Novel coronavirus mutations: Vaccine development and challenges

The Current Progress in the Quest for Vaccines Against the Semliki Forest Virus Complex

The Semliki Forest virus (SFV) complex comprises of arboviruses that are transmitted by arthropod vectors and cause acute febrile illness in humans. In the last seven decades, re-emergence of these viruses has resulted in numerous outbreaks globally, affecting regions including Africa, Americas, Asia, Europe and the Caribbean. These viruses are transmitted to humans by the bite of infected mosquitoes. Symptoms of infection include high fever, severe joint pain, skin rash, muscle pain and headache. Fatal cases were reported, and mortality rate increased during the epidemic of these viruses. There is therefore a need to control the spread of these emerging arboviruses. Given that vaccination is one of the most effective ways to protect populations against viral outbreaks, efforts have been made to develop and test potential vaccine candidates. However, there are still no licensed vaccines available against the medically important viruses in the SFV complex. This review first summarizes the current knowledge of the SFV complex disease pathogenesis. Next, seven strategies that have been applied in vaccine development against these viruses are reviewed, indicating the immune response and efficacies of these vaccine candidates in in vivo models of infection. Finally, the more promising candidates that have entered clinical trials are discussed and insights into the future development of vaccines for viruses of the SFV complex are given.

Impact of Newcastle disease virus vaccines and genetic variations on interleukin-4 activation in broiler chicken

Background

Newcastle disease virus is a virus that causes a significant economic impact on the poultry industry and is primarily controlled through vaccination. Most of the vaccinations with the LaSota strain are either live attenuated or inactivated vaccines, both of which are from the Lentogenic pathotype.

Aim

This study aimed to investigate the influence of vaccine type and genetic variations on Chicken Interleukin-4 (ChIL4) activation.

Methods

Three groups were examined: Group K received the killed vaccine, Group L received the live vaccine, and Group C served as the control. Blood samples were collected on days 15, 25, and 35 post-vaccinations to assess ChIL4 levels using Enzyme-Linked Immunosorbent Assay and for molecular analysis using polymerase chain reaction.

Results

Group K showed a gradual increase in ChIL4 levels from 11.19 ± 0.17 to 13.70 ± 0.38, while Group L exhibited an initial increase on day 15 followed by stabilization on days 25 and 35. In contrast, ChIL4 levels in Group C declined over time from 4.84 ± 0.39 to 4.32 ± 0.25. Molecular analysis revealed four genetic variations of the single nucleotide polymorphism (SNPs) type at locations (3044, 3132, 3261, 3499) bp, with the third SNP at location (3261 bp) resulting in an amino acid change from valine to isoleucine. Analysis indicated that variants for most of these SNPs occur more likely in Group K compared to the other two groups.

Conclusion

These findings suggest that genetic variations, particularly SNPs, may play a significant role in ChIL4 activation, potentially impacting vaccine efficacy and immune response.

Impact of Newcastle disease virus vaccines and genetic variations on interleukin-4 activation in broiler chicken

Background

Newcastle disease virus is a virus that causes a significant economic impact on the poultry industry and is primarily controlled through vaccination. Most of the vaccinations with the LaSota strain are either live attenuated or inactivated vaccines, both of which are from the Lentogenic pathotype.

Aim

This study aimed to investigate the influence of vaccine type and genetic variations on Chicken Interleukin-4 (ChIL4) activation.

Methods

Three groups were examined: Group K received the killed vaccine, Group L received the live vaccine, and Group C served as the control. Blood samples were collected on days 15, 25, and 35 post-vaccinations to assess ChIL4 levels using Enzyme-Linked Immunosorbent Assay and for molecular analysis using polymerase chain reaction.

Results

Group K showed a gradual increase in ChIL4 levels from 11.19 ± 0.17 to 13.70 ± 0.38, while Group L exhibited an initial increase on day 15 followed by stabilization on days 25 and 35. In contrast, ChIL4 levels in Group C declined over time from 4.84 ± 0.39 to 4.32 ± 0.25. Molecular analysis revealed four genetic variations of the single nucleotide polymorphism (SNPs) type at locations (3044, 3132, 3261, 3499) bp, with the third SNP at location (3261 bp) resulting in an amino acid change from valine to isoleucine. Analysis indicated that variants for most of these SNPs occur more likely in Group K compared to the other two groups.

Conclusion

These findings suggest that genetic variations, particularly SNPs, may play a significant role in ChIL4 activation, potentially impacting vaccine efficacy and immune response.

The Potential of mRNA Vaccines to Fight Against Viruses

Vaccines have always been a critical tool in preventing infectious diseases. However, the development of traditional vaccines often takes a long time and may struggle to address the challenge of rapidly mutating viruses. The emergence of mRNA technology has brought revolutionary changes to vaccine development, particularly in rapidly responding to the threat of emerging viruses. The global promotion of mRNA vaccines against severe acute respiratory syndrome coronavirus 2 has demonstrated the importance of mRNA technology. Also, mRNA vaccines targeting viruses such as influenza, respiratory syncytial virus, and Ebola are under development. These vaccines have shown promising preventive effects and safety profiles in clinical trials, although the duration of immune protection is still under evaluation. However, the development of mRNA vaccines also faces many challenges, such as stability, efficacy, and individual differences in immune response. Researchers adopt various strategies to address these challenges. Anyway, mRNA vaccines have shown enormous potential in combating viral diseases. With further development and technological maturity, mRNA vaccines are expected to have a profound impact on public health and vaccine equity. This review discussed the potential of mRNA vaccines to fight against viruses, current progress in clinical trials, challenges faced, and future prospects, providing a comprehensive scientific basis and reference for future research.

