SARS-associated Coronavirus Research Articles

Randomized controlled trial to study the safety and efficacy of probiotics supplementation in addition to the standard treatment in novel coronavirus (SARS‑CoV‑2) positive patients

Background: The severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) infection spread at a catastrophic rate, rapidly becoming a pandemic. Apart from the symptoms related to viral infection, a few patients with Coronavirus Disease 2019 (COVID-19) also experienced gastrointestinal symptoms. There was initial evidence of intestinal microbial dysbiosis in COVID-19 cases, and a few international studies showed the benefits of probiotics in reducing gastrointestinal (GI) symptoms and favorably altering the course of COVID-19 disease. Aims and Objectives: This study was planned to investigate if probiotics show any beneficial effects on COVID-19 disease in Indian patients. Materials and Methods: A prospective, randomized, open-label study was conducted to evaluate the effect of probiotic supplements added to the existing standard treatment in patients with the novel coronavirus SARS-CoV2 and compared them with the control group. Ninety patients were included in this study and were observed on day 1, day 3, day 5, day 10, day 14, and day of discharge for progression or recovery. Patients were monitored for symptom progression, the need for oxygen therapy, ventilation needs, etc. Results: There was no significant difference in the parameters at baseline in either of the groups. Cough was significantly less in group A (the standard control group) compared to group B (the probiotic group) only on day 5. No significant difference in the number of patients with coughs was seen on the other days. Other important parameters were not significantly different on any day of observation. Conclusion: The study results do not support the use of probiotics for the treatment of GI symptoms related to COVID19 and do not alter the course of COVID-19 disease or symptoms so as to be used as adjunct therapy for COVID-19 patients.

Lentiviral Production Platform.

Lentiviral-mediated transfection technique is a powerful tool for gene modification in preclinical studies. By using this technique, the desired gene modification can be achieved easily in immune cells, nondividing, and terminally differentiated cells, including hematopoietic stem cells, neurons, and even tumor cells, which other viral vectors cannot do. The main considerations of therapeutic gene delivery using a lentiviral system are the risk of insertional mutagenesis and the immune reaction elicited by infected cells. Although some biosafety concerns need to be addressed before clinical trials in rheumatoid arthritis, the lentiviral system targeting therapeutic targets has been widely used for in vivo gene transfer in animal models. In this chapter, the protocols for production of viral particles and viral concentration are provided. As an alternative utilization, this lentiviral production platform could also be employed to produce a pseudotype severe acute respiratory syndrome-related coronavirus 2 in which the spike glycoprotein of SARS-CoV-2 was incorporated into pseudovirions for viral study.

Epidemiology and clinical featuresof respiratory syncytial virus (RSV) infection in hospitalized children during the COVID-19 pandemic in Gorgan,Iran.

Respiratory syncytial virus (RSV)is a leading cause of acute respiratory infection in infants and young children. Given the altered circulation patterns of respiratory viruses during the coronavirus disease pandemic-2019 (COVID-19),the study aimed to evaluate epidemiology and clinical features of RSV infections in hospitalized children during the COVID-19pandemic in Gorgan, northeastern Iran. Molecular epidemiology studies on respiratory viral infections are necessary to monitor circulating viruses, disease severity, and clinical symptoms, in addition to early warning of new outbreaks. Overall, 411 respiratory swab samples from hospitalized children from October 2021 to March 2022 were collected at Taleghani Children's Hospital, Gorgan, Iran. The incidence of RSV, as well as the circulating subgroups and genotypes, were investigated and confirmed using PCR methods. Additionally, all samples tested for severe acute respiratory syndrome-associated coronavirus 2 (SARS-CoV-2)and influenza, and demographic and clinical data were analyzed using SPSS software. The share of RSV, SARS-CoV-2, and influenza among hospitalized children with acute lower respiratory infections (ALRI)were 27%, 16.5%, and 4.1%, respectively. The RSV subgroup A (genotype ON1) was dominant over subgroup B (genotype BA9),with more severe clinical symptoms. Compared with the prepandemic era there were high numbers of hospitalized SARS-CoV-2 positive children and low numbers of other respiratory viruses. Despite this, the prevalence of ALRI-relatedRSV-disease among hospitalized children in our specialized pediatric center was higher than COVID-19disease in the same cohort. Studying the epidemiology of respiratory viruses and determining the circulating strains can contribute to effective infection control and treatment strategies.

