Mutant Virus Research Articles

The Role of nsp5 in SARS-CoV-2

SARS-CoV-2, the causative agent of the COVID-19 pandemic, is a single-stranded positive-sense RNA virus belonging to the coronavirus family. It emerged at the end of 2019 and has swiftly disseminated globally, presenting an unparalleled threat to public health worldwide. The non-structural protein 5 (nsp5) is a key component in the SARS-CoV-2 replication process, also known as the main protease (Mpro or 3CLpro), which is essential for cleaving viral polyproteins into functional proteins required for replication and transcription. The conserved characteristics and essential role of nsp5 render it an attractive target for antiviral pharmacological development. Recent developments in nsp5-targeted treatments, like Paxlovid, exhibit significant effectiveness in decreasing COVID-19-associated hospitalizations and fatalities. However, the development of nsp5 inhibitors continues to face challenges due to viral mutations and specific administration requirements. This review explores the structural and biochemical properties of nsp5, with particular attention to its catalytic dyad, substrate recognition sites, and three-domain architecture that underpin its role in viral replication. It highlights the potential impact of nsp5 research on advancing antiviral strategies, aiding in the fight against current SARS-CoV-2 infections, and laying the groundwork for future coronavirus outbreak preparedness.

Expert consensus on the benefits of neuraminidase in conventional influenza vaccines: a Delphi study

BackgroundSeasonal vaccination is the mainstay of human influenza prevention. Licensed influenza vaccines are regularly updated to account for viral mutations and antigenic drift and are standardised for their haemagglutinin content. However, vaccine effectiveness remains suboptimal. Neuraminidase (NA) evolves more gradually than hemagglutinin and has been demonstrated to provide added clinical benefits. However, NA is not currently a mandated or standardised component of influenza vaccines.MethodsHere, we collated expert opinions on the importance of NA in influenza vaccines in a two-stage Delphi survey. Nine statements about NA were formulated by a steering committee based on a targeted literature review. In the survey’s first round, panellists recruited from three continents were requested to report on their agreement with each statement and estimate the strength of evidence for each statement. Panellists were also requested to explain their choice of answer and suggest revisions to the statements. Consensus was considered reached if ≥ 75% of panellists agreed with a statement. If consensus was not reached for a statement, this statement was revised and included in the survey’s second round.ResultsNine panellists with a broad range of NA-related expertise, including clinical, research, and public health experience, completed the survey. They agreed that anti-NA responses acquired via natural infection or vaccination are associated with protective immunity independently of haemagglutinin and that NA provided additional advantages including improving disease severity metrics. The experts identified several knowledge gaps concerning heterologous cross-reactivity of vaccine-induced anti-NA antibodies, correlations between anti-NA titres and reduced transmission or infection risks, and differences in anti-NA responses to seasonal influenza vaccines.ConclusionsNA is an important influenza vaccine component and is associated with specific benefits. These benefits would likely be greater if NA content were standardised. Additional research is needed to optimise vaccines for anti-NA effects.

The coronavirus nsp14 exoribonuclease interface with the cofactor nsp10 is essential for efficient virus replication and enzymatic activity.

Coronaviruses (CoVs) encode non-structural proteins (nsp's) 1-16, which assemble to form replication-transcription complexes that function in viral RNA synthesis. All CoVs encode a proofreading 3'-5' exoribonuclease in non-structural protein 14 (nsp14-ExoN) that mediates proofreading and high-fidelity replication and is critical for other roles in replication and pathogenesis. The in vitro enzymatic activity of nsp14-ExoN is enhanced in the presence of the cofactor nsp10. We introduced alanine substitutions in nsp14 of murine hepatitis virus (MHV) at the nsp14-nsp10 interface and recovered mutant viruses with a range of impairments in replication and in vitro biochemical exonuclease activity. Two of these substitutions, nsp14 K7A and D8A, had impairments intermediate between wild type-MHV nsp14 and the known ExoN(-) D89A/E91A nsp14 catalytic inactivation mutant. All introduced nsp14-nsp10 interface alanine substitutions impaired in vitro exonuclease activity. Passage of the K7A and D8A mutant viruses selected second-site non-synonymous mutations in nsp14 associated with improved mutant virus replication and exonuclease activity. These results confirm the essential role of the nsp14-nsp10 interaction for efficient enzymatic activity and virus replication, identify proximal and long-distance determinants of nsp14-nsp10 interaction, and support targeting the nsp14-nsp10 interface for viral inhibition and attenuation.IMPORTANCECoronavirus replication requires assembly of a replication transcription complex composed of nsp's, including polymerase, helicase, exonuclease, capping enzymes, and non-enzymatic cofactors. The coronavirus nsp14 exoribonuclease mediates several functions in the viral life cycle including genomic and subgenomic RNA synthesis, RNA recombination, RNA proofreading and high-fidelity replication, and native resistance to many nucleoside analogs. The nsp-14 exonuclease activity in vitro requires the non-enzymatic cofactor nsp10, but the determinants and importance of the nsp14-nsp10 interactions during viral replication have not been defined. Here we show that for the coronavirus murine hepatitis virus, nsp14 residues at the nsp14-nsp10 interface are essential for efficient viral replication and in vitro exonuclease activity. These results shed new light on the requirements for protein interactions within the coronavirus replication transcription complex, and they may reveal novel non-active-site targets for virus inhibition and attenuation.

