COVID-19: emergence and mutational diversification of SARS-CoV-2

Evolutionary trajectory of diverse SARS-CoV-2 variants at the beginning of COVID-19 outbreak

Despite extensive scientific efforts directed toward the evolutionary trajectory of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in humans at the beginning of the COVID-19 epidemic, it remains unclear how the virus jumped into and evolved in humans so far. Herein, we recruited almost all adult coronavirus disease 2019 (COVID-19) cases appeared locally or imported from abroad during the first 8 months of the outbreak in Shanghai. From these patients, SARS-CoV-2 genomes occupying the important phylogenetic positions in the virus phylogeny were recovered. Phylogenetic and mutational landscape analyses of viral genomes recovered here and those collected in and outside of China revealed that all known SARS-CoV-2 variants exhibited the evolutionary continuity despite the co-circulation of multiple lineages during the early period of the epidemic. Various mutations have driven the rapid SARS-CoV-2 diversification, and some of them favor its better adaptation and circulation in humans, which may have determined the waxing and waning of various lineages.

Identification of inhibitors against SARS-CoV-2 variants of concern using virtual screening and metadynamics-based enhanced sampling

Among the variants of SARS-CoV-2, some are more infectious than the Wild-type. Interestingly, these mutations enable the virus to evade the therapeutic efforts. Hence, there is a need for candidate drug molecules that can potently bind with all the variants. We have adopted a strategy combining virtual screening, molecular docking followed by rigorous sampling by metadynamics simulations to find candidate molecules. From our results we found four highly potent drug candidates that can bind to the Spike-RBD of all the variants of the virus. Additionally, we also found that certain signature residues on the RBM region commonly bind to each of these inhibitors. Thus, our study not only gives information on the chemical compounds, but also residues on the proteins which could be targeted for future drug and vaccine development studies.

Advances of CRISPR-Cas13 system in COVID-19 diagnosis and treatment

The ongoing global pandemic of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in over 570 million infections and 6 million deaths worldwide. Early detection and quarantine are essential to arrest the spread of the highly contagious COVID-19. High-risk groups, such as older adults and individuals with comorbidities, can present severe symptoms, including pyrexia, pertussis, and acute respiratory distress syndrome, on SARS-CoV-2 infection that can prove fatal, demonstrating a clear need for high-throughput and sensitive platforms to detect and eliminate SARS-CoV-2. CRISPR-Cas13, an emerging CRISPR system targeting RNA with high specificity and efficiency, has recently drawn much attention for COVID-19 diagnosis and treatment. Here, we summarized the current research progress on CRISPR-Cas13 in COVID-19 diagnosis and treatment and highlight the challenges and future research directions of CRISPR-Cas13 for effectively counteracting COVID-19.

B.1.1.7 (Alpha) variant is the most antigenic compared to Wuhan strain, B.1.351, B.1.1.28/triple mutant and B.1.429 variants

The rapid spread of the SARS-CoV-2 virus and its variants has created a catastrophic impact worldwide. Several variants have emerged, including B.1.351 (Beta), B.1.1.28/triple mutant (P.1), B.1.1.7 (Alpha), and B.1.429 (Epsilon). We performed comparative and comprehensive antigenicity mapping of the total S-glycoprotein using the Wuhan strain and the other variants and identified 9-mer, 15-mer, and 20-mer CTL epitopes through in silico analysis. The study found that 9-mer CTL epitope regions in the B.1.1.7 variant had the highest antigenicity and an average of the three epitope types. Cluster analysis of the 9-mer CTL epitopes depicted one significant cluster at the 70% level with two nodes (KGFNCYFPL and EGFNCYFPL). The phage-displayed peptides showed mimic 9-mer CTL epitopes with three clusters. CD spectra analysis showed the same band pattern of S-glycoprotein of Wuhan strain and all variants other than B.1.429. The developed 3D model of the superantigen (SAg)-like regions found an interaction pattern with the human TCR, indicating that the SAg-like component might interact with the TCR beta chain. The present study identified another partial SAg-like region (ANQFNSAIGKI) from the S-glycoprotein. Future research should examine the molecular mechanism of antigen processing for CD8⁺ T cells, especially all the variants’ antigens of S-glycoprotein.

