Antibody isotype epitope mapping of SARS-CoV-2 Spike RBD protein: Targets for COVID-19 symptomatology and disease control.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still poses a challenge for biomedicine and public health. To advance the development of effective diagnostic, prognostic, and preventive interventions, our study focused on high-throughput antibody binding epitope mapping of the SARS-CoV-2 spike RBD protein by IgA, IgM and IgG antibodies in saliva and sera of different cohorts from healthy uninfected individuals to SARS-CoV-2-infected unvaccinated and vaccinated asymptomatic, recovered, nonsevere, and severe patients. Identified candidate diagnostic (455-LFRKSNLKPFERD-467), prognostic (395-VYADSFVIRGDEV-407-C-KLH, 332-ITNLCPFGEV-342-C-KLH, 352-AWNRKRI-358-C-KLH, 524-VCGPKKSTNLVKN-536-KLH), and protective (MKLLE-487-NCYFPLQSYGFQPTNGVG-504-GGGGS-446-GGNYNYLYRLFRKSNLKPFERD-467) epitopes were validated with sera from prevaccine and postvaccine cohorts. The results identified neutralizing epitopes and support that antibody recognition of linear B-cell epitopes in RBD protein is associated with antibody isotype and disease symptomatology. The findings in asymptomatic individuals suggest a role for anti-RBD antibodies in the protective response against SARS-CoV-2. The possibility of translating results into diagnostic interventions for the early diagnosis of asymptomatic individuals and prognosis of disease severity provides new tools for COVID-19 surveillance and evaluation of risks in hospitalized patients. These results, together with other approaches, may contribute to the development of new vaccines for the control of COVID-19 and other coronavirus-related diseases using a quantum vaccinomics approach through the combination of protective epitopes.

Serum biomarkers for nutritional status as predictors in COVID-19 patients before and after vaccination.

The aim of this study was to characterize serum protein biomarkers for nutritional status that may be used as predictors for disease symptomatology in COVID-19 patients before and after vaccination. In pre-vaccine cohorts, proteomics analysis revealed significant differences between groups, with serum proteins alpha-1-acid glycoproteins (AGPs) 1 and 2, C-reactive protein (CRP) and retinol binding protein (RBP) increasing with COVID-19 severity, in contrast with serum albumin, transthyretin (TTR) and serotransferrin (TF) reduction as the symptomatology increased. Immunoassay reproduced and validated proteomics results of serum proteins albumin and RBP. In post-vaccine cohorts, the results showed the same pattern as in pre-vaccine cohorts for serum proteins AGPs, CRP, albumin and TTR. However, TF levels were similar between groups and RBP presented a slight reduction as COVID-19 symptomatology increased. In these cohorts, immunoassay validated proteomics results of serum proteins albumin, TTR and TF. Additionally, immune response to α-Gal in pre-vaccine cohorts varied in predominant immunoglobulin type profile, while post-vaccine groups presented mainly anti-α-Gal protective IgG antibodies. The study identified serum nutritional biomarkers that could potentially predict an accurate prognostic of COVID-19 disease to provide an appropriate nutritional care and guidance in non-vaccinated and vaccinated individuals against SARS-CoV-2. These results highlight the importance of designing personalized nutrition protocols to improve diet along with the application of prebiotics or probiotics for the control of COVID-19 and other infectious diseases.

Approaching Challenges Posed by SARS-CoV-2 Genetic Variants.

In this new collection of the most viewed and cited papers, one of the Editor's chosen articles, published in Pathogens in 2021, addressed the impact and the concerns relating to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants [...].

A study of viral pathogens in bat species in the Iberian Peninsula: identification of new coronavirus genetic variants.

