Get started
Work

Viruses in the upper respiratory tract of individuals at risk of zoonotic infection and their animals in Vietnam : follow-up and virus discovery

Year: 2021
Type: dissertation
Study design: Observational Study
Abstract: The ongoing COVID-19 pandemic emphasizes the importance of understanding exposures to zoonotic reservoirs, active surveillance for pathogens and novel viruses and having feasible testing for quick identification of emerging viruses in future outbreaks. A cohort of 581 individuals working with animals in Vietnam was established (2013–2016). Nasal-throat swabs of the participants and their animals were collected at beginning of each year (no any respiratory symptoms) for baseline data, and whenever the participants reported any respiratory symptom and fever. The analysis shows that the participants were frequently exposed to zoonotic sources by both occupational activities and non-occupational activities (e.g. farming animals surrounding their house, consuming of raw animal blood or meat), or by no or limited use of personal protective equipment, or by exposure to a large variety of animal species. Multiplex RT-PCRs screening for 15 common respiratory viral viruses reveals that enteroviruses and rhinoviruses were predominant viruses detected throughout the study. mNGS analysis of 91 disease-episodes swabs in 2013 successfully detected rhinovirus, enterovirus, influenza A virus, coronavirus OC43, and RSV A in 13 of 15 (86.7%) RT-PCR positive samples (positive controls). Additionally, rotavirus, torque teno virus, human papillomavirus and human betaherpesvirus 7 were also detected. Notably, a vientovirus of a recently discovered Redondoviridae family, a novel cyclovirus, a novel gemycircularvirus and a novel statovirus were also detected and genetically characterized. The results offer important insights into the virome of acute respiratory infections in individuals at high risk of zoonotic infections. The mNGS protocol used here is highly sensitive for sequence-independent detection of a wide range of viruses. Using PCR to screen in all mNGS samples, the virus detection of mNGS were successfully replicated by PCR. However, redondoviruses were additionally detected in 29, the novel cyclovirus in 5, the novel gemycircularvirus in 12 mNGS-negative samples. This result reveals the prevalence of these viruses and emphasizes that standard PCR remains a more sensitive diagnostic test for known viruses than mNGS. No evidence of redondoviruses was found by PCR screenings in nasal-throat swabs of pigs, chicken, Muscovy ducks, ducks and dogs that the virus-positive participants were exposed to. Similarly, the novel statovirus was not detected in animal samples. In contrast, sequences of the novel cyclovirus and gemycircularvirus were found in pig swabs. However, passive contamination in respiratory tracts of both humans and their animals cannot be excluded. Additionally, the same replication gene sequence of redondoviruses was detected in longitudinal samples of several participants, indicating likelihood of redondovirus persistence in the human nasopharynx. Phylogenetic analysis suggests a wide geographic distribution and diversity of redondoviruses. Collectively, these data provided new insights into the high prevalence, widespread, possible chronic shedding in human respiratory tracts and lack of evidence about zoonotic origin of redondoviruses
Language: English
Field: Medicine
Open Access status: green
OpenAlex ID: W3179992698
Cites: 249
Cited by: 1
Related to: 10