A polymorphic residue that attenuates the antiviral potential of interferon lambda 4 in hominid lineages

Abstract

As antimicrobial signalling molecules, type III or lambda interferons (IFNλs) are critical for defence against infection by diverse pathogens, including bacteria, fungi and viruses. Counter-intuitively, expression of one member of the family, IFNλ4, is associated with decreased clearance of hepatitis C virus (HCV) in the human population; by contrast, a natural frameshift mutation that abrogates IFNλ4 production improves HCV clearance. To further understand how genetic variation between and within species affects IFNλ4 function, we screened a panel of all known extant coding variants of human IFNλ4 for their antiviral potential and identify three that substantially affect activity: P70S, L79F and K154E. The most notable variant was K154E, which was found in African Congo rainforest ‘Pygmy’ hunter-gatherers. K154E greatly enhanced in vitro activity in a range of antiviral (HCV, Zika virus, influenza virus and encephalomyocarditis virus) and gene expression assays. Remarkably, E154 is the ancestral residue in mammalian IFNλ4s and is extremely well conserved, yet K154 has been fixed throughout evolution of the hominid genus Homo, including Neanderthals. Compared to chimpanzee IFNλ4, the human orthologue had reduced activity due to amino acid K154. Comparison of published gene expression data from humans and chimpanzees showed that this difference in activity between K154 and E154 in IFNλ4 correlates with differences in antiviral gene expression in vivo during HCV infection. Mechanistically, our data show that the human-specific K154 negatively affects IFNλ4 activity through a novel means by reducing its secretion and potency. We thus demonstrate that attenuated activity of IFNλ4 is conserved among humans and postulate that differences in IFNλ4 activity between species contribute to distinct host-specific responses to—and outcomes of—infection, such as HCV infection. The driver of reduced IFNλ4 antiviral activity in humans remains unknown but likely arose between 6 million and 360,000 years ago in Africa.

Interferon lambda 4 impacts the genetic diversity of hepatitis C virus

“…Using these data, we observed that the haplotype coding for the IFN-λ4-S70 variant had a smaller effect on viral amino acid variability compared to the haplotype coding for the IFN-λ4-P70 variant. This observation agrees with previous independent studies showing the reduced antiviral activity for IFN-λ4-S70 in vitro (Bamford et al, 2018; Terczyńska-Dyla et al, 2014). Moreover, the mean viral load in IFN-λ4-Null carrying patients was similar to those carrying the IFN-λ4-S70 variant; by contrast, those carrying an IFN-λ4-P70 variant had a reduced viral load, which correlates with its higher antiviral activity.…”

“…This variant [ΔG > TT] causes a frameshift, abrogating production of functional IFN-λ4 protein (Prokunina-Olsson et al, 2013). Moreover, several amino acid substitutions within IFN-λ4 have been shown to alter its antiviral activity (Bamford et al, 2018; Terczyńska-Dyla et al, 2014). In particular, a common amino acid substitution (coded by the SNP rs117648444 [G > A]) in the IFN-λ4 protein, which changes a proline residue at position 70 (P70) to a serine residue (S70), reduces its antiviral activity in vitro (Terczyńska-Dyla et al, 2014).…”

An interferon lambda 4-associated variant in the hepatitis C virus RNA polymerase affects viral replication in infected cells

“…These results were similar to our previous analyses (11). SGRs containing mutations had reduced replication in EGFP-CM-treated cells compared to WT (Fig 2C), consistent with data presented in Fig 2A at 48hpt (Fig 2A).…”

“…One of our main objectives in the study was to examine whether A150V, which is associated with host IFNL4 genotype, would affect multicycle HCV replication in the presence or absence of IFNλ4 using an in vitro model system. We have previously established a system to test the antiviral activity of WT human IFNλ3 and IFNλ4 on HCV infection (11). Huh7 cells, treated with exogenous transfected-cell 'conditioned media' (CM) containing IFNs, were transfected with WT and mutant SGR RNAs or infected with WT and mutant HCVcc; GLuc activity was assayed at 48hpt (for SGR) and viral RNA measured at 72hpi (for HCVcc).…”

Bovine Interferon Lambda Is a Potent Antiviral Against SARS-CoV-2 Infection in vitro

“…One of the limitations of using human IFN-λ as a universal therapeutic molecule resides in the fact that it has several genetic variants (20,21) that might have different stability and affinity in the interaction with the IFNLR. Engineering of IFN-λ to assess natural or in silico predicted mutations critical to maintaining the antiviral activity proved that the strength of the interaction of between IFN-λ and its receptor could modulate downstream functions (22)(23)(24)(25)(26).…”