Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater DOI Creative Commons
Megan Lott, Amanda Sullivan, Leah Lariscy

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 17, 2024

ABSTRACT During the COVID-19 pandemic, detection and sequencing of SARS-CoV-2 from wastewater proved to be a valuable tool in assessing trends at community level. Several whole genome enrichment methods have been proposed for mixed community, but there is little consensus on most appropriate variant or abundance estimations. Few studies elucidated errors associated with these established minimum requirements correct interpretation results. To address needs, we systematically assessed efficacy three tiled amplicon (Freed/Midnight, ARTIC V4, NEB VarSkip) variants using mock communities known proportions. We found V4 approach yielded accurate results identification estimation, followed by VarSkip approach. Conversely, method obtained highest genomic coverage, achieving second coverage. Finally, determined that Freed/Midnight library preparation are not well-suited use short read sequencing. Based present results, workflow appears robust cost-effective monitoring circulating surveillance. IMPORTANCE This work informative practitioners wastewater-based epidemiology. Here, detail systematic comparison approaches wastewater. Using composition, validate analysis previously published Baaijens et al. Genome Biology (2022) estimating an RNAseq pipeline, kallisto. provide recommendations estimates The sequences generated uploaded NCBI’s Sequence Read Archive will useful other seeking their bioinformatic pipelines.

Язык: Английский

Comparison of three tiled amplicon sequencing approaches for SARS-CoV-2 variant detection from wastewater DOI Creative Commons
Megan Lott, Amanda Sullivan, Leah Lariscy

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 17, 2024

ABSTRACT During the COVID-19 pandemic, detection and sequencing of SARS-CoV-2 from wastewater proved to be a valuable tool in assessing trends at community level. Several whole genome enrichment methods have been proposed for mixed community, but there is little consensus on most appropriate variant or abundance estimations. Few studies elucidated errors associated with these established minimum requirements correct interpretation results. To address needs, we systematically assessed efficacy three tiled amplicon (Freed/Midnight, ARTIC V4, NEB VarSkip) variants using mock communities known proportions. We found V4 approach yielded accurate results identification estimation, followed by VarSkip approach. Conversely, method obtained highest genomic coverage, achieving second coverage. Finally, determined that Freed/Midnight library preparation are not well-suited use short read sequencing. Based present results, workflow appears robust cost-effective monitoring circulating surveillance. IMPORTANCE This work informative practitioners wastewater-based epidemiology. Here, detail systematic comparison approaches wastewater. Using composition, validate analysis previously published Baaijens et al. Genome Biology (2022) estimating an RNAseq pipeline, kallisto. provide recommendations estimates The sequences generated uploaded NCBI’s Sequence Read Archive will useful other seeking their bioinformatic pipelines.

Язык: Английский

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