The Role of SARS-CoV Non-structural protein 1 in Regulating RNA stability

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infected more than 600 million people across 219 countries during the past three years. SARS-CoV-2 consists of a positive-strand RNA genome that encodes structural and nonstructural proteins and shares a 79% sequence homology with severe acute respiratory syndrome coronavirus 1 (SARS-CoV-1). Nonstructural proteins are necessary for viral replication and suppression of the host cell immune response. Nonstructural protein 1 (nsp1), a small protein conserved among most beta-coronaviruses, inhibits host messenger RNA (mRNA) translation by binding to ribosomal mRNA channels. Nsp1 also triggers degradation of host mRNA while viral RNA remains intact. We have previously shown that nsp1 localizes within stress granules (SGs), non-membranous vesicles of stalled mRNA that form in response to viral infection. We also found that upon induction of stress, SGs disperses within 60- 120 minutes in the presence of nsp1. Since SGs are known to store and protect translationally stalled mRNAs that are target of nsp1, we sought to analyze the level of mRNAs accumulation in SGs in the presence of nsp1. The goal of this project is to identify the impact of nsp1 on stress granule formation during SARS-CoV infection. We used human embryonic kidney cells (HEK293) and transfected them with DNA expressing SARSCoV- 1 nsp1 or a control plasmid. Cells were then incubated at 37degreeC under 5% CO2 concentration for 16 hours. Following incubation, cells were subjected to 30 min of oxidative stress using sodium arenite. Cells were collected and lysed using lysis buffer, then centrifuge at 18 000xg to collect SG pellets used for RNA isolation. Isolated mRNAs were quantified using quantitative RT-PCR. We specifically targeted mRNAs that tend to show a preferential accumulation in SGs without any viral infection. When nsp1 was expressed, we found majority of mRNAs have shown a 2-fold decrease in accumulation in SGs. These results suggest there is a direct effect of nsp1 in dispersing of RNA from SGs. We are currently investigating the effect of viral leader sequence in their accumulation in SGs in the presence of nsp1. This project was supported by the DRP award from SC INBRE (NIGMS, P20GM103499).Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Insights Gained from an Inquiry-Driven Biochemistry Laboratory during the COVID-19 Pandemic

The early stages of the COVID-19 pandemic required us to implement innovative ideas, especially in upper-level chemistry laboratory courses that train students to implement critical thinking and problem-solving skills. Due to the pandemic-enforced close down of the campus in the spring of 2020, many students lacked laboratory skills. At the same time our university, like many others, adopted the HyFlex model to accommodate multiple waves of COVID-19 and to provide flexibility for the students to learn materials from home. In accordance with these changes, the senior-level biochemistry laboratory course was restructured into a hybrid course focusing on the study of a SARS coronavirus protein. To establish inquiry-driven learning, this hybrid course included two modules: Module I included computer-based studies that allowed students to propose a hypothesis, and Module II included in-person laboratory sessions that allowed students to verify the hypothesis. The computer-based module was offered in synchronous hybrid (virtual and in-person) mode, while the hands-on activities were run in a synchronous in-person mode. This computer-based module could be adapted in any biochemistry lecture or laboratory course as a separate module or as a semester-long project to study the structure-function relationship of a protein of interest. In this communication, I present the activities and the key lessons learned from the inquiry-driven biochemistry laboratory course. Based on this experience, several adjustments are made for future courses to offer flexibility to students. © 2023 The Author. Published by American Chemical Society and Division of Chemical Education, Inc.

