Whole Genome Sequence Analysis to Identify SARS-CoV-2 Variant in Nepal

Background The spread of SARS-CoV-2 has become a global public health crisis. Nepal is facing the second wave of COVID-19 pandemic but, there is still a limited data on the genomic sequence of SARS-CoV-2 variants circulating in Nepal. Objective The objective of this study is to sequence the whole genome of SARS-CoV-2 in Nepal to detect possible mutation profiles and phylogenetic lineages of circulating SARS-CoV-2 variants. Method In this study, swab samples tested positive for SARS-CoV-2 were investigated. After RNA extraction, the investigation was performed through real-time PCR followed by whole genome sequencing. The consensus genome sequences were, then, analyzed with appropriate bioinformatics tools. Result Sequence analysis of two SARS-CoV-2 genomes from patient without travel history (Patient A1 and A2) were found to be of lineage B.1.1. Similarly, among other four samples from subjects returning from the United Kingdom, genomes of two samples were of lineage B.1.36, and the other two were of lineage B.1.1.7 (Alpha Variant). The mutations in the consensus genomes contained the defining mutations of the respective lineages of SARS-CoV-2. Conclusion We confirmed two genomic sequences of variant of concern VOC-202012/01 in Nepal. Our study provides the concise genomic evidence for spread of different lineages of SARS-CoV-2 - B.1.1, B.1.36 and B.1.1.7 of SARS-CoV-2 in Nepal.Copyright © 2021, Kathmandu University. All rights reserved.

Liver injury in COVID-19: prevalence and association with patient-centered outcomes- an analysis of the international severe acute respiratory and emerging infection consortium (ISARIC) database

Background and Aim: Extrapulmonary manifestations are common in COVID-19 and elevations in components of liver function tests have been reported. Multiple mechanisms may contribute to these derangements. Using a large clinical dataset, we evaluated the prevalence and severity of derangements in liver function tests and their association with patient-centered outcomes. Methods: Using information available on the International Severe Acute Respiratory and emerging Infection Consortium database, we included patients with laboratory confirmed or suspected SARS-COV2 infection admitted to the hospital. The main exposure was the baseline liver function and main outcomes were hospital mortality, admission to an intensive care unit (ICU), receipt of oxygen therapy, non-invasive ventilation (NIV) or invasive ventilation, inotropes/vasopressors, renal replacement therapy, and the durations of hospital and ICU stay. We used generalized linear models to determine the association between exposure variables and outcomes. Results: From 708052 patients in the database, we included 17531 after excluding those with missing baseline information on liver function tests and outcomes. Nearly14% of patients had stage 2 liver injury at baseline and over 75% of the cohort had stage 3 liver injury. Stage 2 and 3 were associated with higher odds of mortality [ Stage 2- OR 1.82 (95%CI: 1.47-2.25) p value<0.001 and Stage 3- OR 1.50 (95%CI: 1.24-1.82) p value<0.001]. Stage 2 was also associated with higher odds of mechanical ventilation [ Stage 2- OR 1.6 (95%CI:1.34-2.06) p value<0.001] and a higher odds of ICU admission [ OR 1.13 (95%CI:0.95-1.35) p value=0.17]. For stage 3, this association with a higher probability of mechanical ventilation [OR 0.84 (95% CI:0.69-1.02) p value 0.08] and ICU admission [OR 0.24 (95% CI:0.21-0.28) p value<0.001)] was not observed. Conclusion: Liver function abnormalities are common among COVID-19 patients and are associated with worse clinical outcomes.

