tetano
Editor, Senior Moderator
Viruses
. 2023 Mar 21;15(3):801.
doi: 10.3390/v15030801.
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[SUP] 1 [/SUP], Sara Mesquita Costa[SUP] 1 2 [/SUP], Priscila da Silva Figueiredo Celestino Gomes[SUP] 1 3 [/SUP], Nádia Vaez Gonçalves da Cruz[SUP] 4 [/SUP], Isadora Alonso Corrêa[SUP] 2 [/SUP], Marcos Romário Matos de Souza[SUP] 2 [/SUP], Marcos Dornelas-Ribeiro[SUP] 4 [/SUP], Tatiana Lucia Santos Nogueira[SUP] 4 [/SUP], Caleb Guedes Miranda Dos Santos[SUP] 4 [/SUP], Luísa Hoffmann[SUP] 5 [/SUP], Amilcar Tanuri[SUP] 6 [/SUP], Rodrigo Soares de Moura-Neto[SUP] 6 [/SUP], Clarissa R Damaso[SUP] 1 [/SUP], Luciana Jesus da Costa[SUP] 2 [/SUP], Rosane Silva[SUP] 1 [/SUP]
Affiliations
Abstract
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.
Keywords: B.1.1.33 lineage; COVID-19; ORF7a; SARS-CoV-2; sgRNAs; viral fitness.
. 2023 Mar 21;15(3):801.
doi: 10.3390/v15030801.
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[SUP] 1 [/SUP], Sara Mesquita Costa[SUP] 1 2 [/SUP], Priscila da Silva Figueiredo Celestino Gomes[SUP] 1 3 [/SUP], Nádia Vaez Gonçalves da Cruz[SUP] 4 [/SUP], Isadora Alonso Corrêa[SUP] 2 [/SUP], Marcos Romário Matos de Souza[SUP] 2 [/SUP], Marcos Dornelas-Ribeiro[SUP] 4 [/SUP], Tatiana Lucia Santos Nogueira[SUP] 4 [/SUP], Caleb Guedes Miranda Dos Santos[SUP] 4 [/SUP], Luísa Hoffmann[SUP] 5 [/SUP], Amilcar Tanuri[SUP] 6 [/SUP], Rodrigo Soares de Moura-Neto[SUP] 6 [/SUP], Clarissa R Damaso[SUP] 1 [/SUP], Luciana Jesus da Costa[SUP] 2 [/SUP], Rosane Silva[SUP] 1 [/SUP]
Affiliations
- PMID: 36992509
- DOI: 10.3390/v15030801
Abstract
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.
Keywords: B.1.1.33 lineage; COVID-19; ORF7a; SARS-CoV-2; sgRNAs; viral fitness.