Modelling the response to vaccine in non-human primates to define SARS-CoV-2 mechanistic correlates of protection

The definition of correlates of protection is critical for the development of next-generation SARS-CoV-2 vaccine platforms. Here, we propose a model-based approach for identifying mechanistic correlates of protection based on mathematical modelling of viral dynamics and data mining of immunological markers. The application to three different studies in non-human primates evaluating SARS-CoV-2 vaccines based on CD40-targeting, two-component spike nanoparticle and mRNA 1273 identifies and quantifies two main mechanisms that are a decrease of rate of cell infection and an increase in clearance of infected cells. Inhibition of RBD binding to ACE2 appears to be a robust mechanistic correlate of protection across the three vaccine platforms although not capturing the whole biological vaccine effect. The model shows that RBD/ACE2 binding inhibition represents a strong mechanism of protection which required significant reduction in blocking potency to effectively compromise the control of viral replication.Initiative for the creation of a Vaccine Research InstituteInfrastructure nationale pour la modélisation des maladies infectieuses humaine

Optimization of the doxycycline-dependent simian immunodeficiency virus through in vitro evolution

<p>Abstract</p> <p>Background</p> <p>Vaccination of macaques with live attenuated simian immunodeficiency virus (SIV) provides significant protection against the wild-type virus. The use of a live attenuated human immunodeficiency virus (HIV) as AIDS vaccine in humans is however considered unsafe because of the risk that the attenuated virus may accumulate genetic changes during persistence and evolve to a pathogenic variant. We earlier presented a conditionally live HIV-1 variant that replicates exclusively in the presence of doxycycline (dox). Replication of this vaccine strain can be limited to the time that is needed to provide full protection through transient dox administration. Since the effectiveness and safety of such a conditionally live virus vaccine should be tested in macaques, we constructed a similar dox-dependent SIV variant. The Tat-TAR transcription control mechanism in this virus was inactivated through mutation and functionally replaced by the dox-inducible Tet-On regulatory system. This SIV-rtTA variant replicated in a dox-dependent manner in T cell lines, but not as efficiently as the parental SIVmac239 strain. Since macaque studies will likely require an efficiently replicating variant, we set out to optimize SIV-rtTA through in vitro viral evolution.</p> <p>Results</p> <p>Upon long-term culturing of SIV-rtTA, additional nucleotide substitutions were observed in TAR that affect the structure of this RNA element but that do not restore Tat binding. We demonstrate that the bulge and loop mutations that we had introduced in the TAR element of SIV-rtTA to inactivate the Tat-TAR mechanism, shifted the equilibrium between two alternative conformations of TAR. The additional TAR mutations observed in the evolved variants partially or completely restored this equilibrium, which suggests that the balance between the two TAR conformations is important for efficient viral replication. Moreover, SIV-rtTA acquired mutations in the U3 promoter region. We demonstrate that these TAR and U3 changes improve viral replication in T-cell lines and macaque peripheral blood mononuclear cells (PBMC) but do not affect dox-control.</p> <p>Conclusion</p> <p>The dox-dependent SIV-rtTA variant was optimized by viral evolution, yielding variants that can be used to test the conditionally live virus vaccine approach and as a tool in SIV biology studies and vaccine research.</p

Influence du polymorphisme du promoteur des sous-types du VIH-1 sur la dynamique de la réplication virale in vivo

Viral promoters modulate transcription and hence viral replication. The HIV-1 promoter is polymorph in its transcription factors binding sites. The impact of this polymorphism on viral replication in vivo has never been addressed. On the background of a SIVmac239 genome, we have engineered three chimeras bearing the minimal promoters of HIV-1 clade B, C and E. By co-infection of four rhesus macaques, a discrepancy between the genotypes of rPBMCs-associated chimeras and of virions in the serum has been highlighted. A shift in viral genotype profiles was observed between the acute and the asymptomatic phase. These results show that subtype-specific HIV-1 promoter polymorphism is a major determinant influencing viral replication and dissemination. Notably, primary infection viremia is mainly due to HIV-1 replication in the gut.Le promoteur viral module la transcription et par conséquent la réplication virale. Le promoteur du VIH-1 est polymorphe pour une variété de sites de fixation de facteurs de transcription, toutefois l'impact de ce polymorphisme sur la réplication virale in vivo n'est pas élucidé. Nous avons construit des virus chimères isogèniques portant le promoteur minimal des sous-types B, C, et E du VIH-1 dans le génome du VISmac239. Dans quatre macaques rhésus co-infectés avec les trois chimères, une discordance entre les génotypes des virus associés aux rPBMCs et des virions du sérum est observée lors de la primo-infection. Un changement dans le génotype viral est également visible entre la primo-infection et la phase asymptomatique. Nos résultats montrent que le polymorphisme du promoteur des sous-types du VIH-1 constitue un déterminant majeur pour la réplication et la dissémination virale, et que la virémie en primo-infection est majoritairement due à la réplication virale dans l'intestin