Bats have long been associated with multiple pathogens, including viruses affecting humans such as henipaviruses, filoviruses, bunyaviruses and coronaviruses. The alpha and beta coronaviruses genera can infect most mammalian species. Among them, betacoronavirus SARS-CoV, MERS-CoV and SARS-CoV-2, which have caused the three major pandemics in the last two decades, have been proposed to originate in bats. In this study, 194 oral swabs from 22 bats species sampled in 19 locations of the Iberian Peninsula were analysed and characterized by three different PCR tests (coronavirus generic real-time RT-PCR, multiplex conventional PCR, and SARS-CoV-2 specific real-time RT-PCR) to detect bat coronaviruses. Screening with coronavirus generic PCR showed 102 positives out of 194 oral swabs analysed. Then, metabarcoding with multiplex PCR amplified 15 positive samples. Most of the coronaviruses detected in this study belong to alphacoronavirus (α-CoV) genus, with multiple alphacoronaviruses identified by up to five different genetic variants coexisting in the same bat. One of the positive samples identified in a Miniopterus schreibersii bat positive for the generic coronavirus PCR and the specific SARS-CoV-2 PCR was classified as betacoronavirus (-CoV) through phylogenetic analysis. These results support the rapid evolution of coronaviruses to generate new genomic potentially pathogenic variants likely through co-infection and recombination.

HEPA filters of portable air cleaners as a tool for the surveillance of SARS-CoV-2.

Studies about the identification of SARS-CoV-2 in indoor aerosols have been conducted in hospital patient rooms and to a lesser extent in nonhealthcare environments. In these studies, people were already infected with SARS-CoV-2. However, in the present study, we investigated the presence of SARS-CoV-2 in HEPA filters housed in portable air cleaners (PACs) located in places with apparently healthy people to prevent possible outbreaks. A method for detecting the presence of SARS-CoV-2 RNA in HEPA filters was developed and validated. The study was conducted for 13 weeks in three indoor environments: school, nursery, and a household of a social health center, all in Ciudad Real, Spain. The environmental monitoring of the presence of SARS-CoV-2 was conducted in HEPA filters and other surfaces of these indoor spaces for a selective screening in asymptomatic population groups. The objective was to limit outbreaks at an early stage. One HEPA filter tested positive in the social health center. After analysis by RT-PCR of SARS-CoV-2 in residents and healthcare workers, one worker tested positive. Therefore, this study provides direct evidence of virus-containing aerosols trapped in HEPA filters and the possibility of using these PACs for environmental monitoring of SARS-CoV-2 while they remove airborne aerosols and trap the virus.

Correlates with Vaccine Protective Capacity and COVID-19 Disease Symptoms Identified by Serum Proteomics in Vaccinated Individuals.

In the last two years, the coronavirus disease 19 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been a scientific and social challenge worldwide. Vaccines have been the most effective intervention for reducing virus transmission and disease severity. However, genetic virus variants are still circulating among vaccinated individuals with different disease symptomatology. Understanding the protective- or disease-associated mechanisms in vaccinated individuals is relevant to advances in vaccine development and implementation. To address this objective, serum-protein profiles were characterized by quantitative proteomics and data-analysis algorithms in four cohorts of uninfected and SARS-CoV-2-infected vaccinated individuals with asymptomatic, non-severe, and severe disease symptomatology. The results show that immunoglobulins were the most overrepresented proteins in infected cohorts when compared to PCR-negative individuals. The immunoglobulin profile varied between different infected cohorts and correlated with protective- or disease-associated capacity. Overrepresented immunoglobulins in PCR-positive individuals correlated with protective response against SARS-CoV-2, other viruses, and thrombosis in asymptomatic cases. In non-severe cases, correlates of protection against SARS-CoV-2 and HBV together with risk of myasthenia gravis and allergy and autoantibodies were observed. Patients with severe symptoms presented risk for allergy, chronic idiopathic thrombocytopenic purpura, and autoantibodies. The analysis of underrepresented immunoglobulins in PCR-positive compared to PCR-negative individuals identified vaccine-induced protective epitopes in various coronavirus proteins, including the spike receptor-binding domain RBD. Non-immunoglobulin proteins were associated with COVID-19 symptoms and biological processes. These results evidence host-associated differences in response to vaccination and the possibility of improving vaccine efficacy against SARS-CoV-2.

