SARS-CoV-2 Variants in Paraguay: Detection and Surveillance with an Economical and Scalable Molecular Protocol

• Published in: Viruses 2022-04, Vol.14 (5), p.873
• Main Authors: Martinez, Magaly, Nguyen, Phuong-Vi, Su, Maxwell, Cardozo, Fátima, Valenzuela, Adriana, Franco, Laura, Galeano, María Eugenia, Rojas, Leticia Elizabeth, Díaz Acosta, Chyntia Carolina, Fernández, Jonás, Ortiz, Joel, Del Puerto, Florencia, Mendoza, Laura, Nara, Eva, Rojas, Alejandra, Waggoner, Jesse J
• Format: Article
• Language: English
• Subjects: COVID-19 - diagnosis; COVID-19 - epidemiology; Genomes; Genotypes; Humans; Mutation; Pandemics; Paraguay; Paraguay - epidemiology; real-time RT-PCR; SARS-CoV-2; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Software; variants; Whole genome sequencing
• ISSN: 1999-4915; 1999-4915
• DOI: 10.3390/v14050873

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.