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

Nurlan Sandybayev; Vyacheslav Beloussov; Vitaliy Strochkov; Maxim Solomadin; Joanna Granica; Sergey Yegorov

doi:10.7717/peerj.15008

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

PeerJ. 2023 Mar 13:11:e15008. doi: 10.7717/peerj.15008. eCollection 2023.

Authors

Nurlan Sandybayev¹, Vyacheslav Beloussov^{1

2}, Vitaliy Strochkov¹, Maxim Solomadin³, Joanna Granica², Sergey Yegorov^{4

5}

Affiliations

¹ Kazakhstan-Japan Innovation Center, Kazakh National Agrarian Research University, Almaty, Kazakhstan.
² TreeGene Molecular Genetics Laboratory, Almaty, Kazakhstan.
³ School of Pharmacy, Karaganda Medical University, Karaganda, Kazakhstan.
⁴ Michael G. DeGroote Institute for Infectious Disease Research; McMaster Immunology Research Centre; Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
⁵ School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan.

Abstract

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.

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

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Adult
COVID-19* / epidemiology
Humans
Influenza A virus*
Multiplex Polymerase Chain Reaction
Pandemics
Parainfluenza Virus 1, Human
Parainfluenza Virus 2, Human
Pilot Projects
Respiratory Tract Infections* / diagnosis
Rhinovirus / genetics
SARS-CoV-2 / genetics

Grants and funding

This work was supported by the Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan, Grant No. AP09259192. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.