Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.

Autor: Baaijens JA; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA. j.a.baaijens@tudelft.nl.; Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands. j.a.baaijens@tudelft.nl., Zulli A; Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA., Ott IM; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA., Nika I; Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands., van der Lugt MJ; Department of Intelligent Systems, Delft University of Technology, Delft, Netherlands., Petrone ME; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA., Alpert T; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA., Fauver JR; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.; Department of Epidemiology, University of Nebraska Medical Center, Omaha, NE, USA., Kalinich CC; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA., Vogels CBF; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA., Breban MI; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA., Duvallet C; Biobot Analytics, Inc., Cambridge, MA, USA., McElroy KA; Biobot Analytics, Inc., Cambridge, MA, USA., Ghaeli N; Biobot Analytics, Inc., Cambridge, MA, USA., Imakaev M; Biobot Analytics, Inc., Cambridge, MA, USA., Mckenzie-Bennett MF; Ginkgo Bioworks, Inc., Boston, MA, USA., Robison K; Ginkgo Bioworks, Inc., Boston, MA, USA., Plocik A; Ginkgo Bioworks, Inc., Boston, MA, USA., Schilling R; Ginkgo Bioworks, Inc., Boston, MA, USA., Pierson M; Ginkgo Bioworks, Inc., Boston, MA, USA., Littlefield R; Ginkgo Bioworks, Inc., Boston, MA, USA., Spencer ML; Ginkgo Bioworks, Inc., Boston, MA, USA., Simen BB; Ginkgo Bioworks, Inc., Boston, MA, USA., Hanage WP; Center for Communicable Disease Dynamics and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA., Grubaugh ND; Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA., Peccia J; Department of Chemical and Environmental Engineering, Yale University, New Haven, CT, USA., Baym M; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Jazyk: angličtina
Zdroj: Genome biology [Genome Biol] 2022 Nov 08; Vol. 23 (1), pp. 236. Date of Electronic Publication: 2022 Nov 08.
DOI: 10.1186/s13059-022-02805-9
Abstrakt: Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable.
(© 2022. The Author(s).)
Databáze: MEDLINE
Externí odkaz: