Characterisation of human astrovirus in a diarrhoea outbreak using nanopore and Sanger sequencing protocols.

Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance hospital in Beijing. Samples were evaluated immediately using parallel multiplex RT-qPCR and nanopore sequencing, and were then amplified by designed primers and Sanger sequencing to obtain whole genome sequences. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution. Full genome analysis revealed low genetic variation (99.38–100% identity) among isolates. Phylogenetic analysis showed that all isolates were closely related to domestic strains Yu/1-CHN and 2013/Fuzhou/85. The recombination breakpoint of the six isolates was located at 2741 bp in the overlap region of ORF1a and ORF1b, similar to those of Yu/1-CHN and 2013/Fuzhou/85. Overall, our study highlights the combined use of RT-qPCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV. Highlights: We parallel used multiplex RT-PCR and nanopore sequencing to identify Human astroviruse from 10 stool samples of a diarrhea outbreak from a diarrhea sentinel surveillance hospital in this study. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution.It is showed that the combined use of RT-PCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV. [ABSTRACT FROM AUTHOR]