We obtained the same information for the 1,708 coronavirus disease cases of November 2021, when the Delta variant of SARS-CoV-2 represented 100% (1,299/1,299) of samples. We obtained data on sociodemographic characteristics (age), vaccination status (nonvaccinated or fully vaccinated), and presence or absence of symptoms, as well as symptom onset date (SOD) or diagnosis date (DD) for asymptomatic cases, from the Contact Tracing Program of Cantabria ( Appendix). Lineage assignment was done by Pangolin ( 3) by using consensus fasta. Next-generation sequencing data were analyzed using Torrent suite software and were assembled by IRMA ( 2). Libraries were constructed by using Ion AmpliSeq SARS-CoV-2 Insight Research Assay and were sequenced with Ion GeneStudio S5 system (both Thermo Fisher Scientific). The analysis method was validated through whole-genome sequencing of 63 samples. Samples positive for the K417N mutation and negative for L452R were considered compatible with Omicron. The Omicron cases were detected among the samples with no amplification of the spike (S) gene (non-S gene target failure) by real-time reverse transcription PCR using the TaqMan SARS-CoV-2 mutation panel (Thermo Fisher Scientific, ) for single-nucleotide polymorphism genotyping focused on the K417N and L452R mutations.
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