SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Interference between SARS-CoV-2 and influenza B virus during coinfection is mediated by induction of specific interferon responses in the lung epithelium

Coinfections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza virus have represented a major health concern since the beginning of the COVID-19 pandemic. The continued spread and constant emergence of new SARS-CoV-2 variants mean that cocirculation and coinfection with seasonal respiratory viruses will continue. Despite the considerable contribution of influenza B virus (IBV) infections to global disease burdens, its interactions with SARS-CoV-2 remain largely unstudied. In this study, we sequentially coinfected lung epithelial cells with representative SARS-CoV-2 variants and IBV strains. We found that prior infection with IBV impaired SARS-CoV-2 D614G, Delta and Omicron BA.1 replication, but did not affect replication of the more recent Omicron EG.5.1 variant. We additionally show that pre-infection with SARS-CoV-2 reduces live attenuated influenza vaccine (LAIV) replication, suggesting vaccine effectiveness in children carrying SARS-CoV-2 pre-infections can be negatively impacted in coinfection. Both SARS-CoV-2 and IBV induced strong type III interferon (IFN) responses, whereas SARS-CoV-2 drove type I IFN production not seen in IBV infection, suggesting viral interference through specific IFN responses. Treatment with innate immune response inhibitors BX795 and Ruxolitinib abrogated viral interference between IBV and SARS-CoV-2 in coinfection, demonstrating that IFN-stimulated gene (ISG) responses play a vital role in viral interference. More specifically, we show that the magnitude and timing of ISG expression, triggered by the primary infecting virus in sequential coinfection, facilitates viral interference between IBV and SARS-CoV-2.

Differential clearance rate of proteins encoded on a self-amplifying mRNA COVID-19 vaccine in muscle and lymph nodes

ARCT-154, a recently approved self-amplifying mRNA (saRNA) vaccine for SARS-CoV-2, has shown superior induction and prolonged maintenance of neutralizing antibodies compared to the conventional mRNA vaccine BNT162b2. However, the scientific evidence explaining this superiority remained elusive. Hence, we explored the temporal changes in spike protein and replicase components following a single dose of ARCT-154 vaccination in mice. The encoded spike protein reached its highest level approximately 3 days after vaccination and quickly disappeared from the rectus femoris muscle, the injection site. Although the spike protein levels also peaked at an early time point in the lymph nodes, it remained detectable 28 days after the vaccination and then disappeared by 44 days after the vaccination. Expression of nsP1, nsP2 and nsP4 was observed in the injected muscle and/or the lymph nodes for up to 15 days post-vaccination. Data were analyzed using unpaired two-tailed Mann-Whitney U-tests. These data suggest that prolonged expression of spike proteins in lymph nodes may, if not entirely, be responsible for the induction of higher and prolonged levels of neutralizing antibodies by the saRNA vaccine.

The role of DAMP cytotoxic fractions in the immune markers' disruption in patients with urgent surgical pathology and against the background of post-COVID-19 syndrome

BACKGROUND

As a result of the SARS-CoV-2 pandemic, various population groups were formed that had acute and asymptomatic COVID-19. A survey in these groups revealed with equal frequency an asthenic symptom complex, the so-called post-COVID-19 syndrome (PCS). The frequency of urgent surgical pathology against the background of PCS and structural and functional disorders of various organs was increased. The aim - to study the dynamics of immunoresistance factors changes in patients with urgent surgical pathology that developed against the background of PCS and to identify pathogenic markers of the severe course and the risk of mortality.

MATERIALS AND METHODS

To examine patients with PCS and urgent cardiovascular (n = 103) and abdominal (n = 106) pathology we used the following methods: fluorescence microscopy, confocal microscopy, flow cytometry, spectrophotometry, ELISA.

RESULTS

We revealed a temporal dependence of immune dysfunction in patients with a comorbid course of urgent surgical pathology and PCS. The nature of the DAMP (damage-associated molecular patterns) cytotoxic fractions ratio was associated with certain changes in innate and adaptive immunity factors, severity of the condition and risk of mortality. At the first stage (2020-2021), patients with PCS has disorders of the humoral and cellular components of innate immunity against the background of an increase in the oligopeptide and peptide DAMP fractions. At the second stage (2022-2024) of PCS development, changes in innate as well as adaptive immunity were observed against the background of an increase in the cytotoxic oligonucleotide DAMP fraction (mortality was 17.3%).

CONCLUSIONS

The identified markers of impaired immunoresistance in cardiovascular and abdominal urgent pathology can be used to select targeted therapy tactics.

Upstream SARS-CoV-2 variant surveillance at Breede Valley municipality using wastewater-based epidemiology

The COVID-19 pandemic has strained economies and health systems worldwide, particularly in low- and middle-income countries, where limited resources were further stretched by the crisis. In response, innovative strategies like wastewater-based epidemiology (WBE) have emerged as cost-effective and efficient alternatives to traditional surveillance. In Breede Valley Municipality, Western Cape, South Africa, weekly monitoring of wastewater treatment plants (WWTPs) showed consistently high SARS-CoV-2 viral loads in Rawsonville, especially of the Delta variant (AY.32 and B.1.617.2), despite Omicron's dominance in other regions. Total RNAs of all samples were extracted using the Qiagen RNeasy PowerSoil Kit, from which both RT-qPCR and whole genome sequencing were performed to determine the amount of SARS-CoV-2 RNA and their variants, respectively. Rawsonville had the highest median viral load, measured in genome copies per millilitre (gc/mL) at 2211 gc/mL, compared to Worcester (1790 gc/mL), De Doorns (1438 gc/mL), and Touws River (1253 gc/mL). Neighbourhoods in Rawsonville (RV) upstream of the main WWTP, where manholes were sampled, indicated that the suburban manhole on Grey Street (RV_G, 2347 gc/mL) and the peri-urban manhole on Rugby Street (RV_R, 714 gc/mL) were the primary contributors to the SARS-CoV-2 viral load. In contrast, the manhole near public toilets (RV_P, 470 gc/mL) had the lowest viral load. Notably, sequencing data indicated that only Omicron (BA.5) was detected in upstream sites RV_G and RV_R when Deltacron was present in Rawsonville, suggesting complex transmission dynamics requiring further study. These findings underscore the importance of targeted upstream surveillance to trace variant emergence and inform public health interventions.

SARS-CoV-2 spike protein: structure, viral entry and variants

Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been a devastating global pandemic for 4 years and is now an endemic disease. With the emergence of new viral variants, COVID-19 is a continuing threat to public health despite the wide availability of vaccines. The virus-encoded trimeric spike protein (S protein) mediates SARS-CoV-2 entry into host cells and also induces strong immune responses, making it an important target for development of therapeutics and vaccines. In this Review, we summarize our latest understanding of the structure and function of the SARS-CoV-2 S protein, the molecular mechanism of viral entry and the emergence of new variants, and we discuss their implications for development of S protein-related intervention strategies.

