In a recent study published in PNAS, researchers compared the potency of 17 human interferons (IFNs) against multiple variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent variants of concern (VOCs) of SARS-CoV-2 showed increased resistance to IFN, indicating that evasion of innate immunity or human IFNs could be a driving force in the evolution of SARS – CoV-2.
Study: Interferon resistance of emerging SARS-CoV-2 variants. Image credit: WhiteDragon/Shutterstock
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Previous studies have linked the emergence of SARS-CoV-2 variants to spike (S) mutations. However, studies have not uncovered the role of other viral protein mutations that can inhibit human IFNs, for example, IFNα2 and IFNβ, which are being repurposed for the treatment of coronavirus disease 2019 (COVID-19 ).
About the study
In the present study, the researchers obtained representative isolates of SARS-CoV-2 from lineages B, B.1, B.1.1.7, and B.1.351 from beiresources.org. They incubated human alveolar epithelial cell line type II (A549)-angiotensin-converting enzyme 2 (ACE2) cells with 17 recombinant IFNs overnight in parallel and in triplicate. They infected these cells with a non-saturating dose of virus for 2 hours.
They used a quantitative polymerase chain reaction (qPCR) assay to determine the amounts of virus produced 24 hours after infection. The researchers also evaluated the qPCR assay against a VeroE6 plaque assay using triplicate serial dilutions of SARS-CoV-2 isolate B.1.351, with one plaque-forming unit detected by this assay corresponding to ∼900 nucleocapsids 1 of SARS-CoV-2 (N1). ) copies.
In addition, the team used immunofluorescence to quantify the number of viral copies in primary airway epithelial cells infected with different SARS-CoV-2 variants. Finally, they generated a heat map to visualize the antiviral potency of the 17 IFNs against the five SARS-CoV-2 isolates.
Results of the study
Although the doses of IFNβ and IFNλ1 did not substantially affect cell viability, a 2-picomolar (pM) concentration maximally distinguished the antiviral activities of IFNβ and IFNλ1, two widely divergent IFNs. Although the authors observed a strong correlation between the virus titers obtained using the two assays, compared to the VeroE6 plate assay, the qPCR assay robustly distinguished the antiviral activity of the different IFNs.
All 17 IFNs showed antiviral activities against SARS-CoV-2, with a correlation observed between IFN potencies against the five isolates. All three IFNλ subtypes showed antiviral activities of none to less than twofold compared to most IFN-Is. IFNα8, IFNβ, and IFNω were the most potent, type III IFNs (λ) the least potent, and IFNα5, IFNα17, and IFNα14 showed moderate potency.
The heat map data confirmed that the IFN resistance of the emerging SARS-CoV-2 variants was particularly striking compared to the ancestral USA-WA1/2020 strain, with an IFN-I resistance of 25 to 322 times greater. However, the study’s experiments did not reveal how different doses of IFN-I affected the replication of all SARS-CoV-2 strains. It was also unclear whether the emerging variants were resistant to IFN-III. Inhibition curves for five IFNs showed that IFNλ1 had a 100-fold higher mean inhibitory concentration (IC50) than IFNα2, which exhibited 14-fold higher IC50 than IFNβ, IFNα5, and IFNα8. Both IFNβ and IFNλ1 similarly inhibited A and B isolate lineages.
Interestingly, both IFNβ and IFNλ1 failed to achieve maximal inhibition against VOC alpha, saturating at levels 15- to 20-fold higher than the lineage B isolate. In particular, Omicron had the highest levels of virus replication residual at the highest doses of one of the most potent IFNs, IFNβ.
Conclusions
The study demonstrated the antiviral potency of various human IFNs in a specific order, indicating how SARS-CoV-2 evolved after host switching to become more resistant to human IFNs. The study’s findings could help identify IFN subtypes that might be most useful in treating early SARS-CoV-2 infections. For example, for SARS-CoV-2, higher doses of IFNλ were required to achieve a similar antiviral effect in vivo, as IFN-Is and IFNβ showed potential as therapeutics against COVID-19 .
Among the IFNα subtypes, IFNα8 showed anti-SARS-CoV-2 potency similar to that of IFNβ. It also showed high antiviral activity against human immunodeficiency virus 1 (HIV-1), raising a potential treatment approach for both viruses. While IFNα6 restricted HIV-1, IFNα subtypes were weakest against SARS-CoV-2. In contrast, IFNα5 strongly inhibited SARS-CoV-2 but weakly inhibited HIV-1. Genes limiting IFN responses to emerging SARS-CoV-2 variants suggested that IFNs may also influence the evolution of SARS-CoV-2. Similarly, previous studies with HIV-1 suggested that IFNs may shape the evolution of pandemic viruses.
Overall, the current study reinforced the importance of continued genomic surveillance of SARS-CoV-2 to assess emerging variants that evade host IFN responses. Indeed, the role of the innate immune response in driving the evolution of SARS-CoV-2 could have implications for IFN-based therapies.