Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya
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 vir...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2022-01-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-021-03987-1 |
| _version_ | 1798033452984958976 |
|---|---|
| author | My V. T. Phan Charles N. Agoti Patrick K. Munywoki Grieven P. Otieno Mwanajuma Ngama Paul Kellam Matthew Cotten D. James Nokes |
| author_facet | My V. T. Phan Charles N. Agoti Patrick K. Munywoki Grieven P. Otieno Mwanajuma Ngama Paul Kellam Matthew Cotten D. James Nokes |
| author_sort | My V. T. Phan |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-11T20:30:36Z |
| format | Article |
| id | doaj.art-b8674ec557a840ed853590141e4613ce |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-11T20:30:36Z |
| publishDate | 2022-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-b8674ec557a840ed853590141e4613ce2022-12-22T04:04:31ZengNature PortfolioScientific Reports2045-23222022-01-0112111110.1038/s41598-021-03987-1Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from KenyaMy V. T. Phan0Charles N. Agoti1Patrick K. Munywoki2Grieven P. Otieno3Mwanajuma Ngama4Paul Kellam5Matthew Cotten6D. James Nokes7Virus Genomics, Wellcome Trust Sanger InstituteEpidemiology and Demography Department, KEMRI –Wellcome Trust Research ProgrammeEpidemiology and Demography Department, KEMRI –Wellcome Trust Research ProgrammeEpidemiology and Demography Department, KEMRI –Wellcome Trust Research ProgrammeEpidemiology and Demography Department, KEMRI –Wellcome Trust Research ProgrammeVirus Genomics, Wellcome Trust Sanger InstituteVirus Genomics, Wellcome Trust Sanger InstituteEpidemiology and Demography Department, KEMRI –Wellcome Trust Research ProgrammeAbstract 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.https://doi.org/10.1038/s41598-021-03987-1 |
| spellingShingle | My V. T. Phan Charles N. Agoti Patrick K. Munywoki Grieven P. Otieno Mwanajuma Ngama Paul Kellam Matthew Cotten D. James Nokes Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya Scientific Reports |
| title | Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya |
| title_full | Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya |
| title_fullStr | Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya |
| title_full_unstemmed | Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya |
| title_short | Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya |
| title_sort | identification of missed viruses by metagenomic sequencing of clinical respiratory samples from kenya |
| url | https://doi.org/10.1038/s41598-021-03987-1 |
| work_keys_str_mv | AT myvtphan identificationofmissedvirusesbymetagenomicsequencingofclinicalrespiratorysamplesfromkenya AT charlesnagoti identificationofmissedvirusesbymetagenomicsequencingofclinicalrespiratorysamplesfromkenya AT patrickkmunywoki identificationofmissedvirusesbymetagenomicsequencingofclinicalrespiratorysamplesfromkenya AT grievenpotieno identificationofmissedvirusesbymetagenomicsequencingofclinicalrespiratorysamplesfromkenya AT mwanajumangama identificationofmissedvirusesbymetagenomicsequencingofclinicalrespiratorysamplesfromkenya AT paulkellam identificationofmissedvirusesbymetagenomicsequencingofclinicalrespiratorysamplesfromkenya AT matthewcotten identificationofmissedvirusesbymetagenomicsequencingofclinicalrespiratorysamplesfromkenya AT djamesnokes identificationofmissedvirusesbymetagenomicsequencingofclinicalrespiratorysamplesfromkenya |