Viruses (Mar 2023)

Evaluation of SARS-CoV-2 ORF7a Deletions from COVID-19-Positive Individuals and Its Impact on Virus Spread in Cell Culture

  • Maria Clara da Costa Simas,
  • Sara Mesquita Costa,
  • Priscila da Silva Figueiredo Celestino Gomes,
  • Nádia Vaez Gonçalves da Cruz,
  • Isadora Alonso Corrêa,
  • Marcos Romário Matos de Souza,
  • Marcos Dornelas-Ribeiro,
  • Tatiana Lucia Santos Nogueira,
  • Caleb Guedes Miranda dos Santos,
  • Luísa Hoffmann,
  • Amilcar Tanuri,
  • Rodrigo Soares de Moura-Neto,
  • Clarissa R. Damaso,
  • Luciana Jesus da Costa,
  • Rosane Silva

DOI
https://doi.org/10.3390/v15030801
Journal volume & issue
Vol. 15, no. 3
p. 801

Abstract

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The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing the COVID-19 outbreak, posed a primary concern of public health worldwide. The most common changes in SARS-CoV-2 are single nucleotide substitutions, also reported insertions and deletions. This work investigates the presence of SARS-CoV-2 ORF7a deletions identified in COVID-19-positive individuals. Sequencing of SARS-CoV-2 complete genomes showed three different ORF7a size deletions (190-nt, 339-nt and 365-nt). Deletions were confirmed through Sanger sequencing. The ORF7a∆190 was detected in a group of five relatives with mild symptoms of COVID-19, and the ORF7a∆339 and ORF7a∆365 in a couple of co-workers. These deletions did not affect subgenomic RNAs (sgRNA) production downstream of ORF7a. Still, fragments associated with sgRNA of genes upstream of ORF7a showed a decrease in size when corresponding to samples with deletions. In silico analysis suggests that the deletions impair protein proper function; however, isolated viruses with partial deletion of ORF7a can replicate in culture cells similarly to wild-type viruses at 24 hpi, but with less infectious particles after 48 hpi. These findings on deleted ORF7a accessory protein gene, contribute to understanding SARS-CoV-2 phenotypes such as replication, immune evasion and evolutionary fitness as well insights into the role of SARS-CoV-2_ORF7a in the mechanism of virus-host interactions.

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