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Wahaab A, Mustafa BE, Hameed M, Stevenson NJ, Anwar MN, Liu K, Wei J, Qiu Y, Ma Z. Potential Role of Flavivirus NS2B-NS3 Proteases in Viral Pathogenesis and Anti-flavivirus Drug Discovery Employing Animal Cells and Models: A Review. Viruses 2021; 14:44. [PMID: 35062249 PMCID: PMC8781031 DOI: 10.3390/v14010044] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 02/07/2023] Open
Abstract
Flaviviruses are known to cause a variety of diseases in humans in different parts of the world. There are very limited numbers of antivirals to combat flavivirus infection, and therefore new drug targets must be explored. The flavivirus NS2B-NS3 proteases are responsible for the cleavage of the flavivirus polyprotein, which is necessary for productive viral infection and for causing clinical infections; therefore, they are a promising drug target for devising novel drugs against different flaviviruses. This review highlights the structural details of the NS2B-NS3 proteases of different flaviviruses, and also describes potential antiviral drugs that can interfere with the viral protease activity, as determined by various studies. Moreover, optimized in vitro reaction conditions for studying the NS2B-NS3 proteases of different flaviviruses may vary and have been incorporated in this review. The increasing availability of the in silico and crystallographic/structural details of flavivirus NS2B-NS3 proteases in free and drug-bound states can pave the path for the development of promising antiflavivirus drugs to be used in clinics. However, there is a paucity of information available on using animal cells and models for studying flavivirus NS2B-NS3 proteases, as well as on the testing of the antiviral drug efficacy against NS2B-NS3 proteases. Therefore, on the basis of recent studies, an effort has also been made to propose potential cellular and animal models for the study of flavivirus NS2B-NS3 proteases for the purposes of exploring flavivirus pathogenesis and for testing the efficacy of possible drugs targets, in vitro and in vivo.
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Affiliation(s)
- Abdul Wahaab
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Bahar E Mustafa
- Sub Campus Toba Tek Singh, University of Agriculture, Faisalabad 36050, Pakistan;
| | - Muddassar Hameed
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute, State University, Fralin Life Sciences Building, 360 W Campus Blacksburg, Blacksburg, VA 24061, USA
| | - Nigel J. Stevenson
- Royal College of Surgeons in Ireland, Medical University of Bahrain, Busaiteen, Adliya 15503, Bahrain;
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland
| | - Muhammad Naveed Anwar
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
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Youseff BH, Brewer TG, McNally KL, Izuogu AO, Lubick KJ, Presloid JB, Alqahtani S, Chattopadhyay S, Best SM, Hu X, Taylor RT. TRAF6 Plays a Proviral Role in Tick-Borne Flavivirus Infection through Interaction with the NS3 Protease. iScience 2019; 15:489-501. [PMID: 31129244 PMCID: PMC6536497 DOI: 10.1016/j.isci.2019.05.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 01/18/2019] [Accepted: 05/08/2019] [Indexed: 02/08/2023] Open
Abstract
Tick-borne flaviviruses (TBFVs) can cause life-threatening encephalitis and hemorrhagic fever. To identify virus-host interactions that may be exploited as therapeutic targets, we analyzed the TBFV polyprotein in silico for antiviral protein-binding motifs. We obtained two putative tumor necrosis factor receptor-associated factor 6 (TRAF6)-binding motifs (TBMs) within the protease domain of the viral nonstructural 3 (NS3) protein. Here, we show that TBFV NS3 interacted with TRAF6 during infection and that TRAF6 supports TBFV replication. The proviral role of TRAF6 was not seen with mosquito-borne flaviviruses, consistent with the lack of conserved TBMs. Mutation of the second TBM within NS3 disrupted TRAF6 binding, coincident with reduced abundance of mature, autocatalytically derived form of the NS3 protease and significant virus attenuation in vitro. Our studies reveal insights into how flaviviruses exploit innate immunity for the purpose of viral replication and identify a potential target for therapeutic design. Langat virus (LGTV) NS3 protease interacts with TRAF6 during infection Tick-borne, unlike mosquito-borne, flaviviruses use TRAF6 for optimal replication E117A mutation of LGTV NS3 reduces TRAF6 binding and mature protease abundance LGTV with a mutated TRAF6-binding motif is attenuated in vitro
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Affiliation(s)
- Brian H Youseff
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Thomas G Brewer
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Kristin L McNally
- Innate Immunity and Pathogenesis Unit, Laboratory of Virology, Rocky Mountain Laboratories, DIR, NIAID, NIH, Hamilton, MT 59840, USA
| | - Adaeze O Izuogu
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Kirk J Lubick
- Innate Immunity and Pathogenesis Unit, Laboratory of Virology, Rocky Mountain Laboratories, DIR, NIAID, NIH, Hamilton, MT 59840, USA
| | - John B Presloid
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Saad Alqahtani
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - Saurabh Chattopadhyay
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA
| | - Sonja M Best
- Innate Immunity and Pathogenesis Unit, Laboratory of Virology, Rocky Mountain Laboratories, DIR, NIAID, NIH, Hamilton, MT 59840, USA
| | - Xiche Hu
- Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA
| | - R Travis Taylor
- Department of Medical Microbiology and Immunology, University of Toledo College of Medicine and Life Sciences, Toledo, OH 43614, USA.
