Publications
Adventitious Virus Detection in Cells by High-Throughput Sequencing of Newly Synthesized RNAs: Unambiguous Differentiation of Cell Infection from Carryover of Viral Nucleic Acids
The use of high-throughput sequencing (HTS) to identify viral contamination of biological products is extremely sensitive and provides a broad range of detection. Nevertheless, viral sequences identified can also be inert. Read how we developed a method that relies on the sequencing of newly synthesized RNAs, an unequivocal sign of the presence of active viruses.
Use of a new RNA next-generation sequencing approach for the specific detection of virus infection in cells
In order to improve NGS specificity, we have designed a new NGS approach which targets subsets of viral RNAs only synthesized during cell infection.
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- Pérot P, Biton A, Marchetta J, Pourcelot AG, Nazac A, Marret H, Hébert T, Chrétien D, Demazoin MC, Falguières M, Arowas L, Laude H, Heard I, Eloit M. Broad-range papillomavirus transcriptome as a biomarker of papillomavirus-associated cervical high-grade cytology. J Mol Diagn. 2019 Aug 6. pii: S1525-1578.
- Ng SH, Braxton C, Eloit M, FenSF, Fragnoud R, Mallet L, Mee ET, Sathiamoorthy S, Vandeputte O, and Khan AS. Current perspectives on High-Throughput Sequencing (HTS) for adventitious virus Ddtection: Upstream sample processing and library preparation. Viruses. 2018, 10(10), 566.
- Lambert C, Braxton C, Charlebois RL, Deyati A, Duncan P, La Neve F, Malicki HD, Ribrioux S, Rozelle DK, Michaels B, Sun W, Yang Z, Khan AS. Considerations for optimization of high-throughput sequencing bioinformatics pipelines for virus detection. Viruses. 2018 Sep 27;10(10). pii: E528.
- Khan AS, Benetti L, Blumel J, Deforce D, Egan WM, Knezevic I, Krause PR, Mallet L, Mayer D, Minor PD, Neels P, Wang G.
Report of the international conference on next generation sequencing for adventitious virus detection in biologicals. Biologicals. 2018 Sep;55:1-16.
- Eiden M, Gil P, Ziegler U, Rakotoarivony I, Marie A, Frances B, L’Ambert G, Simonin Y, Foulongne V, Groschup MH, Gutierrez S, Eloit M. Emergence of two Usutu virus lineages in Culex pipiens mosquitoes in the Camargue, France, 2015. Infect Genet Evol. 2018 Jul;61:151-154.
- Comoy EE, Mikol J, Jaffré N, Lebon V, Levavasseur E, Streichenberger N, Sumian C, Perret-Liaudet A, Eloit M, Andreoletti O, Haïk S, Hantraye P, Deslys JP. Experimental transfusion of variant CJD-infected blood reveals previously uncharacterised prion disorder in mice and macaque. Nat Commun. 2017 Nov 2;8(1):1268.
- Moutailler S, Popovici I, Devillers E, Vayssier-Taussat M, Eloit M. Diversity of viruses in Ixodes ricinus, and characterization of a neurotropic strain of Eyach virus. New Microbes New Infect. 2016 Mar 5;11:71-81.
- Mee ET, Preston MD, Minor PD, Schepelmann S; CS533 Study Participants. Development of a candidate reference material for adventitious virus detection in vaccine and biologicals manufacturing by deep sequencing. Vaccine. 2016 Apr 12;34(17):2035-43.
- Denesvre C, Dumarest M, Rémy S, Gourichon D, Eloit M. Chicken skin virome analyzed by high-throughput sequencing shows a composition highly different from human skin. Virus Genes. 2015 Oct;51(2):209-16.
- Dumarest M, Muth E, Cheval J, Gratigny M, Hébert C, Gagnieur L, Eloit M. Viral diversity in swine intestinal mucus used for the manufacture of heparin as analyzed by high-throughput sequencing. Biologicals. 2015 Jan;43(1):31-6. doi: 10.1016/j.biologicals.2014.10.004.
- Cabannes E, Hébert C, Eloit M. Whole genome: next-generation sequencing as a virus safety test for biotechnological products. PDA J Pharm Sci Technol. 2014; 68:631-8. doi: 10.5731/pdajpst.2014.01015.
- Gagnieur L, Cheval J, Cochet M, Breard E, Gratigny M, Hébert C, Muth E, Viarouge C, Dumarest M, Coulpier M, Eloit M. Analysis by high throughput sequencing of Specific Pathogen Free eggs. Biologicals. 2014 Jul;42(4):218-9. doi: 10.1016/j.biologicals.2014.05.004.
- Bonnet S, Michelet L, Moutailler S, Cheval J, Hébert C, Vayssier-Taussat M, Eloit M. Identification of parasitic communities within European ticks using next-generation sequencing. PLoS Negl Trop Dis. 2014 Mar 27;8(3):e2753. doi: 10.1371/journal.pntd.0002753.
- Gagnieur L, Cheval J, Gratigny M, Hébert C, Muth E, Dumarest M, Eloit M. Unbiased analysis by high throughput sequencing of the viral diversity in fetal bovine serum and trypsin used in cell culture. Biologicals. 2014; 42:145-52. doi: 10.1016/j.biologicals.2014.02.002.
- Vayssier-Taussat M, Moutailler S, Michelet L, Devillers E, Bonnet S, Cheval J, Hébert C, Eloit M. Next generation sequencing uncovers unexpected bacterial pathogens in ticks in western Europe. PLoS One. 2013 Nov 27;8(11):e81439. doi: 10.1371/journal.pone.0081439. eCollection 2013.
- 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. J Virol. 2012 Sep;86(18):10036-46. doi: 10.1128/JVI.00046-12. Epub 2012 Jul 11.
- Bouquet J, Cheval J, Rogée S, Pavio N, Eloit M. Identical consensus sequence and conserved genomic polymorphism of hepatitis E virus during controlled interspecies transmission. J Virol. 2012 Jun;86(11):6238-45. doi: 10.1128/JVI.06843-11. Epub 2012 Mar 28.
- 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. Emerg Infect Dis. 2011 Aug;17(8):1364-70. doi: 10.3201/eid1708.110278.
- 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. J Virol. 2011 Aug;85(15):7948-50. doi: 10.1128/JVI.00639-11. Epub 2011 Jun 1.
- 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. J Clin Microbiol. 2011; 49:3268-75. doi: 10.1128/JCM.00850-11.
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