Abstract
SARS-CoV-2 variant detection relies on resource-intensive whole-genome sequencing methods. We sought to develop a scalable protocol for variant detection and surveillance in Paraguay, pairing rRT-PCR for spike mutations with Nanopore sequencing. A total of 201 acute-phase nasopharyngeal samples were included. Samples were positive for the SARS-CoV-2 N2 target and tested with the Spike SNP assay to detect mutations associated with the following variants: alpha (501Y), beta/gamma (417variant/484K/501Y), delta (452R/478K), and lambda (452Q/490S). Spike SNP calls were confirmed using amplicon (Sanger) sequencing and whole-genome (Nanopore) sequencing on a subset of samples with confirmed variant lineages. Samples had a mean N2 Ct of 20.8 (SD 5.6); 198/201 samples (98.5%) tested positive in the Spike SNP assay. The most common genotype was 417variant/484K/501Y, detected in 102/198 samples (51.5%), which was consistent with the P.1 lineage (gamma variant) in Paraguay. No mutations (K417 only) were found in 64/198 (32.3%), and K417/484K was identified in 22/198 (11.1%), consistent with P.2 (zeta). Seven samples (3.5%) tested positive for 452R without 478K, and one sample with genotype K417/501Y was confirmed as B.1.1.7 (alpha). The results were confirmed using Sanger sequencing in 181/181 samples, and variant calls were consistent with Nanopore sequencing in 29/29 samples. The Spike SNP assay could improve population-level surveillance for mutations associated with SARS-CoV-2 variants and inform the judicious use of sequencing resources.
Keywords: Paraguay; SARS-CoV-2; real-time RT-PCR; variants.
【저자키워드】 SARS-CoV-2, variants, real-time RT-PCR, Paraguay, 【초록키워드】 whole-genome sequencing, Mutation, protocol, spike, Nanopore, Sequencing, variant, SARS-CoV-2 variant, variants, rRT-PCR, Sanger sequencing, Surveillance, SARS-CoV-2 variants, B.1.1.7, spike mutation, P.1, Genotype, Lineage, SNP, nanopore sequencing, Alpha, P.2, spike mutations, real-time RT-PCR, lineages, Lambda, Amplicon, Zeta, K417, positive, variant calls, nasopharyngeal sample, whole-genome, resources, IMPROVE, tested, detect, Sample, develop, subset, the Spike, the SARS-CoV-2, variant call, 【제목키워드】 detection,