SARS-CoV-2 variants retain high airborne transmissibility by different strategies

SARS-CoV-2 variants evolve to balance immune evasion and airborne transmission, yet the mechanisms remain unclear. In hamsters, first-wave, Alpha, and Delta variants transmitted efficiently via aerosols. Alpha emitted fewer viral particles than first-wave virus but compensated with a lower infectious dose (ID50). Delta exhibited higher airborne emission but required a higher ID50. A fall in airborne emission of infectious Delta virus over time after infection correlated with a decrease in its infectivity to RNA ratio in nasal wash and a decrease in contagiousness to sentinel animals. Omicron subvariants (BA.1, EG.5.1, BA.2.86, JN.1) displayed varying levels of airborne transmissibility, partially correlated with airborne emissions. Mutations in the non-spike genes contributed to reduced airborne transmissibility, since recombinant viruses with spike genes of BA.1 or JN.1 and non-spike genes from first-wave virus are more efficiently transmitted between hamsters. These findings reveal distinct viral strategies for maintaining airborne transmission. Early assessment of ID50 and aerosolized viral load may help predict transmissibility of emerging variants.

A Genomic Surveillance Circuit for Emerging Viral Pathogens

Genomic surveillance has been crucial in monitoring the evolution and spread of SARS-CoV-2. In Andalusia (Spain), a coordinated genomic surveillance circuit was established to systematically sequence and analyze viral genomes across the region. This initiative organizes sample collection through 27 hospitals, which act as regional hubs within their respective health districts. Sequencing is performed at three reference laboratories, with downstream data analysis and reporting centralized at a bioinformatics platform. From 2021 to 2025, over 42,500 SARS-CoV-2 genomes were sequenced, enabling the identification of major variants and their evolutionary dynamics. The circuit tracked the transition from Alpha and Delta to successive Omicron waves, including both recombinant and non-recombinant clades. The integration of genomic and epidemiological data facilitated rapid variant detection, outbreak investigation, and public health decision making. This surveillance framework at a regional granularity demonstrates the feasibility of large-scale sequencing within a decentralized healthcare system and has expanded to monitor other pathogens, reinforcing its value for epidemic preparedness. Continued investment in genomic surveillance is critical for tracking viral evolution, guiding interventions, and mitigating future public health threats.

Cathepsins in cellular entry of human pathogenic viruses

In the life cycle of a virus, host cell entry represents the first step that a virus needs to undertake to gain access to the cell interior for replication. Once a virus attaches itself to its target cell receptor, it activates endogenous cellular responses and exploits host cell factors for its internalization, fusion, and genome release. Among the host factors that critically contribute to the viral entry processes are cathepsins, which are the most abundant endo/lysosomal proteases with diverse physiological functions. This review summarizes previous findings on how different cathepsins contribute to the host cell entry of human pathogenic viruses, focusing on their specific roles in the entry processes of both enveloped and non-enveloped RNA viruses. A comprehensive knowledge of the functions of different cathepsins in viral entry will provide valuable insights into the molecular mechanisms underlying viral infections and can be useful in the development of new antiviral strategies.

Integrated renin angiotensin system dysregulation and immune profiles predict COVID-19 disease severity in a South African cohort

Renin-angiotensin system (RAS) dysregulation is an important component of the complex pathophysiology of SARS-CoV-2 and other coronavirus infections. Thus, angiotensin-converting enzyme 2 (ACE2), the entry receptor and key to the alternative RAS, was proposed as a severity/prognostic biomarker for risk-stratification. However, experimental RAS data from diverse cohorts are limited, particularly analyses integrating RAS with immune biomarkers. Participants (n = 172) in Cape Town were sampled longitudinally (including a recovery timepoint [> 3-month]), across WHO asymptomatic to critical severity. Using fluorometric assays and LC-MS/MS RAS Fingerprinting®, results show serum ACE1 activity significantly decreases with increasing COVID-19 severity (P < 0.01) and mortality (P < 0.05), while increased ACE2 activity is associated with worse severity (P < 0.01). Neither enzyme activity correlates with viral load proxy or nasal ACE mRNA levels. ACE1 and ACE2 activities were the most effective severity biomarkers compared to 96 established immune markers obtained via proximity extension assay, as demonstrated by principal component analysis. A multivariate variable selection model using random forest classification identified biomarkers discriminating COVID-19 severity (AUC = 0.82), the strongest being HGF, EN-RAGE, cathepsin L. Adding ACE1 activity and anti-SARS-CoV-2 antibody titres improved differentiation between ambulatory and hospitalised participants. Notably, RAS dysregulation has unique severity associations in coronavirus infections with implications for treatment and pathophysiological mechanisms.

From N-0385 to N-0920: Unveiling a Host-Directed Protease Inhibitor with Picomolar Antiviral Efficacy against Prevalent SARS-CoV-2 Variants

The worldwide spread of new SARS-CoV-2 variants emphasizes the need to diversify existing therapeutic strategies. TMPRSS2, a host protease crucial for SARS-CoV-2 entry, has garnered significant research attention as a potential target for therapeutic intervention. Here, we optimized N-0385, a previously reported TMPRSS2 ketobenzothiazole-based peptidomimetic inhibitor, by screening 135 derivatives for target affinity and antiviral potency. Among the top candidates, N-0695 exhibited low nanomolar Ki values against three TTSPs associated with respiratory virus entry: TMPRSS2, matriptase, and TMPRSS13. Notably, N-0920 demonstrated exceptional potency in reducing SARS-CoV-2 variants EG.5.1 and JN.1 entry in Calu-3 cells, representing the first in cellulo picomolar inhibitor with EC50 values of 300 and 90 pM, respectively. Additionally, molecular modeling provided insights into the binding interactions between the compounds and their targets. This study underscores the effectiveness of our screening approach in refining an existing peptidomimetic scaffold to enhance selectivity and antiviral activity.

Cross-variant immune shield: computational multiepitope vaccine design against B.617.2 to Omicron sub-lineages in SARS-CoV-2

The COVID-19 pandemic had a profound impact on global health. This study focuses on an in-depth analysis of the structural proteins (Spike (S), Nucleocapsid (N), Membrane (M), and Envelope (E) protein) of SARS-CoV-2 and its variants, aiming to develop a multiepitope vaccine construct that targets the virus independently of its variants. The analysis began by examining genetic variations in viral proteins relative to the reference strain Wuhan-Hu2, particularly in the S, M, N, and E proteins. T-cell epitope predictions for MHC Class-I and Class-II binding were conducted, shedding light on potential cytotoxic and helper T lymphocyte recognition. Identification of linear B-cell epitopes laid the groundwork for antibody-based humoral immune responses. The safety and efficacy of these epitopes were assessed for antigenicity, allergenicity, toxicity, immunogenicity, and conservancy. Population coverage analysis indicated promising global effectiveness of the designed vaccine construct. By incorporating 28 epitopes, we validated that was designed vaccine construct for stability through structural analysis. Molecular dynamics simulations and docking studies revealed its robust interaction with Toll-like receptor 4 (TLR4). Immune simulation studies suggested that the vaccine construct could induce a potent immune response by enhancing antibody titers, B-cell proliferation, memory cell development, and activation of T cells and natural killer cells upon administration. This comprehensive approach offers a promising multiepitope vaccine against SARS-CoV-2, with the potential for broad global coverage and strong immunogenicity. Further experimental validation holds the prospect of introducing a novel candidate vaccine to aid in the ongoing battle against the COVID-19 pandemic.

