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

Nguyen Thi Kha Tu,Le Van Tan,Nguyen Thi Thu Hong,Guy Thwaites,Olli Vapalahti,Eric Delwart,Anna-Maija K Virtala,Pham Thi Thanh Tam,Luu Thi Thu Ha,Dang Thao Huong,H Rogier Van Doorn,Tran My Phuc,Xutao Deng,Stephen Baker,Ho Dang Trung Nghia,Duong An Han,Nguyen Thi Han Ny

doi:10.3390/v12090960

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.

Highlights

Acute respiratory infections are the leading cause of morbidity and mortality worldwide [1,2].Despite intensive laboratory investigations, a substantial proportion of acute respiratory infections are of unknown etiology, resulting in difficulties in clinical management [3,4,5,6]
We first applied metagenomic next-generation sequencing (mNGS) to nasal-throat swab samples collected during disease episodes in 2013
Sequences related to 5 viral pathogens detected by diagnostic RT-PCRs were detected by mNGS in 13 of 15 (86.7%, 95% CI: 62.1–96.3%) samples, including 8 human rhinovirus (HRV), 1 enterovirus (EVs), 1 mix-detection of humanhuman rhinovirus (HRV) and EVs, 1 influenza A virus, 1 coronavirus (CoV), and 1 respiratory syncytial virus (RSV) A. mNGS failed to detect RSV (cycle threshold (Ct): 36.3) and human metapneumovirus (MPV) (Ct: 40) in 2/15 RT-PCR-positive samples (Table 2) but detected in only 2 other samples, which were negative in RT-PCR (Table 3)

Summary

Introduction

Acute respiratory infections are the leading cause of morbidity and mortality worldwide [1,2].Despite intensive laboratory investigations, a substantial proportion of acute respiratory infections are of unknown etiology, resulting in difficulties in clinical management [3,4,5,6]. Acute respiratory infections are the leading cause of morbidity and mortality worldwide [1,2]. Viruses are the main causes of acute respiratory infections with the potential to cause pandemics [9,10,11,12]. Most emerging viral agents of acute respiratory diseases are of zoonotic origin and pose a major threat to human health [10,11,12,13]. The ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exemplifies problems resulting from emerging zoonotic pathogens [9]. The early detection of emerging viral pathogens of animal origin that exhibit potential for human-to-human transmission remains a difficult but essential step to mitigate their propagation

Methods

Results

Conclusion