Art-science multidisciplinary collaborations to address the scientific challenges posed by COVID-19.

The ongoing coronavirus pandemic COVID-19 constitutes a scientific and social challenge. The application of mixed-methods research with multidisciplinary collaborations increases the success of experimental design and interpretation of results to approach scientific challenges. The objective is to develop and implement protean art algorithms with interactions between artists and scientists for scientific research in areas of molecular biology, immunology, ecology and biomedicine. In this perspective, artists were invited to contribute pieces related to the pandemic, and scientists were then challenged to contribute their view and proposed research inspired by artist contribution to face COVID-19 scientific challenges. Proposed research objectives inspired by artist contributions contribute to approach COVID-19 scientific and social challenges with results that may translate into new diagnosis and control interventions. The proposed research objectives approach vaccine protective mechanisms and the development of nutritional interventions with possible impact on boosting protective response to vaccination, the impact of fuel pollutants on host immunity and virus transmission, the possible role of ectoparasite vectors in the appearance of SARS-CoV-2 variants and virus transmission, collaboration between different sectors to contribute to virus surveillance and reduce risks of contagion, characterization of the incidence of zoonotic diseases during and after the COVID-19 pandemic in relation to modifications in the interactions between humans and reservoir animal species, evaluation of the risks associated with sexual or congenital transmission of SARS-CoV-2, development of new methods for the easy and rapid detection of very low SARS-CoV-2 virus amounts in infected but asymptomatic individuals, and understanding society perceptions about the socio-ecological relationships between decoupled environments and the risks and effects of pandemics. This approach may be used to promote social participation in science through combined scientific and artistic perspectives with impact on science and society.KEY MESSAGEMixed-methods research with multidisciplinary collaborations increases the success of experimental design and interpretation of results.Implementation of protean art algorithms through interactions between artists and scientists advances scientific research.Proposed research objectives inspired by artist contributions contribute to approach COVID-19 scientific and social challenges with results that may translate into new diagnosis and control interventions.

Good and bad get together: Inactivation of SARS-CoV-2 in particulate matter pollution from different fuels.

Air pollution and associated particulate matter (PM) affect environmental and human health worldwide. The intense vehicle usage and the high population density in urban areas are the main causes of this public health impact. Epidemiological studies have provided evidence on the effect of air pollution on airborne SARS-CoV-2 transmission and COVID-19 disease prevalence and symptomatology. However, the causal relationship between air pollution and COVID-19 is still under investigation. Based on these results, the question addressed in this study was how long SARS-CoV-2 survives on the surface of PM from different origin to evaluate the relationship between fuel and atmospheric pollution and virus transmission risk. The persistence and viability of SARS-CoV-2 virus was characterized in 5 engine exhaust PM and 4 samples of atmospheric PM10. The results showed that SARS-CoV-2 remains on the surface of PM10 from air pollutants but interaction with engine exhaust PM inactivates the virus. Consequently, atmospheric PM10 levels may increase SARS-CoV-2 transmission risk thus supporting a causal relationship between these factors. Furthermore, the relationship of pollution PM and particularly engine exhaust PM with virus transmission risk and COVID-19 is also affected by the impact of these pollutants on host oxidative stress and immunity. Therefore, although fuel PM inactivates SARS-CoV-2, the conclusion of the study is that both atmospheric and engine exhaust PM negatively impact human health with implications for COVID-19 and other diseases.

Current and Future Strategies for the Diagnosis and Treatment of the Alpha-Gal Syndrome (AGS).

