SARS-CoV-2 Variants of Concern: Presumptive Identification via Sanger Sequencing Analysis of the Receptor Binding Domain (RBD) Region of the S Gene

• Published in: Diagnostics (Basel) Vol. 13; no. 7; p. 1256
• Main Authors: Rodrigues, Grazielle Motta, Volpato, Fabiana Caroline Zempulski, Wink, Priscila Lamb, Paiva, Rodrigo Minuto, Barth, Afonso Luís, de-Paris, Fernanda
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 27-03-2023; MDPI
• Subjects: Brief Report; Genomes; Mutation; Proteins; RBD; Sanger sequencing; SARS-CoV-2; Severe acute respiratory syndrome coronavirus 2; Software; Surveillance; VOCs; United States > US; VOCs; SARS-CoV-2; Sanger sequencing; RBD
• ISSN: 2075-4418; 2075-4418
• DOI: 10.3390/diagnostics13071256

Variants of concern (VOCs) of SARS-CoV-2 are viral strains that have mutations associated with increased transmissibility and/or increased virulence, and their main mutations are in the receptor binding domain (RBD) region of the viral spike. This study aimed to characterize SARS-CoV-2 VOCs via Sanger sequencing of the RBD region and compare the results with data obtained via whole genome sequencing (WGS). Clinical samples (oro/nasopharyngeal) with positive RT-qPCR results for SARS-CoV-2 were used in this study. The viral RNA from SARS-CoV-2 was extracted and a PCR fragment of 1006 base pairs was submitted for Sanger sequencing. The results of the Sanger sequencing were compared to the lineage assigned by WGS using next-generation sequencing (NGS) techniques. A total of 37 specimens were sequenced via WGS, and classified as: VOC gamma (8); delta (7); omicron (10), with 3 omicron specimens classified as the BQ.1 subvariant and 12 specimens classified as non-VOC variants. The results of the partial Sanger sequencing presented as 100% in agreement with the WGS. The Sanger protocol made it possible to characterize the main SARS-CoV-2 VOCs currently circulating in Brazil through partial Sanger sequencing of the RBD region of the viral spike. Therefore, the sequencing of the RBD region is a fast and cost-effective laboratory tool for clinical and epidemiological use in the genomic surveillance of SARS-CoV-2.