Truncated NS1 Influenza A Virus Induces a Robust Antigen-Specific Tissue-Resident T-Cell Response and Promotes Inducible Bronchus-Associated Lymphoid Tissue Formation in Mice

Background: Influenza viruses with truncated NS1 proteins show promise as viral vectors and candidates for mucosal universal influenza vaccines. These mutant NS1 viruses, which lack the N-terminal half of the NS1 protein (124 a.a.), are unable to antagonise the innate immune response. This creates a self-adjuvant effect enhancing heterologous protection by inducing a robust CD8+ T-cell response together with immunoregulatory mechanisms. However, the effects of NS1 modifications on T-follicular helper (Tfh) and B-cell responses remain less understood. Methods: C57bl/6 mice were immunised intranasally with 10 μL of either an influenza virus containing a truncated NS1 protein (PR8/NS124), a cold-adapted influenza virus with a full-length NS1 (caPR8/NSfull), or a wild-type virus (PR8/NSfull). Immune responses were assessed on days 8 and 28 post-immunisation by flow cytometry, ELISA, and HAI assay. Results: In this study, we demonstrate that intranasal immunisation with PR8/NS124 significantly increases tissue-resident CD4+ and CD8+ T cells in the lungs and activates Tfh cells in regional lymph nodes as early as day 8 post-immunisation. These effects are not observed in mice immunised with caPR8/NSfull or PR8/NSfull. Notably, PR8/NS124 immunisation also leads to the development of inducible bronchus-associated lymphoid tissue (iBALT) in the lungs by day 28, characterised by the presence of antigen-specific Tfh cells and GL7+Fas+ germinal centre B cells. Conclusions: Our findings further underscore the potential of NS1-truncated influenza viruses to drive robust mucosal immune responses and enhance vaccine efficacy.

The viral serpin SPI-1 directly inhibits the host cell serine protease FAM111A.

The host-range mutant of rabbitpox virus (RPXV) with a deletion in the gene encoding the serpin serine protease inhibitor 1 (SPI-1) fails to replicate efficiently in restrictive host cells. Depletion of the host cell serine protease FAM111A restores viral replication in these cells, suggesting that SPI-1 targets FAM111A to facilitate infection. However, direct evidence of SPI-1 inhibiting FAM111A has been lacking. Here, we demonstrate that SPI-1 directly inhibits FAM111A's protease activity in vitro through covalent complex formation, a hallmark of the serpin inhibition mechanism. SPI-1 also exhibits specificity for FAM111A compared to other serine proteases in vitro. Through mutagenesis studies, we identified residues and regions within SPI-1's reactive center loop (RCL) that are critical for FAM111A inhibition and covalent complex formation in vitro, with varying degrees of impact. Notably, these RCL mutations showed a spectrum of effects on SPI-1's ability to support RPXV replication in non-permissive cells, which strongly correlated with their impact on SPI-1's capacity to inhibit FAM111A activity in vitro. Altogether, our study provides direct evidence that SPI-1 inhibits FAM111A protease activity, highlighting FAM111A's antiviral role and its significance as a target of SPI-1 during orthopoxvirus infection.

A Comprehensive Review of mRNA-based Vaccines for COVID-19, A New Era in Pharmaceuticals: Unspecified and Unknown Aspects, Effects and Challenges.