Cryptococcus laurentii: A rare and serious fungal infection, and a rising cause of concern in post-COVID-19 era

Coronaviruses are a large group of viruses that infect humans and animals. Rarely, coronaviruses that infect animals can evolve and infect humans and spread between them. Current evidence for coronavirus disease-2019 (COVID-19) suggests that the causative virus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a strain of coronavirus that causes COVID-19, the respiratory illness responsible for COVID-19 pandemic, has a zoonotic origin, closely related to the bat-origin SARS-like coronavirus. The present case report describes the case of a 63-year-old male patient who presented with post-COVID-19 symptoms including fever, and was later diagnosed positive for Cryptococcus laurentii on a urine culture sensitivity test. The following core competencies are addressed in this article: Practice-based learning and improvement, Patient care and procedural skills, Medical knowledge.

SARS CoV 2 (COVID-19) Diagnosis in Wildlife Animals using Rt-Polymerase Chain Reaction (PCR) in Dubai Safari Park

Coronaviruses (CoVs) are enveloped, positive-sense, single-stranded RNA viruses. SARS-CoV-2 is a beta coronavirus, a genus that includes several coronaviruses (SARS-CoV, MERS-CoV, bat SARS-like CoV, and others) isolated from humans, bats, camels, civets, and other animals. Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the pathogenic agent that causes the disease COVID-19. SARS-CoV-2 is thought to have emerged from an animal source, most likely a bat, and subsequently spread to humans. While genetically closely related viruses have been isolated from Rhinolophus bats, the exact source of SARS-CoV-2 and its route of introduction into the human population have not been established. Monitoring animal infections is imperative to better understanding their epidemiological significance for animal health, biodiversity, and human health. According to evidence from risk assessments, epidemiological investigations, and experimental studies, animals play no significant role in the spread of SARS-CoV-2, which is sustained by human-to-human transmission. The possibility of Coronavirus testing by veterinary labs was considered after the Iowa State veterinary lab discovered the COVID-19 virus has a similar DNA testing process to porcine epidemic diarrhea virus (PED). PED is another form of coronavirus that killed many piglets in 2013 and was unresponsive to treatment. Several vet labs optimized their equipment and processes to test for PED, helping them determine that older pigs could recover and develop immunity against the virus. Those same labs are still set up for coronavirus testing. We in Dubai Safari Park, particularly within the laboratory Veterinary Hospital, are conducting RT-PCR analysis to test diverse animal species including non-human primates, Carnivores, small mammals, and Ungulates. Even though none of our animals show any respiratory signs, we have conducted this study to ensure that our animal collection is healthy and free of SARS-COV-2.

Probiotics, An Approach towards Modern Medication

Coronaviruses (CoVs) are enveloped, positive-sense, single-stranded RNA viruses. SARS-CoV-2 is a beta coronavirus, a genus that includes several coronaviruses (SARS-CoV, MERS-CoV, bat SARS-like CoV, and others) isolated from humans, bats, camels, civets, and other animals. Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the pathogenic agent that causes the disease COVID-19. SARS-CoV-2 is thought to have emerged from an animal source, most likely a bat, and subsequently spread to humans. While genetically closely related viruses have been isolated from Rhinolophus bats, the exact source of SARS-CoV-2 and its route of introduction into the human population have not been established. Monitoring animal infections is imperative to better understanding their epidemiological significance for animal health, biodiversity, and human health. According to evidence from risk assessments, epidemiological investigations, and experimental studies, animals play no significant role in the spread of SARS-CoV-2, which is sustained by human-to-human transmission. The possibility of Coronavirus testing by veterinary labs was considered after the Iowa State veterinary lab discovered the COVID-19 virus has a similar DNA testing process to porcine epidemic diarrhea virus (PED). PED is another form of coronavirus that killed many piglets in 2013 and was unresponsive to treatment. Several vet labs optimized their equipment and processes to test for PED, helping them determine that older pigs could recover and develop immunity against the virus. Those same labs are still set up for coronavirus testing. We in Dubai Safari Park, particularly within the laboratory Veterinary Hospital, are conducting RT-PCR analysis to test diverse animal species including non-human primates, Carnivores, small mammals, and Ungulates. Even though none of our animals show any respiratory signs, we have conducted this study to ensure that our animal collection is healthy and free of SARS-COV-2.

