Identification of a novel neurovirulence factor encoded by the cryptic orphan gene UL31.6 of herpes simplex virus 1.

Although the herpes simplex virus type 1 (HSV-1) genome was thought to contain approximately 80 different protein coding sequences (CDSs), recent multi-omics analyses reported HSV-1 encodes more than 200 potential CDSs. However, few of the newly identified CDSs were confirmed to be expressed at the peptide or protein level in HSV-1-infected cells. Furthermore, the impact of the proteins they encode on HSV-1 infection is largely unknown. This study focused on a newly identified CDS, UL31.6. Re-analyzation of our previous chemical proteomics data verified that UL31.6 was expressed at the peptide level in HSV-1-infected cells. Antisera raised against a viral protein encoded by UL31.6 (pUL31.6) reacted with a protein with an approximate molecular mass of 37 kDa in lysates of Vero cells infected with each of three HSV-1 strains. pUL31.6 was efficiently dissociated from virions in high-salt solution. A UL31.6-null mutation had a minimal effect on HSV-1 gene expression, replication, cell-to-cell spread, and morphogenesis in Vero cells; in contrast, it significantly reduced HSV-1 cell-to-cell spread in three neural cells but not in four non-neural cells including Vero cells. The UL31.6-null mutation also significantly reduced the mortality and viral replication in the brains of mice after intracranial infection, but had minimal effects on pathogenic manifestations in and around the eyes, and viral replication detected in the tear films of mice after ocular infection. These results indicated that pUL31.6 was a tegument protein and specifically acted as a neurovirulence factor by potentially promoting viral transmission between neuronal cells in the central nervous system.IMPORTANCERecent multi-omics analyses reported the herpes simplex virus type 1 (HSV-1) genome encodes an additional number of potential coding sequences (CDSs). However, the expressions of these CDSs at the peptide or protein levels and the biological effects of these CDSs on HSV-1 infection remain largely unknown. This study annotated a cryptic orphan CDS, termed UL31.6, an HSV-1 gene that encodes a tegument protein with an approximate molecular mass of 37 kDa, which specifically acts as a neurovirulence factor. Our study indicates that HSV-1 proteins important for viral pathogenesis remain to be identified and a comprehensive understanding of the pathogenesis of HSV-1 will require not only the identification of cryptic orphan CDSs using emerging technologies but also step-by-step and in-depth analyses of each of the cryptic orphan CDSs.

Sparse Bayesian Learning With Weakly Informative Hyperprior and Extended Predictive Information Criterion.

This article considers the regression problem with sparse Bayesian learning (SBL) when the number of weights P is larger than the data size N , i.e., P >> N . The situation induces overfitting and makes regression tasks, such as prediction and basis selection, challenging. We show a strategy to address this problem. Our strategy consists of two steps. The first is to apply an inverse gamma hyperprior with a shape parameter close to zero over the noise precision of automatic relevance determination (ARD) prior. This hyperprior is associated with the concept of a weakly informative prior in terms of enhancing sparsity. The model sparsity can be controlled by adjusting a scale parameter of inverse gamma hyperprior, leading to the prevention of overfitting. The second is to select an optimal scale parameter. We develop an extended predictive information criterion (EPIC) for optimal selection. We investigate the strategy through relevance vector machine (RVM) with a multiple-kernel scheme dealing with highly nonlinear data, including smooth and less smooth regions. This setting is one form of the regression task with SBL in the P >> N situation. As an empirical evaluation, regression analyses on four artificial datasets and eight real datasets are performed. We see that the overfitting is prevented, while predictive performance may be not drastically superior to comparative methods. Our methods allow us to select a small number of nonzero weights while keeping the model sparse. Thus, the methods are expected to be useful for basis and variable selection.

Multi-Task Learning for Compositional Data via Sparse Network Lasso.

Multi-task learning is a statistical methodology that aims to improve the generalization performances of estimation and prediction tasks by sharing common information among multiple tasks. On the other hand, compositional data consist of proportions as components summing to one. Because components of compositional data depend on each other, existing methods for multi-task learning cannot be directly applied to them. In the framework of multi-task learning, a network lasso regularization enables us to consider each sample as a single task and construct different models for each one. In this paper, we propose a multi-task learning method for compositional data using a sparse network lasso. We focus on a symmetric form of the log-contrast model, which is a regression model with compositional covariates. Our proposed method enables us to extract latent clusters and relevant variables for compositional data by considering relationships among samples. The effectiveness of the proposed method is evaluated through simulation studies and application to gut microbiome data. Both results show that the prediction accuracy of our proposed method is better than existing methods when information about relationships among samples is appropriately obtained.

