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Human infection with G12 rotaviruses, Germany.

Pietsch C, Liebert UG - Emerging Infect. Dis. (2009)

Bottom Line: Rotavirus group A G12 genotypes were detected in 3 (1.5%) of 198 stool samples positive for human rotavirus.G12P[6] was present in 2 samples, and a mixed G3G12P[8] was found in 1 sample.Phylogenetic analysis of complete open reading frames of all 11 genomic RNA segments proved their Wa-like genogroup affiliation.

View Article: PubMed Central - PubMed

Affiliation: Institute of Virology, Leipzig University, Leipzig, Germany. corinna.pietsch@medizin.uni-leipzig.de

ABSTRACT
Rotavirus group A G12 genotypes were detected in 3 (1.5%) of 198 stool samples positive for human rotavirus. G12P[6] was present in 2 samples, and a mixed G3G12P[8] was found in 1 sample. Phylogenetic analysis of complete open reading frames of all 11 genomic RNA segments proved their Wa-like genogroup affiliation.

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Phylogenetic dendrogram of viral protein 4 (VP4) P[6] and P[8] rotaviruses at the amino acid level. Bootstraps values (1,000 replicates) >65% are shown. The strain name is prefixed by the country of origin (AUS, Australia; BRA, Brazil; BAN, Bangladesh; BEL, Belgium; DRC, Democratic Republic of Congo; GER, Germany; JAP, Japan; MAL, Malawi; PRC, People’s Republic of China; SKO, South Korea; UK, United Kingdom; USA, United States of America; VEN, Venezuela) as well as the viral host (Hu, human) and followed by the associated G genotype. Boldface indicates strains of this study. GenBank accession numbers of VP4 genes compared: P[6] B1711 ABU49763, CAU195 ABK62863, CAU214 ABK62864, Dhaka12–03 ABA34207, DRC86 AAY55972, M37 AAA57560, Matlab13–03 ABA34208, MMC147 ACJ54810, MMC24 ACJ54809, MMC29 ACJ54804, MW23 CAB92920, N26–02 ABA34209, NnB1 AAC68884, RV161–00 ABF67555, RV176–00 ABF67561, RV3 AAB05652, S12/85 AAC68883, SK277 ACJ54805, SK423 ACJ54803, ST3 ABV53292, US1205 AAC28852, XJ00–486 ABC49694, XJ99–468 ABC49698; P[8] 90–513 BAF80182, 95–87 BAA77555, B3458 ABV66093, B4633–03 ABA34205, CAU202 ABK62865, CAU219 ACD50869, D ABV53244, DH402 ACJ54815, Dhaka16–03 ABF50136, Dhaka25–02 ABA34206, DRC88 AAY55961, Hochi BAB32852, IAL28 ABV53260, KU BAE76023, MO BAA77543, P ABV53276, SK424 ACJ54811, SK430 ACJ54817, Wa AAA47290, Wi61 ABV53300, YO BAA77544.
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Figure 2: Phylogenetic dendrogram of viral protein 4 (VP4) P[6] and P[8] rotaviruses at the amino acid level. Bootstraps values (1,000 replicates) >65% are shown. The strain name is prefixed by the country of origin (AUS, Australia; BRA, Brazil; BAN, Bangladesh; BEL, Belgium; DRC, Democratic Republic of Congo; GER, Germany; JAP, Japan; MAL, Malawi; PRC, People’s Republic of China; SKO, South Korea; UK, United Kingdom; USA, United States of America; VEN, Venezuela) as well as the viral host (Hu, human) and followed by the associated G genotype. Boldface indicates strains of this study. GenBank accession numbers of VP4 genes compared: P[6] B1711 ABU49763, CAU195 ABK62863, CAU214 ABK62864, Dhaka12–03 ABA34207, DRC86 AAY55972, M37 AAA57560, Matlab13–03 ABA34208, MMC147 ACJ54810, MMC24 ACJ54809, MMC29 ACJ54804, MW23 CAB92920, N26–02 ABA34209, NnB1 AAC68884, RV161–00 ABF67555, RV176–00 ABF67561, RV3 AAB05652, S12/85 AAC68883, SK277 ACJ54805, SK423 ACJ54803, ST3 ABV53292, US1205 AAC28852, XJ00–486 ABC49694, XJ99–468 ABC49698; P[8] 90–513 BAF80182, 95–87 BAA77555, B3458 ABV66093, B4633–03 ABA34205, CAU202 ABK62865, CAU219 ACD50869, D ABV53244, DH402 ACJ54815, Dhaka16–03 ABF50136, Dhaka25–02 ABA34206, DRC88 AAY55961, Hochi BAB32852, IAL28 ABV53260, KU BAE76023, MO BAA77543, P ABV53276, SK424 ACJ54811, SK430 ACJ54817, Wa AAA47290, Wi61 ABV53300, YO BAA77544.

