Bibliography

Scientific articles

Publications in international peer-review journals
• Articles/letters

  1. Lagal V, Pérez-Ramírez E, Mikaty G, Amato L, Robbiati C, Pajovic I, Sekulic N, Ignjatović Ćupina A, Kavran M, Haddad N i j, Feghali R, Karam S, Fares W, Triki H, Seguy M, Fernández-Pinero J, Aguilera-Sepúlveda P, Declich S, Marsboom C, Jiménez-Clavero MA, Manuguerra JC
    MediLabSecure: A decade of One Health actions to prevent emerging vector-borne diseases in the Mediterranean, Sahel and Black Sea regions
    One Health. 2026; 22. DOI.org/10.1016/j.onehlt.2026.101393.
  2. Chung KK, Aubry M, PhD1; Teiti I, Mapotoeke M, White R, Mathieu-Daudé F, Dian L, Paoaafaite T, Wattiaux A, Mallet HP, Vanhomwegen J, Manuguerra JC, Cao-Lormeau VM
    Social Mixing Patterns and Chikungunya Reemergence Risk in French Polynesia
    JAMA Netw Open. 2026; 9(3):e262270. doi:10.1001/jamanetworkopen.2026.2270
  3. Venter M, Manuguerra JC, Watson JM, Fischer TK, Blacksell SD, Summermatter, K, Damon IK, Drosten C, Alviola C, Assiri P, Farag E, Gangakhedkar R, Ghosn N, Guzman, MG, Happi C, Kalema-Zikusoka G, Labbé N, Myint K, Nguyen-Viet H, Ochu C, Saijo M, Sang R, Wacharapluesadee S
    COVID’s origins: what we do and don’t know
    Nature. 2026 ; 650(8103), 829-833. DOI :10.1038/d41586-026-00530-y
  4. Van Kerkhove MD., Simniceanu A, Gilbert J, Yang Y, Watson J, Wacharapluesadee S, Summermatter K, Sang R, Saijo M, Ochu CL, Nguyen-Viet H, Morel C, Myint K, Ly S, Labbe N, Kalema-Zikusoka G, Happi C, Guzman MG, Ghosn N, Gangakhedkar R, Fischer TK., Farag E, Drosten C, Dedkov V, Damon IK., Blacksell SD., Assiri A, Alviola P, Manuguerra JC, Venter, M
    A WHO global framework to guide investigations into origins of potentially epidemic and pandemic pathogens
    Nature Communications. 2025; 16(1). DOI: 10.1038/s41467-025-57218-6
  5. Ramasindrazana B, Rahalison ZA., Gauthier P, Mikaty G, Bodoarison ZI, Maminirina LA., Rahajandraibe S, Randriamanantsoa MG, Kayoko G, Manuguerra JC, Le Guern AS , Rasamindrakotroka AJ, Rajerison M
    Development and evaluation of a triplex real-time PCR assay for enhanced plague diagnostics in Madagascar
    PLOS Neglected Tropical Diseases. 2025; 19(7), e0013278. DOI: 10.1371/journal.pntd.0013278
  6. Tamietti C, Stephen T, Rouvinski A, Tenebray B, Leparc-Goffard I, de Laval, F, Fernandes-Pellerin S, Manuguerra JC, Rey R, Hasan M, Badaut C, Flamand M, Matheus S, Briolant S
    Prolonged Zika Virus NS1 Protein Circulation in Patient Sera Impacts Clinical Outcome Before the Rise of a Specific IgM Response
    Journal of Medical Virology. 2025;97(5), e70368. DOI: 10.1002/jmv.70368
  7. Postal J, Guivel-Benhassine F, Porrot F, Grassin Q, Crook JM, Vernuccio R, Caro V, Vanhomwegen J, Guardado-Calvo P, Simon-Lorière E, Dacheux L, Manuguerra JC, Schwartz O
    Antiviral activity of tecovirimat against monkeypox virus clades 1a, 1b, 2a, and 2b
    The Lancet Infectious Diseases. 2025; 25(3), e126 - e127. DOI: 10.1016/S1473-3099(25)00014-3
  8. Mendiboure V, Teiti I, Aubry M, Teissier A, Paoaafaite T, Vanhomwegen J, Manuguerra JC, Fontanet A, Cao-Lormeau VM, Madec Y
    SARS-CoV-2 seroprevalence and associated factors of infection before and after the Delta wave in French Polynesia: a cross-sectional study
    BMC Public Health. 2024; 24(1). DOI: 10.1186/s12889-024-17869-4
  9. Hourdel V, Balière C, Vanhomwegen J, Brisebarre A, Grassin Q, Manuguerra JC, Kallel H, Demar M, Dacheux L, Caro V
    Complete genome sequence of a vampire bat-related rabies virus obtained by metagenomics from a patient with encephalitis of unknown etiology, French Guiana
    Microbiology Resource Announcements. 2024; 13(11), e0051424. DOI: 10.1128/mra.00514-24
  10. Besombes C, Mbrenga F, Malaka C, Gonofio E, Schaeffer L, Konamna X, Selekon B, Namsenei-Dankpea J, Gildas Lemon C, Landier J, von Platen C, Gessain A, Manuguerra JC, Fontanet A, Nakouné E.
    Investigation of a mpox outbreak in Central African Republic, 2021-2022.
    One Health [Internet]. 2023;16. PMID: 36950196 DOI: 10.1016/j.onehlt.2023.100523 HAL: pasteur-04079299v1
  11. Balière C, Hourdel V, Kwasiborski A, Grassin Q, Feher M, Hoinard D, Vanhomwegen J, Taieb F, Consigny PH, Manuguerra JC, Leclercq I, Batéjat C, Caro V.
    Complete Genome Sequences of Monkeypox Virus from a French Clinical Sample and the Corresponding Isolated Strain, Obtained Using Nanopore Sequencing.
    Microbiol Resour Announc [Internet]. 2023;12(4). PMID: 36971577 DOI: 10.1128/mra.00009-23 HAL: hal-04127243v1
  12. Hubert M, Guivel-Benhassine F, Bruel T, Porrot F, Planas D, Vanhomwegen J, Wiedemann A, Burrel S, Marot S, Palich R, Monsel G, Diombera H, Gallien S, Lopez-Zaragoza JL, Vindrios W, Taieb F, Fernandes-Pellerin S, Delhaye M, Laude H, Arowas L, Ungeheuer MN, Hocqueloux L, Pourcher V, Prazuck T, Marcelin AG, Lelièvre JD, Batéjat C, Lévy Y, Manuguerra JC, Schwartz O.
    Complement-dependent mpox-virus-neutralizing antibodies in infected and vaccinated individuals.
    Cell Host Microbe. 2023;31(6):937-948.e4. PMID: 37196656 DOI: 10.1016/j.chom.2023.05.001 HAL: hal-04309033 , v1
  13. Vandenbogaert M, Kwasiborski A, Gonofio E, Descorps‐Declère S, Selekon B, Nkili Meyong AA, Ouilibona RS, Gessain A, Manuguerra JC, Caro V, Nakoune E, Berthet N.
    Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic.
    Scientific Reports [Internet]. 2022;12(1). PMID: 35750759 DOI: 10.1038/s41598-022-15073-1 HAL: pasteur-03720772
  14. Sett S, dos Santos Ribeiro C, Prat C, Haringhuizen G, Avšič T, Batten C, Beato MS, Bourhy H, Di Caro A, Charrel R, Coutard B, Drexler JF, Drosten C, Fooks AR, Klempa B, Koopmans M, Klimkait T, Günther S, Manuguerra JC, Mirazimi A, Mettenleiter TC, Komurian-Pradel F, Reiche S, Reusken C, Romette JL, van der Werf S, Williams D, Scholz AH.
    Access and benefit-sharing by the European Virus Archive in response to COVID-19.
    The Lancet Microbe. 2022;3(4):e316–e323. PMID: 34806057 DOI: 10.1016/s2666-5247(21)00211-1 HAL: pasteur-03915037, v1
  15. Mikaty G, Matheus S, Donoso Mantke O, McCulloch E, Zeichhardt H, Manuguerra JC.
    Evaluation of the diagnostic capacities for emerging arboviral diseases in the international network MediLabSecure from 2014 to 2018 - Importance of external quality assessments.
    Journal of Infection and Public Health. 2022;15(2):203–209. PMID: 35038668 DOI: 10.1016/j.jiph.2021.12.005 HAL: pasteur-03526119
  16. Chaix E, Boni M, Guillier L, Bertagnoli S, Mailles A, Collignon C, Kooh P, Ferraris O, Martin-Latil S, Manuguerra JC, Haddad N.
    Risk of Monkeypox virus (MPXV) transmission through the handling and consumption of food.
    Microbial Risk Analysis [Internet]. 2022;22. PMID: 36320929 DOI: 10.1016/j.mran.2022.100237 HAL: anses-03898801
  17. Besombes C, Mbrenga F, Schaeffer L, Malaka C, Gonofio E, Landier J, Vickos U, Konamna X, Selekon B, Dankpea JN, Von Platen C, Houndjahoue FG, Ouaïmon DS, Hassanin A, Berthet N, Manuguerra JC, Gessain A, Fontanet A, Nakouné-Yandoko E.
