SEARCHCROSS-SECTIONALinfectious disease, epidemiology

cross-sectional·infectious disease, epidemiology, public health, family medicine, internal medicine·PMC10022499

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

PeerJ · 6 authors, 5 centres

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TL;DR

This cross-sectional pilot study tested 1,812 symptomatic adults in Kazakhstan for COVID-19 and other respiratory viruses during a low transmission period in 2021.

Full summary

1,036 CHARS

This cross-sectional pilot study characterized viral causes of symptomatic upper respiratory tract infection (RTI) in 1,812 adults presenting at outpatient clinics in Almaty, Kazakhstan during May-June 2021, a period of low COVID-19 transmission. Initial screening found 21/1,812 (1.2%) were SARS-CoV-2 positive. A subset of 50 SARS-CoV-2-negative adults underwent further testing, revealing 33/50 (66%) had a positive PCR for another virus: 25/50 (50%) had human parainfluenza virus (predominantly type 4), 2/50 (4%) had rhinovirus, 4/50 (8%) had a co-infection of hPIV-4 and rhinovirus, and 2/50 (4%) had adenovirus or a coronavirus (HKU-1/OC43). Virome sequencing characterized rhinovirus and hPIV-3 in 6 of 33 PCR-positive samples. Limitations include the small subset size, cross-sectional design preventing seasonality analysis, and the fact that pathogen detection does not prove causation. The findings suggest non-COVID-19 viruses were predominant causes of symptomatic RTI in this population during low SARS-CoV-2 circulation.

STUDY TYPE

cross-sectional

SPECIALTY

infectious disease

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AI pipeline

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ORIGINAL PAPER

PMC10022499

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

PeerJ

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ABSTRACT

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

CITATION EXPORT

Nurlan Sandybayev, Vyacheslav Beloussov, Vitaliy Strochkov et al.. Characterization of viral pathogens associated with symptomatic upper respiratory tract infection in adults during a low COVID-19 transmission period. PeerJ. (2023). https://doi.org/10.7717/peerj.15008

AUTHORS

6 · 5 CENTRES

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

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