Zygosaccharomyces bailii virus Z (ZbV-Z) is a monosegmented dsRNA virus that infects the yeast Zygosaccharomyces bailii and remains unclassified to date despite its discovery >20 years ago. The previously reported nucleotide sequence of ZbV-Z (GenBank AF224490) encompasses two nonoverlapping long ORFs: upstream ORF1 encoding the putative coat protein and downstream ORF2 encoding the RNA-dependent RNA polymerase (RdRp). The lack of overlap between these ORFs raises the question of how the downstream ORF is translated. After examining the previous sequence of ZbV-Z, we predicted that it contains at least one sequencing error to explain the nonoverlapping ORFs, and hence we redetermined the nucleotide sequence of ZbV-Z, derived from the same isolate of Z. bailii as previously studied, to address this prediction. The key finding from our new sequence, which includes several insertions, deletions, and substitutions relative to the previous one, is that ORF2 in fact overlaps ORF1 in the +1 frame. Moreover, a proposed sequence motif for +1 programmed ribosomal frameshifting, previously noted in influenza A viruses, plant amalgaviruses, and others, is also present in the newly identified ORF1–ORF2 overlap region of ZbV-Z. Phylogenetic analyses provided evidence that ZbV-Z represents a distinct taxon most closely related to plant amalgaviruses (genus Amalgavirus, family Amalgaviridae). We conclude that ZbV-Z is the prototype of a new species, Zygosaccharomyces bailii virus Z, which we propose to assign as type species of a new genus of monosegmented dsRNA mycoviruses in family Amalgaviridae. Comparisons involving other unclassified mycoviruses with RdRps apparently related to those of plant amalgaviruses, and having either mono- or bisegmented dsRNA genomes, are also discussed.

Highlights d CD94/NKG2A educates uterine NK cells d NKG2A-deficient dams display reduced utero-placental hemodynamic adaptations d Asymmetric growth restriction and abnormal brain development in NKG2A-deficient dams d Non-functional HLA-B/HLA-E/NKG2A pathway exposes women to greater pre-eclampsia risk

Freshwater planarians, flatworms from order Tricladida, are experimental models of stem cell biology and tissue regeneration. An aspect of their biology that remains less well studied is their relationship with viruses that may infect them. In this study, we identified a taxon of monosegmented dsRNA viruses in five planarian species, including the well-characterized model Schmidtea mediterranea. Sequences for the S. mediterranea virus (abbreviated SmedTV for S. mediterranea tricladivirus) were found in public transcriptome data from multiple institutions, indicating that SmedTV is prevalent in S. mediterranea lab colonies, though without causing evident disease. Presence of SmedTV in discrete cells was shown through in situ hybridization methods for detecting the viral RNA. SmedTV-staining cells were found to be concentrated in neural structures (eyes and brain) but were also scattered in other worm tissues as well. In contrast, few SmedTV-staining cells were seen in stem cell compartments (also consistent with RNA-sequencing data) or early blastema tissue. RNAi targeted to the SmedTV sequence led to apparent cure of infection, though effects on worm health or behavior were not observed. Efforts to transmit SmedTV horizontally through microinjection were unsuccessful. Based on these findings, we conclude that SmedTV infects S. mediterranea in a persistent manner and undergoes vertical transmission to progeny worms during serial passage in lab colonies. The utility of S. mediterranea as a regeneration model, coupled with the apparent capacity of SmedTV to evade normal host immune/RNAi defenses under standard conditions, argues that further studies are warranted to explore this newly recognized virus–host system. IMPORTANCE Planarians are freshwater flatworms, related more distantly to tapeworms and flukes, and have been developed as models to study the molecular mechanisms of stem cell biology and tissue regeneration. These worms live in aquatic environments, where they are likely to encounter a variety of viruses, bacteria, and eukaryotic organisms with pathogenic potential. How the planarian immune system has evolved to cope with these potential pathogens is not well understood, and only two types of planarian viruses have been described to date. Here we report discovery and inaugural studies of a novel taxon of dsRNA viruses in five different planarian species. The virus in the best-characterized model species, Schmidtea mediterranea, appears to persist long term in that host while avoiding endogenous antiviral or RNAi mechanisms. The S. mediterranea virus–host system thus seems to offer opportunity for gaining new insights into host defenses and their evolution in an important lab model.

