Performance of Long-Read Single-Molecule Real-Time Sequencing for SARS-CoV-2 Genotyping in Clinical Samples

Due to the continuous genetic evolution of SARS-CoV-2, numerous variants have emerged and different whole genome sequencing techniques, necessary for accurate virus typing, have been developed. In this study, we evaluated the performance of PacBio single-molecule real-time (SMRT) sequencing for SARS-CoV-2 typing. Reproducibility was assessed on two internal quality controls, whose median reading depths were 1154X and 1059X. The overall sensitivity on 1646 clinical samples collected between January 2023 and June 2024 was 83.6% and was correlated to the viral load. By comparison, the overall sensitivity of short-read illumina sequencing over the same period of time on 271 samples was 90.8%. Although less sensitive, SMRT sequencing was more efficient for the identification of the two lineages in a co-infection case due to the amplification of long fragments. Comparing the results obtained by the two techniques, 10 out of 50 samples were identified with the same clade but not the exact same lineage at the time of analysis, because of the very frequent updates of the Pango taxonomy. Nevertheless, we obtained very similar fasta consensus sequences with a maximum difference of 4 nucleotides, showing that both methods provide accurate typing of SARS-CoV-2, useful for epidemiological or clinical studies.