    National Monkeypox Surveillance, Central African Republic, 2001-2021.
    Emerging infectious diseases. 2022;28(12):2435–2445. PMID: 36328951 DOI: 10.3201/eid2812.220897 HAL: pasteur-03915036, v1
  18. Batéjat C, Grassin Q, Feher M, Hoinard D, Vanhomwegen J, Manuguerra JC, Leclercq I.
    Heat inactivation of monkeypox virus.
    Journal of Biosafety and Biosecurity. 2022;4(2):121–123. PMID: 36245694 DOI: 10.1016/j.jobb.2022.08.001 HAL: pasteur-03915042, v1
  19. Vanhomwegen J, Kwasiborski A, Diop A, Boizeau L, Hoinard D, Vray M, Bercion R, Ndiaye B, Dublineau A, Michiyuki S, Manuguerra JC, Sauvage V, Candotti D, Seck A, Laperche S, Shimakawa Y.
    Development and clinical validation of loop-mediated isothermal amplification (LAMP) assay to diagnose high HBV DNA levels in resource-limited settings.
    Clinical Microbiology and Infection. 2021;27(12):1858.e9-1858.e15. PMID: 33838304 DOI: 10.1016/j.cmi.2021.03.014 HAL: inserm-03237803
  20. Simo Tchetgna H, Descorps-Declère S, Selekon B, Kwasiborski A, Vandenbogaert M, Manuguerra JC, Gessain A, Caro V, Nakouné E, Berthet N.
    Molecular characterization of a new highly divergent Mobala related arenavirus isolated from Praomys sp. rodents.
    Scientific Reports [Internet]. 2021;11(1). PMID: 33986310 DOI: 10.1038/s41598-021-88046-5 HAL: pasteur-03264401
  21. Marchio A, Batejat C, Vanhomwegen J, Feher M, Grassin Q, Chazal M, Raulin O, Farges-Berth A, Reibel F, Estève V, Dejean A, Jouvenet N, Manuguerra JC, Pineau P.
    ddPCR increases detection of SARS-CoV-2 RNA in patients with low viral loads.
    Archives of Virology. 2021;166(9):2529–2540. PMID: 34251549 DOI: 10.1007/s00705-021-05149-0 HAL: hal-03365425
  22. Labadie T, Grassin Q, Batéjat C, Manuguerra JC, Leclercq I.
    Monitoring influenza virus survival outside the host using real-time cell analysis.
    Journal of Visualized Experiments [Internet]. 2021;2021(168). PMID: 33682860 DOI: 10.3791/61133 HAL: pasteur-03915043, v1
  23. Garneret P, Coz E, Martin E, Manuguerra JC, Brient-Litzler E, Enouf V, González Obando DF, Olivo-Marin JC, Monti F, van der Werf S, Vanhomwegen J, Tabeling P.
    Performing point-of-care molecular testing for SARS-CoV-2 with RNA extraction and isothermal amplification.
    PLoS ONE [Internet]. 2021;16(1 January). PMID: 33428641 DOI: 10.1371/journal.pone.0243712 HAL: pasteur-02916049
  24. Fares W, Chouikha A, Ghedira K, Gdoura M, Rezig D, Boubaker SH, Dhifallah IB, Touzi H, Hammami W, Meddeb Z, Sadraoui A, Hogga N, Abouda I, Kwasiborski A, Hourdel V, Mikaty G, Caro V, Manuguerra JC, Alaya NB, Triki H.
    Whole genome sequencing and phylogenetic analysis of six SARS-CoV-2 strains isolated during COVID-19 pandemic in Tunisia, North Africa.
    BMC Genomics [Internet]. 2021;22(1). PMID: 34261445 DOI: 10.1186/s12864-021-07870-10 HAL: pasteur-03574784
  25. Betton M, Livrozet M, Planas D, Fayol A, Monel B, Védie B, Bruel T, Tartour E, Robillard N, Manuguerra JC, Blanchard A, Ghosn J, Visseaux B, Péré H, Lebeaux D, Schwartz O, Veyer D, Hulot JS.
    Sera Neutralizing Activities Against Severe Acute Respiratory Syndrome Coronavirus 2 and Multiple Variants 6 Months After Hospitalization for Coronavirus Disease 2019.
    Clinical Infectious Diseases. 2021;73(6):E1337–E1344. PMID: 33851216 DOI: 10.1093/cid/ciab308 HAL: pasteur-03229817
  26. Berthet N, Descorps-Declère S, Besombes C, Curaudeau M, Nkili Meyong AA, Selekon B, Labouba I, Gonofio EC, Ouilibona RS, Simo Tchetgna HD, Feher M, Fontanet A, Kazanji M, Manuguerra JC, Hassanin A, Gessain A, Nakoune E.
    Genomic history of human monkey pox infections in the Central African Republic between 2001 and 2018.
    Scientific Reports [Internet]. 2021;11(1). PMID: 34158533 DOI: 10.1038/s41598-021-92315-8 HAL: hal-03270046
  27. Batéjat C, Grassin Q, Manuguerra JC, Leclercq I.
    Heat inactivation of the severe acute respiratory syndrome coronavirus 2.
    Journal of Biosafety and Biosecurity. 2021;3(1):1–3. PMID: 33521591 DOI: 10.1016/j.jobb.2020.12.001 HAL: pasteur-03915049, v1
  28. Bailly S, Rousset D, Fritzell C, Hozé N, Ben Achour S, Berthelot L, Enfissi A, Vanhomwegen J, Salje H, Fernandes-Pellerin S, Saout M, Lavergne A, Manuguerra JC, Carod JF, Djossou F, Cauchemez S, Flamand C.
    Spatial distribution and burden of emerging arboviruses in french guiana.
    Viruses [Internet]. 2021;13(7). PMID: 34372505 DOI: 10.3390/v13071299 HAL: pasteur-03325602
  29. Serris A, Stass R, Bignon EA, Muena NA, Manuguerra JC, Jangra RK, Li S, Chandran K, Tischler ND, Huiskonen JT, Rey FA, Guardado-Calvo P.
    The Hantavirus Surface Glycoprotein Lattice and Its Fusion Control Mechanism.
    Cell. 2020;183(2):442-456.e16. PMID: 32937107 DOI: 10.1016/j.cell.2020.08.023 HAL: pasteur-03207940
  30. Sailleau C, Dumarest M, Vanhomwegen J, Delaplace M, Caro V, Kwasiborski A, Hourdel V, Chevaillier P, Barbarino A, Comtet L, Pourquier P, Klonjkowski B, Manuguerra JC, Zientara S, Le Poder S.
    First detection and genome sequencing of SARS-CoV-2 in an infected cat in France.
    Transboundary and Emerging Diseases. 2020;67(6):2324–2328. PMID: 32500944 DOI: 10.1111/tbed.13659 HAL: hal-02874788
  31. Hozé N, Salje H, Rousset D, Fritzell C, Vanhomwegen J, Bailly S, Najm M, Enfissi A, Manuguerra JC, Flamand C, Cauchemez S.
    Reconstructing Mayaro virus circulation in French Guiana shows frequent spillovers.
    Nature Communications [Internet]. 2020;11(1). PMID: 32503971 DOI: 10.1038/s41467-020-16516-x HAL: pasteur-02875125
  32. Hourdel V, Kwasiborski A, Balière C, Matheus S, Batéjat CF, Manuguerra JC, Vanhomwegen J, Caro V.
    Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100TM System.
    Frontiers in Microbiology [Internet]. 2020;11. PMID: 33101244 DOI: 10.3389/fmicb.2020.571328 HAL: pasteur-02976015
  33. Henderson AD, Aubry M, Kama M, Vanhomwegen J, Teissier A, Mariteragi-Helle T, Paoaafaite T, Teissier Y, Manuguerra JC, Edmunds J, Whitworth J, Watson CH, Lau CL, Cao-Lormeau VM, Kucharski AJ.
    Zika seroprevalence declines and neutralizing antibodies wane in adults following outbreaks in French Polynesia and Fiji.
    eLife [Internet]. 2020;9. PMID: 31987069 DOI: 10.7554/eLife.48460 HAL: pasteur-02875145
  34. Dente MG, Riccardo F, Van Bortel W, Marrama L, Mollet T, Derrough T, Sudre B, Calistri P, Nacca G, Ranghiasci A, Escadafal C, Gaayeb L, Guillot A, Jiménez-Clavero MA, Manuguerra JC, Mikaty G, Picard M, Fernández-Pinero J, Pérez-Ramírez E, Robert V, Victoir K, Declich S.
    Enhancing Preparedness for Arbovirus Infections with a One Health Approach: The Development and Implementation of Multisectoral Risk Assessment Exercises.
