Search Results (651)

Background: The Delta variant of SARS-CoV-2 virus, one of the alarming variants of concern (VOC) with a distinct mutation characteristic, was immensely detrimental and a significant cause of the prolonged pandemic waves. This study aimed to analyze the genetic characteristics of the predominant Delta variant in acute febrile illness (AFI) patients in Ethiopia. Method: Nasopharyngeal swab samples were collected from AFI patients in four hospitals from February 2021 to June 2022 and tested for SARS-CoV-2 by using RT-qPCR. Of 101 positive samples, 48 stored specimens were re-tested, and 26 with sufficient RNA quality (Ct < 30) were sequenced using whole-genome sequencing to identify variants of concern, specific virus lineages and mutation features. Result: Delta variants (21J clade) were found predominant among all the sequenced SARS-CoV-2 isolate (80.8%, 21/26). AY.120 (46.2%) and B.1.617.2 (26.9%) were the predominant sub-lineages of the Delta variant. Omicron (21k, Pango BA.1.1/BA.1.17/BA.1) and Alpha (20I, Pango B.1.1.7) variants accounted for 11.5% and 7.7% of the total sequenced samples. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Ethiopia. The number of mutations increases dramatically from Alpha (~35 avg) to Delta (~42 avg) to Omicron (~56 avg). The Delta variant revealed a spike mutation on L452R and T478K and P681R, and was characterized by the double deletion E156-F157- in Spike protein. Conclusions: The findings are indicative of a gradual change in the genetic coding of the virus underscoring the importance of ongoing genomic surveillance to track the evolution and spread of SARS-CoV-2 and other emerging virus. Full article

Furin, a calcium-dependent serine endoprotease of the proprotein convertase family, plays a pivotal role in both physiological homeostasis and viral pathogenesis. By cleaving polybasic motifs within viral glycoproteins, furin enables the maturation of structural proteins essential for viral entry, fusion, and replication. This mechanism has been documented across a broad spectrum of human pathogens, including SARS-CoV-2, influenza virus, human immunodeficiency virus, human papilloma virus, hepatitis B virus, flaviviruses, herpesviruses, and paramyxoviruses, highlighting furin as a conserved molecular hub in host–virus interactions. Genetic variability within the FURIN gene further modulates infection outcomes. Several single-nucleotide polymorphisms (SNPs), such as rs6226 and rs1981458, are associated with altered COVID-19 severity, whereas variants like rs17514846 confer protection against human papilloma virus infection. Conversely, mutations predicted to reduce enzymatic activity have been linked to attenuated SARS-CoV-2 pathogenesis in certain populations. These findings underscore the importance of considering population genetics when evaluating viral susceptibility and disease progression. Despite advances, unresolved questions remain regarding furin’s non-canonical roles in viral life cycles, tissue-specific regulation, and interactions with other host proteases and immune modulators. Targeted inhibition of furin and related convertases represents a promising avenue for broad-spectrum antiviral interventions. Collectively, current evidence positions furin as a central node at the intersection of viral pathogenesis, host genetic variability, and translational therapeutic potential. Full article

Background: In response to the emergence of immune-evasive variants of SARS-CoV-2, this study explores a novel heterologous vaccination strategy using a microparticulate formulation approach that is delivered via oral dissolving film (ODF) formulations into the buccal cavity. Heterologous administration has the potential to generate cross-reactive antibodies, which can be especially beneficial against viruses with ever-mutating variants. Moreover, the microparticulate oral dissolving film-based vaccine approach is a non-invasive vaccine delivery platform. Methods: The vaccine design incorporated whole inactivated Delta and Omicron variants of the virus, administered at prime and booster doses, respectively, effectively encapsulated in a Poly(lactic-co-glycolic) acid (PLGA) polymer matrix, and adjuvanted with Alum to enhance immune activation. Following vaccination, serum, mucosal, and tissue samples were analyzed to evaluate humoral and cellular immune responses against the model antigen, as well as other variants such as Alpha and Beta variants, to understand the cross-reactive response. Result: In vitro evaluations confirmed the vaccine’s safety and its ability to stimulate immune responses. On administering microparticulate oral dissolving films to mice, whole inactivated delta and omicron variant-specific antibodies were observed in serum samples along with neutralizing titers in terminal week. The formulated vaccine showed significant secretory IgA antibody levels in mucosal samples. Moreover, CD4⁺ and CD8a cellular responses were observed in tissue samples of spleen and lymph nodes, along with antibodies (IgG, IgA, and IgM) detected in lung supernatant samples. Humoral and cellular cross-reactive antibodies were observed in the samples. Conclusions: This approach offers a promising platform for developing next-generation vaccines capable of inducing broad immunity. Full article

