How SARS-CoV-2 variant B.1.1.7 adapted to evade innate immunity

Researchers in the United States and the UK have conducted a study showing how the B.1.1.7 (Alpha) lineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) adapted to suppress host innate immune responses in lung epithelial cells.

The SARS-CoV-2 virus is the agent responsible for the coronavirus disease 2019 (COVID-19) pandemic that continues to threaten global public health and has now claimed the lives of more than 3.74 million people worldwide.

Nevan Krogan from the Quantitative Biosciences Institute (QBI) Coronavirus Research Group in San Francisco, California, and colleagues found that B.1.1.7 isolates have dramatically increased levels of subgenomic RNA and increased expression of innate immune antagonists.

“Our data reveal how the SARS-CoV-2 B.1.1.7 lineage has adapted to the host by enhancing antagonism of the innate immune response,” writes the team. “We propose that enhanced innate immune antagonism by the B.1.1.7 lineage contributes to its transmission advantage.”

The team says the findings have important implications for management of the ongoing pandemic and that expanding ongoing sequencing efforts to monitor subgenomic RNA levels will be critical in the identification of future SARS-CoV-2 variants of concern.

A pre-print version of the research paper is available on the bioRxiv* server, while the article undergoes peer review.

More about the B.1.1.7 variant

Following its initial detection in the UK in September 2020, the B.1.1.7 lineage of SARS-CoV-2 rapidly became the dominant variant worldwide.

Due to its increased transmissibility and potential threat to public health containment measures, the B.1.1.7 lineage was categorized as a variant of concern by Public Health England in December 2020.

The B.1.1.7 variant contains 23 mutations, eight of which lie in the viral spike protein. This spike mediates the initial stage of the infection process by binding to the human host cell receptor angiotensin-converting enzyme 2 (ACE2).

While research efforts have focused on this adaption of the spike protein for viral entry and immune escape, little attention has been paid to B.1.1.7 variant of concern (VOC)-defining mutations lying outside of the spike that may contribute to the transmission advantage.

Most B.1.1.7 mutations are found in the non-structural proteins Nsp3 and Nsp6, the accessory protein Orf8, and the nucleocapsid protein, all of which have previously been shown to modulate the innate immune response.

“Furthermore, it is not yet clear whether any of the B.1.1.7-specific mutations impact the expression levels of viral proteins,” says Krogan and colleagues.

“In sum, the impact of these additional mutations on viral replication, transmission and pathogenesis has not been characterized,” they write. “Innate immune responses can exert strong selective pressure during viral transmission and play an important role in determining clinical outcomes to SARS-CoV-2 infection.”

What did the current study involve?

Using the Calu-3 human lung epithelial cell model, the researchers investigated differences between B.1.1.7 isolates and “wave one” SARS-CoV-2 viruses.

Studies that employed unbiased abundance proteomics, phosphoproteomics, messenger RNA (mRNA) sequencing and viral replication assays showed that B.1.1.7 isolates are more effective at suppressing host innate immune responses in these airway epithelial cells.

SARS-CoV-2 B.1.1.7 antagonises innate immune activation more efficiently than earlylineage isolates. a. SARS-CoV-2 viruses compared in this study. Protein coding changes in B.1.1.7
SARS-CoV-2 B.1.1.7 antagonizes innate immune activation more efficiently than early lineage isolates. a. SARS-CoV-2 viruses compared in this study. Protein coding changes in B.1.1.7 (red), IC19 (grey) and VIC (blue) are indicated in comparison to the Wuhan-Hu-1 reference genome (MN908947). B.1.1.7 changes include 23 lineage-defining mutations, plus additional changes compared to Wuhan-Hu-1, totaling 29. b and c. Calu-3 cells were infected with either (b) 5000 E copies/cell or (c) 5 E copies/cell of B.1.1.7, VIC and IC19. Measurements of replication of SARS-CoV-2 genomic and subgenomic E RNAs (RT-qPCR) (left), % infection by intracellular nucleocapsid positivity (center) or infectious virion production by TCID50/ml (right) over time are shown. d and e. Fold induction of IFNβ gene expression and protein secretion over time from cells in (b) and (c) respectively. f. Replication (24hpi), IFNβ induction (24hpi) and IFNβ secretion (48hpi) by multiple independent B.1.1.7 isolates compared to IC19 and VIC at 250 E copies/cell. g. SARS-CoV-2 infection at 2000 E copies/cell after 8h pre-treatment with IFNβ at the indicated concentrations. Infection is shown as intracellular N levels normalized to untreated controls at 24hpi. Data shown are mean +/- SEM of one of three representative experiments performed in triplicate. Statistical comparisons are performed by Two Way ANOVA (a,b,c,d,g) or One Way ANOVA with a Tukey post-comparison test (f). Blue stars indicate comparison between B.1.1.7 and VIC (blue lines and symbols), grey stars indicate comparison between B.1.1.7 and IC19 (grey lines and symbols). * (p<0.05), ** (p<0.01), *** (p<0.001), **** (p<0.0001). ns: non-significant. E: viral envelope gene. Hpi: hours post-infection.