New challenges in modern vaccinology

International audienceVaccination has been a major advance for health care, allowing eradication or reduction of incidence and mortality of various infectious diseases. However, there are major pathogens, such as Human Immunodeficiency Virus (HIV) or the causative agent of malaria, for which classical vaccination approaches have failed, therefore requiring new vaccination strategies. The development of new vaccine strategies relies on the ability to identify the challenges posed by these pathogens. Understanding the pathogenesis and correlates of protection for these diseases, our ability to accurately direct immune responses and to vaccinate specific populations are such examples of these roadblocks. In this respect, the use of a robust, cost-effective and predictive animal model that recapitulates features of both human infection and vaccination is currently a much-needed tool. We discuss here the major limitations faced by modern vaccinology and notably, the development of humanized mice for assessing the immune system, along with their potential as vaccine models

Influence du polymorphisme du promoteur des sous-types du VIH-1 sur la dynamique de la réplication virale in vivo

PARIS-BIUSJ-Thèses (751052125) / SudocPARIS-BIUSJ-Physique recherche (751052113) / SudocSudocFranceF

Functional Analysis of the Complex trans-Activating Response Element RNA Structure in Simian Immunodeficiency Virus▿

Transcription of human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) is activated through binding of the viral Tat protein to the trans-activating response (TAR) element at the 5′ end of the nascent transcript. Whereas HIV type 1 (HIV-1) TAR folds a simple hairpin structure, the corresponding domains of HIV-2 and SIVmac exhibit a more complex structure composed of three stem-loops. This structural polymorphism may be attributed to additional functions of TAR in HIV-2/SIVmac replication. We recently constructed an SIVmac variant that does not require the Tat-TAR interaction for transcription. We used this variant to study additional roles of TAR in SIVmac replication and generated mutants with a truncated TAR structure. We demonstrate that partial or nearly complete removal of TAR does not impair viral transcription, RNA processing, and translation. Moreover, these deletions do not significantly affect virus replication in the PM1 T-cell line and macaque peripheral blood mononuclear cells. These results demonstrate that the complex TAR structure in SIVmac has no other essential function in virus replication in vitro besides its role in Tat-mediated activation of transcription

Clade-specific differences in active viral replication and compartmentalization

This review focuses on the impact of HIV-1 clade-specific polymorphisms on the dynamics of viral replication and compartmentalization in vivo. HIV-1 transcription and compartmentalization are essentially modulated by interconnected parameters: cellular activation by T-cell receptor engagement or cytokine signalling in different tissues, and viral polymorphisms in the long terminal repeat and Tat protein. Moreover, the gut-associated lymphoid tissue plays a central role in HIV-1 pathogenesis. It selectively supports viral replication in primary infection and may influence viral quasispeciation during interleukin-7 treatment. In addition, interleukin-7, permanently released by the intestinal epithelial cells, preferentially activates the HIV-1 clade C promoter versus the B and E counterparts. In view of the influence of long terminal repeat polymorphisms on the replication of different clades and the importance of HIV-1 replication in the gut-associated lymphoid tissue during primary infection, it will be important to show whether the amplitude and speed of gut-associated lymphoid tissue depletion in primary infection are also clade dependent and can impact disease progression. In the context of therapeutic interleukin-7 treatment, this cytokine might well foster growth of HIV-1 clade C and perhaps clade A viruses. This needs attentio

In HIV-1 pathogenesis the die is cast during primary infection.

International audienceThe chronic stage of HIV-1 infection has been extensively described as a slowly evolving phase, in which the virus induces T-cell death slightly faster than the human body is able to recover. In contrast, T-cell and viral replication dynamics during primary infection have been less well studied. Recent studies in the SIV-macaque model and in HIV-positive patients during the acute infection period have highlighted the massive and irreversible depletion of CD4 memory T cells in the mucosa, particularly in the gut. Hence, gut-associated lymphoid tissue (GALT) plays a central role in the early stages of HIV-1 pathogenesis. Due to its particular cytokine expression pattern, GALT may favour the differential replication of certain HIV-1 subtypes during primary infection, particularly of subtype C. This could enhance the chance of a successful transmission. Moreover, these early events taking place in GALT during primary infection have major implications for therapy and vaccine design

Optimisation of secretion of recombinant HBsAg virus-like particles: Impact on the development of HIV-1/HBV bivalent vaccines.

International audienceThe hepatitis B surface antigen (HBsAg) assembles into virus-like particles (VLPs) that can be used as carrier of immunogenic peptides for the development of bivalent vaccine candidates. It is shown here that by respecting certain qualitative features of mammalian preS1 and preS2 protein domains upstream of HBsAg, foreign sequences can be inserted in their place while maintaining efficient secretion of VLPs. A polyepitope bearing HIV-1 epitopes restricted to the HLA-A*0201 class I allele was optimised for secretion as an HBsAg fusion protein by counterbalancing the generally hydrophobic class I epitopes with hydrophilic spacers, eliminating epitopes bearing cysteine residues, limiting the number of internal methionine residues to a minimum and adopting Homo sapiens codon usage. The optimised HIV-1 polyepitope-HBsAg recombinant protein with up to 138 residues assembled into efficiently secreted recombinant VLPs. DNA immunisation in HLA-A*0201 and HLA-A*0201/HLA-DR1 transgenic mice resulted in the recovery of humoral response against the carrier and enhanced levels of HIV-1 specific CD8(+) T lymphocyte activation. Efficient self-assembly of recombinant HBsAg VLPs opens up the possibility of making efficient bivalent HBV/HIV vaccine candidates, which is particularly apposite given that the two viruses are frequently associated