S. Kalluri, P. Gilruth, D. Rogers, and M. Szczur, Surveillance of arthropod vector-borne infectious diseases using remote sensing techniques: a review, PLoS pathogens, vol.3, issue.10, p.2042005, 2007.

S. Bhatt, P. W. Gething, O. J. Brady, J. P. Messina, A. W. Farlow et al., The global distribution and burden of dengue, Nature, vol.496, issue.7446, p.3651993, 2013.

L. Lambrechts, T. W. Scott, and D. J. Gubler, Consequences of the expanding global distribution of Aedes albopictus for dengue virus transmission, PLoS neglected tropical diseases, vol.4, issue.5, p.2876112, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-02011027

W. H. , Dengue haemorrhagic fever: diagnosis, treatment prevention and control. 2 nd Edition, 1997.

K. Clyde, J. L. Kyle, and E. Harris, Recent advances in deciphering viral and host determinants of dengue virus replication and pathogenesis, Journal of virology, vol.80, issue.23, p.1642597, 2006.

S. S. Whitehead, J. E. Blaney, A. P. Durbin, and B. R. Murphy, Prospects for a dengue virus vaccine, Nature reviews Microbiology, vol.5, issue.7, pp.518-546, 2007.

E. C. Holmes and S. S. Burch, The causes and consequences of genetic variation in dengue virus, Trends in microbiology, vol.8, issue.2, p.10664600, 2000.

B. T. Teoh, S. S. Sam, K. K. Tan, J. Johari, M. B. Danlami et al., Detection of dengue viruses using reverse transcription-loop-mediated isothermal amplification, BMC infectious diseases, vol.13, p.3846474, 2013.

L. C. Katzelnick, J. M. Fonville, G. D. Gromowski, B. Arriaga, J. Green et al., Dengue viruses cluster antigenically but not as discrete serotypes, Science, vol.349, issue.6254, p.4876809, 2015.

C. S. Vinodkumar, N. K. Kalapannavar, K. G. Basavarajappa, D. Sanjay, C. Gowli et al., Episode of coexisting infections with multiple dengue virus serotypes in central Karnataka, vol.6, p.23806706, 2013.

L. Franco, I. Pagan, S. Del-cor, N. Schunk, M. Neumayr et al., Clinical microbiology and infection: the official publication of the European Society of Clinical Microbiology and Infectious Diseases, vol.21, p.25843502, 2015.

L. C. Ng, Y. K. Chem, C. Koo, R. N. Mudin, F. M. Amin et al., dengue outbreaks in Singapore and Malaysia caused by different viral strains. The American journal of tropical medicine and hygiene, vol.92, p.4458818, 2013.

Y. Takamatsu, T. Nabeshima, T. T. Nguyen, D. T. Dang, L. H. Pham et al., Journal of clinical virology: the official publication of the Pan American Society for Clinical Virology, vol.66, p.25866331, 2013.

K. Z. Thant, M. M. Tun, P. Mdel, C. Inoue, S. Lwin et al., Molecular Epidemiology of Dengue Viruses Co-circulating in Upper Myanmar in 2006. Tropical medicine and health, vol.43, p.4361346, 2015.

T. R. Poloni, F. P. Dornas, D. Santos, . Nn, A. M. Soares et al., High prevalence of clinically unsuspected dengue disease among children in Ribeirao Preto city, Brazil. Journal of medical virology, vol.88, issue.10, p.27004990, 2016.

A. P. Durbin, . A-dengue, and . Vaccine, Cell, vol.166, issue.1, p.27368091, 2016.

A. Igarashi, Isolation of a Singh's Aedes albopictus cell clone sensitive to Dengue and Chikungunya viruses, The Journal of general virology, vol.40, issue.3, p.690610, 1978.

R. B. Tesh, A method for the isolation and identification of dengue viruses, using mosquito cell cultures. The American journal of tropical medicine and hygiene, vol.28, p.41456, 1979.

M. G. Guzman and G. Kouri, Advances in dengue diagnosis. Clinical and diagnostic laboratory immunology, vol.3, p.170421, 1996.

R. S. Lanciotti, C. H. Calisher, D. J. Gubler, G. J. Chang, and A. V. Vorndam, Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction, Journal of clinical microbiology, vol.30, issue.3, p.265106, 1992.

J. D. Callahan, S. J. Wu, A. Dion-schultz, B. E. Mangold, L. F. Peruski et al., Development and evaluation of serotype-and group-specific fluorogenic reverse transcriptase PCR (TaqMan) assays for dengue virus, Journal of clinical microbiology, vol.39, issue.11, p.88496, 2001.

D. Wagner, K. De-with, D. Huzly, F. Hufert, M. Weidmann et al., Nosocomial acquisition of dengue, Emerging infectious diseases, vol.10, issue.10, p.3323263, 2004.

