A Pseudomonas aeruginosa small RNA regulates chronic and acute infection.

The ability to switch between different lifestyles allows bacterial pathogens to thrive in diverse ecological niches1,2. However, a molecular understanding of their lifestyle changes within the human host is lacking. Here, by directly examining bacterial gene expression in human-derived samples, we discover a gene that orchestrates the transition between chronic and acute infection in the opportunistic pathogen Pseudomonas aeruginosa. The expression level of this gene, here named sicX, is the highest of the P. aeruginosa genes expressed in human chronic wound and cystic fibrosis infections, but it is expressed at extremely low levels during standard laboratory growth. We show that sicX encodes a small RNA that is strongly induced by low-oxygen conditions and post-transcriptionally regulates anaerobic ubiquinone biosynthesis. Deletion of sicX causes P. aeruginosa to switch from a chronic to an acute lifestyle in multiple mammalian models of infection. Notably, sicX is also a biomarker for this chronic-to-acute transition, as it is the most downregulated gene when a chronic infection is dispersed to cause acute septicaemia. This work solves a decades-old question regarding the molecular basis underlying the chronic-to-acute switch in P. aeruginosa and suggests oxygen as a primary environmental driver of acute lethality.

DUSP11-mediated control of 5'-triphosphate RNA regulates RIG-I sensitivity.

Deciphering the mechanisms that regulate the sensitivity of pathogen recognition receptors is imperative to understanding infection and inflammation. Here we demonstrate that the RNA triphosphatase dual-specificity phosphatase 11 (DUSP11) acts on both host and virus-derived 5'-triphosphate RNAs rendering them less active in inducing a RIG-I-mediated immune response. Reducing DUSP11 levels alters host triphosphate RNA packaged in extracellular vesicles and induces enhanced RIG-I activation in cells exposed to extracellular vesicles. Virus infection of cells lacking DUSP11 results in a higher proportion of triphosphorylated viral transcripts and attenuated virus replication, which is rescued by reducing RIG-I expression. Consistent with the activity of DUSP11 in the cellular RIG-I response, mice lacking DUSP11 display lower viral loads, greater sensitivity to triphosphorylated RNA, and a signature of enhanced interferon activity in select tissues. Our results reveal the importance of controlling 5'-triphosphate RNA levels to prevent aberrant RIG-I signaling and demonstrate DUSP11 as a key effector of this mechanism.

The Sequence Read Archive: a decade more of explosive growth.

The Sequence Read Archive (SRA, https://www.ncbi.nlm.nih.gov/sra/) stores raw sequencing data and alignment information to enhance reproducibility and facilitate new discoveries through data analysis. Here we note changes in storage designed to increase access and highlight analyses that augment metadata with taxonomic insight to help users select data. In addition, we present three unanticipated applications of taxonomic analysis.

Viral predation pressure on coral reefs.

BACKGROUND: Predation pressure and herbivory exert cascading effects on coral reef health and stability. However, the extent of these cascading effects can vary considerably across space and time. This variability is likely a result of the complex interactions between coral reefs' biotic and abiotic dimensions. A major biological component that has been poorly integrated into the reefs' trophic studies is the microbial community, despite its role in coral death and bleaching susceptibility. Viruses that infect bacteria can control microbial densities and may positively affect coral health by controlling microbialization. We hypothesize that viral predation of bacteria has analogous effects to the top-down pressure of macroorganisms on the trophic structure and reef health. RESULTS: Here, we investigated the relationships between live coral cover and viruses, bacteria, benthic algae, fish biomass, and water chemistry in 110 reefs spanning inhabited and uninhabited islands and atolls across the Pacific Ocean. Statistical learning showed that the abundance of turf algae, viruses, and bacteria, in that order, were the variables best predicting the variance in coral cover. While fish biomass was not a strong predictor of coral cover, the relationship between fish and corals became apparent when analyzed in the context of viral predation: high coral cover (> 50%) occurred on reefs with a combination of high predator fish biomass (sum of sharks and piscivores > 200 g m-2) and high virus-to-bacteria ratios (> 10), an indicator of viral predation pressure. However, these relationships were non-linear, with reefs at the higher and lower ends of the coral cover continuum displaying a narrow combination of abiotic and biotic variables, while reefs at intermediate coral cover showed a wider range of parameter combinations. CONCLUSIONS: The results presented here support the hypothesis that viral predation of bacteria is associated with high coral cover and, thus, coral health and stability. We propose that combined predation pressures from fishes and viruses control energy fluxes, inhibiting the detrimental accumulation of ecosystem energy in the microbial food web.

