The bat connection: The heterogeneity of COVID-19 makes it challenging to predict the course of infection in an individual. Upon virus infection, interferons (IFNs) generate the initial signals for cellular defenses. Knowing that defects in IFN signaling are associated with more severe COVID-19, Wickenhagen et al . used IFN-stimulated gene expression screening on human lung cells from which they identified a gene for 2′-5′-oligoadenylate synthetase 1 (OAS1) (see the Perspective by Schoggins). OAS1 stimulates RNase L to inhibit the virus with a surprising degree of specificity, targeting the membranous organelles in which it replicates. In most mammals, OAS1 is attached to membranes by a prenyl group. However, billions of humans do not have the prenylated OAS1 haplotype, including many experiencing severe COVID-19. The same is true for horseshoe bats, prolific sources of betacoronaviruses, because of an ancient retrotransposition event. —CA

The recent emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the underlying cause of Coronavirus Disease 2019 (COVID-19), has led to a worldwide pandemic causing substantial morbidity, mortality, and economic devastation. In response, many laboratories have redirected attention to SARS-CoV-2, meaning there is an urgent need for tools that can be used in laboratories unaccustomed to working with coronaviruses. Here we report a range of tools for SARS-CoV-2 research. First, we describe a facile single plasmid SARS-CoV-2 reverse genetics system that is simple to genetically manipulate and can be used to rescue infectious virus through transient transfection (without in vitro transcription or additional expression plasmids). The rescue system is accompanied by our panel of SARS-CoV-2 antibodies (against nearly every viral protein), SARS-CoV-2 clinical isolates, and SARS-CoV-2 permissive cell lines, which are all openly available to the scientific community. Using these tools, we demonstrate here that the controversial ORF10 protein is expressed in infected cells. Furthermore, we show that the promising repurposed antiviral activity of apilimod is dependent on TMPRSS2 expression. Altogether, our SARS-CoV-2 toolkit, which can be directly accessed via our website at https://mrcppu-covid.bio/, constitutes a resource with considerable potential to advance COVID-19 vaccine design, drug testing, and discovery science.

Pestiviruses are highly variable RNA viruses belonging to the continuously growing family Flaviviridae. A genetically very distinct pestivirus was recently discovered in the USA, designated atypical porcine pestivirus (APPV). Here, a screening of 369 sera from apparently healthy adult pigs demonstrated the existence of APPV in Germany with an estimated individual prevalence of 2.4% and ~10% at farm level. Additionally, APPV genomes were detected in newborn piglets affected by congenital tremor (CT), but genomes were absent in unaffected piglets. High loads of genomes were identified in glandular epithelial cells, follicular centers of lymphoid organs, the inner granular cell layer of the cerebellum, as well as in the trigeminal and spinal ganglia. Retrospective analysis of cerebellum samples from 2007 demonstrated that APPV can be found in piglets with CT of unsolved aetiology. Determination of the first European APPV complete polyprotein coding sequence revealed 88.2% nucleotide identity to the APPV sequence from the USA. APPV sequences derived from different regions in Germany demonstrated to be highly variable. Taken together, the results of this study strongly suggest that the presence of APPV genomes in newborn piglets correlates with CT, while no association with clinical disease could be observed in viremic adult pigs.

The so-called Schmallenberg virus (SBV), first detected in a German town of the same name in October 2011, is a novel emerging orthobunyavirus in Europe causing malformations and severe economic loss in ruminants. This report describes lesions in 40 sheep, 2 goats, and 16 cattle naturally infected with SBV as determined by real-time quantitative reverse transcription polymerase chain reaction. The most common macroscopic changes were arthrogryposis, vertebral malformations, brachygnathia inferior, and malformations of the central nervous system, including hydranencephaly, porencephaly, hydrocephalus, cerebellar hypoplasia, and micromyelia. Histologic lesions included lymphohistiocytic meningoencephalomyelitis in some cases, glial nodules mainly in the mesencephalon and hippocampus of lambs and goats, and neuronal degeneration and necrosis mainly in the brain stem of calves. Micromyelia was characterized by a loss of gray and white matter, with few neurons remaining in the ventral horn in calves. The skeletal muscles had myofibrillar hypoplasia in lambs and calves. The lesions of SBV-associated abortion and perinatal death are similar to those attributed to Akabane virus and other viruses in the Simbu group of bunyaviruses.

