Accepted Manuscript First Complete Genome Sequence of Circulating Dengue Virus Serotype 3 in Jeddah, Saudi Arabia Anwar M. Hashem, Sayed S. Sohrab, Sherif A. El-Kafrawy, Saeid Abo El-Ela, Adly MM. Abd-Alla, Suha A. Farraj, Norah A. Othman, Ahmed M. Hassan, Mai M. El-Daly, Remi N. Charrel, Tariq A. madani, Esam I. Azhar PII:
S2052-2975(17)30076-8
DOI:
10.1016/j.nmni.2017.09.005
Reference:
NMNI 364
To appear in:
New Microbes and New Infections
Received Date: 7 August 2017 Revised Date:
11 September 2017
Accepted Date: 19 September 2017
Please cite this article as: Hashem AM, Sohrab SS, El-Kafrawy SA, El-Ela SA, Abd-Alla AM, Farraj SA, Othman NA, Hassan AM, El-Daly MM, Charrel RN, madani TA, Azhar EI, First Complete Genome Sequence of Circulating Dengue Virus Serotype 3 in Jeddah, Saudi Arabia, New Microbes and New Infections (2017), doi: 10.1016/j.nmni.2017.09.005. This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain.
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First Complete Genome Sequence of Circulating Dengue Virus Serotype 3 in
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Jeddah, Saudi Arabia
3 Anwar M Hashem1,2, Sayed S Sohrab1, Sherif A El-Kafrawy1, Saeid Abo El-Ela1,
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Adly MM Abd-Alla3, Suha A Farraj1, Norah A Othman1, Ahmed M Hassan1, Mai M
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El-Daly1, Remi N Charrel1,4, Tariq A madani5, Esam I Azhar1,6*
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*Corresponding Author Prof. Esam Ibraheem Azhar Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, Post Box No- 80216 Jeddah -21589, Saudi Arabia. Phone: +966-566615222 ; +966-64001000. Ext. 25297 Email:
[email protected]
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Special Infectious Agent Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.
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Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia. Insect Pest Control Laboratory, Joint FAO/IAEA Programme of Nuclear Techniques in Food and Agriculture, Vienna, Austria, Pests and Plant Protection Department, National Research Center, Cairo, Egypt.
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UMR "Emergence des Pathologies Virales" (EPV: Aix-Marseille University - IRD 190 - Inserm 1207 - EHESP) & Fondation IHU Méditerranée Infection, APHM Public Hospitals of Marseille, Marseille, France. Department of Medicine, Faculty of Medicine, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia.
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Department of medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
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First Complete Genome Sequence of Circulating Dengue Virus Serotype 3 in
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Jeddah, Saudi Arabia
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ACCEPTED MANUSCRIPT 1 2 3 Abstract
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Here we report the first full-length genome sequence of dengue virus serotype 3
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(DENV-3) from a strain isolated from a patient in Jeddah city, Saudi Arabia in 2014.
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The genome consists of 10,635 bp and shows close similarity to circulating genotype
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III isolates from Singapore suggesting possible importation most probably during
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religious pilgrimages to Saudi Arabia.
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Keywords: Dengue virus, DENV, full genome, genotypes, Saudi Arabia.
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ACCEPTED MANUSCRIPT 1 2 Dengue virus (DENV) is an arbovirus transmitted primarily by Aedes aegypti and
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albopictus mosquitos. It causes a disease ranging from acute dengue fever (DF) to
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severe dengue hemorrhagic fever (DHF) or dengue shock syndrome (DSS) (1).
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Dengue is endemic in ~100 countries in tropical and subtropical regions of the world
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(2). Current estimates suggest that ~40% of the world’s population are at high risk of
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dengue infection and there are 50-100 million annual DF cases with 500,000 DHF and
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22,000 deaths (2). There are four antigenicaly and genetically distinct DENV
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serotypes (DENV-1 to 4) which are further classified into different genotypes
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genetically.
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DENV-3 have been classified into five different genotypes (3) with genotypes I, II
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and III being responsible for most DENV-3 infections and DHF outbreaks compared
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to genotypes IV and V (3,4,5). DENV-3 has been circulating and causing several
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outbreaks in the western region of Saudi Arabia (Jeddah and Makkah cities) since its
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first isolation, in 1997 in Jeddah, until now, although with lower prevalence compared
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to DENV-1 and DENV-2 (6-11). However, there has been no report of any DENV-3
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full genome sequence from Saudi Arabia. Therefore, in this study we report the first
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full genome of DENV-3 strain isolated from Jeddah, Saudi Arabia.
