Circulating rotavirus G and P strains post rotavirus vaccination in Eastern Mediterranean Region

Almalki, Shaia Saleh R.

doi:10.15537/smj.2018.6.21394

Cited by 11 publications

(12 citation statements)

References 52 publications

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“…19 reported G1P[4] as the common genotype in sewage isolates in Nigeria. In addition, a previous study in Detroit, MI reported G1P[4] as the dominant circulating strain in children with severe diarrhea, 55 and a review by Almalki and colleagues 63 identified G1P[4] as the dominant strain in Yemen. The emergence of G1P[4] might have resulted from reassortment with G2P[4].…”

Section: Discussionmentioning

confidence: 99%

Human rotavirus VP4 and VP7 genetic diversity and detection of GII norovirus in Ibadan as Nigeria introduces rotavirus vaccine

et al. 2022

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Objective This cross-sectional study investigated the circulating strains of rotavirus and screened for noravirus in Ibadan, Nigeria as the country introduces the rotavirus vaccine into its national immunization program. Methods Sixty-five stool samples were collected from children younger than 5 years with clinically diagnosed diarrhea and screened for the presence of rotavirus and norovirus using RT-PCR. Rotavirus-positive samples were further analyzed to determine the G and P genotypes using semi-nested multiplex PCR. Results The rates of rotavirus and norovirus positivity were 30.8% and 10.8%, respectively, whereas the rate of rotavirus and norovirus mixed infection was 4.6%. G1 was the predominant VP7 genotype, followed by G2, G9, and G1G2G9, whereas the predominant VP4 genotype was P[4], followed by P[6], P[8], and P[9]. The mixed P types P[4]P[8] and P[4]P[6] were also detected. G1P[4] was the most common VP4 and VP7 combination, followed by G2P[4], G1[P6], G1P[8], G2P[6], G2P[9], G9P[6], G2G9P[4], G2P[4]P[6], G1P[4]P[8], G2G9P[8], G1G2G9P[8], and G1[non-typable] P[non-typable], which were detected in at least 5% of the samples. Four samples had a combination of non-typable G and P types. Conclusions It is essential to monitor the circulation of virus strains prior to and during the implementation of the immunization program.

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Section: Discussionmentioning

confidence: 99%

Human rotavirus VP4 and VP7 genetic diversity and detection of GII norovirus in Ibadan as Nigeria introduces rotavirus vaccine

et al. 2022

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“…However, vaccine effectiveness varied substantially by region [ 119 ] and resulted in changes to the circulating strain prevalence. For example, in a post-vaccine era, the prevalence of G9P [8], G2P [4], and G9P [4], G9P [8] increased, while the prevalence of G1P [8] and G3P [8] declined [ 120 , 121 , 122 , 123 ]. The emergence of rare genotypes or animal RVA reassortments in children also appears to be connected to the selective pressure imposed by vaccination.…”

Section: Discussionmentioning

confidence: 99%

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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“…The sequences obtained were cleaned by removing the overlapping sequences after comparison with the sequences obtained from paired-end sequencing using Bioedit v7.2 (Nucleics Co., Sydney, Australia). To compare nucleotide sequences obtained from water samples, phylogenetic analyses were performed for the resulting HRVA sequences against the HRVA G1 lineage represented by G1P[8], G9 lineage, including G9P[8], G2 lineage, including G2P[4] and G2P[8], as the later genotypes were reported as highly prevalent in Saudi Arabia and nearby countries 20 – 23 . The G12 lineage was designated as the outgroup.…”

Section: Methodsmentioning

confidence: 99%

“…So far, 36 G and 51 P types demonstrate intratypic variation 19 . The G1, G2, and G9 and the P 1 , P 4 , and P 8 genotypes have been frequently recorded at high prevalence in Saudi Arabia and its surrounding countries 20 – 23 . Moreover, fluctuations in rotavirus G-P type combinations are influenced by seasonal variations and geographical locations 19 .…”

Section: Introductionmentioning

confidence: 99%

Novel insights of waterborne human rotavirus A in Riyadh (Saudi Arabia) involving G2 predominance and emergence of a thermotolerant sequence

Nour

Hanif

Alanazi

et al. 2021

Sci Rep

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The routine evaluation of water environments is necessary to manage enteric virus-mediated fecal contamination and the possible emergence of novel variants. Here, we detected human rotavirus A (HRVA) circulating in two wastewater treatment plants, two lakes, irrigation water and a wastewater landfill located in Riyadh. VP7-derived surface protein sequences were assessed by phylogenetic analyses and inspection of thermotolerance-mediated secondary structure and seasonal variation. HRVA was most prevalent at An-Nazim wastewater landfill (AN-WWLF; 63.89%). Phylogenetic analyzes revealed the predominance of HRVA G2 lineage for the first time in Saudi Arabia. Moreover, a single HRVA sequence (2B64I-ANLF3/2018) was recovered at 45 °C from AN-WWLF; secondary structure prediction indicated that this sequence was thermotolerant with a high hydrophobicity, an absence of Ramachandran outliers, and a higher content of proline patches on the protein surface. Varied relationships were significantly observed between sampling areas influenced by temperature ranges (p < 0.05). HRVA prevalence was influenced by seasonal variations, favoring moderate temperatures in late autumn and early winter in all locations. However, a significant temperature impact was detected in Wadi-Hanifah Lake (p = 0.01). Our study extends the knowledge of currently circulating HRVA genotypes, and indicates the probable emergence of thermotolerant strains and seasonally mediated HRVA prevalence.

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Circulating rotavirus G and P strains post rotavirus vaccination in Eastern Mediterranean Region

Cited by 11 publications

References 52 publications

Human rotavirus VP4 and VP7 genetic diversity and detection of GII norovirus in Ibadan as Nigeria introduces rotavirus vaccine

Human rotavirus VP4 and VP7 genetic diversity and detection of GII norovirus in Ibadan as Nigeria introduces rotavirus vaccine

Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns

Novel insights of waterborne human rotavirus A in Riyadh (Saudi Arabia) involving G2 predominance and emergence of a thermotolerant sequence

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