Mentions: Direct sequencing of gel-purified GER126-08 VP7 amplicons resulted in peak superpositions in sequencing gels; the sequencing of clones of this isolate showed a mixture of G3 and G12 genotypes. Contamination was excluded by a second RNA extraction and by comparing sequences to all G3 and G12 types detected in 2008, which were distinct. An amino acid alignment of VP7 G3 showed highest identity (97.5%) to G3 strains from Southeast Asia (data not shown). The G12 genotype belonged to G12-III lineage but was distinct from published full-length sequences, including the only European sequence from Belgium (Figure 1). Highest homology (97.8%) was shown in comparison to the Indian strain 14B2 (Appendix Table). Partial sequence data from European isolates showed no closer relationship, and G12 was not detected in 19 porcine rotaviruses from different piggeries of Saxony (data not shown). Amplification of VP1–4, VP6, and NSP1–5 by gene segment-specific consensus primers within conserved regions in the respective 5′ and 3′ ends was performed. No peak superposition occurred in sequencing of these amplicons, that is, only 1 variant of each genomic RNA segment could be detected. This finding indicates recent reassortment events. Although less likely, minor species of these 10 genomic RNA segments are not entirely excluded; they might have been missed in amplification or cloning and sequencing. The deduced amino acid sequences (Appendix Table) signified a Wa-like genogroup virus (G3G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1) (11,12). Its VP4 genomic RNA segment was phylogenetically related to those of Japanese G3 and G4 genotypes (Figure 2) and distinct from all other P[8] genotypes of this collection (data not shown). The origin of the associated genomic RNA segments from either a G3 or a G12 type rotavirus remains unclear, due to the lack of substantial numbers of available full-length sequences.


Human infection with G12 rotaviruses, Germany.

Pietsch C, Liebert UG - Emerging Infect. Dis. (2009)

