SARS-CoV-2 variants, spike mutations and immune escape

Neutralizing antibody levels as a key factor in determining the immunogenic efficacy of the novel PEDV alpha coronavirus vaccine

Porcine epidemic diarrhea virus (PEDV) causes significant global agricultural losses. Despite commercial inactivated and live attenuated vaccines, persistent outbreaks underscore the need for more effective solutions. Here, we isolated a novel Chinese PEDV variant, PEDV ShXXY2-2023, with amino acid substitutions in key neutralizing epitopes (N-terminal domain, receptor-binding domain, and CO-26K equivalent epitope) compared to vaccine strains. An inactivated ShXXY2-2023 vaccine induced higher neutralizing antibodies and superior cross-protection versus commercial vaccines. Vaccinated sows conferred enhanced protection to offspring, improving piglet survival post-challenge. Maternal serum neutralizing antibody titers correlated strongly with piglet survival; titers of 1:377-1:774 at one week prepartum yielded >80% protective efficacy. These findings emphasize neutralizing antibodies' critical role in PEDV prevention and position ShXXY2-2023 as a promising vaccine candidate, with broader implications for coronavirus vaccine development.

Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants

To generate antibodies (Abs) against SARS-CoV-2 emerging variants, we integrated multiple tools and engineered molecules with excellent neutralizing breadth and potency. Initially, the screening of an immune library identified a nanobody (Nb), termed Nb4, specific to the receptor-binding domain (RBD) of the Omicron BA.1 variant. A Nb4-derived heavy chain antibody (hcAb4) recognized the spike (S) of the Wuhan, Beta, Delta, Omicron BA.1, and BA.5 SARS-CoV-2 variants. A high-resolution crystal structure of the Nb4 variable (VHH) domain in complex with the SARS-CoV-2 RBD (Wuhan) defined the Nb4 binding mode and interface. The Nb4 VHH domain grasped the RBD and covered most of its outer face, including the core and the receptor-binding motif (RBM), which was consistent with hcAb4 blocking RBD binding to the SARS-CoV-2 receptor. In mouse models, a humanized hcAb4 showed therapeutic potential and prevented the replication of SARS-CoV-2 BA.1 virus in the lungs of the animals. In vitro, hcAb4 neutralized Wuhan, Beta, Delta, Omicron BA.1, and BA.5 viral variants, as well as the BQ.1.1 subvariant, but showed poor neutralization against the Omicron XBB.1.5. Structure-based computation of the RBD-Nb4 interface identified three Nb4 residues with a reduced contribution to the interaction with the XBB.1.5 RBD. Site-saturation mutagenesis of these residues resulted in two hcAb4 mutants with enhanced XBB.1.5 S binding and virus neutralization, further improved by mutant Nb4 trimers. This research highlights an approach that combines library screening, Nb engineering, and structure-based computational predictions for the generation of SARS-CoV-2 Omicron-specific Abs and their adaptation to emerging variants.

Neutralizing antibody responses after a two-dose regimen with BNT162b2, CoronaVac or ChAdOx1-S in Brazil: Differential neutralization of SARS-CoV-2 omicron variants

The emergence of SARS-CoV-2 variants has reduced antibody effectiveness, affecting vaccine protection. This study evaluated neutralizing antibodies against Wuhan strain and several variants, including Alpha, Beta, Gamma, Delta, and Omicron, in Brazilians vaccinated twice with CoronaVac, ChAdOx1-S, or BNT162b2 before Delta and Omicron emerged. After the booster, strong antibody responses to the Wuhan strain were seen in all groups, but BNT162b2 resulted in higher anti-Spike and anti-RBD IgG levels. While all vaccines showed some cross-neutralization against Alpha, Beta, Gamma, and Delta, only BNT162b2 was effective against Omicron BA.2 and BA.4/5 subvariants. Furthermore, BNT162b2 vaccination showed a positive correlation between Wuhan RBD-specific IgG and Omicron neutralizing antibodies. This group demonstrated distinct clustering patterns of neutralizing antibodies against all variants, unlike those from CoronaVac and ChAdOx1-S. The findings suggest BNT162b2 offers broader neutralization capability, highlighting the benefit of booster shots with bivalent mRNA vaccines to enhance immune responses against emerging variants.

Electrochemical pan-variant detection of SARS-CoV-2 through host cell receptor-mimicking molecular recognition

The persistent emergence of new SARS-CoV-2 variants has presented significant challenges to vaccines and antiviral therapeutics, highlighting the need for the development of methods that ensure variant-independent responses. This study introduces a unique sensor capable of electrochemically detecting SARS-CoV-2 across a wide range of variants. The comprehensive detection is achieved by using a peptide-DNA hybrid, R7-02, as the capture probe, mimicking the binding interface between a SARS-CoV-2 spike protein and a host cell receptor, hACE2. Since the first step of viral infection is the binding of the spike protein to hACE2 regardless of variant type, the hACE2-mimicking probe can naturally acquire the pan-variant recognition capability. In constructing the sensor, the R7-02 probes are positioned on electrodes via a tetrahedral DNA nanostructure for enhanced detection efficiency. Since R7-02 directly captures the externally-exposed spike protein, our approach does not require sample pretreatments, such as virus particle lysis, unlike conventional diagnostic methods. The R7-02-embedded sensor demonstrated high sensitivity towards Omicron and its major subvariants-commonly known as 'stealth Omicron' (BA.5, BA.2.75, BQ.1.1, and XBB.1.5)-with a detection limit as low as 811.9 pM, along with robust specificity for SARS-CoV-2 against influenza and other human coronaviruses. The sensor also successfully detected SARS-CoV-2 directly from non-treated saliva samples of COVID-19-positive patients. Given the comprehensive and sensitive detection capability, combined with its simple operation, our receptor-mimicking probe-based electrochemical sensor holds the potential to be a sustainable and effective point-of-care diagnostic tool, offering a promising solution to the constant challenges posed by the endemic presence of SARS-CoV-2.

Development of Ni-ZnO-ACE-2 peptide hybrids as electrochemical devices for SARS-CoV-2 spike protein detection

Owing to fast SARS-CoV-2 mutations, biosensors employing antibodies as biorecognition elements have presented problems with sensitivity and accuracy. To face these challenges, antibodies can be replaced with the human angiotensin converting enzyme 2 (ACE-2), where it has been shown that the affinity between ACE-2 and the receptor binding domain (RBD) increases with the emergence of new variants. Herein, we report on Ni-doped ZnO nanorod electrochemical biosensors employing an ACE-2 peptide (IEEQAKTFLDKFNHEAEDLFYQS-NH2) as a biorecognition element for detecting Spike (S) Wild-Type (WT) protein. The electrode was fully characterized in terms of electrochemical and physical properties. The sensor showed high cross reactivity with Spike protein B.1.1.7 and Spike protein B.1.351. Still, there was no cross reactivity with the Nucleocapsid protein WT, showing that the biosensor can identify ancestral WT S protein and S protein variants of concern. The device exhibited a LOD of 60.13 ng mL-1 across an S protein WT concentration range from 200 ng mL-1 to 1000 ng mL-1 and a LOQ of 182.22 ng mL-1. The calculated sensitivity and specificity were 88.88 and 100 %, respectively. These results proved that the Ni-ZnO sensor has promising prospects for SARS-CoV-2 detection and diagnosis of other viruses, employing peptides as biorecognition elements.

The pan-variant potential of light: 425 nm light inactivates SARS-CoV-2 variants of concern and non-cytotoxic doses reduce viral titers in human airway epithelial cells

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) prolonged the coronavirus disease 2019 (COVID-19) pandemic. The continued development of novel pan-variant therapeutics to treat currently circulating and future VOCs is critically important. Photomedicine may offer broadly applicable, pan-variant treatments. In this study, we show that visible light centered around 425 nm inactivates each of the five SARS-CoV-2 VOC lineages that have been identified by the World Health Organization (Alpha, Beta, Delta, Gamma, and Omicron) in cell-free suspensions in a dose-dependent manner, including bamlanivimab-resistant variants. Specifically, 60 J/cm2 of 425 nm light reduced SARS-CoV-2 titers by >4 log10 relative to unilluminated controls. We observed that 425 nm light inactivates SARS-CoV-2 through restricted entry to host cells. In addition, a non-cytotoxic dosing regimen of 32 J/cm2 of 425 nm light reduced infectious virus titers in well-differentiated air-liquid interface (ALI) human airway epithelial (HAE) cells infected with the Beta, Delta, and Omicron variants that incorporate mutations associated with immune evasion and/or increased transmissibility. Infectious SARS-CoV-2 titers were reduced when dosing began during the early stages of infection or in more established infections. Finally, we translated these findings to the RD-X19, a novel medical device that emits 425 nm light; our results showed that the RD-X19 restricted spike binding to ACE-2 and reduced SARS-CoV-2 titers in cell-free suspensions (by >2 log10) and in the ALI HAE model (by >1 log10). These findings indicate that photomedicine utilizing 425 nm visible light may serve as a novel, pan-variant treatment modality for COVID-19.IMPORTANCEThe continued spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the emergence of variants that can evade public health measures, including vaccines and therapeutics. Thus, the continued development of broadly applicable measures to supplement current public health measures and standards of care remains critical. Photomedicine is one such approach. In this study, we show that non-ultraviolet visible light can inactivate each SARS-CoV-2 variant of concern (VOC) by preventing entry to host cells. Furthermore, visible light reduced the amount of virus produced in an infection model of the human airway at multiple stages of infection, demonstrating the antiviral capability of visible light. This study provides preclinical support for the development of visible light to serve as a SARS-CoV-2 countermeasure and warrants further investigation.

