The Critical Role of Genome Maintenance Proteins in Immune Evasion During Gammaherpesvirus Latency

Gammaherpesviruses are important pathogens that establish latent infection in their natural host for lifelong persistence. During latency, the viral genome persists in the nucleus of infected cells as a circular episomal element while the viral gene expression program is restricted to non-coding RNAs and a few latency proteins. Among these, the genome maintenance protein (GMP) is part of the small subset of genes expressed in latently infected cells. Despite sharing little peptidic sequence similarity, gammaherpesvirus GMPs have conserved functions playing essential roles in latent infection. Among these functions, GMPs have acquired an intriguing capacity to evade the cytotoxic T cell response through self-limitation of MHC class I-restricted antigen presentation, further ensuring virus persistence in the infected host. In this review, we provide an updated overview of the main functions of gammaherpesvirus GMPs during latency with an emphasis on their immune evasion properties

Varicella Virus-Host Interactions During Latency and Reactivation: Lessons From Simian Varicella Virus

Varicella zoster virus (VZV) is a neurotropic alphaherpesvirus and the causative agent of varicella (chickenpox) in humans. Following primary infection, VZV establishes latency in the sensory ganglia and can reactivate to cause herpes zoster, more commonly known as shingles, which causes significant morbidity, and on rare occasions mortality, in the elderly. Because VZV infection is highly restricted to humans, the development of a reliable animal model has been challenging, and our understanding of VZV pathogenesis remains incomplete. As an alternative, infection of rhesus macaques with the homologous simian varicella virus (SVV) recapitulates the hallmarks of VZV infection and thus constitutes a robust animal model to provide critical insights into VZV pathogenesis and the host antiviral response. In this model, SVV infection results in the development of varicella during primary infection, generation of an adaptive immune response, establishment of latency in the sensory ganglia, and viral reactivation upon immune suppression. In this review, we discuss our current knowledge about host and viral factors involved in the establishment of SVV latency and reactivation as well as the important role played by T cells in SVV pathogenesis and antiviral immunity

Cross-sectional Ct distributions from qPCR tests can provide an early warning signal for the spread of COVID-19 in communities

BackgroundSARS-CoV-2 PCR testing data has been widely used for COVID-19 surveillance. Existing COVID-19 forecasting models mainly rely on case counts obtained from qPCR results, even though the binary PCR results provide a limited picture of the pandemic trajectory. Most forecasting models have failed to accurately predict the COVID-19 waves before they occur. Recently a model utilizing cross-sectional population cycle threshold (Ct—the number of cycles required for the fluorescent signal to cross the background threshold) values obtained from PCR tests (Ct-based model) was developed to overcome the limitations of using only binary PCR results. In this study, we aimed to improve on COVID-19 forecasting models using features derived from the Ct-based model, to detect epidemic waves earlier than case-based trajectories.MethodsPCR data was collected weekly at Northeastern University (NU) between August 2020 and January 2022. Campus and county epidemic trajectories were generated from case counts. A novel forecasting approach was developed by enhancing a recent deep learning model with Ct-based features and applied in Suffolk County and NU campus. For this, cross-sectional Ct values from PCR data were used to generate Ct-based epidemic trajectories, including effective reproductive rate (Rt) and incidence. The improvement in forecasting performance was compared using absolute errors and residual squared errors with respect to actual observed cases at the 7-day and 14-day forecasting horizons. The model was also tested prospectively over the period January 2022 to April 2022.ResultsRt curves estimated from the Ct-based model indicated epidemic waves 12 to 14 days earlier than Rt curves from NU campus and Suffolk County cases, with a correlation of 0.57. Enhancing the forecasting models with Ct-based information significantly decreased absolute error (decrease of 49.4 and 221.5 for the 7 and 14-day forecasting horizons) and residual squared error (40.6 and 217.1 for the 7 and 14-day forecasting horizons) compared to the original model without Ct features.ConclusionCt-based epidemic trajectories can herald an earlier signal for impending epidemic waves in the community and forecast transmission peaks. Moreover, COVID-19 forecasting models can be enhanced using these Ct features to improve their forecasting accuracy. In this study, we make the case that public health agencies should publish Ct values along with the binary positive/negative PCR results. Early and accurate forecasting of epidemic waves can inform public health policies and countermeasures which can mitigate spread

Pathogenesis of wildebeest-derived malignant catarrhal fever: lessons from micro-RNAs and the genome maintenance protein of alcelaphine herpesvirus 1

