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V-pipe 3.0: a sustainable pipeline for within-sample viral genetic diversity estimation.
Fuhrmann L, Jablonski KP, Topolsky I, Batavia AA, Borgsmüller N, Baykal PI, Carrara M, Chen C, Dondi A, Dragan M, Dreifuss D, John A, Langer B, Okoniewski M, du Plessis L, Schmitt U, Singer F, Stadler T, Beerenwinkel N. Fuhrmann L, et al. Among authors: dreifuss d. Gigascience. 2024 Jan 2;13:giae065. doi: 10.1093/gigascience/giae065. Gigascience. 2024. PMID: 39347649 Free PMC article.
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.
Sutcliffe SG, Kraemer SA, Ellmen I, Knapp JJ, Overton AK, Nash D, Nissimov JI, Charles TC, Dreifuss D, Topolsky I, Baykal PI, Fuhrmann L, Jablonski KP, Beerenwinkel N, Levy JI, Olabode AS, Becker DG, Gugan G, Brintnell E, Poon AFY, Valieris R, Drummond RD, Defelicibus A, Dias-Neto E, Rosales RA, Tojal da Silva I, Orfanou A, Psomopoulos F, Pechlivanis N, Pipes L, Chen Z, Baaijens JA, Baym M, Shapiro BJ. Sutcliffe SG, et al. Among authors: dreifuss d. Microb Genom. 2024 May;10(5):001249. doi: 10.1099/mgen.0.001249. Microb Genom. 2024. PMID: 38785221 Free PMC article.
Early detection and surveillance of SARS-CoV-2 genomic variants in wastewater using COJAC.
Jahn K, Dreifuss D, Topolsky I, Kull A, Ganesanandamoorthy P, Fernandez-Cassi X, Bänziger C, Devaux AJ, Stachler E, Caduff L, Cariti F, Corzón AT, Fuhrmann L, Chen C, Jablonski KP, Nadeau S, Feldkamp M, Beisel C, Aquino C, Stadler T, Ort C, Kohn T, Julian TR, Beerenwinkel N. Jahn K, et al. Among authors: dreifuss d. Nat Microbiol. 2022 Aug;7(8):1151-1160. doi: 10.1038/s41564-022-01185-x. Epub 2022 Jul 18. Nat Microbiol. 2022. PMID: 35851854 Free PMC article.
Wastewater monitoring of SARS-CoV-2 shows high correlation with COVID-19 case numbers and allowed early detection of the first confirmed B.1.1.529 infection in Switzerland: results of an observational surveillance study.
Bagutti C, Alt Hug M, Heim P, Maurer Pekerman L, Ilg Hampe E, Hübner P, Fuchs S, Savic M, Stadler T, Topolsky I, Icer Baykal P, Dreifuss D, Beerenwinkel N, Tschudin Sutter S. Bagutti C, et al. Among authors: dreifuss d. Swiss Med Wkly. 2022 Jun 27;152:w30202. doi: 10.4414/smw.2022.w30202. eCollection 2022 Jun 20. Swiss Med Wkly. 2022. PMID: 35822578 Free article.
Inferring transmission fitness advantage of SARS-CoV-2 variants of concern from wastewater samples using digital PCR, Switzerland, December 2020 through March 2021.
Caduff L, Dreifuss D, Schindler T, Devaux AJ, Ganesanandamoorthy P, Kull A, Stachler E, Fernandez-Cassi X, Beerenwinkel N, Kohn T, Ort C, Julian TR. Caduff L, et al. Among authors: dreifuss d. Euro Surveill. 2022 Mar;27(10):2100806. doi: 10.2807/1560-7917.ES.2022.27.10.2100806. Euro Surveill. 2022. PMID: 35272748 Free PMC article.
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland.
Chen C, Nadeau SA, Topolsky I, Manceau M, Huisman JS, Jablonski KP, Fuhrmann L, Dreifuss D, Jahn K, Beckmann C, Redondo M, Noppen C, Risch L, Risch M, Wohlwend N, Kas S, Bodmer T, Roloff T, Stange M, Egli A, Eckerle I, Kaiser L, Denes R, Feldkamp M, Nissen I, Santacroce N, Burcklen E, Aquino C, de Gouvea AC, Moccia MD, Grüter S, Sykes T, Opitz L, White G, Neff L, Popovic D, Patrignani A, Tracy J, Schlapbach R, Dermitzakis ET, Harshman K, Xenarios I, Pegeot H, Cerutti L, Penet D, Blin A, Elies M, Althaus CL, Beisel C, Beerenwinkel N, Ackermann M, Stadler T. Chen C, et al. Among authors: dreifuss d. Epidemics. 2021 Dec;37:100480. doi: 10.1016/j.epidem.2021.100480. Epub 2021 Aug 9. Epidemics. 2021. PMID: 34488035 Free PMC article.