Author, as appears in the article.: Garcia-Pedemonte D; Carcereny A; Gregori J; Quer J; Garcia-Cehic D; Guerrero L; Ceretó-Massagué A; Abid I; Bosch A; Costafreda MI; Pintó RM; Guix S
Department: Bioquímica i Biotecnologia
URV's Author/s: Cereto Massagué, Adrián José
Keywords: Twist rna Sars-cov-2 Ngs Miseq Minion Lofreq Ivar Freyja
Abstract: Shortly after the beginning of the SARS-CoV-2 pandemic, many countries implemented sewage sentinel systems to monitor the circulation of the virus in the population. A fundamental part of these surveillance programs is the variant tracking through sequencing approaches to monitor and identify new variants or mutations that may be of importance. Two of the main sequencing platforms are Illumina and Oxford Nanopore Technologies. Here, we compare the performance of MiSeq (Illumina) and MinION (Oxford Nanopore Technologies), as well as two different data processing pipelines, to determine the effect they may have on the results. MiSeq showed higher sequencing coverage, lower error rate, and better capacity to detect and accurately estimate variant abundances than MinION R9.4.1 flow cell data. The use of different variant callers (LoFreq and iVar) and approaches to calculate the variant proportions had a remarkable impact on the results generated from wastewater samples. Freyja, coupled with iVar, may be more sensitive and accurate than LoFreq, especially with MinION data, but it comes at the cost of having a higher error rate. The analysis of MinION R10.4.1 flow cell data using Freyja combined with iVar narrows the gap with MiSeq performance in terms of read quality, accuracy, sensitivity, and number of detected mutations. Although MiSeq should still be considered as the standard method for SARS-CoV-2 variant tracking, MinION’s versatility and rapid turnaround time may represent a clear advantage during the ongoing pandemic.
Thematic Areas: Zootecnia / recursos pesqueiros Spectroscopy Saúde coletiva Química Psicología Physical and theoretical chemistry Organic chemistry Odontología Nutrição Molecular biology Medicine (miscellaneous) Medicina veterinaria Medicina iii Medicina ii Medicina i Materiais Interdisciplinar Inorganic chemistry Geociências Farmacia Engenharias iv Engenharias ii Engenharias i Educação física Computer science applications Ciências biológicas iii Ciências biológicas ii Ciências biológicas i Ciências ambientais Ciências agrárias i Ciência de alimentos Ciência da computação Chemistry, multidisciplinary Catalysis Biotecnología Biodiversidade Biochemistry & molecular biology Astronomia / física
licence for use: https://creativecommons.org/licenses/by/3.0/es/
Author's mail: adrianjose.cereto@urv.cat adrianjose.cereto@urv.cat
Record's date: 2024-01-13
Papper version: info:eu-repo/semantics/publishedVersion
Link to the original source: https://www.mdpi.com/1422-0067/24/24/17184
Papper original source: International Journal Of Molecular Sciences. 24 (24):
APA: Garcia-Pedemonte D; Carcereny A; Gregori J; Quer J; Garcia-Cehic D; Guerrero L; Ceretó-Massagué A; Abid I; Bosch A; Costafreda MI; Pintó RM; Guix S (2023). Comparison of Nanopore and Synthesis-Based Next-Generation Sequencing Platforms for SARS-CoV-2 Variant Monitoring in Wastewater. International Journal Of Molecular Sciences, 24(24), -. DOI: 10.3390/ijms242417184
Licence document URL: https://repositori.urv.cat/ca/proteccio-de-dades/
Article's DOI: 10.3390/ijms242417184
Entity: Universitat Rovira i Virgili
Journal publication year: 2023
Publication Type: Journal Publications
Repositori URV