Antibody Response Following the Intranasal Administration of SARS-CoV-2 Spike Protein-CpG Oligonucleotide Vaccine.

The new coronavirus infection causes severe respiratory failure following respiratory tract infection with severe acute respiratory syndrome-related coronavirus (SARS-CoV-2). All currently approved vaccines are administered intramuscularly; however, intranasal administration enhances mucosal immunity, facilitating the production of a less invasive vaccine with fewer adverse events. Herein, a recombinant vaccine combining the SARS-CoV-2 spike protein receptor-binding domain (RBD), or S1 protein, with CpG-deoxyoligonucleotide (ODN) or aluminum hydroxide (alum) adjuvants was administered intranasally or subcutaneously to mice. Serum-specific IgG titers, IgA titers in the alveolar lavage fluid, and neutralizing antibody titers were analyzed. The nasal administration of RBD protein did not increase serum IgG or IgA titers in the alveolar lavage fluid. However, a significant increase in serum IgG was observed in the intranasal group administered with S1 protein with CpG-ODN and the subcutaneous group administered with S1 protein with alum. The IgA and IgG levels increased significantly in the alveolar lavage fluid only after the intranasal administration of the S1 protein with CpG-ODN. The neutralizing antibody titers in serum and bronchoalveolar lavage were significantly higher in the intranasal S1-CpG group than in every other group. Hence, the nasal administration of the S1 protein vaccine with CpG adjuvant might represent an effective vaccine candidate.

Mapping Potential Regions of Human Interaction with Acuminate Horseshoe Bats (Rhinolophus acuminatus) in Thailand

Bats are reservoirs for various pathogens, including SARS-like coronaviruses (CoVs). Understanding the distribution of bat species is crucial to identifying areas where viral spillover from bats to other animals or humans might occur. In this study, we performed species distribution modeling to predict suitable habitats within Thailand under current and predicted future climate conditions for Rhinolophus acuminatus, a bat species that has been found to host SARS-CoV-2-related viruses. Our assessment of current conditions revealed that temperature seasonality had the greatest impact on habitat suitability and that suitable habitats were primarily restricted to the southern and eastern regions of Thailand. Over time, the projections indicate a diminishing availability of suitable habitats, suggesting a potential trend toward migration into neighboring areas. We next combined modeled bat distribution with urbanization data to estimate regions in Thailand where bat–human interactions might occur. The resulting map highlighted regions of heightened interaction risk, encompassing approximately 46,053.94 km2 across 58 provinces and representing approximately 9.24% of Thailand’s total area. These risk concentrations are prominently situated in the southern, central, and eastern Thai regions, with extensions into neighboring border areas. Our findings will significantly aid future risk surveillance efforts and enhance the effectiveness of monitoring and managing emerging diseases within the country and in contiguous regions.

A Modified Recombinant DNA-Based SARS-CoV-2 Vaccine Expressing Stabilized Uncleavable Spike Protein Elicits Humoral and Cellular Immunity against Various SARS-CoV-2 Variants of Concern