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Palanisamy N, Akaberi D, Lennerstrand J, Lundkvist Å. Comparative genome analysis of Alkhumra hemorrhagic fever virus with Kyasanur forest disease and tick-borne encephalitis viruses by the in silico approach. Pathog Glob Health 2018; 112:210-226. [PMID: 29745301 PMCID: PMC6151960 DOI: 10.1080/20477724.2018.1471187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Alkhumra hemorrhagic fever virus (AHFV), a relatively new member of the Flaviviruses, was discovered in Saudi Arabia 23 years ago. AHFV is classified in the tick-borne encephalitis virus serocomplex, along with the Kyasanur forest disease virus (KFDV) and tick-borne encephalitis virus (TBEV). Currently, very little is known about the pathologies of AHFV. In this study, using the available genome information of AHFV, KFDV and TBEV, we have predicted and compared the following aspects of these viruses: evolution, nucleotide and protein compositions, recombination, codon frequency, substitution rate, N- and O-glycosylation sites, signal peptide and cleavage site, transmembrane region, secondary structure of 5' and 3' UTRs and RNA-RNA interactions. Additionally, we have modeled the 3D protease and RNA-dependent RNA polymerase structures for AHFV, KFDV and TBEV. Recombination analysis showed no evidence of recombination in the AHFV genome with that of either KFDV or TBEV, although single break point analysis showed that nucleotide position 7399 (in the NS4B) is a breakpoint location. AHFV, KFDV and TBEV are very similar in terms of codon frequency, the number of transmembrane regions, properties of the polyprotein, RNA-RNA interaction sequences, NS3 protease and NS5 polymerase structures and 5' UTR structure. Using genome sequences, we showed the similarities between these closely- related viruses on several different areas.
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Affiliation(s)
- Navaneethan Palanisamy
- Molecular and Cellular Engineering Group, University of Freiburg, Institute of Biology II, Freiburg, Germany
- The Hartmut Hoffmann-Berling International Graduate School of Molecular and Cellular Biology (HBIGS), University of Heidelberg, Heidelberg, Germany
| | - Dario Akaberi
- Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Johan Lennerstrand
- Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, Uppsala University, Uppsala, Sweden
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Armstrong N, Hou W, Tang Q. Biological and historical overview of Zika virus. World J Virol 2017; 6:1-8. [PMID: 28239566 PMCID: PMC5303855 DOI: 10.5501/wjv.v6.i1.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/21/2016] [Accepted: 08/15/2016] [Indexed: 02/05/2023] Open
Abstract
The recent outbreak of the Zika virus attracts worldwide attention probably because the most recently affected country (Brazil) will host the 2016 Olympic Game. Zika virus infected cases are now spreading to many other countries and its infection might be linked to some severe medical sequelae. Since its first isolation from the infected monkey in 1947 in Uganda, only a few studies had been taken until recent outbreak. According to the history of referenced publications, there is a 19-year gap from 1989 to 2007. This might be because only mild diseases were diagnosed from Zika virus infected populations. Obviously, the recent reports that Zika virus infection is probably associated with microcephaly of the neonates makes us reevaluate the medical significance of the viral pathogen. It can be transmitted sexually or by mosquito biting. Sexual transmission of the Zika virus distinguishes it from other members of the Genus Flavivirus. Detailed information of the Zika virus is needed through a thorough investigation covering basic, epidemical, subclinical and clinical studies. Here, we reviewed the published information of Zika virus.
