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

• Type of Material: Article
• Authors: Magaly Martinez, Universidad Nacional de Asunción, San Lorenzo; Phuong-Vi Nguyen, Emory University; Maxwell Su, Emory University; Fátima Cardozo, Universidad Nacional de Asunción; Adriana Valenzuela, Universidad Nacional de Asunción; Laura Franco, Universidad Nacional de Asunción; María Eugenia Galeano, Universidad Nacional de Asunción; Leticia E Rojas, Universidad Nacional de Asunción; Chyntia Carolina Díaz Acosta, Universidad Nacional de Asunción; Jonás Fernandez, Universidad Nacional de Asunción; Joel Ortiz, Universidad Nacional de Asunción; Florencia Del Puerto, Universidad Nacional de Asunción; Laura Mendoza, Universidad Nacional de Asunción; Eva Nara, Universidad Nacional de Asunción; Alejandra Rojas, Universidad Nacional de Asunción; Jesse Waggoner, Emory University
• Language: English
• Date: 2022-05-01
• Publisher: MDPI
• Publication Version: Final Published Version
• Copyright Statement: © 2022 by the authors.
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.3390/v14050873
• Title of Journal or Parent Work: VIRUSES-BASEL
• Volume: 14
• Issue: 5
• Grant/Funding Information: This work was supported by funding from Consejo Nacional de Ciencia y Tecnología with FEEI support, CONACYT, Paraguay, PINV20-239 (M.M.); National Institutes of Health grants U54 EB027690 02S1, U54 EB027690 03S1, U54EB027690 03S2, and UL1TR002378; and the Doris Duke Charitable Foundation, Clinical Scientist Development Award 2019089 (J.J.W.).
• Keywords: Paraguay; real-time RT-PCR; SARS-CoV-2; Virology; Life Sciences & Biomedicine; variants; Science & Technology
• Research Categories: Health Sciences, Public Health; Health Sciences, Medicine and Surgery

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.