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

Abstract

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.

Molecular Epidemiology and Surveillance of Human Adenovirus and Rotavirus A Associated Gastroenteritis in Riyadh, Saudi Arabia

“…The yielded RNA was initially reverse transcribed using the Sensiscript ® RT Kit (SensRT; Qiagen GmbH, Hilden, Germany) in a 20 μL reaction mixture consisting of 2 μL template RNA and 18 μL RT mixture (containing 2 μL 10× RT buffer, 2 μL dNTPs, 2 μL random hexamers [final concentration of 10 μM], 1 μL Sensiscript RT, 1 μL RNase inhibitor [40 U·μL −1 ], and 10 μL nuclease-free water with incubation at 37 °C for 1 h). For HRV detection, PCR was conducted in a 20 μL reaction mixture consisting of 2 μL cDNA template, 500 nM RComb-F: 5′-CCACAAYTDTATTGTGATTA-3′ and RComb-R: 5′-CCCATYGATATCCAYTTATT-3′ [ 18 ], 500 nM reverse primer, and 1× Phusion Master Mix (Thermo Fisher Scientific, Waltham, MA, USA). This was performed under the following reaction conditions: 98 °C for 30 s, followed by 40 cycles of 98 °C for 10 s, 50 °C for 30 s, and 72 °C for 30 s each, and a final extension at 72 °C for 5 min.…”

Insights into Gastrointestinal Virome: Etiology and Public Exposure

“…This could be owing to its broad tolerance to a wide range of temperatures (−20 • C to 37 • C) and pH levels (3 to 11) without a significant infectivity loss [100][101][102][103][104]. However, rotavirus A prevalence is influenced by seasonal variations, favoring lower temperatures in temperate countries [22,105], unlike the endemic manner of rotavirus in tropical countries [106]. In terms of rotavirus frequency, sewage influent of Brazil and, surprisingly, wastewater treatment plant (WWTP) effluents in China recorded the highest frequency, even higher than that reported in Chinese raw water, indicating a deficiency in the WWTP performance or probable sampling cross-contamination, as shown in Table 2.…”

“…People are frequently exposed to wastewater via surface water usage, toilet flushing, recreation water, and wastewater-or greywater-dependent irrigation [17][18][19][20][21]. Most commonly occurring enteric viruses are self-limiting, whereas their infection risk is determined by the prevalence of infectious viral particles in the appropriate environmental condition, since some enteric viruses are significantly influenced by seasonal variation (e.g., rotavirus favoring late autumn and early winter [22]) or their prevalence in water environments that people are exposed to. For instance, the prevalence of HAV was found to be higher in raw water (16/27; 59%), than in treated water (5/26; 19%) [23].…”

Dynamic and Seasonal Distribution of Enteric Viruses in Surface and Well Water in Riyadh (Saudi Arabia)

“…Twenty-five percent of tertiary treated wastewater is used to irrigate landscapes in public parks in a number of cities and crop-irrigated areas across Saudi Arabia. Wadi Hanifa Lake, which is the city's main drainage system and is used for irrigation, receives treated wastewater from the Manfuha sewage treatment plant [34].…”