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Identification of Viral Signatures Using High-Throughput Sequencing on Blood of Patients With Kawasaki Disease.

L'Huillier AG, Brito F, Wagner N, Cordey S, Zdobnov E, Posfay-Barbe KM, Kaiser L.

Front Pediatr. 2019 Dec 19;7:524. doi: 10.3389/fped.2019.00524. eCollection 2019.


Nearly Complete Genome Sequence of a Novel Phlebovirus-Like Virus Detected in a Human Plasma Sample by High-Throughput Sequencing.

Laubscher F, Cordey S, Hartley MA, Vieille G, Boillat-Blanco N, Samaka J, Mlaganile T, d'Acremont V, Kaiser L.

Microbiol Resour Announc. 2019 Aug 29;8(35). pii: e00764-19. doi: 10.1128/MRA.00764-19.


Viral Metagenomics in the Clinical Realm: Lessons Learned from a Swiss-Wide Ring Trial.

Junier T, Huber M, Schmutz S, Kufner V, Zagordi O, Neuenschwander S, Ramette A, Kubacki J, Bachofen C, Qi W, Laubscher F, Cordey S, Kaiser L, Beuret C, Barbié V, Fellay J, Lebrand A.

Genes (Basel). 2019 Aug 28;10(9). pii: E655. doi: 10.3390/genes10090655.


Enterovirus, parechovirus, adenovirus and herpes virus type 6 viraemia in fever without source.

L'Huillier AG, Mardegan C, Cordey S, Luterbacher F, Papis S, Hugon F, Kaiser L, Gervaix A, Posfay-Barbe K, Galetto-Lacour A.

Arch Dis Child. 2020 Feb;105(2):180-186. doi: 10.1136/archdischild-2019-317382. Epub 2019 Aug 28.


Viral Sequences Detection by High-Throughput Sequencing in Cerebrospinal Fluid of Individuals with and without Central Nervous System Disease.

Schibler M, Brito F, Zanella MC, Zdobnov EM, Laubscher F, L'Huillier AG, Ambrosioni J, Wagner N, Posfay-Barbe KM, Docquier M, Schiffer E, Savoldelli GL, Fournier R, Lenggenhager L, Cordey S, Kaiser L.

Genes (Basel). 2019 Aug 19;10(8). pii: E625. doi: 10.3390/genes10080625.


Sequencing and analysis of globally obtained human parainfluenza viruses 1 and 3 genomes.

Bose ME, Shrivastava S, He J, Nelson MI, Bera J, Fedorova N, Halpin R, Town CD, Lorenzi HA, Amedeo P, Gupta N, Noyola DE, Videla C, Kok T, Buys A, Venter M, Vabret A, Cordey S, Henrickson KJ.

PLoS One. 2019 Jul 18;14(7):e0220057. doi: 10.1371/journal.pone.0220057. eCollection 2019.


Detection of dicistroviruses RNA in blood of febrile Tanzanian children.

Cordey S, Laubscher F, Hartley MA, Junier T, Pérez-Rodriguez FJ, Keitel K, Vieille G, Samaka J, Mlaganile T, Kagoro F, Boillat-Blanco N, Mbarack Z, Docquier M, Brito F, Eibach D, May J, Sothmann P, Aldrich C, Lusingu J, Tapparel C, D'Acremont V, Kaiser L.

Emerg Microbes Infect. 2019;8(1):613-623. doi: 10.1080/22221751.2019.1603791.


High-throughput sequencing for the aetiologic identification of viral encephalitis, meningoencephalitis, and meningitis. A narrative review and clinical appraisal.

Zanella MC, Lenggenhager L, Schrenzel J, Cordey S, Kaiser L.

Clin Microbiol Infect. 2019 Apr;25(4):422-430. doi: 10.1016/j.cmi.2018.12.022. Epub 2019 Jan 11. Review.


Erratum for Williams et al., "Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches".

Williams SH, Cordey S, Bhuva N, Laubscher F, Hartley MA, Boillat-Blanco N, Mbarack Z, Samaka J, Mlaganile T, Jain K, d'Acremont V, Kaiser L, Lipkin WI.

mSphere. 2018 Sep 19;3(5). pii: e00477-18. doi: 10.1128/mSphere.00477-18. No abstract available.


