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

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 respi...

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Autores principales: Thi Kha Tu, Nguyen, Thi Thu Hong, Nguyen, Thi Han Ny, Nguyen, My Phuc, Tran, Thi Thanh Tam, Pham, van Doorn, H. Rogier, 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552073/
https://www.ncbi.nlm.nih.gov/pubmed/32872469
http://dx.doi.org/10.3390/v12090960
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author Thi Kha Tu, Nguyen
Thi Thu Hong, Nguyen
Thi Han Ny, Nguyen
My Phuc, Tran
Thi Thanh Tam, Pham
van Doorn, H. Rogier
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
author_facet Thi Kha Tu, Nguyen
Thi Thu Hong, Nguyen
Thi Han Ny, Nguyen
My Phuc, Tran
Thi Thanh Tam, Pham
van Doorn, H. Rogier
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
author_sort Thi Kha Tu, Nguyen
collection PubMed
description 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.
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spelling pubmed-75520732020-10-14 The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections Thi Kha Tu, Nguyen Thi Thu Hong, Nguyen Thi Han Ny, Nguyen My Phuc, Tran Thi Thanh Tam, Pham van Doorn, H. Rogier 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 Viruses Article 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. MDPI 2020-08-29 /pmc/articles/PMC7552073/ /pubmed/32872469 http://dx.doi.org/10.3390/v12090960 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Thi Kha Tu, Nguyen
Thi Thu Hong, Nguyen
Thi Han Ny, Nguyen
My Phuc, Tran
Thi Thanh Tam, Pham
van Doorn, H. Rogier
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
The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections
title The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections
title_full The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections
title_fullStr The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections
title_full_unstemmed The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections
title_short The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections
title_sort virome of acute respiratory diseases in individuals at risk of zoonotic infections
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7552073/
https://www.ncbi.nlm.nih.gov/pubmed/32872469
http://dx.doi.org/10.3390/v12090960
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