Interaction Between the Viral RNA Leader Sequence and nsp1 in SARS Coronavirus

Nonstructural protein 1 (nsp1) of severe acute respiratory syndrome coronavirus (SARS-CoV), inhibits host translation thorough cleaving host mRNA and blocking the translation initiation site on the 40S ribosome. Stem-Loop-1 (SL-1) of the viral RNA leader sequence has been identified to bind to nsp1, allowing viral RNA to escape translation repression. However, the specific residues on nsp1 and the specific sequences on SL-1 important to binding have not been experimentally verified. To investigate this binding, we used gel-shift assay and RNA pull-down to verify binding between nsp1 and SL-1. By mutating SL- 1, we seek to identify the nucleotides of SL-1 that bind to nsp1. Based on recent literature, we hypothesized that disrupting the stem region of SL-1 will decrease binding between nsp1 and SL-1. Moreover, we seek to identify the residues important to binding to SL-1 by mutating specific amino acids of nsp1. Interestingly, nsp1 is a small protein (180 amino acids) with intrinsically unstructured regions at both C- and N-terminal ends of the protein. Based on recent literature we hypothesize that disrupting the R124 and K125 residues will decrease binding to SL-1. The results of this study will increase the knowledge of how viral RNA is able to escape suppression of host gene expression. To investigate the binding of nsp1 to SL1, we used nsp1 purified from bacterial lysate using glutathione beads followed by precision protease cleavage of GST-nsp1, and biotinylated RNA. LightShift Chemiluminescence RNA EMSA Kit (Promega) was used to detect the RNA in complex with nsp1 using a gel shift assay. Contrary to our hypothesis, we found an increase in nsp1 binding to the RNA carrying stem mutation, and a decrease in nsp1 binding to the RNA with the loop mutation. Moreover, we observed two distinct bands in the stem mutant indicating two possible binding sites on SL-1. Using an electrophoretic mobility shift assay, the loop region of SL-1 has been determined to be vital for binding to nsp1 in vitro. We hypothesize when the stem was mutated, we created a new binding site for nsp1. Currently we are further investigating several mutations in SL-1 to identify the actual binding site. This project was supported by the DRP award from SC INBRE (NIGMS, P20GM103499).Copyright © 2023 The American Society for Biochemistry and Molecular Biology, Inc.

Machine Learning in Clinical Text Classification: Specialty Identification and COVID-19 Risk

A report from the World Health Organization reveals that many people lack access to good healthcare services. Primary health care is often inaccessible, not only in developing countries, but also in developed nations like the United States. The lack of sufficient primary care physicians is one of the chief factors contributing to healthcare inaccessibility. Prior research has attempted to address the issue by examining patient symptoms and transcripts through the use of machine learning algorithms, but because numerous illnesses can produce identical symptoms, these efforts have struggled to correctly diagnose and guide patients. We sought to increase the access to healthcare services by utilizing a machine learning system to guide a patient to the appropriate specialist based on the symptoms indicated in their transcripts. In this study, we developed and evaluated an algorithm-based solution that would give the public credible, data-driven, and personalized information about their symptoms, enabling patients and their doctors to make better-educated decisions based on statistics and text transcripts. To do so, we built three models: (1) a transcript model, which uses clinical transcripts to predict the appropriate medical specialist;(2) a keyword model, which uses keyword extraction to reduce noise and isolate the symptoms from the clinical transcripts, and then uses these keywords to predict the appropriate medical specialist;and (3) a COVID-19 risk detection model, which predicts the COVID-19 risk of a patient, something that has not been fully investigated in this field of research. © 2022 IEEE.

COVID‐19 Detection from Chest X‐Ray (CXR) Images Using Deep Learning Models

Due to the tremendous rise in COVID cases around the world, early detection of Covid-19 has become critical. Deep learning technology has recently sparked a lot of attention as a means of detecting and classifying diseases quickly, automatically, and accurately. The goal of this study is to develop a deep learning based automatic COVID‐19 detection system for better, faster, and more accurate COVID‐19 detection from chest X‐Ray (CXR) images. In our work, we have used pre-trained deep learning models such as VGG16, ResNet50, DenseNet201, InceptionV3 and Xception utilizing openly accessible dataset. Experimental results show that the DenseNet201 model performs the best with more than 97% accuracy. Moreover, in terms of size, DenseNet121 is beating the rest of the models. As a results, DenseNet201 is most suitable Deep Convolutional neural networks (CNN) architecture for developing an automatic covid-19 detection tool. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

Cryo-Ground Mango Kernel Powder: Characterization, LC-MS/MS Profiling, Purification of Antioxidant-Rich Gallic Acid, and Molecular Docking Study of Its Major Polyphenols as Potential Inhibitors SARS-CoV-2 M-pro

