Metagenomic identification and winter seasonality of picobirnavirus in stool of hospitalized patients with acute gastroenteritis
Refereed conference paper presented and published in conference proceedings


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AbstractAim: To use metagenomic next-generation sequencing (mNGS) to identify the causative agent in patients hospitalized for acute gastroenteritis with unknown etiology.

Method: A total of 300 stool samples collected from in-patients with gastroenteritis from April to June 2018 were investigated (discovery cohort). These samples had tested negative for common diarrheagenic bacterial and viral pathogens. Nextera XT libraries targeting virome were prepared and sequenced on NextSeq 500. Taxonomic classification of sequencing reads was performed using Taxonomer. Seasonality and prevalence of any newly identified viruses were studied in an independent cohort of 246 stool samples collected from December 2018 to February 2019 (validation cohort).

Results: In the discovery cohort, 10 (3.3%) samples were positive by mNGS for picobirnavirus, a RNA virus currently not included in any in-house diagnostic workflows and commercial gastrointestinal virus testing panels. On-target reads ranged from 0.06%-8.5%. In the validation cohort, 15 (6.1%) samples were positive for picobirnavirus by a virus-specific RT-PCR assay. The virus was present in both children and adults but had a higher prevalence towards middle-aged adults: 0-4 years (0%; 0/73), 5-40 years (7%; 2/29), 41-64 years (13%; 8/63), 65-84 years (7%; 4/54), and ≥85 years (4%; 1/27). Picobirnavirus exhibited a winter seasonality typical to other gastroenteritis viruses: 3% (3/90) in December 13% (10/80) in January, and 2% (2/76) in February.

Conclusions: mNGS identified picobirnavirus in gastroenteritis patients with unknown etiology. The winter seasonality implies picobirnavirus is not opportunistic and may be pathogenic and cause gastroenteritis.

Acknowledgements: This study was supported in part by HMRF CU-17-B8.
All Author(s) ListMartin Chi-Wai Chan, Lin-Yao Zhang, Liutao Guo, Paul K.S. Chan
Name of Conference22nd Annual Meeting of the European Society for Clinical Virology
Start Date of Conference11/09/2019
End Date of Conference14/09/2019
Place of ConferenceCopenhagen
Country/Region of ConferenceDenmark
Year2019
Month9
LanguagesEnglish-United Kingdom

Last updated on 2020-06-03 at 14:18