The appearance of several variants of concern (VOCs) of SARS-CoV-2 affects the efficacy of currently available vaccines and causes continuous spread and reinfection between humans. These variants possess different spike (S) protein mutations, which could affect viral pathogenicity, transmission, and immune escape. Herein, we develop a synthetic codon-optimized DNA vaccine (VIU-1007) expressing full-length S protein. The developed vaccine is stabilized by two K986P and V987P proline substitutions and resistant to cleavage by proteases such as furin by deletion of arginine residues (R682, R683, and R685) in multibasic furin cleavage site (RRAR). Additionally, it carries K417N, E484K, N501Y, and D614G substitutions in the receptor binding domain (RBD) derived from the beta VOC. Following the validation and characterization of the in vitro S protein expression, the humoral and cellular immunogenicity of VIU-1007 was assessed in immunized Balb/c mice. While both regimens elicited a Th-1-biased immune response based on S1-specific binding IgG isotypes, three vaccine doses significantly enhanced IgG levels. Furthermore, CD4+ and CD8+ memory T cell responses in spleens and draining inguinal lymph nodes were significantly higher in mice received three doses of VIU-1007 when compared to those received two doses only. Importantly, sera from mice immunized with three doses showed broad neutralization breadth against several SARS-CoV-2 variants, including alpha, beta, gamma, delta, and omicron VOCs. Moreover, the sera showed limited neutralization capacity against SARS-CoV-1, Bat SARS-like coronavirus WIV1, and MERS-CoV. Together, while these data suggest the presence of common neutralizing-rich epitopes between SARS-CoV-2 variants and some other betacoronaviruses, the ongoing evolution of SARS-CoV-2 could result in escape from vaccine-induced immunity, which requires a continuous update of vaccines.

Analysis of the humoral and cell-mediated immune response in heterologous and homologous SARS-CoV-2 revaccination

The effectiveness of humoral and cell-mediated immunity as a result of primary vaccination for Severe Acute Respiratory Syndrome- related CoronaVirus 2 (SARS-CoV-2), as well as the effectiveness of revaccination, is an important research problem. Studying and selecting optimal revaccination regimens will allow for long-term protection against coronavirus disease 2019 (COVID-19).Aim. To study the severity of humoral and cell-mediated immune response in various (homo- and heterologous) SARS-CoV-2 revaccination regimens as part of a prospective observational study 18 and 24 months after primary vaccination.Material and methods. The study was carried out within the prospective registry SATURN, which included individuals who received various SARS-CoV-2 revaccination (homo- and heterologous regimens) based on a combination of two following vaccines: Gam- COVID-Vac and CoviVac. Depending on the chosen regimen, 3 following groups were formed: group I (n=106) — participants with a homologous Gam- COVID-Vac regimen at each stage of vaccination and revaccination; group II (n=54) — participants with a heterologous regimen of sequential administration of Gam- COVID-Vac and CoviVac at the stage of vaccination and revaccination; group III (n=40) — participants with a homologous CoviVac regimen at the stage of vaccination and revaccination. At the first visit, all participants underwent a medical history collection, examination, and identification of potential contraindications to vaccination. At each subsequent visit, the level of anti- SARS-CoV-2 S-glycoprotein IgG antibodies was additionally determined. At visits 1, 3 and 5, the activity of specifically sensitized T-lymphocytes to the surface and nuclear antigen of SARS-CoV-2 was assessed. The IgG concentration was analyzed using the Abbott Architect SARS-CoV-2 IgG reagent kit, while T-cell immunity was assessed using the T-Spot.COVID test system (Oxford Immunotec). Visit 1 corresponded to the 1st stage of primary vaccination, visit 2 — 2nd stage of primary vaccination, visit 3 (12 months after visit 1) — 1st stage of revaccination, visit 3 (21 days after visit 3) — 2nd stage of revaccination, visit 5 –18 months after primary vaccination, visit 6 — 24 months after primary vaccination.Results. The average level of anti- SARS-CoV-2 S-glycoprotein IgG antibodies in group I at visit 3 was 520 [478; 540] BAU/ml, in group II — 499 [199,5; 540] BAU/ml and in group III — 456 [389; 509,5] BAU/ml. The values were comparable to those obtained at visit 6. However, in group II, IgG level at visit 5 was significantly higher compared to visit 6 (p=0,001). The greatest decrease by visit 5 in the number of active T cells responding to SARS-CoV-2 Spike stimulation was recorded in group III (5,00 [0,50; 11,50] vs 1,00 [0,00; 5,50]; relative changes -80,0%; p=0,067). Also, among patients in group III, there was a significant decrease in the number of active T cells responding to stimulation with SARS-CoV-2 nucleocapsid (10,00 [3,00; 22,50] vs 1,00 [0,00; 11,50]; relative changes -90,0%; p=0,0160). Participants in groups I and II demonstrated stable results on visit 5, relative to visit 3. In all studied groups, no significant relationship was found between IgG levels to SARS-CoV-2 S-glycopeptide and the number of active T cells. Strong positive relationships were found between the level of active T cells responding to SARS-CoV-2 spike stimulation and the level of active T cells responding to SARS-CoV-2 nucleocapsid stimulation: group I (ρ=0,807; p<0,001), group II (ρ=0,748; p<0,001) and group III (ρ=0,902; p<0,001).Conclusion. The use of homologous and heterologous SARS-CoV-2 vaccination demonstrates relatively stable level of both humoral and cell-mediated 18 and 24 months after the first stage of vaccination. Revaccination with a homologous regimen (CoviVac at both stages) ensured stable level of anti- SARS-CoV-2 S-glycopeptide IgG antibodies. However, this regimen was characterized by a significant decrease in the long-term period in the number of active T cells responding to stimulation of SARS-CoV-2 surface and nuclear antigen.

