedly collected from 56 calves born during the years 1992-1993, regardless of whether they had diarrhea. Most of the 32 strains were isolated from fecal specimens obtained from 2- to 6-week-old calves. After electrophoresis of double-stranded viral RNA from the 32 strains, genomic RNA migration patterns were similar to those of the predominant BRV strains isolated at the same farm during the years 1990-1991. All representative strains were identified as G serotype 6 (G6) and P type 5 (P5) by results of the virus-neutralization test and polymerase chain reaction procedure. Thus, BRV had no change in genomic RNA electropherotypes and serologic antigenicities in a closed dairy herd over a period of several years.

Preferential selection of VP7 gene from a parent rotavirus strain (SA11) in sequential passages after mixed infection with SA11 and SA11-human rotavirus single-VP7 gene-substitution reassortants

We studied the competitive growth among SA11-L2(G3) and its single-human VP7 gene-substitution reassortants SA11-L2/KU-R1(G1) and SA11-L2/DS1-R1(G2), which have the genetic background of SA11-L2, during sequential passages after mixed infection. When the same infectious units (m.o.i. of 5 p.f.u./cell) of SA11-L2 and a reassortant SA11-L2/KU-R1 were inoculated onto and passaged in MA104 cells, 88% of the virus clones isolated from the culture fluid at the 3rd passage belonged to G3, and all the clones from the 10th passage had G3 specificity. Even when SA11-L2/KU-R1 with titer 10 times higher than that of SA11-L2 was used in the coinfection, the predominance of clones with G3-VP7 was observed. Although G2 clones slightly surpassed G1 clones in number in the mixed culture of SA11-L2/KU-R1 and SA11-L2/DS1-R1, G3 clones predominated in the virus progeny from a mixed culture infected with the same titers of SA11-L2, SA11-L2/KU-R1, and SA11-L2/DS1-R1. However, no significant difference in viral growth was detected among SA11-L2 and the two reassortants.

Non-random selection of gene segment 3 and random selection of gene segment 5 observed in reassortants generated in vitro between rotavirus SA11 and RRV

A total of 154 clones of reassortants between rotavirus RRV and SA11 were isolated in vitro in order to compare the selection modes of each RNA segment in reassortant formation with those in the in vivo experiment (carried out by Gombold and Ramig) using the same parent strains in which the occurrence of non-random selection of gene segments 3 and 5 was observed. In reassortants isolated from a cross RRV x SA11-L2 (66 isolates) and a cross RRV x SA11-S1 (88 isolates), 36 and 57 different genotypes were identified, respectively. Segregation rates of SA11 RNA segments 1, 5, 8, 9 and 11 were significantly different as compared with those previously reported in the in vivo experiment. While RNA segment 3 was preferentially selected from an SA11 parent, the segregation rate of SA11 gene 5 was relatively low in vitro. Thus, the selection mode of rotavirus RNA segments was found to be different between in vivo and in vitro reassortments.

Detection of mecA, femA, and femB genes in clinical strains of staphylococci using polymerase chain reaction

MecA, a structural gene located on the chromosome of Staphylococcus aureus, characterizes methicillin-resistant S. aureus (MRSA), and femA and femB(fem) genes encode proteins which influence the level of methicillin resistance of S. aureus. In order to examine effectiveness of detecting mecA and fem genes in identification of MRSA, the presence of these genes in 237 clinically isolated strains of staphylococci was investigated by polymerase chain reaction (PCR). An amplified mecA DNA fragment of 533 base pairs (bp) was detected in 100% of oxacillin-resistant S. aureus, in 16.7% of oxacillin-sensitive S. aureus, in 81.5% of S. epidermidis, and in 58.3% of other coagulase-negative staphylococci (CNS). While the PCR product of femA (509 bp) or femB (651 bp) was obtained from almost all the S. aureus strains except for five oxacillin-resistant strains (2.5%), neither of these genes were detected in CNS. Therefore, the detection of femA and femB together with mecA by PCR was considered to be a more reliable indicator to identify MRSA by differentiating it from mecA-positive CNS than single detection of mecA.

