Combining Short- and Long-Read Sequencing Technologies to Identify SARS-CoV-2 Variants in Wastewater.
| Title: | Combining Short- and Long-Read Sequencing Technologies to Identify SARS-CoV-2 Variants in Wastewater. |
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| Authors: | Jayme G; Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Liu JL; McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada.; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada.; Galvez JH; Canadian Centre for Computational Genomics, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada.; Reiling SJ; McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada.; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada.; Celikkol S; Department of Civil Engineering, McGill University, Montreal, QC H3A 0C3, Canada.; N'Guessan A; Department of Biochemistry and Molecular Medicine, Université de Montréal, Montreal, QC H3C 3J7, Canada.; Research Centre, Montreal Heart Institute, Montreal, QC H1T 1C8, Canada.; Lee S; McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada.; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada.; Chen SH; McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada.; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada.; Tsitouras A; Department of Civil Engineering, McGill University, Montreal, QC H3A 0C3, Canada.; Sanchez-Quete F; Department of Civil Engineering, McGill University, Montreal, QC H3A 0C3, Canada.; Maere T; modelEAU, Département de génie civil et de génie des eaux, Université Laval, Québec City, QC G1V 0A6, Canada.; Goitom E; Department of Geography & Environmental Studies, Toronto Metropolitan University, Toronto, ON M5B 2K3, Canada.; Hachad M; Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montreal, QC H3C 3A7, Canada.; Mercier E; Department of Civil Engineering, University of Ottawa, Ottawa, ON K1N 6N5, Canada.; Loeb SK; Department of Civil Engineering, McGill University, Montreal, QC H3A 0C3, Canada.; Vanrolleghem PA; modelEAU, Département de génie civil et de génie des eaux, Université Laval, Québec City, QC G1V 0A6, Canada.; Dorner S; Department of Civil, Geological and Mining Engineering, Polytechnique Montréal, Montreal, QC H3C 3A7, Canada.; Delatolla R; Department of Civil Engineering, University of Ottawa, Ottawa, ON K1N 6N5, Canada.; Shapiro BJ; McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada.; Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 2B4, Canada.; Frigon D; Department of Civil Engineering, McGill University, Montreal, QC H3A 0C3, Canada.; Ragoussis J; McGill Genome Centre, Victor Phillip Dahdaleh Institute of Genomic Medicine, McGill University, Montreal, QC H3A 0G1, Canada.; Department of Human Genetics, McGill University, Montreal, QC H3A 0C7, Canada.; Department of Bioengineering, McGill University, Montreal, QC H3A 0E9, Canada.; Snutch TP; Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.; Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada. |
| Source: | Viruses [Viruses] 2024 Sep 21; Vol. 16 (9). Date of Electronic Publication: 2024 Sep 21. |
| Publication Type: | Journal Article; Research Support, Non-U.S. Gov't |
| Language: | English |
| Journal Info: | Publisher: MDPI Country of Publication: Switzerland NLM ID: 101509722 Publication Model: Electronic Cited Medium: Internet ISSN: 1999-4915 (Electronic) Linking ISSN: 19994915 NLM ISO Abbreviation: Viruses Subsets: MEDLINE |
| Imprint Name(s): | Original Publication: Basel, Switzerland : MDPI |
| MeSH Terms: | Wastewater*/virology ; SARS-CoV-2*/genetics ; SARS-CoV-2*/isolation & purification ; SARS-CoV-2*/classification ; COVID-19*/virology ; COVID-19*/diagnosis ; COVID-19*/epidemiology ; High-Throughput Nucleotide Sequencing*/methods ; Mutation*; RNA, Viral/genetics ; Ontario/epidemiology ; Nanopore Sequencing/methods ; Humans ; Quebec ; Genome, Viral |
| Abstract: | During the COVID-19 pandemic, the monitoring of SARS-CoV-2 RNA in wastewater was used to track the evolution and emergence of variant lineages and gauge infection levels in the community, informing appropriate public health responses without relying solely on clinical testing. As more sublineages were discovered, it increased the difficulty in identifying distinct variants in a mixed population sample, particularly those without a known lineage. Here, we compare the sequencing technology from Illumina and from Oxford Nanopore Technologies, in order to determine their efficacy at detecting variants of differing abundance, using 248 wastewater samples from various Quebec and Ontario cities. Our study used two analytical approaches to identify the main variants in the samples: the presence of signature and marker mutations and the co-occurrence of signature mutations within the same amplicon. We observed that each sequencing method detected certain variants at different frequencies as each method preferentially detects mutations of distinct variants. Illumina sequencing detected more mutations with a predominant lineage that is in low abundance across the population or unknown for that time period, while Nanopore sequencing had a higher detection rate of mutations that are predominantly found in the high abundance B.1.1.7 (Alpha) lineage as well as a higher sequencing rate of co-occurring mutations in the same amplicon. We present a workflow that integrates short-read and long-read sequencing to improve the detection of SARS-CoV-2 variant lineages in mixed population samples, such as wastewater. |
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| Grant Information: | FRN#175622 Canada CIHR; CFI 33406 Canada Foundation for Innovation; CFI-MSI 35444 Canada Foundation for Innovation; #41012 Canada Foundation for Innovation |
| Contributed Indexing: | Keywords: Illumina sequencing; Nanopore sequencing; SARS-CoV-2; coronaviruses; variants; wastewater surveillance |
| Molecular Sequence: | BioProject PRJNA1127571 |
| Substance Nomenclature: | 0 (Wastewater); 0 (RNA, Viral) |
| SCR Organism: | SARS-CoV-2 variants |
| Entry Date(s): | Date Created: 20240928 Date Completed: 20240928 Latest Revision: 20250522 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC11437403 |
| DOI: | 10.3390/v16091495 |
| PMID: | 39339971 |
| Database: | MEDLINE |
Journal Article; Research Support, Non-U.S. Gov't