Influenza A Virus Genetic Tools: From Clinical Sample to Molecular Clone.

Anchisi S, Gonçalves AR, Mazel-Sanchez B, Cordey S, Schmolke M.

Methods Mol Biol. 2018;1836:33-58. doi: 10.1007/978-1-4939-8678-1_3.


Investigation of the Plasma Virome from Cases of Unexplained Febrile Illness in Tanzania from 2013 to 2014: a Comparative Analysis between Unbiased and VirCapSeq-VERT High-Throughput Sequencing Approaches.

Williams SH, Cordey S, Bhuva N, Laubscher F, Hartley MA, Boillat-Blanco N, Mbarack Z, Samaka J, Mlaganile T, Jain K, d'Acremont V, Kaiser L, Lipkin WI.

mSphere. 2018 Aug 22;3(4). pii: e00311-18. doi: 10.1128/mSphere.00311-18. Erratum in: mSphere. 2018 Sep 19;3(5):.


Metagenomics analysis of the virome of 300 concentrates from a Swiss platelet bank.

Brito F, Cordey S, Delwart E, Deng X, Tirefort D, Lemoine-Chaduc C, Zdobnov E, Lecompte T, Kaiser L, Waldvogel-Abramowski S, Preynat-Seauve O.

Vox Sang. 2018 Jul 18. doi: 10.1111/vox.12695. [Epub ahead of print]


Novel human astroviruses in pediatric respiratory samples: A one-year survey in a Swiss tertiary care hospital.

Cordey S, Zanella MC, Wagner N, Turin L, Kaiser L.

J Med Virol. 2018 Nov;90(11):1775-1778. doi: 10.1002/jmv.25246. Epub 2018 Jul 16.


Human pegivirus persistence in human blood virome after allogeneic haematopoietic stem-cell transplantation.

Vu DL, Cordey S, Simonetta F, Brito F, Docquier M, Turin L, van Delden C, Boely E, Dantin C, Pradier A, Roosnek E, Chalandon Y, Zdobnov EM, Masouridi-Levrat S, Kaiser L.

Clin Microbiol Infect. 2019 Feb;25(2):225-232. doi: 10.1016/j.cmi.2018.05.004. Epub 2018 May 19.


Detection of novel astroviruses MLB1 and MLB2 in the sera of febrile Tanzanian children.

Cordey S, Hartley MA, Keitel K, Laubscher F, Brito F, Junier T, Kagoro F, Samaka J, Masimba J, Said Z, Temba H, Mlaganile T, Docquier M, Fellay J, Kaiser L, D'Acremont V.

Emerg Microbes Infect. 2018 Mar 14;7(1):27. doi: 10.1038/s41426-018-0025-1. No abstract available.


Usutu virus in cerebrospinal fluid: A 2-year survey in a Tertiary Care Hospital, Geneva, Switzerland.

Cordey S, Vieille G, Turin L, Kaiser L.

J Med Virol. 2018 Mar;90(3):609-611. doi: 10.1002/jmv.24967. Epub 2017 Nov 9.


Novel and classical human astroviruses in stool and cerebrospinal fluid: comprehensive screening in a tertiary care hospital, Switzerland.

Cordey S, Vu DL, Zanella MC, Turin L, Mamin A, Kaiser L.

Emerg Microbes Infect. 2017 Sep 20;6(9):e84. doi: 10.1038/emi.2017.71.


Severe viral respiratory infections in children with IFIH1 loss-of-function mutations.

Asgari S, Schlapbach LJ, Anchisi S, Hammer C, Bartha I, Junier T, Mottet-Osman G, Posfay-Barbe KM, Longchamp D, Stocker M, Cordey S, Kaiser L, Riedel T, Kenna T, Long D, Schibler A, Telenti A, Tapparel C, McLaren PJ, Garcin D, Fellay J.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):8342-8347. doi: 10.1073/pnas.1704259114. Epub 2017 Jul 17.


Metagenomics analysis of red blood cell and fresh-frozen plasma units.

Lau P, Cordey S, Brito F, Tirefort D, Petty TJ, Turin L, Guichebaron A, Docquier M, Zdobnov EM, Waldvogel-Abramowski S, Lecompte T, Kaiser L, Preynat-Seauve O.

