Impact of reference design on estimating SARS-CoV-2 lineage abundances from wastewater sequencing data

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

Genomic surveillance of Canadian airport wastewater samples allows early detection of emerging SARS-CoV-2 lineages

Scientific Reports, Journal Year: 2024, Volume and Issue: 14(1)

Published: Nov. 3, 2024

Abstract The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has shown wastewater (WW) surveillance to be an effective means of tracking the emergence viral lineages which arrive by many routes transmission including via transportation hubs. In Canadian province Ontario, numerous municipal treatment plants (WWTPs) participate in WW infectious disease targets such as SARS-CoV-2 qPCR and whole genome sequencing (WGS). Greater Toronto Airports Authority (GTAA), operator Pearson International Airport (Toronto Pearson), been participating since January 2022. As a major international airport Canada largest national hub, this is ideal location for globally emerging variants concern (VOCs). study, collected from Pearson’s two terminals pooled aircraft sewage was processed WGS using tiled-amplicon approach targeting virus genome. Data generated analyzed monitor trends lineage frequencies. Initial detections were compared between samples, samples surrounding regions, Ontario clinical data published Public Health Ontario. Results enabled early detection VOCs individual mutations On average, novel at preceded 1–4 weeks, up 16 weeks one case. This project illustrates efficacy transitory hubs sets example that could applied other viruses part preparedness strategy provide monitoring on mass scale.

Language: Английский