Efficacy of Favipiravir in treatment of mild & moderate COVID-19 infection in Nepal: a multi-center, randomized, open-labelled, phase III clinical trial

To study tolerability and outcome of oral favipiravir treatment among COVID-19 patients in Nepal. In this multi-centered randomized, open-labelled phase III clinical trial, we enrolled 18-80 years old, RT-PCR confirmed patients with mild to moderate COVID-19 infection from 9 participating hospitals of Nepal, within 6 days of onset of symptoms. The investigational product (Favipiravir) was compared against placebo in patients with mild infection and against Remdesivir in moderate infection. Patients who met the eligibility criteria were randomly enrolled in the study after taking informed consent. This is a preliminary report of the data analysis. At the time of this preliminary data analysis, 90 cases were enrolled in the study including 70 mild and 20 moderate cases (see table). Among the participants with mild COVID19 infection, clinical improvement was noted in 30 (78.9%) and 27 (84.4%) patients who received Favipiravir and placebo, respectively (p=0.78). While among the participants with moderate infection, 9 (81%) and 8 (88.9%) patients who received Favipiravir and Remdesivir, respectively, had clinical improvement (p=1). Patients tolerated Favipiravir well with only 3 (6.12 %) patients showing adverse events, which were mainly elevated liver function test & uric acid level, both considered minor. None of the patients receiving placebo or remdesivir reported any adverse events. The investigational product has been tolerated well by this group of patients with only mild and reversible side effects in 6.12 % cases. The outcomes between the study groups were comparable. [ FROM AUTHOR] Copyright of International Journal of Infectious Diseases is the property of Elsevier B.V. and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

Whole Genome Sequence Analysis to Identify SARS-CoV-2 Variant in Nepal

Background The spread of SARS-CoV-2 has become a global public health crisis. Nepal is facing the second wave of COVID-19 pandemic but, there is still a limited data on the genomic sequence of SARS-CoV-2 variants circulating in Nepal. Objective The objective of this study is to sequence the whole genome of SARS-CoV-2 in Nepal to detect possible mutation profiles and phylogenetic lineages of circulating SARSCoV-2 variants. Method In this study, swab samples tested positive for SARS-CoV-2 were investigated. After RNA extraction, the investigation was performed through real-time PCR followed by whole genome sequencing. The consensus genome sequences were, then, analyzed with appropriate bioinformatics tools. Result Sequence analysis of two SARS-CoV-2 genomes from patient without travel history (Patient A1 and A2) were found to be of lineage B.1.1. Similarly, among other four samples from subjects returning from the United Kingdom, genomes of two samples were of lineage B.1.36, and the other two were of lineage B.1.1.7 (Alpha Variant). The mutations in the consensus genomes contained the defining mutations of the respective lineages of SARS-CoV-2. Conclusion We confirmed two genomic sequences of variant of concern VOC-202012/01 in Nepal. Our study provides the concise genomic evidence for spread of different lineages of SARS-CoV-2 - B.1.1, B.1.36 and B.1.1.7 of SARS-CoV-2 in Nepal.

Dissecting the Drug Development Strategies Against SARS-CoV-2 Through Diverse Computational Modeling Techniques

The world of the twenty-first century has not experienced such a lockdown situation before, which leads to a complete shutdown of economy not until the novel coronavirus disease 2019 (COVID-19) came caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It becomes an unacceptable global threat to human lives. The COVID-19 has been known only worldwide in the last few months, but it is spreading in a speed of light from Wuhan, China, to the rest of the world. About 2 crore of people have been infected and more than 7 lakh of people have died worldwide till now due to the deadly SARS-CoV-2 infection. There are still no drugs exclusively available in the market for the treatment of SARS-CoV-2 infection, though supportive treatment of hydroxychloroquine, ribavirin, favipiravir, and remdesivir have shown clinical evidences to treat COVID-19. Therefore, it is utmost importance for the medicinal chemists to design and discover novel drugs urgently to rescue or to protect the humanity worldwide from this deadly virus. However, lack of experimental evidences and understanding the behavior of the SARS-CoV-2 within this short period may hinder the process of drug discovery. Still a ray of hope resides in the structural features of SARS-CoV-2 and related coronaviruses (SARS-CoV and MERS-CoV) as these are homologous. Therefore, depending on the established viral target proteins (spike protein, ACE-2, 3CLpro, PLpro, RdRp, helicase, as well as other viral proteins), novel chemical entities may be designed. In this context, several computational modeling approaches (generally structure-based modeling techniques) may be utilized which are cost-effective and less time-consuming. Different structure-based modeling techniques, namely, homology modeling, robust molecular docking, molecular dynamics simulation, and structure-based pharmacophore mapping followed by in silico virtual screening, may be effective and fruitful approaches to design compounds against SARS-CoV-2. In this chapter, various structure-based drug design and discovery strategies from target identification that could be optimized against SARS-CoV-2 have been discussed in detail. Additionally, ongoing and previously reported computational modeling techniques performed by different groups of researchers on various SARS-CoV-2 target proteins have been highlighted elaborately. In addition to the identification techniques of drugs, this chapter also discloses their binding mode of action along with the pharmacokinetics and toxicity criteria computed by modeling techniques. This chapter, therefore, may be a stepping-stone for the researchers to open up a new horizon in the discovery of novel anti-coronavirus drugs in the future.