The interaction between immune cells and virus-infected targets involves multiple plasma membrane (PM) proteins. A systematic study of PM protein modulation by vaccinia virus (VACV), the paradigm of host regulation, has the potential to reveal not only novel viral immune evasion mechanisms, but also novel factors critical in host immunity. Here, >1000 PM proteins were quantified throughout VACV infection, revealing selective downregulation of known T and NK cell ligands including HLA-C, downregulation of cytokine receptors including IFNAR2, IL-6ST and IL-10RB, and rapid inhibition of expression of certain protocadherins and ephrins, candidate activating immune ligands. Downregulation of most PM proteins occurred via a proteasome-independent mechanism. Upregulated proteins included a decoy receptor for TRAIL. Twenty VACV-encoded PM proteins were identified, of which five were not recognised previously as such. Collectively, this dataset constitutes a valuable resource for future studies on antiviral immunity, host-pathogen interaction, poxvirus biology, vector-based vaccine design and oncolytic therapy.

Reproductive immunology has moved on from the classical Medawar question of 60 years ago “why doesn’t the mother reject the fetus?”. Looking beyond fetal-maternal tolerance, modern reproductive immunology focuses on how the maternal immune system supports fetal growth. Maternal uterine natural killer (uNK) cells, in partnership with fetal trophoblast cells, regulate physiological vascular changes in the uterus of pregnant women and mice. These vascular changes are necessary to build the placenta and sustain fetal growth. NK cell functions in the uterus and elsewhere, including anti-viral and anti-tumour immunity mediated mostly by blood NK cells, are modulated by NK cell education, a quantifiable process that determines cellular activation thresholds. This process relies largely on interactions between self-MHC class I molecules and inhibitory NK cell receptors. By getting to know self, the maternal immune system sets up uNK cells to participate to tissue homeostasis in the womb. Placentation can be viewed as a form of natural transplantation unique in vertebrates and this raises the question of how uNK cell education or missing-self recognition affect their function and, ultimately fetal growth. Here, using combinations of MHC-sufficient and -deficient mice, we show that uNK cell education is linked to maternal and not fetal MHC, so that MHC-deficient dams produce more growth-restricted fetuses, even when the fetuses themselves express self-MHC. We also show that, while peripheral NK cells reject bone marrow cells according to the established rules of missing-self recognition, uNK cells educated by maternal MHC do not reject fetuses that miss self-MHC and these fetuses grow to their full potential. While these results are not directly applicable to clinical research, they show that NK education by maternal MHC-I is required for optimal fetal growth.

26The phylum Platyhelminthes is composed of both parasitic and non-parasitic flatworms. While 27 the parasitic species have drawn attention for their wide effects on human and livestock heath, 28 free-living flatworms, such as freshwater planarians, have become molecular models of 29 regeneration and stem cell biology in the laboratory. However, one aspect of planarian biology 30 that remains understudied is the relationship between host and any endemic viruses. Here we 31 used searches of multiple transcriptomes from Schmidtea mediterranea asexual strain CIW4 and 32 detected a novel, double-stranded RNA (dsRNA) virus, named S. mediterranea tricladivirus 33 (SmedTV), which represents a distinct taxon (proposed new genus) within a larger taxon of 34 monosegmented dsRNA viruses of diverse hosts. Experimental evidence for SmedTV in S. 35 mediterranea CIW4 was obtained through whole-mount in situ hybridization (WISH). SmedTV 36 "expression" (detected by both sense and anti-sense probes) was discrete yet variable from worm 37 to worm and cell type to cell type, suggesting a persistent infection. Single-cell RNA sequencing 38 (scRNAseq) further supported that SmedTV expression was low in stem cells, but substantially 39 higher in multiple, though not all, differentiated tissues, with notable neural enrichment. 40Interestingly, knockdown of SmedTV by RNA-interference resulted in a "cure" of SmedTV after 41 10 RNAi doses, and expression remained undetectable by WISH even after 90 days. Due to 42 being able to evade host defenses and the endogenous RNAi pathway, we believe SmedTV 43 represents a novel animal model to study host-virus evolution. 45 Planarians are freshwater flatworms and emerging models to study the molecular mechanisms of 46 adult stem cell and regenerative biology. However, they also live in aquatic environments with 47 high amounts of viruses, bacteria, fungi, and protist pathogens. How the planarian immune 48 system copes with all of these is largely unknown and only 2 types of virus have been described. 44 Statement of significance 49Here we find a novel dsRNA virus, endemic to multiple types of flatworms. We show that it is a 50 persistent infection, and likely transmits from stem cell to differentiated cell in the planarian, 51 while avoiding endogenous RNA-interference machinery and mechanisms used to suppress 52 viruses. We present this as a new model to study host-virus defense and evolution. 53 54 55 The phylum Platyhelminthes encompasses both parasitic and nonparasitic species of 56 flatworms. Two classes, Cestoda and Trematoda, include globally important parasites of humans 57 (tapeworms and flukes, respectively) and another class, Monogenea, includes parasites of fish 58 (Verneau, Du Preez et al. 2009, Ramm 2017). Planarians fall outside these three classes of 59 parasitic flatworms, and species commonly used as laboratory models are members of order 60 Tricladida. Of these free-living (nonparasitic) species, Schmidtea mediterranea (S. mediterranea) 61 is the most extensively used as a ...