Early studies on the evolution of SARS-CoV-2 revealed mutations that favored host transmission of the virus and more efficient viral entry. However, cell-free virus spread is vulnerable to host-neutralizing antibodies. As population immunity developed, mutations that confer escape from neutralization were selected. Notably, cell syncytia formation wherein an infected cell fuses with a noninfected cell is a more efficient route of transmission that bypasses humoral immunity. Cell syncytia formation has been implicated in the pathogenicity of SARS-CoV-2 infection whilst compromising host transmission due to impaired whole virion release. Therefore, understanding the mechanisms of virus-mediated cell–cell fusion will aid in identifying and targeting more pathogenic strains of SARS-CoV-2. Whilst the general kinetics of cell–cell fusion have been known for decades, the specific mechanisms by which SARS-CoV-2 induces fusion are beginning to be elucidated. This is partially due to emergence of more reliable, high throughput methods of quantifying and comparing fusion efficiency in experimental models. Moreover, the ongoing inflammatory response and emerging health burden of long COVID may point to cell–cell fusion in the pathogenesis. In this review, we synthesize current understanding of SARS-CoV-2-mediated cell–cell fusion and its consequences on immune escape, viral persistence, and the innate immune response. Full article

The emergence or mutation of aggressive viruses represents a latent threat to human health that could lead to new pandemics, so it is important to constantly monitor and analyze the behavior of the diseases they can cause. In this sense, the purpose of this work was to generate models to predict the behavior of recoveries and deaths from COVID-19 in Mexico in the post-pandemic era, applying machine learning techniques to data related to this disease, published by the Mexican government. Models based on artificial neural networks, logistic regression, and classification algorithms were generated and validated, yielding high rates of correct classification, accuracy, and recall, so that they could be used to make predictions about future cases of patients infected with the SARS-CoV-2 virus. Full article

The Coronavirus disease 2019 (COVID-19) pandemic had a profound global impact, yet children exhibited distinct clinical and epidemiological patterns compared to adults. Pediatric cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were generally characterized by milder disease, lower hospitalization rates, and few long-term sequelae. However, a subset of children developed severe complications such as multisystem inflammatory syndrome in children (MIS-C), highlighting the heterogeneity in disease presentation. Differences in immune system maturity and comorbidities likely contribute to the age-dependent manifestation of SARS-CoV-2 and other respiratory viruses. Persistent SARS-CoV-2 infection, particularly in immunocompromised individuals, has been implicated in the emergence of new viral variants with immune escape characteristics due to ongoing viral replication in the presence of selective pressure. While SARS-CoV-2 evolution in persistently infected adults has been well-documented, it is less clear how the virus evolves during persistent infection in the pediatric population. To address this question, we performed viral whole genome sequencing of longitudinal specimens collected from immunocompetent and immunocompromised pediatric COVID-19 patients. Similarly to what has been observed in adult cohorts, mutations associated with enhanced viral fitness and immune escape arose intra-host over time. Intra-host diversity accumulated at similar rates in immunocompetent and immunocompromised children, though more mutations overall were observed in the immunocompromised cohort due to the longer infection time courses. Overall, we identified similar viral evolutionary trends over the course of infection despite clinical differences in pediatric COVID-19 manifestation and severity. This similarity suggests that persistent infection in children may be an additional, but not unique, source of ongoing viral diversification. Full article

