The impact of sequencing errors and contaminating viruses on SARS-CoV-2 variant detection by sequencing wastewater-sourced viral RNA

The impact of sequencing errors and contaminating viruses on SARS-CoV-2 variant detection by sequencing wastewater-sourced viral RNA

van der Lugt, Mart (TU Delft Electrical Engineering, Mathematics and Computer Science)

Baaijens, J.A. (mentor)
Hildebrandt, K.A. (graduation committee)

Delft University of Technology

Computer Science and Engineering

CSE3000 Research Project

2022-01-28

Since the start of the SARS-CoV-2 pandemic, the monitoring of SARS-CoV-2 by way of viral RNA sequencing of wastewater has proven to be an efficient and effective way of estimating COVID-19 cases in population groups. A recently developed pipeline also enables us to estimate SARS-CoV-2 variant abundance using viral samples from wastewater. This is done by repurposing an RNA-seq quantification algorithm to quantify reads, belonging to variants, from DNA-sequencing data. However, the impact of sequencing errors and contaminating viruses on this process is unknown. Here I show that, in simulated data, the credibility of the prediction results is dependent on the error rate of the sequencing machines used. I also show that contaminating the simulated dataset with certain human coronaviruses has a significant effect on prediction accuracy. However, most viruses currently found in wastewater have no effect. Furthermore, adding a reference genome for these human corona-viruses to the reference set removes any impact. The results demonstrate that it is important to assess the credibility of the pipeline on a case by case basis and to tailor the testing setup and reference set to this assessment.

DNA Sequencing
sars-cov-2
variant detection
errors
wastewater
Contamination

http://resolver.tudelft.nl/uuid:6617adbe-1d0e-4c26-9ba9-40ed4700d3ad

Student theses

bachelor thesis

© 2022 Mart van der Lugt