Mango processing waste (MPW) is an inexpensive and rich source of valuable substances. Hence, the mango kernel powder (MKP) from four cultivars (Chausa, Neelum, Barahmasi, and Dashehari) was characterized for the selection of the best cultivar. The MKP of the best cultivar (Dashehari) was analyzed for the profiling of polyphenols using LC-MS/MS in both modes of ionization (positive and negative) and indicated the presence of 50 compounds with specific retention times. After identification, gallic acid (GA), an important industrial compound, was targeted and purified followed by its confirmation using NMR (600 MHz) and HRMS. The antioxidant activity (IC50: 1.96 mu g/mL) of extracted GA proposes its use as a natural antioxidant in novel food formulations. Additionally, SARS-CoV-2 main protease (M-pro) was selected for molecular docking based virtual screening of seven major polyphenols (MKP), and the results were compared with hydroxychloroquine. The docking scores of targeted polyphenols revealed that three compounds (epicatechin, mangiferin, and quercetin) exhibited appreciable proteolytic activity against M-pro. In this way, it is a favorable approach toward environmental safety on the standpoint of green chemistry owing to the use of food processing waste and elimination of the waste dumping/composting problems.

Hematopoietic Stem/Progenitor Cells and Engineering: HALF-TRUTH: GRAFT CRYOPRESERVATION DOES NOT IMPACT ENGRAFTMENT AFTER ALLOGENEIC HEMATOPOIETIC CELL TRANSPLANT (ALLO-HCT)-A SINGLE CENTER EXPERIENCE FROM INDIA

Background & Aim: Background: Traditionally, ‘fresh’ Hematopoietic progenitors cell (HPC) infusions have been preferred over cryopreserved HPC in Allo-HCT because cryopreservation and thawing leads to cell loss, besides DMSO-related adverse reactions in patients. Emergence of COVID-19 pandemic has severely affected fresh HPC infusions and most professional bodies recommend cryopreservation of HPC products before initiating conditioning chemotherapy. Although some western studies suggest no significant impact of graft manipulation on patient outcome, there is no available data from the developing world.Aim: We compare neutrophil and platelet engraftment in patients undergoing Allo-HCT with fresh and cryopreserved HPC products. Methods, Results & Conclusion: Material and Method: Allo-HCT data from October 2018 to October 2021 were analyzed. Cryopreservation was performed by controlled-rate freezing using 10% DMSO, plasmalyte- A and human albumin ( 1:2:1) as cryoprotectant. Cryopreserved products were stored in vapour-phase of Liquid nitrogen tank. CD34+ enumeration and viablity( by 7-AAD) was done on Flow-cytometry on fresh and post-thaw HPC samples. Neutrophil engraftment was defined as absolute neutrophil count >0.5 ×109/L for 3 days. Platelet engraftment was defined as independence from platelet transfusion for at least 7 days with a platelet count >20 × 109/L. Statistical analysis using Wilcoxon Rank Sum test. Results: Ninety-six patients underwent allo-HCT (46 received fresh and 50 received cryopreserved HPC products) (Table 1). There was no significant difference in neutrophil engraftment with fresh and cryopreserved grafts (p>0.05) in different types of transplants( Matched related/unrelated and haploidentical). 22% (11/50) of cryopreserved graft infusions were associated with Grade-1 DMSO-related adverse reactions, which were managed with symptomatic treatment. Cryopreservation increased the cost of related allogeneic transplants by USD1100. No cryopreserved HPC product was culture positive on microbiological assessment. Conclusion: In our experience, the engraftment kinetics were similar with fresh and cryopreserved HPC products as CD34+cell dose administered was almost the same. Cryopreserved grafts had a median 7% CD34+cell loss, associated with mild DMSO-related adverse reactions and cost increment. Even though, graft cryopreservation is a feasible alternative during the pandemic, it is crucial to ensure graft quality and promptly manage DMSO-related adverse reactions.(Table Presented) Table 1 Comparison of Fresh and cryopreserved HPC products in Allo-HCT

Neologism Related to COVID-19 Pandemic: A Corpus-Based Study for the Bengali Language

