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: | Journal article |
| Language: | English |
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MDPI
2020
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| _version_ | 1826297273309462528 |
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| author | Thi Kha Tu, N Thi Thu Hong, N Thi Han Ny, N My Phuc, T Thi Thanh Tam, P Doorn, HRV Dang Trung Nghia, H Thao Huong, D An Han, D Thi Thu Ha, L Deng, X Thwaites, G Delwart, E Virtala, A-MK Vapalahti, O Baker, S Van Tan, L |
| author_facet | Thi Kha Tu, N Thi Thu Hong, N Thi Han Ny, N My Phuc, T Thi Thanh Tam, P Doorn, HRV Dang Trung Nghia, H Thao Huong, D An Han, D Thi Thu Ha, L Deng, X Thwaites, G Delwart, E Virtala, A-MK Vapalahti, O Baker, S Van Tan, L |
| author_sort | Thi Kha Tu, N |
| collection | OXFORD |
| 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 | 2024-03-07T04:29:04Z |
| format | Journal article |
| id | oxford-uuid:cdae97ed-4aae-437c-a231-14f5eaa82638 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T04:29:04Z |
| publishDate | 2020 |
| publisher | MDPI |
| record_format | dspace |
| spelling | oxford-uuid:cdae97ed-4aae-437c-a231-14f5eaa826382022-03-27T07:30:24ZThe virome of acute respiratory diseases in individuals at risk of zoonotic infectionsJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:cdae97ed-4aae-437c-a231-14f5eaa82638EnglishSymplectic ElementsMDPI2020Thi Kha Tu, NThi Thu Hong, NThi Han Ny, NMy Phuc, TThi Thanh Tam, PDoorn, HRVDang Trung Nghia, HThao Huong, DAn Han, DThi Thu Ha, LDeng, XThwaites, GDelwart, EVirtala, A-MKVapalahti, OBaker, SVan Tan, LThe 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. |
| spellingShingle | Thi Kha Tu, N Thi Thu Hong, N Thi Han Ny, N My Phuc, T Thi Thanh Tam, P Doorn, HRV Dang Trung Nghia, H Thao Huong, D An Han, D Thi Thu Ha, L Deng, X Thwaites, G Delwart, E Virtala, A-MK Vapalahti, O Baker, S Van Tan, L 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 |
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