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Memish ZA, Charrel RN, Zaki AM, Fagbo SF. Alkhurma haemorrhagic fever—a viral haemorrhagic disease unique to the Arabian Peninsula. Int J Antimicrob Agents 2010; 36 Suppl 1:S53-7. [DOI: 10.1016/j.ijantimicag.2010.06.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Chappell KJ, Stoermer MJ, Fairlie DP, Young PR. Mutagenesis of the West Nile virus NS2B cofactor domain reveals two regions essential for protease activity. J Gen Virol 2008; 89:1010-1014. [PMID: 18343843 DOI: 10.1099/vir.0.83447-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The flavivirus NS2B/NS3 protease has received considerable attention as a target for the development of antiviral compounds. While substrate based inhibitors have been the primary focus to date, an approach focussing on NS2B cofactor displacement could prove to be an effective alternative. To understand better the role of the NS2B cofactor in protease activation, we conducted an alanine mutagenesis screen throughout the 42-residue central cofactor domain (NS2B(51-92)) of West Nile virus (WNV). Two sites critical for proteolytic activity were identified (NS2B(59-62) and NS2B(75-87)), where the majority of substitutions were found to significantly decrease proteolytic activity of a recombinant WNV NS2B/NS3 protease. These findings provide mechanistic insights into the structural and functional role that the cofactor may play in the substrate-bound and free protease complexes as well as providing novel sites for targeting new antiviral inhibitors.
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Affiliation(s)
- Keith J Chappell
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, QLD 4072, Australia
| | - Martin J Stoermer
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - David P Fairlie
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
| | - Paul R Young
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- School of Molecular and Microbial Sciences, University of Queensland, Brisbane, QLD 4072, Australia
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Radichev I, Shiryaev SA, Aleshin AE, Ratnikov BI, Smith JW, Liddington RC, Strongin AY. Structure-based mutagenesis identifies important novel determinants of the NS2B cofactor of the West Nile virus two-component NS2B–NS3 proteinase. J Gen Virol 2008; 89:636-641. [DOI: 10.1099/vir.0.83359-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
West Nile virus (WNV) is an emerging mosquito-borne flavivirus that causes neuronal damage in the absence of treatment. In many flaviviruses, including WNV, the NS2B cofactor promotes the productive folding and the functional activity of the two-component NS3 (pro)teinase. Based on an analysis of the NS2B–NS3pro structure, we hypothesized that the G22 residue and the negatively charged patch D32DD34 of NS2B were part of an important configuration required for NS2B–NS3pro activity. Our experimental data confirmed that G22 and D32DD34 substitution for S and AAA, respectively, inactivated NS2B–NS3pro. An additional D42G mutant, which we designed as a control, had no dramatic effect on either the catalytic activity or self-proteolysis of NS2B–NS3pro. Because of the significant level of homology in flaviviral NS2B–NS3pro, our results will be useful for the development of specific allosteric inhibitors designed to interfere with the productive interactions of NS2B with NS3pro.
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Affiliation(s)
- Ilian Radichev
- Inflammatory and Infectious Disease Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Sergey A. Shiryaev
- Inflammatory and Infectious Disease Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Alexander E. Aleshin
- Inflammatory and Infectious Disease Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Boris I. Ratnikov
- Inflammatory and Infectious Disease Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Jeffrey W. Smith
- Inflammatory and Infectious Disease Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Robert C. Liddington
- Inflammatory and Infectious Disease Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
| | - Alex Y. Strongin
- Inflammatory and Infectious Disease Center, Burnham Institute for Medical Research, La Jolla, CA 92037, USA
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Johnston PA, Phillips J, Shun TY, Shinde S, Lazo JS, Huryn DM, Myers MC, Ratnikov BI, Smith JW, Su Y, Dahl R, Cosford NDP, Shiryaev SA, Strongin AY. HTS identifies novel and specific uncompetitive inhibitors of the two-component NS2B-NS3 proteinase of West Nile virus. Assay Drug Dev Technol 2008; 5:737-50. [PMID: 18181690 DOI: 10.1089/adt.2007.101] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
West Nile virus (WNV), a member of the Flavividae family, is a mosquito-borne, emerging pathogen. In addition to WNV, the family includes dengue, yellow fever, and Japanese encephalitis viruses, which affect millions of individuals worldwide. Because countermeasures are currently unavailable, flaviviral therapy is urgently required. The flaviviral two-component nonstructural NS2B-NS3 proteinase (protease [pro]) is essential for viral life cycle and, consequently, is a promising drug target. We report here the results of the miniaturization of an NS2B-NS3pro activity assay, followed by high-throughput screening of the National Institutes of Health's 65,000 compound library and identification of novel, uncompetitive inhibitors of WNV NS2B-NS3pro that appear to interfere with the productive interactions of the NS2B cofactor with the NS3pro domain. We anticipate that following structure optimization, the identified probes could form the foundation for the design of novel and specific therapeutics for WNV infection. We also provide the structural basis for additional species-selective allosteric inhibitors of flaviviruses.