Phylogenetic dendrogram of viral protein 4 (VP4) P[6] and P[8] rotaviruses at the amino acid level. Bootstraps values (1,000 replicates) >65% are shown. The strain name is prefixed by the country of origin (AUS, Australia; BRA, Brazil; BAN, Bangladesh; BEL, Belgium; DRC, Democratic Republic of Congo; GER, Germany; JAP, Japan; MAL, Malawi; PRC, People’s Republic of China; SKO, South Korea; UK, United Kingdom; USA, United States of America; VEN, Venezuela) as well as the viral host (Hu, human) and followed by the associated G genotype. Boldface indicates strains of this study. GenBank accession numbers of VP4 genes compared: P[6] B1711 ABU49763, CAU195 ABK62863, CAU214 ABK62864, Dhaka12–03 ABA34207, DRC86 AAY55972, M37 AAA57560, Matlab13–03 ABA34208, MMC147 ACJ54810, MMC24 ACJ54809, MMC29 ACJ54804, MW23 CAB92920, N26–02 ABA34209, NnB1 AAC68884, RV161–00 ABF67555, RV176–00 ABF67561, RV3 AAB05652, S12/85 AAC68883, SK277 ACJ54805, SK423 ACJ54803, ST3 ABV53292, US1205 AAC28852, XJ00–486 ABC49694, XJ99–468 ABC49698; P[8] 90–513 BAF80182, 95–87 BAA77555, B3458 ABV66093, B4633–03 ABA34205, CAU202 ABK62865, CAU219 ACD50869, D ABV53244, DH402 ACJ54815, Dhaka16–03 ABF50136, Dhaka25–02 ABA34206, DRC88 AAY55961, Hochi BAB32852, IAL28 ABV53260, KU BAE76023, MO BAA77543, P ABV53276, SK424 ACJ54811, SK430 ACJ54817, Wa AAA47290, Wi61 ABV53300, YO BAA77544.
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Figure 2: Phylogenetic dendrogram of viral protein 4 (VP4) P[6] and P[8] rotaviruses at the amino acid level. Bootstraps values (1,000 replicates) >65% are shown. The strain name is prefixed by the country of origin (AUS, Australia; BRA, Brazil; BAN, Bangladesh; BEL, Belgium; DRC, Democratic Republic of Congo; GER, Germany; JAP, Japan; MAL, Malawi; PRC, People’s Republic of China; SKO, South Korea; UK, United Kingdom; USA, United States of America; VEN, Venezuela) as well as the viral host (Hu, human) and followed by the associated G genotype. Boldface indicates strains of this study. GenBank accession numbers of VP4 genes compared: P[6] B1711 ABU49763, CAU195 ABK62863, CAU214 ABK62864, Dhaka12–03 ABA34207, DRC86 AAY55972, M37 AAA57560, Matlab13–03 ABA34208, MMC147 ACJ54810, MMC24 ACJ54809, MMC29 ACJ54804, MW23 CAB92920, N26–02 ABA34209, NnB1 AAC68884, RV161–00 ABF67555, RV176–00 ABF67561, RV3 AAB05652, S12/85 AAC68883, SK277 ACJ54805, SK423 ACJ54803, ST3 ABV53292, US1205 AAC28852, XJ00–486 ABC49694, XJ99–468 ABC49698; P[8] 90–513 BAF80182, 95–87 BAA77555, B3458 ABV66093, B4633–03 ABA34205, CAU202 ABK62865, CAU219 ACD50869, D ABV53244, DH402 ACJ54815, Dhaka16–03 ABF50136, Dhaka25–02 ABA34206, DRC88 AAY55961, Hochi BAB32852, IAL28 ABV53260, KU BAE76023, MO BAA77543, P ABV53276, SK424 ACJ54811, SK430 ACJ54817, Wa AAA47290, Wi61 ABV53300, YO BAA77544.
Mentions: Direct sequencing of gel-purified GER126-08 VP7 amplicons resulted in peak superpositions in sequencing gels; the sequencing of clones of this isolate showed a mixture of G3 and G12 genotypes. Contamination was excluded by a second RNA extraction and by comparing sequences to all G3 and G12 types detected in 2008, which were distinct. An amino acid alignment of VP7 G3 showed highest identity (97.5%) to G3 strains from Southeast Asia (data not shown). The G12 genotype belonged to G12-III lineage but was distinct from published full-length sequences, including the only European sequence from Belgium (Figure 1). Highest homology (97.8%) was shown in comparison to the Indian strain 14B2 (Appendix Table). Partial sequence data from European isolates showed no closer relationship, and G12 was not detected in 19 porcine rotaviruses from different piggeries of Saxony (data not shown). Amplification of VP1–4, VP6, and NSP1–5 by gene segment-specific consensus primers within conserved regions in the respective 5′ and 3′ ends was performed. No peak superposition occurred in sequencing of these amplicons, that is, only 1 variant of each genomic RNA segment could be detected. This finding indicates recent reassortment events. Although less likely, minor species of these 10 genomic RNA segments are not entirely excluded; they might have been missed in amplification or cloning and sequencing. The deduced amino acid sequences (Appendix Table) signified a Wa-like genogroup virus (G3G12-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1) (11,12). Its VP4 genomic RNA segment was phylogenetically related to those of Japanese G3 and G4 genotypes (Figure 2) and distinct from all other P[8] genotypes of this collection (data not shown). The origin of the associated genomic RNA segments from either a G3 or a G12 type rotavirus remains unclear, due to the lack of substantial numbers of available full-length sequences.

Bottom Line: Rotavirus group A G12 genotypes were detected in 3 (1.5%) of 198 stool samples positive for human rotavirus.G12P[6] was present in 2 samples, and a mixed G3G12P[8] was found in 1 sample.Phylogenetic analysis of complete open reading frames of all 11 genomic RNA segments proved their Wa-like genogroup affiliation.

View Article: PubMed Central - PubMed

Affiliation: Institute of Virology, Leipzig University, Leipzig, Germany. corinna.pietsch@medizin.uni-leipzig.de

ABSTRACT
Rotavirus group A G12 genotypes were detected in 3 (1.5%) of 198 stool samples positive for human rotavirus. G12P[6] was present in 2 samples, and a mixed G3G12P[8] was found in 1 sample. Phylogenetic analysis of complete open reading frames of all 11 genomic RNA segments proved their Wa-like genogroup affiliation.

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Related in: MedlinePlus