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 G. Ksiazek

doi:10.1159/000362334

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 G. Ksiazek

Pathology

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

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 language	English (US)
Pages (from-to)	300-310
Number of pages	11
Journal	Intervirology
Volume	57
Issue number	5
DOIs	https://doi.org/10.1159/000362334
State	Published - Aug 2014

Keywords

Alkhumra hemorrhagic fever virus
Flavivirus
Genome sequence
Hemorrhagic fever
Phylogenetic analysis

ASJC Scopus subject areas

Virology
Infectious Diseases

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10.1159/000362334

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Madani, T. A., Azhar, E. I., Abuelzein, E. T. M. E., Kao, M., Al-Bar, H. M. S., Farraj, S. A., Masri, B. E., Al-Kaiedi, N. A., Shakil, S., Sohrab, S. S., Santalucia, J., & Ksiazek, T. G. (2014). Complete genome sequencing and genetic characterization of alkhumra hemorrhagic fever virus isolated from Najran, Saudi Arabia. Intervirology, 57(5), 300-310. https://doi.org/10.1159/000362334

@article{d030e828a2ce4f9dbb181531ca18b9bc,

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. 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.",

keywords = "Alkhumra hemorrhagic fever virus, Flavivirus, Genome sequence, Hemorrhagic fever, Phylogenetic analysis",

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

year = "2014",

month = aug,

doi = "10.1159/000362334",

language = "English (US)",

volume = "57",

pages = "300--310",

journal = "Intervirology",

issn = "0300-5526",

publisher = "S. Karger AG",

number = "5",

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TY - JOUR

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 G.

PY - 2014/8

Y1 - 2014/8

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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M3 - Article

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AN - SCOPUS:84906003438

SN - 0300-5526

VL - 57

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EP - 310

JO - Intervirology

JF - Intervirology

IS - 5

ER -

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

Abstract

Keywords

ASJC Scopus subject areas

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