The Role of Lebanon in the COVID-19 Butterfly Effect: The B.1.398 Example

In the present study, we provide a retrospective genomic surveillance of the SARS-CoV-2 pandemic in Lebanon; we newly sequence the viral genomes of 200 nasopharyngeal samples collected between July 2020 and February 2021 from patients in different regions of Lebanon and from travelers crossing the Lebanese-Syrian border, and we also analyze the Lebanese genomic dataset available at GISAID. Our results show that SARS-CoV-2 infections in Lebanon during this period were shaped by the turnovers of four dominant SARS-CoV-2 lineages, with B.1.398 being the first to thoroughly dominate. Lebanon acted as a dispersal center of B.1.398 to other countries, with intercontinental transmissions being more common than within-continent. Within the country, the district of Tripoli, which was the source of 43% of the total B.1.398 sequences in our study, was identified as being an important source of dispersal in the country. In conclusion, our findings exemplify the butterfly effect, by which a lineage that emerges in a small area can be spread around the world, and highlight the potential role of developing countries in the emergence of new variants.

Molecular insights into the differential dynamics of SARS-CoV-2 variants of concern

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has affected the lives and livelihood of millions of individuals around the world. It has mutated several times after its first inception, with an estimated two mutations occurring every month. Although we have been successful in developing vaccines against the virus, the emergence of variants has enabled it to escape therapy. Few of the generated variants are also reported to be more infectious than the wild-type (WT). In this study, we analyze the attributes of all RBD/ACE2 complexes for the reported VOCs, namely, Alpha, Beta, Gamma, and Delta through computer simulations. Results indicate differences in orientation and binding energies of the VOCs from the WT. Overall, it was observed that electrostatic interactions play a major role in the binding of the complexes. Detailed residue level energetics revealed that the most prominent changes in interaction energies were seen particularly at the mutated residues which were present at RBD/ACE2 interface. We found that the Delta variant is one of the most tightly bound variants of SARS-CoV-2 with dynamics similar to WT. The high binding affinity of RBD towards ACE2 is indicative of an increase in viral transmission and infectivity. The details presented in our study provide additional information for the design and development of effective therapeutic strategies for the emerging variants of the virus in the future.

Critical View on the Importance of Host Defense Strategies on Virus Distribution of Bee Viruses: What Can We Learn from SARS-CoV-2 Variants?

Bees, both wild and domesticated ones, are hosts to a plethora of viruses, with most of them infecting a wide range of bee species and genera. Although viral discovery and research on bee viruses date back over 50 years, the last decade is marked by a surge of new studies, new virus discoveries, and reports on viral transmission in and between bee species. This steep increase in research on bee viruses was mainly initiated by the global reports on honeybee colony losses and the worldwide wild bee decline, where viruses are regarded as one of the main drivers. While the knowledge gained on bee viruses has significantly progressed in a short amount of time, we believe that integration of host defense strategies and their effect on viral dynamics in the multi-host viral landscape are important aspects that are currently still missing. With the large epidemiological dataset generated over the last two years on the SARS-CoV-2 pandemic, the role of these defense mechanisms in shaping viral dynamics has become eminent. Integration of these dynamics in a multi-host system would not only greatly aid the understanding of viral dynamics as a driver of wild bee decline, but we believe bee pollinators and their viruses provide an ideal system to study the multi-host viruses and their epidemiology.

Molecular Evolution of Severe Acute Respiratory Syndrome Coronavirus 2: Hazardous and More Hazardous Strains Behind the Coronavirus Disease 2019 Pandemic and Their Targeting by Drugs and Vaccines

Within almost the last 2 years, the world has been shaken by the coronavirus disease 2019 (COVID-19) pandemic, which has affected the lives of all people. With nearly 4.92 million deaths by October 19, 2021, and serious health damages in millions of people, COVID-19 has been the most serious global challenge after the Second World War. Besides lost lives and long-term health problems, devastating impact on economics, education, and culture will probably leave a lasting impression on the future. Therefore, the actual extent of losses will become obvious only after years. Moreover, despite the availability of different vaccines and vaccination programs, it is still impossible to forecast what the next steps of the virus are or how near we are to the end of the pandemic. In this article, the route of molecular evolution of the coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is thoroughly compiled, highlighting the changes that the virus has undergone during the last 2 years and discussing the approaches that the medical community has undertaken in the fight against virus-induced damages.

