E-Mail karger@karger.com Orginal Paper Intervirology 2014;57:300–310 DOI: 10.1159/000362334 Complete Genome Sequencing and Genetic Characterization of Alkhumra Hemorrhagic Fever Virus Isolated from Najran, Saudi Arabia Tariq A. Madani a Esam I. Azhar b, c El-Tayeb M.E. Abuelzein c, d Moujahed Kao c Hussein M.S. Al-Bar e Suha A. Farraj c Badr E. Masri c Noora A. Al-Kaiedi c Shazi Shakil c Sayed S. Sohrab c John SantaLucia Jr. f Thomas G. Ksiazek g a Department of Medicine, Faculty of Medicine, b Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, c Special Infectious Agents Unit, King Fahd Medical Research Center, d Scientific Chair of Sheikh Mohammad Hussein Al-Amoudi for Viral Hemorrhagic Fever, and e Department of Family and Community Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia; f Department of Chemistry, Wayne State University, Detroit, Mich., and g Galveston National Laboratory, Departments of Pathology and Microbiology and Immunology, University of Texas Medical Branch, Galveston, Tex., USA ein, whereas the previously reported AHFV strains were com- posed 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 ho- mology. The most important variations were observed in the core protein and NS4a gene sequences of two AHFV isolates. Conclusion: The variation in the number of nucleotides and phylogenetic analysis with the other AHFV isolates could have resulted from recombination of circulating virus strains. © 2014 S. Karger AG, Basel Introduction Alkhumra hemorrhagic fever virus (AHFV) is a new- ly described flavivirus associated with hemorrhagic fever that was first identified in Saudi Arabia. It is a member of the tick-borne encephalitis group in the genus Flavivi- rus of the family Flaviviridae. It was first isolated in 1994– 1995 from 6 patients living in the Alkhumra district in Key Words Alkhumra hemorrhagic fever virus · Flavivirus · Hemorrhagic fever · Phylogenetic analysis · Genome sequence 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. Subse- quently, 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 ampli- fied 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 nu- cleotides encoding for a single 3,416-amino acid polyprot- Received: July 17, 2013 Accepted after revision: March 19, 2014 Published online: July 30, 2014 Prof. Tariq Ahmed Madani Department of Medicine Faculty of Medicine, King Abdulaziz University PO Box 80215, Jeddah 21589 (Saudi Arabia) E-Mail tmadani  @  kau.edu.sa © 2014 S. Karger AG, Basel 0300–5526/14/0575–0300$39.50/0 www.karger.com/int