A comprehensive review of SARS-CoV-2 genetic mutations and lessons from animal coronavirus recombination in one health perspective

Distinctive Combinations of RBD Mutations Contribute to Antibody Evasion in the Case of the SARS-CoV-2 Beta Variant

Since its first report in 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed a grave threat to public health. Virus-specific countermeasures, such as vaccines and therapeutics, have been developed and have contributed to the control of the viral pandemic, which has become endemic. Nonetheless, new variants continue to emerge and could cause a new pandemic. Consequently, it is important to comprehensively understand viral evolution and the roles of mutations in viral infectivity and transmission. SARS-CoV-2 beta variant encode mutations (D614G, N501Y, E484K, and K417N) in the spike which are frequently found in other variants as well. While their individual role in viral infectivity has been elucidated against various therapeutic antibodies, it still remains unclear whether those mutations may act additively or synergistically when combined. Here, we report that N501Y mutation shows differential effect on two therapeutic antibodies tested. Interestingly, the relative importance of E484K and K417N mutations in antibody evasion varies depending on the antibody type. Collectively, these findings suggest that continuous efforts to develop effective antibody therapeutics and combinatorial treatment with multiple antibodies are more rational and effective forms of treatment.

An integrative pan-cancer analysis reveals the carcinogenic effects of NCAPH in human cancer

BACKGROUND

Non-chromosomal structure maintenance protein condensin complex I subunit H (NCAPH) has been reported to play a regulatory role in a variety of cancers and is associated with tumor poor prognosis. This study aims to explore the potential role of NCAPH with a view to providing insights on pathologic mechanisms.

METHODS

The expression of NCAPH in different tumors was explored by The Cancer Genome Atlas (TCGA) and Genotype Tissue Expression (GTEx). The prognostic value of NCAPH was retrieved through GEPIA and Kaplan-Meier Plotter databases. Tumor Immunity Estimation Resource (TIMER) and Single-Sample Gene Set Enrichment Analysis (GSEA) to search for the association of NCAPH with tumor immune infiltration. The cBioPortal and PhosphoSite Plus databases showed NCAPH phosphorylation status in tumors. Gene set enrichment analysis (GSEA) was performed using bioinformatics.

RESULTS

Our findings revealed that NCAPH showed high expression levels in a wide range of tumor types, and was strongly correlated with the prognosis of patients. Moreover, a higher phosphorylation level at S59, S67, S76, S190, S222 and T38 site was discovered in head and neck squamous cell carcinoma (HNSC). NCAPH overexpression was positively correlated with the infiltration level of CD8+T cells and myeloid dendritic infiltration in breast cancer and thymoma.

CONCLUSIONS

The up-regulation of NCAPH was significantly correlated with the poor prognosis and immune infiltration in pan-cancer, and NCAPH could be served as a potential immunotherapeutic target for cancers.

Impact of X-radiation in the management of COVID-19 disease

Coronaviruses are a diverse group of viruses that infect both animals and humans. Even though the existence of coronavirus and its infection to humans is not new, the 2019-novel coronavirus (nCoV) caused a major burden to individuals and society i.e., anxiety, fear of infection, extreme competition for hospitalization, and more importantly financial liability. The nCoV infection/disease diagnosis was based on non-specific signs and symptoms, biochemical parameters, detection of the virus using reverse-transcription polymerase chain reaction (RT-PCR), and X-ray-based imaging. This review focuses on the consolidation of potentials of X-ray-based imaging modality [chest-X radiography (CXR) and chest computed tomography (CT)] and low-dose radiation therapy (LDRT) for screening, severity, and management of COVID-19 disease. Reported studies suggest that CXR contributed significantly toward initial rapid screening/diagnosis and CT- imaging to monitor the disease severity. The chest CT has high sensitivity up to 98% and low specificity for diagnosis and severity of COVID-19 disease compared to RT-PCR. Similarly, LDRT compliments drug therapy in the early recovery/Less hospital stays by maintaining the physiological parameters better than the drug therapy alone. All the results undoubtedly demonstrated the evidence that X-ray-based technology continues to evolve and play a significant role in human health care even during the pandemic.

Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview

With the unexpected emergence of the novel 2019 Wuhan coronavirus, the world was faced with a sudden uproar that quickly shifted into a serious life-threatening pandemic. Affecting the lives of the global population and leaving drastic damage in various sections and systems, several measures have been constantly taken to tackle down this crisis. For instance, numerous vaccines have been developed in the past two years, some of which have been granted emergency use, thus providing sufficient immunity to the vaccinated individuals. However, the appearance of newly emerged SARS-CoV-2 variants with accelerated transmission and fatality has led the world towards another pandemic. Having undergone various mutations in genomic and/or amino acid profiles, some of the emerged variants of concern (VOCs) including Alpha, Beta, Gamma, and Delta have displayed immune evasion and pathogenicity even in the vaccinated population, hence raising concerns regarding the efficacy of current vaccines against new VOCs of COVID-19. Therefore, genomic investigations of SARS-CoV-2 mutations are expected to provide valuable insight into the evolution of SARS-CoV-2, while also determining the impact of different mutations on infection severity. This study was constructed with the aim of shining light on recent advances regarding mutations in major COVID-19 VOCs, as well as vaccination efficacy against those VOCs.

BCG-Based Vaccines Elicit Antigen-Specific Adaptive and Trained Immunity against SARS-CoV-2 and Andes orthohantavirus

Background:Mycobacterium bovis Bacillus Calmette-Guérin (BCG) is a live attenuated vaccine mainly administered to newborns and used for over 100 years to prevent the disease caused by Mycobacterium tuberculosis (M. tb). This vaccine can induce immune response polarization towards a Th1 profile, which is desired for counteracting M. tb, other mycobacteria, and unrelated intracellular pathogens. The vaccine BCG has been used as a vector to express recombinant proteins and has been shown to protect against several diseases, particularly respiratory viruses. Methods: BCG was used to develop recombinant vaccines expressing either the Nucleoprotein from SARS-CoV-2 or Andes orthohantavirus. Mice were immunized with these vaccines with the aim of evaluating the safety and immunogenicity parameters. Results: Immunization with two doses of 1 × 10⁸ CFU or one dose of 1 × 10⁵ CFU of these BCGs was safe in mice. A statistically significant cellular immune response was induced by both formulations, characterized as the activation of CD4⁺ and CD8⁺ T cells. Stimulation with unrelated antigens resulted in increased expression of activation markers by T cells and secretion of IL-2 and IFN-γ, while increased secretion of IL-6 was found for both recombinant vaccines; all of these parameters related to a trained immunity profile. The humoral immune response elicited by both vaccines was modest, but further exposure to antigens could increase this response. Conclusions: The BCG vaccine is a promising platform for developing vaccines against different pathogens, inducing a marked antigen-specific immune response.

COVID-19 Recovery Patterns Across Alpha (B.1.1.7) and Delta (B.1.617.2) Variants of SARS-CoV-2

Background

B.1.1.7 (alpha) and B.1.617.2 (delta) variants of concern for SARS-CoV-2 have been reported to have differential infectivity and pathogenicity. Difference in recovery patterns across these variants and the interaction with vaccination status has not been reported in population-based studies.

Objective

The objective of this research was to study the length of stay and temporal trends in RT-PCR cycle times (Ct) across alpha and delta variants of SARS-CoV-2 between vaccinated and unvaccinated individuals.

Methods

Participants consisted of patients admitted to national COVID-19 treatment facilities if they had a positive RT-PCR test for SARS-CoV-2, and analysis of variants was performed (using whole genome sequencing). Information on vaccination status, age, sex, cycle times (Ct) for four consecutive RT-PCR tests conducted during hospital stay, and total length of hospital stay for each participant were ascertained from electronic medical records.

Results

Patients infected with the delta variant were younger (mean age = 35years vs 39 years for alpha, p<0.001) and had lesser vaccination coverage (54% vs 72% for alpha, p<0.001). RT-PCR Ct values were similar for both variants at the baseline test; however by the fourth test, delta variant patients had significantly lower Ct values (27 vs 29, p=0.05). Length of hospital stay was higher in delta variant patients in vaccinated (3 days vs 2.9 days for alpha variant) as well as in unvaccinated patients (5.2 days vs 4.4 days for alpha variant, p<0.001). Hazards of hospital discharge after adjusting for vaccination status, age, and sex was higher for alpha variant infections (HR=1.2, 95% CI: 1.01-1.41, p=0.029).

Conclusion

Patients infected with the delta variant of SARS-CoV-2 were found to have a slower recovery as indicated by longer length of stay and higher shedding of the virus compared to alpha variant infections, and this trend was consistent in both vaccinated and unvaccinated patients.

Profiles in conspiracism: Associations with two psychiatric syndromes, religiosity and pandemic-related health behaviors

INTRODUCTION

Conspiratorial beliefs are often maladaptive for individuals and dangerous for societies. Other prevalent belief systems such as (normative) religious belief and (pathological) delusional belief show parallels to conspiratorial beliefs, which may also be linked to excessive social media exposure. We conducted an online survey to characterize heterogeneous profiles of conspiracy-mindedness, with respect to these other phenomena.

