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. 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.

Phylogenetic characterization of circulating Dengue and Alkhumra Hemorrhagic Fever viruses in western Saudi Arabia and lack of evidence of Zika virus in the region: A retrospective study, 2010‐2015

“…Many of these viruses are human pathogens causing a wide range of clinical symptoms . In Saudi Arabia, at least five flaviviruses are circulating including DENV‐1, DENV‐2, DENV‐3, and AHFV in addition to recent detection of DENV‐4 in Jeddah (personal communication). However, whether other flaviviral species are circulating in the Kingdom is not known because of the few number of surveillance studies.…”

“…AHFV is a newly characterized flavivirus first isolated in Jeddah, Saudi Arabia, in 1995 . Until now, AHFV has been isolated sporadically from humans and ticks in Saudi Arabia and Egypt and shown to have high mortality rate (∼25%) . Whether the reported numbers of cases reflect the actual incidence of AHFV infections is not known mostly due to the limited epidemiological studies and/or misdiagnosis.…”

“…Cycle sequencing was performed on an ABI 3500 Automatic Sequencer (Applied Biosystems, Foster City, CA) using PF1 and PFR2 primers and Bigdye Terminator V3.1 Reaction Cycle Kit (Applied Biosystems) according to manufacturer's instructions. Complete genome of AHFV was sequenced as previously described . All generated sequences were deposited in GenBank database with the following accession numbers for DENV‐2 (KU886699, KU886700, KU886701, KU886702, KU886703, KU886704, KU886705, KU886706, KU886707, KU886708, KU886709, KU886710, KU886712, and KU886713), for DENV‐3 (KU886711) and for AHFV (KU884971).…”

“…In Saudi Arabia, at least five vector‐borne flaviviruses are circulating including DENV‐1, DENV‐2, DENV‐3, DENV‐4, and AHFV in addition to two other arboviruses (Rift Valley fever virus [RVFV] and Crimean‐Congo haemorrhagic fever virus [CCHF]) . These viruses are known to be endemic and causing outbreaks or sporadic infections in several regions in Saudi Arabia.…”

Al-Khurma Haemorrhagic Fever

“…Daha sonra AHFV'nin, 3416 aminoasidden ibaret uzun bir poliproteini kodlayan 10 248 nükleotidden oluşan tam genom dizisi belirlenerek ve tam poliprotein ve zarf (E) proteininin bağım-sız analizleri yapılarak, KFDV ile ortak bir filogenetik atadan geldiği gösterilmiştir (16). Dolaşımdaki AHFV suşları arasın-daki rekombinasyona bağlı olarak, nükleotid sayılarında kü-çük farklılıklar gözlenebilmektedir (17 (23). Ancak suşun referans suşla da özdeş olması, sonradan bir laboratuvar kontaminasyonu olarak yorumlanmıştır (24).…”