SEARCHCROSS-SECTIONALinfectious_disease, virology

cross-sectional·infectious_disease, virology, public_health, epidemiology, otolaryngology, pulmonology·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

AI SUMMARY

FIDELITY 100%

POPULATIONAdults aged 17–45 presenting with upper respiratory tract symptoms at two public outpatient clinics in Almaty, Kazakhstan (May–June 2021)

INTERVENTIONMultiplex PCR testing for common respiratory viruses and influenza A virus (IAV), plus virome sequencing of PCR-positive samples

COMPARISONNot applicable (descriptive cross-sectional study without a comparator group)

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AGENT 01 · STRUCTURED SUMMARY

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TL;DR

During a low COVID-19 transmission period in spring 2021 in Almaty, Kazakhstan, only 1.2% of symptomatic adults tested positive for SARS-CoV-2, while 66% of COVID-negative participants had detectable non-COVID respiratory viruses, predominantly human parainfluenza virus (hPIV) and rhinovirus (hRV). This pilot study highlights that respiratory viruses other than SARS-CoV-2 remain major causes of symptomatic upper respiratory tract infections in the post-pandemic era, particularly in Central Asia where regional RTI surveillance data are scarce. The findings underscore the need to include non-COVID pathogens in clinical management and public health preparedness for adult RTI.

Full summary

3,466 CHARS

**Background:** The COVID-19 pandemic has altered the epidemiology of common community respiratory tract infections (RTI), with some pathogens (e.g., influenza, RSV) declining while others (e.g., rhinovirus) have risen. In Central Asia, particularly Kazakhstan, data on regional RTI dynamics are limited. By spring–summer 2021, up to 60% of Kazakhstan's population had been exposed to SARS-CoV-2, and national surveillance reported a rise in non-COVID symptomatic RTI. This pilot study aimed to characterize viral pathogens associated with symptomatic upper RTI in adults during a low COVID-19 transmission period in Almaty, Kazakhstan.

**Methods:** Adults (aged 17–45) presenting with RTI symptoms (cough, sore throat, runny nose, fever) at two public outpatient clinics in Almaty were screened using SARS-CoV-2 PCR on nasopharyngeal swabs (Syntol kits, targeting orf1ab). A subset of 50 COVID-19-negative participants was then tested using a multiplex PCR panel (Amplisens ARVI-screen-FRT) for common RNA viruses (RSV, MPV, hPIV-1–4, coronaviruses OC43/HKU-1 and NL63/229E, rhinovirus) and DNA viruses (adenovirus B/C/E, bocavirus), plus a separate IAV PCR. Positivity threshold was Ct ≤ 32. Virome sequencing was performed on all PCR-positive samples using the Ion Torrent S5 platform, with bioinformatic analysis via EDGE, GOTTCHA2, Kraken2, BWA, MethaPhlAn2, and Diamond. Phylogenetic trees were constructed using MEGA 11 with maximum likelihood and 500 bootstrap replicates.

**Key Results:** Of 1,812 symptomatic adults screened, 21 (1.16%) tested SARS-CoV-2-positive. Among the 50 COVID-negative participants (median age 31 years, 76% female), 33/50 (66%) had a positive multiplex PCR result for a non-COVID respiratory virus. Specifically, 25/50 (50%) had hPIV mono-infection (24 hPIV-4, 1 hPIV-3), 2/50 (4%) had hRV mono-infection, 4/50 (8%) had hPIV4-hRV co-infection, and 2/50 (4%) had adenovirus or OC43/HKU-1 coronavirus mono-infection. No IAV, RSV, MPV, bocavirus, or NL63/229E coronavirus was detected. Virome sequencing successfully characterized viral sequences in 6/33 (18%) PCR-positive samples: 5 rhinoviruses (all species A: A56, A30, A100, and two A1B strains) and 1 hPIV-3 (respirovirus-3). One hRV-A1B sample achieved 100% linear coverage with 69,393 reads. Phylogenetic analysis showed the hRV-A strains were diverse with global origins, while the hPIV-3 clustered distinctly with other hPIV-3 sequences.

**Clinical Implications:** This study provides the first pilot data on RTI dynamics in a Central Asian population during a low COVID-19 transmission period. The finding that only 1.2% of symptomatic adults had COVID-19, while 66% of COVID-negative individuals had detectable non-COVID respiratory viruses (predominantly hPIV and hRV), suggests that clinical management and prevention strategies for adult RTI in the post-pandemic era should not focus exclusively on SARS-CoV-2. The high proportion of hPIV-4 (50% of tested subset) is notable and warrants further investigation. Limitations include the small sample size (n=50 for multiplex testing), cross-sectional design precluding seasonality analysis, limited PCR panel (not covering all viral/bacterial pathogens), and low sequencing success rate (18% of PCR-positive samples). Despite these limitations, the study highlights the need for more comprehensive, adequately powered RTI surveillance in Central Asia to inform healthcare resource allocation and outbreak preparedness.

PICO

PPOPULATION

Adults aged 17–45 presenting with upper respiratory tract symptoms at two public outpatient clinics in Almaty, Kazakhstan (May–June 2021)

IINTERVENTION

Multiplex PCR testing for common respiratory viruses and influenza A virus (IAV), plus virome sequencing of PCR-positive samples

OOUTCOME

Proportion of SARS-CoV-2-positive cases among symptomatic adults; proportion and types of non-COVID respiratory viruses detected in COVID-negative subset; viral sequence diversity via NGS

STUDY TYPE

cross-sectional

SPECIALTY

infectious_disease

SUMMARISED BY

AI pipeline

FIDELITY CHECK

100% · A

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