Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis of SARS-CoV-2-Related Viruses

Abstract

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was recently identified as the causative agent for the coronavirus disease 2019 (COVID-19) outbreak that has generated a global health crisis. We use a combination of genomic analysis and sensitive profile-based sequence and structure analysis to understand the potential pathogenesis determinants of this virus. As a result, we identify several fast-evolving genomic regions that might be at the interface of virus-host interactions, corresponding to the receptor binding domain of the Spike protein, the three tandem Macro fold domains in ORF1a, and the uncharacterized protein ORF8. Further, we show that ORF8 and several other proteins from alpha- and beta-CoVs belong to novel families of immunoglobulin (Ig) proteins. Among them, ORF8 is distinguished by being rapidly evolving, possessing a unique insert, and having a hypervariable position among SARS-CoV-2 genomes in its predicted ligand-binding groove. We also uncover numerous Ig domain proteins from several unrelated metazoan viruses, which are distinct in sequence and structure but share comparable architectures to those of the CoV Ig domain proteins. Hence, we propose that SARS-CoV-2 ORF8 and other previously unidentified CoV Ig domain proteins fall under the umbrella of a widespread strategy of deployment of Ig domain proteins in animal viruses as pathogenicity factors that modulate host immunity. The rapid evolution of the ORF8 Ig domain proteins points to a potential evolutionary arms race between viruses and hosts, likely arising from immune pressure, and suggests a role in transmission between distinct host species. IMPORTANCE The ongoing COVID-19 pandemic strongly emphasizes the need for a more complete understanding of the biology and pathogenesis of its causative agent SARS-CoV-2. Despite intense scrutiny, several proteins encoded by the genomes of SARS-CoV-2 and other SARS-like coronaviruses remain enigmatic. Moreover, the high infectivity and severity of SARS-CoV-2 in certain individuals make wet-lab studies currently challenging. In this study, we used a series of computational strategies to identify several fast-evolving regions of SARS-CoV-2 proteins which are potentially under host immune pressure. Most notably, the hitherto-uncharacterized protein encoded by ORF8 is one of them. Using sensitive sequence and structural analysis methods, we show that ORF8 and several other proteins from alpha- and beta-coronavirus comprise novel families of immunoglobulin domain proteins, which might function as potential immune modulators to delay or attenuate the host immune response against the viruses.

Functional and druggability analysis of the SARS-CoV-2 proteome

“…The SARS-CoV-2 orf7a is a transmembrane protein of 121 amino acids (106 if only the mature protein is considered, excluding the signaling peptide), with 86% identity and 94% similarity with respect to its SARS-CoV counterpart. Interestingly, it exhibits structural similarity to Igs ( Nelson et al, 2005 ; Tan et al, 2020 ), but shares poor sequence identity with proteins of the Ig superfamily (within the 2–16% range). Like orf3a, orf7a is also included in the virion, and both proteins have been shown to interact with each other in SARS-CoV ( Tan et al, 2004 ) and in SARS-CoV-2 ( Li et al, 2020a ).…”

“…Orf8 is one of the fastest evolving genes in SARS-CoV-2, as can be inferred by its high variability ( Tan et al, 2020 ). The orf8 expression is not essential for SARS-CoV and SARS-CoV-2 replication; it was observed, however, that a 29 nucleotide deletion in SARS-CoV may correlate with milder disease ( Muth et al, 2018 ).…”

A unique view of SARS-CoV-2 through the lens of ORF8 protein

“…Among these accessory proteins, ORF8 is a significantly exclusive protein as it is different from another known SARS-CoV and thus associated with high efficiency in pathogenicity transmission [11,12]. The SARS-CoV-2 ORF8 displays arrays of functions; inhibition of interferon 1, promoting viral replication, inducing apoptosis and modulating ER stress [13,14,15].…”

Structure of SARS-CoV-2 ORF8, a rapidly evolving coronavirus protein implicated in immune evasion

“…A 382 nucleotide deletion (Δ382) in SARS-CoV-2 (9,10) was also found to correlate with milder disease and a lower incidence of hypoxia (11). SARS-CoV-2 ORF8 is a 121 amino acid protein consisting of an N-terminal signal sequence followed by a predicted Ig-like fold (12). With <20% sequence identity to SARS-CoV ORF8, SARS-CoV-2 ORF8 is remarkably divergent.…”

“…These observations show how recent evolutionary changes in the sequence of SARS-CoV-2 relative to its more benign precursors could contribute to a unique higher-order assembly mediating unique functions in immune evasion and suppression. (12). Asterisks designate residues contributing to the 'covalent' dimer interface.…”