HERC5-mediated ISGylation of SARS-CoV-2 nsp8 facilitates its degradation and inhibits viral replication

Severe acute respiratory syndrome coronavirus 2 non-structural protein 8 (SARS-CoV-2 nsp8) is a multifunctional protein essential for viral replication and immune evasion. However, the host factors that regulate nsp8 stability and function remain unclear. In this study, we identify HECT and RCC-like domain-containing protein 5 (HERC5) as an essential E3 ligase that regulates nsp8 stability through ISGylation, a ubiquitin-like post-translational modification that facilitates proteasome-dependent degradation. HERC5 overexpression significantly enhances nsp8 degradation in an enzymatic activity-dependent manner, whereas SARS-CoV-2 papain-like protease (PLpro) counteracts this process by deconjugating interferon-stimulated gene 15 (ISG15) from nsp8-thereby preventing its degradation and facilitating viral replication. Mass spectrometry and mutational analyses revealed that the N2 domain of nsp8 is indispensable for ISGylation, with multiple lysine residues acting as primary modification sites. Additionally, we demonstrated that the ISGylation system, including HERC5, ubiquitin-like modifier activating enzyme 7 (UBA7), and ISG15, effectively suppresses SARS-CoV-2 replication across multiple variants, including Omicron BA.5 and XBB.1.5.15. These findings provide novel insights into the role of ISGylation in host antiviral defense and highlight the interplay between HERC5 and PLpro in modulating viral replication. This study establishes a foundation for developing therapeutic strategies targeting HERC5 or PLpro to inhibit SARS-CoV-2 replication.

Integrative Metabolomic and Lipidomic Signatures of SARS-CoV-2 VOCs: Correlations with Hematological and Biochemical Markers

In the present study, we investigated biochemical, hematological, lipidomic, and metabolomic alterations associated with different SAR-CoV-2 variants of concern (VOCs), such as WT, α, β, γ, and δ, as well as their impact on COVID-19 severity. Across the first and second waves in India, a machine learning approach was used in 3134 COVID-19 patients, and nine critical biochemical and hematological parameters, namely, C-reactive protein (CRP), D-dimer, ferritin, neutrophil, WBC count, lymphocyte, urea, creatine, and lactate dehydrogenase (LDH), were identified. Furthermore, through metabolic and lipidomic profiles of lung and colon cells transfected with spike VOCs, notable dysregulation was exhibited by the delta variant correlated with characteristic pathways such as catecholamine and thyroid hormone synthesis. A corroborating meta-analysis also highlighted the involvement of urea and amino acid metabolism pathways. Overall, our study provides crucial insights into metabolic and biochemical disruptions caused by VOCs, contributing to a better understanding of COVID-19 pathogenesis and the development of targeted interventions.

P.1 and P.2 SARS-CoV-2 Brazilian variants activate the unfolded protein response with a time and pathway specificity

COVID-19 is a human respiratory syndrome caused by the infection of the SARS-CoV-2 virus that has a high rate of infection and mortality. Viruses modulate the host machinery by altering cellular mechanisms that favor their replication. One of the mechanisms that viruses exploit is the protein folding and processing of post-translational modifications that occur in the endoplasmic reticulum (ER). When ER function is impaired, there is an accumulation of misfolded proteins leading to endoplasmic reticulum stress (ER stress). To maintain homeostasis, cells trigger an adaptive signaling mechanism called the Unfolded Protein Response (UPR) which helps cells deal with stress, but under severe conditions, can activate the apoptotic cell death mechanism. This study elucidated an activation of a diversity of molecular mechanisms by Brazilian variants of SARS-CoV-2 by a time-resolved and large-scale characterization of SARS-CoV-2-infected cells proteomics and immunoblotting. Furthermore, it was shown that pharmacological UPR modulation could reduce viral release by counteracting the different viral activations of its cellular response. Analysis of human clinical specimens and disease outcomes focusing on ER stress reinforces the importance of UPR modulation as a host regulatory mechanism during viral infection and could point to novel therapeutic targets. SIGNIFICANCE: Since the emergence of SARS-CoV-2 and the consequent COVID-19 pandemic, the rapid emergence of variants of this new coronavirus has been a cause for concern since many of them have significantly higher rates of transmissibility and virulence, being called Variants of Concern (VOC). In this work, we studied the VOCs Gamma (P.1) and Zeta (P.2), also known as Brazilian variants. Constant evidence has reported that there are particularities related to each variant of SARS-CoV-2, with different rates of transmissibility, replication and modulation of host biological processes being observed, in addition to the mutations present in the variants. For this reason, this work focused on infections caused by the Brazilian variants of SARS-CoV-2 in different cell lines, in which we were able to observe that the infections caused by the variants induced endoplasmic reticulum stress in the infected cells and activated the UPR pathways, presenting specific modulations of each variant in this pathway. Furthermore, transcriptome analysis of patients revealed a correlation between ER-related genes and COVID-19 progression. Finally, we observed that the use of UPR modulators in host cells decreased viral release of all variants without affecting cell viability. The data presented in this work complement the observations of other studies that aim to understand the pathogenicity of SARS-CoV-2 VOCs and possible new therapeutic strategies, mainly targeting biological processes related to the endoplasmic reticulum.

Infectivity and structure of SARS-CoV-2 after hydrogen peroxide treatment

Hydrogen peroxide (H2O2) exhibits broad-spectrum antiviral activity and is commonly used as an over-the-counter disinfecting agent. However, its potential activities against SARS-CoV-2 have not been systematically evaluated, and mechanisms of action are not well understood. In this study, we investigate H2O2's antiviral activity against SARS-CoV-2 infection and its impact on the virion's structural integrity as compared to the commonly used fixative agent paraformaldehyde (PFA). We show that H2O2 rapidly and directly inactivates SARS-CoV-2 with a half-maximal inhibitory concentration (IC50) of 0.0015%. Cryogenic electron tomography (cryo-ET) with subtomogram averaging reveals that treatment with PFA induced the viral trimeric spike protein (S) to adopt a post-fusion conformation, and treatment of viral particles with H2O2 locked S in its pre-fusion conformation. Therefore, H2O2 treatment likely has induced modifications, such as oxidation of cysteine residues within the S subunits of the spike trimer that locked them in their pre-fusion conformation. Locking of the meta-stable pre-fusion trimer prevents its transition to the post-fusion conformation, a process essential for viral fusion with host cells and entry into host cells. Together, our cellular, biochemical, and structural studies established that hydrogen peroxide can inactivate SARS-CoV-2 in tissue culture and uncovered its underlying molecular mechanism.IMPORTANCEHydrogen peroxide (H2O2) is the commonly used, over-the-counter antiseptic solution available in pharmacies, but its effect against the SARS-CoV-2 virus has not been evaluated systematically. In this study, we show that H2O2 inactivates the SARS-CoV-2 infectivity and establish the effective concentration of this activity. Cryogenic electron tomography and sub-tomogram averaging reveal a detailed structural understanding of how H2O2 affects the SARS-CoV-2 spike in comparison with that of the commonly used fixative PFA under identical conditions. We found that PFA promoted a post-fusion conformation of the viral spike protein, while H2O2 could potentially lock the spike in its pre-fusion state. Our findings not only substantiate the disinfectant efficacy of H2O2 as a potent agent against SARS-CoV-2 but also lay the groundwork for future investigations into targeted antiviral therapies that may leverage the virus' structural susceptibilities. In addition, this study may have significant implications for developing new antiviral strategies and improving existing disinfection protocols.

Development of monoclonal antibodies against SARS-CoV-2 nucleocapsid protein for COVID-19 antigen detection

BACKGROUND

The coronavirus disease 2019 (COVID-19) pandemic underscored the global need for reliable diagnostic tools with quick turnaround time for effective patient management and mitigation of virus spread. This study aimed to express severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein and produce monoclonal antibodies (mAbs) against the expressed protein.

METHODS

Following successful expression and purification of His-tagged SARS-CoV-2 N protein using a wheat germ cell-free protein expression system (WGCFS), BALB/c mice were immunized, and generated hybridomas screened for mAb production. Indirect and sandwich ELISA were used to screen the reactivity of the monoclonal antibody against both our recombinant antigen and commercial antigen. The mAbs were also assessed for their performance using RT-PCR confirmed positive samples with varying cycle threshold (CT) values and their specificity screened using virus isolates of other respiratory viruses.

RESULTS

Our mAb demonstrated high reactivity against our recombinant antigen, commercial antigen, SARS-CoV-2 Beta and Omicron variants. There was no significant difference in the binding affinity of our mAb and commercial mAb against the study recombinant (p = 0.12) and commercial (p = 0.072) antigens. Our mAb detected SARS-CoV-2 from clinical samples with varying CT values and exhibited no cross-reactivity against other respiratory viruses.

CONCLUSIONS

We successfully expressed SARS-CoV-2 N protein leveraging WGCFS in a resource-limited setting. Our mAb had a high binding affinity to the recombinant antigen, making it a suitable candidate for antigen detection kit development. Beyond diagnostics, the mAb holds potential for therapeutic applications as well as use in clinical and environmental surveillance platforms.

Fast screening of COVID-19 inpatient samples by integrating machine learning and label-free SERS methods

BACKGROUND

Advances in bio-analyte detection demonstrate the need for innovation to overcome the limitations of traditional methods. Emerging viruses evolve into variants, driving the need for fast screening to minimize the time required for positive detection and establish standardized detection. In this study, a SERS-active substrate with Au NPs on a regularly arranged ZrO2 nanoporous structure was utilized to obtain the SERS spectrum of inpatient samples from COVID-19 patients. Two analytical approaches were applied to classify clinical samples - empirical method to identify peak assignments corresponding to the target SARS-CoV-2 BA.2 variant, and machine learning (ML) method to build classifier models.

