Single-cell analysis reveals an antiviral network that controls Zika virus infection in human dendritic cells.

Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10× Genomics Chromium single-cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human monocyte-derived dendritic cells infected with ZIKV at the single-cell level. The bystander cells, which lacked detectable viral RNA, expressed an antiviral state that was enriched for genes coinciding predominantly with a type I interferon (IFN) response. Within the infected cells, viral RNA negatively correlated with type I IFN-dependent and -independent genes (the antiviral module). We modeled the ZIKV-specific antiviral state at the protein level, leveraging experimentally derived protein interaction data. We identified a highly interconnected network between the antiviral module and other host proteins. In this work, we propose a new paradigm for evaluating the antiviral response to a specific virus, combining an unbiased list of genes that highly correlate with viral RNA on a per-cell basis with experimental protein interaction data. IMPORTANCE: Zika virus (ZIKV) remains a public health threat given its potential for re-emergence and the detrimental fetal outcomes associated with infection during pregnancy. Understanding the dynamics between ZIKV and its host is critical to understanding ZIKV pathogenesis. Through ZIKV-inclusive single-cell RNA sequencing (scRNA-seq), we demonstrate on the single-cell level the dynamic interplay between ZIKV and the host: the transcriptional program that restricts viral infection and ZIKV-mediated inhibition of that response. Our ZIKV-inclusive scRNA-seq assay will serve as a useful tool for gaining greater insight into the host response to ZIKV and can be applied more broadly to the flavivirus field.

Single cell analysis reveals an antiviral network that controls Zika virus infection in human dendritic cells.

Zika virus (ZIKV) is a mosquito-borne flavivirus that caused an epidemic in the Americas in 2016 and is linked to severe neonatal birth defects, including microcephaly and spontaneous abortion. To better understand the host response to ZIKV infection, we adapted the 10x Genomics Chromium single cell RNA sequencing (scRNA-seq) assay to simultaneously capture viral RNA and host mRNA. Using this assay, we profiled the antiviral landscape in a population of human moDCs infected with ZIKV at the single cell level. The bystander cells, which lacked detectable viral RNA, expressed an antiviral state that was enriched for genes coinciding predominantly with a type I interferon (IFN) response. Within the infected cells, viral RNA negatively correlated with type I IFN dependent and independent genes (antiviral module). We modeled the ZIKV specific antiviral state at the protein level leveraging experimentally derived protein-interaction data. We identified a highly interconnected network between the antiviral module and other host proteins. In this work, we propose a new paradigm for evaluating the antiviral response to a specific virus, combining an unbiased list of genes that highly correlate with viral RNA on a per cell basis with experimental protein interaction data. Our ZIKV-inclusive scRNA-seq assay will serve as a useful tool to gaining greater insight into the host response to ZIKV and can be applied more broadly to the flavivirus field.

Assessment of Knowledge Regarding Furcation Defects among Dental Practitioners: A Multinational Survey

@#This study was undertaken to assess knowledge regarding furcation defects among dental fraternity. This is an open-ended, randomized, web-based cross-sectional multinational online survey. A total of 904 responses were gathered by sending 13 questions through a google form. Data were expressed in frequency and percentages. Chi-square test was performed to determine significant difference between gender, education level and variation between dentists of India and other countries. P value <0.05 was considered to be statistically significant. Present study had 650 dentists from India and 254 dentists from other countries. For overall knowledge regarding furcation, 90.7% (average of first and second question) of dentists had knowledge regarding furcation. There was no significant difference between males (range 54%-93%) and females (range 46%- 95%) (p>0.05) in terms of knowledge. Majority (88.7%) of post-graduates knew about the use of Nabers probe for furcation measurements and values were significant (p<0.05). Present study also revealed 65%-67% of undergraduates and post-graduates knew that Degree II furcation defects showed predictable periodontal regeneration, however values were non-significant (p>0.05). There was no statistical significance (p>0.05) between dentists of India and other countries. Dental fraternity in general had adequate knowledge regarding the furcation defects, their treatment modalities and expected complications.

