Identification of rotavirus genogroups by RNA-RNA hybridization

Nakagomi, Osamu; Nakagomi, Toyoko; Akatani, Kaoru; Ikegami, Nobuko

doi:10.1016/0890-8508(89)90006-6

Cited by 147 publications

(122 citation statements)

References 30 publications

Supporting

Mentioning

116

Contrasting

Unclassified

Order By: Relevance

“…The 95H115 probe formed 8 hybrid bands with the genomic RNA from Wa, whereas it formed but two faintly visible hybrid bands with either the KUN or the AU-1 genome (Fig. 1), indicating that the 95H115 strain belongs to the Wa genogroup of human rotavirus (17). When hybridized with the genomic RNAs from earlier G9 strains available in our laboratory, the 95H115 probe formed 10 hybrid bands with the AU32 genome, 9 with the WI61 genome, and 8 with the 116E genome ( Fig.…”

mentioning

confidence: 99%

See 1 more Smart Citation

Genogroup Characterization of Reemerging Serotype G9 Human Rotavirus Strain 95H115 in Comparison with Earlier G9 and Other Human Prototype Strains

Nakagomi

2002

Microbiology and Immunology

Self Cite

View full text Add to dashboard Cite

Group A rotavirus, or species Rotavirus A, is the single most important etiological agent of acute gastroenteritis in infants and young children worldwide (12). Although 15 G serotypes have been described in the literature (12), G1 G4 were shown to be the G serotypes most frequently found in human rotaviruses (14). G9 human rotaviruses, however, emerged globally in the mid-'90s and thereafter, and these G9 strains were reported to predominate in some geographic settings (1,2,10,15). A human rotavirus strain 95H115 is a G9 isolate detected in Japan in the 1994 95 season, the first time after a 9-year interval (19) since prototype G9 strains AU32 and F45 were discovered in the 1985 86 season (8, 18). We recently sequenced the VP7 genes of AU32 and 95H115, compared them with other G9 VP7 genes, and concluded that the 95H115 VP7 gene did not directly evolve from the AU32 VP7 gene. We found that it was much more closely related to its contemporary G9 VP7 genes found in the United States, such as the one carried by US1205 (19). This observation was confirmed and extended by phylogenetic analysis with an increasing number of recently emerging G9 strains (23). Because the genetic background of the U.S. G9 strains was the DS-1 genogroup (13, 23), Kirkwood et al. (13) speculated that unlike Indian 116E, which resulted from reassortment between strains from the Wa and bovine genogroups (7), US1205 arose through a reassortment between two human strains belonging to the DS-1 and Wa genogroups. Since 95H115 had a long RNA pattern, we presumed that 95H115 was a Wa genogroup strain and that 95H115, or its relatives, could be the candidate of the G9 VP7 gene donor strain that Kirkwood et al. had speculated on. As a first step to examine this hypothesis, we thought it necessary to determine by RNA-RNA hybridization the genogroup of 95H115 together with its overall genetic relationships to Indian 116E and prototype G9 strains in the mid-'80s, i.e., AU32 and WI61.From the stool specimen 95H115, in which we previously reported to contain a G9 rotavirus, a rotavirus was isolated in cell culture and designated strain 95H115. Although this virus grew poorly and resisted plaque cloning, polyacrylamide gel electrophoresis of its genomic RNA showed a single electropherotype. Other human rotavirus strains used in this study were Wa (G1, P1A [8] Abstract: Serotype G9 human rotaviruses have emerged globally since the mid-1990s. The 95H115 strain was derived from a stool specimen collected in Japan in the 1994 95 season, thus it is the earliest of the globally reemerging G9 human rotaviruses that were adapted to cell culture. Genogrouping by RNA-RNA hybridization was performed to examine the genetic background of 95H115. The 95H115 strain belonged to the Wa genogroup, the most common human rotavirus genogroup, and it had a high degree of homology with AU32 and WI61, the prototype G9 isolates in the 1980s. However, the divergent genomic RNA constellation as indicated by the aberrant hybridization patterns between 95H115 and earlier G9 strains ...

show abstract

mentioning

confidence: 99%

“…Genogrouping by RNA-RNA hybridization was performed as previously described (17). Briefly, the 32 Plabeled single-stranded RNA probes from strains 95H115 and 116E were hybridized to the denatured genomic RNAs from a panel of human rotaviruses.…”

mentioning

confidence: 99%

Genogroup Characterization of Reemerging Serotype G9 Human Rotavirus Strain 95H115 in Comparison with Earlier G9 and Other Human Prototype Strains