RESULTS

Comparison of spectral profiles of pure BA.2 variant and inpatient samples showed significant differences in the occurrence of SERS peaks, requiring the selection of regions of interest for further analysis through the empirical method. SERS spectra are classified into CoV (+) and CoV (-) using both empirical and machine learning methods, each demonstrating a sensitivity of 85.7 % and a specificity of 60 %. The former method relies on peak assignment, which is performed manually relying on established and results in a longer turnaround time. In contrast, the latter method is based on the mathematical correlations between variables across the entire spectrum. The machine must continuously learn from larger datasets, and the response time for interpretation is short. Nonetheless, both methods demonstrated their suitability in classifying clinical samples.

SIGNIFICANCE

This study demonstrated that a more comprehensive discussion can be formed with the integration of machine learning classification with biochemical profiling with the empirical analysis approach. Further improvement is expected by combining these two methods by utilizing only the regions of interest instead of the entire spectrum as input for machine learning, as a feature extraction technique.

Estimation of Respiratory States Based on a Measurement Model of Airflow Characteristics in Powered Air-Purifying Respirators Using Differential Pressure and Pulse Width Modulation Control Signals-In the Development of a Public-Oriented Powered Air-Purifying Respirator as an Alternative to Lockdown Measures

Fluid dynamics modeling was conducted for the supply unit of a Powered Air-Purifying Respirator (PAPR) consisting of a nonwoven fabric filter and a pump, as well as for the exhaust filter (nonwoven fabric). The supply flow rate Q1 was modeled as a function of the differential pressure ΔP and the duty value d of the PWM control under a constant pump voltage of V = 12.0 [V]. In contrast, the exhaust flow rate Q2 was modeled solely as a function of ΔP. To simulate the pressurized hood compartment of the PAPR, a pressure buffer and a connected "respiratory airflow simulator" (a piston-cylinder mechanism) were developed. The supply unit and exhaust filter were connected to this pressure buffer, and simulated respiratory flow was introduced as an external disturbance flow. Under these conditions, it was demonstrated that the respiratory state-i.e., the expiratory state (flow from the simulator to the pressure buffer) and the inspiratory state (flow from the pressure buffer to the simulator)-can be estimated from the differential pressure ΔP, the pump voltage V, and the PWM duty value d, with respect to the disturbance flow generated by the respiratory airflow simulator. It was also confirmed that such respiratory state estimation remains valid even when the duty value d of the pump is being actively modulated to control the internal pressure of the PAPR hood. Furthermore, based on the estimated respiratory states, a theoretical investigation was conducted on constant pressure control inside the PAPR and on the inverse pressure control aimed at supporting respiratory activity-namely, pressure control that assists breathing by depressurizing when expiratory motion is detected and pressurizing when inspiratory motion is detected. This study was conducted as part of a research and development project on public-oriented PAPR systems, which are being explored as alternatives to lockdown measures in response to airborne infectious diseases such as COVID-19. The present work specifically focused on improving the wearing comfort of the PAPR.

Characterization of SARS-CoV-2 intrahost genetic evolution in vaccinated and non-vaccinated patients from the Kenyan population

Vaccination is a key control measure of coronavirus disease 2019 by preventing severe effects of disease outcomes, reducing hospitalization rates and death, and increasing immunity. However, vaccination can affect the evolution and adaptation of SARS-CoV-2 largely through vaccine-induced immune pressure. Here, we investigated intrahost recombination and single nucleotide variations (iSNVs) on the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome in non-vaccinated and vaccinated sequences from the Kenyan population to profile intrahost viral genetic evolution and adaptations driven by vaccine-induced immune pressure. We identified recombination hotspots in the S, N, and ORF1a/b genes and showed the genetic evolution landscape of SARS-CoV-2 by comparing within- and inter-wave recombination events from the beginning of the pandemic (June 2020 to December 2022) in Kenya. We further reveal differential expression of recombinant RNA species between vaccinated and non-vaccinated individuals and perform an in-depth analysis of iSNVs to identify and characterize the functional properties of non-synonymous mutations found in ORF-1 a/b, S, and N genes. Lastly, we detected a minority variant in non-vaccinated patients in Kenya, with an immune escape mutation S255F of the spike gene, and showed differential recombinant RNA species. Overall, this work identified unique in vivo mutations and intrahost recombination patterns in SARS-CoV-2, which could have significant implications for virus evolution, virulence, and immune escape.IMPORTANCEThe impact of vaccination on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity in Kenya and much of Africa remains unknown. This can be attributed to lower sequencing rates; however, this information is relevant to improvement in vaccine and antiviral research. In this study, we investigated how vaccination and SARS-CoV-2 transmission waves affect intrahost non-homologous recombination and single nucleotide variations (iSNVs). We identified unique in vivo mutations and intrahost recombination patterns in SARS-CoV-2, which could have significant implications for virus evolution, virulence, and immune escape. We also demonstrate a methodology for studying genetic changes in a pathogen by a simultaneous analysis of both intrahost single nucleotide variations and recombination events. The study reveals the diversity of SARS-CoV-2 in Kenya and highlights the need for sustained genomic surveillance in Kenya and Africa to better understand how the virus evolves. Such surveillance ensures detection of drifts in evolution, allowing information for updates in vaccines, policy making, and containment of future variants of SARS-CoV-2.

Role of Glycoprotein 3 in neutralizing antibody recognition of porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome virus (PRRSV) has been causing significant economic losses in the global swine industry since its emergence. Insufficient knowledge of the structural glycoprotein characteristics of NADC30-like strains has hindered the development of effective control strategies. In this study, we found that the neutralizing antibodies (NAbs) in pig sera against NADC30-like PRRSV strain FJ1402 (lineage 1) and highly pathogenic PRRSV (HP-PRRSV) strain BB0907 (lineage 8) exhibited low cross-neutralizing activity against each other. Subsequently, six chimeric recombinant viruses were generated based on the infectious cDNA clone of HP-PRRSV strain BB0907, in which specific structural protein genes were replaced by those from the NADC30-like strain. Cross-neutralization assays revealed that the NAbs against NADC30-like strain primarily target glycoprotein 3 (GP3), glycoprotein 4 (GP4), and glycoprotein 5 (GP5). Furthermore, we constructed six additional infectious cDNA clones with point mutations in GP3, and found that the residues 66I and 85S in GP3 play critical roles during NAbs recognition. These findings provide molecular insights into the host neutralizing antibody recognition against PRRSV, highlighting the role of GP3 in the recognition process. This study offers a foundation for rational antigen selection strategies in developing PRRSV NADC30-like strain vaccines.

An Improved Rapid and Sensitive Long Amplicon Method for Nanopore-Based RSV Whole-Genome Sequencing

BACKGROUND

Whole-genome sequencing (WGS) provides critical insights into the respiratory syncytial virus (RSV) transmission and any emerging mutations that could impair the efficacy of monoclonal antibodies or vaccines that have been recently licenced for clinical use worldwide. However, the ability to sequence RSV genomes at large scale is limited by expensive and time-consuming sequencing methods. Oxford Nanopore Technology (ONT) offers significant improvements in next generation sequencing (NGS) both in turnaround time and cost, compared with other platforms for viral WGS.

METHODS

We have developed and modified an RSV long amplicon-based WGS protocol for the ONT platform using a one-step multiplex RT-PCR assay and the rapid barcoding kit. One hundred thirty-five RSV positive Australian clinical specimens (91 RSV-A and 44 RSV-B) sampled in 2023 with cycle threshold (Ct) values between 14 to 35 were tested in this study. This ONT workflow was compared with other recent RSV WGS amplification assays based on short amplicons.

RESULTS

A PCR amplicon clean-up step prior to library preparation significantly improved WGS result for samples with poor amplicon generation, but it is not necessary or beneficial for ones that generated high concentrations of amplicons. Overall, a success rate of 85.9% was achieved for WGS. This method performed as well as the more complex short amplicon methods in terms of genome coverage and sequencing depth.

CONCLUSIONS

The workflow described here was highly successful in generating RSV WGS on ONT platform and had improved turnaround times and excellent results with RSV clinical samples with Ct values up to 30.

The consequences of SARS-CoV-2 within-host persistence

SARS-CoV-2 causes an acute respiratory tract infection that resolves in most people in less than a month. Yet some people with severely weakened immune systems fail to clear the virus, leading to persistent infections with high viral titres in the respiratory tract. In a subset of cases, persistent SARS-CoV-2 replication results in an accelerated accumulation of adaptive mutations that confer escape from neutralizing antibodies and enhance cellular infection. This may lead to the evolution of extensively mutated SARS-CoV-2 variants and introduce an element of chance into the timing of variant evolution, as variant formation may depend on evolution in a single person. Whether long COVID is also caused by persistence of replicating SARS-CoV-2 is controversial. One line of evidence is detection of SARS-CoV-2 RNA and proteins in different body compartments long after SARS-CoV-2 infection has cleared from the upper respiratory tract. However, thus far, no replication competent virus has been cultured from individuals with long COVID who are immunocompetent. In this Review, we consider mechanisms of viral persistence, intra-host evolution in persistent infections, the connection of persistent infections with SARS-CoV-2 variants and the possible role of SARS-CoV-2 persistence in long COVID. Understanding persistent infections may therefore resolve much of what is still unclear in COVID-19 pathophysiology, with possible implications for other emerging viruses.