    BioMed Research International [Internet]. 2020;2020. PMID: 32382554 DOI: 10.1155/2020/4832360 HAL: pasteur-02917615
  35. Aubry M, Kama M, Henderson AD, Teissier A, Vanhomwegen J, Mariteragi-Helle T, Paoaafaite T, Manuguerra JC, Christi K, Watson CH, Lau CL, Kucharski AJ, Cao-Lormeau VM.
    Low chikungunya virus seroprevalence two years after emergence in Fiji.
    International Journal of Infectious Diseases. 2020;90:223–225. PMID: 31689529 DOI: 10.1016/j.ijid.2019.10.040 HAL: pasteur-02875151
  36. Rabenandrasana MAN, Rafetrarivony LF, Rivoarilala LO, Enouf V, Robinson AL, Rakotozanany A, Vanhomwegen J, Caro V, Platen CV, Manuguerra JC, Collard JM.
    Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar.
    Microbiology Resource Announcements [Internet]. 2019;8(35). PMID: 31467100 DOI: 10.1128/MRA.00752-19 HAL: hal-02875195
  37. Mekanda FMO, Monamele CG, Nemg FBS, Yonga GM, Ouapi D, Beng VP, Batéjat C, Caro V, Manuguerra JC, Demanou M.
    Molecular characterization of measles virus strains circulating in Cameroon during the 2013-2016 epidemics.
    PLoS ONE [Internet]. 2019;14(9). PMID: 31553766 DOI: 10.1371/journal.pone.0222428 HAL: pasteur-02921762
  38. Kama M, Aubry M, Naivalu T, Vanhomwegen J, Mariteragi-Helle T, Teissier A, Paoaafaite T, Hué S, Hibberd ML, Manuguerra JC, Christi K, Watson CH, Nilles EJ, Aaskov J, Lau CL, Musso D, Kucharski AJ, Cao-Lormeau VM.
    Sustained Low-Level Transmission of Zika and Chikungunya Viruses after Emergence in the Fiji Islands.
    Emerging Infectious Diseases. 2019;25(8):1535–1538. PMID: 31310218 DOI: 10.3201/eid2508.180524 HAL: pasteur-02916041
  39. Flamand C, Bailly S, Fritzell C, Berthelot L, Vanhomwegen J, Salje H, Paireau J, Matheus S, Enfissi A, Fernandes-Pellerin S, Djossou F, Linares S, Carod JF, Kazanji M, Manuguerra JC, Cauchemez S, Rousset D.
    Impact of Zika Virus Emergence in French Guiana: A Large General Population Seroprevalence Survey.
    Journal of Infectious Diseases. 2019;220(12):1915–1925. PMID: 31418012 DOI: 10.1093/infdis/jiz396 HAL: hal-02615896
  40. Filippone C, Castel G, Murri S, Ermonval M, Korva M, Avšič-Županc T, Sironen T, Vapalahti O, McElhinney LM, Ulrich RG, Groschup MH, Caro V, Sauvage F, van der Werf S, Manuguerra JC, Gessain A, Marianneau P, Tordo N.
    Revisiting the genetic diversity of emerging hantaviruses circulating in Europe using a pan-viral resequencing microarray.
    Scientific Reports [Internet]. 2019;9(1). PMID: 31455867 DOI: 10.1038/s41598-019-47508-7 HAL: hal-02618353
  41. Besombes C, Gonofio E, Konamna X, Selekon B, Gessain A, Berthet N, Manuguerra JC, Fontanet A, Nakouné E.
    Intrafamily transmission of monkeypox virus, Central African Republic, 2018.
    Emerging Infectious Diseases. 2019;25(8):1602–1604. PMID: 31216261 DOI: 10.3201/eid2508.190112 HAL: pasteur-02917509
  42. Aubry M, Kama M, Vanhomwegen J, Teissier A, Mariteragi-Helle T, Hue S, Hibberd ML, Manuguerra JC, Christi K, Watson CH, Nilles EJ, Lau CL, Aaskov J, Musso D, Kucharski AJ, Cao-Lormeau VM.
    Ross river virus antibody prevalence, Fiji Islands, 2013–2015.
    Emerging Infectious Diseases. 2019;25(4):827–830. PMID: 30882332 DOI: 10.3201/eid2504.180694 HAL: hal-02263771
  43. Simon O, Acket B, Forfait C, Girault D, Gourinat AC, Millon P, Daures M, Vanhomwegen J, Billot S, Biron A, Hoinard D, Descloux E, Guyon D, Manuguerra JC, Laumond S, Molko N, Dupont-Rouzeyrol M.
    Zika virus outbreak in New Caledonia and Guillain-Barré syndrome: a case-control study.
    Journal of NeuroVirology. 2018;24(3):362–368. PMID: 29594985 DOI: 10.1007/s13365-018-0621-9 HAL: pasteur-01831514
  44. Phan NT, Ar Gouilh M, Paireau J, Do LP, Cheval J, Ngu ND, Hébert C, Nguyen TH, Lortholary O, Tondeur L, Manuguerra JC, Barouki R, Sander J, Janzen N, Nguyen HT, Brey PT, Fontanet A, Eloit M.
    Hypoglycemic toxins and enteroviruses as causes of outbreaks of acute encephalitis-like syndrome in children, Bac Giang province, northern Vietnam.
    Emerging Infectious Diseases. 2018;24(8):1435–1443. PMID: 30014832 DOI: 10.3201/eid2408.171004 HAL: hal-02146362
  45. Labadie T, Batéjat C, Manuguerra JC, Leclercq I.
    Influenza virus segment composition influences viral stability in the environment.
    Frontiers in Microbiology [Internet]. 2018;9(JUL). PMID: 30038604 DOI: 10.3389/fmicb.2018.01496 HAL: pasteur-02917110
  46. Kucharski AJ, Kama M, Watson CH, Aubry M, Funk S, Henderson AD, Brady OJ, Vanhomwegen J, Manuguerra JC, Lau CL, Edmunds WJ, Aaskov J, Nilles EJ, Cao-Lormeau VM, Hué S, Hibberd ML.
    Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji.
    eLife [Internet]. 2018;7. PMID: 30103854 DOI: 10.7554/eLife.34848 HAL: pasteur-02917604
  47. Gaidet N, Leclercq I, Batéjat C, Grassin Q, Daufresne T, Manuguerra JC.
    Avian influenza virus surveillance in high arctic breeding geese, Greenland.
    Avian Diseases. 2018;62(2):237–240. PMID: 29944408 DOI: 10.1637/11793-010418-ResNote.1 HAL: hal-02620939
  48. Aubry M, Teissier A, Huart M, Merceron S, Vanhomwegen J, Mapotoeke M, Mariteragi-Helle T, Roche C, Vial AL, Teururai S, Sicard S, Paulous S, Desprès P, Manuguerra JC, Mallet HP, Imrie A, Musso D, Deparis X, Cao-Lormeau VM.
    Seroprevalence of dengue and chikungunya virus antibodies, French Polynesia, 2014–2015.
    Emerging Infectious Diseases. 2018;24(3):558–561. PMID: 29460745 DOI: 10.3201/eid2403.171149 HAL: hal-01702664
  49. Ar Gouilh M, Puechmaille SJ, Diancourt L, Vandenbogaert M, Serra-Cobo J, Lopez Roïg M, Brown P, Moutou F, Caro V, Vabret A, Manuguerra JC.
    SARS-CoV related Betacoronavirus and diverse Alphacoronavirus members found in western old-world.
    Virology. 2018;517:88–97. PMID: 29482919 DOI: 10.1016/j.virol.2018.01.014 HAL: hal-01872415
  50. Vanhomwegen J, Beck C, Desprès P, Figuerola A, García R, Lecollinet S, López-Roig M, Manuguerra JC, Serra-Cobo J.
    Circulation of Zoonotic Arboviruses in Equine Populations of Mallorca Island (Spain).
    Vector-Borne and Zoonotic Diseases. 2017;17(5):340–346. PMID: 28346868 DOI: 10.1089/vbz.2016.2042 HAL: hal-01702948
  51. Simo Tchetgna HD, Nakoune E, Selekon B, Gessain A, Manuguerra JC, Kazanji M, Berthet N.
    Molecular characterization of the kamese virus, an unassigned rhabdovirus, isolated from culex pruina in the Central African Republic.
    Vector-Borne and Zoonotic Diseases. 2017;17(6):447–451. PMID: 28350284 DOI: 10.1089/vbz.2016.2068 HAL: pasteur-03516019
  52. Nakoune E, Lampaert E, Ndjapou SG, Janssens C, Zuniga I, Van Herp M, Fongbia JP, Koyazegbe TD, Selekon B, Komoyo GF, Garba-Ouangole SM, Manengu C, Manuguerra JC, Kazanji M, Gessain A, Berthet N.
    A Nosocomial Outbreak of Human Monkeypox in the Central African Republic.
    Open Forum Infectious Diseases [Internet]. 2017;4(4). PMID: 29732376 DOI: 10.1093/ofid/ofx168 HAL: pasteur-03516016
  53. Magro L, Jacquelin B, Escadafal C, Garneret P, Kwasiborski A, Manuguerra JC, Monti F, Sakuntabhai A, Vanhomwegen J, Lafaye P, Tabeling P.
