Understanding the Role of SARS-CoV-2 ORF3a in Viral Pathogenesis and COVID-19.

Jiantao Zhang,J Marc Simard,Volodymyr Gerzanich,Mohamed Nasr,Amara Ejikemeuwa,Richard Y Zhao,Qiyi Tang

doi:10.3389/fmicb.2022.854567

Abstract

The ongoing SARS-CoV-2 pandemic has shocked the world due to its persistence, COVID-19-related morbidity and mortality, and the high mutability of the virus. One of the major concerns is the emergence of new viral variants that may increase viral transmission and disease severity. In addition to mutations of spike protein, mutations of viral proteins that affect virulence, such as ORF3a, also must be considered. The purpose of this article is to review the current literature on ORF3a, to summarize the molecular actions of SARS-CoV-2 ORF3a, and its role in viral pathogenesis and COVID-19. ORF3a is a polymorphic, multifunctional viral protein that is specific to SARS-CoV/SARS-CoV-2. It was acquired from β-CoV lineage and likely originated from bats through viral evolution. SARS-CoV-2 ORF3a is a viroporin that interferes with ion channel activities in host plasma and endomembranes. It is likely a virion-associated protein that exerts its effect on the viral life cycle during viral entry through endocytosis, endomembrane-associated viral transcription and replication, and viral release through exocytosis. ORF3a induces cellular innate and pro-inflammatory immune responses that can trigger a cytokine storm, especially under hypoxic conditions, by activating NLRP3 inflammasomes, HMGB1, and HIF-1α to promote the production of pro-inflammatory cytokines and chemokines. ORF3a induces cell death through apoptosis, necrosis, and pyroptosis, which leads to tissue damage that affects the severity of COVID-19. ORF3a continues to evolve along with spike and other viral proteins to adapt in the human cellular environment. How the emerging ORF3a mutations alter the function of SARS-CoV-2 ORF3a and its role in viral pathogenesis and COVID-19 is largely unknown. This review provides an in-depth analysis of ORF3a protein’s structure, origin, evolution, and mutant variants, and how these characteristics affect its functional role in viral pathogenesis and COVID-19.

Highlights

SARS-CoV-2 and Genome OrganizationSevere acute respiratory syndrome coronavirus 2 (SARSCoV-2) is an enveloped, positive-sense, single-stranded RNA (+ssRNA) virus that belongs to the genus Betacoronavirus of Coronaviridae family (Coronaviridae Study Group of the International Committee on Taxonomy of Viruses, 2020)
ORF3a protein has a number of well-conserved functional motifs (Figure 1B) that are presumably responsible for its multifunctionalities, including ion channel activity, viral replication, and cytopathogenic effects that link to COVID-19 (Issa et al, 2020; Kern et al, 2021)
A single a.a. change (Q57E) within TM1 at top of the cavity, or double mutations (S58L/Q116L) at the base of the TM2– TM3 grooves reduce Ca2+ and NMDG+ permeability without altering its Na+ or K+ permeability (Kern et al, 2021; Figure 3C). These data indicate that SARS-CoV-2 ORF3a may act as a non-selective cationic channel with a large pore and high single-channel conductance

Summary

INTRODUCTION

Severe acute respiratory syndrome coronavirus 2 (SARSCoV-2) is an enveloped, positive-sense, single-stranded RNA (+ssRNA) virus that belongs to the genus Betacoronavirus of Coronaviridae family (Coronaviridae Study Group of the International Committee on Taxonomy of Viruses, 2020). ORF3a protein has a number of well-conserved functional motifs (Figure 1B) that are presumably responsible for its multifunctionalities, including ion channel activity, viral replication, and cytopathogenic effects that link to COVID-19 (Issa et al, 2020; Kern et al, 2021). The main function of a viroporin affects virion morphogenesis, viral entry, viral replication, and virus release (egress; Nieva et al, 2012) Since both SARS ORF3a are transmembrane proteins with similar structures (Figure 2A) and SARS-CoV ORF3a is a viroporin (Lu et al, 2006; Castano-Rodriguez et al, 2018), it was predicted that SARS-CoV-2 ORF3a might be a viroporin. A single a.a. change (Q57E) within TM1 at top of the cavity, or double mutations (S58L/Q116L) at the base of the TM2– TM3 grooves reduce Ca2+ and NMDG+ permeability without altering its Na+ or K+ permeability (Kern et al, 2021; Figure 3C) These data indicate that SARS-CoV-2 ORF3a may act as a non-selective cationic channel with a large pore and high single-channel conductance. For more comprehensive reviews of ion channel activities and the differences between SARS-CoV ORF3a and SARS-CoV-2 ORF3a, see (McClenaghan et al, 2020; Gargan and Stevenson, 2021)

A Role of ORF3a-Mediated Ion Channel Activity in Viral Release

A Prominent Role of ORF3a in Virus Reproduction