Genomic surveillance of SARS-CoV-2 Spike gene by sanger sequencing

PLoS One. 2022 Jan 20;17(1):e0262170. doi: 10.1371/journal.pone.0262170. eCollection 2022.

Abstract

The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike gene. Monitoring the S gene mutations is crucial for successful controlling measures and detecting variants that can evade vaccine immunity. Even after the costs reduction resulting from the pandemic, the new generation sequencing methodologies remain unavailable to a large number of scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S gene, this work describes a new feasible protocol for complete nucleotide sequencing of the S gene using the Sanger technique. Such a methodology could be easily adopted by any laboratory with experience in sequencing, adding to effective surveillance of SARS-CoV-2 spreading and evolution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Brazil / epidemiology
  • COVID-19 / diagnosis*
  • COVID-19 / epidemiology*
  • COVID-19 / virology
  • COVID-19 Nucleic Acid Testing / methods*
  • Diagnostic Tests, Routine / methods
  • Electrophoresis, Agar Gel / methods
  • Epidemiological Monitoring
  • Genes, Viral*
  • Humans
  • Mutation
  • Pandemics / prevention & control*
  • RNA, Viral / genetics
  • RNA, Viral / isolation & purification
  • Reverse Transcriptase Polymerase Chain Reaction / methods*
  • SARS-CoV-2 / genetics*
  • Sequence Analysis, RNA / methods*
  • Spike Glycoprotein, Coronavirus / genetics*

Substances

  • RNA, Viral
  • Spike Glycoprotein, Coronavirus
  • spike protein, SARS-CoV-2

Grants and funding

This work was material supported by Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro-FAPERJ [grant number E-26/201.840/2017] (RCA) and Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES) – Public Notice Number 09/2020 - Prevention and Combat against Outbreaks, Endemics, Epidemics and Pandemics. Process number 223038.014313/2020-19 (TSS and FBC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.