RT info:eu-repo/semantics/article
T1 SARS-CoV-2 variants in Paraguay : detection and surveillance with an economical and scalable molecular protocol
A1 Martínez Pereira, Iara Magaly
A1 Nguyen, Phuong-Vi
A1 Su, Maxwell
A1 Cardozo Segovia, Fátima María
A1 Valenzuela, Adriana Beatriz
A1 Franco, Laura Ximena
A1 Galeano, María Eugenia
A1 Rojas, Leticia Elizabeth
A1 Díaz Acosta, Chyntia Carolina
A1 Fernández, Jonás
A1 Ortíz, Joel
A1 del Puerto Rodas, Ramona Florencia
A1 Mendoza Torres, Laura Patricia
A1 Nara, Eva
A1 Rojas Segovia, Alejandra María
A1 Waggoner, Jesse J.
A2 Centro de Estudios y Formación para el Ecodesarrollo
AB 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.
PB Multidisciplinary Digital Publishing Institute
SN 1999-4915
YR 2022
FD 2022-04-22
LK http://hdl.handle.net/20.500.14066/4369
UL http://hdl.handle.net/20.500.14066/4369
LA eng
NO Martínez, M.; Nguyen, P.-V.; Su, M.; Cardozo, F.; Valenzuela, A.; Franco, L.; Galeano, M.E.; Rojas, L.E.; Díaz Acosta, C.C.; Fernández, J.; et al. SARS-CoV-2 Variants in Paraguay: Detection and Surveillance with an Economical and Scalable Molecular Protocol. Viruses 2022, 14, 873. https://doi.org/10.3390/v14050873
NO Correspondence: arojass@iics.una.py (A.R.); jjwaggo@emory.edu (J.J.W.); Tel.: +595-982-414456 (A.R.); +1-404-712-2360 (J.J.W.)
NO Consejo Nacional de Ciencia y Tecnología
DS MINDS@UW
RD 31-ago-2024