CRISPR-Cas9 genetic screens reveal regulation of TMPRSS2 by the Elongin BC-VHL complex

The TMPRSS2 cell surface protease is used by a broad range of respiratory viruses to facilitate entry into target cells. Together with ACE2, TMPRSS2 represents a key factor for SARS-CoV-2 infection, as TMPRSS2 mediates cleavage of viral spike protein, enabling direct fusion of the viral envelope with the host cell membrane. Since the start of the COVID-19 pandemic, TMPRSS2 has gained attention as a therapeutic target for protease inhibitors which would inhibit SARS-CoV-2 infection, but little is known about TMPRSS2 regulation, particularly in cell types physiologically relevant for SARS-CoV-2 infection. Here, we performed an unbiased genome-wide CRISPR-Cas9 library screen, together with a library targeted at epigenetic modifiers and transcriptional regulators, to identify cellular factors that modulate cell surface expression of TMPRSS2 in human colon epithelial cells. We find that endogenous TMPRSS2 is regulated by the Elongin BC-VHL complex and HIF transcription factors. Depletion of Elongin B or treatment of cells with PHD inhibitors resulted in downregulation of TMPRSS2 and inhibition of SARS-CoV-2 infection. We show that TMPRSS2 is still utilised by SARS-CoV-2 Omicron variants for entry into colonic epithelial cells. Our study enhances our understanding of the regulation of endogenous surface TMPRSS2 in cells physiologically relevant to SARS-CoV-2 infection.

Capture of fusion-intermediate conformations of SARS-CoV-2 spike requires receptor binding and cleavage at either the S1/S2 or S2' site

Although structures of pre- and post-fusion conformations of SARS-CoV-2 spikes have been solved by cryo-electron microscopy, the transient spike conformations that mediate virus fusion with host cell membranes remain poorly understood. In this study, we used a peptide fusion inhibitor corresponding to the heptad repeat 2 (HR2) in the S2 transmembrane subunit of the spike to investigate fusion-intermediate conformations that involve exposure of the highly conserved heptad repeat 1 (HR1). The HR2 peptide disrupts the assembly of the HR1 and HR2 regions of the spike, which form a six-helix bundle during the transition to the post-fusion conformation. We show that binding of the spike S1 subunit to ACE2 is sufficient to induce conformational changes that allow S1 shedding and enable the HR2 peptide to bind to fusion-intermediate conformations of S2 and inhibit membrane fusion. When TMPRSS2 is also present, the peptide captures an S2' fusion intermediate though the proportion of the S2' intermediate relative to the S2 intermediate is lower in Omicron variants than pre-Omicron variants. In spikes lacking the natural S1/S2 furin cleavage site, ACE2 binding alone is not sufficient for trapping fusion intermediates, but the presence of ACE2 and TMPRSS2 allows peptide trapping of an S2' intermediate. These results indicate that, in addition to ACE2 engagement, at least one spike cleavage is needed for unwinding S2 into an HR2 peptide-sensitive, fusion-intermediate conformation. Our findings elucidate fusion-intermediate conformations of SARS-CoV-2 spike variants that expose conserved sites on spike that could be targeted by inhibitors or antibodies.

Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City

The COVID-19 pandemic in New York City (NYC) was characterized by marked disparities in disease burdens across neighborhoods. Accurate neighborhood-level forecasts are critical for planning more equitable resource allocation to reduce health inequalities; however, such spatially high-resolution forecasts remain scarce in operational use. In this study, we analyze aggregated foot traffic data derived from mobile devices to measure the connectivity among 42 NYC neighborhoods driven by various human activities such as dining, shopping, and entertainment. Using real-world time-varying contact patterns in different place categories, we develop a parsimonious behavior-driven epidemic model that incorporates population mixing, indoor crowdedness, dwell time, and seasonality of virus transmissibility. We fit this model to neighborhood-level COVID-19 case data in NYC and further couple this model with a data assimilation algorithm to generate short-term forecasts of neighborhood-level COVID-19 cases in 2020. We find differential contact patterns and connectivity between neighborhoods driven by different human activities. The behavior-driven model supports accurate modeling of neighborhood-level SARS-CoV-2 transmission throughout 2020. In the best-fitting model, we estimate that the force of infection (FOI) in indoor settings increases sublinearly with crowdedness and dwell time. Retrospective forecasting demonstrates that this behavior-driven model generates improved short-term forecasts in NYC neighborhoods compared to several baseline models. Our findings indicate that aggregated foot-traffic data for routine human activities can support neighborhood-level COVID-19 forecasts in NYC. This behavior-driven model may be adapted for use with other respiratory pathogens sharing similar transmission routes.

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.

Coronavirus disease 2019 (COVID-19) in children: Evolving epidemiology, immunology, symptoms, diagnostics, treatment, post-COVID-19 conditions, prevention strategies, and future directions

The epidemiology of coronavirus disease 2019 (COVID-19) in children has evolved throughout the pandemic, with initially low infection rates rising significantly as a result of the emergence of the more transmissible Omicron variant. Adolescents, children from ethnic minorities and lower-income households, and those with obesity are at increased risk of contracting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The immune response in children leads to milder symptoms compared to adults, with fever and cough being most frequent; tough symptoms vary by SARS-CoV-2 variant and age. Diagnostic methods to confirm current or past infection include reverse transcription PCR, rapid antigen tests, and serology. Treatment is mainly supportive, with antivirals and glucocorticoids reserved for severe cases. While serious conditions like multisystem inflammatory syndrome in children and other post-COVID-19 conditions are rare, they require careful management. Vaccination has proven effective in reducing severe disease and protecting against post-COVID-19 conditions. Continued surveillance, including wastewater monitoring and universal or pooled testing, remains crucial for controlling community spread. Key questions remain regarding the duration and quality of immunity after reinfection or vaccination, the impact of coinfections, and optimal treatment protocols for different pediatric populations.

Viral and host factors associated with SARS-CoV-2 disease severity in Georgia, USA

While SARS-CoV-2 vaccines have shown strong efficacy, the continued emergence of new viral variants raises concerns about the ongoing and future public health impact of COVID-19, especially in locations with suboptimal vaccination uptake. We investigated viral and host factors, including vaccination status, that were associated with SARS-CoV-2 disease severity in a setting with low vaccination rates. We analyzed clinical and demographic data from 1,957 individuals in the state of Georgia, USA, coupled with viral genome sequencing from 1,185 samples. We found no specific mutations associated with disease severity. Compared to those who were unvaccinated, vaccinated individuals experienced less severe SARS-CoV-2 disease, and the effect was similar for both variants. Vaccination within the prior 3-9 months was associated with decreased odds of moderate disease, severe disease, and death. Older age and underlying health conditions, especially immunosuppression and renal disease, were associated with increased disease severity. Overall, this study provides insights into the impact of vaccination status, variants/mutations, and clinical factors on disease severity in SARS-CoV-2 infection when vaccination rates are low. Understanding these associations will help refine and reinforce messaging around the crucial importance of vaccination in mitigating the severity of SARS-CoV-2 disease.