1726. Characterization of humoral immune responses to COVID-19 vaccination in children in Canada: interim analysis from the Severe acute respiratory syndrome-related coronavirus 2 PRevalence In children and youNG adults in British Columbia (SPRING) Study

Abstract Background A vaccine series consisting of two doses of coronavirus disease 2019 (COVID-19) mRNA vaccines plus one booster dose is currently recommended for healthy children aged 5-11 years in Canada. Additional studies are needed to understand the longitudinal immunity to COVID-19 vaccination in the pediatric population. The Severe acute respiratory syndrome-related coronavirus 2 PRevalence In children and youNG adults in British Columbia (SPRING) sub-study aimed to specifically investigate antibody responses to COVID-19 vaccination in children aged 5-11 years. Methods Fifty-four children without immunocompromising conditions or taking immunosuppressive medications were enrolled prior to dose one or dose two of their COVID-19 vaccine. Responses were quantified via: anti-index virus spike protein specific IgG (S-IgG) geometric mean concentrations (GMCs) (binding antibody units, BAU/mL) and S-IgG avidity reported as total relative IgG avidity index (TRAI) (avidity units, AU) at pre-dose two, as well as one and six months post-dose two. A Welch’s t-test compared responses between timepoints. Results The cohort consisted of 55% male and 45% female with a median age of 8 years. The interval between first and second doses ranged from 7 – 18 (median 11) weeks. Concentrations of S-IgG increased from pre-dose two to one month post-dose two (222 vs. 1152 BAU/mL, p < 0.0001). GMCs then decreased by six months post-dose two (1152 vs. 343 BAU/mL, p < 0.0001) to levels similar to pre-dose two (p = 0.0696). TRAI increased between time points. By six months post-dose two, S-IgG TRAI (68 AU) remained higher than pre-dose two (46 AU, p < 0.0001) and one month post-dose two (65 AU, p = 0.0495). This increase in avidity was due to higher concentrations of medium high, high and very high avidity S-IgG as well as a decrease in very low avidity S-IgG at six months post-dose two. Conclusion Concentrations of S-IgG waned significantly by six months post-dose two. The results suggest that due to repeated exposure to the S-protein, affinity maturation has resulted in the production of higher avidity antibodies post-dose two. This suggests that both S-IgG concentrations and avidity should be considered when determining protection against COVID-19 and need to be further explored to support future booster recommendations. Disclosures Sofia R. Bartlett, PhD, Abbvie: Advisor/Consultant|Abbvie: Grant/Research Support|Cepheid: Advisor/Consultant|Gilead: Advisor/Consultant|Gilead: Grant/Research Support Manish Sadarangani, BM BCh, FRCPC, DPhil, GlaxoSmithKline: Grant/Research Support|Merck: Grant/Research Support|Moderna: Grant/Research Support|Pfizer: Grant/Research Support|Sanofi Pasteur: Grant/Research Support|Seqirus: Grant/Research Support|Symvivo: Grant/Research Support|VBI Vaccines: Grant/Research Support

