{"doi":"10.3390/v14050873","title":"SARS-CoV-2 Variants in Paraguay: Detection and Surveillance with an Economical and Scalable Molecular Protocol","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.","journal":"Viruses","year":2022,"id":259734,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":16,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9525,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":804922,"name":"Phuong-Vi Nguyen","orcid":null,"position":1,"is_corresponding":false},{"id":698336,"name":"Maxwell Su","orcid":"0000-0002-6601-3723","position":2,"is_corresponding":false},{"id":390250,"name":"Fátima Cardozo","orcid":"0000-0001-8290-4625","position":3,"is_corresponding":false},{"id":912391,"name":"Adriana Valenzuela","orcid":"0000-0002-0785-8371","position":4,"is_corresponding":false},{"id":912392,"name":"Laura Franco","orcid":"0000-0001-6567-5146","position":5,"is_corresponding":false},{"id":646097,"name":"María E. Galeano","orcid":"0000-0002-4476-3486","position":6,"is_corresponding":false},{"id":912393,"name":"Leticia Elizabeth Rojas","orcid":"0000-0002-7678-7327","position":7,"is_corresponding":false},{"id":912394,"name":"Chyntia Carolina Díaz Acosta","orcid":"0000-0002-8541-8312","position":8,"is_corresponding":false},{"id":912395,"name":"Jonás Fernández","orcid":"0000-0003-1011-483X","position":9,"is_corresponding":false},{"id":912396,"name":"Joel Ortiz","orcid":"0000-0003-3042-5184","position":10,"is_corresponding":false},{"id":912397,"name":"Florencia del Puerto","orcid":"0000-0003-0631-8805","position":11,"is_corresponding":false},{"id":900980,"name":"Laura Mendoza","orcid":"0000-0001-6124-1244","position":12,"is_corresponding":false},{"id":912398,"name":"Eva Nara","orcid":"0000-0002-8575-325X","position":13,"is_corresponding":false},{"id":390249,"name":"Alejandra Rojas","orcid":"0000-0001-5519-3442","position":14,"is_corresponding":false},{"id":168177,"name":"Jesse J. Waggoner","orcid":"0000-0002-0244-5957","position":15,"is_corresponding":false},{"id":647138,"name":"Magaly Martinez","orcid":null,"position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":null,"created_at":"2026-07-19T00:25:58.993402Z","pmid":"35632615","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}