Clearance Of Viral Infections Research Articles

Activation of the antiviral factor RNase L triggers translation of non-coding mRNA sequences.

Ribonuclease L (RNase L) is activated as part of the innate immune response and plays an important role in the clearance of viral infections. When activated, it endonucleolytically cleaves both viral and host RNAs, leading to a global reduction in protein synthesis. However, it remains unknown how widespread RNA decay, and consequent changes in the translatome, promote the elimination of viruses. To study how this altered transcriptome is translated, we assayed the global distribution of ribosomes in RNase L activated human cells with ribosome profiling. We found that RNase L activation leads to a substantial increase in the fraction of translating ribosomes in ORFs internal to coding sequences (iORFs) and ORFs within 5' and 3' UTRs (uORFs and dORFs). Translation of these alternative ORFs was dependent on RNase L's cleavage activity, suggesting that mRNA decay fragments are translated to produce short peptides that may be important for antiviral activity.

Selective Interferon Responses of Intestinal Epithelial Cells Minimize Tumor Necrosis Factor Alpha Cytotoxicity.

Interferon (IFN) family cytokines stimulate genes (interferon-stimulated genes [ISGs]) that are integral to antiviral host defense. Type I IFNs act systemically, whereas type III IFNs act preferentially at epithelial barriers. Among barrier cells, intestinal epithelial cells (IECs) are particularly dependent on type III IFN for the control and clearance of virus infection, but the physiological basis of this selective IFN response is not well understood. Here, we confirm that type III IFN treatment elicits robust and uniform ISG expression in neonatal mouse IECs and inhibits the replication of IEC-tropic rotavirus. In contrast, type I IFN elicits a marginal ISG response in neonatal mouse IECs and does not inhibit rotavirus replication. In vitro treatment of IEC organoids with type III IFN results in ISG expression that mirrors the in vivo type III IFN response. However, IEC organoids have increased expression of the type I IFN receptor relative to neonate IECs, and the response of IEC organoids to type I IFN is strikingly increased in magnitude and scope relative to type III IFN. The expanded type I IFN-specific response includes proapoptotic genes and potentiates toxicity triggered by tumor necrosis factor alpha (TNF-α). The ISGs stimulated in common by type I and III IFNs have strong interferon-stimulated response element (ISRE) promoter motifs, whereas the expanded set of type I IFN-specific ISGs, including proapoptotic genes, have weak ISRE motifs. Thus, the preferential responsiveness of IECs to type III IFN in vivo enables selective ISG expression during infection that confers antiviral protection but minimizes disruption of intestinal homeostasis.IMPORTANCE Enteric viral infections are a major cause of gastroenteritis worldwide and have the potential to trigger or exacerbate intestinal inflammatory diseases. Prior studies have identified specialized innate immune responses that are active in the intestinal epithelium following viral infection, but our understanding of the benefits of such an epithelium-specific response is incomplete. Here, we show that the intestinal epithelial antiviral response is programmed to enable protection while minimizing epithelial cytotoxicity that can often accompany an inflammatory response. Our findings offer new insight into the benefits of a tailored innate immune response at the intestinal barrier and suggest how dysregulation of this response could promote inflammatory disease.

The Effects of Androgens on T Cells: Clues to Female Predominance in Autoimmune Liver Diseases?

The immune system responds differently in women and in men. Generally speaking, adult females show stronger innate and adaptive immune responses than males. This results in lower risk of developing most of the infectious diseases and a better ability to clear viral infection in women (1–5). On the other hand, women are at increased risk of developing autoimmune diseases (AID) such as rheumatoid arthritis, multiple sclerosis (MS), systemic lupus erythematosus (SLE), Sjögren's syndrome, and the autoimmune liver diseases autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) (6). Factors contributing to the female sex bias in autoimmune diseases include environmental exposure, e.g., microbiome, behavior, and genetics including X chromosomal inactivation of genes. Several lines of evidence and clinical observations clearly indicate that sex hormones contribute significantly to disease pathogenesis, and the role of estrogen in autoimmune diseases has been extensively studied. In many of these diseases, including the autoimmune liver diseases, T cells are thought to play an important pathogenetic role. We will use this mini-review to focus on the effects of androgens on T cells and how the two major androgens, testosterone and dihydrotestosterone, potentially contribute to the pathogenesis of autoimmune liver diseases (AILD).