Incidence and Risk Factors of Immediate Hypersensitivity Reactions and Immunization Stress-Related Responses With COVID-19 mRNA Vaccine.

BACKGROUND: With the implementation of mass vaccination campaigns against COVID-19, the safety of vaccine needs to be evaluated. OBJECTIVE: We aimed to assess the incidence and risk factors for immediate hypersensitivity reactions (IHSR) and immunization stress-related responses (ISRR) with the Moderna COVID-19 vaccine. METHODS: This nested case-control study included recipients who received the Moderna vaccine at a mass vaccination center, Japan. Recipients with IHSR and ISRR were designated as cases 1 and 2, respectively. Controls 1 and 2 were selected from recipients without IHSR or ISRR and matched (1 case: 4 controls) with cases 1 and cases 2, respectively. Conditional logistic regression analysis was used to identify risk factors associated with IHSR and ISRR. RESULTS: Of the 614,151 vaccine recipients who received 1,201,688 vaccine doses, 306 recipients (cases 1) and 2478 recipients (cases 2) showed 318 events of IHSR and 2558 events of ISRR, respectively. The incidence rates per million doses were estimated as IHSR: 266 cases, ISRR: 2129 cases, anaphylaxis: 2 cases, and vasovagal syncope: 72 cases. Risk factors associated with IHSR included female, asthma, atopic dermatitis, thyroid diseases, and a history of allergy; for ISRR, the risk factors were younger age, female, asthma, thyroid diseases, mental disorders, and a history of allergy and vasovagal reflex. CONCLUSION: In the mass vaccination settings, the Moderna vaccine can be used safely owing to the low incidence rates of IHSR and anaphylaxis. However, providers should be aware of the occurrence of ISRR. Although recipients with risk factors are associated with slightly increased risks of IHSR and ISRR, this is not of sufficient magnitude to warrant special measures regarding their vaccination.

Assessment of Delayed Large Local Reactions After the First Dose of the SARS-CoV-2 mRNA-1273 Vaccine in Japan.

Importance: A delayed large local reaction (DLLR) is a delayed-onset adverse skin reaction that may occur after injection of the mRNA-1273 vaccine against SARS-CoV-2. Objective: To examine the associations between sex and age and susceptibility of DLLRs after mRNA-1273 vaccination. Design, Setting, and Participants: This retrospective cross-sectional study was conducted at the Self-Defense Forces large-scale vaccination center in Tokyo, Japan, from May 24 to November 30, 2021. Participants were recipients of the second dose of the mRNA-1273 vaccine who had received the first dose 4 to 6 weeks earlier. Five experienced dermatologists interviewed participants to assess whether they had experienced symptoms of DLLR after administration of the first dose of the vaccine. Exposure: Receipt of the first dose of the mRNA-1273 vaccine. Main Outcomes and Measures: The primary outcome was the incidence rate of DLLR stratified by sex and age group. Odds ratios (ORs) were calculated to evaluate the differences between groups. Outcomes were tested for significance using the Pearson χ2 test with 95% CIs. Results: Of 5893 participants in the study, 3318 (56.3%) were male (median age, 55 years [IQR, 38-68 years]) and 2575 (43.7%) were female (median age, 50 years [IQR, 34-67 years]). A total of 747 participants (12.7%) experienced DLLR symptoms after the first dose of the mRNA-1273 vaccine. Symptoms were mild and not considered as contraindications to the vaccine. The incidence rate was significantly higher among females (22.4% [577 participants]; OR, 5.30; 95% CI, 4.42-6.34) than among males (5.1% [170 participants]; reference). Moreover, the incidence rate was significantly higher among participants aged 30 to 39 years (14.3% [129 participants]; OR, 1.68; 95% CI, 1.25-2.26), 40 to 49 years (15.8% [136 participants]; OR, 1.89; 95% CI, 1.41-2.53), 50 to 59 years (14.9% [104 participants]; OR, 1.76; 95% CI, 1.29-2.40), and 60 to 69 years (12.6% [182 participants]; OR, 1.45; 95% CI, 1.10-1.91) than among participants aged 18 to 29 years (9.0% [81 participants]; reference). Conclusions and Relevance: In this cross-sectional study, the first dose of the SARS-CoV-2 mRNA-1273 vaccine was associated with a higher incidence of DLLR among females and among individuals aged 30 to 69 years. The findings suggest that DLLR may be a type IV allergic skin reaction.

