Characterization of viral pathogens associated with symptomatic upper respiratory tract infection in adults during a low COVID-19 transmission period

PeerJ

article

Nurlan Sandybayev¹  Vyacheslav Beloussov¹  Vitaliy Strochkov¹  Maxim Solomadin³  Joanna Granica²  Sergey Yegorov⁴ 

[1] Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University;TreeGene Molecular Genetics Laboratory;School of Pharmacy, Karaganda Medical University;Michael G. DeGroote Institute for Infectious Disease Research;McMaster Immunology Research Centre;Department of Biochemistry and Biomedical Sciences, McMaster University;School of Sciences and Humanities, Nazarbayev University

关键词: Respiratory tract infections;    COVID-19;    SARS-CoV-2;    Human parainfluenza;    Rhinovirus;    PCR;    Central Asia;    NGS;    Influenza;    Rhinovirus;   

DOI  :  10.7717/peerj.15008

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Background The epidemiology of respiratory tract infections (RTI) has dramatically changed over the course of the COVID-19 pandemic. A major effort in the clinical management of RTI has been directed toward diagnosing COVID-19, while the causes of other, common community RTI often remain enigmatic. To shed light on the etiological causes of RTI during a low COVID-19 transmission period in 2021, we did a pilot study using molecular testing for virologic causes of upper RTI among adults with respiratory symptoms from Almaty, Kazakhstan. Methods Adults presenting at two public hospitals with respiratory symptoms were screened using SARS-CoV-2 PCR on nasopharyngeal swabs. A subset of RTI+, COVID-19-negative adults (n = 50) was then tested for the presence of common RTI viruses and influenza A virus (IAV). Next generation virome sequencing was used to further characterize the PCR-detected RTI pathogens. Results Of 1,812 symptomatic adults, 21 (1.2%) tested SARS-CoV-2-positive. Within the COVID-19 negative outpatient subset, 33/50 subjects (66%) had a positive PCR result for a common community RTI virus, consisting of human parainfluenza virus 3-4 (hPIV 3-4) in 25/50 (50%), rhinovirus (hRV) in 2 (4%), hPIV4-hRV co-infection in four (8%) and adenovirus or the OCR43/HKU-1 coronavirus in two (4%) cases; no IAV was detected. Virome sequencing allowed to reconstruct sequences of most PCR-identified rhinoviruses and hPIV-3/human respirovirus-3. Conclusions COVID-19 was cause to a low proportion of symptomatic RTI among adults. Among COVID-negative participants, symptomatic RTI was predominantly associated with hPIV and hRV. Therefore, respiratory viruses other than SARS-CoV-2 should be considered in the clinical management and prevention of adult RTI in the post-pandemic era.

【 授权许可】

CC BY