title: Complete genome sequencing and genetic characterization of Alkhumra hemorrhagic fever virus isolated from Najran, Saudi Arabia.
abstract: BACKGROUND
  Alkhumra hemorrhagic fever virus (AHFV) is a newly described flavivirus first isolated in 1994-1995 from the Alkhumra district south of Jeddah, Saudi Arabia. Subsequently, the virus was also isolated from Makkah (2001-2003) and Najran (2008-2009), Saudi Arabia.
  
  
  METHODS
  The full-length genome of an AHFV strain isolated from patients in Najran (referred to as AHFV/997/NJ/09/SA) was PCR amplified and sequenced, and compared with the sequences of 18 other AHFV strains previously isolated from Jeddah and Makkah, dengue virus (DENV), Kyasanur forest disease virus (KFDV), Langat virus, Omsk hemorrhagic fever virus (OHFV), and tick-borne encephalitis virus (TBEV).
  
  
  RESULTS
  The RNA of the AHFV/997/NJ/09/SA strain was found to have 10,546 nucleotides encoding for a single 3,416-amino acid polyprotein, whereas the previously reported AHFV strains were composed of 10,685-10,749 nucleotides. The AHFV/997/NJ/09/SA strain showed about 99% homology with the previously reported AHFV strains. The KFDV, Langat virus, TBEV, and OHFV isolates formed a separate cluster with a variable homology. The most important variations were observed in the core protein and NS4a gene sequences of two AHFV isolates.
  
  
  CONCLUSIONS
  The variation in the number of nucleotides and phylogenetic analysis with the other AHFV isolates could have resulted from recombination of circulating virus strains.
authors.affiliation: Department of Medicine, Faculty of Medicine, Faculty of Applied Medical Sciences, Jeddah, Saudi Arabia.
authors.forename: Tariq A
authors.initials: TA
authors.lastname: Madani
authors.forename: Esam I
authors.initials: EI
authors.lastname: Azhar
authors.forename: El-Tayeb M E
authors.initials: el-TM
authors.lastname: Abuelzein
authors.forename: Moujahed
authors.initials: M
authors.lastname: Kao
authors.forename: Hussein M S
authors.initials: HM
authors.lastname: Al-Bar
authors.forename: Suha A
authors.initials: SA
authors.lastname: Farraj
authors.forename: Badr E
authors.initials: BE
authors.lastname: Masri
authors.forename: Noora A
authors.initials: NA
authors.lastname: Al-Kaiedi
authors.forename: Shazi
authors.initials: S
authors.lastname: Shakil
authors.forename: Sayed S
authors.initials: SS
authors.lastname: Sohrab
authors.forename: John
authors.initials: J
authors.lastname: SantaLucia
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Ksiazek
mesh_terms: D016000:Cluster Analysis; D004669:Encephalitis Viruses, Tick-Borne / Q000235:genetics* / Q000302:isolation & purification; D004675:Encephalitis, Tick-Borne / Q000821:virology*; D016679:Genome, Viral; D006801:Humans; D010802:Phylogeny; D020815:Polyproteins / Q000235:genetics; D012367:RNA, Viral / Q000235:genetics*; D012529:Saudi Arabia; D017422:Sequence Analysis, DNA; D017385:Sequence Homology
chemical_list: D020815:Polyproteins; D012367:RNA, Viral