HIV-1 Vpr antagonizes innate immune activation by targeting karyopherin-mediated NF-κB/IRF3 nuclear transport.

HIV-1 must replicate in cells that are equipped to defend themselves from infection through intracellular innate immune systems. HIV-1 evades innate immune sensing through encapsidated DNA synthesis and encodes accessory genes that antagonize specific antiviral effectors. Here, we show that both particle associated, and expressed HIV-1 Vpr, antagonize the stimulatory effect of a variety of pathogen associated molecular patterns by inhibiting IRF3 and NF-κB nuclear transport. Phosphorylation of IRF3 at S396, but not S386, was also inhibited. We propose that, rather than promoting HIV-1 nuclear import, Vpr interacts with karyopherins to disturb their import of IRF3 and NF-κB to promote replication in macrophages. Concordantly, we demonstrate Vpr-dependent rescue of HIV-1 replication in human macrophages from inhibition by cGAMP, the product of activated cGAS. We propose a model that unifies Vpr manipulation of nuclear import and inhibition of innate immune activation to promote HIV-1 replication and transmission

Neutralization potency of monoclonal antibodies recognizing dominant and subdominant epitopes on SARS-CoV-2 Spike is impacted by the B.1.1.7 variant

Interaction of the SARS-CoV-2 Spike receptor binding domain (RBD) with the receptor ACE2 on host cells is essential for viral entry. RBD is the dominant target for neutralizing antibodies, and several neutralizing epitopes on RBD have been molecularly characterized. Analysis of circulating SARS-CoV-2 variants has revealed mutations arising in the RBD, N-terminal domain (NTD) and S2 subunits of Spike. To understand how these mutations affect Spike antigenicity, we isolated and characterized >100 monoclonal antibodies targeting epitopes on RBD, NTD, and S2 from SARS-CoV-2-infected individuals. Approximately 45% showed neutralizing activity, of which ∼20% were NTD specific. NTD-specific antibodies formed two distinct groups: the first was highly potent against infectious virus, whereas the second was less potent and displayed glycan-dependant neutralization activity. Mutations present in B.1.1.7 Spike frequently conferred neutralization resistance to NTD-specific antibodies. This work demonstrates that neutralizing antibodies targeting subdominant epitopes should be considered when investigating antigenic drift in emerging variants

Investigating antagonism of innate immunity by HIV-1 accessory protein Vpr

The role of the HIV-1 accessory protein Vpr has been obscure. Recent studies suggested that HIV-1 is sensitive to type-I Interferon stimulated by activation of cytoplasmic DNA sensor cGAS. Given that Vpr is packaged into HIV-1 particles and present during early stages of the viral lifecycle when its DNA is prone to detection by cGAS, it was hypothesised that Vpr may antagonise cGAS activation of innate immune responses. Consistent with this hypothesis, HIV-1 replication was Vpr dependent in macrophages activated with cGAMP, a product of activated cGAS. High dose infection of THP-1 cells by HIV-1 triggered a Vpr sensitive ISG response, which depended on cGAS but not MAVS. Vpr expression inhibited interferon stimulated genes (ISGs) mRNA and protein expression stimulated by cGAMP. Vpr mutants revealed that this activity required interaction with the DCAF1 E3 ubiquitin ligase complex and importin-α but is independent of Vpr cell cycle arrest function. DCAF1 requirement was further confirmed by DCAF1 depletion. Surprisingly, Vpr expression also inhibited LPS or Sendai virus activated ISG expression suggesting that Vpr targets a conserved step downstream of several innate immune sensors. Indeed, Vpr potently inhibited nuclear translocation of IRF3 without affecting IRF3 phosphorylation at serine386 which is necessary and sufficient for IRF3 activation. In addition to IRF3, Vpr also inhibited NF-ĸB nuclear translocation downstream of DNA sensing. Immunofluorescence analysis of Vpr correlated antagonism of immune signalling with localisation of Vpr to the nuclear envelope, suggesting that Vpr may target nuclear translocation of IRF3 and NF-ĸB at the nuclear pore. In parallel, investigation of Vpr in HEK293T cells revealed that Vpr inhibits mRNA expression from various promoters except the ubiquitin or EF1α promoter which lack NFĸB binding sites. This function correlated with Vpr localisation to the nuclear envelope and was independent of the cell cycle arrest function of Vpr. Interestingly, Vpr did not inhibit HIV-1 gene expression or infectivity. Moreover, nucleofection or integration of a reporter overcame the Vpr-mediated block to expression, suggesting that Vpr may inhibit nuclear import of co-transfected plasmids. In conclusion, I propose that during infection Vpr acts to suppress cGAS activation induced by inappropriately exposed HIV-1 DNA in infected cells and Vpr mediated block to expression from the co-transfected plasmids is a consequence of Vpr inhibition of IRF3 and NF-ĸB nuclear impor

MX2-mediated innate immunity against HIV-1 is regulated by serine phosphorylation

