Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010–2018

Arana, Ainara; Jere, Khuzwayo C.; Chaguza, Chrispin; Montes, Milagrosa; Alkorta, Miriam; Iturriza‐Gómara, Miren; Cilla, Gustavo

doi:10.1016/j.meegid.2019.03.016

Cited by 9 publications

(13 citation statements)

References 46 publications

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“…33,34 In this study, we observed that children infected with G12 strains tended to be younger, which is in contrast with the earlier reports form Gipuzkoa and eastern Brazilian coast. 35,36 In contrast to previous reports, we found the significant association of ages of children infected with G12 RVAs versus other strains. 10,37 Based on epidemiological data and phylogenetic analysis, G12…”

Section: Discussioncontrasting

confidence: 99%

“…The differences in disease severity may be due to the variations in virulence between rotavirus strains and the immune status of the community towards an infecting strain/serotype(s) 33,34 . In this study, we observed that children infected with G12 strains tended to be younger, which is in contrast with the earlier reports form Gipuzkoa and eastern Brazilian coast 35,36 . In contrast to previous reports, we found the significant association of ages of children infected with G12 RVAs versus other strains 10,37 …”

Section: Discussioncontrasting

confidence: 99%

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Phylogenetic analysis of VP7 and VP4 genes of the most predominant human group A rotavirus G12 identified in children with acute gastroenteritis in Himachal Pradesh, India during 2013–2016

Gupta

Gauhar

Bubber

et al. 2021

Journal of Medical Virology

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G12 strains are now considered to be the sixth most prevalent human rotaviruses globally. India has introduced rotavirus vaccine Rotavac® into the national immunization program in 2016 and Himachal Pradesh (HP) is the first state to launch it. During epidemiological rotavirus surveillance in HP, predominance of G12 rotaviruses was observed. This study investigated the genetic variability and evolution of HP G12 strains (n = 15) associated with P-genotypes P[6], P[4], and P[8] identified between 2013 and 2016. Phylogenetic analysis of VP7 gene revealed that all characterized G12 strains clustered in lineage-III and diversified into three subclusters indicating that these strains may have originated from three different ancestral G12 strains. The comparative sequence analysis of HP strains with Rotavac® and Rotarix® vaccine strains revealed various amino acid substitutions in epitope regions of VP7 and VP4 proteins especially at the antibody neutralization sites. Only 12/29 VP7 epitope residues and 2/25 VP4 epitope residues were found to be conserved between HP rotavirus strains and vaccine strains. Both long and short electropherotypes were observed in G12P[4] strains, while a single long electropherotype was observed in G12P[6] strains. Children of ≤11 months were significantly infected with G12 rotaviruses. The frequency of vomiting episodes (≥5/ day) was significantly higher in children infected with G12 rotavirus strains as compared to non-G12 rotaviruses (p = 0.0405). Our study provides the comprehensive data on clinical characteristics and evolutionary pattern of the G12 rotavirus, the most prevalent strain in HP and emphasizes the need to monitor these strains for inclusion in future vaccine.

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Section: Discussioncontrasting

confidence: 99%

Section: Discussioncontrasting

confidence: 99%

Phylogenetic analysis of VP7 and VP4 genes of the most predominant human group A rotavirus G12 identified in children with acute gastroenteritis in Himachal Pradesh, India during 2013–2016

Gupta

Gauhar

Bubber

et al. 2021

Journal of Medical Virology

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“…Our results show a coincident decline in the relative diversities and effective population sizes of all RVA segments after 2006. Supporting this analysis, several studies, including an analysis of G12 strains in Africa, G12 strains in Spain, and a lineage of P [8] strains also show a general decline in diversity/effective population size after 2008 [ 116 , 117 , 118 ].…”

Section: Discussionmentioning

confidence: 64%

Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

Dennehy

2021

Viruses

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Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.

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Section: Rotavirus Evolution Following the Introduction Of Rotavirus mentioning

confidence: 54%

Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

Dennehy

2021

Preprint

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Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortant-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different treespaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable treespaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the least conservation by host species. Bayesian skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to common host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.

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Molecular epidemiology of G12 rotavirus strains during eight consecutive epidemic seasons in the Basque Country (North of Spain), 2010–2018

Cited by 9 publications

References 46 publications

Phylogenetic analysis of VP7 and VP4 genes of the most predominant human group A rotavirus G12 identified in children with acute gastroenteritis in Himachal Pradesh, India during 2013–2016

Phylogenetic analysis of VP7 and VP4 genes of the most predominant human group A rotavirus G12 identified in children with acute gastroenteritis in Himachal Pradesh, India during 2013–2016

Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

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