title: Development and evaluation of a panel of filovirus sequence capture probes for pathogen detection by next-generation sequencing.
abstract: A detailed understanding of the circulating pathogens in a particular geographic location aids in effectively utilizing targeted, rapid diagnostic assays, thus allowing for appropriate therapeutic and containment procedures. This is especially important in regions prevalent for highly pathogenic viruses co-circulating with other endemic pathogens such as the malaria parasite. The importance of biosurveillance is highlighted by the ongoing Ebola virus disease outbreak in West Africa. For example, a more comprehensive assessment of the regional pathogens could have identified the risk of a filovirus disease outbreak earlier and led to an improved diagnostic and response capacity in the region. In this context, being able to rapidly screen a single sample for multiple pathogens in a single tube reaction could improve both diagnostics as well as pathogen surveillance. Here, probes were designed to capture identifying filovirus sequence for the ebolaviruses Sudan, Ebola, Reston, Taï Forest, and Bundibugyo and the Marburg virus variants Musoke, Ci67, and Angola. These probes were combined into a single probe panel, and the captured filovirus sequence was successfully identified using the MiSeq next-generation sequencing platform. This panel was then used to identify the specific filovirus from nonhuman primates experimentally infected with Ebola virus as well as Bundibugyo virus in human sera samples from the Democratic Republic of the Congo, thus demonstrating the utility for pathogen detection using clinical samples. While not as sensitive and rapid as real-time PCR, this panel, along with incorporating additional sequence capture probe panels, could be used for broad pathogen screening and biosurveillance.
authors.affiliation: Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America.
authors.forename: Jeffrey W
authors.initials: JW
authors.lastname: Koehler
authors.affiliation: Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America.
authors.forename: Adrienne T
authors.initials: AT
authors.lastname: Hall
authors.affiliation: Pathogenica, Inc., Boston, Massachusetts, United States of America.
authors.forename: P Alexander
authors.initials: PA
authors.lastname: Rolfe
authors.affiliation: Virology Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America.
authors.forename: Anna N
authors.initials: AN
authors.lastname: Honko
authors.affiliation: Center for Genomic Sciences, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America.
authors.forename: Gustavo F
authors.initials: GF
authors.lastname: Palacios
authors.affiliation: Metabiota, San Francisco, California, United States of America.
authors.forename: Joseph N
authors.initials: JN
authors.lastname: Fair
authors.affiliation: Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo.
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Muyembe
authors.affiliation: Kinshasa School of Public Health, Kinshasa, Democratic Republic of the Congo.
authors.forename: Prime
authors.initials: P
authors.lastname: Mulembekani
authors.affiliation: Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America.
authors.forename: Randal J
authors.initials: RJ
authors.lastname: Schoepp
authors.affiliation: Pathogenica, Inc., Boston, Massachusetts, United States of America.
authors.forename: Adeyemi
authors.initials: A
authors.lastname: Adesokan
authors.affiliation: Diagnostic Systems Division, United States Army Medical Research Institute of Infectious Diseases, Fort Detrick, Maryland, United States of America.
authors.forename: Timothy D
authors.initials: TD
authors.lastname: Minogue
mesh_terms: D000818:Animals; D015342:DNA Probes / Q000138:chemical synthesis*; D018076:DNA, Complementary / Q000235:genetics; D015023:Democratic Republic of the Congo; D029043:Ebolavirus / Q000235:genetics* / Q000302:isolation & purification; D016563:Filoviridae / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D019142:Hemorrhagic Fever, Ebola / Q000175:diagnosis / Q000662:veterinary* / Q000821:virology; D006801:Humans; D008253:Macaca mulatta; D016133:Polymerase Chain Reaction / Q000379:methods*; D012367:RNA, Viral / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA
chemical_list: D015342:DNA Probes; D018076:DNA, Complementary; D012367:RNA, Viral