Challenges and Innovations in Pharmacovigilance and Signal Management During the COVID-19 Pandemic: An Industry Perspective

Vaccine marketing authorization holders (MAHs) are responsible for the conduction of global vaccine pharmacovigilance on their vaccine products. A safety signal is detected when a new adverse event (AE) or aspect of an AE occurs after exposure to the vaccine and warrants further investigation to determine whether a causal association may exist. Signal detection and evaluation (signal management) begins at the start of vaccine development, before an MAH submits an application for authorization to regulatory authorities, continues through the course of all clinical trials, and carries on beyond development into the post-marketing phase. As long as the vaccine remains authorized anywhere in the world, pharmacovigilance continues. During the time that the COVID-19 vaccine became widely available after authorization and approval, clinical trials were also ongoing, and therefore all clinical development and post-authorization safety information was closely monitored for safety by the MAH. MAH pharmacovigilance activities were adapted to manage the unprecedented volume of safety information that became available within a very short timeframe following worldwide vaccination campaigns. No vaccine had previously been administered to such a large number of individuals in such a short time, nor had there previously been a public health vaccine experience that was the subject of so many medical and non-medical writings. The MAH's COVID-19 vaccine signal detection methods included the continuous review of accruing clinical trial data and the quantitative and qualitative analyses of spontaneously reported experiences. Review of published and unpublished medical literature and epidemiology-based analyses such as observed vs. expected analysis based on reported adverse events following immunization (AEFIs) played key roles in pharmacovigilance and signal management. All methods of signal detection and evaluation have caveats, but when considered in totality, can advance our understanding of a vaccine's safety profile and therefore the risk-benefit considerations for vaccinating both individuals and large populations of people. All COVID-19 vaccines authorized for use were subject to an unprecedented level of pharmacovigilance by their individual MAHs, national regulatory authorities, public health organizations, and others during the years immediately following regulatory authorization and full approval. The intense worldwide focus on pharmacovigilance and the need for MAHs and regulatory/health authorities to quickly evaluate incoming safety information, spurred frequent and timely communications between national and regional health authorities and between MAHs and regulatory/health authorities, spotlighting a unique opportunity for individuals committed to patient safety to share important accruing safety information in a collegial and less traditionally formal manner than usual. The global pandemic precipitated by the SARS-CoV-2 virus created a significant impetus for MAHs to develop innovative vaccines to change the course of the COVID-19 pandemic. Pharmacovigilance also had to meet unprecedented needs. In this article, unique aspects of COVID-19 vaccine pharmacovigilance encountered by one MAH will be summarized.

Characterization of binding affinity changes of SARS-CoV-2 omicron variant peptides to population-specific HLA

BACKGROUND

The evolution of SARS-CoV-2, particularly through new variants, presents significant global health challenges due to their potential for immune evasion and reduced vaccine effectiveness. This study aims to investigate the impact of mutations in the Spike protein of Omicron EG.5 and XBB.1.16 variants on the binding affinities of viral peptides to common human leukocyte antigen (HLA) class I and II alleles across Taiwanese, British, and Russian populations. Understanding these interactions is crucial for elucidating differences in immune responses and disease severity among diverse populations.

METHODS

We updated the T-CoV portal to incorporate and analyze EG.5 and XBB.1.16 variants. Binding affinities between mutated Spike protein peptides and HLA class I and II alleles were predicted and compared across the three populations. Statistical analyses, including chi-squared tests, were conducted to assess the significance of binding affinity differences across the three populations and between HLA classes.

RESULTS

Our findings revealed that mutations in the Spike protein had a more pronounced effect on HLA class II binding affinities than on HLA class I. While binding affinity profiles for HLA class I were largely consistent across populations, significant population-specific variations were observed for HLA class II alleles. Specifically, the British population exhibited lower proportions of tightly binding mutated peptides compared to the Taiwanese and Russian populations. Furthermore, substantial differences were identified in the binding affinity changes of mutated Spike peptides for HLA class II across Taiwanese, British, and Russian populations, as well as between the Omicron EG.5 and XBB.1.16 variants. Subsequent analyses revealed significant differences in the conservation and evolutionary trajectories of binding affinities between mutated Spike peptides and common HLA class II alleles, both between the EG.5 and XBB.1.16 variants and across the three populations for the XBB.1.16 variant.

CONCLUSIONS

In summary, Spike protein mutations in SARS-CoV-2 variants significantly influence immune responses by altering HLA-peptide interactions, with pronounced population-specific effects on HLA class II alleles. These findings underscore the critical role of HLA class II diversity in shaping immune responses and susceptibility to COVID-19. Integrating population-specific HLA profiles into vaccine development and public health strategies is essential for improving interventions against evolving SARS-CoV-2 variants.

Hypericin Suppresses SARS-CoV-2 Replication and Synergizes with Antivirals via Dual Targeting of RdRp and 3CLpro

The continuous emergence of SARS-CoV-2 variants underscores the need for novel antiviral candidates. Hypericin (HY), a compound derived from Hypericum perforatum, exhibited potent in vitro activity against SARS-CoV-2 in Vero E6 cells, with low cytotoxicity (CC50 > 200 nM). HY showed no significant activity against Influenza A (H1N1) or dengue virus serotype 2, supporting its selective action. Antiviral effects were most evident when HY was administered post-infection, in a concentration-dependent manner, while cellular pretreatment or viral pre-incubation produced limited effects. Notably, HY also displayed virucidal activity, significantly reducing viral titers at 4 °C, 22 °C, and 37 °C. Combination treatments with remdesivir or nirmatrelvir enhanced antiviral efficacy by 50-70% relative to monotherapy, depending on compound concentration. Molecular simulations revealed stable interactions with conserved residues in RdRp and 3CLpro, suggesting a low risk of resistance. Together, these findings highlight the potential of HY as a selective antiviral and virucidal agent against SARS-CoV-2, particularly in combination regimens.

The COVID-19 Infection Did Not Aggravate the Mortality of Long-Term Care Facility Residents Under Strict Infection Control and with Immediate Anti-Viral Treatment: Real-World Analysis

BACKGROUND

Long-term care facilities (LTCFs) remain highly vulnerable to COVID-19. Despite reduced virulence, Omicron's high transmissibility poses ongoing risks. The effect of infection under strict control measures and early antiviral treatment remains unclear.

METHODS

We conducted a retrospective cohort study in a 450-bed LTCF, which implemented rigorous infection control and early antiviral use, evaluating survival outcomes during repeated Omicron outbreaks from January 2022 to December 2023 using Cox regression with time-dependent covariates, adjusted for age, sex, comorbidities, and vaccination status. Mortality trends were also compared across three periods: pre-COVID-19 (2018-2019), COVID-19 present in Japan but absent in our facility (2020-2021), and the Omicron outbreak period (2022-2023).

RESULTS

Among 623 residents, 253 were infected. Mortality was lower in the infected group than in the uninfected group (16% vs. 26%), and infection was not significantly associated with increased mortality (HR = 1.36; 95% CI: 0.91-2.04; p = 0.14). Although stratified analysis showed higher mortality among infected females, overall mortality during the outbreak period was unexpectedly lower than in prior periods.

CONCLUSIONS

In LTCFs with rigorous infection control and early antiviral use, Omicron infection did not raise mortality. Enhanced protocols may have improved survival, even among uninfected residents.

A Modular Mathematical Model of the Immune Response for Investigating the Pathogenesis of Infectious Diseases

The COVID-19 pandemic highlighted the importance of mathematical modeling for understanding viral infection dynamics and accelerated its application into immunological research. Collaborative efforts among international research groups yielded a wealth of experimental data, which facilitated model development and validation. This study focuses on developing a modular mathematical model of the immune response, capturing the interactions between innate and adaptive immunity, with an application to SARS-CoV-2 infection. The model was validated using experimental data from middle-aged individuals with moderate COVID-19 progression, including measurements of viral load in the upper and lower airways, serum antibodies, CD4+ and CD8+ T cells, and interleukin-6 levels. Parameter optimization and sensitivity analysis were performed to improve the model accuracy. Additionally, identifiability analysis was conducted to assess whether the data were sufficient for reliable parameter estimation. The verified model simulates the dynamics of moderate, severe, and critical COVID-19 progressions using measured data on lung epithelium damage, viral load, and IL-6 levels as key indicators of disease severity. We also performed a series of validation scenarios to assess whether the model correctly reproduces biologically relevant behaviors under various conditions, such as immunity hyperactivation, co-infection with HIV, and interferon administration as a therapeutic strategy. The model was developed as a component of the Digital Twin project and represents a general immune module that integrates both innate and adaptive immunity. It can be utilized for further COVID-19 research or serve as a foundation for studying other infectious diseases, provided sufficient data are available.

Beyond the Pandemic Era: Recent Advances and Efficacy of SARS-CoV-2 Vaccines Against Emerging Variants of Concern

Vaccination has been instrumental in curbing the transmission of SARS-CoV-2 and mitigating the severity of clinical manifestations associated with COVID-19. Numerous COVID-19 vaccines have been developed to this effect, including BioNTech-Pfizer and Moderna's mRNA vaccines, as well as adenovirus vector-based vaccines such as Oxford-AstraZeneca. However, the emergence of new variants and subvariants of SARS-CoV-2, characterized by enhanced transmissibility and immune evasion, poses significant challenges to the efficacy of current vaccination strategies. In this review, we aim to comprehensively outline the landscape of emerging SARS-CoV-2 variants of concern (VOCs) and sub-lineages that have recently surfaced in the post-pandemic years. We assess the effectiveness of existing vaccines, including their booster doses, against these emerging variants and subvariants, such as BA.2-derived sub-lineages, XBB sub-lineages, and BA.2.86 (Pirola). Furthermore, we discuss the latest advancements in vaccine technology, including multivalent and pan-coronavirus approaches, along with the development of several next-generation coronavirus vaccines, such as exosome-based, virus-like particle (VLP), mucosal, and nanomaterial-based vaccines. Finally, we highlight the key challenges and critical areas for future research to address the evolving threat of SARS-CoV-2 subvariants and to develop strategies for combating the emergence of new viral threats, thereby improving preparedness for future pandemics.