DUSP11 activity on triphosphorylated transcripts promotes Argonaute association with noncanonical viral microRNAs and regulates steady-state levels of cellular noncoding RNAs.

RNA silencing is a conserved eukaryotic gene expression regulatory mechanism mediated by small RNAs. In Caenorhabditis elegans, the accumulation of a distinct class of siRNAs synthesized by an RNA-dependent RNA polymerase (RdRP) requires the PIR-1 phosphatase. However, the function of PIR-1 in RNAi has remained unclear. Since mammals lack an analogous siRNA biogenesis pathway, an RNA silencing role for the mammalian PIR-1 homolog (dual specificity phosphatase 11 [DUSP11]) was unexpected. Here, we show that the RNA triphosphatase activity of DUSP11 promotes the RNA silencing activity of viral microRNAs (miRNAs) derived from RNA polymerase III (RNAP III) transcribed precursors. Our results demonstrate that DUSP11 converts the 5' triphosphate of miRNA precursors to a 5' monophosphate, promoting loading of derivative 5p miRNAs into Argonaute proteins via a Dicer-coupled 5' monophosphate-dependent strand selection mechanism. This mechanistic insight supports a likely shared function for PIR-1 in C. elegans Furthermore, we show that DUSP11 modulates the 5' end phosphate group and/or steady-state level of several host RNAP III transcripts, including vault RNAs and Alu transcripts. This study shows that steady-state levels of select noncoding RNAs are regulated by DUSP11 and defines a previously unknown portal for small RNA-mediated silencing in mammals, revealing that DUSP11-dependent RNA silencing activities are shared among diverse metazoans.

Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus.

Circular RNAs (circRNAs) are a conserved class of RNAs with diverse functions, including serving as messenger RNAs that are translated into peptides. Here we describe circular RNAs generated by human polyomaviruses (HPyVs), some of which encode variants of the previously described alternative large T antigen open reading frame (ALTO) protein. Circular ALTO RNAs (circALTOs) can be detected in virus positive Merkel cell carcinoma (VP-MCC) cell lines and tumor samples. CircALTOs are stable, predominantly located in the cytoplasm, and N6-methyladenosine (m6A) modified. The translation of MCPyV circALTOs into ALTO protein is negatively regulated by MCPyV-generated miRNAs in cultured cells. MCPyV ALTO expression increases transcription from some recombinant promoters in vitro and upregulates the expression of multiple genes previously implicated in MCPyV pathogenesis. MCPyV circALTOs are enriched in exosomes derived from VP-MCC lines and circALTO-transfected 293T cells, and purified exosomes can mediate ALTO expression and transcriptional activation in MCPyV-negative cells. The related trichodysplasia spinulosa polyomavirus (TSPyV) also expresses a circALTO that can be detected in infected tissues and produces ALTO protein in cultured cells. Thus, human polyomavirus circRNAs are expressed in human tumors and infected tissues and express proteins that have the potential to modulate the infectious and tumorigenic properties of these viruses.

Interpreting and de-noising genetically engineered barcodes in a DNA virus.

The concept of a nucleic acid barcode applied to pathogen genomes is easy to grasp and the many possible uses are straightforward. But implementation may not be easy, especially when growing through multiple generations or assaying the pathogen long-term. The potential problems include: the barcode might alter fitness, the barcode may accumulate mutations, and construction of the marked pathogens may result in unintended barcodes that are not as designed. Here, we generate approximately 5,000 randomized barcodes in the genome of the prototypic small DNA virus murine polyomavirus. We describe the challenges faced with interpreting the barcode sequences obtained from the library. Our Illumina NextSeq sequencing recalled much greater variation in barcode sequencing reads than the expected 5,000 barcodes-necessarily stemming from the Illumina library processing and sequencing error. Using data from defined control virus genomes cloned into plasmid backbones we develop a vetted post-sequencing method to cluster the erroneous reads around the true virus genome barcodes. These findings may foreshadow problems with randomized barcodes in other microbial systems and provide a useful approach for future work utilizing nucleic acid barcoded pathogens.

Retrospective Review of Antecustodial Deaths Referred for Medicolegal Autopsy at the Medical University of South Carolina.

