Metagenomic profiling of nasopharyngeal samples from adults with acute respiratory infection
Sandybayev N. Beloussov V. Strochkov V. Solomadin M. Granica J. Yegorov S.
10 July 2024Royal Society Publishing
Royal Society Open Science
2024#11Issue 7
Diagnosis of acute respiratory infections (ARIs) is challenging due to the broad diversity of potential microbial causes. We used metagenomic next-generation sequencing (mNGS) to analyze the nasopharyngeal virome of ARI patients, who had undergone testing with a clinical multiplex PCR panel (Amplisens ARVI-screen-FRT). We collected nasopharyngeal swabs from 49 outpatient adults, 32 of whom had ARI symptoms and were PCR-positive, and 4 asymptomatic controls in Kazakhstan during Spring 2021. We assessed the biodiversity of the mNGS-derived virome and concordance with PCR results. PCR identified common ARI viruses in 65% of the symptomatic cases. mNGS revealed viral taxa consisting of human, non-human eukaryotic and bacteriophage groups, comprising 15, 11 and 28 genera, respectively. Notable ARI-associated human viruses included rhinovirus (16.3%), betaherpesvirus 7 (14.3%) and Epstein-Barr virus (8.16%). The primary phage hosts were Streptococcus spp. (32.7%), Pseudomonas aeruginosa (24.5%) and Burkholderia spp. (20.4%). In total, 47% of ARIs were linked solely to bacterial pathogens, a third to viral-bacterial co-infections, and less than 10% to only viral infections by mNGS. PCR showed low concordance with mNGS, except for rhinovirus. These results underscore the importance of broad diagnostic methods and question the effectiveness of commonly used PCR panels in ARI diagnosis.
acute respiratory infection , metagenomics , nasopharyngeal swab , virome
Text of the article Перейти на текст статьи
Kazakhstan-Japan Innovation Centre, Kazakh National Agrarian Research University (KazNARU), 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, ON, Canada
Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
Kazakhstan-Japan Innovation Centre
TreeGene Molecular Genetics Laboratory
School of Pharmacy
Michael G. DeGroote Institute for Infectious Disease Research
Department of Biology
10 лет помогаем публиковать статьи Международный издатель
Книга Публикация научной статьи Волощук 2026 Book Publication of a scientific article 2026