Language is changing over time, and it is a common phenomenon for all languages. Generally, it is a slow but continuous process. The new words come or adopt in the languages, and some existing words become less frequent use or becoming obsolete in written or verbal communication. The term neologism is implying a newly coined word or expression or a phrase that is entering for common use. But sometimes or some special events like War, New disease, Computer, Internet, etc. make the change rapidly, and the COVID-19 pandemic is one such latest event. Note that the infectious disease caused by a newly discovered coronavirus is termed COVID-19, and it is now the official name of coronavirus disease. It has led to an explosion of neologism in the context of disease and several other social contexts. During this period, many new words were coined in the languages and many of these terminologies are rapidly becoming a part of our daily life. For example, some established terms like “lockdown”, “quarantine”, “isolation”, “pandemic”, etc. increased quickly the use in our daily terminology. From the linguistic point of view, the study of such change or adaptation and its quantization is very much important. This study attempted a corpus-based computational approach to explore the adaptation or creation of new words during the outbreak of COVID-19 in the Bengali language. The main components of this work are the creation of the corpus related to the COVID-19 and an algorithm to find out the neologism. For this study, a news corpus has been used. The corpus is created from the news article related to the COVID-19 from January 2020 to February 2021. © 2022, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

An update of safety and efficacy results from phase 1 dose-escalation and expansion study of vodobatinib, a novel oral BCR-ABL1 tyrosine kinase inhibitor (TKI), in patients with chronic myeloid leukemia (CML) and philadelphia chromosome positive acute lymphoblastic leukemia (Ph+ All) failing prior tki therapies

