About: Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda

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About: Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda
Creator	Tokarz, Rafal Bakamutumaho, Barnabas Lutwama, Julius Byaruhanga, Timothy Kayiwa, John Mathema, Barun Namagambo, Barbara Owor, Nicholas Wolf, Allison Lipkin, W Cummings, Matthew O'donnell, Max Schluger, Neil
Source	Medline; PMC
abstract	BACKGROUND: Precision 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. METHODS: Using 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. RESULTS: Among 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. CONCLUSIONS: Using 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.
has issue date	2018-08-07(xsd:dateTime)
bibo:doi	10.1093/cid/ciy656
bibo:pmid	30099510
has license	green-oa
sha1sum (hex)	d259dce085930f831390ee1f66b1b33504611b2a
schema:url	https://doi.org/10.1093/cid/ciy656
resource representing a document's title	Precision Surveillance for Viral Respiratory Pathogens: Virome Capture Sequencing for the Detection and Genomic Characterization of Severe Acute Respiratory Infection in Uganda
has PubMed Central identifier	PMC6424078
has PubMed identifier	30099510
schema:publication	Clinical Infectious Diseases
resource representing a document's body	covid:d259dce085930f831390ee1f66b1b33504611b2a#body_text
is schema:about of	named entity 'UGANDA' named entity 'CAPTURE' named entity 'SEVERE ACUTE RESPIRATORY INFECTION' named entity 'public health' named entity 'Viral' named entity 'GENOMIC' named entity 'DETECTION' named entity 'CLINICAL' named entity 'UGANDA' named entity 'IS A' named entity 'TO DETECT' named entity 'VIRAL' named entity 'SURVEILLANCE' named entity 'INFECTIOUS DISEASES' named entity 'PUBLIC HEALTH' named entity 'DISEASE PREVENTION' named entity 'EPIDEMIC' named entity 'SET' named entity 'METHODS' named entity 'SYNDROMIC SURVEILLANCE' named entity 'BACKGROUND' named entity 'GENOMIC SEQUENCING' named entity 'NOVEL' named entity 'VIRAL' named entity 'SEQUENCING' named entity 'STRATEGY' named entity 'POTENTIAL' named entity 'PRECISION' named entity 'APPLIED' named entity 'MITIGATION' named entity 'COMBINING' named entity 'RESPIRATORY PATHOGENS' named entity 'SEVERE ACUTE RESPIRATORY INFECTION' named entity 'INTERVENTIONS' named entity 'RESPIRATORY PATHOGENS' named entity 'CHARACTERIZATION' named entity 'PRECISION' named entity 'set' named entity 'Uganda' named entity 'public health' named entity 'precision' named entity 'Pathogens' named entity 'Viral' named entity 'Clinical Infectious Diseases' named entity 'polymerase chain reaction' named entity 'sequenced' named entity 'virus' named entity 'coinfection' named entity 'high-throughput sequencing' named entity 'homology' named entity 'RSV' named entity 'PBV' named entity 'influenza' named entity 'genomic sequencing' named entity 'central Uganda' named entity 'Uganda' named entity 'SARI' named entity 'shortness of breath' named entity 'influenza' named entity 'CMV' named entity 'SARI' named entity 'virus' named entity 'RSV' named entity 'low-income' named entity 'HPIV' named entity 'difficulty breathing' named entity 'viral pathogens' named entity 'PBV' named entity 'SARS'

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