Isolation of Limosilactobacillus mucosae G01 with inhibitory effects on porcine epidemic diarrhea virus in vitro from Bama pig gastroenteritis

Porcine epidemic diarrhea virus (PEDV) is responsible for causing fatal watery diarrhea in piglets, resulting in significant economic losses within the pig farming industry. Although vaccination is currently employed as a preventive measure, certain vaccines do not provide complete protection against PEDV field strains. Probiotics present a promising alternative due to their ability to regulate intestinal flora, enhance host immunity, and improve resistance against pathogenic microorganisms. We isolated six lactic acid bacteria (LAB) from the fecal microorganisms of Bama pigs, compared to Limosilactobacillus mucosae DSM13345 of the same genus in which Limosilactobacillus mucosae G01 (L. mucosae G01) proved to have a potent anti-PEDV effect. In a comprehensive manner, L. mucosae G01 significantly augmented the phosphorylation of IRF3 in IPEC-J2 cells, resulting in the induction of interferons (IFN α, IFN β, IFN λ1, and IFN λ3) and subsequent upregulation of interferon-stimulated genes (ISGs) (MX1, MX2, OAS1, and ZAP) in a dose-dependent fashion, consequently leading to the mitigation of PEDV replication. These findings underscore the promising prospects of L. mucosae G01 as a naturally derived substitute for combating PEDV and other enteric coronavirus infections.

The knowns and unknowns of long COVID-19: from mechanisms to therapeutical approaches

The coronavirus disease 2019 (COVID-19) pandemic caused by SARS-CoV-2 has been defined as the greatest global health and socioeconomic crisis of modern times. While most people recover after being infected with the virus, a significant proportion of them continue to experience health issues weeks, months and even years after acute infection with SARS-CoV-2. This persistence of clinical symptoms in infected individuals for at least three months after the onset of the disease or the emergence of new symptoms lasting more than two months, without any other explanation and alternative diagnosis have been named long COVID, long-haul COVID, post-COVID-19 conditions, chronic COVID, or post-acute sequelae of SARS-CoV-2 (PASC). Long COVID has been characterized as a constellation of symptoms and disorders that vary widely in their manifestations. Further, the mechanisms underlying long COVID are not fully understood, which hamper efficient treatment options. This review describes predictors and the most common symptoms related to long COVID's effects on the central and peripheral nervous system and other organs and tissues. Furthermore, the transcriptional markers, molecular signaling pathways and risk factors for long COVID, such as sex, age, pre-existing condition, hospitalization during acute phase of COVID-19, vaccination, and lifestyle are presented. Finally, recommendations for patient rehabilitation and disease management, as well as alternative therapeutical approaches to long COVID sequelae are discussed. Understanding the complexity of this disease, its symptoms across multiple organ systems and overlapping pathologies and its possible mechanisms are paramount in developing diagnostic tools and treatments.

Epidemiological and clinical features of SARS-CoV-2 Omicron variant infection in Quanzhou, Fujian province: a retrospective study

Epidemiological and clinical data of patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant (BA.2) admitted to three designated hospitals in Quanzhou City, Fujian Province, China, were collected and analyzed. Overall, 2,541 patients infected with BA.2, comprising 1,060 asymptomatic, 1,287 mild, and 194 moderate infections, were enrolled. The percentage of moderate infections was higher in patients aged ≥ 60 years than in those aged < 18 years and 18-59 years. The median hospitalization duration was 17 days. Among the 2,541 patients, 43.52% had a clear history of close contact. The vaccination rate was 87.92%, and the percentage of asymptomatic infections was higher in vaccinated than in unvaccinated patients. Moreover, patients with underlying diseases, including hypertension and diabetes mellitus, had more moderate infections than those without underlying diseases. The three most common clinical manifestations were fever, dry cough, and sore throat. The albumin-to-globulin (A/G) ratio and lymphocyte count decreased in cases with mild and moderate infections, while procalcitonin, erythrocyte sedimentation rate, interleukin-6, D-dimer, and C4 levels increased. Advanced age, non-vaccination, and underlying comorbid diseases were high-risk factors for disease progression in patients. However, dynamic monitoring of blood routine parameters, A/G ratio, and inflammatory indicators facilitated the prediction of disease progression.

Effects of SARS-CoV-2 Vaccines on Sperm Quality: Systematic Review

BACKGROUND

The COVID-19 pandemic, caused by SARS-CoV-2, has triggered a global public health crisis of unprecedented proportions. SARS-CoV-2 vaccination is a highly effective strategy for preventing infections and severe COVID-19 outcomes. Although several studies have concluded that COVID-19 vaccines are unlikely to affect fertility, concerns have arisen regarding adverse events, including the potential impact on fertility; these concerns are plagued by limited and inconsistent evidence.

