Biology subjects

Trkola, A.

Publications and source records attributed to Trkola, A..

7 recordsLinked to original sources

bioRxiv2026

Opposing cell type preferences for binding and replication shape influenza A virus infection in human airways

Influenza A viruses (IAVs) pose a persistent threat to human health through seasonal epidemics and zoonotic spillover from avian reservoirs. As respiratory pathogens, they primarily target the airway epithelium. However, it remains unclear how host cell-specific barriers jointly shape viral tropism and replication in primary human airway cultures. Here, we show that avian IAVs can infect ciliated and secretory cells but preferentially bind to ciliated cells, consistent with higher abundance of their receptor 2,3-linked sialic acids, specifically sialyl Lewis X glycans, present on the apical surface of ciliated cells. Replication levels were comparable between secretory and ciliated cells for the avian strains, resulting in an overall preference for ciliated cells. In contrast, human IAVs also preferentially bind to ciliated cells but independently of 2,6-linked sialic acid abundance. Human IAVs replicate more efficiently than avian IAVs due to their ability to utilize human ANP32 proteins, but they also exhibit cell type-specific differences due to ANP32, allowing for higher viral RNA levels in secretory cells. Thus, preferential binding to ciliated cells coupled with enhanced replication in secretory cells equalizes overall infection levels across cell types for human IAVs. Together, our findings highlight the spatiotemporal complexity and interplay of IAV infection dynamics in the airway epithelium and redefine current models of influenza A virus tropism.

microbiology↗

bioRxiv2024

Assessing bnAb potency in the context of HIV-1 Envelope conformational plasticity

The ability of broadly neutralizing antibodies (bnAbs) to interact with the closed, pre-fusion HIV-1 envelope (Env) trimer distinguishes them from weakly neutralizing antibodies (weak-nAbs) that depend on trimer opening to bind. Comparative analysis of neutralization data from the CATNAP database revealed a nuanced relationship between bnAb activity and Env conformational plasticity, with substantial epitope-specific variation of bnAb potency ranging from increased to decreased activity against open, neutralization-sensitive Env. To systematically investigate the impact of Env conformational dynamics on bnAb potency we screened 126 JR-CSF point mutants for generalized neutralization sensitivity to weak-nAbs and plasma from people with chronic HIV-1 infection. 23 mutations at highly conserved sites resulted in neutralization phenotype with high Tier 1 sensitivity, which was associated with destabilization of the closed, prefusion conformation. Including 19 of these mutants into a Sensitivity Env mutant panel (SENSE-19), we classified bnAbs according to potency variations in response to trimer opening. To verify that these sensitivity patterns are independent of the in vitro assay system, replication-competent SENSE-19 mutant viruses were tested on primary CD4 T cells. While loss of potency on SENSE-19 was registered for bnAbs recognizing quaternary epitopes on pre-triggered Env, structural destabilization benefitted MPER bnAbs and other inhibitors known to have post-CD4 attachment neutralization activity. Importantly, for certain bnAbs targeting CD4bs, V3-glycan and interface epitopes, particularly low potency variation was noted, suggesting that Env conformational tolerance can be achieved but is not the rule. In summary, SENSE-19 screens revealed distinct Env flexibility tolerance levels between bnAb types that provide mechanistic insights in their function and broaden current neutralization breadth assessments. Author summaryConsistently high potency and neutralizing breadth against genetically divergent strains circulating worldwide are central to the applicability of HIV-1 broadly neutralizing antibodies (bnAbs) for prevention and therapy. The trimeric Envelope protein complex on these viruses is the target for nAbs and because of its inherent flexibility can be presented in different shapes. However, the activity of nAbs depends to different degree on the presentation of certain shapes, limiting their potency and breadth. Here we assemble a virus panel that can be used to estimate this dependence, enabling the identification of bnAbs tolerating the presentation of different shapes.

immunology↗

bioRxiv2024

The XbnAb Cohort: 304 people with broadly neutralizing antibody activity to HIV-1

Broadly neutralizing antibodies (bnAbs) recognizing a diversity of HIV-1 strains are widely thought to be essential for an HIV-1 vaccine. Extensive knowledge on bnAbs has been gained from studying natural HIV infection by following bnAb evolution in individual people with HIV (PWH). However, it remains essential to increase knowledge of bnAb responses in large PWH cohorts to assess the feasibility of inducing bnAb activity by vaccination. To allow systematic analysis, we created the XbnAb cohort, a large bnAb-inducer cohort selected by screening plasma of PWH enrolled in the Swiss HIV Cohort Study (SHCS) and the Zurich Primary HIV Infection Study (ZPHI). The XbnAb cohort represents a retrospective, biobank-based cohort comprising data of 305 PWH who developed bnAb activity during HIV-1 infection. Here, we report on the characteristics of the XbnAb cohort and its potential for HIV vaccine research.

immunology↗

bioRxiv2024

Rare twin cysteine residues in the HIV-1 envelope variable region 1 link to neutralization escape and breadth development