    Paper-based RNA detection and multiplexed analysis for Ebola virus diagnostics.
    Scientific Reports [Internet]. 2017;7(1). PMID: 28465576 DOI: 10.1038/s41598-017-00758-9 HAL: pasteur-01570241
  54. Magro L, Escadafal C, Garneret P, Jacquelin B, Kwasiborski A, Manuguerra JC, Monti F, Sakuntabhai A, Vanhomwegen J, Lafaye P, Tabeling P.
    Paper microfluidics for nucleic acid amplification testing (NAAT) of infectious diseases.
    Lab on a Chip. 2017;17(14):2347–2371. PMID: 28632278 DOI: 10.1039/c7lc00013h HAL: pasteur-01671743
  55. Fléche-Matéos AL, Kügler JH, Hansen SH, Syldatk C, Hausmann R, Lomprez F, Vandenbogaert M, Manuguerra JC, Grimont PAD.
    Rouxiella badensis sp. nov. and Rouxiella silvae sp. nov. isolated from peat bog soil and emendation description of the genus Rouxiella.
    International Journal of Systematic and Evolutionary Microbiology. 2017;67(5):1255–1259. PMID: 28100296 DOI: 10.1099/ijsem.0.001794 HAL: pasteur-03690819
  56. Aubry M, Teissier A, Huart M, Merceron S, Vanhomwegen J, Roche C, Vial AL, Teururai S, Sicard S, Paulous S, Desprès P, Manuguerra JC, Mallet HP, Musso D, Deparis X, Cao-Lormeau VM.
    Zika virus seroprevalence, French Polynesia, 2014–2015.
    Emerging Infectious Diseases. 2017;23(4):669–672. PMID: 28084987 DOI: 10.3201/eid2304.161549 HAL: hal-01521256
  57. Aubry M, Teissier A, Huart M, Merceron S, Vanhomwegen J, Roche C, Vial AL, Teururai S, Sicard S, Paulous S, Desprès P, Manuguerra JC, Mallet HP, Musso D, Deparis X, Cao-Lormeau VM.
    Ross river virus seroprevalence, French Polynesia, 2014–2015.
    Emerging Infectious Diseases. 2017;23(10):1751–1753. PMID: 28930020 DOI: 10.3201/eid2310.170583 HAL: hal-01702942
  58. Escadafal C, Gaayeb L, Riccardo F, Pérez-Ramírez E, Picard M, Dente MG, Fernández-Pinero J, Manuguerra JC, Jiménez-Clavero MA, Declich S, Victoir K, Robert V.
    Risk of Zika virus transmission in the Euro-Mediterranean area and the added value of building preparedness to arboviral threats from a One Health perspective.
    BMC Public Health [Internet]. 2016;16(1). PMID: 27914465 DOI: 10.1186/s12889-016-3831-1 HAL: pasteur-03915052, v1
  59. Duong V, Mey C, Eloit M, Zhu H, Danet L, Huang Z, Zou G, Tarantola A, Cheval J, Perot P, Laurent D, Richner B, Ky S, Heng S, Touch S, Sovann L, Van Doorn R, Tran TT, Farrar JJ, Wentworth DE, Das SR, Stockwell TB, Manuguerra JC, Delpeyroux F, Guan Y, Altmeyer R, Buchy P.
    Molecular epidemiology of human enterovirus 71 at the origin of an epidemic of fatal hand, foot and mouth disease cases in Cambodia.
    Emerging Microbes and Infections [Internet]. 2016;5(9). PMID: 27651091 DOI: 10.1038/emi.2016.101 HAL: pasteur-01739359
  60. Cao-Lormeau VM, Blake A, Mons S, Lastère S, Roche C, Vanhomwegen J, Dub T, Baudouin L, Teissier A, Larre P, Vial AL, Decam C, Choumet V, Halstead SK, Willison HJ, Musset L, Manuguerra JC, Despres P, Fournier E, Mallet HP, Musso D, Fontanet A, Neil J, Ghawché F.
    Guillain-Barré Syndrome outbreak associated with Zika virus infection in French Polynesia: A case-control study.
    The Lancet. 2016;387(10027):1531–1539. PMID: 26948433 DOI: 10.1016/S0140-6736(16)00562-6 HAL: pasteur-01453407
  61. Brault JB, Khou C, Basset J, Coquand L, Fraisier V, Frenkiel MP, Goud B, Manuguerra JC, Pardigon N, Baffet AD.
    Comparative Analysis Between Flaviviruses Reveals Specific Neural Stem Cell Tropism for Zika Virus in the Mouse Developing Neocortex.
    EBioMedicine. 2016;10:71–76. PMID: 27453325 DOI: 10.1016/j.ebiom.2016.07.018 HAL: pasteur-01441052
  62. Berthet N, Nakouné E, Gessain A, Manuguerra JC, Kazanji M.
    Complete Genome Characterization of the Arumowot Virus (Unclassified Phlebovirus) Isolated from Turdus libonyanus Birds in the Central African Republic.
    Vector-Borne and Zoonotic Diseases. 2016;16(2):139–143. PMID: 26807610 DOI: 10.1089/vbz.2015.1830 HAL: pasteur-03516024
  63. Berthet N, Descorps-Declère S, Nkili-Meyong AA, Nakouné E, Gessain A, Manuguerra JC, Kazanji M.
    Improved assembly procedure of viral RNA genomes amplified with Phi29 polymerase from new generation sequencing data.
    Biological Research [Internet]. 2016;49(1). PMID: 27605096 DOI: 10.1186/s40659-016-0099-y HAL: pasteur-03516023
  64. Simon-Loriere E, Faye O, Faye O, Koivogui L, Magassouba N, Keita S, Thiberge JM, Diancourt L, Bouchier C, Vandenbogaert M, Caro V, Fall G, Buchmann JP, Matranga CB, Sabeti PC, Manuguerra JC, Holmes EC, Sall AA.
    Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic.
    Nature. 2015;524(7563):102–104. PMID: 26106863 DOI: 10.1038/nature14612 HAL: pasteur-03915059, v1
  65. Hans A, Gaudaire D, Manuguerra JC, Leon A, Gessain A, Laugier C, Berthet N, Zientara S.
    Combination of an unbiased amplification method and a resequencing microarray for detecting and genotyping equine arteritis virus.
    Journal of Clinical Microbiology. 2015;53(1):287–291. PMID: 25339390 DOI: 10.1128/JCM.01935-14 HAL: hal-02946322
  66. Flèche-Matéos AL, Levast M, Lomprez F, Arnoux Y, Andonian C, Perraud M, Vincent V, Gouilh MA, Thiberge JM, Vandenbogaert M, Diancourt L, Caro V, Burguière AM, Manuguerra JC.
    Rouxiella chamberiensis gen. nov., sp. Nov., a member of the family Enterobacteriaceae isolated from parenteral nutrition bags.
    International Journal of Systematic and Evolutionary Microbiology. 2015;65(6):1812–1818. PMID: 25747423 DOI: 10.1099/ijs.0.000179 HAL: pasteur-01134699
  67. Desdouits M, Kamgang B, Berthet N, Tricou V, Ngoagouni C, Gessain A, Manuguerra JC, Nakouné E, Kazanji M.
    Genetic characterization of Chikungunya virus in the Central African Republic.
    Infection, Genetics and Evolution. 2015;33:25–31. PMID: 25911440 DOI: 10.1016/j.meegid.2015.04.006 HAL: pasteur-01443281
  68. Shigematsu S, Dublineau A, Sawoo O, Batéjat C, Matsuyama T, Leclercq I, Manuguerra JC.
    Influenza A virus survival in water is influenced by the origin species of the host cell.
    Influenza and other Respiratory Viruses. 2014;8(1):123–130. PMID: 24112132 DOI: 10.1111/irv.12179 HAL: pasteur-03915063, v1
  69. Sawoo O, Dublineau A, Batéjat C, Zhou P, Manuguerra JC, Leclercq I.
    Cleavage of hemagglutinin-bearing lentiviral pseudotypes and their use in the study of influenza virus persistence.
    PLoS ONE [Internet]. 2014;9(8). PMID: 25166303 DOI: 10.1371/journal.pone.0106192 HAL: pasteur-03915066, v1
  70. Pereyaslov D, Rosin P, Palm D, Zeller H, Gross D, Brown CS, Struelens MJ, Robo A, Hatibi IH, Alis JC, Sargsyan S, Gurbanov S, Gribkova N, Van Ranst M, Ieven G, Patteet S, Tomic S, Korsun N, Drazenovic V, Pieridou-Bagkatzouni D, Jirincova H, Havlickova M, Fomsgaard A, Rae K, Lappalainen M, Ikonen N, Lina B, Van Der Werf S, Manuguerra JC, Machablishvili A, Eickmann M, Wolff T, Dobler G, Schmidt-Chanasit J, Drosten C, Papa A, Mentis AF, Kis Z, Löve A, Coughlan S, Mandelboim M, Capobianchi MR, Landini MP, Baldanti F, Palu G, Ghisetti V, Donatelli I, Nusupbayeva G, Tokhtabakiyeva Z, Kasymbekova K, Storozenko J, Erne S, Griskevicius A, Opp M, Barbara C, Vratnica Z, Reusken C, Dudman SG, Hungnes O, Pancer K, Guiomar R, Eder V, Lupulescu E, Yatsyshina S, Pisareva M, Buzitskaya Z, Sergeev A, Nedeljković J, Staroňová E, Županc TA, Petrovec M, Korva M, Prosenc K, Casas I, Gaines H, Cherpillod P, Zakirova N, Bosevska G, Altas B, Ciblak M, Ciblak M, Mironenko A, Dykhanovska T, Demchyshyna I, Bermingham A, Rakhimov R.