Introduction: Vodobatinib is a novel third generation TKI effective against wild-type and mutated BCR-ABL1 (except T315I) with limited off-target activity. We present updated results from the Phase 1 dose-escalation (DEs) and expansion (DEx) study in CML and Ph+ALL patients (pts) failing ≥ 3 prior TKIs (< 3 prior TKIs if approved TKI is not clinically advised or available);patients with T315I are not eligible (NCT02629692). Methods: This is an open-label, phase 1, multicentre, 3+3 study evaluating maximum tolerated dose (MTD), safety and efficacy of vodobatinib administered once daily in 28 day cycles (dose range: 12 to 240 mg). MTD was established at 204 mg. DEx study enrolled chronic phase CML (CP-CML) patients at 174 mg dose of vodobatinib. Treatment continued until unacceptable toxicity, disease progression, consent withdrawal or death. Adverse events were assessed using NCI-CTCAE v4.03. Results: As of 15 Jul 2021, 52 pts are enrolled in DEs and DEx cohorts. Forty one of these pts received doses from 12 to 240 mg in the DEs cohort;32 chronic phase (CP-CML), 3 accelerated phase CML (AP-CML), 4 blast phase CML (BP-CML), 2 Ph+ ALL. Eleven CPCML pts were enrolled in DEx cohort at 174 mg dose. The baseline demographics and disease history are represented in Table 1. Efficacy: Of the 32 CP-CML pts enrolled in DEs: At baseline, 21 (65%) pts had no cytogenetic response, 4 (12.5%) were in PCyR, 7 (22%) were in CCyR. On vodobatinib therapy, 11(34%) pts achieved CCyR, 3 (9%) achieved PCyR and 7 (22%) maintained baseline CCyR. Baseline major molecular response (MMR) was present in 1 (3%) pt;and 14 pts (44%) achieved MMR on study. Of the remaining 11 pts, 5 (16%) had haematologically stable disease (no CyR and molecular response) and 6 (19%) had disease progression (cytogenetic or hematological) as their best response (Table 2 and 3). Seventeen CP-CML pts had prior ponatinib treatment, of which 11 (65%) had MCyR (4 achieved CCyR, 4 maintained CCyR, 3 achieved PCyR);while 8 (47%) achieved MMR. In the remaining 15 pts ponatinib naïve CP-CML: 10 (66%) had CCyR (7 achieved CCyR, 3 maintained CCyR);with 7 (47%) with MMR (6 achieved, 1 maintained). Two of the 3, AP-CML pts had baseline hematological response (CHR) with absence of cytogenetic and molecular response. The 3 pts further deepened their responses with 1 pt achieving CCyR with MMR and 2 pts in PCyR. Of the 4 BP-CML pts, 2 achieved CHR and 2 patients had disease progression as their best response;Of the 2 Ph+ ALL pts, 1 pt maintained CCyR and MMR while the other reported disease progression as the best response. Median duration of treatment overall was 23 (0.5-51) months [CP-CML 23 (0.5-51);AP-CML 36 (9-40);BP-CML 3 (0.5-18) and Ph+ ALL 4 (0.7-7.3) months]. Twenty one pts continue in study. In the DEx cohort, 1 of the 11 CP-CML pts was in PCyR at baseline. No pts had molecular response. Of the 11 patients, 6 (54 %) pts achieved CCyR, 1(10%) pt achieved PCyR. MMR was achieved by 1 pt (10%). Data is maturing for 1 pt. Median duration of treatment is 16 (0.3-19) months and 10 pts continue in study. Safety: Forty nine of 52 pts reported at least 1 TEAE. Most common any grade TEAEs included thrombocytopenia (33%), cough (19%), anaemia & diarrhoea (17% each). Thirty one pts (60%) reported Grade 3 and 4 treatment emergent AEs: most common were thrombocytopenia (15%), neutropenia and anaemia (12%), increased amylase and lipase (8% each). Ten (19%) pts reported cardiovascular TEAEs (Grade 1: angina pectoris, palpitations, ventricular extra-systoles, arteriosclerosis, hot flush, hypotension, intermittent claudication;Grade 2: hypertension, hypotension;Grade 3: cardiac failure congestive, hypertension);with a Grade 2 hypertension being vodobatinib related. Nineteen pts (37%) reported SAEs;vodobatinib related SAEs were reported in 3 pts (fatal intracranial haemorrhage (ICH), Grade 2 back pain and Grade 3 amnesia reported in 1 pt each). There were 5 deaths on study: 1 was related to use of vodobatinib (1 ICH, confounded by disease progression to blast phase that include extra-medullary sites) and the remaining unrelated (1 sudden death, 1 disease progression, 1 pneumonia fungal, 1 suspected COVID-19). Conclusion: Vodobatinib continues to be associated with favourable long term safety and efficacy in heavily pre-treated CML failing ≥ 3 prior TKIs, including ponatinib. Phase 2 study evaluating vodobatinib in pts failing at least 3 prior lines of therapy, including ponatinib, is ongoing.

Computer Vision-based Social Distancing Surveillance with Automated Camera Calibration for Large-scale Deployment

Social distancing has been suggested as one of the effective measures to break the chain of viral transmission in the ongoing COVID-19 pandemic. We herein describe a computer vision-based AI-assisted solution to aid compliance with social distancing norms. The solution consists of modules to detect and track people, and to identify distance violations. It provides the flexibility to choose between a tool-based mode requiring user input or a fully automated mode of camera calibration (devised in-house), making the latter suitable for large-scale deployments. We also outline a strategy to estimate the number of video feeds which can be supported in parallel for scalability. Finally, we discuss different metrics to assess the risk associated with social distancing violations, including the use of 'violation clusters', and how we can differentiate between transient or persistent violations. Our proposed solution performs satisfactorily under different test scenarios, processes video feed at real-time speed, as well as addresses data privacy regulations by blurring faces of detected people, making it ideal for deployments. © 2021 IEEE.

