A Rare Deletion in SARS-CoV-2 ORF6 Dramatically Alters the Predicted Three-Dimensional Structure of the Resultant Protein

Abstract

The function of the SARS-CoV-2 accessory protein p6, encoded by ORF6, is not fully known. Based upon its similarity to p6 from SARS-CoV, it may play a similar role, namely as an antagonist of type I interferon (IFN) signaling. Here we report the sequencing of a SARS-CoV-2 strain passaged six times after original isolation from a clinical patient in Hong Kong. The genome sequence shows a 27 nt in-frame deletion (Δ27,264-27,290) within ORF6, predicted to result in a 9 aa deletion (ΔFKVSIWNLD) from the central portion of p6. This deletion is predicted to result in a dramatic alteration in the three-dimensional structure of the resultant protein (p6 Δ22-30 ), possibly with significant functional implications. Analysis of the original clinical sample indicates that the deletion was not present, while sequencing of subsequent passages of the strain identifies the deletion as a majority variant. This suggests that the deletion originated ab initio during passaging and subsequently propagated into the majority, possibly due to the removal of selective pressure through the IFN-deficient Vero E6 cell line. The specific function of the SARS-CoV-2 p6 N-terminus, if any, has not yet been determined. However, this deletion is predicted to cause a shift from N-endo to N-ecto in the transmembrane localization of the SARS-CoV-2 p6 Δ22-30 N-terminus, possibly leading to the ablation of its native function.

A novel cell culture system modeling the SARS-CoV-2 life cycle

“…Additionally, we found that the subgenomic RNAs of ORF6, ORF7 and ORF8 were dramatically decreased in the P10-trVLP infected cells compared with that of P1 VLP (Fig. 3E), indicating that ORF6, ORF7 and ORF8 may not be required for virus infection at least in vitro, consistent with other reports that deletions of these regions were observed in clinical samples by deep sequencing analysis [17][18][19][20] .…”

Characterization of SARS-CoV-2 ORF6 deletion variants detected in a nosocomial cluster during routine genomic surveillance, Lyon, France

“…Here, we characterized large ORF6 deletion variants identified through surveillance of patients from the same hospital unit. Reports of similar patterns of genomic deletions in the SARS-CoV-2 genome since its emergence have already been described, including in the ORFs 6,7,and 8 [20,21,29,32].…”

Effects of SARS-CoV-2 Mutations on Protein Structures and Intraviral Protein-Protein Interactions

“…Non-synonymous mutations cause amino acid substitutions, and could alter virus protein structures, which may affect viral reproduction, leading to false-negative diagnoses and drug resistance. It is reported that the depletion of nine amino acids in SARS-CoV-2 Orf6 resulted in a dramatic alteration of protein structure and caused a shift in its transmembrane localization, which would lead to drug resistance of interferon (IFN) [4].…”