Clinical and Environmental Surveillance of Rotavirus Common Genotypes Showed High Prevalence of Common P Genotypes in Egypt

Abstract

The objective of this study was to compare the prevalence of human rotavirus group A common G and P genotypes in human Egyptian stool specimens and raw sewage samples to determine the most common genotypes for future vaccine development. From 1026 stool specimens of children with acute diarrhea and using nested RT-PCR, 250 samples (24.37%) were positive for human rotavirus group A. Using multiplex RT-PCR, rotavirus common P and G genotypes were detected as 89.20% and 46.40% of the positive clinical specimens respectively. This low percentage of common G genotypes frequency may affect the efficiency of the available live attenuated oral rotavirus vaccines [Rotarix® (human rotavirus G1P[8]) and RotaTeq® (reassortant bovine-human rotavirus G1-4P[5] and G6P[8])], however the percentage of clinical specimens which were negative for common G genotypes but positive for P[8] genotype was 12.00%. From 24 positive raw sewage samples for rotavirus group A VP6 collected from Zenin and El-Gabal El-Asfar wastewater treatment plants (WWTPs), 21 samples (87.50%) were typeable for common P genotypes while 13 samples (54.17%) were typeable for common G genotypes. Phylogenetic analysis of a VP8 partial gene of 45 P-typeable clinical isolates and 20 P-typeable raw sewage samples showed high similarity to reference strains and the majority of mutations were silent and showed lower to non-significant similarity with the two vaccine strains. This finding is useful for determining the most common antigens required for future vaccine development.

Molecular characterization of rotavirus Group A VP6 gene in Egyptian surface water, wastewater and diarrheal specimens

“…This has stimulated interest in an alternative non-living parental approach to vaccination. Although genotypes G1P8 and G1P4 were the highest prevalent genotypes in both Egyptian clinical specimens and environmental samples in the last twenty years, high diversity of other genotypes were observed in several studies (Villena et al, 2003;El-Esnawy et al, 2010;El-Senousy et al, 2014a;El-Senousy and Abou-Elela, 2017;El-Senousy et al, 2020). This may suggest the VP6 recombinant subunit vaccine as a candidate RoV vaccine in Egypt and other countries with high diversity of RoV genotypes.…”

“…The testing capability is inconsistent with infectivity of the virus (Li et al, 2002;El-Senousy et al, 2007;Parshionikar et al, 2010;Hamza and Bibby 2019). Although RotaRix vaccine was available in Egypt more than ten years ago and after that Rotateq vaccine became available, RoV prevalence was still high in both clinical specimens and environmental samples in comparison to its prevalence before the commercial vaccines availability in Egypt (Villena et al, 2003;El-Senousy et al, 2004;El-Senousy and ELmahdy, 2009;El-Esnawy et al, 2010;El-Senousy et al, 2013a;El-Senousy et al, 2013b;El-Senousy et al, 2014a;El-Senousy and Abou-Elela, 2017;El-Senousy et al, 2020). One explanation of this might be the fact that RoV vaccines are not in the free obligatory immunization program for children in Egypt and the relatively high price of the vaccines in the private sector.…”

“…These low variations in amino acid sequences in the samples which contained G1P8 genotype may suggest the VP6 recombinant subunit vaccine as a candidate vaccine for RoV which contained G1P8 genotype. However, this genotype in parallel with G1P4 genotype represent the most frequent genotypes in Egyptian clinical specimens and environmental samples (Villena et al, 2003;El-Esnawy et al, 2010;El-Senousy et al, 2014a;El-Senousy and Abou-Elela, 2017;El-Senousy et al, 2020). In our previous study which concerned with the VP8 partial gene (El-Senousy et al, 2020) and using the same samples of our present study, low variations in amino acid sequences in the VP8 partial gene between the samples contained G1P8 genotype in addition to the low number of samples contained non-silent mutations in comparison to the two RoV reference strains (human RoV Wa strain and human RoV A strain USA) were observed.…”

Occurrence of Human Enteric Viruses in Water Sources and Shellfish: A Focus on Africa

“… (Ibrahim et al 2016 ) N.D. Nested RT-PCR, RT-qPCR & ICC PCR VP7 SW (river) South Africa Mar 2011–Jan 2012 (Singh 2012 ) N.D. RT-qPCR VP7 WW (effluent) South Africa Sep 2012–Aug 2013 (Osuolale and Okoh 2017 ) N.D. RT-qPCR N.R. SW (river) & WW (effluent) Kenya Apr 2015–Apr 2016 (van Zyl et al 2019 ) G1, G3 & G9;P[4], P[6] & P[8] Nested RT-PCR † VP4 † , VP6 † & VP7 † Egypt Oct 2015–Mar 2017 (El-Senousy et al 2020 ) Group A Illumina Miseq N.A. DNW Kenya Jun–Aug 2016 (Hendriksen et al 2019 ) N.D. RT-qPCR N.R.…”

“…This review testifies to the extent of the problem on the African continent by reviewing over 100 investigations conducted in 13 African countries in which the occurrence of enteric viruses was described in a wide range of samples including not only raw sewage but also groundwater, open water sources, bivalve shellfish and, alarmingly, drinking water. While many of these studies are limited to simple molecular detection of specific viruses in selected samples a few go further to describe the quantification, prevalence and links to disease outbreaks (see for example: El-Senousy et al 2015 , 2020 ; Elmahdy et al 2019 ; Okubo et al 2019 ). When assessing the public health risks posed by enteric viruses in the environment, it must be acknowledged that standard molecular-based detection methods cannot discriminate between infectious viruses and non-viable virus particles and that additional data is needed for accurate risk estimates (Rodríguez et al 2009 ; Leifels et al 2016 ).…”