A case report of coronavirus disease-2019-induced acute asthma exacerbation in an obese patient.

The coronavirus disease-2019 (COVID-19) has spread worldwide. Previous studies indicated a low prevalence of COVID-19 induced acute exacerbations of asthma. We present a 39-year-old-male obese asthmatic case who experienced acute asthma exacerbation during COVID-19. On day 8 of infection, his cough and dyspnea worsened with hypoxia and wheezing. Laboratory test results revealed elevated interleukin-6 (IL-6) and total immunoglobulin E (IgE) levels without eosinophilia. Two months since the onset, hypoxia disappeared with decreased IL-6 and IgE levels. Our case suggested that obesity and high serum IL-6 and IgE levels may have contributed to atypical asthma exacerbation in COVID-19.

Comparison of CT findings of coronavirus disease 2019 (COVID-19) pneumonia caused by different major variants.

PURPOSE: To explore the CT findings and pneumonnia progression pattern of the Alpha and Delta variants of SARS-CoV-2 by comparing them with the pre-existing wild type. METHOD: In this retrospective comparative study, a total of 392 patients with COVID-19 were included: 118 patients with wild type (70 men, 56.8 ± 20.7 years), 137 with Alpha variant (93 men, 49.4 ± 17.0 years), and 137 with Delta variant (94 men, 45.4 ± 12.4). Chest CT evaluation included opacities and repairing changes as well as lesion distribution and laterality. Chest CT severity score was also calculated. These parameters were statistically compared across the variants. RESULTS: Ground glass opacity (GGO) with consolidation and repairing changes were more frequent in the order of Delta variant, Alpha variant, and wild type throughout the disease course. Delta variant showed GGO with consolidation more conspicuously than did the other two on days 1-4 (vs. wild type, Bonferroni corrected p = 0.01; vs. Alpha variant, Bonferroni corrected p = 0.003) and days 5-8 (vs. wild type, Bonferroni corrected p < 0.001; vs. Alpha variant, Bonferroni corrected-p = 0.003). Total lung CT severity scores of Delta variant were higher than those of wild type on days 1-4 and 5-8 (Bonferroni corrected p = 0.01 and Bonferroni corrected p = 0.005, respectively) and that of Alpha variant on days 1-4 (Bonferroni corrected p = 0.002). There was no difference in the CT findings between wild type and Alpha variant. CONCLUSIONS: Pneumonia progression of Delta variant may be more rapid and severe in the early stage than in the other two.

Endpoint Recombinase Polymerase Amplification (RPA) Assay for Enumeration of Thiocyanate-degrading Bacteria.

An endpoint recombination amplification reaction (RPA) assay for assessing the abundance of the gene encoding thiocyanate dehydrogenase (TcDH) in Thiohalobacter has been developed. The RPA reaction was performed at 37°C for 30| |min, terminated by the addition of sodium dodecyl sulfate (SDS) solution, and the DNA concentration of the RPA product was fluorometrically measured. The abundance of TcDH in 22 activated sludge samples and 7 thiocyanate-degrading enrichment cultures ranged between 2.5×103 and 1.5×106 copies µL-1, showing a linear relationship (R2=0.83) with those measured using a conventional quantitative PCR assay.

Federated learning for predicting clinical outcomes in patients with COVID-19.

Federated learning (FL) is a method used for training artificial intelligence models with data from multiple sources while maintaining data anonymity, thus removing many barriers to data sharing. Here we used data from 20 institutes across the globe to train a FL model, called EXAM (electronic medical record (EMR) chest X-ray AI model), that predicts the future oxygen requirements of symptomatic patients with COVID-19 using inputs of vital signs, laboratory data and chest X-rays. EXAM achieved an average area under the curve (AUC) >0.92 for predicting outcomes at 24 and 72 h from the time of initial presentation to the emergency room, and it provided 16% improvement in average AUC measured across all participating sites and an average increase in generalizability of 38% when compared with models trained at a single site using that site's data. For prediction of mechanical ventilation treatment or death at 24 h at the largest independent test site, EXAM achieved a sensitivity of 0.950 and specificity of 0.882. In this study, FL facilitated rapid data science collaboration without data exchange and generated a model that generalized across heterogeneous, unharmonized datasets for prediction of clinical outcomes in patients with COVID-19, setting the stage for the broader use of FL in healthcare.