Background/Objectives: Despite the lifting of the COVID-19 public health emergency, SARS-CoV-2 infections continue to be recorded worldwide. The continued prevalence of infection has been attributed to the ability of the virus to evade host immune responses, including neutralizing antibody-derived immunity. The vast majority of antibody escape mutations has been associated with the S1 subunit of the spike protein. The other region of the spike, the S2 subunit, is the most conserved region amongst coronaviruses. We hypothesized that S2-specific antibody levels are modest in vaccinated and SARS-CoV-2-infected patients, resulting in suboptimal neutralization of distant coronaviruses. Methods: Here, we analyzed S1- and S2-specific antibody levels in SARS-CoV-2-infected individuals, including a mixed cohort of those with and without immunosuppression and prior vaccination. Results: We found that S2-specific antibody responses were generally lower than S1-specific antibody responses. Intriguingly, Omicron-S1-specific antibody levels were higher than Wuhan-S1-specific antibody levels despite all vaccinated participants having received Wuhan-spike-based immunogens. This emphasizes the importance of the infecting variant and vaccine immunogen in the production of spike-targeting antibodies and associated hybrid immunity. Although S1-specific antibody levels were generally higher than their S2-specific counterparts, the correlation between neutralization and binding antibody levels was mostly higher in S2- compared with S1-specific responses. Conclusions: We conclude that S2-based immunogens are suitable for the induction of antibody-based immunity against novel SARS-CoV-2 variants but also against more distant coronaviruses, which would support a better protection for the immunocompromised as well as other vulnerable populations. Full article

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus are major respiratory pathogens associated with substantial morbidity and a risk of severe disease. However, the effectiveness of current vaccines and antiviral drugs is limited by viral mutations. Umeboshi, a traditional Japanese food prepared from pickled Prunus mume, is known for its health benefits; certain components of P. mume have exhibited antimicrobial properties. However, the efficacy of P. mume against SARS-CoV-2 and influenza virus remains unknown. We aimed to examine the antiviral activity of P. mume extracts against SARS-CoV-2 and influenza virus. Cytopathic effect (CPE) assays and reverse transcription–quantitative polymerase chain reaction (RT-qPCR) analyses with full-time treatment demonstrated that four extracts (PM2, PM3, PM4, and PM6) among eight tested inhibited the replication of both viruses. Subsequent time-of-addition assays, plaque assays, and transmission electron microscopy (TEM) confirmed that PM2 directly inactivated viral particles of both viruses by disrupting their structural integrity. Additional evaluations of virion integrity and infectivity suggested that the antiviral activity of PM2 may also involve mechanisms other than direct virion disruption. These findings suggest that P. mume-derived components exhibit direct antiviral activities against SARS-CoV-2 and influenza virus, supporting their potential development as antiviral agents or infection-preventive dietary products. Full article

The SARS-CoV-2 main protease (M^pro) is a well-established target for antiviral drug development. One such inhibitor, nirmatrelvir, in combination with ritonavir as a booster, has already been introduced into the market, under the name Paxlovid. However, being an RNA virus, SARS-CoV-2 is prone to the emergence of resistance mutations. A number of such mutations have been characterized, although they have not yet been shown to play a significant role in clinical settings; these include S144A, E166V, H172Y, and Q189K. We recombinantly produced these mutants and studied the corresponding proteins using X-ray crystallography, enzymology, and biophysical approaches. We discuss the potential of each mutant to lead to a widespread nirmatrelvir resistance scenario. We also demonstrate that one of our own inhibitors (13b-K), while showing some degree of cross-resistance with nirmatrelvir, exhibits much higher inhibitory activity against the M^pro carrying the E166V mutation. Full article