Characteristics and predictors of severe outcomes of COVID-19 cases presenting to the emergency department of a major Australian referral hospital: A record linkage study

OBJECTIVE

To describe the characteristics, outcomes and predictors of a severe outcome of patients presenting with a SARS-CoV-2 infection to the ED of a major urban referral hospital in New South Wales, Australia, from January 2020 through February 2022.

METHODS

Linked healthcare and death registration records were used and included any person assigned a diagnosis potentially related to an acute respiratory infection in the ED and that had a linked positive COVID-19 detection. Logistic regression was used to determine predictors of a severe outcome (ICU admission or death) within 28 days.

RESULTS

Of 2081 included COVID-19 patients, 238 (11.4%) had a severe outcome within 28 days of arrival at the ED. Among adults, the odds of a severe outcome increased with age, although the rate of increase in odds within age groups was statistically significant only in 30-64-year-olds (4% per year of age; confidence interval [CI] 2-6). Ambulance arrival (odds ratio [OR] 2.85; CI 1.76-4.78), higher triage urgency (category 1 or 2 compared with 4 or 5: OR 8.63; CI 4.41-18.12), and presentation during the pre-Delta (OR 6.18; CI 3.59-10.66) and Delta (OR 3.64; 95% CI 2.49-5.35) variant periods (compared with Omicron) were independently associated with increased risk of a severe outcome.

CONCLUSION

Age, ambulance arrival, higher triaged urgency, and presentation earlier in the pandemic were predictors of a severe COVID-19 outcome. Aged care measures and prioritising vaccination of older persons and aged care workers may have reduced severe outcomes in the elderly.

Structural and Mechanistic Insights into the Main Protease (Mpro) Dimer Interface Destabilization Inhibitor: Unveiling New Therapeutic Avenues against SARS-CoV-2

SARS-CoV-2 variant recurrence has emphasized the imperative prerequisite for effective antivirals. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication, making it one of the prime and promising antiviral targets. Mpro features several druggable sites, including active sites and allosteric sites near the dimerization interface, that regulate its catalytic activity. This study identified six highly efficacious antiviral SARS-CoV-2 compounds (WIN-62577, KT185, bexarotene, ledipasvir, diacerein, and simepervir) using structure-based virtual screening of compound libraries against Mpro. Using SPR and ITC, the binding of selected inhibitory compounds to the target Mpro was validated. The FRET-based protease assay demonstrated that the identified molecules effectively inhibit Mpro with IC50 values in the range from 0.64 to 11.98 μM. Additionally, in vitro cell-based antiviral assays showed high efficacy with EC50 values in the range of 1.51 to 18.92 μM. The crystal structure of the Mpro-minocycline complex detailed the possible inhibition mechanism of minocycline, an FDA-approved antibiotic. Minocycline binds to an allosteric site, revealing residues critical for the loss of protease activity due to destabilization of molecular interactions at the dimeric interface, which are crucial for the proteolytic activity of Mpro. The study suggests that the binding of minocycline to the allosteric site may play a role in Mpro dimer destabilization and direct the rational design of minocycline derivatives as antiviral drugs.

SARS-CoV-2: The Interplay Between Evolution and Host Immunity

The persistence of SARS-CoV-2 infections at a global level reflects the repeated emergence of variant strains encoding unique constellations of mutations. These variants have been generated principally because of a dynamic host immune landscape, the countermeasures deployed to combat disease, and selection for enhanced infection of the upper airway and respiratory transmission. The resulting viral diversity creates a challenge for vaccination efforts to maintain efficacy, especially regarding humoral aspects of protection. Here, we review our understanding of how SARS-CoV-2 has evolved during the pandemic, the immune mechanisms that confer protection, and the impact viral evolution has had on transmissibility and adaptive immunity elicited by natural infection and/or vaccination. Evidence suggests that SARS-CoV-2 evolution initially selected variants with increased transmissibility but currently is driven by immune escape. The virus likely will continue to drift to maintain fitness until countermeasures capable of disrupting transmission cycles become widely available.

RBD-depleted SARS-CoV-2 spike generates protective immunity in cynomolgus macaques

The SARS-CoV-2 pandemic revealed the rapid evolution of circulating strains. This led to new variants carrying mostly mutations within the receptor binding domain, which is immunodominant upon immunization and infection. In order to steer the immune response away from RBD epitopes to more conserved domains, we generated S glycoprotein trimers without RBD and stabilized them by formaldehyde cross-linking. The cryoEM structure demonstrated that SΔRBD folds into the native prefusion conformation, stabilized by one specific cross-link between S2 protomers. SΔRBD was coated onto lipid vesicles, to produce synthetic virus-like particles, SΔRBD-LV, which were utilized in a heterologous prime-boost strategy. Immunization of cynomolgus macaques either three times with the mRNA Comirnaty vaccine or two times followed by SΔRBD-LV showed that the SΔRBD-LV boost induced similar antibody titers and neutralization of different variants, including omicron. Upon challenge with omicron XBB.3, both the Comirnaty only and Comirnaty/SΔRBD-LV vaccination schemes conferred similar overall protection from infection for both the Comirnaty only and Comirnaty/SΔRBD-LV vaccination schemes. However, the SΔRBD-LV boost indicated better protection against lung infection than the Comirnaty strategy alone. Together our findings indicate that SΔRBD is highly immunogenic and provides improved protection compared to a third mRNA boost indicative of superior antibody-based protection.

Management of SARS-CoV-2 Infection-Clinical Practice Guidelines of the Polish Association of Epidemiologists and Infectiologists, for 2025

The first Polish recommendations for the management of COVID-19 were published by the Polish Society of Epidemiologists and Infectiologists (PTEiLChZ) on 31 March 2020, and the last three years ago. The emergence of new SARS-CoV-2 variants, a different course of the disease, as well as new knowledge about therapies and vaccines, requires updating diagnostic, therapeutic, and prophylactic guidelines. Despite the reduction in the threat associated with COVID-19, there is a risk of another epidemic caused by coronaviruses, which was an additional reason for developing a new version of the guidelines. In preparing these recommendations, the Delphi method was used, reaching a consensus after three survey cycles. Compared to the 2022 version, the names of the individual stages of the disease have been changed, adapting them to the realities of clinical practice, and attention was paid to the differences observed in immunosuppressed patients and in children. Some previously recommended drugs have been discontinued, including monoclonal antibodies. In addition, general principles of vaccination were presented, as well as issues related to the post-COVID syndrome.

Protection conferred by SARS-CoV-2 infection across a spectrum of reinfection symptoms and severities

BACKGROUND

SARS-CoV-2 infection is associated with protection against reinfection. This study analysed this protection across different reinfection symptoms and severities, comparing the preomicron and omicron eras.