Efficacy and Safety of Favipiravir in Moderate COVID-19 Pneumonia Patients without Oxygen Therapy: A Randomized, Phase III Clinical Trial.

INTRODUCTION: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the cause of coronavirus disease 2019 (COVID-19), is an enveloped, single-stranded RNA virus. Favipiravir is an orally administrable antiviral drug whose mechanism of action is to selectively inhibit RNA-dependent RNA polymerase. A preliminary trial in COVID-19 patients reported significant improvements across a multitude of clinical parameters, but these findings have not been confirmed in an adequate well-controlled trial. We conducted a randomized, single-blind, placebo-controlled Phase III trial assessing the efficacy and safety of favipiravir in patients with moderate pneumonia not requiring oxygen therapy. METHODS: COVID-19 patients with moderate pneumonia (SpO2 ≥ 94%) within 10 days of onset of fever (temperature ≥ 37.5 °C) were assigned to receive either placebo or favipiravir (1800 mg twice a day on Day 1, followed by 800 mg twice a day for up to 13 days) in a ratio of 1:2. An adaptive design was used to re-estimate the sample size. The primary endpoint was a composite outcome defined as the time to improvement in temperature, oxygen saturation levels (SpO2), and findings on chest imaging, and recovery to SARS-CoV-2-negative. This endpoint was re-examined by the Central Committee under blinded conditions. RESULTS: A total of 156 patients were randomized. The median time of the primary endpoint was 11.9 days in the favipiravir group and 14.7 days in the placebo group, with a significant difference (p = 0.0136). Favipiravir-treated patients with known risk factors such as obesity or coexisting conditions provided better effects. Furthermore, patients with early-onset in the favipiravir group showed higher odds ratio. No deaths were documented. Although adverse events in the favipiravir group were predominantly transient, the incidence was significantly higher. CONCLUSIONS: The results suggested favipiravir may be one of options for moderate COVID-19 pneumonia treatment. However, the risk of adverse events, including hyperuricemia, should be carefully considered. TRIAL REGISTRATION: Clinicaltrials.jp number: JapicCTI-205238.

Efficacy of Chest Radiography as a Primary Care Triage Tool in Severe Coronavirus Disease.

Objective Severe acute respiratory syndrome coronavirus 2 has spread globally, and it is important to utilize medical resources properly, especially in critically ill patients. We investigated the validity of chest radiography as a tool for predicting aggravation in coronavirus disease (COVID-19) cases. Methods A total of 104 laboratory-confirmed COVID-19 cases were referred from the cruise ship "Diamond Princess" to the Self-Defense Forces Central Hospital in Japan from February 11 to 25, 2020. Fifty-nine symptomatic patients were selected. Chest radiography was performed upon hospitalization; subsequently, patients were categorized into the positive radiograph (Group A) and negative radiograph (Group B) groups. Radiographic findings were analyzed with a six-point semiquantitative score. Group A was further classified into two additional subgroups: patients who required oxygen therapy during their clinical courses (Group C) and patients who did not (Group D). Clinical records, laboratory data, and radiological findings were collected for an analysis. Results Among 59 patients, 34 were men with a median age of 60 years old. Groups A, B, C, and D consisted of 33, 26, 12, and 21 patients, respectively. The number of patients requiring oxygen administration was significantly larger in Group A than in Group B. The consolidation score on chest radiographs was significantly higher in Group C than in Group D. When chest radiographs showed consolidation in more than two lung fields, the positive likelihood ratio of deterioration was 10.6. Conclusions Chest radiography is a simple and easy-to-use clinic-level triage tool for predicting the severity of COVID-19 and may contribute to the allocation of medical resources.

Multilinear Common Component Analysis via Kronecker Product Representation.

We consider the problem of extracting a common structure from multiple tensor data sets. For this purpose, we propose multilinear common component analysis (MCCA) based on Kronecker products of mode-wise covariance matrices. MCCA constructs a common basis represented by linear combinations of the original variables that lose little information of the multiple tensor data sets. We also develop an estimation algorithm for MCCA that guarantees mode-wise global convergence. Numerical studies are conducted to show the effectiveness of MCCA.

Complete Genome Sequence of Thiohalobacter sp. Strain COW1, Isolated from Activated Sludge Treating Coke Oven Wastewater.

