Global status of COVID-19 diagnosis: an overview. (Special Issue: Coronaviruses and COVID-19- Past, Present, and Future.)

Since the beginning of the New Year 2020, countries around the world are stumbling due to the coronavirus disease (COVID-19) pandemic. Better approaches of diagnostics and medical facilities have helped some countries recover early. Previous exposures to epidemics have imparted lessons to handle such a pandemic with a high level of preparedness. The World Health Organization (WHO) and national health authorities are taking great efforts via efficient and impactful interventions to contain the virus. Diagnostic tests such as reverse transcription-polymerase chain reaction are increasingly being used to confirm the diagnosis because testing biological samples for the presence of the virus is the definitive method to identify the disease, analyze the risk for transmission, and determine whether someone has been cured or not. It is also important to screen asymptomatic individuals to get the exact overview of the virus spread. Antibody detection plays a pivotal role in diagnosis;however, using it at the wrong time yields negative results and conveys dissenting opinion about the tests. Although the scaling up of testing has been significant, overall testing has been limited by the availability of diagnostics. Rapid diagnoses and discontinuation of transmission are keys to ending this pandemic. Diagnostics manufacturers are developing test kits and distributing them to different countries. Therefore, more than 500 commercial test kits for molecular- and immunoassays, most with Emergency Use Authorization, are now becoming available in the market. In this review, we discuss the importance of diagnostics, approaches of different countries toward the epidemic, global testing situation, and lessons to countries at the start of the epidemic for better preparedness.

Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2.

Interaction of SARS-CoV-2 spike glycoprotein with the ACE2 cell receptor is very crucial for virus attachment to human cells. Selected mutations in SARS-CoV-2 S-protein are reported to strengthen its binding affinity to mammalian ACE2. The N501T mutation in SARS-CoV-2-CTD furnishes better support to hotspot 353 in comparison with SARS-CoV and shows higher affinity for receptor binding. Recombination analysis exhibited higher recombination events in SARS-CoV-2 strains, irrespective of their geographical origin or hosts. Investigation further supports a common origin among SARS-CoV-2 and its predecessors, SARS-CoV and bat-SARS-like-CoV. The recombination events suggest a constant exchange of genetic material among the co-infecting viruses in possible reservoirs and human hosts before SARS-CoV-2 emerged. Furthermore, a comprehensive analysis of codon usage bias (CUB) in SARS-CoV-2 revealed significant CUB among the S-genes of different beta-coronaviruses governed majorly by natural selection and mutation pressure. Various indices of codon usage of S-genes helped in quantifying its adaptability in other animal hosts. These findings might help in identifying potential experimental animal models for investigating pathogenicity for drugs and vaccine development experiments.

In silico Molecular Docking Analysis Targeting SARS-CoV-2 Spike Protein and Selected Herbal Constituents

In modern drug discovery, molecular docking analysis is routinely used to understand and predict the interaction between a drug molecule and a target protein from a microbe. Drugs identified in this way may inhibit the entry and replication of pathogens in host cells. The SARS-CoV-2 associated coronavirus disease, COVID-19, has become the most contagious and deadly pandemic disease in the world today. In abeyance of any specific vaccine or therapeutic against SARS-CoV-2, the burgeoning situation urges a need for effective drugs to treat the virus-infected patients. Herbal medicines have been used as natural remedies for treating various infectious diseases since ancient times. The spike (S) protein of SARS-CoV-2 is important for the attachment and pathogenesis of the virus. Therefore, this study focused on the search of useful ligands for S protein among active constituents present in common herbs that could serve as efficient remedies for COVID-19. We analysed the binding efficiency of twelve compounds present in common herbs with the S protein of SARS-CoV-2 through molecular docking analysis and also results are validated with two different docking tools. The binding efficiency of ligands was scored based on their predicted pharmacological interactions coupled with binding energy estimates. In docking analysis, compound "I" (Epigallocatechin gallate (EGCG)) was found to have the highest binding affinity with the viral S protein, followed by compounds, "F" (Curcumin),"D" (Apigenin) and "E" (Chrysophanol). The present study corroborates that compound "I" (EGCG) mostly present in the integrants of green tea, shows the highest potentiality for acting as an inhibitor of SARS-CoV-2. Further, characterization of the amino acid residues comprising the viral binding site and the nature of the hydrogen bonding involved in the ligand-receptor interaction revealed significant findings with herbal compound "I" (EGCG) binding to the S protein at eight amino acid residues. The binding sites are situated near to the amino acids which are required for virus pathogenicity. The findings of the present study need in vivo experiments to prove the utility of "I", "F","D" and "E" compounds and their further use in making herb-based anti-SARS-CoV-2 product in near future. This analysis may help to create a new ethno-drug formulation for preventing or curing the COVID-19.