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Affiliation(s)
- Paul A Johnston
- Pittsburgh Molecular Library Screening Center, Department of Pharmacology, University of Pittsburgh Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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Lin CW, Huang HD, Shiu SY, Chen WJ, Tsai MH, Huang SH, Wan L, Lin YJ. Functional determinants of NS2B for activation of Japanese encephalitis virus NS3 protease. Virus Res 2007; 127:88-94. [PMID: 17467838 DOI: 10.1016/j.virusres.2007.03.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 03/22/2007] [Accepted: 03/23/2007] [Indexed: 11/19/2022]
Abstract
Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus, causing severe central nerve system diseases without specific treatments. The NS2B-NS3 protease of flaviviruses mediates several cleavages on the flavivirus polyprotein, being believed to be a target for antiviral therapy. NS2B is the cofactor of the viral serine protease, correlating with stabilization and substrate recognition of the NS3 protease. In this study, we investigate the functional determinants in the JEV NS2B for the activation of the NS3 protease. Cis- and trans-cleavage assays of the deletions at the N-terminal of NS2B demonstrated that the NS2B residues Ser(46) to Ile(60) were the essential region required for both cis and trans activity of the NS3 protease. In addition, alanine substitution at the residues Trp53, Glu55, and Arg56 in NS2B significantly reduced the cis- and trans-cleavage activities of the NS3 protease. Sequence alignment and modeled structures suggested that functional determinants at the JEV NS2B residues Ser46 to Ile60, particularly in Trp53, Glu55 and Arg56 could play an important configuration required for the activity of the flavivirus NS3 protease. Our results might be useful for development of inhibitors that block the interaction between NS2B and NS3.
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Affiliation(s)
- Cheng-Wen Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung 404, Taiwan, ROC.
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Peyrefitte CN, Pastorino BAM, Grandadam M, Rolland D, Tolou HJ, Bessaud M. Enzymatic characterization of a trypsin-like serine protease encoded by the genome of Cell fusing agent virus. Virus Genes 2006; 34:185-91. [PMID: 17143721 DOI: 10.1007/s11262-006-0052-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Accepted: 10/12/2006] [Indexed: 11/26/2022]
Abstract
Cell fusing agent virus (CFAV) is a positive strand RNA insect virus first isolated from a mosquito cell line. Based on viral morphology, phenotypic and phylogenetic studies, CFAV had been tentatively assigned to the genus Flavivirus (family Flaviviridae). The determination of the CFAV polyprotein complete sequence showed a putative serine protease domain analogue to the flaviviral NS2B/NS3 complex. This complex had been extensively studied, because it represented one of the main targets for antiflavivirus therapy development. We report herein the biochemical characterization of CFAV DeltaNS2B-NS3pro protease complex. CFAV polyprotein sequence was computationally analysed to identify the amino-acid regions involved in protease activity. We designed, expressed and purified a catalytically active protease whose enzymatic properties were determined using fluorogenic substrates. Our results showed that, despite the low level of conservation of its amino-acid sequence, CFAV protease exhibited physico-chemical properties of other flaviviruses (high pH value requirement for optimal activity, inhibition by salt and preference for substrates featuring a basic residue at P(1) position).
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Affiliation(s)
- Christophe N Peyrefitte
- Unité de virologie tropicale, Institut de médecine tropicale du Service de santé des armées, BP 46, 13 998, Marseille armées, France.
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