Genotypic diversity of reassortants between simian rotavirus SA11 and human rotaviruses having different antigenic specificities and RNA patterns

A total of 200 clones of reassortants were generated in vitro between simian rotavirus SA11 (SA11-L2 strain) and each of five human rotavirus (HRV) strains with different antigenic specificities and RNA patterns. When culture fluid coinfected with parent viruses was subjected to repeated selection with anti-HRV-VP4 and anti-SA11-VP7 neutralizing monoclonal antibodies, all yielded progenies were antigenic mosaic reassortants possessing VP4 and VP7 derived from SA11 and HRV, respectively. In genomic analysis of viral RNA by PAGE, two and five different genotypes were identified in 40 clones, generated between SA11 and HRV strain Hochi (G serotype 4, G4) and between SA11 and KU (G1), respectively. In contrast, 11 and 17 genotypes were found in progenies between SA11 and subgroup I G2 HRV strain HN126 or DS-1, respectively. Although SA11 genes, except for the VP7 gene, were predominant in most reassortants, gene 5 was preferentially selected from HRV. Incorporation of HRV segments 1, 3 and 10 into progenies was more frequent in SA11 x HN126 and SA11 x DS-1 reassortants than in other reassortants. These results indicated that the extent of diversity of reassortant genotypes differs between the two groups of the parental HRV strain; one has subgroup I specificity and a short RNA pattern (DS-1 genogroup), while the other has subgroup II specificity and a long RNA pattern (Wa genogroup).

Effect of the selection pressure with anti-VP7 and anti-VP4 neutralizing monoclonal antibodies on reassortant formation between two human rotaviruses

In order to study the effect of selection pressure of anti-VP4 and anti-VP7 neutralizing monoclonal antibodies(N-MAbs) on reassortant formation, 424 reassortant clones were produced from mixed cultures of human rotavirus strains Wa and HN126 and their genotypes were analysed. Reassortant selection was done with four types of N-MAb: anti-VP4 MAb to Wa and anti-VP7 MAb to HN126(selection A); anti-VP4 MAb to HN126 and anti-VP7 MAb to Wa(selection B); anti-VP7 MAb to Wa(selection C); and anti-VP4 MAb to Wa(selection D). In each selection experiment, more than 100 clones were isolated, and the parental origin of RNA segments was identified by polyacrylamide gel electrophoresis. All clones isolated by selections A and B were found to be antigenic mosaic reassortants with the VP4 gene of HN126 and the VP7 gene of Wa and antigenic mosaic reassortants with the VP4 gene of Wa and the VP7 gene of HN126, respectively. Although in reassortants of both selections, RNA segments 2, 3, 5 and 6 were selected from strain Wa at considerably high rates, selection rates of RNA segments 1, 7, 8, and 11 were significantly different between selection A and B. In reassortants from selection C and D, selection rates of RNA segments 1, 3, 6, 7, 8, and 11 from Wa were significantly lower than those in selection A and B, whereas RNA segments 2 and 5 were almost exclusively selected from Wa as observed in selection A and B. These results indicated the presence of two types of nonrandom gene selection in reassortant formation, one strongly dependent on, and another irrespective of, the selection pressure with N-MAbs.

Survey on the distribution of the gene 4 alleles of human rotaviruses by polymerase chain reaction

The presence of six gene 4 alleles (or VP4 genotypes) in human rotaviruses has been recognized. Using 16 representative cultivable human rotavirus strains, we confirmed the specificity of VP4 genotyping by polymerase chain reaction (PCR) using the nested oligonucleotides specific to each of the four representative gene 4 alleles. Using the PCR, we surveyed the gene 4 alleles of 199 human rotaviruses in stools collected in Japan and Thailand. Strains with the gene 4 allele, corresponding to P1A serotype, were shown to be the most prevalent, but two strains with P2 gene 4 allele and one strain with P3 gene 4 allele were detected in Thailand and in Japan, respectively.