The identification of HIV-1 Envelope glycoprotein (Env) traits associated with development of neutralization cross-reactivity in natural infection is critical for vaccine design. Here we describe the presence of additional Cysteine (Cys) residues in V1 that are enriched among people with elite neutralization breadth. Using >65,000 V1 sequences from the CATNAP database, the AMP trials and three large longitudinal HIV infection cohorts, the SHCS, ZPHI and CAPRISA studies, we show that Env variants with extra V1 Cys are present at low levels throughout infection and fluctuate in frequency over time within participants. We demonstrate an independent association of extra V1 Cys with elite plasma neutralization, and a strong preference for two versus one extra Cys, suggesting certain Envs introduce an additional disulfide bond for stabilization. We observed high levels of neutralization resistance among Envs from 34 bNAb donors, of which 17.6% had elongated V1 regions with extra Cys. We show that extra V1 Cys moderately increase neutralization resistance in an Env from a V2- Apex bNAb-inducer. Modulation of the accessibility of bNAb epitopes on this Env by extra V1 Cys enhanced epitope shielding of several regions, but increased V2 exposure. This suggests that escape from autologous neutralizing activity drove insertion of the extra V1 Cys, creating a modified antigen that may have favored V2 bNAb induction in this donor. Overall, we identify a rare motif of twin Cys in V1 that confers increased neutralization resistance and Env stabilization, is associated with bNAb induction, and may hold potential for incorporation into future HIV bNAb immunogens.

immunology↗

bioRxiv2020

Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies

The HIV-1 gp120/gp41 trimer undergoes a series of conformational changes in order to catalyze gp41-induced fusion of viral and cellular membranes. Here, we present the crystal structure of gp41 locked in a fusion intermediate state by an MPER-specific neutralizing antibody. The structure illustrates the conformational plasticity of the six membrane anchors arranged asymmetrically with the fusion peptides and the transmembrane regions pointing into different directions. Hinge regions located adjacent to the fusion peptide and the transmembrane region facilitate the conformational flexibility that allows high affinity binding of broadly neutralizing anti-MPER antibodies. Molecular dynamics simulation of the MPER Ab-induced gp41 conformation reveals the transition into the final post-fusion conformation with the central fusion peptides forming a hydrophobic core with flanking transmembrane regions. This, thus, suggests that MPER-specific broadly neutralizing antibodies can block final steps of refolding of the fusion peptide and the transmembrane region, which is required for completing membrane fusion.

microbiology↗

bioRxiv2020

Distinct Phenotypes of SARS-CoV-2 Isolates Reveal Viral Traits Critical for Replication in Primary Human Respiratory Cells

Since entering the human population, SARS-CoV-2 (the causative agent of COVID-19) has spread worldwide, causing >100 million infections and >2 million deaths. While large-scale sequencing efforts have identified numerous genetic variants in SARS-CoV-2 during its circulation, it remains largely unclear whether many of these changes impact adaptation, replication or transmission of the virus. Here, we characterized 14 different low-passage replication-competent human SARS-CoV-2 isolates representing all major European clades observed during the first pandemic wave in early 2020. By integrating viral sequencing data from patient material, virus stocks, and passaging experiments, together with kinetic virus replication data from non-human Vero-CCL81 cells and primary differentiated human bronchial epithelial cells (BEpCs), we observed several SARS-CoV-2 features that associate with distinct phenotypes. Notably, naturally-occurring variants in Orf3a (Q57H) and nsp2 (T85I) were associated with poor replication in Vero-CCL81 cells but not in BEpCs, while SARS-CoV-2 isolates expressing the Spike D614G variant generally exhibited enhanced replication abilities in BEpCs. Strikingly, low-passage Vero-derived stock preparation of 3 SARS-CoV-2 isolates selected for substitutions at positions 5/6 of E, and were highly attenuated in BEpCs, revealing a key cell-specific function to this region. Rare isolate-specific deletions were also observed in the Spike furin-cleavage site during Vero-CCL81 passage, but these were rapidly selected against in BEpCs, underscoring the importance of this site for SARS-CoV-2 replication in primary human cells. Overall, our study uncovers sequence features in SARS-CoV-2 variants that determine cell-specific virus replication, and highlights the need to monitor SARS-CoV-2 stocks carefully when phenotyping newly emerging variants or potential variants-of-concern.

microbiology↗

bioRxiv2017

Development of a high-throughput bead based assay system to measure HIV-1 specific immune signatures in clinical samples

The monitoring and assessment of a broadly neutralizing antibody (bnAb) based HIV-1 vaccine require detailed measurements of HIV-1 binding antibody responses to support the detection of correlates of protection. Here we describe the development of a flexible, high-throughput microsphere based multiplex assay system that allows monitoring complex binding antibody signatures. Studying a panel of 13 HIV-1 antigens in a parallel assessment of different IgG subclasses (IgG1, IgG2 and IgG3) we demonstrate the potential of our strategy. The technical advances we describe include means to improve antigen reactivity using directed neutravidin-biotin immobilization of antigens and biotin saturation to reduce background. A particular emphasis of our study was to provide tools for the assessment of reproducibility and stability of the assay system and strategies to control for variations allowing the application in high-throughput assays, where reliability of single measurements needs to be guaranteed.

immunology↗