Bortezomib-Pomalidomide-Dexamethasone (VPD) As Novel Induction Therapy in Newly-Diagnosed Multiple Myeloma: Early Safety Data from an Ongoing Single Arm Phase-II Investigator-Initiated Clinical Trial (PRIME Study)

Introduction: Pomalidomide is a third-generation immunomodulatory drug approved for relapsed and/or refractory Multiple Myeloma (RRMM). In the phase 3 OPTIMISMM trial, pomalidomide, bortezomib, and dexamethasone demonstrated superior efficacy in patients with RRMM. PRIME study (CTRI/2019/10/021618) is testing this combination in Newly Diagnosed Multiple Myeloma (NDMM) Aim: To determine safety of Pomalidomide in combination with Bortezomib and dexamethasone (VPD) in NDMM Study design: A prospective, single arm, phase II study from a tertiary center. Both transplant eligible and ineligible patients with NDMM aged between 18-70 years are being recruited in the study. Patients with Plasma cell leukemia, POEMS and amyloidosis were excluded. The regimen consists of weekly Bortezomib 1.3mg/sq.m (subcutaneous), Tab. Pomalidomide 2-4mg once daily for 21days, and Tab Dexamethasone 20mg twice weekly, with the cycle repeating every 28 days, 9-12 cycles. Here we report the adverse events (AE) by NCI CTCAE v5.0, upon recruiting 26 patients, as predetermined in the study. Results: Of the proposed 45-50 patients, 26 patients were enrolled in the study between April 2020 to May 2021 and 23 (88.4%) have completed 4 cycles of VPD. The median age is 55years (18-70), and gender ratio 1:1. At disease presentation, bone lesions were the commonest (96.2%, n=25), IMWG high risk cytogenetics were seen in 42.4% (n=11), RISS-2 in 69.3% (n=18), IgG kappa paraproteinemia in 54% (n=14) patients and ECOG performance score 2-3 in 57.6%(n=15). Ten (38.5%) patients have completed 9 cycles, and 3 underwent auto-transplant (between Cycle 4 & 6). Protocol adherence was 96.1% (25/26 patients). Table-1 shows drug-induced toxicity, hematological toxicities were the commonest. Two patients withdrew consent in view of bortezomib-induced peripheral neuropathy. Serious adverse events (SAE) were reported in 9 (34.6%) patients and were considered unrelated to the regimen by the safety committee (PSVT=1, Bony pain=2, dyspnea=1, pneumonia=1, constipation=1, diarrhea=1, hypotension=1) and one death due to SARS-CoV2 pneumonia. Treatment delays of 2 weeks in 4 patients (SARS-CoV2 = 3, Syncope = 1) After 4 cycles (n=23), 6 (26%) patients were in stringent Complete Response (sCR), 17(74%) in Very Good partial response (VGPR) and 13 (56.5%) are Measurable Residual Disease (MRD) negative. Of 10 patients who completed cycle 9, 9 were MRD negative and 1 showed disease progression. Conclusion: Safety data from the PRIME study demonstrates that VPD regimen has a favorable tolerance profile in patients with NDMM. Early efficacy signals are encouraging, and recruitment continues. [Formula presented] Disclosures: Radhakrishnan: Dr Reddy's Laboratories: Honoraria, Membership on an entity's Board of Directors or advisory committees;Emcure Pharmaceuticals: Research Funding;Intas Pharmaceuticals: Research Funding;Janssen India: Honoraria;NATCO Pharmaceuticals: Research Funding;Novartis India: Membership on an entity's Board of Directors or advisory committees;Roche India: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding;AstraZeneca India: Honoraria, Speakers Bureau;Bristol-Myers-Squibb India: Membership on an entity's Board of Directors or advisory committees, Research Funding;Cipla Pharmaceuticals India: Research Funding;Aurigene: Speakers Bureau. Garg: Dr Reddys Laboratories: Honoraria, Speakers Bureau. Nair: Dr Reddy's Laboratories: Honoraria, Membership on an entity's Board of Directors or advisory committees, Speakers Bureau;Intas pharmaceuticals: Honoraria, Speakers Bureau;Mylan pharmaceuticals: Honoraria;Novartis India: Honoraria;Fresenius Kabi India: Honoraria;Cipla Pharmaceuticals: Honoraria, Speakers Bureau;Janssen India: Honoraria, Speakers Bureau. Chandy: Janssen: Honoraria;Pfizer: Honoraria;Intas Pharmaceuticals: Research Funding.