    Laboratory capability and surveillance testing for middle east respiratory syndrome coronavirus infection in the WHO European region, June 2013.
    Eurosurveillance [Internet]. 2014;19(40). PMID: 25323078 DOI: 10.2807/1560-7917.es2014.19.40.20923 HAL: pasteur-03915067, v1
  71. Maganga GD, Kapetshi J, Berthet N, Ilunga BK, Kabange F, Kingebeni PM, Mondonge V, Muyembe JJT, Bertherat E, Briand S, Cabore J, Epelboin A, Formenty P, Kobinger G, González-Angulo L, Labouba I, Manuguerra JC, Okwo-Bele JM, Dye C, Leroy EM.
    Ebola virus disease in the Democratic Republic of Congo.
    New England Journal of Medicine. 2014;371(22):2083–2091. PMID: 25317743 DOI: 10.1056/NEJMoa1411099 HAL: pasteur-03516027
  72. Leclercq I, Batéjat C, Burguière AM, Manuguerra JC.
    Heat inactivation of the Middle East respiratory syndrome coronavirus.
    Influenza and other Respiratory Viruses. 2014;8(5):585–586. PMID: 25074677 DOI: 10.1111/irv.12261 HAL: pasteur-03915081, v1
  73. Berthet N, Nakouné E, Kamgang B, Selekon B, Descorps-Declère S, Gessain A, Manuguerra JC, Kazanji M.
    Molecular characterization of three zika flaviviruses obtained from sylvatic mosquitoes in the Central African Republic.
    Vector-Borne and Zoonotic Diseases. 2014;14(12):862–865. PMID: 25514122 DOI: 10.1089/vbz.2014.1607 HAL: pasteur-03516033
  74. Vanhomwegen J, Berthet N, Mazuet C, Guigon G, Vallaeys T, Stamboliyska R, Dubois P, Kennedy GC, Cole ST, Caro V, Manuguerra JC, Popoff MR.
    Application of High-Density DNA Resequencing Microarray for Detection and Characterization of Botulinum Neurotoxin-Producing Clostridia.
    PLoS ONE [Internet]. 2013;8(6). PMID: 23818983 DOI: 10.1371/journal.pone.0067510 HAL: pasteur-01765377
  75. Page AL, de Rekeneire N, Sayadi S, Aberrane S, Janssens AC, Rieux C, Djibo A, Manuguerra JC, Ducou-le-Pointe H, Grais RF, Schaefer M, Guerin PJ, Baron E.
    Infections in Children Admitted with Complicated Severe Acute Malnutrition in Niger.
    PLoS ONE [Internet]. 2013;8(7). PMID: 23874731 DOI: 10.1371/journal.pone.0068699 HAL: pasteur-03915086, v1
  76. Mailles A, Blanckaert K, Chaud P, van der Werf S, Lina B, Caro V, Campese C, Guéry B, Prouvost H, Lemaire X, Paty MC, Haeghebaert S, Antoine D, Ettahar N, Noel H, Behillil S, Hendricx S, Manuguerra JC, Enouf V, La Ruche G, Semaille C, Coignard B, Lévy-Bruhl D, Weber F, Saura C, Che D.
    First cases of middle east respiratory syndrome coronavirus (MERS-COV) infections in France, investigations and implications for the prevention of human-to-human transmission, France, May 2013.
    Eurosurveillance [Internet]. 2013;18(24). PMID: 23787161 DOI: 10.2807/ese.18.24.20502-en HAL: pasteur-03915090, v1
  77. Guery B, Poissy J, El Mansouf L, Séjourné C, Ettahar N, Lemaire X, Vuotto F, Goffard A, Behillil S, Enouf V, Caro V, Mailles A, Che D, Manuguerra JC, Mathieu D, Fontanet A, Van Der Werf S.
    Clinical features and viral diagnosis of two cases of infection with Middle East Respiratory Syndrome coronavirus: A report of nosocomial transmission.
    The Lancet. 2013;381(9885):2265–2272. PMID: 23727167 DOI: 10.1016/S0140-6736(13)60982-4 HAL: hal-02266768
  78. Dereure O, Cheval J, Du Thanh A, Pariente K, Sauvage V, Manuguerra JC, Caro V, Foulongne V, Eloit M.
    No evidence for viral sequences in mycosis fungoides and Sézary syndrome skin lesions: A high-throughput sequencing approach.
    Journal of Investigative Dermatology. 2013;133(3):853–855. PMID: 23096719 DOI: 10.1038/jid.2012.371 HAL: hal-02645452
  79. Le Flèche-Matéos A, Berthet N, Lomprez F, Arnoux Y, Le Guern AS, Leclercq I, Burguière AM, Manuguerra JC.
    Recurrent Breast Abscesses due to Corynebacterium kroppenstedtii, a Human Pathogen Uncommon in Caucasian Women.
    Case Rep Infect Dis. 2012;2012:120968. Epub 2012 Sep 13. PubMed PMID: 23008788; PubMed Central PMCID: PMC3449112.
  80. Abdallat MM, Abroug F, Al Dhahry SHS, Alhajri MM, Al-Hakeem R, Al Hosani FI, Al Qasrawi SMA, Al-Romaihi HE, Assiri A, Baillie JK, Ben Embarek PK, Ben Salah A, Blümel B, Briese T, Buchholz U, Cognat SBF, Defang GN, De La Rocque S, Donatelli I, Drosten C, Drury PA, Eremin SR, Ferguson NM, Fontanet A, Formenty PBH, Fouchier RAM, Gao CQ, Garcia E, Gerber SI, Guery B, Haagmans BL, Haddadin AJ, Hardiman MC, Hensley LE, Hugonnet SAL, Hui DSC, Isla N, Karesh WB, Koopmans M, Kuehne A, Lipkin WI, Mafi AR, Malik M, Manuguerra JC, Memish Z, Mounts AW, Mumford E, Opoka L, Osterhaus A, John Oxenford C, Pang J, Pebody R, Peiris JSM, Jay Plotkin B, Poumerol G, Reusken C, Rezza G, Roth CE, Shindo N, Shumate AM, Siwula M, Slim A, Smallwood C, van der Werf S, Van Kerkhove MD, Zambon M.
    State of knowledge and data gaps of middle east respiratory syndrome coronavirus (MERS-CoV) in humans.
    PLoS Currents [Internet]. 2013;5(Outbreaks). PMID: 24270606 DOI: 10.1371/currents.outbreaks.0bf719e352e7478f8ad85fa30127ddb8 HAL: pasteur-02024923
  81. Sauvage V, Ar Gouilh M, Cheval J, Muth E, Pariente K, Burguiere A, Caro V, Manuguerra JC, Eloit M.
    A member of a new Picornaviridae genus is shed in pig feces.
    Journal of Virology. 2012;86(18):10036–10046. PMID: 22787214 DOI: 10.1128/JVI.00046-12 HAL: hal-01191193
  82. Paireau J, Tuan NH, Lefrançois R, Buckwalter MR, Nghia ND, Hien NT, Lortholary O, Poirée S, Manuguerra JC, Gessain A, Albert ML, Brey PT, Nga PT, Fontanet A.
    Litchi-associated acute encephalitis in children, northern Vietnam, 2004-2009.
    Emerging Infectious Diseases. 2012;18(11):1817–1824. PMID: 23092599 DOI: 10.3201/eid1811.111761 HAL: pasteur-00830992
  83. Foulongne V, Sauvage V, Hebert C, Dereure O, Cheval J, Gouilh MA, Pariente K, Segondy M, Burguière A, Manuguerra JC, Caro V, Eloit M.
    Human skin Microbiota: High diversity of DNA viruses identified on the human skin by high throughput sequencing.
    PLoS ONE [Internet]. 2012;7(6). PMID: 22723863 DOI: 10.1371/journal.pone.0038499 HAL: hal-02646448
  84. Weidmann M, Sall AA, Manuguerra JC, Koivogui L, Adjami A, Traoré FF, Hedlund KO, Lindegren G, Mirazimi A.
    Quantitative analysis of particles, genomes and infectious particles in supernatants of haemorrhagic fever virus cell cultures.
