The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections

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VIZIONS Consortium , Thi Kha Tu , N , Thi Thu Hong , N , Thi Han Ny , N , My Phuc , T , Thi Thanh Tam , P , Doorn , H R V , Dang Trung Nghia , H , Thao Huong , D , An Han , D , Thi Thu Ha , L , Deng , X , Thwaites , G , Delwart , E , Virtala , A-M K , Vapalahti , O , Baker , S & Van Tan , L 2020 , ' The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections ' , Viruses-Basel , vol. 12 , no. 9 , 960 . https://doi.org/10.3390/v12090960

Title: The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections
Author: VIZIONS Consortium; Thi Kha Tu, Nguyen; Thi Thu Hong, Nguyen; Thi Han Ny, Nguyen; My Phuc, Tran; Thi Thanh Tam, Pham; Doorn, H. Rogier van; Dang Trung Nghia, Ho; Thao Huong, Dang; An Han, Duong; Thi Thu Ha, Luu; Deng, Xutao; Thwaites, Guy; Delwart, Eric; Virtala, Anna-Maija K.; Vapalahti, Olli; Baker, Stephen; Van Tan, Le
Contributor: University of Helsinki, Veterinary Biosciences
University of Helsinki, Helsinki One Health (HOH)
Date: 2020-09
Language: eng
Number of pages: 15
Belongs to series: Viruses-Basel
ISSN: 1999-4915
URI: http://hdl.handle.net/10138/321130
Abstract: The ongoing coronavirus disease 2019 (COVID-19) pandemic emphasizes the need to actively study the virome of unexplained respiratory diseases. We performed viral metagenomic next-generation sequencing (mNGS) analysis of 91 nasal-throat swabs from individuals working with animals and with acute respiratory diseases. Fifteen virus RT-PCR-positive samples were included as controls, while the other 76 samples were RT-PCR negative for a wide panel of respiratory pathogens. Eukaryotic viruses detected by mNGS were then screened by PCR (using primers based on mNGS-derived contigs) in all samples to compare viral detection by mNGS versus PCR and assess the utility of mNGS in routine diagnostics. mNGS identified expected human rhinoviruses, enteroviruses, influenza A virus, coronavirus OC43, and respiratory syncytial virus (RSV) A in 13 of 15 (86.7%) positive control samples. Additionally, rotavirus, torque teno virus, human papillomavirus, human betaherpesvirus 7, cyclovirus, vientovirus, gemycircularvirus, and statovirus were identified through mNGS. Notably, complete genomes of novel cyclovirus, gemycircularvirus, and statovirus were genetically characterized. Using PCR screening, the novel cyclovirus was additionally detected in 5 and the novel gemycircularvirus in 12 of the remaining samples included for mNGS analysis. Our studies therefore provide pioneering data of the virome of acute-respiratory diseases from individuals at risk of zoonotic infections. The mNGS protocol/pipeline applied here is sensitive for the detection of a variety of viruses, including novel ones. More frequent detections of the novel viruses by PCR than by mNGS on the same samples suggests that PCR remains the most sensitive diagnostic test for viruses whose genomes are known. The detection of novel viruses expands our understanding of the respiratory virome of animal-exposed humans and warrant further studies.
Subject: virome
acute respiratory disease
NGS
metagenomics
zoonoses
novel cyclovirus
novel statovirus
novel gemycircularvirus
CYCLOVIRUS
DNA
VIRUSES
11832 Microbiology and virology
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