Identification of Rotavirus Genotypes in Children under Five Years in the United Arab Emirates Using Nanopore Sequencing Technology

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.