Discovery and optimization of phenazopyridine hydrochloride as novel SARS-CoV-2 RdRp inhibitors

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the pathogen of coronavirus disease (COVID-19) causing a pandemic with growing global transmission. The viral RNA-dependent RNA polymerase (RdRp) is conserved especially for variants of concern (VOCs), making it as an effective antivirals target. Due to the proofreading activity of coronavirus nsp14/nsp10, limited the efficacy of nucleoside analogs in vivo. Herein, we identified that Phenazopyridine hydrochloride (PAP) inhibits SARS-CoV-2 with EC50 of 5.37 μmol/L. Furthermore, PAP can effectively inhibit SARS-CoV-2 RdRp with EC50 value of 7.37 μmol/L, after further optimization, compound PAP-22 exhibits the most potential inhibition, with EC50 of 1.11 μmol/L. PAP and its derivatives can bind directly to SARS-CoV-2 RdRp, fully resistance to the exoribonuclease (ExoN) and exhibit broad spectrum anti-CoV activities. Combined with the current data available on the safe and pharmacokinetics of PAP as an approved drug in clinical use, these results provide a path for the urgently needed antivirals to combat SARS-CoV-2.

The spread of the Delta variant in Catalonia during summer 2021: Modelling and interpretation

BACKGROUND

The emergence of highly transmissible SARS-CoV-2 variants has posed significant challenges to public health efforts worldwide. During the summer of 2021, the Delta variant (B.1.617.2) rapidly displaced the Alpha variant (B.1.1.7) in Catalonia, Spain, leading to a resurgence in infections despite ongoing vaccination campaigns. Understanding the epidemiological drivers of this outbreak is critical for refining future mitigation strategies.

METHODS

We employed a Bayesian age-stratified epidemiological model, incorporating vaccination status and variant-specific transmission dynamics, to analyze the outbreak in Catalonia. The model was calibrated using daily reported cases, hospitalizations, sequencing data, and vaccination coverage across age groups. We inferred contact patterns dynamically to assess their role in the epidemic resurgence and estimated the transmission advantage of the Delta variant over Alpha.

RESULTS

Our analysis revealed that increased social interactions among younger, less vaccinated populations significantly contributed to the surge in infections. The long weekend of Sant Joan (June 23-24) coincided with a peak in contact rates, driving a rise in the reproduction number, particularly among individuals aged 20-29. We estimated that the Delta variant had a 40-60.

CONCLUSIONS

Our findings underscore the critical role of vaccination coverage in mitigating the impact of emerging variants. The combination of increased social interactions and uneven vaccine distribution exacerbated the Delta-driven resurgence. NPIs alone proved insufficient in controlling transmission, highlighting the necessity of targeted vaccination strategies to achieve robust epidemic control. This study provides a framework for assessing future variant-specific threats and informing tailored public health interventions.

Optimisation of the cultured ELISpot/Fluorospot technique for the selective investigation of SARS-CoV-2 reactive central memory T cells

Introduction

This study presents an optimised cultured ELISpot protocol for detecting central memory T-cell interferon gamma (IFNγ) responses against SARS-CoV-2 peptides following an initial priming with either peptides, or whole spike protein.

Methods

Key variations optimised include the culture length, timing of exogenous survival signals (IL-2), and endpoint analysis modality and cell density to enhance assay sensitivity without compromising specificity for central memory T-cell IFNγ recall responses to cognate antigen.

Results

We noted a culture duration of 10 days, combined with a delayed IL-2 administration on day 5 to enhance assay sensitivity while maintaining response specificity towards cognate antigen when compared with shorter culture periods or earlier exogenous survival signal provision. With regards to lower-frequency T-cell interactions, as we observed with our donor SARS-CoV-2 epitope responses, our findings suggest Fluorospot to be preferable to the chromogenic ELISpot modality, and an immediate cell washing after culture collection to better facilitate cognate antigen responses. Fluorospot enabled a higher cell density while minimising the generation of visual artefacts, meanwhile immediate cell washing was critical for improving endpoint assay sensitivity. CCR7+ cell depletion was used to demonstrate our optimised protocol to selectively demonstrate central memory T-cell responses. Lastly, we provide evidence for the capacity of our assay to delineate individual responding peptides following peptide pool priming, and to explore cross-reactivity between viral variant peptides.

Conclusion

This work advances the methodology for investigating T-cell immunity, particularly in the context of SARS-CoV-2, and emphasises the balance between enhancing specific cognate central memory responses while limiting non-specific activation.

Safety and Immunogenicity of SARS-CoV-2 Spike Receptor-Binding Domain and N-Terminal Domain mRNA Vaccine

BACKGROUND

mRNA-1283 is an investigational coronavirus disease 2019 (COVID-19) mRNA vaccine encoding the receptor-binding and N-terminal domains of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein in contrast to the original mRNA-1273 vaccine, which encodes the full-length spike protein.

METHODS

A phase 2a, dose-ranging, observer-blind, randomized study conducted in adults (aged ≥18 years) previously vaccinated with mRNA-1273 evaluated the safety and immunogenicity of a single dose of mRNA-1283 (2.5, 5, and 10 µg) and its bivalent formulation, mRNA-1283.211 (5 and 10 µg; encoding original SARS-CoV-2 and Beta) against the comparator mRNA-1273 vaccine, 50 µg (part A). A subsequent, open-label study (part B) evaluated the safety and immunogenicity of a monovalent Omicron BA.1 vaccine, mRNA-1283.529 (5 and 10 µg).

RESULTS

A total of 340 participants were randomized in part A, and 200 participants were enrolled in part B. All dose levels of mRNA-1283 vaccines were well tolerated and increased the neutralizing antibody (nAb) responses at day 29 compared to baseline against SARS-CoV-2 D614G and Beta. The nAb responses elicited by mRNA-1283 were higher than those elicited by mRNA-1273. mRNA-1283.529 (part B) increased nAb at day 29 against Omicron BA.1. Antibody responses remained detectable for a year postvaccination.

CONCLUSIONS

mRNA-1283 was well tolerated and exhibited improved immunogenicity compared to mRNA-1273.

CLINICAL TRIALS REGISTRATION

NCT05137236.

Impact of SARS-CoV-2 Wuhan and Omicron Variant Proteins on Type I Interferon Response

SARS-CoV-2 has demonstrated a remarkable capacity for immune evasion. While initial studies focused on the Wuhan variant and adaptive immunity, later emerging strains such as Omicron exhibit mutations that may alter their immune-modulatory properties. We performed a comprehensive review of immune evasion mechanisms associated with SARS-CoV-2 viral proteins to focus on the evolutionary dynamics of immune modulation. We systematically analyzed and compared the impact of all currently known Wuhan and Omicron SARS-CoV-2 proteins on type I interferon (IFN) responses using a dual-luciferase reporter assay carrying an interferon-inducible promoter. Results revealed that Nsp1, Nsp5, Nsp14, and ORF6 are potent type I IFN inhibitors conserved across Wuhan and Omicron strains. Notably, we identified strain-specific differences, with Nsp6 and Spike proteins exhibiting enhanced IFN suppression in Omicron, whereas the Envelope protein largely retained this function. To extend these findings, we investigated selected proteins in primary human endothelial cells and also observed strain-specific differences in immune response with higher type I IFN response in cells expressing the Wuhan strain variant, suggesting that Omicron's adaptational mutations may contribute to a damped type I IFN response in the course of the pandemic's trajectory.

Discovery of Nirmatrelvir (PF-07321332): A Potent, Orally Active Inhibitor of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS CoV-2) Main Protease

In early 2020, severe acute respiratory syndrome coronavirus 2 (SARS CoV-2) infections leading to COVID-19 disease reached a global level leading to the World Health Organization (WHO) declaration of a pandemic. Scientists around the globe rapidly responded to try and discover novel therapeutics and repurpose extant drugs to treat the disease. This work describes the preclinical discovery efforts that led to the invention of PF-07321332 (nirmatrelvir, 14), a potent and orally active inhibitor of the SARS CoV-2 main protease (Mpro) enzyme. At the outset we focused on modifying PF-00835231 (1) discovered in 2004 as a potent inhibitor of the SARS CoV-1 Mpro with poor systemic exposure. Our effort was focused on modifying 1 with the goal of engineering in oral bioavailability by design, while maintaining cellular potency and low metabolic clearance. Modifications of 1 ultimately led to the invention of nirmatrelvir 14, the Mpro inhibitor component in PAXLOVID.