Computational modeling of SARS-CoV-2 Nsp1 binding to human ribosomal 40S complex

Molecular docking and Targeted Molecular Dynamics Simulations were conducted to elucidate binding properties of SARS-CoV-2 nonstructural protein 1 (nspl) onto the human ribosomal 40S complex. Nspl serves as a host shutoff factor by blocking ribosome assembly on host mRNAs, thereby suppressing host gene expression. Recently, cryo-electron microscope structure of both 40S and 80S ribosome purified in the presence of SARS-CoV-2 nspl revealed the presence of the C-terminal region of nspl in the mRNA binding site of the 40S ribosome. This structure gives the first insight into the molecular mechanism of nspl-mediated suppression of host protein translation. In this study we have utilized the most recent emerging partial structures of nspl bound to 40S ribosome as the reference point of implementing a Targeted Molecular Dynamics Simulation of the entire nspl bound to the 40S complex. Our final bound structure of nspl exhibits the previously reported helix-turn-helix conformation of the C-terminal region of nspl and satisfies all the previously reported proximity restraints. Finally, we have established the interaction and stability of this final bound state of the full nspl and 40S. The observation that C-terminal region of nspl folds into a helix-turn-helix structure to occupy the mRNA binding site in the 40S ribosome enables further inquiry into the understanding of the entire nspl structure bound to the 40S ribosome to reveal relative positioning of the two termini when nspl is bound to ribosome. © 2021 ACM.

Clinical and Biochemical Profile of COVID-19 Patients Admitted in a Tertiary Care Hospital of Kolkata

Introduction: The disease caused by Coronavirus (COVID19), is now pandemic all over the world including India. There are different manifestations of the disease from asymptomatic and mild to severe form. Clinical severity varies from country to country. This study was conducted to document different clinical and biochemical profiles in this Tertiary Care Hospital of Kolkata. Aim: The study was done to observe and to compare the clinical and biochemical profile in asymptomatic to mild and moderate to severe symptomatic patients. Materials and Methods: This was an observational study conducted in Medical College, Kolkata, West Bengal, India. The study was conducted from June 2019 to mid-August 2019. Total 573 Real Time Polymerase Chain Reaction (RT PCR) positive COVID patients were included in this study. All patients were examined and investigated with blood parameters. Patients were divided into two groups (Group A-asymptomatic and mild symptoms and Group B moderate and severe symptoms) clinically. Statistical calculators like Statistical Package for Social Sciences (SPSS) and Soccalculator were used and different biochemical parameters were analysed using Chisquare, unpaired T-test to find out significance among these two groups. Results: Among 573 patients, 222 were in group A and 351 were in group B. Fever was the most common presenting feature (69.6%) followed by dry cough and shortness of breath. Other features were malaise/fatigability, diarrhoea and anosmia. Among the co-morbidities hypertension and diabetes were significantly different between the two groups. Among the biochemical parameters Neutrophil- Lymphocyte Ratio (NLR), C-Reactive Protein (CPR), D-dimer, Prothrombin time, Serum Glutamic Oxaloacetic Transaminase (SGOT), Serum Glutamic Pyruvic Transaminase (SGPT) were significantly different between the two groups. Conclusion: In a tertiary care hospital of Kolkata, fever is the most common presentation followed by dry cough and fatigability in COVID patients. Diabetes and hypertension are the common co morbidities. CRP, NLR, D-dimer, prothrombin time, SGOT and SGPT should be monitored to differentiate between mild and severe cases.

Outcome of sars-cov2 infection in hematological disorders: A tertiary-care cancer center experience