1348. Identification of GB-0669, a Novel S-2 Targeted Spike Monoclonal Antibody in Development for SARS-CoV-2 Prophylaxis

Abstract Background The clinical benefit of anti-spike mAbs for prophylaxis and treatment of SARS-CoV-2 is now well established (Baum 2020, Loo 2022, Westendorf 2022, Jones 2021, Kreuzberger 2021, Cathcart 2021, Hirsch 2022, Shi 2020); However, the evolution of SARS CoV-2 due to immune pressure has compromised the utility of all previously approved mAbs which target the variable, immune dominant receptor binding domain of the Spike protein. Despite the success of vaccination protecting the general population, the immunocompromised and elderly remain at high risk of serious disease and mortality from SARS CoV-2 infection. Therefore, there is a need to develop mAbs that remain active across current and emergent SARS CoV-2 variants for such populations. Methods The Generate Platform uses machine learning (ML) models to generate therapeutics with desirable properties. We used this platform to explore the amino acid sequence landscape compatible with the binding conformation and breadth of neutralization for mAbs targeting the conserved S-2 stem helix of Spike. While S-2 directed antibodies can broadly neutralize diverse coronaviruses, they are generally limited by potency. We employed an iterative computation- experimentation loop to design antibodies that bind to the S-2 stem helix, optimizing for potency, breadth and developability. Results The Generate Platform was employed to identify S-2 targeted Spike antibodies with high potency and breadth of neutralization resulting in GB-0669. GB-0669 exhibits sub-nM neutralization against all SARS-CoV-2 variants and Omicron sublineages including the highly immune evasive strain XBB. GB-0669 also displays sub-nM neutralization against sarbecoviruses associated with previous epidemics (SARS-CoV-1) and those of pandemic potential (WIV1, bat SARS-like coronavirus). The GB 0669 epitope was mapped by co-crystallization and is consistent with the observed breadth; all key interactions are >99% conserved with no evidence of immune escape. Conclusion GB-0669, a novel mAB targeting the conserved S-2 region of Spike, is hypothesized to be effective for prophylaxis of COVID-19 across all Omicron sublineages and future variants as well as CoVs with pandemic potential. Disclosures Francesco Borriello, MD PhD, Generate Biomedicines: Employee Gevorg Grigoryan, PhD, Generate Biomedicines: Chief Technology Officer|Generate Biomedicines: Ownership Interest|Generate Biomedicines: Stocks/Bonds Daria Hazuda, PhD, Generate Biomedicines: Employee|Generate Biomedicines: Stocks/Bonds|Merck and Co: Employee|Merck and Co: Stocks/Bonds Nathan H. Joh, PhD, Generate Biomedicines: Employee at Generate Biomedicines

Mapping IgA Epitope and Cross-Reactivity between Severe Acute Respiratory Syndrome-Associated Coronavirus 2 and DENV.

The newly introduced COVID-19 vaccines have reduced disease severity and hospitalizations. However, they do not significantly prevent infection or transmission. In the same context, measuring IgM and IgG antibody levels is important, but it does not provide information about the status of the mucosal immune response. This article describes a comprehensive mapping of IgA epitopes of the S protein, its cross-reactivity, and the development of an ELISA-peptide assay. IgA epitope mapping was conducted using SPOT synthesis and sera from RT-qPCR COVID-19-positive patients. Specific and cross-reacting epitopes were identified, and an evolutionary analysis from the early Wuhan strain to the Omicron variant was performed using bioinformatics tools and a microarray of peptides. The selected epitopes were chemically synthesized and evaluated using ELISA-IgA. A total of 40 IgA epitopes were identified with 23 in S1 and 17 in the S2 subunit. Among these, at least 23 epitopes showed cross-reactivity with DENV and other organisms and 24 showed cross-reactivity with other associated coronaviruses. Three MAP4 polypeptides were validated by ELISA, demonstrating a sensitivity of 90-99.96% and a specificity of 100%. Among the six IgA-RBD epitopes, only the SC/18 epitope of the Omicron variants (BA.2 and BA.2.12.1) presented a single IgA epitope. This research unveiled the IgA epitome of the S protein and identified many epitopes that exhibit cross-reactivity with DENV and other coronaviruses. The S protein of variants from Wuhan to Omicron retains many conserved IgA epitopes except for one epitope (#SCov/18). The cross-reactivity with DENV suggests limitations in using the whole S protein or the S1/S2/RBD segment for IgA serological diagnostic tests for COVID-19. The expression of these identified specific epitopes as diagnostic biomarkers could facilitate monitoring mucosal immunity to COVID-19, potentially leading to more accurate diagnoses and alternative mucosal vaccines.

