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...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-08-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/12/9/960 |
| _version_ | 1797555214631305216 |
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| author | Nguyen Thi Kha Tu Nguyen Thi Thu Hong Nguyen Thi Han Ny Tran My Phuc Pham Thi Thanh Tam H. Rogier van Doorn Ho Dang Trung Nghia Dang Thao Huong Duong An Han Luu Thi Thu Ha Xutao Deng Guy Thwaites Eric Delwart Anna-Maija K. Virtala Olli Vapalahti Stephen Baker Le Van Tan |
| author_facet | Nguyen Thi Kha Tu Nguyen Thi Thu Hong Nguyen Thi Han Ny Tran My Phuc Pham Thi Thanh Tam H. Rogier van Doorn Ho Dang Trung Nghia Dang Thao Huong Duong An Han Luu Thi Thu Ha Xutao Deng Guy Thwaites Eric Delwart Anna-Maija K. Virtala Olli Vapalahti Stephen Baker Le Van Tan |
| author_sort | Nguyen Thi Kha Tu |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T16:43:21Z |
| format | Article |
| id | doaj.art-dd38c10718bd4e56b66062c44f212b35 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-10T16:43:21Z |
| publishDate | 2020-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-dd38c10718bd4e56b66062c44f212b352023-11-20T11:50:34ZengMDPI AGViruses1999-49152020-08-0112996010.3390/v12090960The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic InfectionsNguyen Thi Kha Tu0Nguyen Thi Thu Hong1Nguyen Thi Han Ny2Tran My Phuc3Pham Thi Thanh Tam4H. Rogier van Doorn5Ho Dang Trung Nghia6Dang Thao Huong7Duong An Han8Luu Thi Thu Ha9Xutao Deng10Guy Thwaites11Eric Delwart12Anna-Maija K. Virtala13Olli Vapalahti14Stephen Baker15Le Van Tan16Doctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, FinlandOxford University Clinical Research Unit, Ho Chi Minh City 7000, VietnamOxford University Clinical Research Unit, Ho Chi Minh City 7000, VietnamOxford University Clinical Research Unit, Ho Chi Minh City 7000, VietnamOxford University Clinical Research Unit, Ho Chi Minh City 7000, VietnamOxford University Clinical Research Unit, Ha Noi 8000, VietnamOxford University Clinical Research Unit, Ho Chi Minh City 7000, VietnamOxford University Clinical Research Unit, Ho Chi Minh City 7000, VietnamDong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, VietnamDong Thap Provincial Center for Disease Control, Cao Lanh City 660273, Dong Thap Province, VietnamDepartment of Laboratory Medicine, University of California, San Francisco, CA 94143, USAOxford University Clinical Research Unit, Ho Chi Minh City 7000, VietnamDepartment of Laboratory Medicine, University of California, San Francisco, CA 94143, USADepartment of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, 00014 Helsinki, FinlandDoctoral School in Health Sciences, Faculty of Medicine, University of Helsinki, 00014 Helsinki, FinlandCambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UKOxford University Clinical Research Unit, Ho Chi Minh City 7000, VietnamThe 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.https://www.mdpi.com/1999-4915/12/9/960viromeacute respiratory diseaseNGSmetagenomicszoonosesnovel cyclovirus |
| spellingShingle | Nguyen Thi Kha Tu Nguyen Thi Thu Hong Nguyen Thi Han Ny Tran My Phuc Pham Thi Thanh Tam H. Rogier van Doorn Ho Dang Trung Nghia Dang Thao Huong Duong An Han Luu Thi Thu Ha Xutao Deng Guy Thwaites Eric Delwart Anna-Maija K. Virtala Olli Vapalahti Stephen Baker Le Van Tan The Virome of Acute Respiratory Diseases in Individuals at Risk of Zoonotic Infections Viruses virome acute respiratory disease NGS metagenomics zoonoses novel cyclovirus |
| 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 | virome acute respiratory disease NGS metagenomics zoonoses novel cyclovirus |
| url | https://www.mdpi.com/1999-4915/12/9/960 |
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