Immunotherapy in patients with local HPV infection and high-grade squamous intraepithelial lesion following uterine cervical conization

Objective To establish the clearance of cervical human papillomavirus (HPV) infection following postoperative immunotherapy with inosine pranobex in women receiving surgical treatment of established high-grade squamous intraepithelial lesion (HSIL) of the uterine cervix. Materials and methods Over the six-year study period, 32 women with cervical HPV infection following electroconization (loop electrosurgical excision procedure) of the uterine cervix for established HSIL were randomly divided into two groups: I (n = 10) without and II (n = 22) with postoperative inosine pranobex immunotherapy. Follow-up after 24 and 48 months included cervical testing for HPV persistence and after 12, 24, and 48 months with cytology and colposcopy for dysplasia relapse (confirmed histologically). Results Relapse monitoring in 32 women after 12 months revealed 1 and 0 HSIL positive in groups I and II, respectively; after 24 months an additional 3 patients in each group were positive; and after 48 months an additional 3 and 1 patients were positive in groups I and II, respectively (p < .05). The groups significantly differed (p < .05) with regard to clearing the most common high-risk HPV genotypes (HPV 16 and HPV 56). Conclusions Inosine pranobex immunotherapy in HPV-positive patients following cervical conization significantly increased the clearance of viral infection with high-risk genotypes and reduced relapse of HSIL.

The Pro-autoimmune allele of tyrosine phosphatase PTPN22 enhances anti-viral and anti-tumor immunity

Abstract The 1858C&amp;gt;T allele of the tyrosine phosphatase PTPN22 (causing amino acid substitution R620W) is present in 5–10% of the North American population and is strongly associated with numerous autoimmune diseases. Specifically, this alternative allele affects lymphocyte activation, toll-like receptor signaling, and cytokine production in various autoimmune contexts. Despite the importance of these inflammatory networks to clear pathogens and tumors, the influence of PTPN22, and its pro-autoimmune allele, have on viral and tumorigenic conditions is still being defined. To interrogate these roles, we used CRISPR/Cas9 to generate mice expressing the Ptpn22 R619W molecule, which is the ortholog of R620W in humans. Using LCMV-cl13 infection and B16 tumor models, we tested the hypothesis that pleiotropic effects of Ptpn22 R619W enhances anti-viral and anti-tumor immunity. Importantly, R619W-bearing mice have less tumor burden and clear chronic viral infection faster than wild-type mice. Consistent with these results, R619W mice have enhanced antigen-specific T cell activation during viral infection and increased tumor-infiltrating Th1 CD4 T cells. Additionally, we define an underlying mechanism by which Ptpn22 promotes PD-L1 expression on conventional dendritic cells (cDCs) in wild-type mice, but is abrogated in R619W mice during disease. Lastly, R619W expression in lymphocytes alone can enhance T cell activation; however, the combination of R619W expressing lymphocytes and DCs enhances T cell activation even more. Our results suggest that a pro-autoimmune allele can be beneficial by promoting anti-viral and anti-tumor immune responses through multiple immune cell types, and may have a protective effect in these diseases.

BPIFB3 interacts with ARFGAP1 and TMED9 to regulate non-canonical autophagy and RNA virus infection.

