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Identification of missed respiratory viruses by metagenomic sequencing of clinical respiratory samples from Kenya
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Phan, My V. T., Agoti, Charles N., Munywoki, Patrick K., Otieno, Grieven Paul, Ngama, Mwanajuma, Kellam, Paul, Cotton, Matthew and Nokes, D. James (2022) Identification of missed respiratory viruses by metagenomic sequencing of clinical respiratory samples from Kenya. Scientific Reports, 12 . 202. doi:10.1038/s41598-021-03987-1 ISSN 2045-2322.
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Official URL: https://doi.org/10.1038/s41598-021-03987-1
Abstract
Pneumonia remains a major cause of mortality and morbidity. Most molecular diagnoses of viruses rely on polymerase chain reaction (PCR) assays that however can fail due to primer mismatch. We investigated the performance of routine virus diagnostics in Kilifi, Kenya, using random-primed viral next generation sequencing (viral NGS) on respiratory samples which tested negative for the common viral respiratory pathogens by a local standard diagnostic panel. Among 95 hospitalised pneumonia patients and 95 household-cohort individuals, analysis of viral NGS identified at least one respiratory-associated virus in 35 (37%) and 23 (24%) samples, respectively. The majority (66%; 42/64) belonged to the Picornaviridae family. The NGS data analysis identified a number of viruses that were missed by the diagnostic panel (rhinovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus), and these failures could be attributed to PCR primer/probe binding site mismatches. Unexpected viruses identified included parvovirus B19, enterovirus D68, coxsackievirus A16 and A24 and rubella virus. The regular application of such viral NGS could help evaluate assay performance, identify molecular causes of missed diagnoses and reveal gaps in the respiratory virus set used for local screening assays. The results can provide actionable information to improve the local pneumonia diagnostics and reveal locally important viral pathogens.
Item Type: | Journal Article | ||||||
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||||
Journal or Publication Title: | Scientific Reports | ||||||
Publisher: | Nature Publishing Group | ||||||
ISSN: | 2045-2322 | ||||||
Official Date: | 7 January 2022 | ||||||
Dates: |
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Volume: | 12 | ||||||
Article Number: | 202 | ||||||
DOI: | 10.1038/s41598-021-03987-1 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||
Date of first compliant deposit: | 6 December 2021 | ||||||
Date of first compliant Open Access: | 10 January 2022 | ||||||
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