Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data DOI Creative Commons
Eva Aßmann, Shelesh Agrawal, Laura Orschler

et al.

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Abstract Background Sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from wastewater samples has emerged as a valuable tool for detecting the presence and relative abundances SARS-CoV-2 variants in community. By analyzing viral genetic material present wastewater, researchers public health authorities can gain early insights into spread virus lineages emerging mutations. Constructing reference datasets known their mutation profiles become state-of-the-art assigning sequencing data. However, selecting sequences or mutations directly affects predictive power. Results Here, we show impact mutation- sequence-based reconstruction abundance estimation. We benchmark 3 datasets: (i) synthetic “spike-in”’ mixtures; (ii) German 2021, mainly comprising Alpha; (iii) obtained at an international airport Germany end including first signals Omicron. The approaches differ sublineage detection, with marker mutation-based method, particular, being challenged by increasing number lineages. estimations both depend on representative references optimized parameter settings. performing escalation experiments, demonstrate effects size alternative allele frequency cutoffs how different settings lead to results our test illustrate lineage composition references. Conclusions Our study highlights current computational challenges, focusing general design, which impacts allocations. advantages disadvantages that may be relevant further developments community context defining robust quality metrics.

Language: Английский

Leveraging wastewater sequencing to strengthen global public health surveillance DOI Creative Commons
Victor Gordeev, Martin Hölzer, Daniel Desirò

et al.

BMC Global and Public Health, Journal Year: 2025, Volume and Issue: 3(1)

Published: March 21, 2025

Language: Английский

Citations

0
Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data DOI Creative Commons
Eva Aßmann, Shelesh Agrawal, Laura Orschler

et al.

GigaScience, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 1, 2024

Abstract Background Sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA from wastewater samples has emerged as a valuable tool for detecting the presence and relative abundances SARS-CoV-2 variants in community. By analyzing viral genetic material present wastewater, researchers public health authorities can gain early insights into spread virus lineages emerging mutations. Constructing reference datasets known their mutation profiles become state-of-the-art assigning sequencing data. However, selecting sequences or mutations directly affects predictive power. Results Here, we show impact mutation- sequence-based reconstruction abundance estimation. We benchmark 3 datasets: (i) synthetic “spike-in”’ mixtures; (ii) German 2021, mainly comprising Alpha; (iii) obtained at an international airport Germany end including first signals Omicron. The approaches differ sublineage detection, with marker mutation-based method, particular, being challenged by increasing number lineages. estimations both depend on representative references optimized parameter settings. performing escalation experiments, demonstrate effects size alternative allele frequency cutoffs how different settings lead to results our test illustrate lineage composition references. Conclusions Our study highlights current computational challenges, focusing general design, which impacts allocations. advantages disadvantages that may be relevant further developments community context defining robust quality metrics.

Language: Английский

Citations

2