Field Detection of Multiple Infectious Diseases with Naked Eye Using Plasmonic-Enhanced Fluorescent Nanoparticles

Accurately diagnosing infectious diseases in a resource-limited setting is a major challenge. Plasmonic materials, via localized surface plasmon resonance (LSPR), have greatly enhanced fluorescence signal and detection sensitivity. However, traditional plasmonic-enhanced fluorescence methods largely rely on near-infrared or visible-light fluorophores with small Stokes shift, limiting naked-eye visibility without filters. In this study, we developed a novel plasmonic silver film (pSilverF) to enhance visible-light fluorescence with large Stokes shift, allowing for improved biomarker detection sensitivity under naked-eye observation. Integrated with bright fluorescent nanoparticles, we designed a multiplexed assay for detecting Hepatitis C Virus (HCV), Hepatitis B Virus (HBV), and Human Immunodeficiency Virus (HIV) antibodies, achieving detection sensitivities down to 0.0032, 0.023, and 0.168 NCU/mL, respectively. In a cohort of 68 clinical samples, our method achieved 100% sensitivity and specificity for HIV and HCV detection and 96% sensitivity and 100% specificity for HBV detection. Notably, the results can be visualized by the naked eye and directly captured by a standard mobile phone camera without any modification for signal analysis using RGB image splitting. This platform demonstrated potential for field detection of multiple infectious diseases with simple settings, providing a useful tool for disease control in communities and areas with limited medical resources.

Increased preference for lysine over arginine in spike proteins of SARS-CoV-2 BA.2.86 variant and its daughter lineages

The COVID-19 pandemic offered an unprecedented glimpse into the evolution of its causative virus, SARS-CoV-2. It has been estimated that since its outbreak in late 2019, the virus has explored all possible alternatives in terms of missense mutations for all sites of its polypeptide chain. Spike protein of the virus exhibits the largest sequence variation in particular, with many individual mutations impacting target recognition, cellular entry, and endosomal escape of the virus. Moreover, recent studies unveiled a significant increase in the total charge on the spike protein during the evolution of the virus in the initial period of the pandemic. While this trend has recently come to a halt, we perform a sequence-based analysis of the spike protein of 2665 SARS-CoV-2 variants which shows that mutations in ionizable amino acids continue to occur with the newly emerging variants, with notable differences between lineages from different clades. What is more, we show that within mutations of amino acids which can acquire positive charge, the spike protein of SARS-CoV-2 exhibits a prominent preference for lysine residues over arginine residues. This lysine-to-arginine ratio increased at several points during spike protein evolution, most recently with BA.2.86 and its sublineages, including the recently dominant JN.1, KP.3, and XEC variants. The increased ratio is a consequence of mutations in different structural regions of the spike protein and is now among the highest among viral species in the Coronaviridae family. The impact of high lysine-to-arginine ratio in the spike proteins of BA.2.86 and its daughter lineages on viral fitness remains unclear; we discuss several potential mechanisms that could play a role and that can serve as a starting point for further studies.

Subtle Changes at the RBD/hACE2 Interface During SARS-CoV-2 Variant Evolution: A Molecular Dynamics Study

The SARS-CoV-2 Omicron variants show different behavior compared to the previous variants, especially with respect to the Delta variant, which promotes a lower morbidity despite being much more contagious. In this perspective, we performed molecular dynamics (MD) simulations of the different spike RBD/hACE2 complexes corresponding to the WT, Delta and four Omicron variants. Carrying out a comprehensive analysis of residue interactions within and between the two partners allowed us to draw the profile of each variant by using complementary methods (PairInt, hydrophobic potential, contact PCA). PairInt calculations highlighted the residues most involved in electrostatic interactions, which make a strong contribution to the binding with highly stable interactions between spike RBD and hACE2. Apolar contacts made a substantial and complementary contribution in Omicron with the detection of two hydrophobic patches. Contact networks and cross-correlation matrices were able to detect subtle changes at point mutations as the S375F mutation occurring in all Omicron variants, which is likely to confer an advantage in binding stability. This study brings new highlights on the dynamic binding of spike RBD to hACE2, which may explain the final persistence of Omicron over Delta.

Entry Efficiency, Protease Dependence, and Antibody-Mediated Neutralization of SARS-CoV-2 Sublineages KP.3.1.1 and XEC

BACKGROUND

The SARS-CoV-2 variants KP.3.1.1 and XEC currently dominate the COVID-19 epidemic. However, their cell tropism, proteolytic processing, and susceptibility to neutralization by monoclonal antibodies remain incompletely characterized.

METHODS

We employed pseudotyped viruses to assess the entry efficiency of KP.3.1.1 and XEC in various cell lines, their dependence on TMPRSS2 for lung cell entry, and their ability to use ACE2 for infection. Additionally, we evaluated their susceptibility to neutralization by monoclonal antibodies BD55-4637 and BD55-5514.

RESULTS

KP.3.1.1 and XEC entered cell lines with similar efficiency as the parental JN.1 lineage and utilized TMPRSS2 for Calu-3 lung cell entry. Unlike JN.1, KP.3.1.1 and XEC failed to efficiently use murine ACE2 for cell entry. Both variants were effectively neutralized by the monoclonal antibodies BD55-4637 and BD55-5514, suggesting therapeutic potential.

CONCLUSIONS

Our findings demonstrate that JN.1, KP.3.1.1, and XEC, like their predecessor BA.2.86, rely on TMPRSS2 for lung cell entry and remain sensitive to certain neutralizing monoclonal antibodies. However, these variants differ in their ability to utilize ACE2 species orthologs for cell entry.

The SARS-CoV-2 NSP4 T492I mutation promotes double-membrane vesicle formation to facilitate transmission

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in mutations not only in the spike protein, aiding immune evasion, but also in the NSP3/4/6 proteins, crucial for regulating double-membrane vesicle (DMV) formation. However, the functional consequences of these NSP3/4/6 mutations remain poorly understood. In this study, a systematic analysis was conducted to investigate the evolutionary patterns of NSP3/4/6 mutations and their impact on DMV formation. The findings revealed that the NSP4 T492I mutation, a prevalent mutation found in all Delta and Omicron sub-lineages, notably enhances DMV formation. Mechanistically, the NSP4 T492I mutation enhances its homodimerization, leading to an increase in the size of puncta induced by NSP3/4, and also augments endoplasmic reticulum (ER) membrane curvature, resulting in a higher DMV density per fluorescent puncta. This study underscores the significance of the NSP4 T492I mutation in modulating DMV formation, with potential implications for the transmission dynamics of SARS-CoV-2. It contributes valuable insights into how these mutations impact viral replication and pathogenesis.

Balancing stability and function: impact of the surface charge of SARS-CoV-2 Omicron spike protein

The ectodomain of the Omicron SARS-CoV-2 spike has an increased positive surface charge, favoring binding to the host cell surface, but may affect the stability of the ectodomain. Thermal stability studies identified two transitions associated with the flexibility of the receptor binding domain and the unfolding of the whole ectodomain, respectively. Despite destabilizing effects of some mutations, compensatory mutations maintain ECD stability and functional advantages thus supporting viral fitness.

Pan-Variant SARS-CoV-2 Vaccines Induce Protective Immunity by Targeting Conserved Epitopes

The development of a globally effective COVID-19 vaccine faces significant challenges, particularly in redirecting the B-cell response from immunodominant yet variable regions of viral proteins toward their conserved domains. To address this, an integrated strategy is implemented that combines classical B-cell epitope prediction with protein-antibody cluster docking and antibody titer analysis from 30 vaccinated and convalescent individuals. This approach yields stable immunodominant and immunoprevalent B-cell epitopes capable of eliciting robust antibody responses in BALB/c mice and effectively neutralizing pseudoviruses expressing the Spike protein of SARS-CoV-2 variants of concern, including Alpha, Beta, Gamma, Delta, and Omicron. To achieve a broader T-cell-based immune response, promiscuous T-cell epitopes are identified by integrating classical T-cell epitope predictions, differential scanning fluorimetry, and peptide-MHC structural analysis. Unique peptides with conserved MHC-anchoring residues are identified, enabling binding to a spectrum of MHC-I and MHC-II haplotypes. These peptides elicit strong interferon gamma responses in human peripheral blood mononuclear cells and demonstrate cross-species efficacy by activating both CD4+ and CD8+ T-cells in BALB/c mice. Collectively, these findings highlight the significance of innovative vaccine strategies targeting immunodominant/immunoprevalent B-cell and promiscuous T-cell epitopes to drive broad and robust humoral and cellular immune responses against a wide range of SARS-CoV-2 variants.

T-Cell-Dependent Bispecific IgGs Protect Aged Mice From Lethal SARS-CoV-2 Infection

T-cell ageing may be a key factor in the disproportionate severity of coronavirus disease 2019 (COVID-19) in older populations. For hospitalized COVID-19 patients, treatment involving the use of monoclonal antibodies with the ability to neutralize SARS-CoV-2 usually involves the administration of high doses but has not been very effective at preventing complications or fatality, highlighting the need for additional research into anti-SARS-CoV-2 therapies, particularly for older populations. In this study, it is discovered that older persons with a severe SARS-CoV-2 infection has weaker T-cell responses. Therefore the development and characterization of spike-targeting T-cell-dependent bispecific (TDB) full-length human immunoglobulin Gs with enhanced efficacy in the treatment of COVID-19 is described. Using S-targeting TDBs, polyclonal T cells are guided to target and destroy S-expressing cells, preventing the cell-to-cell transmission of SARS-CoV-2 and thereby eliminating the need for SARS-CoV-2-specific immunity. Using animal models of COVID-19, it is shown that the selective activation of T cells improves the efficiency of treatment in preinfected mice by attenuating disease-induced weight loss and death. The significance of T-cell-based immunity during infection is highlighted by the findings. These results have implications for better clinical effectiveness of therapies for COVID-19 and the development of T-cell-dependent medicines for the elderly population.