Strikingly, the team found that B.1.1.7 isolates have dramatically increased levels of subgenomic RNA and increased expression of the key viral innate antagonists Orf9b and Orf6.

“This remarkable and novel observation suggests evolution of B.1.1.7 nucleotide sequences that modulate specific single-guide RNA (sgRNA) production, and selection for increased sgRNA synthesis and protein expression,” writes Krogan and colleagues.

Inhibition of innate immunity by Orf9b may be regulated by the host innate response itself

The researchers found that expression of Orf9b alone suppressed the innate immune response through interaction with the mitochondrial protein TOM70, which is involved in the activation of mitochondrial antiviral signaling.

However, the study also revealed that Orf9b activation is regulated by phosphorylation.

“It is striking that Orf9b is not only enhanced in expression in B.1.1.7, but appears to be regulated by phosphorylation, which is, in turn, particularly repressed during B.1.1.7 infection,” say the researchers.

Krogan and colleagues say this suggests that inhibition of innate immunity by Orf9b is regulated by the host innate response itself.

Model schematic depicting how B.1.1.7 antagonises innate immune activation. Highly transmissible SARS-CoV-2 B.1.1.7 has evolved to more effectively antagonise the innate immune response. SARS-CoV-2 wave one isolates activate a delayed innate response in airway epithelial cells relative to rapid viral replication, indicative of viral antagonism of innate immune responses early in infection. It is known that Orf9b, Orf6 and N are innate immune antagonists, acting at different levels to inhibit RNA sensing. Orf6 inhibits IRF3 and STAT1 nuclear translocation13,24, N prevents activation of RNA sensor RIG-I16 and here we show that Orf9b inhibits RNA sensing through interaction with TOM70 regulated by phosphorylation. We find that B.1.1.7 has evolved to produce more sgRNA for these key innate immune antagonists leading to increased protein levels and enhanced innate immune antagonism as compared to first wave isolates.
Model schematic depicting how B.1.1.7 antagonizes innate immune activation. Highly transmissible SARS-CoV-2 B.1.1.7 has evolved to more effectively antagonize the innate immune response. SARS-CoV-2 wave one isolates activate a delayed innate response in airway epithelial cells relative to rapid viral replication, indicative of viral antagonism of innate immune responses early in infection. It is known that Orf9b, Orf6 and N are innate immune antagonists, acting at different levels to inhibit RNA sensing. Orf6 inhibits IRF3 and STAT1 nuclear translocation13,24, N prevents activation of RNA sensor RIG-I16 and here we show that Orf9b inhibits RNA sensing through interaction with TOM70 regulated by phosphorylation. We find that B.1.1.7 has evolved to produce more sgRNA for these key innate immune antagonists leading to increased protein levels and enhanced innate immune antagonism as compared to first wave isolates.

Unphosphorylated Orf9b was maximally active during the early stage of infection, which enabled effective innate antagonism and, therefore, viral production. However, as host activation began, Orf9b was phosphorylated and switched off to enable innate immune activation.

“Such an inflammatory switch may have evolved by coronaviruses to enhance transmission by increasing inflammation at the site of infection once virus production is high, leading to symptoms that promote transmission such as mucosal secretions and coughing,” suggests the team.

Monitoring subgenomic RNA levels will be critical in the identification of future variants

Krogan and colleagues say the findings have important implications for managing the ongoing COVID-19 pandemic.

“It is expected that expanding ongoing sequencing efforts to monitor subgenomic RNA levels will be critical in the identification of future SARS-CoV-2 variants of concern,” they write.

“Our findings highlight the importance of studying changes outside Spike to understand the phenotype of B.1.1.7, other current variants, and future variants, and to emphasize the importance of innate immune evasion in the ongoing process of adaptation of SARS-CoV-2 to a new host,” concludes the team.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:
Sally Robertson

Written by

Sally Robertson

Sally first developed an interest in medical communications when she took on the role of Journal Development Editor for BioMed Central (BMC), after having graduated with a degree in biomedical science from Greenwich University.

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