Abstract
ABSTRACTDuring an outbreak of acute gastroenteritis in Sweden when laboratory routine diagnostics failed to detect a causative agent, Sapporo virus was detected in stool specimens using electron microscopy (M.-P. Hergens, J. Nederby Öhd, E. Alm, H. Hervius Askling, S. Helgesson, M. Insulander, N. Lagerkvist, B. Svennungsson, M. Tihane, T. Tolfvenstam, P. Follin, unpublished data). Whole-genome sequencing revealed a Sapporo virus variant clustering with genogroup V.
Highlights
During an outbreak of acute gastroenteritis in Sweden when laboratory routine diagnostics failed to detect a causative agent, Sapporo virus was detected in stool specimens using electron microscopy
The libraries were amplified on a Veriti Thermal Cycler according to the protocol in the manual of the Ion total RNA-seq kit (Thermo Fisher Scientific) with the following modification: a total of 22 cycles for libraries prepared from sample S3 and a total of 16 cycles for libraries prepared from samples S6 were applied for the amplification step
The libraries were pooled to a final concentration of 50 pM and clonally amplified using the Ion Chef system and used for sequencing on an Ion S5 XL instrument using a 540 chip and Ion 540 Kit-Chef (Thermo Fisher Scientific)
Summary
During an outbreak of acute gastroenteritis in Sweden when laboratory routine diagnostics failed to detect a causative agent, Sapporo virus was detected in stool specimens using electron microscopy Total RNA was extracted from 200-L aliquots of two stool supernatants (S3 and S6) using MagDEA Dx SV reagent and the magLEAD instrument (Precision System Science). The RNA was eluted in 50 L and stored at Ϫ80°C pending analysis.
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