ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2019
Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 28 citations in OpenAlex.
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- Validation of the VirCapSeq-VERT system for differential diagnosis, detection, and surveillance of viral infections.Journal of clinical microbiology · 2024Article
- Emergence of a Distinct Picobirnavirus Genotype Circulating in Patients Hospitalized with Acute Respiratory Illness.Viruses · 2021Article
- Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Article
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- Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses.Microorganisms · 2020Article
- Comparative Analysis of RNA Virome Composition in Rabbits and Associated Ectoparasites.Journal of virology · 2020Article
- Public health in genetic spaces: a statistical framework to optimize cluster-based outbreak detection.Virus evolution · 2020Article
- The True Host/s of Picobirnaviruses.Frontiers in veterinary science · 2020Review
- Broad Virus Detection and Variant Discovery in Fecal Samples of Hematopoietic Transplant Recipients Using Targeted Sequence Capture Metagenomics.Frontiers in microbiology · 2020Article
- Characterization of Stool Virome in Children Newly Diagnosed With Moderate to Severe Ulcerative Colitis.Inflammatory bowel diseases · 2019Article
- Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples.BMC genomics · 2019Article
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13 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundPrecision public health is a novel set of methods to target disease prevention and mitigation interventions to high-risk subpopulations. We applied a precision public health strategy to syndromic surveillance for severe acute respiratory infection (SARI) in Uganda by combining spatiotemporal analytics with genomic sequencing to detect and characterize viral respiratory pathogens with epidemic potential.
methodsUsing a national surveillance network we identified patients with unexplained, influenza-negative SARI from 2010 to 2015. Spatiotemporal analyses were performed retrospectively to identify clusters of unexplained SARI. Within clusters, respiratory viruses were detected and characterized in naso- and oropharyngeal swab samples using a novel oligonucleotide probe capture (VirCapSeq-VERT) and high-throughput sequencing platform. Linkage to conventional epidemiologic strategies further characterized transmission dynamics of identified pathogens.
resultsAmong 2901 unexplained SARI cases, 9 clusters were detected, accounting for 301 (10.4%) cases. Clusters were more likely to occur in urban areas and during biannual rainy seasons. Within detected clusters, we identified an unrecognized outbreak of measles-associated SARI; sequence analysis implicated cocirculation of endemic genotype B3 and genotype D4 likely imported from England. We also detected a likely nosocomial SARI cluster associated with a novel picobirnavirus most closely related to swine and dromedary viruses.
conclusionsUsing a precision approach to public health surveillance, we detected and characterized the genomics of vaccine-preventable and zoonotic respiratory viruses associated with clusters of severe respiratory infections in Uganda. Future studies are needed to assess the feasibility, scalability, and impact of applying similar approaches during real-time public health surveillance in low-income settings.
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