North American bats and their viruses: The effect of stressors on persistent infections and viral shedding

There is direct or circumstantial evidence that several viruses that cause no obvious disease in bats have spilled over into humans and other species causing serious and often fatal disease. The reasons for the lack of disease in bats or for the spillover of these viruses from bats are poorly understood. While there is considerable literature on the interactions of these viruses with their secondary hosts or their surrogates, little is known about the interactions of bat viruses in their natural hosts. We used a coronavirus detected in little brown bat (Myotis lucifugus) and a herpesvirus, detected in the big brown bat (Eptesicus fuscus), as models to understand the factors that might alter bat-virus relationships. We demonstrated that a coronavirus (Myotis lucifugus coronavirus – Myl-CoV) detected in the intestines of little brown bats, could persist in them during the 4 months of hibernation. Using this coronavirus-bat model, we showed that the stress of fungal infection by Pseudogymnoascus destructans (Pd), which causes bat white-nose syndrome (WNS), led to a 60-fold increase in viral replication in intestines than bats with virus alone. Increased viral replication correlated with the severity of Pd-related pathology and the intestine of fungus-infected bats showed changes in gene expression suggesting suppressed innate antiviral response and increased apoptotic responses. Our results suggest that the systemic effects of WNS leads to a resurgence of virus replication and increases the potential of virus shedding. Using a bat cell culture model, we showed that viral persistence could be disrupted by artificially suppressing the host cell’s antiviral response and was mediated through similar pathways that were observed during in-vivo experiments. To ascertain whether the effect of stressor could disrupt viral persistence in other bat-virus relationships, I studied the big brown bat herpesvirus. As herpesviruses inherently establish life-long latent infections in their hosts and reactivate periodically in response to stress, we used this model to study the effects of natural stressors on the bat-virus relationship. We characterized the herpesvirus and developed techniques for detecting the virus as well as for monitoring the adaptive antibody response against the virus. We showed that the bat gammaherpesvirus reactivates at the end of hibernation and was accompanied by a lower antibody level, which subsequently increased upon arousal. Our studies on coronavirus and herpesvirus show that bats have a long-term balanced and benign relationships with viruses and a variety of stressors could disrupt this balance allowing an increase in viral replication

Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged to cause widespread infections in humans. SARS-CoV-2 infections have been reported in the Kingdom of Saudi Arabia, where Middle East respiratory syndrome coronavirus (MERS-CoV) causes seasonal outbreaks with a case fatality rate of ~37 %. Here we show that there exists a theoretical possibility of future recombination events between SARS-CoV-2 and MERS-CoV RNA. Through computational analyses, we have identified homologous genomic regions within the ORF1ab and S genes that could facilitate recombination, and have analysed co-expression patterns of the cellular receptors for SARS-CoV-2 and MERS-CoV, ACE2 and DPP4, respectively, to identify human anatomical sites that could facilitate co-infection. Furthermore, we have investigated the likely susceptibility of various animal species to MERS-CoV and SARS-CoV-2 infection by comparing known virus spike protein–receptor interacting residues. In conclusion, we suggest that a recombination between SARS-CoV-2 and MERS-CoV RNA is possible and urge public health laboratories in high-risk areas to develop diagnostic capability for the detection of recombined coronaviruses in patient samples

Single-cell RNA sequencing of liver fine-needle aspirates captures immune diversity in the blood and liver in chronic hepatitis B patients