EpiCurator: an immunoinformatic workflow to predict and prioritize SARS-CoV-2 epitopes

The ongoing coronavirus 2019 (COVID-19) pandemic, triggered by the emerging SARS-CoV-2 virus, represents a global public health challenge. Therefore, the development of effective vaccines is an urgent need to prevent and control virus spread. One of the vaccine production strategies uses the in silico epitope prediction from the virus genome by immunoinformatic approaches, which assist in selecting candidate epitopes for in vitro and clinical trials research. This study introduces the EpiCurator workflow to predict and prioritize epitopes from SARS-CoV-2 genomes by combining a series of computational filtering tools. To validate the workflow effectiveness, SARS-CoV-2 genomes retrieved from the GISAID database were analyzed. We identified 11 epitopes in the receptor-binding domain (RBD) of Spike glycoprotein, an important antigenic determinant, not previously described in the literature or published on the Immune Epitope Database (IEDB). Interestingly, these epitopes have a combination of important properties: recognized in sequences of the current variants of concern, present high antigenicity, conservancy, and broad population coverage. The RBD epitopes were the source for a multi-epitope design to in silico validation of their immunogenic potential. The multi-epitope overall quality was computationally validated, endorsing its efficiency to trigger an effective immune response since it has stability, high antigenicity and strong interactions with Toll-Like Receptors (TLR). Taken together, the findings in the current study demonstrated the efficacy of the workflow for epitopes discovery, providing target candidates for immunogen development.

Molecular Level Dissection of Critical Spike Mutations in SARS-CoV-2 Variants of Concern (VOCs): A Simplified Review

SARS-CoV-2 virus during its spread in the last one and half year has picked up critical changes in its genetic code i.e. mutations, which have leads to deleterious epidemiological characteristics. Due to critical role of spike protein in cell entry and pathogenesis, mutations in spike regions have been reported to enhance transmissibility, disease severity, possible escape from vaccine-induced immune response and reduced diagnostic sensitivity/specificity. Considering the structure-function impact of mutations, understanding the molecular details of these key mutations of newly emerged variants/lineages is of urgent concern. In this review, we have explored the literature on key spike mutations harbored by alpha, beta, gamma and delta 'variants of concern' (VOCs) and discussed their molecular consequences in the context of resultant virus biology. Commonly all these VOCs i.e. B.1.1.7, B.1.351, P.1 and B.1.617.2 lineages have decisive mutation in Receptor Binding Motif (RBM) region and/or region around Furin cleavage site (FCS) of spike protein. In general, mutation induced disruption of intra-molecular interaction enhances molecular flexibility leading to exposure of spike protein surface in these lineages to make it accessible for inter-molecular interaction with hACE2. A disruption of spike antigen-antibody inter-molecular interactions in epitope region due to the chemical nature of substituting amino acid hampers the neutralization efficacy. Simplified surveillance of mutation induced changes and their consequences at molecular level can contribute in rationalizing mutation's impact on virus biology. It is believed that molecular level dissection of these key spike mutation will assist the future investigations for a more resilient outcome against severity of COVID-19.

COVID-19: vaccine's progress

Under the pressure of the COVID-19 pandemic, vaccines were developed and rolled out into mass vaccination campaigns at incredible speed. What normally takes a decade was worked out within a year. Vaccines were produced along many different platforms ranging from inactivated whole virus vaccines over adenovirus-vectored vaccines, recombinant protein vaccines and nanoparticles to mRNA vaccines. Several vaccines went through preclinical testing and completed successful phase 1 to phase 3 clinical trials. The first evaluations of national vaccination campaigns document astonishing high levels of protection against disease. The present article summarizes the published reports leading to these striking achievements with vaccines based on different concepts.

Rapid diagnostic methods for SARS-CoV-2 (COVID-19) detection: an evidence-based report

Since December 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has been a global health concern. The transmission method is human-to-human. Since this second wave of SARS-CoV-2 is more aggressive than the first wave, rapid testing is warranted to use practical diagnostics to break the transfer chain. Currently, various techniques are used to diagnose SARS-CoV-2 infection, each with its own set of advantages and disadvantages. A full review of online databases such as PubMed, EMBASE, Web of Science, and Google Scholar was analyzed to identify relevant articles focusing on SARS-CoV-2 and diagnosis and therapeutics. The most recent article search was on May 10, 2021. We summarize promising methods for detecting the novel Coronavirus using sensor-based diagnostic technologies that are sensitive, cost-effective, and simple to use at the point of care. This includes loop-mediated isothermal amplification and several laboratory protocols for confirming suspected 2019-nCoV cases, as well as studies with non-commercial laboratory protocols based on real-time reverse transcription-polymerase chain reaction and a field-effect transistor-based bio-sensing device. We discuss a potential discovery that could lead to the mass and targeted SARS-CoV-2 detection needed to manage the COVID-19 pandemic through infection succession and timely therapy.