A thiocyanate-degrading bacterium, Thiohalobacter sp. strain COW1, was isolated from activated sludge treating coke oven wastewater, and the complete genome sequence was determined. COW1 contained a single circular chromosome (3.23 Mb; G+C content, 63.4%) in which 2,788 protein-coding genes, 39 tRNA genes, and 3 rRNA genes were identified.

Virus-like insertions with sequence signatures similar to those of endogenous nonretroviral RNA viruses in the human genome.

Understanding the genetics and taxonomy of ancient viruses will give us great insights into not only the origin and evolution of viruses but also how viral infections played roles in our evolution. Endogenous viruses are remnants of ancient viral infections and are thought to retain the genetic characteristics of viruses from ancient times. In this study, we used machine learning of endogenous RNA virus sequence signatures to identify viruses in the human genome that have not been detected or are already extinct. Here, we show that the k-mer occurrence of ancient RNA viral sequences remains similar to that of extant RNA viral sequences and can be differentiated from that of other human genome sequences. Furthermore, using this characteristic, we screened RNA viral insertions in the human reference genome and found virus-like insertions with phylogenetic and evolutionary features indicative of an exogenous origin but lacking homology to previously identified sequences. Our analysis indicates that animal genomes still contain unknown virus-derived sequences and provides a glimpse into the diversity of the ancient virosphere.

Federated Learning used for predicting outcomes in SARS-COV-2 patients.

'Federated Learning' (FL) is a method to train Artificial Intelligence (AI) models with data from multiple sources while maintaining anonymity of the data thus removing many barriers to data sharing. During the SARS-COV-2 pandemic, 20 institutes collaborated on a healthcare FL study to predict future oxygen requirements of infected patients using inputs of vital signs, laboratory data, and chest x-rays, constituting the "EXAM" (EMR CXR AI Model) model. EXAM achieved an average Area Under the Curve (AUC) of over 0.92, an average improvement of 16%, and a 38% increase in generalisability over local models. The FL paradigm was successfully applied to facilitate a rapid data science collaboration without data exchange, resulting in a model that generalised across heterogeneous, unharmonized datasets. This provided the broader healthcare community with a validated model to respond to COVID-19 challenges, as well as set the stage for broader use of FL in healthcare.

Prediction of an increase in oxygen requirement of SARS-CoV-2 pneumonia using three different scoring systems.

INTRODUCTION: In patients with severe coronavirus disease 2019 (COVID-19), respiratory failure is a major complication and its symptoms occur around one week after onset. The CURB-65, A-DROP and expanded CURB-65 tools are known to predict the risk of mortality in patients with community-acquired pneumonia. In this retrospective single-center retrospective study, we aimed to assess the correlations of the A-DROP, CURB-65, and expanded CURB-65 scores on admission with an increase in oxygen requirement in patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia. METHODS: We retrospectively analyzed 207 patients who were hospitalized with SARS-CoV-2 pneumonia at the Self-Defense Forces Central Hospital in Tokyo, Japan. Performance of A-DROP, CURB-65, and the expanded CURB-65 scores were validated. In addition, we assessed whether there were any associations between an increase in oxygen requirement and known risk factors for critical illness in COVID-19, including elevation of liver enzymes and C-reactive protein (CRP), lymphocytopenia, high D-dimer levels and the chest computed tomography (CT) score. RESULTS: The areas under the curve for the ability of CURB-65, A-DROP, and the expanded CURB-65 scores to predict an increase in oxygen requirement were 0.6961, 0.6980 and 0.8327, respectively, and the differences between the three groups were statistically significant (p < 0.001). Comorbid cardiovascular disease, lymphocytopenia, elevated CRP, liver enzyme and D-dimer levels, and higher chest CT score were significantly associated with an increase in oxygen requirement CONCLUSIONS: The expanded CURB-65 score can be a better predictor of an increase in oxygen requirement in patients with SARS-CoV-2 pneumonia.

Indicators of Acute Kidney Injury as Biomarkers to Differentiate Heatstroke from Coronavirus Disease 2019: A Retrospective Multicenter Analysis.