The α-Gal syndrome (AGS) is a pathognomonic immunoglobulin E (IgE)-mediated delayed anaphylaxis in foods containing the oligosaccharide galactose-α-1,3-galactose (α-Gal) such as mammalian meat or dairy products. Clinical presentation of AGS can also comprise immediate hypersensitivity due to anticancer therapy, gelatin-containing vaccines or mammalian serum-based antivenom. The IgE initial sensitization is caused by hard-bodied tick bites and symptomatic individuals typically develop delayed pruritus, urticaria, angioedema, anaphylaxis, malaise or gut-related symptoms. Due to inapparent presentation, delayed reactions and a wide variety of patients´ clinical history, the AGS diagnosis and treatment remain challenging. This review covers not only current diagnostic methods used for AGS such as the skin prick test (SPT), the oral food challenge (OFC), anti-α-Gal IgE levels measurement and the basophil activation test (BAT), but also potentially relevant next-generation diagnostic tools like the mast cell activation test (MAT), the histamine-release (HR) assay, omics technologies and model-based reasoning (MBR). Moreover, it focuses on the therapeutical medical and non-medical methods available and current research methods that are being applied in order to elucidate the molecular, physiological and immune mechanisms underlying this allergic disorder. Lastly, future treatment and preventive tools are also discussed, being of utmost importance for the identification of tick salivary molecules, with or without α-Gal modifications, that trigger IgE sensitivity as they could be the key for further vaccine development. Bearing in mind climate change, the tick-host paradigm will shift towards an increasing number of AGS cases in new regions worldwide, which will pose new challenges for clinicians in the future.

Citizen science initiative points at childhood BCG vaccination as a risk factor for COVID-19.

Current results do not provide conclusive evidence on the effect of BCG vaccination on COVID-19 alone or in combination with other factors. To address this limitation, in this study we used a citizen science initiative on the COVID-19 pandemic to collect data worldwide during 2 October 2020-30 October 2020 (1,233 individuals) in a structured way for analysing factors and characteristics of affected individuals in relation to BCG vaccination. For the first time, the results of our study suggested that vaccination with BCG may increase the risk for COVID-19 at certain age, particularly in individuals vaccinated at childhood. Childhood BCG vaccination increased the likelihood of being diagnosed with COVID-19 fivefold in COVID-19 low-incidence countries and threefold in high-incidence countries. A reasonable explanation for this effect is the activation of certain innate immunity mechanisms associated with inflammatory reactions. These factors should be considered when analysing the risks associated with this global pandemic.

Characterization by Quantitative Serum Proteomics of Immune-Related Prognostic Biomarkers for COVID-19 Symptomatology.

The COVID-19 pandemic caused by SARS-CoV-2 challenges the understanding of factors affecting disease progression and severity. The identification of prognostic biomarkers and physiological processes associated with disease symptoms is relevant for the development of new diagnostic and therapeutic interventions to contribute to the control of this pandemic. To address this challenge, in this study, we used a quantitative proteomics together with multiple data analysis algorithms to characterize serum protein profiles in five cohorts from healthy to SARS-CoV-2-infected recovered (hospital discharge), nonsevere (hospitalized), and severe [at the intensive care unit (ICU)] cases with increasing systemic inflammation in comparison with healthy individuals sampled prior to the COVID-19 pandemic. The results showed significantly dysregulated proteins and associated biological processes and disorders associated to COVID-19. These results corroborated previous findings in COVID-19 studies and highlighted how the representation of dysregulated serum proteins and associated BPs increases with COVID-19 disease symptomatology from asymptomatic to severe cases. The analysis was then focused on novel disease processes and biomarkers that were correlated with disease symptomatology. To contribute to translational medicine, results corroborated the predictive value of selected immune-related biomarkers for disease recovery [Selenoprotein P (SELENOP) and Serum paraoxonase/arylesterase 1 (PON1)], severity [Carboxypeptidase B2 (CBP2)], and symptomatology [Pregnancy zone protein (PZP)] using protein-specific ELISA tests. Our results contributed to the characterization of SARS-CoV-2-host molecular interactions with potential contributions to the monitoring and control of this pandemic by using immune-related biomarkers associated with disease symptomatology.

Vaccinomics: a future avenue for vaccine development against emerging pathogens.