Schmallenberg virus (SBV) is an emerging orthobunyavirus of ruminants associated with outbreaks of congenital malformations in aborted and stillborn animals. Since its discovery in November 2011, SBV has spread very rapidly to many European countries. Here, we developed molecular and serological tools, and an experimental in vivo model as a platform to study SBV pathogenesis, tropism and virus-host cell interactions. Using a synthetic biology approach, we developed a reverse genetics system for the rapid rescue and genetic manipulation of SBV. We showed that SBV has a wide tropism in cell culture and “synthetic” SBV replicates in vitro as efficiently as wild type virus. We developed an experimental mouse model to study SBV infection and showed that this virus replicates abundantly in neurons where it causes cerebral malacia and vacuolation of the cerebral cortex. These virus-induced acute lesions are useful in understanding the progression from vacuolation to porencephaly and extensive tissue destruction, often observed in aborted lambs and calves in naturally occurring Schmallenberg cases. Indeed, we detected high levels of SBV antigens in the neurons of the gray matter of brain and spinal cord of naturally affected lambs and calves, suggesting that muscular hypoplasia observed in SBV-infected lambs is mostly secondary to central nervous system damage. Finally, we investigated the molecular determinants of SBV virulence. Interestingly, we found a biological SBV clone that after passage in cell culture displays increased virulence in mice. We also found that a SBV deletion mutant of the non-structural NSs protein (SBVΔNSs) is less virulent in mice than wild type SBV. Attenuation of SBV virulence depends on the inability of SBVΔNSs to block IFN synthesis in virus infected cells. In conclusion, this work provides a useful experimental framework to study the biology and pathogenesis of SBV. Schmallenberg virus (SBV) was discovered in Germany (near the town of Schmallenberg) in November 2011 and since then has been found to be the cause of malformations and stillbirths in ruminants. SBV has spread very rapidly to many European countries including the Netherlands, Belgium, France and the United Kingdom. Very little is known about the biological properties of this virus and there is no vaccine available. In this study (i) we developed an approach (called reverse genetics) that allows the recovery of “synthetic” SBV under laboratory conditions; (ii) we developed a mouse model of infection for SBV; (iii) we showed that SBV replicates in neurons of experimentally infected mice similar to naturally infected lambs and calves; (iv) we developed viral mutants that are not as pathogenic as the original virus due to the inability to counteract the host cell defenses; and v) we identified mutations that are associated with increased virulence. This work provides the experimental tools to understand how this newly emerged virus causes disease in ruminants. In addition, it will now be possible to manipulate the SBV genome in order to develop highly effective vaccines.

Synaptophysin is an abundant membrane protein of synaptic vesicles. The objective of this study was to determine the utility of identifying synaptophysin accumulations (spheroids/ovoids/bulbs) in CNS white matter as an immunohistochemical marker of axonal damage in demyelinating and neuroinflammatory conditions. We studied the cuprizone toxicity and Theiler’s murine encephalomyelitis virus (TMEV) infection models of demyelination and analyzed CNS tissue from patients with multiple sclerosis (MS). Synaptophysin colocalized with the amyloid precursor protein (APP), a well-known marker of axonal damage. In the cuprizone model, numerous pathological synaptophysin/APP-positive spheroids/ovoids were identified in the corpus callosum at the onset of demyelination; the extent of synaptophysin/APP-positive vesicle aggregates correlated with identified reactive microglia; during late and chronic demyelination, the majority of synaptophysin/APP-positive spheroids/ovoids resolved but a few remained, indicating persistent axonal damage; in the remyelination phase, scattered large synaptophysin/APP-positive bulbs persisted. In the TMEV model, only a few large- to medium-sized synaptophysin/APP-positive bulbs were found in demyelinated areas. In MS patient tissue samples, the bulbs appeared exclusively at the inflammatory edges of lesions. In conclusion, our data suggest that synaptophysin as a reliable marker of axonal damage in the CNS in inflammatory/demyelinating conditions.