Ongoing research and development efforts are currently focused on creating COVID-19 vaccines using a variety of platforms. Among these, mRNA technology stands out as a cuttingedge method for vaccine development. There is a growing public awareness of mRNA and its potential in vaccine development. Despite being relatively recent, extensive scientific research has been dedicated to vaccines for a considerable period. mRNA vaccines are created by synthesizing the spike protein from a DNA template. This review delves into the various aspects of these vaccines and thoroughly explores the intricacies of COVID-19 vaccinations. It is essential to choose a reliable, efficient, and widely accessible vaccine to combat COVID-19. However, due to the possibility of virus mutations, developing a dependable and safe vaccine is crucial to prepare for future outbreaks of SARS-CoV-2 variants. Meanwhile, concerns remain regarding the potential risks associated with these vaccines.

Mechanism of THBS1 Regulation of MDCK Cell Proliferation and Apoptosis Through TGF-β/Smad Signalling.

Madin-Darby Canine Kidney (MDCK) cells are a key cell line for influenza vaccine production, due to their high viral yield and low mutation resistance. In our laboratory, we established a tertiary cell bank (called M60) using a standard MDCK cell line imported from American Type Culture Collection (ATCC) in the USA. Due to their controversial tumourigenicity, we domesticated non-tumourigenic MDCK cells (named CL23) for influenza vaccine production via monoclonal screening in the early stage of this study, and the screened CL23 cells were characterised based on their low proliferative capacity, which had certain limitations in terms of expanding their production during cell resuscitation. It was thus our objective to enhance the proliferation efficiency of MDCK cells for influenza vaccine production following cell resuscitation, with a view to improving the production of non-tumourigenic MDCK cells for vaccines and enhancing the production of influenza virus lysate vaccines from MDCK cells through genetic intervention. We concentrated on the protein thrombosponin-1 (THBS1), which was markedly differentiated in the proteomics data of the two MDCK cells. By integrating this finding with related studies, we were able to ascertain that THBS1 exerts a significant influence on the level of cell proliferation and apoptosis. Consequently, our objective was to investigate the impact of THBS1 expression on MDCK cell apoptosis by verifying the differences in THBS1 expression between the two MDCK cells and by interfering with THBS1 expression in the MDCK cells. We found that the knockdown of THBS1 significantly increased the proliferation and apoptosis of CL23 cells without causing significant changes in cell migration and invasion, and its overexpression significantly decreased the proliferation of M60 cells and increased cell migration, invasion, and apoptosis. In addition, the TGF-β/Smad pathway target genes transforming growth factor-β1 (TGF-β1), mothers against decapentaplegic homolog 2 (Smad2), and mothers against decapentaplegic homolog 3 (Smad3), were significantly down-regulated in CL23 cells after THBS1 knockdown and up-regulated in M60 cells after overexpression, with consistent expression identified at both the mRNA and protein levels. The treatment of cells with TGF-β activators and inhibitors further demonstrated that THBS1 regulated MDCK cell proliferation and apoptosis through the TGF-β/Smad signalling pathway. Finally, we found that THBS1 also regulated H1N1 influenza virus replication. These findings enable a comprehensive understanding of the regulatory mechanisms of THBS1 regarding MDCK cell proliferation and apoptosis functions and the effects of influenza virus replication.

Interaction between microRNA and KRAS in Glioblastoma.

Glioblastoma (GBM) characterized byits rapid progression and challenging prognosis, often featuring mutations in the Kirsten rat sarcoma virus (KRAS) gene, which is crucial for numerous cellular signaling mechanisms. Emerging research underscores a significant interaction between KRAS and microRNAs (miRNAs) in these cancers, with miRNAs playing key roles as both regulators and mediators within the KRAS signaling framework. The concept of oncogene-induced senescence (OIS) is explored as a protective mechanism against tumor development, examining how K-RAS signaling is meticulously adjusted to bypass senescence, thereby enhancing cell growth and survival. In this study, we identify certain miRNAs that directly impact KRAS through mRNA targeting or by influencing its downstream signaling cascades. In turn, pathways activated by KRAS can modify the levels of specific miRNAs, establishing a feedback loop that balances cell regulation and tumor progression. We propose a theoretical framework where these interactions are crucial for deciphering the molecular underpinnings of GBM, potentially paving the way for innovative treatment approaches that focus on the miRNA-KRAS connection.