METHODS

A nationwide, matched, test-negative, case-control study was conducted in Qatar from 5 February 2020 to 12 March 2024. The preomicron analysis used a sample of 509 949 positive and 8 494 782 negative tests, while the omicron analysis included 682 257 positive and 6 904 044 negative tests. Data were sourced from Qatar's national databases for COVID-19 laboratory testing, vaccination, hospitalisation and death.

RESULTS

Effectiveness of preomicron infection against preomicron reinfection was estimated at 80.9% (95% CI: 79.1% to 82.6%) for asymptomatic reinfection, 87.5% (95% CI: 86.1% to 88.9%) for symptomatic reinfection, 97.8% (95% CI: 95.7% to 98.9%) for severe COVID-19 reinfection, 100.0% (95% CI: 97.5% to 100.0%) for critical COVID-19 reinfection and 88.1% (95% CI: 50.3% to 97.2%) for fatal COVID-19 reinfection. For omicron infection against omicron reinfection, the estimates were 46.4% (95% CI: 36.9% to 54.4%) for asymptomatic reinfection, 52.8% (95% CI: 44.4% to 60.0%) for symptomatic reinfection, 100.0% (95% CI: 55.4% to 100.0%) for severe COVID-19 reinfection, 100.0% (95% CI: 15.1% to 100.0%) for critical COVID-19 reinfection, and 75.2% (95% CI: -58.8% to 97.5%) for fatal COVID-19 reinfection. Effectiveness over time since previous infection showed no discernible decline in protection against all forms of reinfection in the preomicron era, but a rapid decline against asymptomatic and symptomatic reinfections in the omicron era.

CONCLUSIONS

A gradient of protection against reinfection is evident, with the highest protection observed against severe forms of COVID-19. Over time, this gradient becomes more pronounced, as protection against asymptomatic and symptomatic reinfections decreases, while protection against severe outcomes remains strong.

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.

Cracking the code of a correlate of protection against SARS-CoV-2 breakthrough infection in cancer patients

The level of protection against SARS-CoV-2 breakthrough infections conferred by the presence of anti-S1 SARS-CoV-2 antibodies (IgGs) in cancer patients is still understudied. This work examines the existence of an anti-S1 immunoglobulin G (IgG) -based correlate of protection (CoP) established by prospectively collected observational data about breakthrough infections with different SARS-CoV-2 variants in a large cohort study with vaccinated cancer patients. 760 cancer patients were longitudinally followed-up, starting before first vaccination until six months after second booster. Anti-S1 SARS-CoV-2 IgGs were quantified in serum samples (N = 2958) and breakthrough infections were monitored using questionnaires, routine COVID-19 testing and medical chart review. A Generalized Estimating Equations approach was used to model the binary infection status as endpoint in relation to anti-S1 IgG titers. It is observed that higher anti-S1 IgG titers correspond to a lower probability of breakthrough infection. For the early pandemic phase, a protective anti-S1 IgG titer above 20.42 BAU/mL was observed. However, with the emergence of the Omicron variant, higher anti-S1 IgG titers are required to be protective, but no clear CoP could be identified.

Molecular dynamics of SARS-CoV-2 omicron variants from Philippine isolates against hesperidin as spike protein inhibitor

SARS-CoV-2 remains a global threat with new sublineages posing challenges, particularly in the Philippines. Hesperidin (HD) is being studied as a potential prophylactic for COVID-19. However, the virus's rapid evolution could alter how HD binds to it, affecting its effectiveness. Here, we study the mutation-induced variabilities of HD dynamics and their effects on molecular energetics in SARS-CoV-2 spike receptor complex systems. We considered eight different point mutations present in the Omicron variant. Root-mean-square deviation and binding energy analysis showed that S477N and Omicron did not eject HD throughout the simulation. Hydrogen bond distribution analysis highlighted the involvement of hydrogen bonding in mutant-HD stabilization, especially for S477N and Omicron. Root-mean-square fluctuation analysis revealed evidence of Y505H destabilization on complex systems, while distal-end loop mutations increased loop flexibility for all models bearing the three mutations. Per-residue energy decomposition demonstrated that Q493R substitution increased HD interaction. Free energy landscape and essential dynamics through principal component analysis provided insights into the conformational subspace distribution of mutant model molecular dynamics trajectories. In conclusion, significant mutations contributed to the HD interaction in different ways. S477N has shown significant binding contributions through favorable ligand interaction, while other mutations contribute via conformational modifications, increased affinity due to sidechain mutations, and increased loop flexibility.

Vaccine Impact Bonds: An Alternative Way of Allocating the Economic Risks of Mass Vaccination Programs

Vaccines can be an appropriate tool for combating pandemics. Accordingly, expectations were high when the first Covid-19 vaccines were administered. However, even though the vaccines have not met these high initial expectations, vaccine manufacturers and their investors were making large profits, while most of the associated economic risks have remained with the taxpaying public. Thus, this paper applies the concept of social impact bonds to mass vaccination programs by conceptualizing vaccine impact bonds (VIBs) as an alternative to the advance purchase agreements (APAs) for Covid-19 vaccines. Rather than rewarding vaccine manufacturers and their investors based on the quantity of doses distributed, VIBs intend to link the real-world vaccine impact to the financial returns of vaccine manufacturers and their investors. This paper indicates that VIBs can theoretically shift the economic risks of mass vaccination programs from the taxpaying public to private investors, thereby aligning commercial and public interests. However, it also identifies several major weaknesses such as the complexity of defining and evaluating the vaccine impact as well as the inherent trade-off between relieving taxpayers (through VIBs) and allowing innovation. As these substantial drawbacks outweigh the theoretical strengths of VIBs, this paper calls for further research in order to identify better alternatives to the Covid-19 vaccine contracts.

Differential protection against SARS-CoV-2 reinfection pre- and post-Omicron

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly evolved over short timescales, leading to the emergence of more transmissible variants such as Alpha and Delta1-3. The arrival of the Omicron variant marked a major shift, introducing numerous extra mutations in the spike gene compared with earlier variants1,2. These evolutionary changes have raised concerns regarding their potential impact on immune evasion, disease severity and the effectiveness of vaccines and treatments1,3. In this epidemiological study, we identified two distinct patterns in the protective effect of natural infection against reinfection in the Omicron versus pre-Omicron eras. Before Omicron, natural infection provided strong and durable protection against reinfection, with minimal waning over time. However, during the Omicron era, protection was robust only for those recently infected, declining rapidly over time and diminishing within a year. These results demonstrate that SARS-CoV-2 immune protection is shaped by a dynamic interaction between host immunity and viral evolution, leading to contrasting reinfection patterns before and after Omicron's first wave. This shift in patterns suggests a change in evolutionary pressures, with intrinsic transmissibility driving adaptation pre-Omicron and immune escape becoming dominant post-Omicron, underscoring the need for periodic vaccine updates to sustain immunity.

