Complete genome sequencing and genetic characterization of alkhumra hemorrhagic fever virus isolated from Najran, Saudi Arabia

Tariq A. Madani, Esam I. Azhar, El Tayeb M E Abuelzein, Moujahed Kao, Hussein M S Al-Bar, Suha A. Farraj, Badr E. Masri, Noora A. Al-Kaiedi, Shazi Shakil, Sayed S. Sohrab, John Santalucia, Thomas Ksiazek

Research output: Contribution to journalArticle

5 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)300-310
Number of pages11
JournalIntervirology
Volume57
Issue number5
DOIs
StatePublished - 2014

Fingerprint

Saudi Arabia
Tick-Borne Encephalitis Viruses
Fever
Genome
Viruses
Nucleotides
Flavivirus
Polyproteins
Dengue Virus
Genetic Recombination
RNA

Keywords

  • Alkhumra hemorrhagic fever virus
  • Flavivirus
  • Genome sequence
  • Hemorrhagic fever
  • Phylogenetic analysis

ASJC Scopus subject areas

  • Virology
  • Infectious Diseases

Cite this

Complete genome sequencing and genetic characterization of alkhumra hemorrhagic fever virus isolated from Najran, Saudi Arabia. / Madani, Tariq A.; Azhar, Esam I.; Abuelzein, El Tayeb M E; Kao, Moujahed; Al-Bar, Hussein M S; Farraj, Suha A.; Masri, Badr E.; Al-Kaiedi, Noora A.; Shakil, Shazi; Sohrab, Sayed S.; Santalucia, John; Ksiazek, Thomas.

In: Intervirology, Vol. 57, No. 5, 2014, p. 300-310.

Research output: Contribution to journalArticle

Madani, TA, Azhar, EI, Abuelzein, ETME, Kao, M, Al-Bar, HMS, Farraj, SA, Masri, BE, Al-Kaiedi, NA, Shakil, S, Sohrab, SS, Santalucia, J & Ksiazek, T 2014, 'Complete genome sequencing and genetic characterization of alkhumra hemorrhagic fever virus isolated from Najran, Saudi Arabia', Intervirology, vol. 57, no. 5, pp. 300-310. https://doi.org/10.1159/000362334
Madani, Tariq A. ; Azhar, Esam I. ; Abuelzein, El Tayeb M E ; Kao, Moujahed ; Al-Bar, Hussein M S ; Farraj, Suha A. ; Masri, Badr E. ; Al-Kaiedi, Noora A. ; Shakil, Shazi ; Sohrab, Sayed S. ; Santalucia, John ; Ksiazek, Thomas. / Complete genome sequencing and genetic characterization of alkhumra hemorrhagic fever virus isolated from Najran, Saudi Arabia. In: Intervirology. 2014 ; Vol. 57, No. 5. pp. 300-310.
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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.",
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T1 - Complete genome sequencing and genetic characterization of alkhumra hemorrhagic fever virus isolated from Najran, Saudi Arabia

AU - Madani, Tariq A.

AU - Azhar, Esam I.

AU - Abuelzein, El Tayeb M E

AU - Kao, Moujahed

AU - Al-Bar, Hussein M S

AU - Farraj, Suha A.

AU - Masri, Badr E.

AU - Al-Kaiedi, Noora A.

AU - Shakil, Shazi

AU - Sohrab, Sayed S.

AU - Santalucia, John

AU - Ksiazek, Thomas

PY - 2014

Y1 - 2014

N2 - 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.

AB - 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.

KW - Alkhumra hemorrhagic fever virus

KW - Flavivirus

KW - Genome sequence

KW - Hemorrhagic fever

KW - Phylogenetic analysis

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