Chez les gammaherpèsvirus, le genre Macavirus regroupe des virus associés au coryza gangreneux (CG) et des virus phylogénétiquement proches. Le CG est caractérisé par une maladie lymphoproliférative aigue et fatale affectant de nombreux ruminants, dont le bovin. L’herpèsvirus alcélaphin 1 (AlHV-1) et l’herpèsvirus ovin 2 (OvHV-2) sont capables de persister à vie respectivement chez le gnou et le mouton, sans causer aucun signe clinique ni lésion. Lorsque ces virus sont transmis à d’autres ruminants sensibles, ceux-ci développent respectivement, la forme européenne (FECG) ou africaine du coryza gangreneux (FACG). L’impact économique de la FACG a été largement sous-estimé en Afrique sub-Saharienne ce qui traduit la nécessité de mieux comprendre les mécanismes à l’origine de la pathogénie de la FACG. Le développement de la FACG est étudié chez le lapin qui reproduit la maladie de manière comparable du point de vue macroscopique et histologique à ce qui a été décrit chez les bovins. Des études récentes ont montré que la FACG était associée à une sévère prolifération et infiltration de lymphocytes T CD8+ infectés latents dans la plupart des organes sans détection de particule virale infectieuse (Palmeira et al., 2013). De plus, la protéine de maintenance génomique (PMG) codée par l’ORF73 de l’AlHV-1 (aLANA), qui est responsable du maintien des épisomes viraux dans les cellules infectées, a été démontrée comme étant essentielle au développement de la FACG. Les ARNs non codants, comme par exemple les microARNs (miARNs), ainsi que les PMGs font partie des rares transcrits exprimés pendant la latence des gammaherpèsvirus. Les miARNs exprimés par les herpèsvirus jouent des rôles dans la régulation de la latence, la transformation tumorale des lymphocytes, le cycle cellulaire et l’immuno-évasion. Les PMGs sont responsables de la persistence épisomale dans les cellules infectées latentes au cours de la mitose tout en échappant à leur propre présentation, en contexte CMH-I, aux lymphocytes T cytotoxiques, un mécanisme nommé : immuno-évasion en cis. Ce travail reflète notre volonté de comprendre les mécanismes par lesquels l’AlHV-1 est capable de persister in vivo tout en restant indétectable par le système immunitaire. La première étude de cette thèse a été dédiée à l’identification des miARNs codés par l’AlHV-1 et de leurs rôles potentiels dans l’induction de la FACG. Nous avons identifié 36 miARNs potentiels dans des cellules infectées de veaux développant la FACG, parmi lesquels 32 étaient exprimés en deux groupes sur le brin complémentaire du génome. Après avoir validé l’expression de ces 32 miARNs, nous avons montré que la délétion du groupe comprenant 28 miARNs viraux n’affectait pas la croissance virale in vitro ni l’induction de la FACG chez les lapins. La deuxième étude traite de l’investigation de la propre inhibition, par aLANA, de sa présentation antigénique et du rôle potentiel de ce mécanisme dans le développement de la FACG avec l’aide du modèle lapin. Nous avons démontré que, tout comme ses orthologues, aLANA est capable d’inhiber sa propre présentation aux lymphocytes T cytotoxiques grâce à un mécanisme impliquant la diminution de sa propre synthèse protéique. Nous avons mis en évidence que la présence de la région riche en GE du domaine central répété de aLANA est responsable de ce mécanisme. Pour finir, nous avons généré une souche recombinante de l’AlHV-1 exprimant une protéine aLANA tronquée du domaine GE. Nous avons observé que l’absence de GE n’affectait pas la croissance virale in vitro et n’empêchait pas le développement de la FACG dans le modèle lapin. Ces résultats montrent que GE n’est pas essentiel pour la persistence virale ni la maintenance épisomale. Cependant, l’induction de la FACG a été significativement retardée chez 2 des 4 lapins infectés, ce qui suggère que la région GE de aLANA est potentiellement nécessaire à l’échappement de la réponse cytotoxique anti-virale pendant la FACG. Les macavirus sont capables de persister dans leur hôte naturel alors que la transmission du virus à d’autres espèces sensibles mène au développement de la FACG. Des études récentes ont placé la latence des gammaherpèsvirus au cœur de la pathogénie de la FACG. Il est intéressant de mieux comprendre le mécanisme par lequel l’AlHV-1 est capable de persister in vivo et d’induire la FACG tout en restant caché de la réponse immunitaire afin d’améliorer nos connaissances actuelles sur la pathogénie des macavirus, et plus généralement des gammaherpèsvirus

The Critical Role of Genome Maintenance Proteins in Immune Evasion During Gammaherpesvirus Latency

Gammaherpesviruses are important pathogens that establish latent infection in their natural host for lifelong persistence. During latency, the viral genome persists in the nucleus of infected cells as a circular episomal element while the viral gene expression program is restricted to non-coding RNAs and a few latency proteins. Among these, the genome maintenance protein (GMP) is part of the small subset of genes expressed in latently infected cells. Despite sharing little peptidic sequence similarity, gammaherpesvirus GMPs have conserved functions playing essential roles in latent infection. Among these functions, GMPs have acquired an intriguing capacity to evade the cytotoxic T cell response through self-limitation of MHC class I-restricted antigen presentation, further ensuring virus persistence in the infected host. In this review, we provide an updated overview of the main functions of gammaherpesvirus GMPs during latency with an emphasis on their immune evasion properties