Species specificity and interspecies relatedness in VP4 genotypes demonstrated by VP4 sequence analysis of equine, feline, and canine rotavirus strains

We determined the nucleotide and deduced amino acid sequences of the VP4 genes of five equine, two feline, and two canine rotavirus strains. A high degree of homology (> 97.0%) was found among the VP4 amino acid sequences of the equine strains H2, FI-14, and FI23. Equine strain L338 has a distinct VP4 amino acid sequence from those of the other equine strains (78.1% or less homology), and the L338 VP4 exhibited more than 17.0% divergence at the amino acid level from those of rotavirus strains published so far. The VP4 amino acid sequence of equine strain H1, which showed low homology with those of other equine strains, shares > 95.4% homology to those of porcine strains OSU and YM. VP4 amino acid sequences of feline strain Cat97 and canine strains CU-1 and K9 showed a high degree of homology (96.8 to 97.2%) to one another, and were found to be quite similar (96.0-97.0% homology) to that of a human HCR3 strain recently characterized. Feline strain Cat2, whose VP4 sequence is distinct from that of strain Cat97, has a VP4 similar to those of human strains K8 and AU-1 (97.8 and 97.5% homologies at amino acid level, respectively). Thus, the VP4 sequences of rotaviruses showed species specificity and interspecies relatedness.

Characterization of a G14 equine rotavirus (strain CH3) isolated in Japan

Antigenic and genomic properties of equine rotavirus strain CH3 isolated in Japan were studied by cross-neutralization tests and nucleotide sequence determination of the VP4 and VP7 genes. It was shown that the strain CH3 belongs to G14 and shares VP4 genotype with strain H2.

Differences in plaque size and VP4 sequence found in SA11 virus clones having simian authentic VP4

We isolated five stable SA11 clones (TN-S1, TN-S2, TN-L1, TN-L2, and BN-S4) with different plaque sizes from two SA11 stocks. In polyacrylamide gel electrophoresis, the mobilities of the fourth, fifth, and seventh RNA segments of SA11 clones with large plaque size (TN-L1 and TN-L2) were faster than those of clones with small plaque size (TN-S1, TN-S2, and BN-S4). Nucleotide sequence determination of the fourth RNA segment identified a five-amino-acid difference in VP4s between the clones with large and small plaque sizes. The VP4 sequences of two clones with small plaque size (TN-S1 and BN-S4) were the same as the sequence of SA11-SEM reported by K. Nishikawa et al. (1988, J. Virol. 62, 4022-4026), while the VP4 sequences of the clones with large plaque size (TN-L1 and TN-L2) were similar, but not identical, to that reported by D. B. Mitchell and G. W. Both (1989, Nucleic Acids Res., 17, 2122). A single-gene reassortant, K8-L2.4, in which RNA segment 4 was derived from clone TN-L2 of SA11 virus and the other RNA segments were from strain K8, produced large plaques like TN-L2, suggesting that the five-amino-acid difference in VP4 between the clones with large and small plaque sizes might be associated with the difference in plaque size.

Genomic relatedness of five equine rotavirus strains with different G serotype and P type specificities

Overall genomic relatedness among five equine rotavirus strains and their relatedness to representative human and animal rotavirus strains were investigated by RNA-RNA hybridization tests. The genomes of strains FI-14, FI-23 and H2 were highly related to one another. Strain L338 had only a low degree of genomic relatedness to the other four equine rotavirus strains. Strain H1 also showed little genetic relatedness to the other equine strains. The genome of the strain H1, however, was highly related to those of porcine rotavirus strains OSU, Gottfried and YM. Genomic relatedness of four equine rotavirus strains (FI-14, FI-23, H2 and L338) to human and other animal rotavirus strains was low, whereas several RNA segments of strain H1 showed a relatedness to those of human strain Wa.

Serotyping of human rotavirus by enzyme immuno-assay with monoclonal antibodies

Two series of enzyme immunoassays with monoclonal antibodies produced in two laboratories (A and B) were compared in use for serotyping of human rotavirus in stool samples collected in Japan between 1988 and 1991 from patients with gastroenteritis. Of 358 samples, 222 were determined to be the same serotype, while 61 samples could not be serotyped by either assay. A hundred and one and 92 samples were not serotyped by the A and B antibodies, respectively. We believe that the A and B monoclonal antibodies are useful clinically for serotyping rotaviruses at the present time.