Aims & Objectives: We conducted a clinical audit of patients with hematological disorders and SARS-CoV2 infection. Patients/Materials & Methods: A prospective registry was established in April 2020 for patients from the department of clinical hematology and HCT who were diagnosed to be positive for SARSCoV2 by PCR test. Out patients creening was symptom/contact-exposure driven, and in patients creening was symptomaticorpreemptive. This study is a part of ASHCOVID19 International collaborative and an interim analysis of the institute registry data from April 15, 2020 to October 7, 2020. Results: 1201 new patients were registered and 9539 patient-visits were recorded in the out patient service of the department during this period. 91 (0.08%) patients tested positive for SARS-CoV2. Baseline characteristics of the patients are listed in Table 1. 56 (61.5%) patients needed hospitalization. The median absolute neutrophil count was 3700/cu.mm, while the median absolute lymphocyte count 900/cu.mm. Inflammatory markers (n = 21):median D-dimer was 2845 ng/ml (243-140643) and median CRP level was 14 mg/dl (3.3- 34). Therapy directed against SARS-CoV2 included, Azithromycin (n = 52,60.4%), Dexamethasone (27 patients,29.7%), Remdesivir (n = 10,11.1%) and doxycycline (n = 9,9.9%). 2(2.2%) patients received tocilizumab and 1 patient (1.1%) received convalescent plasma. On univariate analysis, none of the therapies seemed to affect outcomes. The SARS-CoV2 infection mortality was 15% (14/91). 2 patients died due to non-COVID related causes [tumor lysis syndrome (n = 1), leukocytostasis with CVA (n = 1)]. 7/45(15.5%) receiving anti-B-lymphocyte directed therapy died as compared to 7/46(15.21%) not receiving Anti-B-cell therapies. Patients with low grade B-NHL (5/16,31.25%) had the highest mortality rate followed by high grade B-NHL (7/23,30.4%).There was a trend to higher mortality in patients>50 years (12/45,26.6% in those[=50 years age as compared to 4/30,13.33% in those<50 years age). With data available until the date of censoring, most patients were diagnosed in August (n = 32,35.2%) with numbers tailing off in September (n = 20, 22%). Discussion & Conclusion: In our subset of patients with hematological disorders, SARS-COV2 infectivity was found to be low, hospitalization rate was moderate, and mortality was high and commoner in patients>50 yr and a B-cell lymphoma diagnosis. A more aggressive screening approach will potentially improveoutcomes.

A Preliminary Investigation in the Molecular Basis of Host Shutoff Mechanism in SARS-CoV

Recent events leading to the worldwide pandemic of COVID-19 have demonstrated the effective use of genomic sequencing technologies to establish the genetic sequence of this virus. In contrast, the COVID-19 pandemic has demonstrated the absence of computational approaches to understand the molecular basis of this infection rapidly. Here we present an integrated approach to the study of the nsp1 protein in SARS-CoV-1, which plays an essential role in maintaining the expression of viral proteins and further disabling the host protein expression, also known as the host shutoff mechanism. We present three independent methods of evaluating two potential binding sites speculated to participate in host shutoff by nsp1. We have combined results from computed models of nsp1, with deep mining of all existing protein structures (using PDBMine), and binding site recognition (using msTALI) to examine the two sites consisting of residues 55-59 and 73-80. Based on our preliminary results, we conclude that the residues 73-80 appear as the regions that facilitate the critical initial steps in the function of nsp1. Given the 90% sequence identity between nsp1 from SARS-CoV-1 and SARS-CoV-2, we conjecture the same critical initiation step in the function of SARS-CoV-2 nsp1. © 2020 ACM.

Frequency of comorbidities & their association with intensive care unit admission in hospitalised patients with 2019 novel coronavirus infection in tertiary care centres of three states of India

The coronavirus disease 2019 (COVID-19) has created a substantial burden on healthcare services worldwide. Since its first detection in 30th January, it has rapidly spread throughout India. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection results in clusters of severe acute respiratory illness leading to intensive care unit (ICU) admission and considerable mortality. So, there has been an ardent need of data on the frequency of comorbidities in COVID-19 & to assess whether their presence is associated with increased ICU admission. We analysed data from 496 patients with laboratory-confirmed Covid-19 admitted in tertiary care centers of three states of India from 15th to 30th May, 2020. The mean age was 49.7 years & 41.13% of the patients were female. Hypertension (21.97%) was the most frequent comorbidity followed by diabetes (12.90%) & cardiovascular disease (8.87%). 39.92% of the study population had at least one comorbidity. Patients with comorbidities had higher ICU admission than those without comorbidity (35.35% vs. 20.47%). Associated comorbidity was more frequent among ICU patients in comparison to non-ICU patients (53.43% vs. 35.07%). Our study findings suggest that presence of comorbidity is associated with higher ICU admission thereby indicating more severe disease.