Autophagy is a degradative cellular pathway that targets cytoplasmic contents and organelles for turnover by the lysosome. Various autophagy pathways play key roles in the clearance of viral infections, and many families of viruses have developed unique methods for avoiding degradation. Some positive-stranded RNA viruses, such as enteroviruses and flaviviruses, usurp the autophagic pathway to promote their own replication. We previously identified the endoplasmic reticulum (ER)-localized protein BPIFB3 as an important negative regulator of non-canonical autophagy that uniquely impacts the replication of enteroviruses and flaviviruses. Here, we find that many components of the canonical autophagy machinery are not required for BPIFB3 depletion-induced autophagy and identify the host factors that facilitate its role in the replication of enteroviruses and flaviviruses. Using proximity-dependent biotinylation (BioID) followed by mass spectrometry, we identify ARFGAP1 and TMED9 as two cellular components that interact with BPIFB3 to regulate autophagy and viral replication. Importantly, our data demonstrate that non-canonical autophagy in mammalian cells can be controlled outside of the traditional pathway regulators and define the role of two proteins in BPIFB3 depletion mediated non-canonical autophagy.

Immunity to Influenza is dependent on MHC II polymorphism: study with 2 HLA transgenic strains

Major histocompatibility complex II (MHC II) molecules are involved in antigen presentation and the development of a functional adaptive immune response. Evolutionary selection for MHC molecules that effectively clear infectious agents provides an advantage to humans. However, certain class II molecules are associated with autoimmune diseases. In this study we infected autoimmune-susceptible DRB1*0401.AEo and non-susceptible *0402.AEo mice with H1N1 influenza and determined clearance and protective immunity to H3N2 virus. *0401 mice generated a robust TLR-triggered immune response and cleared H1N1 influenza virus infection. After vaccination and challenge with H1N1, *0401 mice, when challenged with H3N2, generated cross-protective immunity to heterosubtypic H3N2 influenza strain whereas *0402 mice cleared the H1N1 infection but did not generate cross-protective immunity against the H3N2 influenza strain. The intracellular trafficking route of MHCII revealed that *0401 molecules traffic through the late endosome/lysosomes while *0402 molecules traffic into early endosomes. This suggested that trafficking of MHCII could affect the functional output of the innate immune response and clearance of viral infections. Also, DRB1*0401 mice live longer than HLA-DRB1*0402 mice. The study provides a potential hypothesis for evolutionary selection of *0401 molecule, even though it is associated with autoreactivity, which may be dependent on the availability of peptide repertoire of self-antigens.

Immunological tolerance of low-risk HPV in recurrent respiratory papillomatosis.

Recurrent respiratory papillomatosis (RRP) is characterized by benign exophytic lesions of the respiratory tract caused by the human papillomavirus (HPV), in particular low-risk HPV6 and HPV11. Aggressiveness varies greatly among patients. Surgical excision is the current standard of care for RRP, with adjuvant therapy used when surgery cannot control disease recurrence. Numerous adjuvant therapies have been used to control RRP with some success, but none are curative. Current literature supports a polarization of the adaptive immune response to a T helper type 2 (Th2)-like or T regulatory phenotype, driven by a complex interplay between innate immunity, adaptive immunity and HPV6/11 proteins. Additionally, certain immunogenetic polymorphisms can predispose individuals to an HPV6/11-tolerant microenvironment. As a result, immunomodulatory efforts are being made to restore the host immune system to a more balanced T cell phenotype and clear viral infection. Literature has shown exciting evidence for the role of HPV vaccination with Gardasil or Gardasil-9 as both primary prevention, by decreasing incidence through childhood vaccinations, and secondary prevention, by treating active RRP disease. Multi-institution randomized clinical trials are needed to better assess their efficacy as treatment for active disease. Interestingly, a DNA vaccine has recently shown in-vitro success in generating a more robust CD8+ T cell response. Furthermore, clinical trials for programmed death 1 (PD-1) inhibitors are under investigation for RRP management. Molecular insights into RRP, in particular the interplay between RRP and the immune system, are needed to advance our understanding of this disease and may lead to the identification of immunomodulatory agents to better manage RRP.