Enhanced RNA replication and pathogenesis in recent SARS-CoV-2 variants harboring the L260F mutation in NSP6

The COVID-19 pandemic has been driven by SARS-CoV-2 variants with enhanced transmission and immune escape. Apart from extensive evolution in the Spike protein, non-Spike mutations are accumulating across the entire viral genome and their functional impact is not well understood. To address the contribution of these mutations, we reconstructed genomes of recent Omicron variants with disabled Spike expression (replicons) to systematically compare their RNA replication capabilities independently from Spike. We also used a single reference replicon and complemented it with various Omicron variant Spike proteins to quantify viral entry capabilities in single-round infection assays. Viral entry and RNA replication were negatively correlated, suggesting that as variants evolve reduced entry functions under growing immune pressure on Spike, RNA replication increases as a compensatory mechanism. We identified multiple mutations across the viral genome that enhanced viral RNA replication. NSP6 emerged as a hotspot with a distinct L260F mutation independently arising in the BQ.1.1 and XBB.1.16 variants. Using mutant and revertant NSP6 viral clones, the L260F mutation was validated to enhance viral replication in cells and increase pathogenesis in mice. Notably, this mutation reduced host lipid droplet content by NSP6. Collectively, a systematic analysis of RNA replication of recent Omicron variants defined NSP6's key role in viral RNA replication that provides insight into evolutionary trajectories of recent variants with possible therapeutic implications.

A humanised ACE2, TMPRSS2, and FCGRT mouse model reveals the protective efficacy of anti-receptor binding domain antibodies elicited by SARS-CoV-2 hybrid immunity

BACKGROUND

Despite the importance of vaccination- and infection-elicited antibodies (Abs) to SARS-CoV-2 immunity, current mouse models do not fully capture the dynamics of Ab-mediated immunity in vivo, including potential contributions of the neonatal Fc receptor, encoded by FCGRT.

METHODS

We generated triple knock-in (TKI) mice expressing human ACE2, TMPRSS2, and FCGRT; and evaluated the protective efficacy of anti-SARS-CoV-2 monoclonal Abs (mAbs) and plasma from individuals with immunity elicited by vaccination alone plus SARS-CoV-2 infection-induced (hybrid) immunity.

FINDINGS

A human anti-SARS-CoV-2 mAb harbouring a half-life-extending mutation, but not the wild-type mAb, exhibited prolonged half-life in TKI mice and protected against lung infection with Omicron BA.2, validating the utility of these mice for evaluating therapeutic Abs. Pooled plasma from individuals with hybrid immunity to Delta, but not from vaccinated-only individuals, cleared infectious Delta from the lungs of TKI mice (P < 0.01), even though the two plasma pools had similar Delta-binding and -neutralising Ab titres in vitro. Similarly, plasma from individuals with hybrid Omicron BA.1/2 immunity, but not hybrid Delta immunity, decreased lung infection (P < 0.05) with BA.5 in TKI mice, despite the plasma pools having comparable BA.5-binding and -neutralising titres in vitro. Depletion of receptor-binding domain-targeting Abs from hybrid immune plasma abrogated their protection against infection.

INTERPRETATION

These results demonstrate the utility of TKI mice as a tool for the development of anti-SARS-CoV-2 mAb therapeutics, show that in vitro neutralisation assays do not accurately predict in vivo protection, and highlight the importance of hybrid immunity for eliciting protective anti-receptor-binding domain Abs.

FUNDING

This work was funded by grants from the e-Asia Joint Research Program (N10A650706 and N10A660577 to MLM, in collaboration with SS); the NIH (U19 AI142790-02S1 to EOS and SS and R44 AI157900 to KJ); the GHR Foundation (to SS and EOS); the Overton family (to SS and EOS); the Arvin Gottlieb Foundation (to SS and EOS), the Prebys Foundation (to SS); and the American Association of Immunologists Fellowship Program for Career Reentry (to FASB).

Skin patch delivery of a SARS-CoV-2 spike DNA vaccine produces broad neutralising antibody responses

The ongoing SARS-CoV-2 pandemic continues to be a major health burden globally, especially in resource-limited areas. Continued research into more effective and accessible vaccines is required to reduce the burden of disease. Here, we use an emerging vaccine delivery system, the high-density microarray patch (HD-MAP) to deliver a plasmid DNA vaccine (Delta 6P) encoding for the SARS-CoV-2 spike protein. HD-MAP delivery of this vaccine resulted in robust IgG responses in mice against multiple domains of the spike protein. The cellular response to vaccination was also measured, and comparative analysis showed that relative to intramuscular vaccination, HD-MAP vaccination elicited spike-specific CD4+ T and CD8+ T cell responses that were largely comparable, but the number of polyfunctional CD4+ T cells was higher in the HD-MAP group. Collectively, this work suggests that HD-MAP delivery of the Delta 6P vaccine is effective against SARS-CoV-2, warranting further investigation.

Designed mosaic nanoparticles enhance cross-reactive immune responses in mice

Nanoparticle vaccines displaying combinations of SARS-like betacoronavirus (sarbecovirus) receptor-binding domains (RBDs) could protect against SARS-CoV-2 variants and spillover of zoonotic sarbecoviruses into humans. Using a computational approach, we designed variants of SARS-CoV-2 RBDs and selected 7 natural sarbecovirus RBDs, each predicted to fold properly and abrogate antibody responses to variable epitopes. RBDs were attached to 60-mer nanoparticles to make immunogens displaying two (mosaic-2COMs), five (mosaic-5COM), or seven (mosaic-7COM) different RBDs for comparisons with mosaic-8b, which elicited cross-reactive antibodies and protected animals from sarbecovirus challenges. Naive and COVID-19 pre-vaccinated mice immunized with mosaic-7COM elicited antibodies targeting conserved RBD epitopes, and their sera exhibited higher binding and neutralization titers against sarbecoviruses than mosaic-8b. Mosaic-2COMs and mosaic-5COM elicited higher antibody potencies against some SARS-CoV-2 variants than mosaic-7COM. However, mosaic-7COM elicited more potent responses against zoonotic sarbecoviruses and highly mutated Omicrons, supporting its use to protect against SARS-CoV-2 variants and zoonotic sarbecoviruses.

Cost-Effectiveness of Introducing Nuvaxovid to COVID-19 Vaccination in the United Kingdom: A Dynamic Transmission Model

Background/Objectives: Vaccination against SARS-CoV-2 remains a key measure to control COVID-19. Nuvaxovid, a recombinant Matrix-M-adjuvanted protein-based vaccine, showed similar efficacy to mRNA vaccines in clinical trials and real-world studies, with lower rates of reactogenicity. Methods: To support decision making on UK vaccine selection, a population-based compartmental dynamic transmission model with a cost-utility component was developed to evaluate the cost-effectiveness of Nuvaxovid compared with mRNA vaccines from a UK National Health Service perspective. The model was calibrated to official epidemiology statistics for mortality, incidence, and hospitalisation. Scenario and sensitivity analyses were conducted. Results: In the probabilistic base case, a Nuvaxovid-only strategy provided total incremental cost savings of GBP 1,338,323 and 1558 additional quality-adjusted life years (QALYs) compared with an mRNA-only vaccination strategy. Cost savings were driven by reduced cold chain-related operational costs and vaccine wastage, while QALY gains were driven by potential differences in vaccine tolerability. Probabilistic sensitivity analysis indicated an approximately 70% probability of cost-effectiveness with Nuvaxovid-only versus mRNA-only vaccination across most cost-effectiveness thresholds (up to GBP 300,000/QALY gained). Conclusions: Nuvaxovid remained dominant over mRNA vaccines in scenario analyses assessing vaccine efficacy waning, Nuvaxovid market shares, and the vaccinated population.