We aimed to explore SARS-CoV-2 evolution during in vitro neutralisation using next generation sequencing, and to determine whether sera from individuals immunised with two doses of the Pfizer-BioNTech vaccine (BNT162b2) were as effective at neutralising the variant of concern (VOC) Delta (B.1.617.2) compared to the earlier lineages Beta (B.1.351) and wild-type (A.2.2) virus. Using a live-virus SARS-CoV-2 neutralisation assay in Vero E6 cells, we determined neutralising antibody titres (nAbT) against three SARS-CoV-2 strains (wild type, Beta, and Delta) in 14 participants (vaccine-naïve (n = 2) and post-second dose of BNT162b2 vaccination (n = 12)), median age 45 years [IQR 29–65]; the median time after the second dose was 21 days [IQR 19–28]. The determination of nAbT was based on cytopathic effect (CPE) and in-house quantitative reverse transcriptase real-time quantitative polymerase chain reaction (RT-qPCR) to confirm SARS-CoV-2 replication. A total of 110 representative samples including inoculum, neutralisation breakpoints at 72 h, and negative and positive controls underwent genome sequencing. By integrating live-virus neutralisation assays with deep sequencing, we characterised both functional antibody responses and accompanying viral genetic changes. There was a reduction in nAbT observed against the Delta and Beta VOC compared with wild type, 4.4-fold (p ≤ 0.0006) and 2.3-fold (p = 0.0140), respectively. Neutralising antibodies were not detected in one vaccinated immunosuppressed participant and the vaccine-naïve participants (n = 2). The highest nAbT against the SARS-CoV-2 variants investigated was obtained from a participant who was vaccinated following SARS-CoV-2 infection 12 months prior. Limited consensus level mutations occurred in the various SARS-CoV-2 lineage genomes during in vitro neutralisation; however, consistent minority allele frequency variants (MFV) were detected in the SARS-CoV-2 polypeptide, spike (S), and membrane protein. Findings from countries with high COVID-19 incidence may not be applicable to low-incidence settings such as Australia; as seen in our cohort, nAbT may be significantly higher in vaccine recipients previously infected with SARS-CoV-2. Monitoring viral evolution is critical to evaluate the impact of novel SARS-CoV-2 variants on vaccine effectiveness, as mutational profiles in the sub-consensus genome could indicate increases in transmissibility and virulence or suggest the development of antiviral resistance. Full article

Since the emergence of SARS-CoV-2, the interplay of human behavior, environmental factors, viral evolution, and public health interventions has resulted in unexpected changes in the timing, intensity, and geography of respiratory virus outbreaks. For example, respiratory syncytial viruses (RSV) exhibited a surge during atypical summer months in several countries. Influenza, on the other hand, nearly vanished in the early years of the pandemic, but returned with unusual strength and altered seasonal patterns. Concurrently, new variants of concern in coronaviruses have demonstrated increased airborne transmissibility, greater resilience to environmental conditions, and the ability to evade both natural and vaccine-induced immunity. In this review article, we have synthesized the current understanding of the aerobiology of respiratory infectious viruses, with a particular emphasis on the paradoxical trends observed in recent years. We examined various aspects, including viral morphology and environmental survivability, shifts in seasonality, the drivers of mutation and resistance, and the impact of environmental and climatic factors. Key issues we explored include viral morphology adaptation in response to airborne selective pressures and climate variability influence on the ecology of airborne viruses. Lastly, we investigated future risks and proposed an interdisciplinary framework for monitoring and mitigating airborne viral threats in an ever-changing world. Full article

In recent years, antiviral therapy has proved crucial in the treatment of infectious diseases, particularly infections by highly variable viruses such as human immunodeficiency virus, hepatitis B, hepatitis C, SARS-CoV-2 or bacteria such as Mycobacterium tuberculosis. Under the effect of selection pressure, this variability induces mutations that lead to resistance to antiviral and antibacterial drugs, and thus to escape from treatment. The use of Advanced Biological Laboratories (ABL) assays technology combined with next-generation sequencing (NGS) and automatized software to detect majority and minority variants involved in treatment resistance has become a mainstay for establishing therapeutic strategies. The present study demonstrated high concordance between majority and minority subtypes and mutations identified in 15 samples across four NGS platforms: ISeq100 (Illumina (San Diego, CA, USA)), MiSeq (Illumina), DNBSEQ-G400 (MGI (Santa Clara, CA, USA)) and Mk1C MinION (Oxford Nanopore (Oxford Science Park, UK)). However, nanopore technology showed a higher number of minority mutations (<20%). The analysis also validated the pooling of microbiological samples as a method for detecting mutations and genotypes in viral and bacterial organisms, using the easy-to-use DeepChek^® bioinformatics software, compatible with all four sequencing platforms. This study underlines the constant evolution of microbiological diagnostic research and the need to adapt rapidly to improve patient care. Full article