METHODS

Eight hundred and thirty six American adults from online panels completed validated questionnaires including the Conspiracy Mindedness Questionnaire (CMQ), Centrality of Religion Scale (CRS), Peters Delusion Inventory (PDI; 21-item version), and Facebook Addiction Scale (FAS). Additionally, they completed 4 questions addressing categorical belief in the origin of SARS-CoV-2, and pandemic-related health behaviors. Total scores on each questionnaire were Z-transformed and entered into K-means cluster analysis. Cluster membership was used in post-hoc analyses to compare pandemic-related items.

RESULTS

An optimal solution included 3 clusters with above-mean (high) CMQ and 3 below-mean (low) CMQ scores. The 3 high-CMQ clusters included: (1) high-religion, low-social media addiction; (2) high religion, social media addiction and delusion; (3) low religion and delusion. High-CMQ clusters 1 and 2 each had rates of zoonotic and malevolent viral origin beliefs that were relatively lower and higher than the grand sample rates, respectively. Significant differences in intended pandemic health-related behaviors among the high-CMQ clusters (compared to the rest of the sample) included Cluster 1-high on Precautions and low on Vaccination; Cluster 2-high on Testing. Respondents who endorsed SARS-CoV-2 origin beliefs (across clusters) that were least plausible and most malevolent were least inclined to engage in pandemic health behaviors.

CONCLUSIONS

Distinct subpopulations of persons with high conspiracy-mindedness exist, which are highly heterogeneous in their other coexisting beliefs and behaviors. Some of these may be pathological, such as delusional belief and social media addiction-like behavior, and they have varied associations with pandemic-related belief and behavior. These results, while cross-sectional, suggest that the psychological origins and consequences of conspiratorial beliefs may not be unitary. Instead, conspiratorial belief may be a common expression of diverse psychological and social/experiential factors, and in turn exert varied influence on decisions and overt behavior.

The oral vaccine based on self-replicating RNA lipid nanoparticles can simultaneously neutralize both SARS-CoV-2 variants alpha and delta

The aim of this study was to evaluate self-replicating RNA lipid nanoparticles (saRNA LNPs) to neutralize SARS-CoV-2 variants delta (B.1.617 lineage) and alpha (B.1.1.7 lineage). Before immunization of mice with saRNA LNPs, we saw high expression of S-protein at both mRNA and protein levels after transfection of HEK293T/17 cells with saRNA LNPs. After oral immunization of BALB/c mice with 0.1 - 10 µg saRNA LNPs , a high quantity of SARS-CoV-2 specific IgG and IgA antibodies were seen with a dose-dependent pattern. Importantly, the ratio of IgG2a/IgG1 in serum of vaccinated mice showed Th1/Th2 skewing response. We also found that the secreted antibodies could neutralize SARS-CoV-2 variants delta (B.1.617 lineage) and alpha (B.1.1.7 lineage). Re-stimulated splenocytes of vaccinated mice showed high secretion of IFN-γ, IL-6, and TNF- α . The authors think that although the preclinical study confirmed the efficacy of saRNA LNPs against SARS-CoV-2, the actual efficacy and safety of the oral vaccine must be evaluated in clinical trials.

Prevalence and molecular characteristics of feline coronavirus in southwest China from 2017 to 2020

Feline coronavirus (FCoV) is the causative agent of feline infectious peritonitis and diarrhoea in kittens worldwide. In this study, a total of 173 feline diarrhoeal faecal and ascetic samples were collected from 15 catteries and six veterinary hospitals in southwest China from 2017 to 2020. FCoV was detected in 80.35 % (139/173) of the samples using the RT-nPCR method; these included infections with 122 type I FCoV and 57 type II FCoV. Interestingly, 51 cases had co-infection with types I and II, the first such report in mainland China. To further analyse the genetic diversity of FCoV, we amplified 23 full-length spike (S) genes, including 18 type I and five type II FCoV. The type I FCoV and type II FCoV strains shared 85.5-98.7% and 97.4-98.9% nucleotide (nt) sequence identities between one another, respectively. The N-terminal domain (NTD) of 23 FCoV strains showed a high degree of variation (73.6-80.3 %). There was six type I FCoV strains with two amino acid insertions (159HL160) in the NTD. In addition, 18 strains of type I FCoV belonged to the Ie cluster, and five strains of type II FCoV were in the IIb cluster based on phylogenetic analysis. Notably, it was first time that two type I FCoV strains had recombination in the NTD, and the recombination regions was located 140-857 nt of the S gene. This study constitutes a systematic investigation of the current infection status and molecular characteristics of FCoV in southwest China.