Viral infection induces the upregulation of MHC-1 expression in infected cancer cells

Abstract Cancer cells can evade immune system by the downregulation of major histocompatibility complex-1 (MHC-1) molecules and upregulation of immunosuppressive ligands such as programmed death ligand 1 (PD-L1). In addition, cancer cells provide inhibitory cytokines so that the microenvironments of cancer maintain as an anti-inflammatory condition. However, it is not clear if cancer cells provide pro-inflammatory microenvironments to help clear viral infection, when they were infected with life-threatning viruses To test this question, we infected EL-4 cells, a lymphoma cell line, with lymphocytic choriomeningitis virus (LCMV) and examined if this infection causes the phenotypic change of cancer cells. On day 7 post infection, we observed that expressions of MHC-1 and PD-L1 molecules increased, while decreased PD-1 expression was found in virus-infected cancer cells. Since the overexpression of MHC-1 molecules was found on virus-infected cells, we further examined whether virus-specific CD8 T cells can recognize the antigen presented by these cancer cells and if these CD8 T cells can mount immune response. When LCMV-specific memory T cells were cultured with virus-infected EL-4 cells, we found that these CD8 T cells were able to produce IFN-γ and TNF-α, but the levels of these proteins were lower compared to positive controls. Altogether, these data suggest that cancer cells infected with viruses presented the viral antigens to CD8 T cells so that the delivery of viral antigen to cancer would be a novel therapeutic strategy.

Self-assembled nanovehicle-mediated co-encapsulation of inactivated EV71 virus and CpG oligonucleotides elicits potent anti-EV71 humoral and cellular immune protective responses

Inactivated vaccines are widely used for prevention of viral disease. Both humoral and cellular immune responses have been shown to play important roles in the control and clearance of virus infections. CpG motif containing oligodeoxynucleotides (ODN) have recently gained considerable interest and been used as vaccine adjuvant due to their potent abilities to modulate host immune response. In this study, CpG-ODN adjuvant and inactivated viral particles of enterovirus 71 (EV71) were co-encapsulated into nanoparticles (NP) generated by using protamine sulfate (PS) and carboxymethyl β-glucan (CMG) through a self-assembly approach. The administration of EV71 nanovaccine elicited not only specific anti-EV71 neutralizing antibody response, but also cellular immune response characterized by strong productions of IFN-α and IFN-γ. The results suggest that CMG/PS-based nanovehicles hold a great potential to be a novel platform for nanovaccine development against viral disease.

Peste des Petits Ruminants Virus Fusion and Hemagglutinin Proteins Trigger Antibody-Dependent Cell-Mediated Cytotoxicity in Infected Cells.

The adaptive immune system utilizes multiple effector mechanisms to clear viral infections. Among those antibody-dependent cell-mediated cytotoxicity (ADCC) can help recognize and clear virus-infected cells. In the present work we evaluated ADCC contribution to immunity in two economically important viral diseases that affect ruminants: bluetongue and peste des petits ruminants. Immune sera obtained from sheep experimentally infected with bluetongue virus (BTV) serotype 8 or peste des petits ruminant virus (PPRV) IC'89 were used for this study. PPRV immune sera could bind to the surface of PPRV-infected ovine B cells while BTV immune sera was unable to bind to the surface of BTV-infected sheep cells but could recognize intracellular BTV antigens. BTV and PPRV immune serum ADCC potency was established using an ovine autologous cytotoxicity assay that employed an NK cell-enriched fraction as effector cells and a virus-infected B cell-enriched fraction as target cells. In this system, immune sera triggered ADCC against PPRV-infected cells, but not against BTV-infected cells. PPRV immune sera could recognize PPRV fusion and hemagglutinin proteins on the surface of transfected cells, and enhanced lysis of these cells in ADCC assays. This indicated that these viral antigens are natural ADCC targets during PPRV infection. The present work describes a novel effector immune mechanism against PPRV in the natural host that could contribute to virus clearance highlighting the importance of studying protective immune mechanisms to improve current vaccines by invoking all effector arms of immunity.