    Virology Journal [Internet]. 2011;8. PMID: 21349180 DOI: 10.1186/1743-422X-8-81 HAL: pasteur-03915094, v1
  85. Sauvage V, Foulongne V, Cheval J, Ar Gouilh M, Pariente K, Dereure O, Manuguerra JC, Richardson J, Lecuit M, Burguière A, Caro V, Eloit M.
    Human polyomavirus related to african green monkey lymphotropic polyomavirus.
    Emerging Infectious Diseases. 2011;17(8):1364–1370. PMID: 21801611 DOI: 10.3201/eid1708.110278 HAL: hal-02647943
  86. Sauvage V, Cheval J, Foulongne V, Gouilh MA, Pariente K, Manuguerra JC, Richardson J, Dereure O, Lecuit M, Burguiere A, Caro V, Eloit M.
    Identification of the first human Gyrovirus, a virus related to chicken anemia virus.
    Journal of Virology. 2011;85(15):7948–7950. PMID: 21632766 DOI: 10.1128/JVI.00639-11 HAL: hal-01004065
  87. Gouilh MA, Puechmaille SJ, Gonzalez JP, Teeling E, Kittayapong P, Manuguerra JC.
    SARS-Coronavirus ancestor's foot-prints in South-East Asian bat colonies and the refuge theory.
    Infection, Genetics and Evolution. 2011;11(7):1690–1702. PMID: 21763784 DOI: 10.1016/j.meegid.2011.06.021 HAL: pasteur-03915097, v1
  88. Dublineau A, Batéjat C, Pinon A, Burguière AM, Leclercq I, Manuguerra JC.
    Persistence of the 2009 pandemic influenza a (H1N1) virus in water and on non-porous surface.
    PLoS ONE [Internet]. 2011;6(11). PMID: 22132205 DOI: 10.1371/journal.pone.0028043 HAL: pasteur-03915100, v1
  89. Cheval J, Sauvage V, Frangeul L, Dacheux L, Guigon G, Dumey N, Pariente K, Rousseaux C, Dorange F, Berthet N, Brisse S, Moszer I, Bourhy H, Manuguerra CJ, Lecuit M, Burguiere A, Caro V, Eloit M.
    Evaluation of high-throughput sequencing for identifying known and unknown viruses in biological samples.
    Journal of Clinical Microbiology. 2011;49(9):3268–3275. PMID: 21715589 DOI: 10.1128/JCM.00850-11 HAL: hal-01191107
  90. Buckwalter MR, Nga PT, Gouilh MA, Fiette L, Bureau JF, Laird ME, Buchrieser J, Ozden S, Cheval J, Eloit M, Manuguerra JC, Gessain A, Brey PT, Fontanet A, Albert ML.
    Identification of a novel neuropathogenic Theiler's murine encephalomyelitis virus.
    Journal of Virology. 2011;85(14):6893–6905. PMID: 21543488 DOI: 10.1128/JVI.00274-11 HAL: pasteur-00830977
  91. Berthet N, Nakouné E, Whist E, Selekon B, Burguire AM, Manuguerra JC, Gessain A, Kazanji M.
    Maculopapular lesions in the Central African Republic.
    The Lancet. 2011;378(9799):1354. PMID: 21982097 DOI: 10.1016/S0140-6736(11)61142-2 HAL: pasteur-00734477
  92. Barakat A, Benjouad A, Manuguerra JC, Aouad RE, van der Werf S.
    Virological surveillance in Africa can contribute to early detection of new genetic and antigenic lineages of influenza viruses.
    Journal of Infection in Developing Countries. 2011;5(4):270–277. PMID: 21537068 DOI: 10.3855/jidc.1065 HAL: pasteur-03915107, v1
  93. Leclercq I, Berthet N, Batéjat C, Rousseaux C, Dickinson P, Old IG, Kong K, Kennedy GC, Cole ST, Manuguerra JC.
    Use of consensus sequences for the design of high density resequencing microarrays: The influenza virus paradigm.
    BMC Genomics [Internet]. 2010;11(1). PMID: 20961419 DOI: 10.1186/1471-2164-11-586 HAL: pasteur-00670619
  94. Formenty P, Muntasir MO, Damon I, Chowdhary V, Opoka ML, Monimart C, Mutasim EM, Manuguerra JC, Davidson WB, Karem KL, Cabeza J, Wang S, Malik MR, Durand T, Khalid A, Rioton T, Kuong-Ruay A, Babiker AA, Karsani MEM, Abdalla MS.
    Human monkeypox outbreak caused by novel virus belonging to Congo Basin clade, Sudan, 2005.
    Emerging Infectious Diseases. 2010;16(10):1539–1545. PMID: 20875278 DOI: 10.3201/eid1610.100713 HAL: pasteur-03915113, v1
  95. Demanou M, Antonio-Nkondjio C, Ngapana E, Rousset D, Paupy C, Manuguerra JC, Zeller H.
    Chikungunya outbreak in a rural area of Western Cameroon in 2006: A retrospective serological and entomological survey.
    BMC Research Notes [Internet]. 2010;3. PMID: 20444282 DOI: 10.1186/1756-0500-3-128 HAL: pasteur-00542414
  96. Dacheux L, Berthet N, Dissard G, Holmes EC, Delmas O, Larrous F, Guigon G, Dickinson P, Faye O, Sall AA, Old IG, Kong K, Kennedy GC, Manuguerra JC, Cole ST, Caro V, Gessain A, Bourhy H.
    Application of broad-spectrum resequencing microarray for genotyping rhabdoviruses.
    Journal of Virology. 2010;84(18):9557–9574. PMID: 20610710 DOI: 10.1128/JVI.00771-10 HAL: pasteur-00507428
  97. Berthet N, Leclercq I, Dublineau A, Shigematsu S, Burguière AM, Filippone C, Gessain A, Manuguerra JC.
    High-density resequencing DNA microarrays in public health emergencies.
    Nature Biotechnology. 2010;28(1):25–27. PMID: 20062034 DOI: 10.1038/nbt0110-25 HAL: pasteur-00460127
  98. Berthet N, Deletoile A, Passet V, Kennedy GC, Manuguerra JC, Cole ST, Brisse S.
    Reconstructed ancestral sequences improve pathogen identification using resequencing DNA microarrays.
    PLoS ONE [Internet]. 2010;5(12). PMID: 21187950 DOI: 10.1371/journal.pone.0015243 HAL: pasteur-03516001
  99. Desvaux S, Marx N, Ong S, Gaidet N, Hunt M, Manuguerra JC, Sorn S, Peiris M, Van Der Werf S, Reynes JM.
    Highly pathogenic avian influenza virus (H5N1) outbreak in captive wild birds and cats, Cambodia.
    Emerging Infectious Diseases. 2009;15(3):475–478. PMID: 19239769 DOI: 10.3201/eid1503.081410 HAL: pasteur-00379880
  100. Berthet N, Reinhardt AK, Leclercq I, Van Ooyen S, Batéjat C, Dickinson P, Stamboliyska R, Old IG, Kong KA, Dacheux L, Bourhy H, Kennedy GC, Korfhage C, Cole ST, Manuguerra JC.
    Phi29 polymerase based random amplification of viral RNA as an alternative to random RT-PCR.
    BMC Molecular Biology [Internet]. 2008;9. PMID: 18771595 DOI: 10.1186/1471-2199-9-77 HAL: pasteur-03516000
  101. Berthet N, Dickinson P, Filliol I, Reinhardt AK, Batejat C, Vallaeys T, Kong KA, Davies C, Lee W, Zhang S, Turpaz Y, Heym B, Coralie G, Dacheux L, Burguière AM, Bourhy H, Old IG, Manuguerra JC, Cole ST, Kennedy GC.
    Massively parallel pathogen identification using high-density microarrays.
    Microbial Biotechnology. 2008;1(1):79–86. PMID: 21261824 DOI: 10.1111/j.1751-7915.2007.00012.x HAL: pasteur-03515998
  102. Medeiros R, Rameix-Welti MA, Lorin V, Ribaud P, Manuguerra JC, Socie G, Scieux C, Naffakh N, Van Der Werf S.
    Failure of zanamivir therapy for pneumonia in a bone-marrow transplant recipient infected by a zanamivir-sensitive influenza A (H1N1) virus.
    Antiviral Therapy. 2007;12(4):571–576. PMID: 17668567 HAL: hal-00167799
  103. Song HD, Tu CC, Zhang GW, Wang SY, Zheng K, Lei LC, Chen QX, Gao YW, Zhou HQ, Xiang H, Zheng HJ, Chern SWW, Cheng F, Pan CM, Xuan H, Chen SJ, Luo HM, Zhou DH, Liu YF, He JF, Qin PZ, Li LH, Ren YQ, Liang WJ, Yu YD, Anderson L, Wang M, Xu RH, Wu XW, Zheng HY, Chen JD, Liang G, Gao Y, Liao M, Fang L, Jiang LY, Li H, Chen F, Di B, He LJ, Lin JY, Tong S, Kong X, Du L, Hao P, Tang H, Bernini A, Yu XJ, Spiga O, Guo ZM, Pan HY, He WZ, Manuguerra JC, Fontanet A, Danchin A, Niccolai N, Li YX, Wu CI, Zhao GP.
    Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human.
    Proceedings of the National Academy of Sciences of the United States of America. 2005;102(7):2430–2435. PMID: 15695582 DOI: 10.1073/pnas.0409608102 HAL: pasteur-03915126, v1
  104. Meijer A, Valette M, Manuguerra JC, Pérez-Breña P, Paget J, Brown C, Van Der Velden K.
    Implementation of the Community Network of Reference Laboratories for Human Influenza in Europe.
    Journal of Clinical Virology. 2005;34(2):87–96. PMID: 16157259 DOI: 10.1016/j.jcv.2005.02.005
  105. Aubin JT, Azebi S, Balish A, Banks J, Bhat N, Bright RA, Brown I, Buchy P, Burguiere AM, Chen HI, Cheng P, Cox NJ, Crosier A, Curns A, Cuvelier F, Deng G, Desheva J, Desvaux S, Diep NH, Donis RO, Douglas A, Dowell SF, Dung NT, Edwards L, Fukuda K, Garten R, Govorkova E, Gregory V, Hampson A, Hanh NTH, Harper S, Hay A, Hoffmann E, Hulse D, Imai M, Itamura S, Jadhao S, Jeannin P, Kang C, Katz J, Kim JH, Klimov A, Kwon YK, Lee CW, Lien PS, Li Y, Lim W, Lin YP, Lindstom S, Loftin L, Mabry J, Mai LQ, Maines T, Manuguerra JC, Mase M, Matsuoka Y, McCarron M, Medina MJ, Nguyen D, Ninomiya A, Obuchi M, Odagiri T, Peiris M, Perdue ML, Reynes JM, Robertson J, Rousseaux C, Saito T, Sangkitporn S, Shaw M, Simmerman JM, Slomka M, Smith C, Sorn S, Spackman E, Stöhr K, Suarez DL, Sung HW, Swayne DE, Tardy-Panit M, Tashiro M, Thawatsupha P, Tumpey T, Uyeki T, Van Tu P, Van Der Werf S, Vong S, Webby R, Webster R, Wood J, Xu X, Yi G, Zhang W.
    Evolution of H5N1 avian influenza viruses in Asia.
    Emerging Infectious Diseases. 2005;11(10):1515–1521. PMID: 16318689 DOI: 10.3201/eid1110.050644 HAL: pasteur-01836582
  106. Medeiros R, Naffakh N, Manuguerra JC, Van Der Werf S.
    Binding of the hemagglutinin from human or equine influenza H3 viruses to the receptor is altered by substitutions at residue 193.
    Archives of Virology. 2004;149(8):1663–1671. PMID: 15290389 DOI: 10.1007/s00705-003-0287-2
  107. Desenclos JC, Van Der Werf S, Bonmarin I, Levy-Bruhl D, Yazdanpanah Y, Hoen B, Emmanuelli J, Lesens O, Dupon M, Natali F, Michelet C, Reynes J, Guery B, Larsen C, Semaille C, Mouton Y, Christmann D, André M, Escriou N, Burguière A, Manuguerra JC, Coignard B, Lepoutre A, Meffre C, Bitar D, Capek I, Antona D, Che D, Herida M, Infuso A, Saura C, Brücker G, Hubert B, LeGoff D, Scheidegger S.
    Introduction of SARS in France, March-April, 2003.
    Emerging Infectious Diseases. 2004;10(2):195–200. PMID: 15030682 DOI: 10.3201/eid1002.030351
  108. Kuiken T, Fouchier RAM, Schutten M, Rimmelzwaan GF, Van Amerongen G, Van Riel D, Laman JD, De Jong T, Van Doornum G, Lim W, Ling AE, Chan PKS, Tam JS, Zambon MC, Gopal R, Drosten C, Van Der Werf S, Escriou N, Manuguerra JC, Stöhr K, Peiris JSM, Osterhaus ADME.
    Newly discovered coronavirus as the primary cause of severe acute respiratory syndrome.
    Lancet. 2003;362(9380):263–270. PMID: 12892955 DOI: 10.1016/S0140-6736(03)13967-0 HAL: pasteur-00167032
  109. Drosten C, Günther S, Preiser W, Van der Werf S, Brodt HR, Becker S, Rabenau H, Panning M, Kolesnikova L, Fouchier RAM, Berger A, Burguière AM, Cinatl J, Eickmann M, Escriou N, Grywna K, Kramme S, Manuguerra JC, Müller S, Rickerts V, Stürmer M, Vieth S, Klenk HD, Osterhaus ADME, Schmitz H, Doerr HW.
    Identification of a novel coronavirus in patients with severe acute respiratory syndrome.
    New England Journal of Medicine. 2003;348(20):1967–1976. PMID: 12690091 DOI: 10.1056/NEJMoa030747 HAL: pasteur-00167033
  110. Medeiros R, Escriou N, Naffakh N, Manuguerra JC, Van Der Werf S.
    Hemagglutinin residues of recent human A(H3N2) influenza viruses that contribute to the inability to agglutinate chicken erythrocytes.
    Virology. 2001;289(1):74–85. PMID: 11601919 DOI: 10.1006/viro.2001.1121
  111. Manuguerra JC, Mosnier A, Paget WJ.
    Monitoring of influenza in the EISS European network member countries from October 2000 to April 2001.
    Euro surveillance : bulletin européen sur les maladies transmissibles = European communicable disease bulletin. 2001;6(9):127–135. PMID: 11891380
  112. Manuguerra JC, Zientara S, Sailleau C, Rousseaux C, Gicquel B, Rijks I, Van Der Werf S.
    Evidence for evolutionary stasis and genetic drift by genetic analysis of two equine influenza H3 viruses isolated in France.
    Veterinary Microbiology. 2000;74(1–2):59–70. PMID: 10799778 DOI: 10.1016/s0378-1135(00)00166-8
  113. Merten OW, Manuguerra JC, Hannoun C, van der Werf S.
    Production of influenza virus in serum-free mammalian cell cultures.
    Developments in biological standardization. 1999;98:23–37; discussion 73-74. PMID: 10494957
  114. Merten OW, Kallel H, Manuguerra JC, Tardy-Panit M, Crainic R, Delpeyroux F, Van Der Werf S, Perrin P.
    The new medium MDSS2N, free of any animal protein supports cell growth and production of various viruses.
    Cytotechnology. 1999;30(1–3):191–201. PMID: 19003369 DOI: 10.1023/A:1008021317639 HAL: pasteur-02044584
  115. Girodon F, Galan P, Monget AL, Boutron-Ruault MC, Brunet-Lecomte P, Preziosi P, Arnaud J, Manuguerra JC, Hercberg S.
    Impact of trace elements and vitamin supplementation on immunity and infections in institutionalized elderly patients: A randomized controlled trial.
    Archives of Internal Medicine. 1999;159(7):748–754. PMID: 10218756 DOI: 10.1001/archinte.159.7.748
  116. Snacken R, Manuguerra JC, Taylor P.
    European Influenza Surveillance Scheme on the Internet.
    Methods of Information in Medicine. 1998;37(3):266–270. PMID: 9787627
  117. Sánchez-Bernal C, Muñoz-Barroso I, Manuguerra JC, Hannoun C, Cabezas JA.
    Study of the O-acetylesterase activity of five influenza C virus strains.
    Archives of Virology. 1998;143(9):1783–1790. PMID: 9787661 DOI: 10.1007/s007050050416
  118. Tourdot S, Oukka M, Manuguerra JC, Magafa V, Vergnon I, Riché N, Bruley-Rosset M, Cordopatis P, Kosmatopoulos K.
    Chimeric peptides: A new approach to enhancing the immunogenicity of peptides with low MHC class I affinity application in antiviral vaccination.
    Journal of Immunology. 1997;159(5):2391–2398. PMID: 9278330
  119. Oukka M, Manuguerra JC, Livaditis N, Tourdot S, Riche N, Vergnon I, Cordopatis P, Kosmatopoulos K.
    Protection Against Lethal Viral Infection by Vaccination with Nonimmunodominant Peptides.
    Journal of Immunology. 1996;157(7):3039–3045. PMID: 8816413
  120. Merten OW, Hannoun C, Manuguerra JC, Ventre F, Petres S.
    Production of influenza virus in cell cultures for vaccine preparation [Internet].
    Advances in Experimental Medicine and Biology. 1996; 397: 141–151. PMID: 8718593 DOI: 10.1007/978-1-4899-1382-1_19
  121. Manuguerra JC, Hannoun C, Saenz MDC, Villar E, Cabezas JA.
    Sero-epidemiological survey of influenza C virus infection in Spain.
    European Journal of Epidemiology. 1994;10(1):91–94. PMID: 7957798 DOI: 10.1007/BF01717459
  122. Kelm S, Schauer R, Manuguerra JC, Gross HJ, Crocker PR.
    Modifications of cell surface sialic acids modulate cell adhesion mediated by sialoadhesin and CD22.