AnnCovDB: a manually curated annotation database for mutations in SARS-CoV-2 spike protein

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been circulating and adapting within the human population for >4 years. A large number of mutations have occurred in the viral genome, resulting in significant variants known as variants of concern (VOCs) and variants of interest (VOIs). The spike (S) protein harbors many of the characteristic mutations of VOCs and VOIs, and significant efforts have been made to explore functional effects of the mutations in the S protein, which can cause or contribute to viral infection, transmission, immune evasion, pathogenicity, and illness severity. However, the knowledge and understanding are dispersed throughout various publications, and there is a lack of a well-structured database for functional annotation that is based on manual curation. AnnCovDB is a database that provides manually curated functional annotations for mutations in the S protein of SARS-CoV-2. Mutations in the S protein carried by at least 8000 variants in the GISAID were chosen, and the mutations were then utilized as query keywords to search in the PubMed database. The searched publications revealed that 2093 annotation entities for 205 single mutations and 93 multiple mutations were manually curated. These entities were organized into multilevel hierarchical categories for user convenience. For example, one annotation entity of N501Y mutation was 'Infectious cycle➔Attachment➔ACE2 binding affinity➔Increase'. AnnCovDB can be used to query specific mutations and browse through function annotation entities. Database URL: https://AnnCovDB.app.bio-it.tech/.

SARS-CoV-2 infection rates and associated risk factors in healthcare workers: systematic review and meta-analysis

To protect healthcare workforce during the COVID-19 pandemic, rigorous efforts were made to reduce infection rates among healthcare workers (HCWs), especially prior to vaccine availability. This study aimed to investigate the prevalence of SARS-CoV-2 infections among HCWs and identify potential risk factors associated with transmission. We searched MEDLINE, Embase, and Google Scholar from 1 December 2019 to 5 February 2024. From 498 initial records, 190 articles were reviewed, and 63 studies were eligible. ROBINS-E tool revealed a lower risk of bias in several domains; however, some concerns related to confounding and exposure measurement were identified. Globally, 11% (95% confidence interval (CI) 9-13) of 283,932 HCWs were infected with SARS-CoV-2. Infection rates were associated with a constellation of risk factors and major circulating SARS-CoV-2 variants. Household exposure (odds ratio (OR) 7.07; 95% CI 3.93-12.73), working as a cleaner (OR 2.72; 95% CI 1.39-5.32), occupational exposure (OR 1.79; 95% CI 1.49-2.14), inadequate training on infection prevention and control (OR 1.46; 95% CI 1.14-1.87), insufficient use of personal protective equipment (OR 1.45; 95% CI 1.14-1.84), performing aerosol generating procedures (OR 1.36; 95% CI 1.21-1.52) and inadequate hand hygiene (OR 1.17; 95% CI 0.79-1.73) were associated with an increased SARS-CoV-2 infection. Conversely, history of quarantine (OR 0.23; 95% CI 0.08-0.60) and frequent decontamination of high touch areas (OR 0.52; 95% CI 0.42-0.64) were protective factors against SARS-CoV-2 infection. This study quantifies the substantial global burden of SARS-CoV-2 infection among HCWs. We underscore the urgent need for effective infection prevention and control measures, particularly addressing factors such as household exposure and occupational practices by HCWs, including cleaning staff.

A computationally designed antigen eliciting broad humoral responses against SARS-CoV-2 and related sarbecoviruses

The threat of spillovers of coronaviruses associated with the severe acute respiratory syndrome (SARS) from animals to humans necessitates vaccines that offer broader protection from sarbecoviruses. By leveraging a viral-genome-informed computational method for selecting immune-optimized and structurally engineered antigens, here we show that a single antigen based on the receptor binding domain of the spike protein of sarbecoviruses elicits broad humoral responses against SARS-CoV-1, SARS-CoV-2, WIV16 and RaTG13 in mice, rabbits and guinea pigs. When administered as a DNA immunogen or by a vector based on a modified vaccinia virus Ankara, the optimized antigen induced vaccine protection from the Delta variant of SARS-CoV-2 in mice genetically engineered to express angiotensin-converting enzyme 2 and primed by a viral-vector vaccine (AZD1222) against SARS-CoV-2. A vaccine formulation incorporating mRNA coding for the optimized antigen further validated its broad immunogenicity. Vaccines that elicit broad immune responses across subgroups of coronaviruses may counteract the threat of zoonotic spillovers of betacoronaviruses.

Variants and vaccines impact nasal immunity over three waves of SARS-CoV-2

Viral variant and host vaccination status impact infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), yet how these factors shift cellular responses in the human nasal mucosa remains uncharacterized. We performed single-cell RNA sequencing (scRNA-seq) on nasopharyngeal swabs from vaccinated and unvaccinated adults with acute Delta and Omicron SARS-CoV-2 infections and integrated with data from acute infections with ancestral SARS-CoV-2. Patients with Delta and Omicron exhibited greater similarity in nasal cell composition driven by myeloid, T cell and SARS-CoV-2hi cell subsets, which was distinct from that of ancestral cases. Delta-infected samples had a marked increase in viral RNA, and a subset of PER2+EGR1+GDF15+ epithelial cells was enriched in SARS-CoV-2 RNA+ cells in all variants. Prior vaccination was associated with increased frequency and activation of nasal macrophages. Expression of interferon-stimulated genes negatively correlated with coronavirus disease 2019 (COVID-19) severity in patients with ancestral and Delta but not Omicron variants. Our study defines nasal cell responses and signatures of disease severity across SARS-CoV-2 variants and vaccination.

Engineering mRNA vaccine with broad-spectrum protection against SARS-cov-2 variants

Herd immunity through mass vaccination is an effective method for preventing infectious diseases. However, the emerging SARS-CoV-2 variants, with their frequent mutations, largely evade the immune response and protection induced by COVID-19 vaccines. Here, we designed messenger RNAs encoding mutant epitopes of the spike protein shared among various COVID-19 variants. These mRNAs were encapsulated in lipid nanoparticles to formulate a vaccine named 'mPANVAX@COVID'. Post-vaccination, this approach elicited effective immunity against multiple SARS-CoV-2 variants, including Delta and Omicron, and demonstrated good safety. This study suggests a novel direction for the design of broadly protective vaccines.