Crystal structure and activity profiling of deubiquitinating inhibitors-bound to SARS-CoV-2 papain like protease revealed new allosteric sites for antiviral therapies

Emerging variants of SARS-CoV-2 still threaten the effectiveness of currently deployed vaccines, and antivirals can prove to be an effective therapeutic option for attenuating it. The papain-like protease (PLpro) is an attractive target due to its sequence conservation and critical role in the replication and pathogenesis of SARS-CoV-2. PLpro also plays very important role in modulation of host immune responses by deubiquitinating (DUBs) or deISGylating host proteins. Thus, targeting PLpro serves as a two-pronged approach to abate SARS-CoV-2. Due to its structural and functional similarities with the host DUB enzymes, an in-house library of DUB inhibitors was constituted in this study. Five promising compounds exhibiting high binding affinities with the substrate binding site of PLpro were identified from a library of 81 compounds with in silico screening, docking, and simulation studies. Interestingly, lithocholic acid, linagliptin, teneligliptin, and flupenthixol significantly inhibited the proteolytic activity of PLpro. Each of these compounds abrogated in vitro replication of SARS-CoV-2 with EC50 values in the range of 5-21 M. In addition, crystal structure of SARS-CoV-2 PLpro and its complex with inhibitors have been determined that revealed their inhibitory mechanism. The findings of this study provide the proof-of-principle that the DUB inhibitors hold high potential as a new class of therapeutics against SARS-CoV-2. Additionally, this is the first study that has opened a new avenue towards not only targeting PLpro active site but also simultaneously directing towards restoration of antiviral immune response of the host for deterring SARS-CoV-2. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/516107v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@90c3fborg.highwire.dtl.DTLVardef@32b4daorg.highwire.dtl.DTLVardef@ff858dorg.highwire.dtl.DTLVardef@198fce7_HPS_FORMAT_FIGEXP M_FIG C_FIG

Biomarkers and Outcomes in Hospitalized Covid-19 Patients: A Prospective Registry

ObjectivesTo determine association of biomarkers high sensitivity C-reactive protein (hsCRP), D-dimer, interleukin-6 (IL-6), lactic dehydrogenase (LDH), ferritin and neutrophil-lymphocyte ratio (NLR) at hospital admission with clinical features and outcomes in Covid-19. MethodsSuccessive virologically confirmed Covid-19 patients hospitalized from April 2020 to July 2021 were recruited in a prospective registry. Details of clinical presentation, investigations, management and outcomes were recorded. All the biomarkers were divided into tertiles to determine associations with clinical features and outcomes. Numerical data are presented in median and interquartile range (IQR 25-75). Univariate and multivariate (age, sex, risk factor, comorbidity adjusted) odds ratio (OR) and 95% confidence intervals (CI) were calculated to determine association of deaths with each biomarker. ResultsWe identified 3036 virologically confirmed Covid-19 patients during the study period, 1215 were hospitalized and included in the present study. Men were 70.0%, aged >60y 44.8%, hypertension 44.8% diabetes 39.6% and cardiovascular disease 18.9%. Median symptom duration was 5 days (IQR 4-7) and SpO2 95% (90-97). Total white cell count was 6.9x103/{micro}l, (5.0-9.8), neutrophils 79.2% (68.1-88.2) and lymphocytes 15.8% (8.7-25.5). Medians (IQR) for biomarkers were hsCRP 6.9 mg/dl (2.2-18.9), D-dimer 464 ng/dl (201-982), IL-6 20.1 ng/dl (6.5-60.4), LDH 284 mg/dl (220-396) and ferritin 351 mg/dl (159-676). Oxygen support at admission was in 38.6%, and non-invasive or invasive ventilatory support in 11.0% and 11.6% respectively. 173 (13.9%) patients died and 15 (1.2%) transferred to hospice care. For each biomarker, those in the second and third tertiles, compared to the first, had worse clinical and laboratory abnormalities, and greater oxygen and ventilatory support. Multivariate adjusted OR (95% CI) for deaths in second and third vs first tertiles, respectively, were for hsCRP 2.29(1.14-4.60) and 13.39(7.23-24.80); D-dimer 3.26(1.31-7.05) and 13.89(6.87-28.27); IL-6 2.61(1.31-5.18) and 10.96(5.88-20.43); ferritin 3.19(1.66-6.11) and 9.13(4.97-16.78); LDH 1.85(0.87-3.97) and 10.51(5.41-20.41); and NLR 3.34(1.62-6.89) and 17.52(9.03-34.00) (p<0.001). ConclusionsIn Covid-19, high levels of biomarkers-hsCRP, D-dimer, IL-6, LDH, ferritin and NLR are associated with more severe illness and significantly greater in-hospital mortality. NLR, a simple, widely available and inexpensive investigation provides prognostic information similar to the more expensive biomarkers.

Lésion d'Antopol-Goldman (Antopol-Goldman lesion): Spontaneous renal pelvic subepithelial hematoma.