Deaths occurring in police custody have dominated public discourse over recent years. However, deaths occurring after law enforcement have initiated nonphysical contact but before active restraint or containment lie outside the strict definition of "in custody." These "antecustodial" deaths demonstrate a unique population and interaction with law enforcement. A retrospective analysis of medicolegal cases referred to the Medical University of South Carolina from September 1, 2012, to April 28, 2022 was performed. Deaths during nonphysical interaction with or during evasion of law enforcement occurred in 78 cases and were categorized by demographic data, cause of death, manner of death, the presence of drugs and/or alcohol, and circumstances surrounding the interaction. Antecustodial deaths occurred primarily during law enforcement pursuit and deescalation scenarios. Decedents were predominantly male (92.3%) with a Black-to-White ratio of 1.1:1. The average age of male and female decedents was 35.7 and 32.2 years, respectively. The most common causes of death were gunshot wounds and blunt trauma sustained in motor vehicle crashes. The most common manner of death was homicide (43.6%), followed by suicide (28.2%) and accident (28.2%).

Spatiotemporal changes in largemouth bass mercury concentrations from Connecticut waterbodies, 1995-2021.

We evaluated spatiotemporal changes in the mean and variation in largemouth bass (Micropterus salmoides) mercury concentrations over three discrete time periods (1995, 2005-2006, and 2019-2021) across 56 Connecticut waterbodies. We detected largemouth bass raw mercury concentrations that exceeded the US Environmental Protection Agency (USEPA) Fish Tissue Residue Criterion (≥ 0.30 µg g-1 ww) in 75.1%, 63.3%, and 47.7% of all fish sampled during 1995, 2005-2006, and 2019-2021, respectively. Total length (TL)-adjusted largemouth bass mercury concentrations declined across all ecoregions in Connecticut between subsequent sampling periods but increased between 2005-2006 and 2019-2021 in the Northwest Hills/Uplands ecoregion. The coefficient of variation (CV) of largemouth bass TL-adjusted mercury concentrations increased through time, increasing from 25.78% during 1995 to 36.47% during 2019-2021. The probability of a largemouth bass having a raw mercury concentration > 0.30 µg g-1 ww increased with total length (TL), but the TL with a 50% probability varied across ecoregions and periods. The variation in largemouth bass mercury concentrations highlights the roles that changes to individual behaviors, food web structure, lake properties, and legacy mercury may play in shaping broad patterns and trends in mercury consumption risks.

A cost-effective maize ear phenotyping platform enables rapid categorization and quantification of kernels.

High-throughput phenotyping systems are powerful, dramatically changing our ability to document, measure, and detect biological phenomena. Here, we describe a cost-effective combination of a custom-built imaging platform and deep-learning-based computer vision pipeline. A minimal version of the maize (Zea mays) ear scanner was built with low-cost and readily available parts. The scanner rotates a maize ear while a digital camera captures a video of the surface of the ear, which is then digitally flattened into a two-dimensional projection. Segregating GFP and anthocyanin kernel phenotypes are clearly distinguishable in ear projections and can be manually annotated and analyzed using image analysis software. Increased throughput was attained by designing and implementing an automated kernel counting system using transfer learning and a deep learning object detection model. The computer vision model was able to rapidly assess over 390 000 kernels, identifying male-specific transmission defects across a wide range of GFP-marked mutant alleles. This includes a previously undescribed defect putatively associated with mutation of Zm00001d002824, a gene predicted to encode a vacuolar processing enzyme. Thus, by using this system, the quantification of transmission data and other ear and kernel phenotypes can be accelerated and scaled to generate large datasets for robust analyses.

Tropical forests can maintain hyperdiversity because of enemies.

Explaining the maintenance of tropical forest diversity under the countervailing forces of drift and competition poses a major challenge to ecological theory. Janzen-Connell effects, in which host-specific natural enemies restrict the recruitment of juveniles near conspecific adults, provide a potential mechanism. Janzen-Connell is strongly supported empirically, but existing theory does not address the stable coexistence of hundreds of species. Here we use high-performance computing and analytical models to demonstrate that tropical forest diversity can be maintained nearly indefinitely in a prolonged state of transient dynamics due to distance-responsive natural enemies. Further, we show that Janzen-Connell effects lead to community regulation of diversity by imposing a diversity-dependent cost to commonness and benefit to rarity. The resulting species-area and rank-abundance relationships are consistent with empirical results. Diversity maintenance over long time spans does not require dispersal from an external metacommunity, speciation, or resource niche partitioning, only a small zone around conspecific adults in which saplings fail to recruit. We conclude that the Janzen-Connell mechanism can explain the maintenance of tropical tree diversity while not precluding the operation of other niche-based mechanisms such as resource partitioning.