Transfusion. 2017 Jul;57(7):1787-1800. doi: 10.1111/trf.14148. Epub 2017 May 11.


Comparative analysis of viral shedding in pediatric and adult subjects with central nervous system-associated enterovirus infections from 2013 to 2015 in Switzerland.

Cordey S, Schibler M, L'Huillier AG, Wagner N, Gonçalves AR, Ambrosioni J, Asner S, Turin L, Posfay-Barbe KM, Kaiser L.

J Clin Virol. 2017 Apr;89:22-29. doi: 10.1016/j.jcv.2017.01.008. Epub 2017 Feb 7.


Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology.

Cordey S, Brito F, Vu DL, Turin L, Kilowoko M, Kyungu E, Genton B, Zdobnov EM, D'Acremont V, Kaiser L.

Emerg Microbes Infect. 2016 Sep 7;5(9):e99. doi: 10.1038/emi.2016.98. No abstract available.


Hospital surveillance of influenza strains: a concordant image of viruses identified by the Swiss Sentinel system?

Gonçalves AR, Iten A, Suter-Boquete P, Schibler M, Kaiser L, Cordey S.

Influenza Other Respir Viruses. 2017 Jan;11(1):41-47. doi: 10.1111/irv.12417. Epub 2016 Aug 31.


Novel human astroviruses: Novel human diseases?

Vu DL, Cordey S, Brito F, Kaiser L.

J Clin Virol. 2016 Sep;82:56-63. doi: 10.1016/j.jcv.2016.07.004. Epub 2016 Jul 11. Review.


Astrovirus VA1 identified by next-generation sequencing in a nasopharyngeal specimen of a febrile Tanzanian child with acute respiratory disease of unknown etiology.

Cordey S, Brito F, Vu DL, Turin L, Kilowoko M, Kyungu E, Genton B, Zdobnov EM, D'Acremont V, Kaiser L.

Emerg Microbes Infect. 2016 Jul 6;5:e67. doi: 10.1038/emi.2016.67. No abstract available. Erratum in: Emerg Microbes Infect. 2016 Sep 07;5(9):e99.


Astrovirus MLB2, a New Gastroenteric Virus Associated with Meningitis and Disseminated Infection.

Cordey S, Vu DL, Schibler M, L'Huillier AG, Brito F, Docquier M, Posfay-Barbe KM, Petty TJ, Turin L, Zdobnov EM, Kaiser L.

Emerg Infect Dis. 2016 May;22(5):846-53. doi: 10.3201/eid2205.151807.


Ebola virus disease diagnosis by real-time RT-PCR: A comparative study of 11 different procedures.

Cherpillod P, Schibler M, Vieille G, Cordey S, Mamin A, Vetter P, Kaiser L.

J Clin Virol. 2016 Apr;77:9-14. doi: 10.1016/j.jcv.2016.01.017. Epub 2016 Feb 2.


Clinical features and viral kinetics in a rapidly cured patient with Ebola virus disease: a case report.

Schibler M, Vetter P, Cherpillod P, Petty TJ, Cordey S, Vieille G, Yerly S, Siegrist CA, Samii K, Dayer JA, Docquier M, Zdobnov EM, Simpson AJH, Rees PSC, Sarria FB, Gasche Y, Chappuis F, Iten A, Pittet D, Pugin J, Kaiser L.

Lancet Infect Dis. 2015 Sep;15(9):1034-1040. doi: 10.1016/S1473-3099(15)00229-7. Epub 2015 Jul 19.


Enterovirus and Parechovirus viraemia in young children presenting to the emergency room: Unrecognised and frequent.

Cordey S, L'Huillier AG, Turin L, Gervaix A, Posfay Barbe K, Kaiser L.

J Clin Virol. 2015 Jul;68:69-72. doi: 10.1016/j.jcv.2015.05.003. Epub 2015 May 11.


E119D Neuraminidase Mutation Conferring Pan-Resistance to Neuraminidase Inhibitors in an A(H1N1)pdm09 Isolate From a Stem-Cell Transplant Recipient.

