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

Sandybayev N. Beloussov V. Strochkov V. Solomadin M. Granica J. Yegorov S.
2023 PeerJ Inc.

PeerJ
2023 #11

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. 2023 Sandybayev et al.

Central Asia , COVID-19 , Human parainfluenza , Influenza , NGS , PCR , Respiratory tract infections , Rhinovirus , SARS-CoV-2

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

Kazakhstan-Japan Innovation Center
TreeGene Molecular Genetics Laboratory
School of Pharmacy
Michael G. DeGroote Institute for Infectious Disease Research
School of Sciences and Humanities

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