Non-Firearm-related Homicides at the Medical University of South Carolina, 2013-2018.

ABSTRACT: After high-profile events involving firearms, gun violence often becomes the center stage of public discourse with national media attention, overshadowing less common causes of homicidal deaths, such as sharp force injury, blunt trauma, and asphyxia. A retrospective analysis of all cases referred for medicolegal autopsy to the Medical and Forensic Autopsy Division of the Department of Pathology and Laboratory Medicine at the Medical University of South Carolina from 2013 to 2018 documented 793 deaths where the manner was classified as homicide. Of these, 18% (144) of the deaths were caused by non-firearm-inflicted injuries. Nonfirearm homicides were further categorized by method; demographic data including decedent age, race, and sex; and other variables such as incident site, decedent relationship status to the alleged perpetrator, number of other homicide fatalities associated with a homicide event, and the presence of drugs and alcohol in the decedents. Data accrued in this review were compared with national statistics published by the Centers for Disease Control and Prevention and to the overall Medical University of South Carolina firearm-related homicide decedent demographic statistics for this same period. Findings augment existing information available regarding non-gun-related homicides and may be valuable in contributing to the ongoing public and political debate regarding firearm and nonfirearm fatalities.

The coronavirus macrodomain is required to prevent PARP-mediated inhibition of virus replication and enhancement of IFN expression.

ADP-ribosylation is a ubiquitous post-translational addition of either monomers or polymers of ADP-ribose to target proteins by ADP-ribosyltransferases, usually by interferon-inducible diphtheria toxin-like enzymes known as PARPs. While several PARPs have known antiviral activities, these activities are mostly independent of ADP-ribosylation. Consequently, less is known about the antiviral effects of ADP-ribosylation. Several viral families, including Coronaviridae, Togaviridae, and Hepeviridae, encode for macrodomain proteins that bind to and hydrolyze ADP-ribose from proteins and are critical for optimal replication and virulence. These results suggest that macrodomains counter cellular ADP-ribosylation, but whether PARPs or, alternatively, other ADP-ribosyltransferases cause this modification is not clear. Here we show that pan-PARP inhibition enhanced replication and inhibited interferon production in primary macrophages infected with macrodomain-mutant but not wild-type coronavirus. Specifically, knockdown of two abundantly expressed PARPs, PARP12 and PARP14, led to increased replication of mutant but did not significantly affect wild-type virus. PARP14 was also important for the induction of interferon in mouse and human cells, indicating a critical role for this PARP in the regulation of innate immunity. In summary, these data demonstrate that the macrodomain is required to prevent PARP-mediated inhibition of coronavirus replication and enhancement of interferon production.

RNA triphosphatase DUSP11 enables exonuclease XRN-mediated restriction of hepatitis C virus.

Seventy percent of people infected with hepatitis C virus (HCV) will suffer chronic infection, putting them at risk for liver disease, including hepatocellular carcinoma. The full range of mechanisms that render some people more susceptible to chronic infection and liver disease is still being elucidated. XRN exonucleases can restrict HCV replication and may help to resolve HCV infections. However, it is unknown how 5' triphosphorylated HCV transcripts, primary products of the viral polymerase, become susceptible to attack by 5' monophosphate-specific XRNs. Here, we show that the 5' RNA triphosphatase DUSP11 acts on HCV transcripts, rendering them susceptible to XRN-mediated attack. Cells lacking DUSP11 show substantially enhanced HCV replication, and this effect is diminished when XRN expression is reduced. MicroRNA-122 (miR-122), a target of current phase II anti-HCV drugs, is known to protect HCV transcripts against XRNs. We show that HCV replication is less dependent on miR-122 in cells lacking DUSP11. Combined, these results implicate DUSP11 as an important component of XRN-mediated restriction of HCV.

Human Trafficking Cases Presenting within Child Advocacy Centers.