Simultaneous Detection of Five Infectious Diseases in a Single Strip: Oligo dT-Utilized Lateral Flow Immunoassay.

The need for accurate and simultaneous diagnosis of multiple respiratory infectious diseases has become increasingly critical due to ongoing viral mutations and the similarity of symptoms among various viruses. Here, we have advanced our detection capabilities by developing a multiplex lateral flow immunoassay (LFA) platform that integrates oligonucleotides and antibodies, enabling the simultaneous detection of five respiratory viruses: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Influenza A (FluA), Influenza B (FluB), Respiratory syncytial virus (RSV), and Adenovirus (ADV), on a single membrane. By applying the oligonucleotide and antibody-conjugated AuNPs, the platform enables highly sensitive and specific detection. In addition, signal amplification using RPA70A-conjugated gold nanoparticles that developed in the previous study can further be applied optionally for low-concentration biomarkers. Our interferences and cross-reactivity tests confirmed that these complexes do not produce false positives, substantiating the assay's utility in clinical settings. This platform, therefore, provides a robust solution for the precise and rapid diagnosis of complex viral infections, positioning it as suitable for application in pandemic response scenarios.

Porcine ISG15 fused IFN-λ3 as a novel antiviral agent for treating porcine reproductive and respiratory syndrome virus infection in vivo.

IFN-λs hold promise as therapeutic candidates against mutable respiratory viruses, but their efficacy against porcine reproductive and respiratory syndrome virus (PRRSV) remains unclear. In this study, we expressed a recombinant fusion protein consisting of porcine ISG15 linked porcine IFN-λ3 (ISG15-IFN-λ3) via a rigid protein linker in Escherichia coli (E. coli). In vitro experiments demonstrated that treatment of porcine alveolar macrophage (PAM)-derived CRL-2843 cells with ISG15-IFN-λ3 induced upregulation of several Interferon-stimulated Genes (ISGs) proteins, including ISG15, ISG56, and HERC5. CRL-2843 cells pretreated with ISG15-IFN-λ3 exhibited heightened resistance to Newcastle disease virus infection, while PRRSV-permissive cells treated with ISG15-IFN-λ3 before and during PRRSV exposure showed significantly inhibited PRRSV replication as well. In animal experiments, at 21days post-infection, ISG15-IFN-λ3-treated piglets displayed milder lung tissue pathology and significantly reduced serum PRRSV-RNA, indicating enhanced viral clearance and faster recovery. Additionally, PAMs collected from ISG15-IFN-λ3-treated piglets showed significantly reduced mRNA expression of representative cytokines, chemokines, suggesting that ISG15-IFN-λ3 treatment may mitigate pneumonia severity by reducing the levels of these inflammatory mediators. These findings indicate that recombinant ISG15-IFN-λ3 expressed in E. coli may serve as a novel, effective, and affordable agent for treating severe PRRSV infection in piglets, potentially benefiting the pork industry.

In silico Binding and Interactions of Known Antivirals to the Dimer Pocket of the SARS-CoV-2 Main Protease

The devastating COVID-19 pandemic began in December 2019, catalyzed by the emergence of the SARS-CoV-2 beta-coronavirus strain. This inflicted global havoc, infecting over 767 million individuals and claiming more than 6.9 million lives by the end of 2023. Despite accelerated vaccine approvals significantly curbing infection rates and fatalities, the persistent spread of COVID-19 cases has been driven by evolving SARS-CoV-2 variants. The risk of future pandemics due to viral mutations emphasizes the urgent need for more effective antiviral drugs to prevent resistance. In this study, we explored the potential binding of small molecules to the dimer site of SARS-CoV-2 main protease (Mpro). We used the DogSiteScore program to predict the druggable sites, and Autodock Vina to evaluate the binding affinities of known antivirals. The results revealed that most of the antivirals exhibit higher binding affinities to the dimer site compared to the catalytic site. Notably, indinavir, nelfinavir, lopinavir, grazoprevir, and dolutegravir are among the top binders, surpassing - 10 kcal/mol in the dimer site. Meanwhile, these antivirals exhibited affinities to the catalytic site that did not exceed -8.7 kcal/mol. These findings highlight the promising potential of the dimer site as an alternative target for developing specific COVID-19 inhibitors.