L'Huillier AG, Abed Y, Petty TJ, Cordey S, Thomas Y, Bouhy X, Schibler M, Simon A, Chalandon Y, van Delden C, Zdobnov E, Boquete-Suter P, Boivin G, Kaiser L.

J Infect Dis. 2015 Dec 1;212(11):1726-34. doi: 10.1093/infdis/jiv288. Epub 2015 May 17.


Human three-dimensional engineered neural tissue reveals cellular and molecular events following cytomegalovirus infection.

Cosset É, Martinez Y, Preynat-Seauve O, Lobrinus JA, Tapparel C, Cordey S, Peterson H, Petty TJ, Colaianna M, Tieng V, Tirefort D, Dinnyes A, Dubois-Dauphin M, Kaiser L, Krause KH.

Biomaterials. 2015;53:296-308. doi: 10.1016/j.biomaterials.2015.02.094. Epub 2015 Mar 17.


Toscana virus meningitis case in Switzerland: an example of the ezVIR bioinformatics pipeline utility for the identification of emerging viruses.

Cordey S, Bel M, Petty TJ, Docquier M, Sacco L, Turin L, Cherpillod P, Emonet S, Louis-Simonet M, Zdobnov EM, Ambrosioni J, Kaiser L.

Clin Microbiol Infect. 2015 Apr;21(4):387.e1-4. doi: 10.1016/j.cmi.2014.11.010. Epub 2014 Nov 26.


Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study.

Petty TJ, Cordey S, Padioleau I, Docquier M, Turin L, Preynat-Seauve O, Zdobnov EM, Kaiser L.

J Clin Microbiol. 2014 Sep;52(9):3351-61. doi: 10.1128/JCM.01389-14. Epub 2014 Jul 9.


Comprehensive metagenomic analysis of glioblastoma reveals absence of known virus despite antiviral-like type I interferon gene response.

Cosset É, Petty TJ, Dutoit V, Cordey S, Padioleau I, Otten-Hernandez P, Farinelli L, Kaiser L, Bruyère-Cerdan P, Tirefort D, Amar El-Dusouqui S, Nayernia Z, Krause KH, Zdobnov EM, Dietrich PY, Rigal E, Preynat-Seauve O.

Int J Cancer. 2014 Sep 15;135(6):1381-9. doi: 10.1002/ijc.28670. Epub 2014 May 8.


Identification of site-specific adaptations conferring increased neural cell tropism during human enterovirus 71 infection.

Cordey S, Petty TJ, Schibler M, Martinez Y, Gerlach D, van Belle S, Turin L, Zdobnov E, Kaiser L, Tapparel C.

PLoS Pathog. 2012;8(7):e1002826. doi: 10.1371/journal.ppat.1002826. Epub 2012 Jul 26.


Pilot Evaluation of RT-PCR/Electrospray Ionization Mass Spectrometry (PLEX-ID/Flu assay) on Influenza-Positive Specimens.

Cordey S, Thomas Y, Suter P, Kaiser L.

Open Virol J. 2012;6:64-7. doi: 10.2174/1874357901206010064. Epub 2012 May 9.


Astrovirus infection in hospitalized infants with severe combined immunodeficiency after allogeneic hematopoietic stem cell transplantation.

Wunderli W, Meerbach A, Güngör T, Berger C, Greiner O, Caduff R, Trkola A, Bossart W, Gerlach D, Schibler M, Cordey S, McKee TA, Van Belle S, Kaiser L, Tapparel C.

PLoS One. 2011;6(11):e27483. doi: 10.1371/journal.pone.0027483. Epub 2011 Nov 11. Erratum in: PLoS One. 2012;7(1). doi:10.1371/annotation/8371c305-a69c-4225-83ae-b0b414eca31a. Guengoer, Tayfun [corrected to Güngör, Tayfun].


T lymphocytes promote the antiviral and inflammatory responses of airway epithelial cells.

Jornot L, Cordey S, Caruso A, Gerber C, Vukicevic M, Tapparel C, Kaiser L, Burger D, Roosnek E, Lacroix JS, Rochat T.

PLoS One. 2011;6(10):e26293. doi: 10.1371/journal.pone.0026293. Epub 2011 Oct 14.