Lésion d'Antopol-Goldman (Antopol-Goldman lesion) is a rare condition characterized by renal pelvic subepithelial hematoma simulating a neoplastic process. A 71-year-old lady presented with macroscopic hematuria and hypoenhancing mass lesion at the upper pole of left kidney. The patient underwent a radical nephrectomy for suspected renal cell carcinoma. Macroscopically a 3.5cm circumscribed hemorrhagic mass lesion was noted flush with the upper pole pelvicalyceal system. Microscopic examination revealed a pelvic subepithelial (suburothelial) organizing hematoma. Extensive sampling did not reveal any neoplastic etiology. The adjacent renal parenchyma and renal vessels were unremarkable. Antopol-Goldman lesion is a diagnostic quagmire, often culminating in unnecessary nephrectomy. This is a rare entity, and clinical awareness as a differential of renal filling defect can preclude a nephrectomy, we hereby discuss its clinico-pathological and treatment implications.

Greater Covid-19 Severity and Mortality in Hospitalized Patients in Second (Delta Variant) Wave Compared to the First: Single Centre Prospective Study in India

Background & ObjectiveCovid-19 pandemic has led to multiple waves secondary to mutations in SARS-CoV-2 and emergence of variants of concern (VOC). Clinical characteristics of delta (B.1.617.2) VOC are not well reported. To compare demographic, clinical and laboratory features and outcomes in the second Covid-19 wave in India (delta VOC) with the previous wave we performed a registry-based study. MethodsSuccessive SARS-CoV-2 reverse transcriptase-polymerase chain reaction (RT-PCR) confirmed Covid-19 patients presenting to our Advanced Covid Care hospital were prospectively recruited. In the first phase (wave) from March-December 2020, 1395 of 7476 (18.7%) suspected patients tested positive and 863 (61.89%) hospitalized, while in second wave from January-July 2021 out of 1641 confirmed cases out of 8680 (19.4%) suspected 388 (23.6%) were hospitalized. Details of clinical and laboratory features at admission to hospital, management and outcomes in the two waves have been compared. ResultsIn both cohorts, majority were men and 20% less than 40 years. Prevalence of hypertension, diabetes and cardiovascular diseases was more than 20%. Second wave patients had similar pre-hospitalization symptom duration but had significantly greater cough, fever and shortness of breath and lower SpO2 at presentation with greater lymphopenia, C-reactive proteins, interleukin-6, ferritin, lactic dehydrogenase and transaminases. In the second vs first wave patients, requirement of supplementary oxygen (47.9% vs 34.3%), prone positioning (89.2 vs 38.6%), high flow nasal oxygen(15.7 vs 9.1%), non-invasive ventilation (14.4 vs 9.5%), invasive ventilation (16.2 vs 9.5%), steroids (94.1 vs 85.9%), remdesivir (91.2 vs 76.0%) and anticoagulants (94.3 vs 76.0%) was greater (p<0.001). Median (IQR) length of stay [8 (6-10) vs 7 (5-10) days] as well as ICU stay [9 (5-13) vs 6 (2-10) days] was more in second wave (p<0.001). In-hospital deaths occurred in 173 patients (13.9%) and were significantly more in the second wave, 75 (19.3%), compared to the first, 98 (11.5%); unadjusted odds ratio (95% CI) 1.84 (1.32-2.55) which did not change significantly with adjustment for age and sex (2.03, 1.44-2.86), and age, sex and comorbidities (2.09, 1.47-2.95). Greater disease severity at presentation was associated with mortality in both the waves. ConclusionsCovid-19 patients hospitalized during the second wave of the epidemic (delta variant) had more severe disease with greater dyspnea, hypoxia, hematological and biochemical abnormalities compared to first wave patients. They had greater length of stay in intensive care unit, oxygen requirement, non-invasive and invasive ventilatory support. The in-hospital mortality in the second wave was double of the first.

Squamous Metaplasia in Pleomorphic Adenoma: A Diagnostic and Prognostic Enigma

Pleomorphic adenoma (PA) is the most common benign salivary gland tumor. Histologically, squamous metaplasia has been reported in PA, but has rarely been documented as being extensive enough to cause significant misdiagnosis. Here, we present an unusual case of PA in a 50-year-old female patient presenting with swelling on the postero-lateral aspect of the palate for a week. Histopathologically, the tumor exhibited the features of conventional PA with extensive squamous metaplasia and giant keratotic lamellae in cyst-like areas. Such exuberant squamous metaplasia and keratin can be a diagnostic and prognostic pitfall and lead to overtreatment of the patient.