A REVIEW OF THE EFFECTS OF SOCIOECONOMIC AND ENVIRONMENTAL FACTORS IN EXPLANING THE PARADOX BETWEEN VACCINATION RATES AND COVID-19 RELATED MORTALITY RATES

This study evaluates vaccination as a primary strategy to reduce COVID-19 deaths across 150 countries. By analyzing the correlation between full vaccination rates and mortality rates in January 2022, the study initially finds a positive association (r = 0.65, p-value < .01). However, further regression analysis reveals a more complex relationship. A 1% increase in full vaccination correlates with a 0.7% rise in deaths per 100,000 people (p-value < .001), even when considering GDP differences. This suggests that factors beyond vaccination, such as socioeconomic conditions, virus mutations, and healthcare resources (e.g., ventilators per capita), play a substantial role in determining mortality rates. The study's findings challenge the notion that vaccination alone can eradicate COVID-19. While vaccination is a crucial tool, it's essential to address the broader factors contributing to the virus's spread and its economic impact, particularly in countries with high vaccination rates but persistent mortality. This comprehensive approach is vital for effectively managing the pandemic and minimizing its long-term consequences.

The PA-X host shutoff site 100 V exerts a contrary effect on viral fitness of the highly pathogenic H7N9 influenza A virus in mice and chickens

ABSTRACT Several viruses, including influenza A virus (IAV), encode viral factors to hijack cellular RNA biogenesis processes to direct the degradation of host mRNAs, termed “host shutoff.” Host shutoff enables viruses to simultaneously reduce antiviral responses and provides preferential access for viral mRNAs to cellular translation machinery. IAV PA-X is one of these factors that selectively shuts off the global host genes. However, the specific role of PA-X host shutoff activity in viral fitness of IAV remains poorly understood. Herein, we successfully mapped PA-X 100 V as a novel site important for host shutoff of the H7N9 and H5N1 viruses. By analysing the polymorphism of this residue in various subtype viruses, we found that PA-X 100 was highly variable in H7N9 viruses. Structural analysis revealed that 100 V was generally close to the PA-X endonuclease active site, which may account for its host shutoff activity. By generating the corresponding mutant viruses derived from the parental H7N9 virus and the PA-X-deficient H7N9 virus, we determined that PA-X 100 V significantly enhanced viral fitness in mice while diminishing viral virulence in chickens. Mechanistically, PA-X 100 V significantly increased viral polymerase activity and viral replication in mammalian cells. Furthermore, PA-X 100 V highly blunted the global host response in 293T cells, particularly restraining genes involved in energy metabolism and inflammatory response. Collectively, our data provided information about the intricate role of the PA-X host shutoff site in regulating the viral fitness of the H7N9 influenza virus, which furthers our understanding of the complicated pathogenesis of the influenza A virus.

The influence of the dynamic context of the pandemic on the predictive performance of mortality predictions over time in older patients hospitalised for COVID-19.

During the COVID-19 pandemic, dynamic factors such as governmental policies, improved treatment and prevention options and viral mutations changed the incidence of outcomes and possibly changed the relation between predictors and outcomes. The aim of the present study was to assess whether the dynamic context of the pandemic influenced the predictive performance of mortality predictions over time in older patients hospitalised for COVID-19. The COVID-OLD study, a multicentre cohort study in the Netherlands, included COVID-19 patients aged 70 years and older hospitalised during the first (early 2020), second (late 2020), third (late 2021) or fourth wave (early 2022). We developed a prediction model for in-hospital mortality that included variables commonly collected at the emergency department with least absolute shrinkage and selection operator (LASSO) regression on patients admitted in the first pandemic wave and temporally validated this model in patients admitted in the second, third or fourth wave. In total, 3067 patients (median age 79 years, 60% men) were included. The final model included demographics, frailty and indicators of disease severity that were generally available within three hours after admission. The model differentiated between death and alive after hospitalization for COVID-19 with an AUC of 0.80 (95% CI: 0.76-0.84) in the internal validation cohort. In terms of discrimination and calibration, predictive performance of the model decreased over time with an AUC of 0.76 (0.73-0.79) and calibration slope of 0.81 (0.68-0.96) in the second wave, an AUC of 0.77 (0.72-0.82) and calibration slope of 0.85 (0.65-1.10) in the third wave and an AUC of 0.59 (0.48-0.70) and calibration slope of 0.35 (-0.05, 0.72) in the fourth wave. Compared to the moderate model performance in the first wave, we observed a slight decrease in terms of discrimination and calibration in the second and third wave with a much larger decrease in the fourth wave. This highlights the importance of ongoing data collection, monitoring of model performance and model updates during a pandemic.