Nanotechnology-Assisted RNA Delivery: From Nucleic Acid Therapeutics to COVID-19 Vaccines

In recent years, the main quest of science has been the pioneering of the groundbreaking biomedical strategies needed for achieving a personalized medicine. Ribonucleic acids (RNAs) are outstanding bioactive macromolecules identified as pivotal actors in regulating a wide range of biochemical pathways. The ability to intimately control the cell fate and tissue activities makes RNA-based drugs the most fascinating family of bioactive agents. However, achieving a widespread application of RNA therapeutics in humans is still a challenging feat, due to both the instability of naked RNA and the presence of biological barriers aimed at hindering the entrance of RNA into cells. Recently, material scientists' enormous efforts have led to the development of various classes of nanostructured carriers customized to overcome these limitations. This work systematically reviews the current advances in developing the next generation of drugs based on nanotechnology-assisted RNA delivery. The features of the most used RNA molecules are presented, together with the development strategies and properties of nanostructured vehicles. Also provided is an in-depth overview of various therapeutic applications of the presented systems, including coronavirus disease vaccines and the newest trends in the field. Lastly, emerging challenges and future perspectives for nanotechnology-mediated RNA therapies are discussed.

SARS-CoV2 spike protein gene variants with N501T and G142D mutation-dominated infections in mink in the United States

Large numbers of mink have been infected with SARS-CoV2 containing the spike protein Y453F mutation in Europe, causing zoonosis concerns. To evaluate the genetic characteristics of the U.S. and Canadian mink-derived SARS-CoV2 sequences, we analyzed all animal-derived (977) and all Canadian (19,529) and U.S. (173,277) SARS-CoV2 sequences deposited in GISAID from December 2019 to March 12, 2021, and identified 2 dominant novel variants, the N501T-G142D variant and N501T-G142D-F486L variant, in the U.S. mink-derived SARS-CoV2 sequences. These variants were not found in mink from Canada or other countries. The Y453F mutation was not identified in the mink-derived sequences in the United States and Canada. The N501T mutation occurred 2 mo earlier in humans than in mink in the United States, and the novel N501T-G142D and N501T-G142D-F486L variants were found in humans prior to mink. Our results suggest that the novel SARS-CoV2 variants may have evolved during human infection and were then transmitted to mink populations in the United States.

Preparedness and activities of the anti-SARS-CoV-2 convalescent plasma bank in the Veneto region (Italy): An organizational model for future emergencies

Background

Convalescent plasma (CP) has been used in the past in various pandemics, in particular in H1N1, SARS and MERS infections. In Spring 2020, when ongoing the SARS-CoV-2 pandemics, the Veneto Region (V-R) has proposed setting-up an anti-SARS-CoV-2 CP (CCP) Bank, with the aim of preparing a supply of CCP immediately available in case of subsequest epidemic waves.

Materials and Methods

Key-points to be developed for a quick set-up of the V-R CCP Bank have been recruitment of donors recovered from COVID-19 infection, laboratory analysis for the biological qualification of the CCP units, including titre of neutralizing antibodies and reduction of pathogens, according to National Blood Centre (CNS) Directives, adaptation of the V-R Information Technology systems and cost analysis. Some activities, including diagnostic and viral inactivation processes, have been centralized in 2 or 3 sites. Laboratory analysis upon preliminary admission of the donor included all tests required by the Italian laws and the CNS directives.

Results

From April to August 2020, 3,298 people have contacted the V-R Blood Transfusion Services: of these, 1,632 have been evaluated and examined as first time donors and those found to be suitable have carried out 955 donations, from which 2,626 therapeutic fractions have been obtained, at a cost around 215,00 Euro. Since October 2020, the number of COVID-19 inpatients has had a surge with a heavy hospital overload. Moreover, the high request of CCP therapy by clinicians has been just as unexpected, showing a wide therapeutic use.

Conclusions

The organizational model here presented, which has allowed the rapid collection of a large amount of CCP, could be useful when facing new pandemic outbreaks, especially in low and middle income countries, with generally acceptable costs.

Omics-based microbiome analysis in microbial ecology: from sequences to information

Microbial ecology is the study of microorganisms present in nature. It particularly focuses on microbial interactions with any biota and with surrounding environments. Microbial ecology is entering its golden age with innovative multi-omics methods triggered by next-generation sequencing technologies. However, the extraction of ecologically relevant information from ever-increasing omics data remains one of the most challenging tasks in microbial ecology. This special issue includes 11 review articles that provide an overview of the state of the art of omics-based approaches in the field of microbial ecology, with particular emphasis on the interpretation of omics data, environmental pollution tracking, interactions in microbiomes, and viral ecology.