549. The Application of Nanopore Sequencing Technology to Characterize Rotavirus Genotypes from Young Children with Diarrhea in the United Arab Emirates

Abstract Background In the United Arab Emirates, rotavirus A (RVA) remains a major cause of gastroenteritis in young children despite the universal use of rotavirus vaccines. Monitoring the genetic diversity of circulating strains is essential to better understand the disease burden. Although semi-nested multiplex-PCR is a popular method for RVA genotyping, some clinically significant strains may not be accurately identified by this method. Nanopore sequencing is a third-generation single-molecule sequencing technology that allows for real-time identification of viral and bacterial isolates at competitive costs. This study aims to investigate the use of nanopore sequencing and multiplex-PCR methods to identify RVA genotypes. Methods Thirty-three RVA isolates, obtained from stool specimens collected from children less than 5 years old who presented with diarrhea between December 2017 and April 2019, were used for genotyping by PCR and nanopore sequencing. Sixteen isolates were genotyped by Taqman-based qRT-PCR based on VP7 (G) and VP4 (P) genes and genotypes were confirmed by nanopore sequencing in thirteen isolates; three isolates were excluded from nanopore sequencing due to poor RNA quality. Another fifteen isolates were genotyped by the nanopore method alone and two samples were excluded due to poor RNA quality. Results The majority of isolates genotyped by qRT-PCR (9 out of 16) were found to harbor VP7 gene of G9 genotype, whereas 5 isolates were of G3 genotype. G12 genotype was rare (2 isolates). For VP4 (P) genotypes, P8 was the most prevalent (8 isolates), followed by P4 (7 isolates), and P6 (1 isolate). When combinations of VP7 and VP4 genotypes are considered, G9P[8] and G9P[4] were the most common genotypes. Nanopore sequencing of 28 isolates revealed G3P8 (29%) as the most prevalent G-P combination, followed by G8P[8] (18%). G9P[8] and G2P[4] were present in 14% of samples. G12P[6] was present in 7% of tested samples. Further, G9P[4], G3P[4], G1P[4], and G4P[2] were detected in 4% of total specimens. One sample was non-typable. Conclusion Nanopore sequencing detected various RVA strains among the studied samples including the recently emerging strain, G8P[8]. Using this method in surveillance studies may advance our understanding of the origin, genetic recombination, and burden of disease. Disclosures All Authors: No reported disclosures.