Although human trafficking of minors is an increasing concern within the United States, very little information is known about how trafficking cases are processed within child advocacy centers (CACs). The current study addresses this gap in the literature by providing descriptive information about victims, service referrals, and prosecutorial outcomes for human trafficking cases presenting at CACs across a Midwestern state. The data originates from a state-wide study focused on understanding the scope of human trafficking cases. Specifically, the dataset includes 210 youth presenting at CACs over a three-year period of time. In this sample, the typical human trafficking case involved sex trafficking of a self-identified white female victim, with an offender known to the victim. Most child survivors passing through CACs were referred to medical and mental health services, although these service referrals did not greatly differ across at-risk versus substantiated trafficking cases. Overall, the findings suggest that CACs are uniquely positioned to encounter human trafficking cases and provide needed services to trafficking survivors. Finally, recommendations are provided for CACs regarding the intake and identification of trafficking cases more broadly.

Experimental metatranscriptomics reveals the costs and benefits of dissolved organic matter photo-alteration for freshwater microbes.

Microbes and sunlight convert terrigenous dissolved organic matter (DOM) in surface waters to greenhouse gases. Prior studies show contrasting results about how biological and photochemical processes interact to contribute to the degradation of DOM. In this study, DOM leached from the organic layer of tundra soil was exposed to natural sunlight or kept in the dark, incubated in the dark with the natural microbial community, and analysed for gene expression and DOM chemical composition. Microbial gene expression (metatranscriptomics) in light and dark treatments diverged substantially after 4 h. Gene expression suggested that sunlight exposure of DOM initially stimulated microbial growth by (i) replacing the function of enzymes that degrade higher molecular weight DOM such as enzymes for aromatic carbon degradation, oxygenation, and decarboxylation, and (ii) releasing low molecular weight compounds and inorganic nutrients from DOM. However, growth stimulation following sunlight exposure of DOM came at a cost. Sunlight depleted the pool of aromatic compounds that supported microbial growth in the dark treatment, ultimately causing slower growth in the light treatment over 5 days. These first measurements of microbial metatranscriptomic responses to photo-alteration of DOM provide a mechanistic explanation for how sunlight exposure of terrigenous DOM alters microbial processing and respiration of DOM.

Identification of virus-encoded microRNAs in divergent Papillomaviruses.

MicroRNAs (miRNAs) are small RNAs that regulate diverse biological processes including multiple aspects of the host-pathogen interface. Consequently, miRNAs are commonly encoded by viruses that undergo long-term persistent infection. Papillomaviruses (PVs) are capable of undergoing persistent infection, but as yet, no widely-accepted PV-encoded miRNAs have been described. The incomplete understanding of PV-encoded miRNAs is due in part to lack of tractable laboratory models for most PV types. To overcome this, we have developed miRNA Discovery by forced Genome Expression (miDGE), a new wet bench approach to miRNA identification that screens numerous pathogen genomes in parallel. Using miDGE, we screened over 73 different PV genomes for the ability to code for miRNAs. Our results show that most PVs are unlikely to code for miRNAs and we conclusively demonstrate a lack of PV miRNA expression in cancers associated with infections of several high risk HPVs. However, we identified five different high-confidence or highly probable miRNAs encoded by four different PVs (Human PVs 17, 37, 41 and a Fringilla coelebs PV (FcPV1)). Extensive in vitro assays confirm the validity of these miRNAs in cell culture and two FcPV1 miRNAs are further confirmed to be expressed in vivo in a natural host. We show that miRNAs from two PVs (HPV41 & FcPV1) are able to regulate viral transcripts corresponding to the early region of the PV genome. Combined, these findings identify the first canonical PV miRNAs and support that miRNAs of either host or viral origin are important regulators of the PV life cycle.

Impact of outcomes data on the management of postoperative hypocalcemia in head and neck endocrine surgery patients.