The antiviral cytokine interferon (IFN) activates expression of IFN-stimulated genes (ISGs) to establish an antiviral state. Myxovirus resistance 2 (MX2/MxB) is an ISG that inhibits the nuclear import of HIV-1 and interacts with the viral capsid and cellular nuclear transport machinery. We identified the myosin light chain phosphatase (MLCP) subunits MYPT1 and PPP1CB as positively-acting regulators of MX2, interacting with its N-terminal domain (NTD). We demonstrated that serine phosphorylation of the NTD at positions 14, 17 and 18 suppresses MX2 antiviral function, prevents interactions with the HIV-1 capsid and nuclear transport factors, and is reversed by MLCP. Importantly, NTD serine phosphorylation also impedes MX2-mediated inhibition of nuclear import of cellular karyophilic cargo. We additionally found that IFN treatment reduces levels of phosphorylation at these serines and outline a homeostatic regulatory mechanism where repression of MX2 by phosphorylation, together with MLCP-mediated dephosphorylation, balances the deleterious effects of MX2 upon normal cell function with innate immunity against HIV-1

TMPRSS2 promotes SARS-CoV-2 evasion from NCOA7-mediated restriction

Interferons play a critical role in regulating host immune responses to SARS-CoV-2, but the interferon (IFN)-stimulated gene (ISG) effectors that inhibit SARS-CoV-2 are not well characterized. The IFN-inducible short isoform of human nuclear receptor coactivator 7 (NCOA7) inhibits endocytic virus entry, interacts with the vacuolar ATPase, and promotes endo-lysosomal vesicle acidification and lysosomal protease activity. Here, we used ectopic expression and gene knockout to demonstrate that NCOA7 inhibits infection by SARS-CoV-2 as well as by lentivirus particles pseudotyped with SARS-CoV-2 Spike in lung epithelial cells. Infection with the highly pathogenic, SARS-CoV-1 and MERS-CoV, or seasonal, HCoV-229E and HCoV-NL63, coronavirus Spike-pseudotyped viruses was also inhibited by NCOA7. Importantly, either overexpression of TMPRSS2, which promotes plasma membrane fusion versus endosomal fusion of SARS-CoV-2, or removal of Spike’s polybasic furin cleavage site rendered SARS-CoV-2 less sensitive to NCOA7 restriction. Collectively, our data indicate that furin cleavage sensitizes SARS-CoV-2 Spike to the antiviral consequences of endosomal acidification by NCOA7, and suggest that the acquisition of furin cleavage may have favoured the co-option of cell surface TMPRSS proteases as a strategy to evade the suppressive effects of IFN-induced endo-lysosomal dysregulation on virus infection

Humoral and cellular immunogenicity to a second dose of COVID-19 vaccine BNT162b2 in people receiving methotrexate or targeted immunosuppression : a longitudinal cohort study

Background: COVID-19 vaccines have robust immunogenicity in the general population. However, data for individuals with immune-mediated inflammatory diseases who are taking immunosuppressants remains scarce. Our previously published cohort study showed that methotrexate, but not targeted biologics, impaired functional humoral immunity to a single dose of COVID-19 vaccine BNT162b2 (Pfizer-BioNTech), whereas cellular responses were similar. Here, we aimed to assess immune responses following the second dose. Methods: In this longitudinal cohort study, we recruited individuals with psoriasis who were receiving methotrexate or targeted biological monotherapy (ie, tumour necrosis factor [TNF] inhibitors, interleukin [IL]-17 inhibitors, or IL-23 inhibitors) from a specialist psoriasis centre serving London and South-East England. The healthy control cohort were volunteers without psoriasis, not receiving immunosuppression. Immunogenicity was evaluated immediately before, on day 28 after the first BNT162b2 vaccination and on day 14 after the second dose (administered according to an extended interval regimen). Here, we report immune responses following the second dose. The primary outcomes were humoral immunity to the SARS-CoV-2 spike glycoprotein, defined as titres of total spike-specific IgG and of neutralising antibody to wild-type, alpha (B.1.1.7), and delta (B.1.617.2) SARS-CoV-2 variants, and cellular immunity defined as spike-specific T-cell responses (including numbers of cells producing interferon-γ, IL-2, IL-21). Findings: Between Jan 14 and April 4, 2021, 121 individuals were recruited, and data were available for 82 participants after the second vaccination. The study population included patients with psoriasis receiving methotrexate (n=14), TNF inhibitors (n=19), IL-17 inhibitors (n=14), IL-23 inhibitors (n=20), and 15 healthy controls, who had received both vaccine doses. The median age of the study population was 44 years (IQR 33–52), with 43 (52%) males and 71 (87%) participants of White ethnicity. All participants had detectable spike-specific antibodies following the second dose, and all groups (methotrexate, targeted biologics, and healthy controls) demonstrated similar neutralising antibody titres against wild-type, alpha, and delta variants. By contrast, a lower proportion of participants on methotrexate (eight [62%] of 13, 95% CI 32–86) and targeted biologics (37 [74%] of 50, 60–85; p=0·38) had detectable T-cell responses following the second vaccine dose, compared with controls (14 [100%] of 14, 77–100; p=0·022). There was no difference in the magnitude of T-cell responses between patients receiving methotrexate (median cytokine-secreting cells per 106 cells 160 [IQR 10–625]), targeted biologics (169 [25–503], p=0·56), and controls (185 [133–328], p=0·41). Interpretation: Functional humoral immunity (ie, neutralising antibody responses) at 14 days following a second dose of BNT162b2 was not impaired by methotrexate or targeted biologics. A proportion of patients on immunosuppression did not have detectable T-cell responses following the second dose. The longevity of vaccine-elicited antibody responses is unknown in this population. Funding: NIHR Biomedical Research Centre at Guy's and St Thomas' NHS Foundation Trust and King's College London; The Psoriasis Association.</p