tetano
Editor, Senior Moderator
Infect Genet Evol
. 2020 Sep 2;104525.
doi: 10.1016/j.meegid.2020.104525. Online ahead of print.
Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene
Filipe Pereira[SUP] 1 [/SUP]
Affiliations
Abstract
The new SARS-CoV-2 poses a significant threat to human health but many aspects of its basic biology remain unknown. Its genome encodes accessory genes that differ significantly within coronaviruses and contribute to the virus pathogenicity. Among accessory genes, open reading frame 8 (ORF8) stands out by being highly variable and showing structural changes suspected to be related with the virus ability to spread. However, the function of ORF8 remains to be elucidated, making it less studied than other SARS-CoV-2 genes. Here I show that ORF8 is poorly conserved among related coronaviruses. The ORF8 phylogeny built using 11,113 SARS-CoV-2 sequences revealed traces of a typical expanding population with a small number of highly frequent lineages. Interestingly, I detected several nonsense mutations and three main deletions in the ORF8 gene that either remove or significantly change the ORF8 protein. These findings suggest that SARS-CoV-2 can persist without a functional ORF8 protein. Deletion breakpoints were found located in predicted hairpins suggesting a possible involvement of these elements in the rearrangement process. Although the function of ORF8 remains to be elucidated, its structural plasticity and high diversity suggest an important role in SARS-CoV-2 pathogenicity.
Keywords: COVID-19; Coronaviruses; ORF8 deletions; RNA structures; SARS-CoV-2 phylogeny.
. 2020 Sep 2;104525.
doi: 10.1016/j.meegid.2020.104525. Online ahead of print.
Evolutionary dynamics of the SARS-CoV-2 ORF8 accessory gene
Filipe Pereira[SUP] 1 [/SUP]
Affiliations
- PMID: 32890763
- DOI: 10.1016/j.meegid.2020.104525
Abstract
The new SARS-CoV-2 poses a significant threat to human health but many aspects of its basic biology remain unknown. Its genome encodes accessory genes that differ significantly within coronaviruses and contribute to the virus pathogenicity. Among accessory genes, open reading frame 8 (ORF8) stands out by being highly variable and showing structural changes suspected to be related with the virus ability to spread. However, the function of ORF8 remains to be elucidated, making it less studied than other SARS-CoV-2 genes. Here I show that ORF8 is poorly conserved among related coronaviruses. The ORF8 phylogeny built using 11,113 SARS-CoV-2 sequences revealed traces of a typical expanding population with a small number of highly frequent lineages. Interestingly, I detected several nonsense mutations and three main deletions in the ORF8 gene that either remove or significantly change the ORF8 protein. These findings suggest that SARS-CoV-2 can persist without a functional ORF8 protein. Deletion breakpoints were found located in predicted hairpins suggesting a possible involvement of these elements in the rearrangement process. Although the function of ORF8 remains to be elucidated, its structural plasticity and high diversity suggest an important role in SARS-CoV-2 pathogenicity.
Keywords: COVID-19; Coronaviruses; ORF8 deletions; RNA structures; SARS-CoV-2 phylogeny.