Julian D. J. Sng

Self-amplifying vaccines based on alphavirus replicons are well established. Preclinical studies of self-amplifying vaccines based on orthoflaviviruses have also been described and include replicons based on Kunjin virus (KUNV). KUNV is an Australian subtype of West Nile virus with typically mild or asymptomatic clinical presentations in humans. Single round infectious particles (SRIPs) have emerged as an effective vaccine delivery modality for KUN replicon RNA vaccines. For instance, a SRIP vaccine encoding the glycoprotein (GP) of Zaire Ebolavirus (EBOV) was previously shown to be effective in guinea pigs and non-human primates. These SRIPs comprise self-amplifying KUN replicon RNA packaged within KUNV structural proteins, and represent virus-like-particles capable of infecting cells and delivering replicon RNA encoding an immunogen. Using EBOV GP as the model immunogen, we describe herein a novel SRIP DNA plasmid construct that illustrates a simplified in vitro methodology for the production of KUN replicon SRIPs. This SRIP DNA was also evaluated as a potential DNA vaccine; however, it performed similarly to a conventional DNA vaccine for eliciting anti-GP antibodies in Ifnar1−/− mice.

Glycosylation is critical for viral-host cell interactions in influenza A virus (IAV) infection, but we lack a comprehensive understanding of how IAV infection shapes the host glycoproteome. Here, we performed liquid chromatography-tandem mass spectrometry (LC-MS/MS) proteomic, glycomic, and glycoproteomic characterisation of the dynamic subcellular responses to an in vitro time course infection of human A549 cells. IAV infection resulted in only modest changes to the subcellular proteome, but robust and significant changes to the host secreted and organelle glycome and glycoproteome. Infection caused reductions in sialylation across the N- and O-glyco(proteo)me; increased oligomannose, paucimannose, and phosphorylated glycans; and shorter hybrid/complex glycans. Desialylation was greater when glycans were fucosylated; for sialic acid linked α2,3 or on the α3 arm; on larger, complex glycans; and on proteins likely to be more accessible to IAV neuraminidase (NA). Subtle activation of the unfolded protein response in infection was associated with a doubling of oligomannose N-glycosylation. Glycans were shorter in infection, implicating IAV-induced disruption of Golgi glycoprotein flux as a mechanism that reduces host glycoprotein sialylation and promotes virion release, independent of NA activity.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the coronavirus disease 2019 (COVID-19) pandemic, remains a global health concern despite vaccines, neutralizing antibodies, and antiviral drugs. The emergence of viral mutations that diminish the effectiveness of current interventions underscores the importance of alternative, host-directed strategies. Here, we show that pharmacological inhibition or knockdown of host N-myristoyltransferase 1 (NMT1), one of the two human enzymes that mediates protein N-myristoylation, significantly impairs SARS-CoV-2, Vesicular Stomatitis Virus (VSV) and Respiratory syncytial virus (RSV) infections. We demonstrate the antiviral efficacy and safety of this host-directed therapeutic strategy across multiple viral tropic sites, including human lung adenocarcinoma cell lines, primary nasal epithelial cells, and human choroid plexus-cortical brain organoids. NMT1 inhibition triggers a Golgi-bypassing pathway for SARS-CoV-2 progeny virion egress, through endoplasmic reticulum and lysosomal structures, which leads to perturbed progeny virion composition and spike maturation, impairing progeny virion infectivity.

Heart disease is the leading cause of morbidity and mortality in individuals with diabetes, due largely to risks associated with ischaemic injuries such as myocardial infarction (MI). We use human population genetic data to demonstrate that classical cardiovascular disease risk biomarkers, including common measures of hyperglycaemia, do not fully account for the increased risk of post-MI mortality in patients with diabetes. This study therefore systematically evaluates glycaemic stress underpinning cardiovascular risk in diabetes. Here, we show using in vivo studies in adult male mice and in vitro models that glycaemic variability, rather than sustained hyperglycaemia alone, is a key risk factor for cardiomyocyte dysfunction and increased susceptibility to myocardial injury in diabetes. We further demonstrate that patient plasma assays can elucidate the predictive potential of glycaemic variability as a primary contributor to cardiomyocyte dysfunction and subclinical cardiac injury in diabetes. These findings provide preclinical models for mechanistic and drug discovery studies and inform strategies for managing cardiovascular outcomes in patients with diabetes.

Dysregulation of the renin-angiotensin system (RAS) contributes to severe influenza and COVID-19, potentially via impaired ACE2/Ang-(1-7)/Mas receptor (MasR) signalling. AVE0991, an orally bioavailable MasR agonist, protects against non-infectious lung inflammation, but its effects in viral respiratory disease are unknown. We evaluated AVE0991 in human lung epithelial cells and murine models of influenza A virus (IAV) and SARS-CoV-2 infection. In vitro , AVE0991 suppressed cytokines IL-6 and TNF-α to both IAV and SARS-CoV-2 and reduced IAV titres. Unexpectedly, in vivo treatment worsened disease. These findings highlight discordant in vitro and in vivo effects and underscore the need for careful evaluation of RAS-targeted therapies in acute viral infection.