Background: Systematic studies providing differentiated insight into the contribution of immunity directed against conserved and non-conserved epitopes of SARS-CoV-2 Spike on long-term protection are rare and insufficiently guide future pan-variant vaccine research. The present observational cohort study aimed to evaluate the correlation of neutralizing antibody levels and cellular immunity against the Spike protein with symptomatic Omicron breakthrough infection. Methods: Neutralizing antibody levels against multiple (sub)variants were analyzed 6 months following the second wild-type mRNA vaccination and 6 months after booster in 107 subjects using a multiplex surrogate virus neutralization assay. To assess cellular immunity, cytokine mRNA expression levels were determined after peptide pool stimulation in whole blood samples of a study subgroup. Results: Neutralizing antibody titers were found to serve as a reasonably reliable correlate of protection prior to booster immunization. However, the predictive power of neutralizing antibody titers was diminished after boosting. This loss appears to be due to a critical remodeling of the antibody repertoire—a process that was dose-dependent on pre-boost humoral immunity. Vaccination against Omicron infection was most effective when a balanced immune response to both conserved and non-conserved epitopes of the viral Spike protein was induced. While neutralizing antibodies against receptor-binding domain epitopes affected by mutations were specifically associated with protection from symptomatic variant infection, cellular immunity was most effective when targeting conserved Spike epitopes. Conclusions: Optimal long-term protection against Omicron infection requires balanced immunity to both conserved and non-conserved epitopes of the viral Spike protein. The limited availability of cross-neutralizing antibodies targeting non-conserved epitopes and their inherently lower efficacy renders them a limiting factor as humoral immunity wanes over time. Future pan-SARS-CoV-2 variant vaccines that primarily target conserved epitopes may therefore provide less effective long-term protection against symptomatic variant infection than vaccines targeting a broader epitope spectrum including both conserved and non-conserved epitopes. Full article

The repeated occurrence of SARS-CoV-2 variants, largely driven by virus–host interactions, was and will remain a public health concern. Spike protein mutations shaped viral infectivity, transmissibility, and immune escape. From February 2022 to April 2024, a local genomic surveillance program in Verona, Italy, was conducted on 1333 SARS-CoV-2-positive nasopharyngeal swabs via next generation full-length genome sequencing. Spike protein mutations were classified based on their prevalence over time. Mutations were grouped into five categories: fixed, emerging, fading, transient, and divergent. Notably, some divergent mutations displayed a “Lazarus effect,” disappearing and later reappearing in new lineages, indicating potential adaptive advantages in specific genomic contexts. This two-year surveillance study highlights the dynamic nature of spike protein mutations and their role in SARS-CoV-2 evolution. The findings underscore the need for ongoing mutation-focused genomic monitoring to detect early signals of variant emergence, especially among mutations previously considered disadvantageous. Such efforts are critical for driving public health responses and guiding future vaccine and therapeutic strategies. Full article

Recombinant vesicular stomatitis virus (rVSV) is a promising viral vaccine vector for addressing the COVID-19 pandemic. Inducing mucosal immunity via the intranasal route is an ideal strategy for rVSV-based vaccines, but it requires extremely stringent safety standards. In this study, we constructed two rVSV variants with amino acid mutations in their M protein: rVSV-M2 with M33A/M51R mutations and rVSV-M4 with M33A/M51R/V221F/S226R mutations, and developed COVID-19 vaccines based on these attenuated vectors. By comparing viral replication capacity, intranasal immunization, intracranial injection, and blood cell counts, we demonstrated that the M protein mutation variants exhibit significant attenuation effects both in vitro and in vivo. Moreover, preliminary investigations into the mechanisms of virus attenuation revealed that these attenuated viruses can induce a stronger type I interferon response while reducing inflammation compared to the wild-type rVSV. We developed three candidate vaccines against SARS-CoV-2 using the wildtype VSV backbone with either wild-type M (rVSV-JN.1) and two M mutant variants (rVSV-M2-JN.1 and rVSV-M4-JN.1). Our results confirmed that rVSV-M2-JN.1 and rVSV-M4-JN.1 retain strong immunogenicity while enhancing safety in hamsters. In summary, the rVSV variants with M protein mutations represent promising candidate vectors for mucosal vaccines and warrant further investigation. Full article