Nakagomi

2002

Microbiology and Immunology

Self Cite

View full text Add to dashboard Cite

show abstract

“…The great diversity of human rotaviruses has been contributed by possible transmission from animal rotaviruses, either as whole viruses [38] or by contributing individual genes during reassortment in mixed infections [60]. Animal rotaviruses are even more flexible and exhibit a greater number of possible G/P combination than human rotaviruses.…”

Section: Animal Strains and The Zoonotic Potential Of Human Rotavirusmentioning

confidence: 99%

Rotavirus Infection: A Perspective on Epidemiology, Genomic Diversity and Vaccine Strategies

Mukherjee

Chawla‐Sarkar

2011

Indian J. Virol.

View full text Add to dashboard Cite

“…Genogrouping by RNA-RNA hybridization RNA-RNA hybridization was carried out as previously described [18]. Briefly, the genomic RNA was transcribed into 11 positive-sense RNAs (i.e., transcription probes) in the presence of [ 32 P]-labelled GTP by using endogenous viral RNA polymerase present in purified double-layered particles.…”

Section: Cell Culture Adaptation Of Strainsmentioning

confidence: 99%

“…While it was reported that there was no statistically significant difference in vaccine efficacy against G1 and non-G1 genotypes in the clinical trial [8], we considered it important to examine whether the strain variation observed for the two surface protein genes extended to the other genome segments. Of note, there is a considerable lack of overall genomic RNA homology between human rotavirus strains with long RNA patterns (as represented by the Wa strain; hence called the Wa genogroup to which RIX4414 belongs), and human rotavirus strains with short RNA patterns (as represented by the DS-1 strain; hence called the DS-1 genogroup to which strains including genotype G2P [4] belong) [18][19][20]. The aim of this study was to compare by RNA-RNA hybridization the whole genomic RNA constellation of circulating wild-type rotaviruses detected during the clinical trial in Malawi with RIX4414 (the strain contained in Rotarix).…”

Section: Introductionmentioning

confidence: 99%

Molecular characterization of rotavirus strains detected during a clinical trial of a human rotavirus vaccine in Blantyre, Malawi

Nakagomi¹,

Nakagomi²,

Dove³

et al. 2012

Vaccine

Self Cite

View full text Add to dashboard Cite

The human, G1P [8] rotavirus vaccine (Rotarix) significantly reduced severe rotavirus gastroenteritis episodes in a clinical trial in South Africa and Malawi, but vaccine efficacy was lower in Malawi (49.5%) than reported in South Africa (76.9%) and elsewhere. The aim of this study was to examine the molecular relationships of circulating wild-type rotaviruses detected during the clinical trial in Malawi to RIX4414 (the strain contained in Rotarix) and to common human rotavirus strains. Of 88 rotavirus-positive, diarrhoeal stool specimens, 43 rotaviruses exhibited identifiable RNA migration patterns when examined by polyacrylamide gel electrophoresis. The genes encoding VP7, VP4, VP6 and NSP4 of 5 representative strains possessing genotypes G12P[6], G1P[8], G9P [8], and G8P[4] were sequenced. While their VP7 (G) and VP4 (P) genotype designations were confirmed, the VP6 (I) and NSP4 (E) genotypes were either I1E1 or I2E2, indicating that they were of human rotavirus origin. RNA-RNA hybridization using 21 culture-adapted strains showed that Malawian rotaviruses had a genomic RNA constellation common to either the Wa-like or DS-1 like human rotaviruses. Overall, the Malawi strains appear similar in their genetic make-up to rotaviruses described in countries where vaccine efficacy is greater, suggesting that the lower efficacy in Malawi is unlikely to be explained by the diversity of circulating strains.

show abstract

Identification of rotavirus genogroups by RNA-RNA hybridization

Cited by 147 publications

References 30 publications

Genogroup Characterization of Reemerging Serotype G9 Human Rotavirus Strain 95H115 in Comparison with Earlier G9 and Other Human Prototype Strains

Genogroup Characterization of Reemerging Serotype G9 Human Rotavirus Strain 95H115 in Comparison with Earlier G9 and Other Human Prototype Strains

Rotavirus Infection: A Perspective on Epidemiology, Genomic Diversity and Vaccine Strategies

Molecular characterization of rotavirus strains detected during a clinical trial of a human rotavirus vaccine in Blantyre, Malawi

Contact Info

Product

Resources

About