T cell dynamics and response of the microbiota after gene therapy to treat X-linked severe combined immunodeficiency

BackgroundMutation of the IL2RG gene results in a form of severe combined immune deficiency (SCID-X1), which has been treated successfully with hematopoietic stem cell gene therapy. SCID-X1 gene therapy results in reconstitution of the previously lacking T cell compartment, allowing analysis of the roles of T cell immunity in humans by comparing before and after gene correction.MethodsHere we interrogate T cell reconstitution using four forms of high throughput analysis. (1) Estimation of the numbers of transduced progenitor cells by monitoring unique positions of integration of the therapeutic gene transfer vector. (2) Estimation of T cell population structure by sequencing of the recombined T cell receptor (TCR) beta locus. (3) Metagenomic analysis of microbial populations in oropharyngeal, nasopharyngeal, and gut samples. (4) Metagenomic analysis of viral populations in gut samples.ResultsComparison of progenitor and mature T cell populations allowed estimation of a minimum number of cell divisions needed to generate the observed populations. Analysis of microbial populations showed the effects of immune reconstitution, including normalization of gut microbiota and clearance of viral infections. Metagenomic analysis revealed enrichment of genes for antibiotic resistance in gene-corrected subjects relative to healthy controls, likely a result of higher healthcare exposure.ConclusionsThis multi-omic approach enables the characterization of multiple effects of SCID-X1 gene therapy, including T cell repertoire reconstitution, estimation of numbers of cell divisions between progenitors and daughter T cells, normalization of the microbiome, clearance of microbial pathogens, and modulations in antibiotic resistance gene levels. Together, these results quantify several aspects of the long-term efficacy of gene therapy for SCID-X1. This study includes data from ClinicalTrials.gov numbers NCT01410019, NCT01175239, and NCT01129544.

Liver clear cell foci and viral infection are associated with non-cirrhotic, non-fibrolamellar hepatocellular carcinoma in young patients from South America

We previously described a divergent clinical and molecular presentation of hepatocellular carcinoma (HCC) in Peru. The present study aimed to further characterize the tissue features associated with this singular nosological form of HCC in order to gain insight into the natural history of the disease. We performed an exploratory analysis of the histology of both tumor and non-tumor liver (NTL) tissues from 50 Peruvian HCC patients, and compared with that of 75 individuals with non-HCC liver tumor or benign liver lesions as a baseline for NTL features. We complemented this approach with a transcriptome analysis in a subset of NTL tissue samples and also performed an ultra-sensitive hepatitis B virus (HBV) detection in liver tissues of the patients. Overall, results highlighted the low rate of liver parenchymal alterations in a young patient cohort (median age: 40 years old), despite a strong prevalence of underlying HBV infection (c. 67%). Withal, liver clear cell foci of cellular alteration were genuinely associated with HCC and appended to some changes in immune and G protein-coupled receptor gene expression ontologies. Our findings confirm the occurrence of a particular setting of HCC in South America, a region where the pathophysiology of liver cancer remains largely unexplored.

Viruses have multiple paths to central nervous system pathology.

Although viral infections of the central nervous system (CNS) are known to acutely cause pathology in the form of cytokine-mediated neural tissue damage and inflammation, the pathophysiology of neurologic sequelae after viral clearance is incompletely understood. Alterations in microglial and glial biology in response to initial infiltration of immune cells that persist within the CNS have recently been shown to promote neuronal dysfunction and cognitive deficits in animal models of viral encephalitis. The current review summarizes the current knowledge on the possible role of innate immune signaling during acute infections as triggers of neurologic sequelae that persist, and may even worsen, after clearance of viral infections within the CNS.

Induction and transcriptional regulation of the co-inhibitory gene module in T cells.