BACKGROUND: Coronavirus disease 2019 (COVID-19) and heat-related illness are systemic febrile diseases. These illnesses must be differentiated during a COVID-19 pandemic in summer. However, no studies have compared and distinguished heat-related illness and COVID-19. We compared data from patients with early heat-related illness and those with COVID-19. METHODS: This retrospective observational study included 90 patients with early heat-related illness selected from the Heatstroke STUDY 2017-2019 (nationwide registries of heat-related illness in Japan) and 86 patients with laboratory-confirmed COVID-19 who had fever or fatigue and were admitted to one of two hospitals in Tokyo, Japan. RESULTS: Among vital signs, systolic blood pressure (119 vs. 125 mm Hg, p = 0.02), oxygen saturation (98% vs. 97%, p < 0.001), and body temperature (36.6°C vs. 37.6°C, p<0.001) showed significant between-group differences in the heatstroke and COVID-19 groups, respectively. The numerous intergroup differences in laboratory findings included disparities in white blood cell count (10.8 × 103/µL vs. 5.2 × 103/µL, p<0.001), creatinine (2.2 vs. 0.85 mg/dL, p<0.001), and C-reactive protein (0.2 vs. 2.8 mg/dL, p<0.001), although a logistic regression model achieved an area under the curve (AUC) of 0.966 using these three factors. A Random Forest machine learning model achieved an accuracy, precision, recall, and AUC of 0.908, 0.976, 0.842, and 0.978, respectively. Creatinine was the most important feature of this model. CONCLUSIONS: Acute kidney injury was associated with heat-related illness, which could be essential in distinguishing or evaluating patients with fever in the summer during a COVID-19 pandemic.

Cucumber Mosaic Virus Infection in Arabidopsis: A Conditional Mutualistic Symbiont?

A cucumber mosaic virus isolate, named Ho [CMV(Ho)], was isolated from a symptomless Arabidopsis halleri field sample containing low virus titers. An analysis of CMV(Ho) RNA molecules indicated that the virus isolate, besides the usual cucumovirus tripartite RNA genome, additionally contained defective RNA3 molecules and a satellite RNA. To study the underlying mechanism of the persistent CMV(Ho) infection in perennial A. halleri, infectious cDNA clones were generated for all its genetic elements. CMV, which consists of synthetic transcripts from the infectious tripartite RNA genomes, and designated CMV(Ho)tr, multiplied in A. halleri and annual Arabidopsis thaliana Col-0 to a similar level as the virulent strain CMV(Y), but did not induce any symptoms in them. The response of Col-0 to a series of reassortant CMVs between CMV(Ho)tr and CMV(Y) suggested that the establishment of an asymptomatic phenotype of CMV(Ho) infection was due to the 2b gene of CMV RNA2, but not due to the presence of the defective RNA3 and satellite RNA. The accumulation of CMV(Ho) 2b protein tagged with the FLAG epitope (2b.Ho-FLAG) in 2b.Ho-FLAG-transformed Col-0 did not induce any symptoms, suggesting a 2b-dependent persistency of CMV(Ho)tr infection in Arabidopsis. The 2b protein interacted with Argonaute 4, which is known to regulate the cytosine methylation levels of host genomic DNA. Whole genomic bisulfite sequencing analysis of CMV(Ho)tr- and mock-inoculated Col-0 revealed that cytosine hypomethylation in the promoter regions of 82 genes, including two genes encoding transcriptional regulators (DOF1.7 and CBP1), was induced in response to CMV(Ho)tr infection. Moreover, the increased levels of hypomethylation in the promoter region of both genes, during CMV(Ho)tr infection, were correlated with the up- or down-regulation of their expression. Taken altogether, the results indicate that during persistent CMV(Ho) infection in Arabidopsis, host gene expression may be epigenetically modulated resulting from a 2b-mediated cytosine hypomethylation of host genomic DNA.

Identification of a herpes simplex virus 1 gene encoding neurovirulence factor by chemical proteomics.

Identification of the complete set of translated genes of viruses is important to understand viral replication and pathogenesis as well as for therapeutic approaches to control viral infection. Here, we use chemical proteomics, integrating bio-orthogonal non-canonical amino acid tagging and high-resolution mass spectrometry, to characterize the newly synthesized herpes simplex virus 1 (HSV-1) proteome in infected cells. In these infected cells, host cellular protein synthesis is shut-off, increasing the chance to preferentially detect viral proteomes. We identify nine previously cryptic orphan protein coding sequences whose translated products are expressed in HSV-1-infected cells. Functional characterization of one identified protein, designated piUL49, shows that it is critical for HSV-1 neurovirulence in vivo by regulating the activity of virally encoded dUTPase, a key enzyme that maintains accurate DNA replication. Our results demonstrate that cryptic orphan protein coding genes of HSV-1, and probably other large DNA viruses, remain to be identified.