J. J. Waggoner, J. Abeynayake, M. K. Sahoo, L. Gresh, Y. Tellez et al., Single-reaction, multiplex, real-time RT-PCR for the detection, quantitation, and serotyping of dengue viruses, PLoS neglected tropical diseases, vol.7, issue.4, p.3630127, 2013.

R. T. Sasmono, A. Aryati, P. Wardhani, B. Yohan, H. Trimarsanto et al., Performance of Simplexa dengue molecular assay compared to conventional and SYBR green RT-PCR for detection of dengue infection in Indonesia, PloS one, vol.9, issue.8, p.4125142, 2014.

E. Alm, G. Lindegren, K. I. Falk, and N. Lagerqvist, One-step real-time RT-PCR assays for serotyping dengue virus in clinical samples, BMC infectious diseases, vol.15, p.4630907, 2015.

M. Simmons, T. Myers, C. Guevara, D. Jungkind, M. Williams et al., Development and Validation of a Quantitative, One-Step, Multiplex, Real-Time Reverse Transcriptase PCR Assay for Detection of Dengue and Chikungunya Viruses, Journal of clinical microbiology, vol.54, issue.7, p.4922117, 2016.

T. Notomi, H. Okayama, H. Masubuchi, T. Yonekawa, K. Watanabe et al., Loop-mediated isothermal amplification of DNA, Nucleic acids research, vol.28, issue.12, p.102748, 2000.

Y. Mori, K. Nagamine, N. Tomita, and T. Notomi, Detection of loop-mediated isothermal amplification reaction by turbidity derived from magnesium pyrophosphate formation. Biochemical and biophysical research communications, vol.289, p.11708792, 2001.

N. Tomita, Y. Mori, H. Kanda, and T. Notomi, Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products, Nature protocols, vol.3, issue.5, p.18451795, 2008.

M. Parida, K. Horioke, H. Ishida, P. K. Dash, P. Saxena et al., Rapid detection and differentiation of dengue virus serotypes by a real-time reverse transcription-loop-mediated isothermal amplification assay, Journal of clinical microbiology, vol.43, issue.6, p.1151941, 2005.

M. Goto, E. Honda, A. Ogura, A. Nomoto, and K. Hanaki, Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue, BioTechniques, vol.46, issue.3, pp.167-72, 2009.

S. Li, M. Fang, B. Zhou, H. Ni, Q. Shen et al., Simultaneous detection and differentiation of dengue virus serotypes 1-4, Japanese encephalitis virus, and West Nile virus by a combined reverse-transcription loop-mediated isothermal amplification assay, Virology journal, vol.8, p.3149006, 2011.

X. Lu, X. Li, Z. Mo, J. F. Wang, B. Zhao et al., Rapid identification of Chikungunya and Dengue virus by a real-time reverse transcription-loop-mediated isothermal amplification method. The American journal of tropical medicine and hygiene, vol.87, p.3516274, 2012.

A. K. Sahni, N. Grover, A. Sharma, I. D. Khan, and J. Kishore, PMID: 24600118; PubMed Central PMCID: PMC3862550. Diagnostic microbiology and infectious disease, Medical journal, Armed Forces India, vol.69, issue.3, p.26032430, 2013.

M. Neeraja, V. Lakshmi, V. Lavanya, E. N. Priyanka, M. M. Parida et al., Rapid detection and differentiation of dengue virus serotypes by NS1 specific reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay in patients presenting to a tertiary care hospital in Hyderabad, India, Journal of virological methods, vol.211, p.25455901, 2015.

Y. L. Lau, M. Y. Lai, B. T. Teoh, J. Abd-jamil, J. Johari et al., Colorimetric Detection of Dengue by Single Tube Reverse-Transcription-Loop-Mediated Isothermal Amplification, PloS one, vol.10, issue.9, p.4575147, 2015.

S. F. Hu, M. Li, L. L. Zhong, S. M. Lu, Z. X. Liu et al., Development of reverse-transcription loop-mediated isothermal amplification assay for rapid detection and differentiation of dengue virus serotypes 1-4, BMC microbiology, vol.15, p.265, 2015.

P. Central and P. , , p.4647581

C. Torres, E. A. Vitalis, B. R. Baker, S. N. Gardner, M. W. Torres et al., LAVA: an open-source approach to designing LAMP (loop-mediated isothermal amplification) DNA signatures, BMC bioinformatics, vol.12, p.3213686, 2011.

R. Huy, P. Buchy, C. A. Ngan, C. Ong, S. Ali et al., National dengue surveillance in Cambodia 1980-2008: epidemiological and virological trends and the impact of vector control, Bulletin of the World Health Organization, vol.88, issue.9, p.2930366, 2010.
URL : https://hal.archives-ouvertes.fr/pasteur-00808323

M. Weidmann, A. A. Sall, J. C. Manuguerra, L. Koivogui, A. Adjami et al., Quantitative analysis of particles, genomes and infectious particles in supernatants of haemorrhagic fever virus cell cultures, Virology journal, vol.8, p.3056813, 2011.

