Adaptive immunity in patients infected with SARS-CoV-2 Δ382 Variant

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first reported in Wuhan, China in 2019 and is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. SARS-CoV-2 is highly contagious, virulent, and has claimed more than 5 million lives worldwide.

Study: Robust virus-specific adaptive immunity in COVID-19 patients with SARS-CoV-2 Δ382 variant infection. Image credit: Kari_Bonit /

The emergence of SARS-CoV-2 variants

Due to genetic mutations of SARS-CoV-2, several variants have emerged, some of which have been classified as either variants of concern (VOC) or variants of interest (VOI). Some of the SARS-CoV-2 VOCs including the B.1.1.7 (Alpha), P.1 (Gamma), B.1.351 (Beta) and B.1.617.2 (Delta) variants are more contagious than the original strain and may also evade the immune protection induced after COVID-19 vaccination or natural infection. At present, the Delta variant is the dominant circulating variant worldwide and has threatened the efficacy of the available COVID-19 vaccines.

Researchers have stated that it is imperative to determine the effects of various mutations present in the VOCs on the host’s immune response elicited through either vaccination or natural infection. The alpha, gamma, and delta variants contain a deletion at the open reading frame 8 region (ORF8), rendering them inactive.

Interestingly, between 2002-2003, ORF8 was identified as a mutation hotspot in SARS-CoV. This mutation is associated with host adaptation and viral replication.

SARS-CoV-2 Δ382 variants

In Singapore and Taiwan, SARS-CoV-2 variants with 382 nucleotide (nt) deletion in the ORF8 regions have been identified and designated Δ382 SARS-CoV-2. SARS-CoV-2 variants with a mutation in the ORF8 region have also been identified in Australia (138-nt deletion), Bangladesh (345-nt deletion) and Spain (52-nt deletion).

Although deletion mutation at ORF8 of SARS-CoV-2 is associated with a mild infection, it accounts for about 5% of infections worldwide. Therefore, understanding the mechanism behind the mild infection would provide better insight into improved handling of SARS-CoV-2 transmission and treatment. In addition, this finding would shed light on the reason behind the high transferability of dominant VOCs.

Although more in vitro studies have shown that SARS-CoV-2 ORF8 downregulates major histocompatibility complex (MHC) I molecules and blocks the type I interferon (IFN) signaling pathway, the functional effects of the ORF8 deletion on the cellular host’s immune response to SARS-CoV-2 are not clear .

To address this research gap and to understand the molecular mechanisms of this natural genetic deletion, a comprehensive characterization of whole blood transcriptomic profiles and adaptive immune responses between SARS-CoV-2 infected wild-type (WT) and Δ382 SARS-CoV-2 was recently performed. by scientists in Singapore. The research is published in Journal of Clinical Immunology.

Survey results

In the current study, researchers performed a high-density ribonucleic acid (RNA) sequencing (RNA-seq) that clearly shows different transcriptomic profiles between WT and Δ382 SARS-CoV-2 strains.

Transcriptomic profiles of patients infected with Δ382 induced more active cellular stress response and an upregulated eIF2 signaling. This finding is consistent with previous studies reporting that coronaviruses elicited cellular stress responses after infection by targeting unfolded protein response (UPR) pathways. As a result, these responses lead to an imbalance in cellular homeostasis and trigger endoplasmic reticulum (ER) stress by specifically targeting activating transcription factor 6 (ATF6), which in turn promotes viral replication.

The authors indicated that the SARS-CoV-2 ORF8 protein triggers protein kinase RNA-like ER kinase (PERK) and eIF2 signaling mechanisms.

The researchers also reported an underexpression of neutrophil activation-associated signature in Δ382 SARS-CoV-2 infected patients. In addition, strong evidence for effector cytotoxic genes was observed, as well as upregulation of SARS-CoV-2-specific T cell immunity and antibody responses, all of which strongly indicated robust T and B cell responses.

Previous studies have also reported that SARS-CoV-2 ORF8 interacts with MHC-I molecules and subsequently downregulates the cytotoxic functions of T lymphocytes. In the current study, the researchers found the presence of several cytotoxic effect genes such as GZMA, GZMB, ID2 and PLAC8 in Δ382 SARS-CoV-2 infected patients.

The researchers also analyzed the plasma of these patients and reported elevated levels of IFN-γ, tumor necrosis factor α (TNF-α) and interleukin 2 (IL-2) during the acute phase of viral infection. These results are consistent with previous reports showing high effector populations with a cytotoxic phenotype associated with effector CD8 +, mucosal-associated invariant T cells (MAIT) and natural killer (NK) T cells in COVID-19 patients with milder symptoms.

The current study also revealed that the deletion of ORF8 could result in increased immunogenicity against SARS-CoV-2. Interestingly, Δ382-infected individuals showed higher immunoglobulin G (IgG) levels in the early acute phase of the infection. However, several studies are needed for a complete understanding of the roles of IgG in SARS-CoV-2 infection.

The researchers also found lower pro-inflammatory cytokines, chemokines and growth factors in Δ382 SARS-CoV-2 infected patients. These factors are strongly associated with severe COVID-19. Pro-inflammatory Th1 responses were found to be more prominent in WT-infected patients.

Molecular mechanisms underlying the milder disease phenotype in Δ382 SARS-CoV-2 infections. A SARS-CoV-2 variant with a 382 nucleotide deletion (Δ382) truncates ORF7b and removes ORF8 transcriptional regulatory sequence, eliminating ORF8 transcription. The ORF8 382-nt deletion has recently been associated with a milder disease phenotype. The attenuation of SARS-CoV-2 ORF8 upregulates eIF2 signaling and cellular stress responses in the acute phase of the infection, potentially interrupting the downregulation of MHC-I molecules by ORF8 and also increasing the activation of both CD4+ and CD8+ T cells, detected by enrichment of effector cytotoxic genes and upregulation of SARS-CoV-2 specific T cell responses in Δ382 SARS-CoV-2 infected patients. Enhanced T cell responses may again mediate rapid and effective antibody responses in Δ382 SARS-CoV-2 infection. More pronounced cellular stress responses may further reduce systemic inflammation and dysfunctional neutrophils in Δ382 SARS-CoV-2 infected patients. Overall, the attenuation of SARS-CoV-2 ORF8 produced a molecular phenotype characterized by more pronounced cellular stress responses and a less dysregulated immune phenotype with more robust T and B cell responses.


Some of the limitations of this study include a limited number of Δ382 SARS-CoV-2 infections for analysis. In addition, the host’s genetic background and demographic data were not evaluated.

However, the main outcome of this study is the functional implication of ORF8 on the host’s immune surveillance. This indicates the use of ORF8 as a possible target for COVID-19 therapy. However, due to mutation, the rapid development of the ORF8 gene compromises its suitability as an antiviral target.

In the future, research related to engineered viruses and animal models may further elucidate the interactions and mechanisms between ORF8 and ER stress or T cell responses during SARS-CoV-2 infection.


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