| Title: |
Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples |
| Authors: |
Bassano, I; Ramachandran, VK; Khalifa, MS; Lilley, CJ; Brown, MR; van Aerle, R; Denise, H; Rowe, W; George, A; Cairns, E; Wierzbicki, C; Pickwell, ND; Carlile, M; Holmes, N; Payne, A; Loose, M; Burke, TA; Paterson, S; Wade, MJ; Grimsley, JMS |
| Contributors: |
Bassano, Irene 0000-0002-6948-2568; Khalifa, Mohammad S. 0000-0002-1747-7337; Wade, Matthew J. 0000-0001-9824-7121 |
| Publisher Information: |
Microbiology Society |
| Publication Year: |
2022 |
| Collection: |
Brunel University London: Brunel University Research Archive (BURA) |
| Subject Terms: |
SARS-CoV-2; sequencing; variant callers; VOC; wastewater |
| Description: |
Impact Statement: Since the declaration of the pandemic in March 2020 by the World Health Organization (WHO), many laboratories have made substantial contributions to understanding the spread of COVID-19 (coronavirus disease 19), the biology and transmission of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), as well as novel studies concerning environmental detection of the virus to support public-health systems around the world. In England, the Environmental Monitoring for Health Protection (EMHP) programme, part of the Department of Health and Social Care, has been monitoring SARS-CoV-2 since 2020, covering up to 75 % of the population. In this article, we have used a portion of the wealth of data collected over the last 2 years to interrogate whether wastewater samples are correctly analysed when it comes to identifying variants of the same circulating virus. While many laboratories have published excellent work in wastewater-based epidemiology (WBE), it is our understanding that a basic investigation regarding the ability of tools to efficiently identify these variants was lacking. Having worked with some of the variant callers within our group, we proposed this article, which we believe covers a good understanding of what tools can be used to analyse wastewater samples. In this work, we describe key parameters used to assess the efficacy of variant callers, namely sensitivity and specificity (also known as recall and precision), as well as comparing the frequency at which known mutations are called. There is a high significance behind these results, as we can clearly show that, using our datasets, some callers do indeed outperform others. To our knowledge, at present, no such comparison work has been done using environmental samples, and we believe this work will lay the basic foundations for future, more detailed and specific studies in WBE. ; Data Summary: All data used to generate figures have been deposited under ENA Accession numbers ERA14897883 and ERA14897645. Codes used to analyse the ... |
| Document Type: |
article in journal/newspaper |
| File Description: |
1–16; Electronic |
| Language: |
English |
| Relation: |
https://bura.brunel.ac.uk/handle/2438/33086; https://doi.org/10.1099/mgen.0.000933 |
| DOI: |
10.1099/mgen.0.000933 |
| Availability: |
https://bura.brunel.ac.uk/handle/2438/33086; https://doi.org/10.1099/mgen.0.000933 |
| Rights: |
Creative Commons Attribution 4.0 International ; https://creativecommons.org/licenses/by/4.0/ ; https://creativecommons.org/licenses/by/4.0/legalcode.en ; The Authors |
| Accession Number: |
edsbas.F032F678 |
| Database: |
BASE |