Characterization of the nasopharyngeal viral microbiome from children with community‐acquired pneumonia but negative for Luminex xTAG respiratory viral panel assay detection

Abstract

In the present study, 50 nasopharyngeal swabs from children with community-acquired pneumonia (CAP) but negative for 18 common respiratory viruses, as measured by the Luminex xTAG Respiratory Viral Panel Assay, were subjected to multiplex metagenomic analyses using a next-generation sequencing platform. Taxonomic analysis showed that all sequence reads could be assigned to a specific species. An average of 95.13% were assigned to the Bacteria kingdom, whereas, only 0.72% were potentially virus derived. This snapshot of the respiratory tract virome revealed most viral reads to be respiratory tract related, classified into four known virus families: Paramyxoviridae, Herpesviridae, Anelloviridae, and Polyomaviridae. Importantly, we detected a novel human parainfluenza virus 3 (HPIV 3) strain with a 32-bp insertion in the haemagglutinin-neuraminidase (HN) gene that produced a negative result in the Luminex assay, highlighting the strength of virome metagenomic analysis to identify not only novel viruses but also viruses likely to be missed by ordinary clinical tests. Thus, virome metagenomic analysis could become a viable clinical diagnostic method.

Detection of Viruses in Clinical Samples by Use of Metagenomic Sequencing and Targeted Sequence Capture

“…The HRV-C was detected both without and with ViroCap, with more than 40,000 reads detected with capture enrichment. It is possible that HRV-C was not detected by the multiplex panel because of sequence differences in the primer binding sites, as has been reported previously for RT-PCR assays directed at human rhinoviruses, which are very diverse (1), and for human parainfluenza virus (43). Because the primer sequences used in the multiplex assay are not available, we cannot directly test this hypothesis.…”

“…Application of MSS to diagnostic virology has great appeal based on the capability for (i) broad-range detection and (ii) detailed taxonomic characterization (40)(41)(42)(43)(44)(45)(46)(47) and for characterization of antiviral resistance genotypes (48). Our findings in this study illustrate and quantitate these advantages using actual clinical samples and measure the further enhancement achieved by the use of targeted sequence capture to improve the sensitivity of standard metagenomic shotgun sequencing.…”

Respiratory viruses in mechanically ventilated patients: a pilot study

“…In a study conducted by Choi et al [18], the main respiratory viruses associated with severe pneumonia in adults admitted in ICU were HRV (23.6%), HPIV (20.8%), HMPV (18.1%), influenza (16.7%) and RSV (13.9%), according to data obtained from real-time PCR analysis in bronchoalveolar lavage samples. In the study by Xu et al [14], 368 samples collected with nasopharyngeal swab from infected children were analyzed with real-time PCR, using a panel of 18 respiratory viruses. The percentage of positive samples was 58.97%.…”

“…At the beginning of the current decade, studies based on culture-independent methods have shown the presence of a small amount of bacterial communities in the lungs of healthy, non-smoker individuals, with some diversity in their elements. There are few studies available in the literature on the characterization of the respiratory tract virome, especially of the lower airways [9][10][11][12][13][14]. Essentialy, most of the studied population was in the pediatric age and the majority of them had respiratory infection.…”

The trigger meaning of persistent intracellular pathogens with prolonged fever and subsequent development of somatic pathology in children

“…Цікавим є і роль назофарінгеального вірому у дітей при тривалих лихоманках та його ідентифіка-ції, що було характеризовано на прикладі досліджень з респіраторної патології у дітей (позашпитальної пневмонії) [12].…”