Glycosylation is critical for viral-host cell interactions in influenza A virus (IAV) infection, but we lack a comprehensive understanding of how IAV infection shapes the host glycoproteome and the implications of these changes. Here, we used a liquid chromatography-tandem mass spectrometry (LC-MS/MS) approach to perform proteomic, glycomic, and glycoproteomic characterisation of the dynamic subcellular responses to an in vitro time course infection of human A549 cells with two IAV strains (A/X-31, H3N2; and A/Puerto Rico/8/1934, H1N1). IAV infection resulted in only modest changes to the subcellular proteome, but robust and significant changes to the host secreted and organelle glycome and glycoproteome. Infection with either virus resulted in a widespread reduction in sialic acid across the N - and O -glyco(proteo)me; increased abundance of oligomannose, paucimannose, and phosphorylated glycans; and shorter hybrid/complex glycans. Reduced sialylation was consistent with desialylation of glycans by viral neuraminidase (NA), but with specific features of the glycan and protein controlling the extent of desialylation. Desialylation was greater when glycans were fucosylated; when the sialic acid was attached via an α2,3 linkage or positioned on the α3 arm; on larger, more complex glycans; and when present on proteins that are more accessible to IAV NA. Subtle but prolonged activation of the unfolded protein response in infection led to a doubling of oligomannose N -glycosylation. Glycans were shorter in infection, implicating IAV-induced disruption of Golgi glycoprotein flux as a mechanism that reduces host glycoprotein sialylation and promotes virion release, independent of NA activity. Our data provide important insights into the host glycoproteome during influenza virus infection, furthering our understanding of how influenza NA acts upon host glycans, and how cell stresses in infection perturb key mediators of protein stability and function, cell signalling and immunity.

SARS-CoV-2 Omicron variants demonstrate greater replication efficiency in the upper respiratory tract than both ancestral virus and Delta variant, potentially due to stronger interactions with motile cilia in human nasal epithelial cells. Despite the emergence of numerous Omicron variants, there has been no comprehensive investigation comparing their interactions with ciliated cells. Here, we use differentiated primary human nasal epithelial cell (NEC) cultures to compare an ancestral isolate (QLD02) to Omicron variants BA.1, BA.5 and XBB. Transcriptomic analysis revealed that BA.5 and XBB infection, unlike BA.1 and QLD02, drives a distinct host response, defined by the profound downregulation of genes essential for cilium assembly and function at 48 hours post-infection. The BA.5/XBB signature was also characterized by the strong upregulation of pro-apoptotic and inflammatory pathways. Immunofluorescence of nucleocapsid-positive cells in NECs showed a significant 13-fold increase for BA.5 relative to QLD02. Additionally, BA.1 and BA.5 exhibited greater tropism for ciliated cells (7.6-fold for BA.1, 9-fold for BA.5) than QLD02. BA.5 and BA.1 infection were associated with elevated apoptosis in both infected and bystander cells, however, the total number of ciliated cells remained unchanged. Consistent with this, BA.5 infection significantly reduced DNAH5 outer dynein arm protein in the cilia, indicating dysfunction of cilia motility rather than overt cilia loss. Overall, we demonstrate a stepwise evolution at the nasal barrier: while enhanced ciliated cell tropism and elevated apoptosis are conserved features of Omicron infection, ciliary dysfunction, evident at both the transcriptional and protein level, is a more pronounced phenotype emerging with BA.5 and preserved in the XBB variant.

Heart disease is the leading cause of morbidity and mortality in individuals with diabetes, due largely to risks associated with ischaemic injuries such as myocardial infarction (MI). We use human population genetic data to demonstrate that current biomarkers of hyperglycaemia do not account for risk of post-MI mortality in diabetes patients. This study therefore systematically evaluates glycaemic stress underpinning cardiovascular risk in diabetes. Using in vivo and in vitro models, we demonstrate that glycaemic variability rather than hyperglycaemia alone is a dominant risk factor for heart muscle dysfunction and myocardial injury sensitivity in diabetes. These findings provide new preclinical models for mechanistic and drug discovery studies and inform strategies for managing cardiovascular outcomes in patients with diabetes.

The spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the main target for vaccine development, as antibodies generated against the spike protein are the most immunodominant and neutralizing against the virus. However, variants of concern (VOC), often containing multiple mutations within neutralizing epitopes, confer immune evasion of the response generated by current SARS-CoV-2 vaccines. To assess the immunogenicity and virus-neutralisation ability of antibodies induced by individual or combination of Vaxzevria (AstraZeneca: AZ) and Comirnaty (Pfizer: PZ) vaccines and of a hybrid immunity induced in people who were also infected with SARS-CoV-2, longitudinal sera samples of participants recruited through the David Serisier Research biobank (Mater Research Hospital) or at the University of Queensland were collected. ELISA with a panel of purified Spike proteins from ancestral, alpha, delta and omicron BA.1 and BA.2 VOCs showed significantly (by ∼2 to 6-fold) reduced IgG antibody titres against Spike proteins from Omicron BA.1 and BA.2 compared to ancestral strain regardless of the number of vaccinations or presence of infection. Neutralisation assays showed reduced activity against delta and omicron BA.1, BA.5 and BA.5 VOCs. However, the differences were in general less pronounced than in the ELISA assay and some were not statistically significant, particularly after four (two AZ and two PZ) vaccinations. We also generated by circular polymerase extension reaction an attenuated SARS-CoV-2 strain with deletion of all accessory genes, ORF 3, 6, 7 and 8, based on the ancestral (QLD02) virus backbone (QLD02 _Δ3678 ) and validated it in virus-neutralization assays with our panel of sera samples. We showed the attenuation of the QLD02 _Δ3678 virus in Vero E6 and human Caco2 cells. We demonstrated that neutralization assays with the wild-type QLD02 virus and QLD02 _Δ3678 virus were concordant, providing a safe platform for neutralisation assays in BSL2/PC2 settings.