Robust classification-based molecular modelling of diverse chemical entities as potential SARS-CoV-2 3CLpro inhibitors: theoretical justification in light of experimental evidences.

COVID-19 is the most unanticipated incidence of 2020 affecting the human population worldwide. Currently, it is utmost important to produce novel small molecule anti-SARS-CoV-2 drugs urgently that can save human lives globally. Based on the earlier SARS-CoV and MERS-CoV infection along with the general characters of coronaviral replication, a number of drug molecules have been proposed. However, one of the major limitations is the lack of experimental observations with different drug molecules. In this article, 70 diverse chemicals having experimental SARS-CoV-2 3CLproinhibitory activity were accounted for robust classification-based QSAR analysis statistically validated with 4 different methodologies to recognize the crucial structural features responsible for imparting the activity. Results obtained from all these methodologies supported and validated each other. Important observations obtained from these analyses were also justified with the ligand-bound crystal structure of SARS-CoV-2 3CLpro enzyme. Our results suggest that molecules should contain a 2-oxopyrrolidine scaffold as well as a methylene (hydroxy) sulphonic acid warhead in proper orientation to achieve higher inhibitory potency against SARS-CoV-2 3CLpro. Outcomes of our study may be able to design and discover highly effective SARS-CoV-2 3CLpro inhibitors as potential anticoronaviral therapy to crusade against COVID-19.

Binding of SARS-CoV-2/SARS-CoV spike protein with human ACE2 receptor

SARS-CoV-2 virus is the serious health concern throughout the world. A comprehensive investigation of binding of SARS-CoV-2 active site with host receptor protein hACE2 is important in designing effective drugs. In the present work, the major amino acid binding partners between the virus CTD and host receptor have been studied and are compared with SARS-CoV RBD binding with hACE2. Our investigation show that some unique hydrogen bond pairs which were not reported in previous work. Along with hydrogen bonding, salt-bridges, hydrophobic interactions and contributions of electrostatic and van der Waals contacts play significant role in binding mechanism. The binding affinity of SARS-CoV-2 CTD/hACE2 is greater than SARS-CoV RBD/hACE2. This outcome is also verified from the free energy estimation by using umbrella sampling.

Structural Insight Into the Viral 3C-Like Protease Inhibitors: Comparative SAR/QSAR Approaches

Severe acute respiratory syndrome (SARS), caused by SARS-coronavirus (SARS-CoV), is a dreadful infection worldwide having economic and medical importance and a global threat for health. It was turned into an epidemic in South China followed by a chain of infections across three generations. A number of pathogeneses in human may occur due to the virus. This infection has not been taken into account before the SARS outbreak, and still it is a neglected one. Therefore, there is an urgent need to develop small molecule antivirals to combat the SARS-CoV. No vaccines are available till date though a number of SARS-CoV 3C-like and 3C protease inhibitors were reported. In this chapter, quantitative structure–activity relationship technique is used for development of anti-SARS and anti-HRV drugs and outcome discussed in details. This approach may be a useful strategy to design novel and potential anti-SARS drugs to combat these dreadful viral diseases. FAU - Adhikari, Nilanjan