Evaluating Neural Network Performance in Predicting Disease Status and Tissue Source of JC Polyomavirus from Patient Isolates Based on the Hypervariable Region of the Viral Genome

JC polyomavirus (JCPyV) establishes a persistent, asymptomatic kidney infection in most of the population. However, JCPyV can reactivate in immunocompromised individuals and cause progressive multifocal leukoencephalopathy (PML), a fatal demyelinating disease with no approved treatment. Mutations in the hypervariable non-coding control region (NCCR) of the JCPyV genome have been linked to disease outcomes and neuropathogenesis, yet few metanalyses document these associations. Many online sequence entries, including those on NCBI databases, lack sufficient sample information, limiting large-scale analyses of NCCR sequences. Machine learning techniques, however, can augment available data for analysis. This study employs a previously compiled dataset of 989 JCPyV NCCR sequences from GenBank with associated patient PML status and viral tissue source to train multilayer perceptrons for predicting missing information within the dataset. The PML status and tissue source models were 100% and 87.8% accurate, respectively. Within the dataset, 348 samples had an unconfirmed PML status, where 259 were predicted as No PML and 89 as PML sequences. Of the 63 sequences with unconfirmed tissue sources, eight samples were predicted as urine, 13 as blood, and 42 as cerebrospinal fluid. These models can improve viral sequence identification and provide insights into viral mutations and pathogenesis.

Viral Oncogenesis: Synergistic Role of Genome Integration and Persistence.

Persistence is a strategy used by many viruses to evade eradication by the immune system, ensuring their permanence and transmission within the host and optimizing viral fitness. During persistence, viruses can trigger various phenomena, including target organ damage, mainly due to an inflammatory state induced by infection, as well as cell proliferation and/or immortalization. In addition to immune evasion and chronic inflammation, factors contributing to viral persistence include low-level viral replication, the accumulation of viral mutants, and, most importantly, maintenance of the viral genome and reliance on viral oncoprotein production. This review focuses on the process of genome integration, which may occur at different stages of infection (e.g., HBV), during the chronic phase of infection (e.g., HPV, EBV), or as an essential part of the viral life cycle, as seen in retroviruses (HIV, HTLV-1). It also explores the close relationship between integration, persistence, and oncogenesis. Several models have been proposed to describe the genome integration process, including non-homologous recombination, looping, and microhomology models. Integration can occur either randomly or at specific genomic sites, often leading to genome destabilization. In some cases, integration results in the loss of genomic regions or impairs the regulation of oncogene and/or oncosuppressor expression, contributing to tumor development.

A predictive language model for SARS-CoV-2 evolution

Modeling and predicting mutations are critical for COVID-19 and similar pandemic preparedness. However, existing predictive models have yet to integrate the regularity and randomness of viral mutations with minimal data requirements. Here, we develop a non-demanding language model utilizing both regularity and randomness to predict candidate SARS-CoV-2 variants and mutations that might prevail. We constructed the “grammatical frameworks” of the available S1 sequences for dimension reduction and semantic representation to grasp the model’s latent regularity. The mutational profile, defined as the frequency of mutations, was introduced into the model to incorporate randomness. With this model, we successfully identified and validated several variants with significantly enhanced viral infectivity and immune evasion by wet-lab experiments. By inputting the sequence data from three different time points, we detected circulating strains or vital mutations for XBB.1.16, EG.5, JN.1, and BA.2.86 strains before their emergence. In addition, our results also predicted the previously unknown variants that may cause future epidemics. With both the data validation and experiment evidence, our study represents a fast-responding, concise, and promising language model, potentially generalizable to other viral pathogens, to forecast viral evolution and detect crucial hot mutation spots, thus warning the emerging variants that might raise public health concern.

Durability of Adaptive Immunity in Immunocompetent and Immunocompromised Patients Across Different Respiratory Viruses: RSV, Influenza, and SARS-CoV-2.