    Glycoconjugate Journal. 1994;11(6):576–585. PMID: 7696861 DOI: 10.1007/BF00731309
  123. Manuguerra JC, Hannoun C, Simón F, Villar E, Cabezas JA.
    Natural infection of dogs by influenza C virus: a serological survey in Spain.
    The new microbiologica : 1993;16(4):367–371. PMID: 8264427
  124. Manuguerra JC, Hannoun C, Nicolson C, Robertson JS.
    Genic amplification of the entire coding region of the HEF RNA segment of influenza C virus.
    Journal of Virological Methods. 1993;41(1):59–76. PMID: 8381795 DOI: 10.1016/0166-0934(93)90163-l
  125. Muñoz-Barroso I, García-Sastre A, Villar E, Manuguerra JC, Hannoun C, Cabezas JA.
    Increased influenza A virus sialidase activity with N-acetyl-9-O-acetylneuraminic acid-containing substrates resulting from influenza C virus O-acetylesterase action.
    Virus Research. 1992;25(1–2):145–153. PMID: 1413991 DOI: 10.1016/0168-1702(92)90106-j
  126. Manuguerra JC, Hannoun C.
    Natural infection of dogs by influenza C virus.
    Research in Virology. 1992;143(C):199–204. PMID: 1325663 DOI: 10.1016/s0923-2516(06)80104-4
  127. Manuguerra JC, Hannoun C, Aymard M.
    Influenza C virus infection in France.
    Journal of Infection. 1992;24(1):91-96,IN15,97-99. PMID: 1312564 DOI: 10.1016/0163-4453(92)91150-a
  128. Duverlie G, Houbart L, Visse B, Chomel JJ, Manuguerra JC, Hannoun C, Orfila J.
    A nylon membrane enzyme immunoassay for rapid diagnosis of influenza A infection.
    Journal of Virological Methods. 1992;40(1):77–84. PMID: 1430074 DOI: 10.1016/0166-0934(92)90009-3
  129. Manuguerra JC, DuBois C, Hannoun C.
    Analytical detection of 9(4)-O-acetylated sialoglycoproteins and gangliosides using influenza C virus.
    Analytical Biochemistry. 1991;194(2):425–432. PMID: 1713751 DOI: 10.1016/0003-2697(91)90252-o
  130. Garcia-Sastre A, Villar E, Manuguerra JC, Hannoun C, Cabezas JA.
    Activity of influenza C virus O-acetylesterase with O-acetyl-containing compounds.
    Biochemical Journal. 1991;273(2):435–441. PMID: 1991039 DOI: 10.1042/bj2730435
  131. Cabezas JA, Villar E, Garcia-Sastre A, Manuguerra JC, Hannoun C.
    New data on influenza virus type C confirm its peculiarities as a new genus.
    Intervirology. 1991;32(6):325–326. PMID: 1938304 DOI: 10.1159/000150216
  132. Dubois C, Manuguerra JC, Hauttecoeur B, Maze J.
    Monoclonal antibody A2B5, which detects cell surface antigens, binds to ganglioside G(T3) (II3 (NeuAc)3LacCer) and to its 9-O-acetylated derivative.
    Journal of Biological Chemistry. 1990;265(5):2797–2803. PMID: 2303428 DOI: 10.1016/S0021-9258(19)39872-2

Publications in international peer-review journals
• Reviews

  1. Labadie T, Batéjat C, Leclercq I, Manuguerra JC.
    Historical Discoveries on Viruses in the Environment and Their Impact on Public Health.
    Intervirology. 2020;63(1–6):17–32. PMID: 33238280 DOI: 10.1159/000511575 HAL: pasteur-03916830, v1
  2. Dente MG, Riccardo F, Nacca G, Ranghiasci A, Escadafal C, Gaayeb L, Jiménez-Clavero MA, Manuguerra JC, Picard M, Fernández-Pinero J, Pérez-Ramírez E, Robert V, Victoir K, Declich S.
    Strengthening preparedness for arbovirus infections in mediterranean and black sea countries: A conceptual framework to assess integrated surveillance in the context of the one health strategy.
    International Journal of Environmental Research and Public Health [Internet]. 2018;15(3). PMID: 29534445 DOI: 10.3390/ijerph15030489 HAL: pasteur-02917553

Publications in national peer-review journals
• Articles/letters

  1. Burdet C, Guégan JF, Duval X, Le Tyrant M, Bergeron H, Manuguerra JC, Raude J, Leport C, Zylberman P.
    Need for integrative thinking to fight against emerging infectious diseases. Proceedings of the 5th seminar on emerging infectious diseases, March 22, 2016 – current trends and proposals.
    Revue d’Epidemiologie et de Sante Publique. 2018;66(1):81–90. PMID: 29223514 DOI: 10.1016/j.respe.2017.08.001
  2. Manuguerra JC, Mosnier A, Autran B, Fleury M, Veyssier P, Patey O, Weil-Olivier C, Beytout J, Bensoussan JL, Nicand E.
    The French Committee for the prevention and control of influenza and the 2009 influenza pandemic: Lessons learnt.
    Presse Medicale. 2012;41(9 PART1):783–792. PMID: 22560684. DOI: 10.1016/j.lpm.2012.02.043
  3. Henry S, Manuguerra JC, Escourolle D, Bessette D, Camus D, Houssin D.
    National plan for the prevention and control “Influenza pandemic.”
    Revue du Praticien. 2008;58(15):1687–1693. PMID: 19044053
  4. Cot S, Thill M, Gillet AM, Desenclos, Manuguerra, Mathiot, Garin MC, Georges MG, Tolou MC.
    Emerging infectious diseases: Which threats?
    Medecine Tropicale. 2006;66(5):517–519
  5. Fleury M, Rathat C, An K, Vu TH, Nguyen NT, Manuguerra JC.
    Severe acute respiratory syndrome (SARS) epidemic: Mission of emergency medical assistance department (French acronym, SAMU) personnel at the French hospital in Hanoi.
    Medecine Tropicale. 2003;63(3):287–290.
  6. Soares JL, Ratsitorahina M, Rakoto Andrianarivelo M, Robinson R, Rousset D, Rasoazanamiarana LN, Rabarijaona LP, Manuguerra JC, Migliani R.
    Epidemics of acute respiratory infections in Madagascar in 2002: from alert to confirmation.
    Archives de l’Institut Pasteur de Madagascar. 2003;69(1–2):12–19. PMID: 15678810

Publications in national peer-review journals
• Reviews

  1. Manuguerra JC.
    Links leading to the emergence of viral diseases in humans, from zoonotic transfer to effective interhuman transmission: The examples of the Severe Acute Respiratory Syndrome (SARS) and Ebola virus disease.
    Bulletin de l’Academie Veterinaire de France. 2019;172(1):123–129. PMID: not found DOI: 10.4267/2042/70854
  2. Berthet N, Leclercq I, Vallaeys T, Gessain A, Manuguerra JC.
    Microarrays in virology: Basic concepts and applications for virus detection.
    Virologie. 2013;17(2):61–80. PMID: 31910535 DOI: 10.1684/vir.2013.0480
  3. Garre M, Le Berre R, Belmin J, Carrat F, Chidiac C, Cohen JM, Garre M, Leophonte P, J, Manuguerra JC, Morer I, Salmon-Ceron D, Veyssier P, Weil-Olivier C.
    Management of extra-pandemic influenza 2005.
    Medecine et Maladies Infectieuses. 2005;35(SUPPL. 4):S237–S273. DOI: 10.1016/j.medmal.2005.09.002
  4. Naffakh N, Manuguerra JC, Van der Werf S.
    Influenza viruses: Zoonosis and interspecies transmission.
    Virologie. 2002;6(SPEC. ISS. NOV.):S73–S82
  5. Medeiros R, Naffakh N, Manuguerra JC, Van der Werf S.
    Influenza viruses: Structure features and mechanisms of genetic and antigenic variations.
    Virologie. 2002;6(SPEC. ISS. NOV.):S63–S72.
  6. Manuguerra JC, Van der Werf S.
    Neuramidase inhibitor: A new class of antivirals to fight against influenza.
    Virologie. 2002;6(SPEC. ISS. NOV.):S129–S138
  7. Manuguerra JC.
    Birds and the ecology of influenza viruses.
    Medecine et Maladies Infectieuses. 2001;31(SUPPL. 2):175–177
  8. Manuguerra JC.
    Ecology, biodiversity and evolution of influenza viruses.
    Virologie. 2001;5(3):195–205
  9. Manuguerra JC, Van Der Werf S.
    Les antiviraux contre la grippe.
    Virologie. 1999;3(6):439–452
  10. Manuguerra JC.
    New influenza viruses.
    Bulletin de l’Academie Nationale de Medecine. 1999;183(7):1377–1390
  11. Manuguerra JC, Hannoun C.
    Influenza : Inter-species transmissions and viral reassortment.
    Bulletin de l’Academie Nationale de Medecine. 1997;181(3):421–430. PMID: 9244574