Variabilidade do gene S do novo coronavírus em pacientes atendidos no complexo Hospitalar Professor Edgard Santos-UFBA

Abstract

Introduction: COVID-19 is a new disease caused by a human coronavirus, whose etiological agent is SARS-CoV-2. Two years have passed and SARS-CoV-2 has a great genetic diversity, which favored the emergence of emergency variants during different periods of the pandemic. Due to the importance employed in viral surveillance and the limitations found in new generation sequencing platforms, the objective of this work was to identify the variability in the Spike region of SARS-CoV2, from a Sanger sequencing platform, in patients with COVID-19 treated at the University Hospital Professor Edgard Santos in Salvador-BA. Methods: This is a cross-sectional observational study with preserved samples, positive for SARS-CoV2, of individuals over 18 years of age, employees, or patients, treated at the Professor Edgard Santos University Hospital (HUPES). All samples from the enrolled participants were confirmed for COVID-19 by an RT-qPCR assay. The extracted viral genetic material was used for a NESTED-PCR assay on the SARS-CoV-2 S gene and the results revealed on a 1.5% agarose gel. The sequencing reaction using the BigDye Terminator V3.1 Cycle Senquencing kit was performed in a region of 1,120 base pairs and the result of this reaction was read by the SeqStudio capillary electrophoresis machine. The files of sequences generated by the machine were analyzed for the construction of the consensus sequence from the reference sequence and identification of mutations throughout the genome. Results: Of all 103 sequenced samples, 69 contained relevant variants represented by 20 BA.1, 13 delta, 22 gamma and 14 zeta, identified between June 2020 and February 2022. All sequences found were aligned with sequences representative of the variants. Conclusions: The protocol developed by this work was able to identify and monitor the variability of the SARS-CoV-2 S gene and, consequently, identify the most relevant variants for the pandemic, which could be an alternative methodology for viral molecular surveillance.