Human immunodeficiency virus-1 (HIV-1) persists as a global health concern, with an incidence rate of approximately 2 million, and estimated global prevalence of over 35 million. Combination antiretroviral treatment is highly effective, but HIV-1 patients that have been treated still suffer from chronic inflammation and residual viral replication. It is therefore paramount to identify therapeutically efficacious strategies to eradicate viral reservoirs and ultimately develop a cure for HIV-1. It has been long accepted that the restriction factor tripartite motif protein 5 isoform alpha (TRIM5α) restricts HIV-1 infection in a species-specific manner, with rhesus macaque TRIM5α strongly restricting HIV-1, and human TRIM5α having a minimal restriction capacity. However, several recent studies underscore human TRIM5α as a cell-dependent HIV-1 restriction factor. Here, we present an overview of the latest research on human TRIM5α and propose a novel conceptualization of TRIM5α as a restriction factor with a varied portfolio of antiviral functions, including mediating HIV-1 degradation through autophagy- and proteasome-mediated mechanisms, and acting as a viral sensor and effector of antiviral signaling. We have also expanded on the protective antiviral roles of autophagy and outline the therapeutic potential of autophagy modulation to intervene in chronic HIV-1 infection.

SARS-CoV-2, the causative virus of COVID-19, continues to threaten global public health. COVID-19 is a multi-organ disease, causing not only respiratory distress, but also extrapulmonary manifestations, including gastrointestinal symptoms with SARS-CoV-2 RNA shedding in stool long after respiratory clearance. Despite global vaccination and existing antiviral treatments, variants of concern are still emerging and circulating. Of note, new Omicron BA.5 sublineages both increasingly evade neutralizing antibodies and demonstrate an increased preference for entry via the endocytic entry route. Alternative to direct-acting antivirals, host-directed therapies interfere with host mechanisms hijacked by viruses, and enhance cell-mediated resistance with a reduced likelihood of drug resistance development. Here, we demonstrate that the autophagy-blocking therapeutic berbamine dihydrochloride robustly prevents SARS-CoV-2 acquisition by human intestinal epithelial cells via an autophagy-mediated BNIP3 mechanism. Strikingly, berbamine dihydrochloride exhibited pan-antiviral activity against Omicron subvariants BA.2 and BA.5 at nanomolar potency, providing a proof of concept for the potential for targeting autophagy machinery to thwart infection of current circulating SARS-CoV-2 subvariants. Furthermore, we show that autophagy-blocking therapies limited virus-induced damage to intestinal barrier function, affirming the therapeutic relevance of autophagy manipulation to avert the intestinal permeability associated with acute COVID-19 and post-COVID-19 syndrome. Our findings underscore that SARS-CoV-2 exploits host autophagy machinery for intestinal dissemination and indicate that repurposed autophagy-based antivirals represent a pertinent therapeutic option to boost protection and ameliorate disease pathogenesis against current and future SARS-CoV-2 variants of concern.

Chronic HIV-1 infection is characterized by T-cell dysregulation that is partly restored by antiretroviral therapy. Autophagy is a critical regulator of T-cell function. Here, we demonstrate a protective role for autophagy in HIV-1 disease pathogenesis. Targeted analysis of genetic variation in core autophagy geneATG16L1reveals the previously unidentified rs6861 polymorphism, which correlates functionally with enhanced autophagy and clinically with improved survival of untreated HIV-1-infected individuals. T-cells carryingATG16L1rs6861(TT) genotype display improved antiviral immunity, evidenced by increased proliferation, revamped immune responsiveness, and suppressed exhaustion/immunosenescence features. In-depth flow-cytometric and transcriptional profiling reveal T-helper-cell-signatures unique to rs6861(TT) individuals with enriched regulation of pro-inflammatory networks and skewing towards immunoregulatory phenotype. Therapeutic enhancement of autophagy recapitulates the rs6861(TT)-associated T-cell traits in non-carriers. These data underscore the in vivo relevance of autophagy for longer-lasting T-cell-mediated HIV-1 control, with implications towards development of host-directed antivirals targeting autophagy to restore immune function in chronic HIV-1 infection.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus disease 19 (COVID-19), continues to circulate globally despite the widespread vaccination and therapeutics like Paxlovid, remdesivir, and molnupiravir. COVID-19 is associated with both respiratory and gastrointestinal manifestations, with persistent intestinal pathology contributing to the post-COVID-19 condition. We have previously demonstrated the antiviral activity of autophagy-blocking drugs, such as Berbamine dihydrochloride, against intestinal SARS-CoV-2 acquisition. In addition, the autophagy blockers restored the barrier function of infected intestinal epithelium. In this addendum, using human intestinal organoids, we present evidence for a protective role of intrinsic higher levels of autophagy flux in limiting intestinal SARS-CoV-2 infection. Pharmacological treatment with Akt inhibitor MK-2206 hydrochloride suppressed viral entry into the intestinal epithelium. This antiviral effect of MK-2206 was shown to be dependent on Synaptosomal-associated protein 29-dependent (SNAP-29)-mediated autophagy flux. Furthermore, extrinsically enhanced autophagy with MK-2206 also prevented SARS-CoV-2-induced intestinal barrier damage. Our findings thus underscore the intricate role of autophagy pathways in the dissemination and pathogenesis of intestinal SARS-CoV-2, highlighting the therapeutic potential of host-directed therapies targeting autophagy to intervene in COVID-19-associated sequelae and improve intestinal health.

Oral vancomycin has a long history as the first-line treatment for Clostridioides difficile infection (CDI), but its use is associated with high relapse rates. Antibiotics that more selectively target C. difficile while sparing protective commensal gut bacteria, have the potential to prevent recurrent CDI (rCDI). Here, we investigate the experimental glycopeptide antibiotic, EVG7, in the context of rCDI. In vitro susceptibility assays reveal that clinical C. difficile isolates are up to 16-times more sensitive to EVG7 (MIC = 0.063–0.25 mg/L) compared to vancomycin (MIC = 0.5–2 mg/L). In a validated mouse model of rCDI in male mice, low dose oral EVG7 (0.04 mg/mL in drinking water) more effectively treats primary CDI and prevents recurrence, outperforming a 10-fold higher dose of vancomycin. Subsequent microbiome analysis and in vitro susceptibility testing reveal that EVG7 preserves Lachnospiraceae, a family of commensal bacteria associated with protection against C. difficile colonization.