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Identification of Rotavirus Genotypes in Children under Five Years in the United Arab Emirates Using Nanopore
Junu A George1, Farah Al-Marzooq2, Hassib Narchi1
1Department of Pediatrics, College of Medicine and Health Sciences, UAE University, Al-Ain, UAE.
Insights
Nanopore sequencing better detects diverse Group A rotavirus (RVA) strains than RT-PCR, crucial for tracking childhood diarrhea in the UAE. This advanced method aids in identifying emerging genotypes and improving RVA surveillance.
Area of Science:
- Virology
- Genetics
- Public Health
Background:
- Group A rotaviruses (RVA) are a primary cause of childhood diarrhea in the UAE, even with widespread vaccination.
- Monitoring RVA genetic diversity is vital for identifying prevalent strains and potential vaccine escape mutants.
- Traditional real-time polymerase chain reaction (RT-PCR) methods may fail to detect novel or emerging RVA strains.
Purpose of the Study:
- To evaluate and compare nanopore sequencing and RT-PCR for RVA genotyping.
- To assess the utility of nanopore sequencing in identifying diverse and emerging RVA genotypes.
- To enhance RVA surveillance and inform preventive strategies against RVA gastroenteritis.
Main Methods:
- Genotyping of 33 RVA strains from young children with diarrhea using both RT-PCR and nanopore sequencing.
- Comparative analysis of genotype detection capabilities between the two methods.
- Identification of common and rare RVA genotypes and their combinations.
Main Results:
- RT-PCR detected thirteen strains, with G9P[8] (56%) being the most common genotype.
- Nanopore sequencing identified a broader range of genotypes in 28 strains, with G3P[8] (29%) being most prevalent.
- Nanopore sequencing revealed emerging genotypes like G8P[8] (18%) that were not detected by RT-PCR.
Conclusions:
- Nanopore sequencing demonstrates superior performance in detecting diverse and emerging RVA genotypes compared to RT-PCR.
- This advanced sequencing technology can significantly improve RVA surveillance in the UAE.
- Enhanced surveillance through nanopore sequencing can guide more effective preventive measures for RVA infections.
Abstract:
Group A rotaviruses (RVA) remain a principal cause of childhood diarrhea in the UAE, despite universal vaccine use. Monitoring genetic diversity is important for identifying prevalent genotypes and escape mutants. Although real-time polymerase chain reaction (RT-PCR) is widely used for RVA genotyping, it may not detect some new strains. This study evaluates nanopore sequencing and RT-PCR for RVA genotyping. Thirty-three RVA strains from children under 5 years presenting with diarrhea were genotyped using both methods. Thirteen strains were genotyped by RT-PCR and confirmed by nanopore sequencing. Fifteen strains were genotyped by nanopore method alone. Most PCR-genotyped strains (56%) had the VP7 G9 genotype, with G3 in five strains and G12 in two. For VP4, P8 (n = 8) and P4 (n = 7) were dominant. The most frequent combinations were G9P[8] (31%) and G9P[4] (25%). Nanopore sequencing of 28 strains revealed G3P[8] (29%) as the most prevalent, followed by G8P[8] (18%). G9P[8] and G2P[4] were present in 14% of samples with G12P[6] being the rarest (7%). Other combinations were detected in 4% the specimens with one nontypeable. Nanopore sequencing was superior to PCR in identifying diverse and emerging genotypes like G8P[8]. This method may enhance surveillance studies and guide preventive measures for RVA gastroenteritis.
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