Self-inhibition of synthesis reduces antigen presentation of the alcelaphine herpesvirus 1-encoded latency-associated protein, aLANA

Alcelalphine herpesvirus 1 (AlHV-1) persistently infects its natural host, the wildebeest, without inducing any clinical signs. However, cross-transmission to other ruminant species leads to the development of a deadly lymphoproliferative disease named malignant catarrhal fever (MCF). AlHV-1 ORF73 encodes the latency-associated nuclear antigen (LANA)-homolog protein termed aLANA. Similarly to other viral genome maintenance proteins encoded by gammaherpesviruses, aLANA has recently been shown to be essential for viral persistence and induction of MCF. Here we have investigated the self-inhibition of antigen presentation by aLANA and the potential role of such mechanism during the development of MCF. We showed that the GE-rich repeat domain of aLANA was sufficient to inhibit the presentation of an epitope linked to it. Though antigen presentation in absence of GE was dependent upon proteasomal degradation of aLANA, a lack of GE did not affect protein turnover. We further found that similarly to EBNA-1 GAr, aLANA GE downregulated protein self-synthesis. Likewise, such mechanism could be associated with reduced antigen presentation in vitro. In addition, in-frame insertion of GE repeat domain in a heterologous eGFP protein significantly down-regulated protein steady-state levels and self-antigen presentation. Next, we modified the AlHV-1 ORF73 gene sequence to reduce the purine bias in GE, without affecting the peptidic sequence. Such codon-modified aLANA GEm construct displayed increased antigen presentation. Finally, we generated an AlHV-1 recombinant strain expressing a GE-deficient aLANA protein and observed that viral growth was not affected in vitro by the absence of aLANA GE domain and MCF could be induced in rabbits irrespective of the expression of full-length aLANA or GE-deficient aLANA protein

Cis-acting inhibition of MHC class I-restricted epitope presentation by Alcelaphine herpesvirus 1 genome maintenance protein

γ-Herpesviruses persist as latent episomes in actively dividing lymphocytes. Their consequent need to express a viral genome maintenance protein (GMP) during latency presents a potential immune target. However, the GMPs from several γ-herpesviruses have evolved related strategies to limit their own MHC class I epitope presentation to cytotoxic T lymphocytes (CTLs). Alcelaphine herpesvirus 1 (AlHV-1) is a γ-herpesvirus that persists asymptomatically in its natural host, the wildebeest. However, AlHV-1 transmission to a large number of susceptible ruminants, including cattle, results in the development of a lethal lymphoproliferative disease named malignant catarrhal fever (MCF). We recently observed that the AlHV-1 GMP-homologue encoded by ORF73 is highly expressed during MCF and that the impairment of its expression renders AlHV-1 unable to induce MCF. With its 1300 aa, AlHV-1 ORF73 is the largest γ-herpesvirus GMP described to date and contains a large acidic internal repeat region that could be involved in the cis-acting CTL evasion mechanism. Here, we sought to determine the CTL evasion properties of AlHV-1 ORF73. We first performed bioinformatic analyses to characterize the protein domains. Then, we used an in vitro assay to demonstrate that ORF73 severely limits the presentation at the cell surface of an MHC class I-restricted epitope linked to ORF73 in cis. These results suggest that AlHV-1 has developed mechanisms to evade cytotoxic anti-viral response during latency. The exact mechanisms explaining the presentation defect remain to be deciphered as well as the role of the cis-acting CTL evasion mechanism of ORF73 in the pathogenesis of MCF

La forme africaine du coryza gangreneux est une maladie lymphoproliférative létale causée par l’herpèsvirus alcélaphin 1

Les gammaherpèsvirus comprennent des virus pouvant induire des maladies lymphoprolifératives et des tumeurs. Ceux-ci peuvent également per- sister à long terme en l’absence de toute manifestation pathologique chez leur hôte naturel. Parmi les gammaherpèsvirus, l’herpèsvirus alcélaphin 1 (AlHV-1) appartient au genre des Macavirus et infecte son hôte naturel, le gnou (Conno- chaetes spp.) de manière asymptomatique. Par ailleurs, lors de sa transmission à de nombreuses espèces sensibles appartenant à l’ordre des artiodactyles, l’AlHV- 1 induit une maladie lymphoproliférative létale dénommée forme africaine du coryza gangreneux (FACG). Le contrôle de cette maladie dans les régions où l’AlHV-1 est endémique est important et dépend directement de la compréhen- sion des mécanismes pathogéniques responsables de l’induction de la FACG. Le but de cette revue est de synthétiser les connaissances actuelles sur l’AlHV-1 et la FACG avec un intérêt particulier porté aux mécanismes par lesquels l’AlHV- 1 induit la maladie. Parmi les différents modèles pathogéniques, nous discuterons du rôle particulier de la latence virale sur base des données actuelles. Enfin, la relation évolutive entre le gnou, l’AlHV-1 et les espèces sensibles à la FACG sera abordée