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Serum and plasma samples were obtained from a DF suspected patient at King
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Abdulaziz University Hospital in 2014 with ethical approval (19–14) from the Unit of
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Biomedical Ethics. The serum sample was found positive for anti-dengue IgM but not
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IgG antibodies, suggesting an acute primary DENV infection which was confirmed by
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real time RT-PCR using the plasma sample as previously described (12). The full
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genome sequence of DENV-3-Jeddah-2014 isolate was then obtained as previously
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described (13). The sequenced length of this isolate was 10,635 bp with an open
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reading frame coding for 3,390 amino acids (aa).
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Phylogenetic analyses based on full genome and complete envelope gene of this strain
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and isolates representing diverse geographical locations were conducted using the
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maximum likelihood (ML) method in MEGA 6.0 software (14). Full genome analysis
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showed close clustering of DENV-3-Jeddah-2014 isolate with genotype III isolates
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collected between 2004 and 2007 from Sri Lanka and Singapore with highest
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similarity to strain GU370053 isolated in 2007 from Singapore (FIG. 1a). However,
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because of the temporal difference between DENV-3-Jeddah-2014 isolate and closely
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related strains and the limited number of available full genome sequences,
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phylogenetic tree based on the envelope (E) gene was constructed using all available
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E gene sequences in the GenBank database within the clade of interest (FIG. 1b). This
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analysis revealed that DENV-3-Jeddah-2014 isolate has a close relationship with
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recent DENV-3 strains from Singapore obtained between 2013 and 2014 (KP685235
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and KX224292) (FIG. 1b). These results suggest that DENV-3-Jeddah-2014 strain
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might have been introduced from Singapore to Jeddah most probably during religious
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pilgrimages (Hajj and Umrah). This is the first report of DENV-3 full genome from
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Saudi Arabia which should help in the study of the evolution of DENV-3 in the
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region. However, more studies and sequences are required to clearly monitor dengue
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importation into Saudi Arabia.
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ACCEPTED MANUSCRIPT 1 2 Nucleotide sequence accession number
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The virus genome sequence described here has been deposited in the GenBank
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database and assigned accession no. KJ830751.
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Acknowledgements
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This work was supported by grants from the Deanship of Scientific Research (DSR),
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King Abdulaziz University (KAU), Jeddah, Saudi Arabia, Grant no. RG/34/2 and
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Grant no. 543/141/1432. The authors, therefore, acknowledge with thanks DSR
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technical and financial support.
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None declared.
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2. Centers for disease control and prevention (CDC). Dengue epidemiology. https://www.cdc.gov/dengue/epidemiology/index.html
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3. Aquino VH, Amarilla AA, Alfonso HL, Batista WC, Figueiredo LT. New genotype of dengue type 3 virus circulating in Brazil and Colombia showed a close relationship to old Asian viruses. PLoS One 2009;4:e7299.
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5. King CC, Chao DY, Chien LJ, Chang GJ, Lin TH, Wu YC, et al. Comparative analysis of full genomic sequences among different genotypes of dengue virus type 3. Virol J 2008;5:63.
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6. Zaki A, Perera D, Jahan SS, Cardosa MJ. Phylogeny of dengue viruses circulating in Jeddah, Saudi Arabia: 1994 to 2006. Trop Med Int Health 2008;13:584-92.
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7. Ahmed MM. Clinical profile of dengue fever infection in King Abdul Aziz University Hospital Saudi Arabia. J Infect Dev Ctries 2010;4:503-10.
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8. Khan NA, Azhar EI, El-Fiky S, Madani HH, Abuljadial MA, Ashshi AM, et al. Clinical profile and outcome of hospitalized patients during first outbreak of dengue in Makkah, Saudi Arabia. Acta Tropica 2008;105:39-44.
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9. Organji SR, Abulreesh HH, Osman GEH. Circulation of Dengue Virus Serotypes in the City of Makkah, Saudi Arabia, as Determined by Reverse Transcription Polymerase Chain Reaction. Can J Infect Dis Med Microbiol 2017;2017:1646701.
