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. 2020 Jun;12(2):99-117.
doi: 10.1007/s12560-020-09426-0. Epub 2020 Apr 11.

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

Waled M El-Senousy  1 , Amel S M Abu Senna  2 , Nabil A Mohsen  3 , Seham F Hasan  2 , Nagwa M Sidkey  2
Affiliations

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

Waled M El-Senousy et al. Food Environ Virol. 2020 Jun.

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.

Keywords: Common P and G genotypes; Diarrhea; Human rotavirus group A; Non-silent mutation; Surveillance.

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Figures

Fig. 1
Fig. 1
Seasonal variations of rotavirus group A in Egyptian cases
Fig. 2
Fig. 2
Distribution of rotavirus group A in different ages
Fig. 3
Fig. 3
Frequency of common and uncommon G genotypes in the total positive rotavirus VP6 clinical specimens
Fig. 4
Fig. 4
Frequency of common and uncommon P genotypes in the total positive rotavirus VP6 clinical specimens
Fig. 5
Fig. 5
Frequency of common and uncommon G genotypes in the total positive rotavirus VP6 raw sewage samples
Fig. 6
Fig. 6
Frequency of common and uncommon P genotypes in the total positive rotavirus VP6 raw sewage samples
Fig. 7
Fig. 7
Phylogenetic tree of partial VP8 gene sequences of group A rotaviruses from P[8], P4], and P[6]. The evolutionary history was inferred using the Neighbor-Joining method. The sequenced studied Egyptian clinical specimens (EGY/SS1-EGY/SS45) and raw sewage samples (EGY/RSS1-EGY/RSS20) are shown with filled circles with ID from EGY/A1 to EGY/A6. EGY/A1 represented 4 isolates (EGY/SS1, SS3, SS10, and RSS3). EGY/A2 represented 17 isolates (EGY/SS2, SS4-SS8, SS11, SS13-SS17, RSS1, RSS2, and RSS5-RSS7). EGY/A3 represented 3 isolates (EGY/SS9, SS12, and RSS4). EGY/A4 represented 23 isolates (EGY/SS18-SS20, SS22, SS24-SS32, SS34, SS35, RSS8-RSS12, and RSS14-RSS16). EGY/A5 represented 4 isolates (EGY/SS21, SS23, SS33, and RSS13). EGY/A6 represented 14 isolates (EGY/SS36-SS45, RSS17-RSS20). The reference strains that showed highest similarity are labeled with empty triangles while the vaccine strains are labeled with empty circles and ID started with their GenBank accession numbers
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