Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.
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ABSTRACT:
SUBMITTER: Baaijens JA
PROVIDER: S-EPMC9643916 | biostudies-literature | 2022 Nov
REPOSITORIES: biostudies-literature
Publications
Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.
Baaijens Jasmijn A JA Zulli Alessandro A Ott Isabel M IM Nika Ioanna I van der Lugt Mart J MJ Petrone Mary E ME Alpert Tara T Fauver Joseph R JR Kalinich Chaney C CC Vogels Chantal B F CBF Breban Mallery I MI Duvallet Claire C McElroy Kyle A KA Ghaeli Newsha N Imakaev Maxim M Mckenzie-Bennett Malaika F MF Robison Keith K Plocik Alex A Schilling Rebecca R Pierson Martha M Littlefield Rebecca R Spencer Michelle L ML Simen Birgitte B BB Hanage William P WP Grubaugh Nathan D ND Peccia Jordan J Baym Michael M
Genome biology 20221108 1
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 sequenci ...[more]
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