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

Yale SARS-CoV-2 Genomic Surveillance Initiative

Research output: Contribution to journalArticlepeer-review

16 Scopus citations

Abstract

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.

Original languageEnglish (US)
Article number236
JournalGenome biology
Volume23
Issue number1
DOIs
StatePublished - Dec 2022

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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