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10. Al-Saeed MS, El-Kafrawy SA, Farraj SA, Al-Subhi TL, Othman NA, Alsultan A, et al. 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. J Med Virol 2017;89:1339-46.
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11. Ashshi AM. The prevalence of dengue virus serotypes in asymptomatic blood donors reveals the emergence of serotype 4 in Saudi Arabia. Virol J 2017;14:107.
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12. Drosten C, Göttig S, Schilling S, Asper M, Panning M, Schmitz H, et al. Rapid detection and quantification of RNA of Ebola and Marburg viruses, 6
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13. Christenbury JG, Aw PP, Ong SH, Schreiber MJ, Chow A, Gubler DJ, et al. A method for full genome sequencing of all four serotypes of the dengue virus. J Virol Methods 2010;169:202-6.
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14. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol 2013;30:2725-9.
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FIG. 1. Phylogenetic trees of DENV-3. (a) Phylogenetic tree based on full genome
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sequences of DENV-3. (b) Phylogenetic tree based on complete E gene sequences of
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DENV-3. Phylogenetic trees were constructed using the maximum likelihood (ML)
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method based on best fit-model of nucleotide substitution and bootstrapping of 1,000
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replicates in MEGA 6.0 software. DENV-3 from in this study indicated by red box.
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FJ882575-Mozambique-1985 FJ882571-Sri Lanka-1989 GQ252674-Sri Lanka-1997 100
b
Sri Lanka 1989
FJ882576-Nicaragua-1994 FJ898440-Mexico-2003 GQ868574-Colombia-2003 99 FJ639763-Venezuela-2001 100 100 KF955468-Puerto Rico-2001 FJ182011-USA-2005 KC425219-Brazil-2002 JX669490-Brazil-2002 GU131872-Brazil-2007 98 JF808122-Paraguay-2003 JX669500-Brazil-2005 99 AY099337-Martinique KU509278-Barbados-2007 100 KF955505-Grenada-2002 99 86 GQ868617-Trinidad and Tobago-2002 100
Nicaragua 2008-2012
EU529703-USA-1998 FJ898457-Ecuador-2000 KT726355-Cuba-2001
100 91 78
Peru 2002-2008
99
KU509281-India-2009
100
India 2013
KY921907-Singapore-2015 JQ922556-India-2005 JQ922557-India-2005
99 100 100
100
India 2007-2008 AY770511-India
86 100 83
China 2009 Pakistan 2006-2009
100 100
KX380841-Singapore-2012 KX380842-Singapore-2013
KJ830751-Saudi-2014
100
GU370053-Singapore-2007 AY099336-Sri Lanka DQ675533-Taiwan-1999 KU509283-Sri Lanka-2006
98 100 99 100
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100
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China 2013
FJ882573-Sri Lanka-1993
Singapore 2004-2005
Sri Lanka 1983-1989
Genotype III
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KU509282-Senegal-2009 KU509286-India-2011
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KP176709-Malaysia-2013 KP176714-Taiwan-2011 KX224283-Singapore-2014 JF968107-Malaysia-2010 KR779787-Singapore-2013 JN030189-Singapore-2010 KX224291-Singapore-2013
KJ830751-Saudi-2014
KP685235-Singapore-2013 KX224292-Singapore-2013 JN030177-Singapore-2009 JF968068-Malaysia-2008 JF968106-Thailand-2010 JN380810-Singapore-2009 JQ686083-India-2009 JN030184-Singapore-2009 KX224280-Singapore-2013 83 JN030180-Singapore-2009 JN575578-Australia-2007 JN022604-Singapore-2007 75 91 GU370053-Singapore-2007 JN030166-Singapore-2008 JN030171-Singapore-2008 JN030185-Singapore-2008 99 JN030165-Singapore-2008 AY099336-Sri_Lanka KX518579-Sri_Lanka-2003 DQ518679-Sri_Lanka-1999 DQ675533-Taiwan-1999 KX518574-Sri_Lanka-1993 99 FJ882573-Sri_Lanka-1993 KX518580-Sri_Lanka-2004 95 99 KX518576-Sri_Lanka-2004 KU509283-Sri_Lanka-2006 KX518578-Sri_Lanka-2004 KX518577-Sri_Lanka-2004 98
Genotype I
82
Genotype II
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0.01
0.002
Singapore 2004-2005
