title: Using next generation sequencing to identify yellow fever virus in Uganda.
abstract: In October and November 2010, hospitals in northern Uganda reported patients with suspected hemorrhagic fevers. Initial tests for Ebola viruses, Marburg virus, Rift Valley fever virus, and Crimean Congo hemorrhagic fever virus were negative. Unbiased PCR amplification of total RNA extracted directly from patient sera and next generation sequencing resulted in detection of yellow fever virus and generation of 98% of the virus genome sequence. This finding demonstrated the utility of next generation sequencing and a metagenomic approach to identify an etiological agent and direct the response to a disease outbreak.
authors.affiliation: Virus Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
authors.forename: Laura K
authors.initials: LK
authors.lastname: McMullan
authors.forename: Mike
authors.initials: M
authors.lastname: Frace
authors.forename: Scott A
authors.initials: SA
authors.lastname: Sammons
authors.forename: Trevor
authors.initials: T
authors.lastname: Shoemaker
authors.forename: Stephen
authors.initials: S
authors.lastname: Balinandi
authors.forename: Joseph F
authors.initials: JF
authors.lastname: Wamala
authors.forename: Julius J
authors.initials: JJ
authors.lastname: Lutwama
authors.forename: Robert G
authors.initials: RG
authors.lastname: Downing
authors.forename: Ute
authors.initials: U
authors.lastname: Stroeher
authors.forename: Adam
authors.initials: A
authors.lastname: MacNeil
authors.forename: Stuart T
authors.initials: ST
authors.lastname: Nichol
mesh_terms: D001483:Base Sequence; D018076:DNA, Complementary; D005787:Gene Frequency; D016679:Genome, Viral; D006801:Humans; D025202:Molecular Diagnostic Techniques; D010802:Phylogeny; D012367:RNA, Viral / Q000097:blood* / Q000235:genetics; D017423:Sequence Analysis, RNA; D014454:Uganda; D015004:Yellow Fever / Q000175:diagnosis* / Q000821:virology; D015005:Yellow fever virus / Q000235:genetics* / Q000302:isolation & purification*
chemical_list: D018076:DNA, Complementary; D012367:RNA, Viral