Natural killer (NK) cells have an established role in controlling poxvirus infection and there is a growing interest to exploit their capabilities in the context of poxvirus-based oncolytic therapy and vaccination. How NK cells respond to poxvirus-infected cells to become activated is not well established. To address this knowledge gap, we studied the NK cell response to vaccinia virus (VACV) in vivo, using a systemic infection murine model. We found broad alterations in NK cells transcriptional activity in VACV-infected mice, consistent with both direct target cell recognition and cytokine exposure. There were also alterations in the expression levels of specific NK surface receptors (NKRs), including the Ly49 family and SLAM receptors, as well as upregulation of memory-associated NK markers. Despite the latter observation, adoptive transfer of VACV-expercienced NK populations did not confer protection from infection. Comparison with the NK cell response to murine cytomegalovirus (MCMV) infection highlighted common features, but also distinct NK transcriptional programmes initiated by VACV. Finally, there was a clear overlap between the NK transcriptional response in humans vaccinated with an attenuated VACV, modified vaccinia Ankara (MVA), demonstrating conservation between the NK response in these different host species. Overall, this study provides new data about NK cell activation, function, and homeostasis during VACV infection, and may have implication for the design of VACV-based therapeutics.

Poverty and inequality are both the starting point, and the ultimate outcome, for most neglected tropical diseases (NTDs). As a group of 20 diseases, NTDs are typified by their prevalence among the poor, excluded, and marginalised within society. In the absence of quality healthcare provision, many NTDs lead to long term disability, disfigurement, and stigma, which in turn act to reinforce the exclusion and poverty experienced by the afflicted. The path leading to illness is often determined by a widespread lack of access to formal education, timely healthcare, adequate living conditions, employment and nutrition. The reasons for such deprivation are complicated, but ultimately reduce to a persistence of inequalities in affected regions. These inequalities can manifest differently depending on the demographic being studied: gender, ethnicity, geographic location, level of formal education, can all determine the ease with which NTDs are transmitted, diagnosed or treated. Yet, regardless of contextual differences, NTDs continue to persist because individuals within endemic regions experience a healthcare system that is, either directly or indirectly, inequitable. The healthcare system referred to in this context is not confined to simply formal healthcare settings. Rather, it encompasses local healers, community healthcare professionals or volunteers, drug administration programmes, community mental health provision, the formal education system, and, in extension, even the infrastructure that exists to physically connect individuals to their healthcare provider. Failing to ensure parity across each of these components for every citizen equates to a discriminatory healthcare system which fails to recognise the individual’s basic human right to “a standard of living adequate for the health and well-being of themselves and of their family, including food, clothing, housing and medical care and necessary social services” (Article 25- Universal Declaration of Human Rights). To ensure NTDs are managed in a way that is sustainable in the long term, the underlying societal inequalities which allow them to persist must be first understood.