OBJECTIVE

This review aims to provide a recent assessment of the literature on the impact of COVID-19 vaccines on male sperm quality. The possible impact of COVID-19 vaccines on fertility potential was also examined to draw a clearer picture and to evaluate the effects of COVID-19 on male reproductive health.

METHODS

PubMed, Scopus, Web of Science, Embase, and Cochrane databases were searched from their inception to October 2023. Eligible studies included articles reporting SARS-CoV-2 vaccination and human semen quality and fertility, as well as the impact of vaccination on assisted reproductive technology treatment outcomes. The quality of cohort studies was assessed using the Newcastle-Ottawa Scale, and the quality of cross-sectional studies was assessed using the quality evaluation criteria recommended by the Agency for Healthcare Research and Quality. The systematic review followed PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines.

RESULTS

The initial literature search yielded 4691 records by searching 5 peer-reviewed databases (PubMed, Scopus, Web of Science, Embase, and Cochrane). Finally, 24 relevant studies were selected for our study. There were evident research inequalities at the regional level, with the United States and Western European countries contributing 38% (9/24) of the studies, Middle Eastern countries contributing 38% (9/24), China accounting for 21% (5/24), and Africa and South America accounting for none. Nonetheless, the overall quality of the included studies was generally good. Our results demonstrated that serious side effects of the COVID-19 vaccine are extremely rare, and men experience few problems with sperm parameters or reproductive potential after vaccination.

CONCLUSIONS

On the basis of the studies published so far, the COVID-19 vaccine is safe for male reproductive health. Obviously, vaccination is a wise option rather than experience serious adverse symptoms of viral infections. These instances of evidence may help reduce vaccine hesitancy and increase vaccination coverage, particularly among reproductive-age couples. As new controlled trials and prospective cohort studies with larger sample sizes emerge, the possibility of a negative effect of the COVID-19 vaccine on sperm quality must be further clarified.

The HLA class I immunopeptidomes of AAV capsid proteins

Introduction

Cellular immune responses against AAV vector capsid represent an obstacle for successful gene therapy. Previous studies have used overlapping peptides spanning the entire capsid sequence to identify T cell epitopes recognized by AAV-specific CD8+ T cells. However, the repertoire of peptides naturally displayed by HLA class I molecules for CD8 T cell recognition is unknown.

Methods

Using mRNA transfected monocyte-derived dendritic cells (MDDCs) and MHC-associated peptide proteomics (MAPPs), we identified the HLA class I immunopeptidomes of AAV2, AAV6 and AAV9 capsids. MDDCs were isolated from a panel of healthy donors that have diverse alleles across the US population. mRNA-transfected MDDCs were lysed, the peptide:HLA complexes immunoprecipitated, and peptides eluted and analyzed by mass spectrometry.

Results

We identified 65 AAV capsid-derived peptides loaded on HLA class I molecules of mRNA transfected monocyte derived dendritic cells. The HLA class I peptides are distributed along the entire capsid and more than 60% are contained within HLA class II clusters. Most of the peptides are organized as single species, however we identified twelve clusters containing at least 2 peptides of different lengths. Only 9% of the identified peptides have been previously identified as T cell epitopes, demonstrating that the immunogenicity potential for the vast majority of the AAV HLA class I immunopeptidome remains uncharacterized. In contrast, 12 immunogenic epitopes identified before were not found to be naturally processed in our study. Remarkably, 11 naturally presented AAV peptides were highly conserved among the three serotypes analyzed suggesting the possibility of cross-reactive AAV-specific CD8 T cells.

Discussion

This work is the first comprehensive study identifying the naturally displayed HLA class I peptides derived from the capsid of AAVs. The results from this study can be used to generate strategies to assess immunogenicity risk and cross-reactivity among serotypes during gene therapies.

SARS-CoV-2 S Mutations: A Lesson from the Viral World to Understand How Human Furin Works

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the etiological agent responsible for the worldwide pandemic and has now claimed millions of lives. The virus combines several unusual characteristics and an extraordinary ability to spread among humans. In particular, the dependence of the maturation of the envelope glycoprotein S from Furin enables the invasion and replication of the virus virtually within the entire body, since this cellular protease is ubiquitously expressed. Here, we analyzed the naturally occurring variation of the amino acids sequence around the cleavage site of S. We found that the virus grossly mutates preferentially at P positions, resulting in single residue replacements that associate with gain-of-function phenotypes in specific conditions. Interestingly, some combinations of amino acids are absent, despite the evidence supporting some cleavability of the respective synthetic surrogates. In any case, the polybasic signature is maintained and, as a consequence, Furin dependence is preserved. Thus, no escape variants to Furin are observed in the population. Overall, the SARS-CoV-2 system per se represents an outstanding example of the evolution of substrate-enzyme interaction, demonstrating a fast-tracked optimization of a protein stretch towards the Furin catalytic pocket. Ultimately, these data disclose important information for the development of drugs targeting Furin and Furin-dependent pathogens.