A Tailored Sequencing Approach for Identifying SARS-CoV-2 Variants in Challenging Samples from Mink
- 1Department of Research Support, National Veterinary Research Institute (PIWet-PIB), 24-100 Puławy, Poland
- 2Department of Virology and Viral Animal Diseases, National Veterinary Research Institute (PIWet-PIB), 24-100 Puławy, Poland
- 3Department of Basic and Preclinical Sciences, Faculty of Biological and Veterinary Sciences, University of Nicolaus Copernicus in Toruń, 87-100 Toruń, Poland
Abstract
High-throughput sequencing (HTS) is an essential tool for genomic surveillance of infectious agents, including SARS-CoV-2 in farmed mink. However, sample quality varies, hindering high-quality sequencing results. In this study, six mink-origin SARS-CoV-2-positive samples were sequenced using two hybrid-capture methods (commercial and custom) and a shotgun metagenomic approach. All methods consistently identified SARS-CoV-2 variants. The metagenomic approach yielded the lowest mapping rate (up to 0.35%), breadth of coverage (97–100%), depth of coverage (9–932×), and mean mapq (30–59), and one sequence did not meet the quality criteria. In contrast, both hybrid-capture methods achieved higher mapping rates (47–99%), breadth of coverage (99.9–100%), and depth of coverage (508–115,846×). The custom hybrid-capture approach was selected because of its superior coverage uniformity, the lowest number of ambiguous bases (N), adjustability to low RNA levels and degraded material, and streamlined laboratory workflow. To further evaluate its applicability, it was applied to 35 clinical samples collected as part of routine genomic surveillance. This method generated sequencing data with high mapping rates (median 95%), depth of coverage (median 13,238×), breadth of coverage (median 100%), and mean mapq (median 60). These findings demonstrate that the custom hybrid-capture approach is a useful tool for genomic surveillance of SARS-CoV-2 in mink-origin samples.
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BibTeX
@article{giza2026tailored,
title = {{A Tailored Sequencing Approach for Identifying SARS-CoV-2 Variants in Challenging Samples from Mink}},
author = {Aleksandra Giza and Ewelina Iwan and Arkadiusz Bomba and Anna Orłowska and Marcin Smreczak and Marta Pietruk and Aleksandra Chudzik and Małgorzata Olejnik and Katarzyna Domańska-Blicharz},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27219638},
url = {https://www.mdpi.com/1422-0067/27/21/9638},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - A Tailored Sequencing Approach for Identifying SARS-CoV-2 Variants in Challenging Samples from Mink
AU - Aleksandra Giza
AU - Ewelina Iwan
AU - Arkadiusz Bomba
AU - Anna Orłowska
AU - Marcin Smreczak
AU - Marta Pietruk
AU - Aleksandra Chudzik
AU - Małgorzata Olejnik
AU - Katarzyna Domańska-Blicharz
PY - 2026
DA - 2026/10/28
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219638
UR - https://www.mdpi.com/1422-0067/27/21/9638
AB - High-throughput sequencing (HTS) is an essential tool for genomic surveillance of infectious agents, including SARS-CoV-2 in farmed mink. However, sample quality varies, hindering high-quality sequencing results. In this study, six mink-origin SARS-CoV-2-positive samples were sequenced using two hybrid-capture methods (commercial and custom) and a shotgun metagenomic approach. All methods consistently identified SARS-CoV-2 variants. The metagenomic approach yielded the lowest mapping rate (up to 0.35%), breadth of coverage (97–100%), depth of coverage (9–932×), and mean mapq (30–59), and one sequence did not meet the quality criteria. In contrast, both hybrid-capture methods achieved higher mapping rates (47–99%), breadth of coverage (99.9–100%), and depth of coverage (508–115,846×). The custom hybrid-capture approach was selected because of its superior coverage uniformity, the lowest number of ambiguous bases (N), adjustability to low RNA levels and degraded material, and streamlined laboratory workflow. To further evaluate its applicability, it was applied to 35 clinical samples collected as part of routine genomic surveillance. This method generated sequencing data with high mapping rates (median 95%), depth of coverage (median 13,238×), breadth of coverage (median 100%), and mean mapq (median 60). These findings demonstrate that the custom hybrid-capture approach is a useful tool for genomic surveillance of SARS-CoV-2 in mink-origin samples.
SN - 1422-0067
ER -