Multi-antigen pan-sarbecovirus DNA vaccines generate protective T cell immune responses.

SARS-CoV-2 is the third zoonotic coronavirus to cause a major outbreak in humans in recent years, and many more SARS-like coronaviruses with pandemic potential are circulating in several animal species. Vaccines inducing T cell immunity against broadly conserved viral antigens may protect against hospitalisation and death caused by outbreaks such viruses. We report the design and pre-clinical testing of two T-cell-based pan-sarbecovirus vaccines, based on conserved regions within viral proteins of sarbecovirus isolates of human and other carrier animals, like bats and pangolins. One vaccine (CoVAX_ORF1ab) encoded antigens derived from non-structural proteins, the other (CoVAX_MNS) antigens from structural proteins. Both multi-antigen DNA vaccines contained a large set of antigens shared across sarbecoviruses and were rich in predicted and experimentally validated human T cell epitopes. In mice, the multi-antigen vaccines generated both CD8 and CD4 T cell responses to shared epitopes. Upon encounter of full-length spike antigen, CoVAX_MNS-induced CD4 T cells were responsible for accelerated CD8 T cell and IgG antibody responses specific to the incoming spike, irrespective of its sarbecovirus origin. Finally, both vaccines elicited partial protection against a lethal SARS-CoV-2 challenge in human-ACE2-transgenic mice. These results support clinical testing of this universal sarbecovirus vaccine for pandemic preparedness.

Interaction of Methylene Blue with Severe Acute Respiratory Syndrome Coronavirus 2 Envelope Revealed by Molecular Modeling.

Methylene blue has multiple antiviral properties against Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2). The ability of methylene blue to inhibit different stages of the virus life cycle, both in light-independent and photodynamic processes, is used in clinical practice. At the same time, the molecular aspects of the interactions of methylene blue with molecular components of coronaviruses are not fully understood. Here, we use Brownian dynamics to identify methylene blue binding sites on the SARS-CoV-2 envelope. The local lipid and protein composition of the coronavirus envelope plays a crucial role in the binding of this cationic dye. Viral structures targeted by methylene blue include the S and E proteins and negatively charged lipids. We compare the obtained results with known experimental data on the antiviral effects of methylene blue to elucidate the molecular basis of its activity against coronaviruses.

Using drivers and transmission pathways to identify SARS-like coronavirus spillover risk hotspots

The emergence of SARS-like coronaviruses is a multi-stage process from wildlife reservoirs to people. Here we characterize multiple drivers—landscape change, host distribution, and human exposure—associated with the risk of spillover of zoonotic SARS-like coronaviruses to help inform surveillance and mitigation activities. We consider direct and indirect transmission pathways by modeling four scenarios with livestock and mammalian wildlife as potential and known reservoirs before examining how access to healthcare varies within clusters and scenarios. We found 19 clusters with differing risk factor contributions within a single country (N = 9) or transboundary (N = 10). High-risk areas were mainly closer (11-20%) rather than far ( < 1%) from healthcare. Areas far from healthcare reveal healthcare access inequalities, especially Scenario 3, which includes wild mammals and not livestock as secondary hosts. China (N = 2) and Indonesia (N = 1) had clusters with the highest risk. Our findings can help stakeholders in land use planning, integrating healthcare implementation and One Health actions.