Enrichment of G-to-U Substitution in SARS-CoV-2 Functional Regions and Its Compensation via Concurrent Mutations

We surveyed single nucleotide variant (SNV) patterns from 5 903 647 complete SARS-CoV-2 genomes. Among 10 012 SNVs, APOBEC-mediated C-to-U (C > U) deamination was the most prevalent, followed by G > U and other RNA editing-related substitutions including (A > G, U > C, G > A). However, C > U mutations were less frequent in functional regions, for example, S protein, intrinsic disordered regions, and nonsynonymous mutations, where G > U were over-represented. Notably, G-loss substitutions rarely appeared together. Instead, G-gain mutations tended to more frequently co-occur with others, with a marked preference in the S protein, suggesting a compensatory mechanism for G loss in G > U mutations. The temporal patterns revealed C > U frequency declined until late 2021 then resurged in early 2022. Conversely, G > U steadily decreased, with a pronounced drop in January 2022, coinciding with reduced COVID-19 severity. Vaccinated individuals exhibited a slightly but significantly higher C > U frequency and a notably lower G > U frequency compared to the unvaccinated group. Additionally, cancer patients had higher G > U frequency than general patients during the same period. Interestingly, none of the C > U SNVs were uniquely identified in 2724 environmental samples. These findings suggest novel functional roles of G > U in COVID-19 symptoms, potentially linked to oxidative stress and reactive oxygen species, while C > U remains the dominant substitution, likely driven by host immune-mediated RNA editing.

Viral escape-inspired framework for structure-guided dual bait protein biosensor design

A generalizable computational platform, CTRL-V (Computational TRacking of Likely Variants), is introduced to design selective binding (dual bait) biosensor proteins. The iteratively evolving receptor binding domain (RBD) of SARS-CoV-2 spike protein has been construed as a model dual bait biosensor which has iteratively evolved to distinguish and selectively bind to human entry receptors and avoid binding neutralizing antibodies. Spike RBD prioritizes mutations that reduce antibody binding while enhancing/ retaining binding with the ACE2 receptor. CTRL-V's through iterative design cycles was shown to pinpoint 20% (of the 39) reported SARS-CoV-2 point mutations across 30 circulating, infective strains as responsible for immune escape from commercial antibody LY-CoV1404. CTRL-V successfully identifies ~70% (five out of seven) single point mutations (371F, 373P, 440K, 445H, 456L) in the latest circulating KP.2 variant and offers detailed structural insights to the escape mechanism. While other data-driven viral escape variant predictor tools have shown promise in predicting potential future viral variants, they require massive amounts of data to bypass the need for physics of explicit biochemical interactions. Consequently, they cannot be generalized for other protein design applications. The publicly availably viral escape data was leveraged as in vivo anchors to streamline a computational workflow that can be generalized for dual bait biosensor design tasks as exemplified by identifying key mutational loci in Raf kinase that enables it to selectively bind Ras and Rap1a GTP. We demonstrate three versions of CTRL-V which use a combination of integer optimization, stochastic sampling by PyRosetta, and deep learning-based ProteinMPNN for structure-guided biosensor design.

Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction

Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions about variant of concerns' (VOCs') landscapes. Here, in this study, we used a new computational algorithm, to predict the mutational pattern in SARS-CoV-2 ssRNA, proteomics, structural identification, mutation stability, and functional correlation, as well as immune escape mechanisms. Interestingly, the sequence diversity of SARS Coronavirus-2 has demonstrated a predominance of G- > A and C- > U substitutions. The best validation statistics are explored here in seven homologous models of the expected mutant SARS-CoV-2 spike ssRNA and employed for hACE2 and IgG interactions. The interactome profile of SARS-CoV-2 spike with hACE2 and IgG revealed a strong correlation between phylogeny and divergence time. The systematic adaptation of SARS-CoV-2 spike ssRNA influences infectivity and immune escape. Data suggest higher propensity of Adenine rich sequence promotes MHC system avoidance, preferred by A-rich codons. Phylogenetic data revealed the evolution of SARS-CoV-2 lineages' epidemiology. Our findings may unveil processes governing the genesis of immune-resistant variants, prompting a critical reassessment of the coronavirus mutation rate and exploration of hypotheses beyond mechanical aspects.

COVID-19 vaccination: 2023 Taiwan Association of Gerontology and Geriatrics (TAGG) consensus statements

The COVID-19 pandemic remains challenging due to the rapid evolution of the severe acute respiratory syndrome coronavirus 2. This article discusses recent findings on high-risk groups for COVID-19 mortality and morbidity, along with consensus statements from the 2023 Taiwan Association of Gerontology and Geriatrics (TAGG) meeting. It examines evidence on viral mutation mechanisms, emerging variants, and their implications for vaccination strategies. The article underscores advanced age, immunocompromised status, chronic medical conditions, occupational exposure, and socioeconomic disparities as significant risk factors for severe COVID-19 outcomes. TAGG's consensus emphasizes robust vaccination promotion, prioritizing elderly, and immunocompromised groups, individualized multi-dose regimens for immunocompromised patients, and simplified clinical guidelines. Discussions on global and regional recommendations for regular, variant-adapted boosters highlight the non-seasonal nature of COVID-19. Key agreements include escalating domestic preparedness, implementing vigorous risk-based vaccination, and adapting global guidelines to local contexts. Given ongoing viral evolution, proactive adjustment of vaccination policies is essential. Scientific consensus, tailored recommendations, and rapid knowledge dissemination are vital for optimizing COVID-19 protection among vulnerable groups in Taiwan. This article seeks to inform clinical practice and public health policy by summarizing expert-driven vaccination perspectives.

Biophysical fitness landscape design traps viral evolution

We introduce foundational principles for designing customizable fitness landscapes for proteins. We focus on crafting antibody ensembles to create evolutionary traps which restrict viral fitness enhancement. By deriving a fundamental relationship between a mutant protein's fitness and its binding affinities to host receptors and antibodies, we show that the fitnesses of different protein sequences are designable, meaning they can be independently tuned by careful choice of antibodies. Given a user-defined target fitness landscape, stochastic optimization can be performed to obtain such an ensemble of antibodies which force the protein to evolve according to the designed target fitness landscape. We conduct in silico serial dilution experiments using microscopic chemical reaction dynamics to simulate viral evolution and validate the fitness landscape design. We then apply the design protocol to control the relative fitnesses of two SARS-CoV-2 neutral genotype networks while ensuring absolute fitness reduction. Finally, we introduce an iterative design protocol which consistently discovers better vaccination target sequences, generating antibodies that restrict the post-vaccination fitness growth of escape variants while simultaneously suppressing wildtype fitness. Biophysical fitness landscape design thus opens the door to prescient vaccine, antibody, and peptide design, thinking several steps ahead of pathogen evolution.

Diversity, Complexity, and Challenges of Viral Infectious Disease Data in the Big Data Era: A Comprehensive Review

Viral infectious diseases, characterized by their intricate nature and wide-ranging diversity, pose substantial challenges in the domain of data management. The vast volume of data generated by these diseases, spanning from the molecular mechanisms within cells to large-scale epidemiological patterns, has surpassed the capabilities of traditional analytical methods. In the era of artificial intelligence (AI) and big data, there is an urgent necessity for the optimization of these analytical methods to more effectively handle and utilize the information. Despite the rapid accumulation of data associated with viral infections, the lack of a comprehensive framework for integrating, selecting, and analyzing these datasets has left numerous researchers uncertain about which data to select, how to access it, and how to utilize it most effectively in their research.This review endeavors to fill these gaps by exploring the multifaceted nature of viral infectious diseases and summarizing relevant data across multiple levels, from the molecular details of pathogens to broad epidemiological trends. The scope extends from the micro-scale to the macro-scale, encompassing pathogens, hosts, and vectors. In addition to data summarization, this review thoroughly investigates various dataset sources. It also traces the historical evolution of data collection in the field of viral infectious diseases, highlighting the progress achieved over time. Simultaneously, it evaluates the current limitations that impede data utilization.Furthermore, we propose strategies to surmount these challenges, focusing on the development and application of advanced computational techniques, AI-driven models, and enhanced data integration practices. By providing a comprehensive synthesis of existing knowledge, this review is designed to guide future research and contribute to more informed approaches in the surveillance, prevention, and control of viral infectious diseases, particularly within the context of the expanding big-data landscape.

Fc-Modified Antibody in Hospitalized Severe COVID-19 Patients

Background: Hospitalized patients with severe COVID-19 are at high risk of clinical deterioration. Methods: A global, randomized, double-blinded, and placebo-controlled phase II trial that investigated the clinical efficacy of SCTA01, an Fc-modified monoclonal antibody, in patients hospitalized with severe COVID-19 during the Delta variant wave was performed. The primary outcome was time to clinical improvement up to Day 29. Secondary outcomes measured the all-cause mortality rate up to Day 29, time to SARS-CoV-2 RNA negativity up to Day 29, and the number of antibody-dependent enhancements. Results: From 27 March 2021, to 11 February 2022, 102 hospitalized adults with severe COVID-19 received a single intravenous infusion of SCTA01 15 mg/kg or 50 mg/kg or placebo in a 1:1:1 ratio. The median time to clinical improvement in the SCTA01 group was numerically shorter than that in the placebo group; however, the between group difference was statistically non-significant (SCTA01 15 mg/kg vs. placebo, HR 0.99, 95% CI 0.55-1.77, p = 0.742; SCTA01 50 mg/kg vs. placebo, HR 1.07, 95% CI 0.61-1.88, p = 0.095). The median time to achieve a negative SARS-CoV-2 status was shorter in the SCTA01 15 mg/kg group (14.0 days vs. 27.0 days) but not in the SCTA01 50 mg/kg group (28.0 days vs. 27.0 days) compared to the placebo group. Adverse events were comparable across all groups, and no treatment-related serious adverse event or antibody-dependent enhancement was reported. Conclusions: The Fc-modified antibody was safe but lacked significant clinical efficacy in vivo, likely due to the SARS-CoV-2 viral mutation.