Expression of co-inhibitory receptors, such as CTLA-4 and PD-1, on effector T cells is a key mechanism for ensuring immune homeostasis. Dysregulated co-inhibitory receptor expression on CD4+ T cells promotes autoimmunity while sustained overexpression on CD8+ T cells promotes T cell dysfunction or exhaustion, leading to impaired ability to clear chronic viral infections and cancer1,2. Here, we used RNA and protein expression profiling at single-cell resolution to identify a module of co-inhibitory receptors that includes not only several known co-inhibitory receptors (PD-1, Tim-3, Lag-3, and TIGIT), but also a number of novel surface receptors. We functionally validated two novel co-inhibitory receptors, Activated protein C receptor (Procr) and Podoplanin (Pdpn). The module of co-inhibitory receptors is co-expressed in both CD4+ and CD8+ T cells and is part of a larger co-inhibitory gene program that is shared by non-responsive T cells in multiple physiological contexts and is driven by the immunoregulatory cytokine IL-27. Computational analysis identified the transcription factors Prdm1 and c-Maf as cooperative regulators of the co-inhibitory module, which we validated experimentally. This molecular circuit underlies the co-expression of co-inhibitory receptors in T cells and identifies novel regulators of T cell function with the potential to regulate autoimmunity and tumor immunity.

Immunomodulatory activity of 2-deoxyguanosine nanoparticles in DNA vaccines

Abstract DNA vaccines induce protective immune responses against several pathogens and tumor cells, but strategies to improve their effectiveness are still under study. Only two adjuvants have been licensed by the FDA, which increases the needs for the discovery of novel adjuvants for HIV vaccines and other infectious diseases. In this regard, we study the immunomodulatory properties of 2-Deoxyguanosine-based nanoparticles (SHS) in DNA vaccines coding for HIV Gag (NL4-3 clone) and Vaccinia Virus Western Reserve (VVWR) A27 proteins. The sequence of A27L was codon optimized and linked to the Outer Domain-1 (OD1) of gp120 HIV-1 protein sequence serving as an additional molecular adjuvant. In this study, female Balb/c mice were immunized three times intramuscularly with plasmids (pGag and pOD1-A27L). Then, seven days after the last dose, cellular and humoral immunity were evaluated through ELISpot and ELISA assays. We found significantly higher frequencies of IFN-γ-producing cells in mouse immunized with pGag and pOD1-A27L co-formulated with SHS versus controls. We also found higher significant levels of IFN-γ over IL-4 in supernatant of splenocytes isolated from mice receiving pGag and pOD1-A27L combined with SHS. Moreover, administration of pOD1-A27L+SHS stimulated a significant higher production of total IgG in mice when compared to Naïve group. Here, we demonstrated that pGag and pOD1-A27L vaccines co-formulated with SHS nanoparticles successfully activate adaptive immunity through production of Th-1 cytokines and/or IgG antibodies. As this type of immunity is essential to clear many viral infections, these data support the evaluation of SHS nanoparticles as a novel adjuvant for DNA vaccines against multiple viral infectious agents.

Utilizing the Multi-parameter Capability of the ZE5 to Monitor T-Cell Exhaustion Following Immunotherapy.

Abstract The immune systems as evolved sophisticated mechanisms to distinguish between self and non-self, and dangerous and non-dangerous signals leading to appropriate and controlled immune responses against infection and cancer or tolerance to avoid attacking the host body. One pathway of immune suppression is T-cell exhaustion which shuts down effector T-cells. T-cells or T-lymphocytes, are an immune cell that help protect the body from infection and fight cancer. T-cell exhaustion is exploited by chronic viral infections and cancers to escape being targeted by the immune system. It results in a sustained expression of suppressive cell surface markers and effector function in these cells, meaning they are no longer able to function to remove the cancerous and infected cells. Recently, researchers have focused on using monoclonal antibody drugs to block these suppressive cell surface markers and re-invigorate the T-cells, restoring their effector capability to clear viral infection and cancer cells from the body. In this study, we use a 15-parameter panel to examine in-depth changes to the T-cell phenotype, exhaustion and cellular subset identity markers before and after chronic stimulation and in combination with a monoclonal antibody drug treatment targeting the receptor Programmed Cell Death 1 (PD-1).