Shared genetic architecture of COVID-19 and Alzheimer’s disease

The severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) and the сoronavirus disease 2019 (COVID-19) have become a global health threat. At the height of the pandemic, major efforts were focused on reducing COVID-19-associated morbidity and mortality. Now is the time to study the long-term effects of the pandemic, particularly cognitive impairment associated with long COVID. In recent years much attention has been paid to the possible relationship between COVID-19 and Alzheimer’s disease, which is considered a main cause of age-related cognitive impairment. Genetic predisposition was shown for both COVID-19 and Alzheimer’s disease. However, the analysis of the similarity of the genetic architecture of these diseases is usually limited to indicating a positive genetic correlation between them. In this review, we have described intrinsic linkages between COVID-19 and Alzheimer’s disease, pointed out shared susceptibility genes that were previously identified in genome-wide association studies of both COVID-19 and Alzheimer’s disease, and highlighted a panel of SNPs that includes candidate genetic risk markers of the long COVID-associated cognitive impairment.

Study of case of the profile of Covid-19 infected in Espirito Santo State in Brazil

The pandemic caused by Severe Acute Respiratory Syndrome - Related Coronavirus 2 (SARS-CoV-2) has made socio-economic inequalities between social classes more evident in the countries in development process. This scenario is also no different in Brazil and it has been demanding from the federal, state and municipal governments broad efforts to combat the consequences of the spread of the disease in Brazil. The rulers have a huge challenge to implement measures to prevent the advance of the transmission of the virus. In addition, state governments need to use the public health system to serve the main population, since the lethality rate is very high directly influenced by social inequality. To minimize the effects of the new coronavirus, the ruler needs planning to give efficient response and requires an understanding of the rich that people about free movement, controlled circulation or total blocking of population movement. In this context, our proposal was to investigate how the disease reached people of different levels of education. And how has been the response of people hospitalized in Brazilian hospitals. We analyzed the public data of reports of Severe Acute Respiratory Syndrome (SRAG). In our research, we considered the variables schooling, ethnicity, gender, time of hospitalization in the Intensive Care Unit (ICU) and use of mechanical ventilators. Our results indicate that the lethality rate is higher for those people who were admitted to the ICU. In addition, people with low schooling and no schooling are 3.6 times more likely to die than people with higher education. This discrepancy highlights the huge disparity of quality treatment in Brazilian states.

Comparative genomics of spike, envelope, and nucleocapsid protein of severe acute respiratory syndrome coronavirus 2.

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) upsurge sprang up in Wuhan, China, in late December 2019. Due to the exceptionally high mutation frequency, comparative genomics of viruses isolated throughout time and in various geographical locations are crucial. To better understand how SARS-CoV-2 heterogeneity has changed around the globe, this research was conducted. Nucleotide and protein sequences of SARS-CoV-2, SARS-CoV, and bat SARS-like CoV were extracted from the NCBI Virus database. The Wuhan SARS-CoV-2 variant was used as a reference. Molecular Evolutionary Genetics Study performed the phylogenetic analysis, while the Genome Detective Coronavirus Typing Tool performed the mutational analysis. The evolutionary research has revealed that bats are the primary host for coronavirus evolution and the origin of the formation of SARS-CoV and SARS-CoV-2. Numerous mutations have been discovered in the spike, envelope, and nucleocapsid protein. The current research findings may have an implication that facilitates the development of prospective immunization candidates/small pharmacological compounds targeting COVID-19.

The abstraction of potentially zoonotic SARS-like coronavirus (BtSY2): A threat to global health.

This article highlights the discovery of a new virus lurking in bats in Yunnan province of China. The virus shows phylogenetic and genomic similarity to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, which was the cause of the COVID-19 pandemic. The virus, named Bat SARS-like virus BtSY2, along with four other viruses, has been named a "virus of concern." Recombination events in the viral genome due to coinfection by multiple viruses in related animal hosts can lead to disease emergence, a process that has repeated itself innumerable times throughout history and has given rise to some major viral pandemics. Zoonotic infections, if not contained at the right time, can cause significant harm to the public health sector as well as the global economy. Studies like this are required to acquire a good understanding of the phylogeny of the virus, mechanisms of its transmission, carriers, probable clinical picture, and similarity to previous outbreaks. This will help to devise preventive strategies and, in case of higher probability and hazardous potential of the disease, develop prototype vaccines and drugs to face the outbreak with adequate preparedness.