Research on respiratory virus immunity duration post-vaccination reveals variable outcomes. This study performed a literature review to assess the efficacy and longevity of immune protection post-vaccination against SARS-CoV-2, influenza, and respiratory syncytial virus (RSV), with a focus on immunocompromised populations. Specific objectives included examining humoral and cellular immune responses and exploring the impact of booster doses and hybrid immunity on extending protection. A literature review was conducted focusing on studies published from January 2014 to November 2024. The search targeted adaptive immunity post-vaccination, natural immunity, and hybrid immunity for SARS-CoV-2, influenza, and RSV. Selection criteria emphasized human populations, adaptive immunity outcomes, and immunocompromised individuals. The PICO framework guided the analysis, culminating in a detailed review of 30 studies. SARS-CoV-2 vaccines exhibited robust initial antibody responses, which waned significantly within six months, necessitating frequent boosters. Influenza and RSV vaccines similarly showed declines in immunity, though some influenza vaccines demonstrated moderate durability. Hybrid immunity, arising from combined natural infection and vaccination, provided more resilient and lasting protection than vaccination alone, especially against emerging variants. Immunocompromised individuals consistently exhibited reduced durability in adaptive immune responses across all studied viruses. Challenges include rapid viral mutations, limiting the broad protection of current vaccines. Immune durability varies significantly across virus types and patient populations. Frequent boosters and hybrid immunity are critical to optimizing protection, particularly for vulnerable groups. The findings underscore the need for adaptable vaccination strategies and advancements in vaccine design to counter rapidly mutating respiratory pathogens effectively.

The alphavirus determinants of intercellular long extension formation.

The alphavirus chikungunya virus (CHIKV) is a serious human pathogen that can cause large-scale epidemics characterized by fever and joint pain and often resulting in chronic arthritis. Infection by alphaviruses including CHIKV and the closely related Semliki Forest virus (SFV) can induce the formation of filopodia-like intercellular long extensions (ILEs). ILEs emanate from an infected cell, stably attach to a neighboring cell, and mediate cell-to-cell viral transmission that is resistant to neutralizing antibodies. However, our mechanistic understanding of ILE formation is limited, and the potential contribution of ILEs to CHIKV virulence or human CHIKV infection is unknown. Here, we used well-characterized virus mutants and monoclonal antibodies with known epitopes to dissect the virus requirements for ILE formation. Our results showed that both the viral E2 and E1 envelope proteins were required for ILE formation, while viral proteins 6K and transframe, and cytoplasmic nucleocapsid formation were dispensable. A subset of CHIKV monoclonal antibodies reduced ILE formation by masking specific regions particularly on the E2 A domain. Studies of the viral proteins from different CHIKV strains showed that ILE formation is conserved across the four major CHIKV lineages. Sera from convalescent human CHIKV patients inhibited ILE formation in cell culture, providing the first evidence for ILE inhibitory antibody production during human CHIKV infections.IMPORTANCEChikungunya virus (CHIKV) infections can cause severe fever and long-lasting joint pain in humans. CHIKV is disseminated by mosquitoes and is now found world-wide, including in the Americas, Asia, and Africa. In cultured cells, CHIKV can induce the formation of long intercellular extensions that can transmit virus to another cell. However, our understanding of the formation of extensions and their importance in human CHIKV infection is limited. We here identified viral protein requirements for extension formation. We demonstrated that specific monoclonal antibodies against the virus envelope proteins or sera from human CHIKV patients can inhibit extension formation. Our data highlight the importance of evaluation of extension formation in the context of human CHIKV infection.

From structure prediction to function: defining the domain on the African swine fever virus CD2v protein required for binding to erythrocytes.

A better understanding of the interactions between viruses and their hosts is a crucial step in the development of strategies for controlling viral diseases, such as vaccines and antivirals. African swine fever, a pig disease with fatality rates approaching 100%, causes very substantial economic losses in affected countries, and new control measures are clearly needed. In this study, we characterized the interaction between the ASFV CD2v protein and host erythrocytes. The interaction plays a key role in viral persistence in blood since it can allow the virus to "hide" from the host immune system. We identified the amino acids in the viral protein that mediate the interaction with erythrocytes and used this information to construct a mutant virus that is no longer able to bind these cells. This virus induces strong immune responses that provide high levels of protection against infection with the deadly parental virus.