INTRODUCTION: Vaccines are a major achievement in medical sciences, but the development of more effective vaccines against infectious diseases is essential for prevention and control of emerging pathogens worldwide. The application of omics technologies has advanced vaccinology through the characterization of host-vector-pathogen molecular interactions and the identification of candidate protective antigens. However, major challenges such as host immunity, pathogen and environmental factors, vaccine efficacy and safety need to be addressed. Vaccinomics provides a platform to address these challenges and improve vaccine efficacy and safety. AREAS COVERED: In this review, we summarize current information on vaccinomics and propose quantum vaccinomics approaches to further advance vaccine development through the identification and combination of antigen protective epitopes, the immunological quantum. The COVID-19 pandemic caused by SARS-CoV-2 is an example of emerging infectious diseases with global impact on human health. EXPERT OPINION: Vaccines are required for the effective and environmentally sustainable intervention for the control of emerging infectious diseases worldwide. Recent advances in vaccinomics provide a platform to address challenges in improving vaccine efficacy and implementation. As proposed here, quantum vaccinomics will contribute to vaccine development, efficacy, and safety by facilitating antigen combinations to target pathogen infection and transmission in emerging infectious diseases.

Anakinra versus Baricitinib: Different Strategies for Patients Hospitalized with COVID-19.

BACKGROUND: Immunomodulatory drugs have been used in patients with severe COVID-19. The objective of this study was to evaluate the effects of two different strategies, based either on an interleukin-1 inhibitor, anakinra, or on a JAK inhibitor, such as baricitinib, on the survival of patients hospitalized with COVID-19 pneumonia. METHODS: Individuals admitted to two hospitals because of COVID-19 were included if they fulfilled the clinical, radiological, and laboratory criteria for moderate-to-severe disease. Patients were classified according to the first immunomodulatory drug prescribed: anakinra or baricitinib. All subjects were concomitantly treated with corticosteroids, in addition to standard care. The main outcomes were the need for invasive mechanical ventilation (IMV) and in-hospital death. Statistical analysis included propensity score matching and Cox regression model. RESULTS: The study subjects included 125 and 217 individuals in the anakinra and baricitinib groups, respectively. IMV was required in 13 (10.4%) and 10 (4.6%) patients, respectively (p = 0.039). During this period, 22 (17.6%) and 36 (16.6%) individuals died in both groups (p = 0.811). Older age, low functional status, high comorbidity, need for IMV, elevated lactate dehydrogenase, and use of a high flow of oxygen at initially were found to be associated with worse clinical outcomes. No differences according to the immunomodulatory therapy used were observed. For most of the deceased individuals, early interruption of anakinra or baricitinib had occurred at the time of their admission to the intensive care unit. CONCLUSIONS: Similar mortality is observed in patients treated with anakinra or baricitinib plus corticosteroids.

Natural SARS-CoV-2 Infection in Kept Ferrets, Spain.

We found severe acute respiratory syndrome coronavirus 2 RNA in 6 (8.4%) of 71 ferrets in central Spain and isolated and sequenced virus from 1 oral and 1 rectal swab specimen. Natural infection occurs in kept ferrets when virus circulation among humans is high. However, small ferret collections probably cannot maintain virus circulation.

The antibody response to the glycan α-Gal correlates with COVID-19 disease symptoms.

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has affected millions of people worldwide. Characterization of the immunological mechanisms involved in disease symptomatology and protective response is important to progress in disease control and prevention. Humans evolved by losing the capacity to synthesize the glycan Galα1-3Galß1-(3)4GlcNAc-R (α-Gal), which resulted in the development of a protective response against pathogenic viruses and other microorganisms containing this modification on membrane proteins mediated by anti-α-Gal immunoglobulin M (IgM)/IgG antibodies produced in response to bacterial microbiota. In addition to anti-α-Gal antibody-mediated pathogen opsonization, this glycan induces various immune mechanisms that have shown protection in animal models against infectious diseases without inflammatory responses. In this study, we hypothesized that the immune response to α-Gal may contribute to the control of COVID-19. To address this hypothesis, we characterized the antibody response to α-Gal in patients at different stages of COVID-19 and in comparison with healthy control individuals. The results showed that while the inflammatory response and the anti-SARS-CoV-2 (Spike) IgG antibody titers increased, reduction in anti-α-Gal IgE, IgM, and IgG antibody titers and alteration of anti-α-Gal antibody isotype composition correlated with COVID-19 severity. The results suggested that the inhibition of the α-Gal-induced immune response may translate into more aggressive viremia and severe disease inflammatory symptoms. These results support the proposal of developing interventions such as probiotics based on commensal bacteria with α-Gal epitopes to modify the microbiota and increase α-Gal-induced protective immune response and reduce severity of COVID-19.

