Phylogenetic analysis of G1P[8] and G12P[8] rotavirus A samples obtained in the pre- and post-vaccine periods, and molecular modeling of VP4 and VP7 proteins

Almeida, Tâmera Nunes Vieira; Sousa, Teresinha Teixeira de; Silva, Roosevelt Alves da; Fiaccadori, Fabíola Souza; Souza, Menira; Badr, Kareem Rady; Cardoso, Divina das Dôres de Paula

doi:10.1016/j.actatropica.2017.06.009

Cited by 6 publications

(5 citation statements)

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“…Similar observations have been reported in several other studies [11,51,53], highlighting the likelihood of the epidemiological fitness of G1 strains in these two lineages, which has led to their prevalent circulation over time. Of the four P [8] lineages that have been established previously [11], the majority (84.2%) of the South African P [8] strains in this study clustered in P [8] lineage III, an observation comparable to other studies [51,[53][54][55]. Additionally, the South African P [8] strains were observed in P [8] lineage I and P [8] lineage IV (also designated as the OP354-like lineage) [56], an observation reported in a study of Indian P [8] strains [57].…”

Section: Discussionsupporting

confidence: 89%

Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years

et al. 2020

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Rotavirus G1P[8] strains account for more than half of the group A rotavirus (RVA) infections in children under five years of age, globally. A total of 103 stool samples previously characterized as G1P[8] and collected seven years before and seven years after introducing the Rotarix® vaccine in South Africa were processed for whole-genome sequencing. All the strains analyzed had a Wa-like constellation (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). South African pre- and post-vaccine G1 strains were clustered in G1 lineage-I and II while the majority (84.2%) of the P[8] strains were grouped in P[8] lineage-III. Several amino acid sites across ten gene segments with the exception of VP7 were under positive selective pressure. Except for the N147D substitution in the antigenic site of eight post-vaccine G1 strains when compared to both Rotarix® and pre-vaccine strains, most of the amino acid substitutions in the antigenic regions of post-vaccine G1P[8] strains were already present during the pre-vaccine period. Therefore, Rotarix® did not appear to have an impact on the amino acid differences in the antigenic regions of South African post-vaccine G1P[8] strains. However, continued whole-genome surveillance of RVA strains to decipher genetic changes in the post-vaccine period remains imperative.

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Section: Discussionsupporting

confidence: 89%

Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years

et al. 2020

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“…The VP7 encoding sequences of the 36 Mozambican G1P [8] strains, collected between 2012 to 2017 from non-vaccinated and vaccinated children ( Supplementary Table S3), were compared with human rotavirus sequences representing VP7 G1 lineages (I-VII) [21][22][23][24][25][26][27][28]. The Mozambican strains clustered into two distinct lineages, I and II ( Figure 1a).…”

Section: Sequence Analyses Of Vp7 and Vp4mentioning

confidence: 99%

“…Prevaccine Mozambican strains are indicated by blue squares, post-vaccine by red circles, the Rotarix ® vaccine strain by a green triangle and Mozambican strains from previous studies [14,19] are indicated by black triangles. Lineages are defined from I-VIII for VP7 and I-IV for VP4 [21][22][23][25][26][27][28]. [8] strains circulating in Mozambique and global strains obtained from GenBank.…”

Section: Sequence Analyses Of Vp7 and Vp4mentioning

confidence: 99%

Whole Genome Characterization and Evolutionary Analysis of G1P[8] Rotavirus A Strains during the Pre- and Post-Vaccine Periods in Mozambique (2012–2017)

et al. 2020

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Mozambique introduced the Rotarix® vaccine (GSK Biologicals, Rixensart, Belgium) into the National Immunization Program in September 2015. Although G1P[8] was one of the most prevalent genotypes between 2012 and 2017 in Mozambique, no complete genomes had been sequenced to date. Here we report whole genome sequence analysis for 36 G1P[8] strains using an Illumina MiSeq platform. All strains exhibited a Wa-like genetic backbone (G1-P[8]-I1-R1-C1-M1-A1-N1-T1-E1-H1). Phylogenetic analysis showed that most of the Mozambican strains clustered closely together in a conserved clade for the entire genome. No distinct clustering for pre- and post-vaccine strains were observed. These findings may suggest no selective pressure by the introduction of the Rotarix® vaccine in 2015. Two strains (HJM1646 and HGM0544) showed varied clustering for the entire genome, suggesting reassortment, whereas a further strain obtained from a rural area (MAN0033) clustered separately for all gene segments. Bayesian analysis for the VP7 and VP4 encoding gene segments supported the phylogenetic analysis and indicated a possible introduction from India around 2011.7 and 2013.0 for the main Mozambican clade. Continued monitoring of rotavirus strains in the post-vaccine period is required to fully understand the impact of vaccine introduction on the diversity and evolution of rotavirus strains.

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“…Responsible for high rates of morbidity and mortality in childhood, group A Rotavirus has a higher incidence and prevalence in underdeveloped countries, with populations without access to basic sanitation, mainly affecting children residing in these regions [3,4]. Immunization through the attenuated virus vaccine is effective in prevention and has reduced epidemiological indices [5][6][7].…”

Section: Introductionmentioning

confidence: 99%

Association among the Presence of Rotavirus Group A and Types of Sources Located in Rural Communities

Gonçalves

Lima

Silva

et al. 2023

Water

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Among the etiological agents of acute gastroenterocolitis, group A Rotavirus stands out. Proper hygiene and basic sanitation are the prophylactic means. The present research aimed to carry out the tracking of Rotavirus in waters of rural communities. The collections were carried out in 86 residences, distributed in 16 communities, considering the types of sources: tubular wells, excavated wells, surface springs, cistern with rainwater and springs. The elution of membranes with negative charges was used to obtain viral particles. Extraction of the genetic material and cDNA synthesis were performed according to the rules of the kit used, then qPCR was performed with an Applied Biosystems StepOne® thermal cycler. Statistical analysis was performed using Stata® 16.0, BioEstat® 5.3 and Minitab® 1. Rotavirus was detected in 47 samples (54.6%), however, there was no significant association among municipalities and the presence of Rotavirus. There was a strong association with shallow excavated well OR = 3.59 [1.05–12.28, p = 0.04]. The virus to infect humans and non-human animals, it can infect poultry, cattle and pigs. The presence of Rotavirus in surface water qualifies it as a biological marker of water quality and would occur through fecal contamination in water surface and underground.

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Phylogenetic analysis of G1P[8] and G12P[8] rotavirus A samples obtained in the pre- and post-vaccine periods, and molecular modeling of VP4 and VP7 proteins

Cited by 6 publications

References 65 publications

Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years

Whole Genome In-Silico Analysis of South African G1P[8] Rotavirus Strains before and after Vaccine Introduction over a Period of 14 Years

Whole Genome Characterization and Evolutionary Analysis of G1P[8] Rotavirus A Strains during the Pre- and Post-Vaccine Periods in Mozambique (2012–2017)

Association among the Presence of Rotavirus Group A and Types of Sources Located in Rural Communities

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