Postoperative hypocalcemia is a well-described outcome following thyroid and parathyroid surgery with symptoms ranging from clinically insignificant laboratory findings to tetany and seizures. The aims of this study were 1. To identify the characteristics and management patterns of postoperative hypocalcemia in head and neck endocrine surgery patients and 2. To compare outcomes between patients treated with empiric calcium and patients treated using a biochemically driven calcium replacement algorithm. Clinical electronic medical record (EMR) data was collected from patients who had undergone total thyroidectomy, completion thyroidectomy, and/or parathyroidectomy at Wake Forest Baptist Medical Center (WFBMC), a tertiary referral and academic institution. Between July 1, 2016, and June 30, 2017, 298 adult patients underwent surgery by a WFBMC Head & Neck (H&N) endocrine surgeon. Objective calcium and parathyroid hormone levels, postoperative supplementation with calcium and Vitamin D, 30-day physician access line (PAL) phone call utilization, emergency department (ED) encounters, and readmission rates were queried. The overall rate of hypocalcemia was 17.4%. No statistically significant difference in PAL utilization, ED visits, or readmissions was found between the empiric supplementation group and those whose supplementation was biochemically directed (PAL 5.0% vs. 5.0% [p = 0.983], ED visit 3.3% vs. 2.5% [p = 0.744], Readmission 1.7% vs. 0% [p = 0.276]). The overall postoperative rates of hypocalcemia and hypoparathyroidism following H&N endocrine surgery were consistent with the reported literature. Neither method of calcium supplementation was superior in reducing PAL utilization, ED encounters, or readmission.

Surgical management of Eagle syndrome: A 17-year experience with open and transoral robotic styloidectomy.

Eagle Syndrome (ES) is a rare disorder that can present with symptoms ranging from globus sensation to otalgia that is attributed to an elongated styloid process and/or calcified stylohyoid ligament. No standardized treatment algorithm exists, and although various surgical approaches have been described, data on the use of transoral robotic surgery (TORS) in this population is limited. To investigate the utility of TORS in the treatment of ES, a retrospective review in 19 ES patients was carried out at a single academic, tertiary medical center between 2000 and 2017. Nineteen patients underwent twenty-one styloid resections: 6 performed via TORS and 15 via transcervical approach. Across all patients, 90% reported some degree of lasting improvement in symptoms while 55% reported significant improvement. When TORS was compared to transcervical resection, there was no difference in the subjective rate of "meaningful" (83 vs. 57%) versus rate of "non-meaningful" symptom improvement (17 vs. 43%) (p = 0.35). There was a trend towards less estimated blood loss (EBL), operative time, and post-operative length of stay (LOS) with TORS versus transcervical cases (9.2 mL vs. 30.0 mL, 98 vs. 156 min, and 0.7 vs. 1.2 days); however, these did not reach statistical significance (p = .11, 0.13, and 0.42, respectively). Three patients experienced complications associated with an open approach, as compared to none with TORS. In select patients, TORS styloidectomy is a reasonable surgical alternative to traditional transoral and transcervical techniques as it provides similar symptom improvement, and reduced length of stay, blood loss, and operative time.

The Murine Polyomavirus MicroRNA Locus Is Required To Promote Viruria during the Acute Phase of Infection.

Polyomaviruses (PyVs) can cause serious disease in immunosuppressed hosts. Several pathogenic PyVs encode microRNAs (miRNAs), small RNAs that regulate gene expression via RNA silencing. Despite recent advances in understanding the activities of PyV miRNAs, the biological functions of PyV miRNAs during in vivo infections are mostly unknown. The studies presented here used murine polyomavirus (MuPyV) as a model to assess the roles of the PyV miRNAs in a natural host. This analysis revealed that a MuPyV mutant that is unable to express miRNAs has enhanced viral DNA loads in select tissues at late times after infection. This is consistent with the PyV miRNAs functioning to reduce viral replication during the persistent phase of infection in a natural host. Additionally, the MuPyV miRNA locus promotes viruria during the acute phase of infection as evidenced by a defect in shedding during infection with the miRNA mutant virus. The viruria defect of the miRNA mutant virus could be rescued by infecting Rag2-/- mice. These findings implicate the miRNA locus as functioning in both the persistent and acute phases of infection and suggest a role for MuPyV miRNA in evading the adaptive immune response.IMPORTANCE MicroRNAs are expressed by diverse viruses, but for only a few is there any understanding of their in vivo function. PyVs can cause serious disease in immunocompromised hosts. Therefore, increased knowledge of how these viruses interact with the immune response is of clinical relevance. Here we show a novel activity for a viral miRNA locus in promoting virus shedding. This work indicates that in addition to any role for the PyV miRNA locus in long-term persistence, it also has biological activity during the acute phase. As this mutant phenotype is alleviated by infection of mice lacking an adaptive immune response, our work also connects the in vivo activity of the PyV miRNA locus to the immune response. Given that PyV-associated disease is associated with alterations in the immune response, our findings help to better understand how the balance between PyVs and the immune response becomes altered in pathogenic states.