Spread of measles virus D4-Hamburg, Europe, 2008-2011.

Mankertz A, Mihneva Z, Gold H, Baumgarte S, Baillot A, Helble R, Roggendorf H, Bosevska G, Nedeljkovic J, Makowka A, Hutse V, Holzmann H, Aberle SW, Cordey S, Necula G, Mentis A, Korukluoğlu G, Carr M, Brown KE, Hübschen JM, Muller CP, Mulders MN, Santibanez S.

Emerg Infect Dis. 2011 Aug;17(8):1396-401. doi: 10.3201/eid1708.101994.


Analytical validation of a lymphocytic choriomeningitis virus real-time RT-PCR assay.

Cordey S, Sahli R, Moraz ML, Estrade C, Morandi L, Cherpillod P, Charrel RN, Kunz S, Kaiser L.

J Virol Methods. 2011 Oct;177(1):118-22. doi: 10.1016/j.jviromet.2011.06.018. Epub 2011 Jul 6.


Rhinovirus genome variation during chronic upper and lower respiratory tract infections.

Tapparel C, Cordey S, Junier T, Farinelli L, Van Belle S, Soccal PM, Aubert JD, Zdobnov E, Kaiser L.

PLoS One. 2011;6(6):e21163. doi: 10.1371/journal.pone.0021163. Epub 2011 Jun 21.


Appearance of a novel measles G3 strain in multiple European countries within a two month period, 2010.

Brown KE, Mulders MN, Freymuth F, Santibanez S, Mosquera MM, Cordey S, Beirnes J, Shulga S, Myers R, Featherstone D.

Euro Surveill. 2011 Apr 28;16(17). pii: 19852.


Rhinovirus genome evolution during experimental human infection.

Cordey S, Junier T, Gerlach D, Gobbini F, Farinelli L, Zdobnov EM, Winther B, Tapparel C, Kaiser L.

PLoS One. 2010 May 11;5(5):e10588. doi: 10.1371/journal.pone.0010588.


New respiratory enterovirus and recombinant rhinoviruses among circulating picornaviruses.

Tapparel C, Junier T, Gerlach D, Van-Belle S, Turin L, Cordey S, Mühlemann K, Regamey N, Aubert JD, Soccal PM, Eigenmann P, Zdobnov E, Kaiser L.

Emerg Infect Dis. 2009 May;15(5):719-26. doi: 10.3201/eid1505.081286.


New molecular detection tools adapted to emerging rhinoviruses and enteroviruses.

Tapparel C, Cordey S, Van Belle S, Turin L, Lee WM, Regamey N, Meylan P, Mühlemann K, Gobbini F, Kaiser L.

J Clin Microbiol. 2009 Jun;47(6):1742-9. doi: 10.1128/JCM.02339-08. Epub 2009 Apr 1.


Simultaneous detection of parainfluenza viruses 1 and 3 by real-time reverse transcription-polymerase chain reaction.

Cordey S, Thomas Y, Cherpillod P, van Belle S, Tapparel C, Kaiser L.

J Virol Methods. 2009 Mar;156(1-2):166-8. doi: 10.1016/j.jviromet.2008.11.006. Epub 2008 Dec 24.


The cis-acting replication elements define human enterovirus and rhinovirus species.

Cordey S, Gerlach D, Junier T, Zdobnov EM, Kaiser L, Tapparel C.

RNA. 2008 Aug;14(8):1568-78. doi: 10.1261/rna.1031408. Epub 2008 Jun 9.


New complete genome sequences of human rhinoviruses shed light on their phylogeny and genomic features.

Tapparel C, Junier T, Gerlach D, Cordey S, Van Belle S, Perrin L, Zdobnov EM, Kaiser L.

BMC Genomics. 2007 Jul 10;8:224.


Transcribing paramyxovirus RNA polymerase engages the template at its 3' extremity.

Cordey S, Roux L.

J Gen Virol. 2006 Mar;87(Pt 3):665-72.


Nature of a paramyxovirus replication promoter influences a nearby transcription signal.

Vulliémoz D, Cordey S, Mottet-Osman G, Roux L.

J Gen Virol. 2005 Jan;86(Pt 1):171-180. doi: 10.1099/vir.0.80435-0.


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