Strategies to enhance NK cell function for the treatment of tumors and infections.

Natural killer (NK) cells are innate immune cells equipped with the ability to rapidly kill stressed cells that are neoplastic or virally infected. These cells are especially important in settings where these stressed cells downregulate MHC class I molecules and evade recognition by cytotoxic T cells. However, the activity of NK cells alone is often suboptimal to fully control tumor growth or to clear viral infections. Thus, the enhancement of NK cell function is necessary to fully harness their antitumor or antiviral potential. In this review, we discuss how NK cell function can be augmented by the modulation of signal transduction pathways, by the manipulation of inhibitory/activating receptors on NK cells, and by cytokine-induced activation. We also discuss how some of these strategies are currently impacting NK cells in the treatment of cancer and infections.

Long-lived CD8+ T cell responses following Crimean-Congo haemorrhagic fever virus infection.

Crimean-Congo haemorrhagic fever virus (CCHFV) is a member of the Orthonairovirus genus of the Nairoviridae family and is associated with haemorrhagic fever in humans. Although T lymphocyte responses are known to play a role in protection from and clearance of viral infections, specific T cell epitopes have yet to be identified for CCHFV following infection. A panel of overlapping peptides covering the CCHFV nucleoprotein and the structural glycoproteins, GN and GC, were screened by ELISpot assay to detect interferon gamma (IFN-γ) production in vitro by peripheral blood mononuclear cells from eleven survivors with previous laboratory confirmed CCHFV infection. Reactive peptides were located predominantly on the nucleoprotein, with only one survivor reacting to two peptides from the glycoprotein GC. No single epitope was immunodominant, however all but one survivor showed reactivity to at least one T cell epitope. The responses were present at high frequency and detectable several years after the acute infection despite the absence of continued antigenic stimulation. T cell depletion studies confirmed that IFN-γ production as detected using the ELISpot assay was mediated chiefly by CD8+ T cells. This is the first description of CD8+ T cell epitopic regions for CCHFV and provides confirmation of long-lived T cell responses in survivors of CCHFV infection.

Genome-Wide Exome Analysis of Cmv5-Disparate Mouse Strains that Differ in Host Resistance to Murine Cytomegalovirus Infection.

Host resistance to murine cytomegalovirus (MCMV) varies in different strains of laboratory mice due to differences in expression of determinants that control and clear viral infection. The major histocompatibility complex class I Dk molecule is one such determinant that controls MCMV through the action of natural killer (NK) cells. However, the extent of NK cell–mediated Dk-dependent resistance to infection varies in different mouse strains. The molecular genetic basis of this variation remains unclear. Previous work to examine the Dk effect on MCMV resistance in MA/My × C57L offspring discovered multiple quantitative trait loci (QTL) that may serve to modify NK cells or their capacity to respond during MCMV infection. One QTL in particular, Cmv5, was found to regulate the frequency of NK cells and secondary lymphoid organ structure in spleen during MCMV infection. Cmv5 alleles, however, have not been identified. We therefore sequenced and analyzed genome-wide exome (GWE) variants, including those aligned to the critical genetic interval, in Cmv5-disparate mouse strains. Their GWE variant profiles were compared to assess strain-specific sequence data integrity and to analyze mouse strain relatedness across the genome. GWE content was further compared against data from the Mouse Genomes Project. This approach was developed as a platform for using GWE variants to define genomic regions of divergence and similarity in different mouse strains while also validating the overall quality of GWE sequence data. Moreover, the analysis provides a framework for the selection of novel QTL candidate sequences, including at the Cmv5 critical region.