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

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.

Redondoviridae: High Prevalence and Possibly Chronic Shedding in Human Respiratory Tract, But No Zoonotic Transmission

“…We previously detected a contig derived from two reads related to the human lung-associated vientovirus AL strain (Accession Number: MK059760.1) in one sample using metagenomic sequencing [ 16 ]. Using inverse PCR, we recovered a full circular genome of this virus, which was 3054-bp.…”

“…Taking into account the results of our previous PCR screening [ 13 ] and mNGS analysis [ 16 ], we identified a mixed infection of redondoviruses and other viruses in 28 samples. The codetected viruses included gemycircularvirus VIZIONS-2013, cyclovirus VIZIONS-2013, human rhinovirus, statovirus VIZIONS-2013, RSV A, gemycircularvirus, enterovirus, statovirus, and influenza A virus ( Table 6 ).…”

“…One source was newly extracted from the original sample using a MagNApure 96 platform (Roche Diagnostics, Mannheim, Germany) [ 13 ]. The other comprised residual nucleic acid materials after mNGS sequencing extracted by the QIAamp 96 Virus QIAcube HT Kit (QIAGEN GmbH, Hilden, Germany) [ 16 ].…”

“…The high-risk sentinel cohort study received approvals from the Ethics Committees at the University of Oxford, United Kingdom, and at the sub-Departments of Animal Health and General Hospital in Dong Thap Province and Dak Lak Province and in the Hospital of Tropical Diseases in Ho Chi Minh City in Vietnam, as reported previously [ 16 , 19 ]. Written consent was obtained from each study participant.…”

Pandemics Throughout History

“…Furthermore, the global virome project was launched to detect and identify viral threats to human health, characterize the host ranges of viruses, identify behaviors that favor spillover, establish a global surveillance network and identify transmission and pathogenicity markers for high-risk viruses ( Carroll et al, 2018 ; Kwok et al, 2020 ). Viral metagenomic next-generation sequencing analysis of nasal/throat swabs from individuals at risk of zoonotic infections was also used to expand the detection of novel viruses and the characterization of the respiratory virome of humans exposed to animals ( Thi Kha Tu et al, 2020 ).…”