T. Nordmann, Entwicklung und optimierung eines cytometric bead array zum nachweis von afrikanischen hämorrhagischen fieberviren, Fakultat der Georg-August, 2011.

S. J. Wu, S. Pal, S. Ekanayake, D. Greenwald, S. Lara et al., A dry-format field-deployable quantitative reverse transcriptase-polymerase chain reaction assay for diagnosis of dengue infections. The American journal of tropical medicine and hygiene, vol.79, p.18840736, 2008.

D. J. Russell, H. H. Otu, and K. Sayood, Grammar-based distance in progressive multiple sequence alignment, BMC bioinformatics, vol.9, p.2478692, 2008.

T. Jombart and A. I. , 3-1: new tools for the analysis of genome-wide SNP data, Bioinformatics, vol.1, issue.21, p.3198581, 2011.

E. C. Holmes, P. H. Tio, D. Perera, J. Muhi, and J. Cardosa, Importation and co-circulation of multiple serotypes of dengue virus in Sarawak, Malaysia. Virus research, vol.143, p.19463715, 2009.

S. C. Weaver and N. Vasilakis, Molecular evolution of dengue viruses: contributions of phylogenetics to understanding the history and epidemiology of the preeminent arboviral disease. Infection, genetics and evolution: journal of molecular epidemiology and evolutionary genetics in infectious diseases, vol.9, p.3609037, 2009.

J. P. Messina, O. J. Brady, T. W. Scott, C. Zou, D. M. Pigott et al., Global spread of dengue virus types: mapping the 70 year history, Trends in microbiology, vol.22, issue.3, p.3946041, 2013.

B. Angel, A. Angel, and V. Joshi, Multiple dengue virus types harbored by individual mosquitoes, Acta tropica, vol.150, p.26209106, 2015.
DOI : 10.1016/j.actatropica.2015.07.007

K. B. Chua, B. Mustafa, A. Wahab, A. H. Chem, Y. K. Khairul et al., A comparative evaluation of dengue diagnostic tests based on single-acute serum samples for laboratory confirmation of acute dengue. The Malaysian journal of pathology, vol.33, p.21874746, 2011.

A. M. Anand, S. Sistla, R. Dhodapkar, A. Hamide, N. Biswal et al., Evaluation of NS1 Antigen Detection for Early Diagnosis of Dengue in a Tertiary Hospital in Southern India, Journal of clinical and diagnostic research: JCDR, vol.10, issue.4, p.4866096, 2016.

S. Pothapregada, The Dilemma of Reactive NS1 Antigen test in Dengue Fever, Indian pediatrics, vol.52, issue.10, p.26499030, 2015.

A. El-wahed, A. Patel, P. Faye, O. Thaloengsok, S. Heidenreich et al., Recombinase Polymerase Amplification Assay for Rapid Diagnostics of Dengue Infection, PloS one, vol.10, issue.6, p.4468249, 2015.
URL : https://hal.archives-ouvertes.fr/pasteur-02082161

B. T. Teoh, S. S. Sam, K. K. Tan, M. B. Danlami, M. H. Shu et al., Early detection of dengue virus by use of reverse transcription-recombinase polymerase amplification, Journal of clinical microbiology, vol.53, issue.3, p.4390637, 2015.

S. N. Gardner, M. W. Lam, J. R. Smith, C. L. Torres, and T. R. Slezak, Draft versus finished sequence data for DNA and protein diagnostic signature development, Nucleic acids research, vol.33, issue.18, p.1266063, 2005.
DOI : 10.1093/nar/gki896

URL : https://academic.oup.com/nar/article-pdf/33/18/5838/7126449/gki896.pdf

D. A. Hysom, P. Naraghi-arani, M. Elsheikh, A. C. Carrillo, P. L. Williams et al., Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments, PloS one, vol.7, issue.4, p.3317645, 2012.

J. C. Manuguerra, Molecular pathogens detection in the field, directly at the point of care, Targeting Ebola 2015 Recent Advances and Studies, 292015-05-28.

M. Panning, R. N. Charrel, D. Mantke, O. Landt, O. Niedrig et al., Coordinated implementation of chikungunya virus reverse transcription-PCR. Emerging infectious diseases, vol.15, p.2681123, 2009.

S. Jacobsen, P. Patel, J. Schmidt-chanasit, I. Leparc-goffart, A. Teichmann et al., External quality assessment studies for laboratory performance of molecular and serological diagnosis of Chikungunya virus infection, vol.76, p.26828561, 2016.

V. J. Lee, A. Chow, X. Zheng, L. R. Carrasco, A. R. Cook et al., Simple clinical and laboratory predictors of Chikungunya versus dengue infections in adults, PLoS neglected tropical diseases, vol.6, issue.9, p.3459852, 2012.

O. Faye, O. Faye, B. Soropogui, P. Patel, E. Wahed et al., Development and deployment of a rapid recombinase polymerase amplification Ebola virus detection assay in Guinea in 2015. Euro surveillance: bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin, vol.20, p.26558690, 2015.