Key result
Nanopore sequencing successfully genotyped 84.8% of rotavirus strains compared to 39.4% with RT-PCR, demonstrating superiority in identifying diverse and emerging genotypes.
Why the study?
Although RT-PCR is widely used for RVA genotyping, it may not detect some new strains, prompting evaluation of nanopore sequencing.
Does nanopore sequencing improve the identification of diverse and emerging rotavirus genotypes compared to RT-PCR in children under 5 years with diarrhea?
Observational (n=33)
Does nanopore sequencing improve the identification of diverse and emerging rotavirus genotypes compared to RT-PCR in children under 5 years with diarrhea?
Absolute Event Rate: 84.8% vs 39.4%
Nanopore sequencing is superior to standard RT-PCR for identifying diverse and emerging rotavirus genotypes, which may enhance surveillance and guide preventive measures.
Nanopore sequencing may enhance RVA detection beyond RT-PCR in vaccinated children; leaves open its role in routine surveillance.
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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George et al. (2024) conducted an observational in Group A rotavirus (RVA) diarrhea (n=33). Nanopore sequencing vs. RT-PCR was evaluated on Successful RVA genotyping. Nanopore sequencing successfully genotyped 84.8% of rotavirus strains compared to 39.4% with RT-PCR, demonstrating superiority in identifying diverse and emerging genotypes.
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