A Tailored Sequencing Approach for Identifying SARS-CoV-2 Variants in Challenging Samples from Mink

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.