Monitoring the Emergence of SARS-CoV-2 VOCs in Wastewater and Clinical Samples-A One-Year Study in Santiago de Compostela (Spain)

Wastewater surveillance has become a valuable tool to monitor the emergence of SARS-CoV-2 variants of concern (VOCs) at the community level. In this study, we aimed to evaluate the presence of Alpha (B.1.1.7), Beta (B.1.351), Delta (B.1617.2), and Omicron (B.1.1.529) VOCs in samples from the inlet of a wastewater treatment plant (WWTP) as well as from two different sewer interceptors (SI-1 and SI-2) from the urban sewage system in Santiago de Compostela (Galicia, NW of Spain) throughout 2021 and January 2022. For this purpose, detection and quantification of the four VOCs was performed using four duplex SARS-CoV-2 allelic discrimination RT-qPCR assays, targeting the S-gene. An N1 RT-qPCR gene assay was used as a reference for the presence of SARS-CoV-2 RNA in wastewater samples. All VOCs were detected in wastewater samples. Alpha, Beta, Delta, and Omicron VOCs were detected in 45.7%, 7.5%, 66.7%, and 72.7% of all samples, respectively. Alpha VOC was dominant during the first part of the study, whereas Delta and Omicron detection peaks were observed in May-June and December 2021, respectively. Some differences were observed among the results obtained for the two city sectors studied, which could be explained by the differences in the characteristics of the population between them. Wastewater-based epidemiology allowed us to track the early circulation and emergence of SARS-CoV-2 variants at a local level, and our results are temporally concordant with clinical data and epidemiological findings reported by the health authorities.

SIV/SARS-CoV-2 co-infection in rhesus macaques impacts viral shedding, host immunity, the microbiome, and viral evolution

People living with HIV (PLWH) have an increased risk of severe COVID-19, including prolonged viral shedding and emergence of mutations. To investigate the simian immunodeficiency virus (SIV) macaque model for HIV/SARS-CoV-2 co-infection, seven SIV+ rhesus macaques were co-infected with SARS-CoV-2. COVID-19 in all macaques was mild. SARS-CoV-2 replication persisted in the upper, but not the lower respiratory tract for 14 days post-infection. Animals showed impaired generation of anti-SARS-CoV-2 antibodies and T-cells. Animals also displayed transient changes in microbial communities in the upper airway and gastrointestinal tract. Evidence of SARS-CoV-2 evolution was observed in the upper respiratory tract. This study demonstrates that SIV/SARS-CoV-2 co-infection in rhesus macaques recapitulates aspects of COVID-19 in PLWH. We show that SIV impairs anti-SARS-CoV-2 immunity, potentially leading to prolonged viral shedding, altered pathogenesis, and viral evolution. This highlights the importance of HIV status in COVID-19 and supports the use of this model for HIV/SARS-CoV-2 co-infection.

Impact in the humoral and cellular immune response to SARS-CoV-2 variants after primary vaccination with AZD1222/COVISHIELD protocol in healthy adults

SARS-CoV-2 emerged rapidly as a pandemic, leading to the urgent development and authorization for the use of several vaccines, with questions relating to immunogenicity in previously infected people or to virus variants. As such, we sought to determine the humoral and cellular immune response of healthy adults to distinct SARS-CoV-2 variants upon AZD1222/COVISHIELD vaccination, using chemiluminescence (CMIA), neutralizing antibody (PRNT) and analysis of activation-induced marker (AIM) by flow cytometry, respectively. We enrolled 75 volunteers, including 26 individuals previously infected with SARS-CoV-2. Our findings demonstrated that AZD1222 vaccine induced increased levels of SARS-CoV-2-specific antibodies after two-dose vaccination scheme, as detected by CMIA (mean = 49 BAU/mL to 743 BAU/mL) and PRNT (GMT = 3, 95 % CI 2-4, to 19, 11-34). After vaccination, all volunteers presented detectable antibodies by CMIA while only 64 % presented positive PRNT. Seroconversion rates were 91 % and 48 % by CMIA and 59 % by PRNT after the first and second dose, respectively. The PRNT to Delta variant demonstrated lower titers as compared to Wuhan-like and a seroconversion of 57 %. Although by CMIA all volunteers were classified as high responders, some volunteers showed no response by PRNT and AIM. In general, previously infected volunteers had higher post-vaccination antibody titers after each dose. CD4+ T cell response was generally higher than CD8+ T cells for all variants. Overall, we observed that AZD1222 vaccination induced cross-reactivity to SARS-CoV-2 variants, in both cellular and humoral responses. During volunteer follow-up, we observed that the elevated antibody titers are lasting and were incremented by the first booster. In conclusion, our findings showed that AZD1222 vaccine was able to induce a robust immune response upon primary immunization, with cross-reactivity for the Delta VOC.

SARS-CoV-2 Genetic Variants Identified in Selected Regions of Ethiopia Through Whole Genome Sequencing: Insights from the Fifth Wave of COVID-19

BACKGROUND

The COVID-19 pandemic highlighted SARS-CoV-2 variants with increased transmissibility and immune evasion. In Ethiopia, where cases surged, the understanding of the virus's dynamics was limited. This study analyzed SARS-CoV-2 variants during the fifth wave, crucial for guiding vaccines, therapeutics, diagnostics, and understanding disease severity.

METHOD

From June to August 2022, 150 SARS-CoV-2-positive samples were randomly selected from the Ethiopian Public Health Institute repository. Sixty-three high-quality genome sequences were analyzed.

RESULTS

Of the 63 sequences, 70% were from males and 30% from females, with a median age of 34. Omicron dominated (97%, 61/63), primarily clade 22A (64%, 40/63), followed by 22B (18%, 11/63) and 21K (14%, 9/63). Delta accounted for 3.2% (2/63). Omicron was identified in all (25) vaccinated study participants. Ethiopian sequences showed limited evolutionary divergence and lower genetic diversity compared to global sequences.

CONCLUSION

Omicron was the predominant variant during Ethiopia's fifth wave, indicating recent community transmission. Despite minor genetic diversity differences, ongoing surveillance remains critical for tracking variants and informing public health interventions.

CAR-NK cell therapy: a potential antiviral platform

Viral infections persist as a significant cause of morbidity and mortality worldwide. Conventional therapeutic approaches often fall short in fully eliminating viral infections, primarily due to the emergence of drug resistance. Natural killer (NK) cells, one of the important members of the innate immune system, possess potent immunosurveillance and cytotoxic functions, thereby playing a crucial role in the host's defense against viral infections. Chimeric antigen receptor (CAR)-NK cell therapy has been developed to redirect the cytotoxic function of NK cells specifically towards virus-infected cells, further enhancing their cytotoxic efficacy. In this manuscript, we review the role of NK cells in antiviral infections and explore the mechanisms by which viruses evade immune detection. Subsequently, we focus on the optimization strategies for CAR-NK cell therapy to address existing limitations. Furthermore, we discuss significant advancements in CAR-NK cell therapy targeting viral infections, including those caused by severe acute respiratory syndrome coronavirus 2, human immunodeficiency virus, hepatitis B virus, human cytomegalovirus, and Epstein-Barr virus.

Genetic Variations of Three Kazakhstan Strains of the SARS-CoV-2 Virus

Prompt determination of the etiological agent is important in an outbreak of pathogens with pandemic potential, particularly for dangerous infectious diseases. Molecular genetic methods allow for arriving at an accurate diagnosis, employing timely preventive measures, and controlling the spread of the disease-causing agent. In this study, whole-genome sequencing of three SARS-CoV-2 strains was performed using the Sanger method, which provides high accuracy in determining nucleotide sequences and avoids errors associated with multiple DNA amplification. Complete nucleotide sequences of samples, KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021 were obtained, with sizes of 29.751 bp, 29.815 bp, and 29.840 bp, respectively. According to the COVID-19 Genome Annotator, 127 mutations were detected in the studied samples compared to the reference strain. The strain KAZ/Britain/2021 contained 3 deletions, 7 synonymous mutations, and 27 non-synonymous mutations, the second strain KAZ/B1.1/2021 contained 1 deletion, 5 synonymous mutations, and 31 non-synonymous mutations, and the third strain KAZ/Delta020/2021 contained 1 deletion, 5 synonymous mutations, and 37 non-synonymous mutations, respectively. The variations C241T, F106F, P314L, and D614G found in the 5' UTR, ORF1ab, and S regions were common to all three studied samples, respectively. According to PROVEAN data, the loss-of-function mutations identified in strains KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021 include 5 mutations (P218L, T716I, W149L, R52I, and Y73C), 2 mutations (S813I and Q992H), and 8 mutations (P77L, L452R, I82T, P45L, V82A, F120L, F120L, and R203M), respectively. Phylogenetic analysis showed that the strains studied (KAZ/Britain/2021, KAZ/B1.1/2021, and KAZ/Delta020/2021) belong to different SARS-CoV-2 lineages, which are closely related to samples from Germany (OU141323.1 and OU365922.1), Mexico (OK432605.1), and again Germany (OV375251.1 and OU375174.1), respectively. The nucleotide sequences of the studied SARS-CoV-2 virus strains were registered in the Genbank database with the accession numbers: ON692539.1, OP684305, and OQ561548.1.