SARS-CoV-2 in animals: potential for unknown reservoir hosts and public health implications.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, previously 2019-nCoV) is suspected of having originated in 2019 in China from a coronavirus infected bat of the genus Rhinolophus. Following the initial emergence, possibly facilitated by a mammalian bridge host, SARS-CoV-2 is currently transmitted across the globe via efficient human-to-human transmission. Results obtained from experimental studies indicate that animal species such as cats, ferrets, raccoon dogs, cynomolgus macaques, rhesus macaques, white-tailed deer, rabbits, Egyptian fruit bats, and Syrian hamsters are susceptible to SARS-CoV-2 infection, and that cat-to-cat and ferret-to-ferret transmission can take place via contact and air. However, natural infections of SARS-CoV-2 have been reported only in pet dogs and cats, tigers, lions, snow leopards, pumas, and gorillas at zoos, and farmed mink and ferrets. Even though human-to-animal spillover has been reported at several instances, SARS-CoV-2 transmission from animals-to-humans has only been reported from mink-to-humans in mink farms. Following the rapid transmission of SARS-CoV-2 within the mink population, a new mink-associated SARS-CoV-2 variant emerged that was identified in both humans and mink. The increasing reports of SARS-CoV-2 in carnivores indicate the higher susceptibility of animal species belonging to this order. The sporadic reports of SARS-CoV-2 infection in domestic and wild animal species require further investigation to determine if SARS-CoV-2 or related Betacoronaviruses can get established in kept, feral or wild animal populations, which may eventually act as viral reservoirs. This review analyzes the current evidence of SARS-CoV-2 natural infection in domestic and wild animal species and their possible implications on public health.

Arthropod Ectoparasites Have Potential to Bind SARS-CoV-2 via ACE.

Coronavirus-like organisms have been previously identified in Arthropod ectoparasites (such as ticks and unfed cat flea). Yet, the question regarding the possible role of these arthropods as SARS-CoV-2 passive/biological transmission vectors is still poorly explored. In this study, we performed in silico structural and binding energy calculations to assess the risks associated with possible ectoparasite transmission. We found sufficient similarity between ectoparasite ACE and human ACE2 protein sequences to build good quality 3D-models of the SARS-CoV-2 Spike:ACE complex to assess the impacts of ectoparasite mutations on complex stability. For several species (e.g., water flea, deer tick, body louse), our analyses showed no significant destabilisation of the SARS-CoV-2 Spike:ACE complex, suggesting these species would bind the viral Spike protein. Our structural analyses also provide structural rationale for interactions between the viral Spike and the ectoparasite ACE proteins. Although we do not have experimental evidence of infection in these ectoparasites, the predicted stability of the complex suggests this is possible, raising concerns of a possible role in passive transmission of the virus to their human hosts.

COVID-19 in the Developing World: Is the Immune Response to α-Gal an Overlooked Factor Mitigating the Severity of Infection?

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19), which has affected millions of people worldwide. Considerably lower prevalence and fatality rates resulting from COVID-19 are reported in Africa and Asia than in the industrialized world. In this Viewpoint, we discuss the possibility that this intriguing phenomenon could be, among other factors, due to protective immunity of the oligosaccharide galactose-α-1,3-galactose (α-Gal). The α-Gal immunity induced by gut microbiota that express the same glycan modification may prevent COVID-19 through the activation of different mechanisms involved in SARS-CoV-2 neutralization and the downregulation of the inflammatory response in the lungs of infected patients.