Background and Aims: HBV infection is restricted to the liver, where it drives exhaustion of virus-specific T and B cells and pathogenesis through dysregulation of intrahepatic immunity. Our understanding of liver-specific events related to viral control and liver damage has relied almost solely on animal models, and we lack useable peripheral biomarkers to quantify intrahepatic immune activation beyond cytokine measurement. Our objective was to overcome the practical obstacles of liver sampling using fine-needle aspiration and develop an optimized workflow to comprehensively compare the blood and liver compartments within patients with chronic hepatitis B using single-cell RNA sequencing. Approach and Results: We developed a workflow that enabled multi-site international studies and centralized single-cell RNA sequencing. Blood and liver fine-needle aspirations were collected, and cellular and molecular captures were compared between the Seq-Well S3 picowell-based and the 10× Chromium reverse-emulsion droplet–based single-cell RNA sequencing technologies. Both technologies captured the cellular diversity of the liver, but Seq-Well S3 effectively captured neutrophils, which were absent in the 10× dataset. CD8 T cells and neutrophils displayed distinct transcriptional profiles between blood and liver. In addition, liver fine-needle aspirations captured a heterogeneous liver macrophage population. Comparison between untreated patients with chronic hepatitis B and patients treated with nucleoside analogs showed that myeloid cells were highly sensitive to environmental changes while lymphocytes displayed minimal differences. Conclusions: The ability to electively sample and intensively profile the immune landscape of the liver, and generate high-resolution data, will enable multi-site clinical studies to identify biomarkers for intrahepatic immune activity in HBV and beyond.</p

Immune System Modulation and Viral Persistence in Bats: Understanding Viral Spillover

Bats harbor a myriad of viruses and some of these viruses may have spilled over to other species including humans. Spillover events are rare and several factors must align to create the &#8220;perfect storm&#8222; that would ultimately lead to a spillover. One of these factors is the increased shedding of virus by bats. Several studies have indicated that bats have unique defense mechanisms that allow them to be persistently or latently infected with viruses. Factors leading to an increase in the viral load of persistently infected bats would facilitate shedding of virus. This article reviews the unique nature of bat immune defenses that regulate virus replication and the various molecular mechanisms that play a role in altering the balanced bat&#8315;virus relationship

Tissue-Resident Memory T Cells in the Liver—Unique Characteristics of Local Specialists

T cells play an important role to build up an effective immune response and are essential in the eradication of pathogens. To establish a long-lasting protection even after a re-challenge with the same pathogen, some T cells differentiate into memory T cells. Recently, a certain subpopulation of memory T cells at different tissue-sites of infection was detected&mdash;tissue-resident memory T cells (TRM cells). These cells can patrol in the tissue in order to encounter their cognate antigen to establish an effective protection against secondary infection. The liver as an immunogenic organ is exposed to a variety of pathogens entering the liver through the systemic blood circulation or via the portal vein from the gut. It could be shown that intrahepatic TRM cells can reside within the liver tissue for several years. Interestingly, hepatic TRM cell differentiation requires a distinct cytokine milieu. In addition, TRM cells express specific surface markers and transcription factors, which allow their identification delimited from their circulating counterparts. It could be demonstrated that liver TRM cells play a particular role in many liver diseases such as hepatitis B and C infection, non-alcoholic fatty liver disease and even play a role in the development of hepatocellular carcinoma and in building long-lasting immune responses after vaccination. A better understanding of intrahepatic TRM cells is critical to understand the pathophysiology of many liver diseases and to identify new potential drug targets for the development of novel treatment strategies

White-nose syndrome is associated with increased replication of a naturally persisting coronaviruses in bats

Abstract Spillover of viruses from bats to other animals may be associated with increased contact between them, as well as increased shedding of viruses by bats. Here, we tested the prediction that little brown bats (Myotis lucifugus) co-infected with the M. lucifugus coronavirus (Myl-CoV) and with Pseudogymnoascus destructans (Pd), the fungus that causes bat white-nose syndrome (WNS), exhibit different disease severity, viral shedding and molecular responses than bats infected with only Myl-CoV or only P. destructans. We took advantage of the natural persistence of Myl-CoV in bats that were experimentally inoculated with P. destructans in a previous study. Here, we show that the intestines of virus-infected bats that were also infected with fungus contained on average 60-fold more viral RNA than bats with virus alone. Increased viral RNA in the intestines correlated with the severity of fungus-related pathology. Additionally, the intestines of bats infected with fungus exhibited different expression of mitogen-activated protein kinase pathway and cytokine related transcripts, irrespective of viral presence. Levels of coronavirus antibodies were also higher in fungal-infected bats. Our results suggest that the systemic effects of WNS may down-regulate anti-viral responses in bats persistently infected with M. lucifugus coronavirus and increase the potential of virus shedding