Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa

Abstract

Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics nextgeneration sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study.The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.

Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus

“…Using RNA-based quantitative sequencing together with a comprehensive and sensitive targeted metagenomic approach capturing over 100 bacterial and viral pathogens, we assessed a broad range of respiratory pathogens in infants with RSV, with the aim of examining disease severity correlates. We found strong genomic evidence for presence of at least one additional virus in 26% of the 433 RSV-infected infants, aligning with reported viral co-detection rates of 10–65% in children of all ages with respiratory infections 12 , 28 – 34 . This co-detection rate is likely a conservative estimate since our stringent detection criteria would necessarily miss very low viral load co-detection.…”

Metagenomic profiling of nasopharyngeal samples from adults with acute respiratory infection

“…Despite the limitations, our study highlights the multifaceted nature of the nasopharyngeal virome in ARI, particularly adding to other studies showing the feasibility of deploying mNGS in the limitedresource settings of developing countries [15,49]. However, the discrepancies between mNGS and multiplex PCR raise questions about the value of the Amplisens PCR panel in the clinical management of ARI and punctuate the need for the integration of complementary clinical and laboratory methods to enhance detection accuracy of ARI pathogens [50].…”

Clinical performance of metagenomic next-generation sequencing for diagnosis of pulmonary Aspergillus infection and colonization

“…Currently, the use of metagenomic next-generation sequence (mNGS) technology is increasingly prevalent in the clinical diagnosis of infectious diseases, particularly when the etiology is not confirmed by conventional microbiological testing (CMT) or when anti-infective treatment proves ineffective. Several studies have demonstrated that mNGS is highly effective in diagnosing mixed infections, and viruses’ infections ( Carpenter et al., 2019 ; Reyes et al., 2021 ; Mei et al., 2023 ; Ogunbayo et al., 2023 ; Xie et al., 2023 ). Compared to culture and other CMT methods, mNGS has a higher positive rate, sensitivity, and specificity in diagnosing invasive fungal infections (IFA) ( Song et al., 2021 ; Li, 2022 ; Wang et al., 2022 ).…”