The respective roles of TMPRSS2 and cathepsins for SARS-CoV-2 infection in human respiratory organoids

A critical aspect of the mechanism of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is the protease-mediated activation of the viral spike (S) protein. The type II transmembrane serine protease TMPRSS2 is crucial for SARS-CoV-2 infection in lung epithelial Calu-3 cells and murine airways. However, the importance of TMPRSS2 needs to be re-examined because the ability to utilize TMPRSS2 is significantly reduced in the Omicron variants that spread globally. For this purpose, replication profiles of SARS-CoV-2 were analyzed in human respiratory organoids. All tested viruses, including Omicron variants, replicated efficiently in these organoids. Notably, all SARS-CoV-2 strains retained replication ability in TMPRSS2-gene knockout (KO) respiratory organoids, suggesting that TMPRSS2 is not essential for SARS-CoV-2 infection in human respiratory tissues. However, TMPRSS2-gene knockout significantly reduces the inhibitory effect of nafamostat, indicating the advantage of TMPRSS2-utilizing ability for the SARS-CoV-2 infection in these organoids. Interestingly, Omicron variants regained the TMPRSS2-utilizing ability in recent subvariants. The basal infectivity would be supported mainly by cathepsins because the cathepsin inhibitor, EST, showed a significant inhibitory effect on infection with any SARS-CoV-2 strains, mainly when used with nafamostat. A supplementary contribution of other serine proteases was also suggested because the infection of the Delta variant was still inhibited partially by nafamostat in TMPRSS2 KO organoids. Thus, various proteases, including TMPRSS2, other serine proteases, and cathepsins, co-operatively contribute to SARS-CoV-2 infection significantly in the respiratory organoids. Thus, SARS-CoV-2 infection in the human respiratory tissues would be more complex than observed in cell lines or mice.

IMPORTANCE

We explored how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus infects human respiratory organoids, which are a cultured cell model made to mimic the physiological conditions of the human airways. We focused on understanding the role of different proteases of host cells in activating the virus spike proteins. Specifically, we looked at TMPRSS2, a transmembrane serine protease, and cathepsin L, a lysosomal enzyme, which helps the virus enter cells by cutting the viral spike protein. We discovered that while TMPRSS2 is crucial for the virus in certain cells and animal models, other proteases, including cathepsins and various serine proteases, also play significant roles in the SARS-CoV-2 infection of human respiratory organoids. We suggest that SARS-CoV-2 uses a more complex mechanism involving multiple proteases to infect human airways, differing from what we see in conventional cell lines or animal models. This complexity might help explain how different variants can spread and infect people effectively.

Tracing Emergence of SARS-CoV-2 Variants: Insights from Comprehensive Assessment Using Reverse Transcription Polymerase Chain Reaction and Whole Genome Sequencing

The emergence and evolution of SARS-CoV-2 variants, such as Delta and Omicron, pose significant challenges to pandemic management. This study evaluated the effectiveness of reverse-transcription polymerase chain reaction (RT-PCR) and whole-genome sequencing (WGS) in detecting and characterizing SARS-CoV-2 variants using 624 samples collected in South Korea from mid-2021 to mid-2022. Two RT-PCR genotyping assays demonstrated a high concordance rate (90.4%) in identifying the Delta variant during its dominance. In contrast, WGS revealed extensive genetic diversity among Omicron sub-lineages, identifying 29 distinct sub-lineages, including two South Korea-specific variants (BA.1.1.5 and BA.2.3.8). Clustering analysis of WGS data highlighted distinct groupings of BA.1, BA.2, and BA.5 sub-lineages, with overlap in shared mutations suggesting evolutionary convergence. Sub-lineage diversity expanded during rapid transmission phases and subsequently consolidated as dominant lineages emerged. These findings highlight the complementary strengths of RT-PCR and WGS and underscore the importance of integrating these methodologies for effective variant monitoring and public health response.

Accelerated Adaptation of SARS-CoV-2 Variants in Mice Lacking IFITM3 Preserves Distinct Tropism and Pathogenesis

Here we investigated whether interferon induced transmembrane protein 3 (IFITM3), a key antiviral protein deficient in certain human populations, affects interspecies adaptation of SARS-CoV-2. We found that SARS-CoV-2 Beta and Omicron variants passaged through IFITM3-deficient versus wild type mice exhibit enhanced replication and pathogenesis in this new host species. Enhancements associated with amino acid substitutions in the viral genome, suggesting that IFITM3 limits accumulation of adaptive mutations. Mouse-adapted viruses enabled comparative studies of variants in mice. Beta caused lung dysfunction and altered cilia-associated gene programs, consistent with broad viral antigen distribution in lungs. Omicron, which shows low pathogenicity and upper respiratory tract preference in humans, replicated to high nasal titers while showing restrained spatial distribution in lungs and diminished lung inflammatory responses compared to Beta. Our findings demonstrate that IFITM3 deficiency accelerates coronavirus adaptation and reveal that intrinsic SARS-CoV-2 variant traits shape tropism, immunity, and pathogenesis across hosts.

HIGHLIGHTS

IFITM3 is a critical barrier to SARS-CoV-2 adaptation in new host speciesMouse-adapted SARS-CoV-2 strains enable comparative pathologyOmicron favors nose and large airways, leading to mild lung pathologyBeta exhibits broad lung replication, driving severe inflammation and dysfunction.

Next generation sequencing of multiple SARS-CoV-2 infections in the Omicron Era

Since the emergence of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the need for an effective vaccine has appeared crucial for stimulating immune system responses to produce humoral/cellular immunity and activate immunological memory. It has been demonstrated that SARS-CoV-2 variants escape neutralizing immunity elicited by previous infection and/or vaccination, leading to new infection waves and cases of reinfection. The study aims to gain into cases of reinfections, particularly infections and/or vaccination-induced protection. We conducted a retrospective descriptive study using data collected during the SARS-CoV-2 pandemic. This analysis involved Reverse Transcriptase Quantitative Polymerase Chain Reaction (RT-qPCR) and Next Generation Sequencing (NGS). RT-qPCR was performed on 416,466 naso-oropharyngeal swabs, with 10,380 samples further analyzed using NGS technology. RT-qPCR identified 350 cases of reinfection, of which 228 were subjected to detailed analysis via NGS. Our findings revealed two interesting cases involving pediatric patients who were not vaccinated. Positive results were observed in these cases within a short interval (< 60 days) and the "nature" of the infection, whether attributable to Reinfection or Viral Persistence, was investigated. Specifically, we discuss a case involving an unvaccinated 18-month-old child, which may represent one of the earliest instances of BA.5/BA.5 reinfection identified worldwide.

The immune landscape and viral shedding of Omicron SARS-CoV-2 variants implicate immune escape

Background

Three years into the SARS-CoV-2 pandemic, the virus continues to mutate despite widespread vaccination, posing ongoing challenges for epidemic prevention and control. The relationship between viral shedding and immune escape remains under investigation. This study aims to examine the association between viral shedding and immune escape in the BA.4/5 and BF.7 variants.

Method

We included 542 patients infected with the Omicron variant from Beijing Xiaotangshan shelter hospital. Based on the viral strain, patients were divided into BA.4/5 group and BF.7 group. Additionally, we categorized patients into rapid viral shedding and slow viral shedding groups according to their viral shedding rates. We explored the relationship between viral shedding and immune-related clinical indicators during this period.

Result

Of the 542 patients, 118 were infected with BA.4/5 variant, and 424 were infected with BF.7 variant. The viral shedding duration differed significantly between BA.4/5 and BF.7 groups (p < 0.0001). However, there was no statistically significant correlation between viral shedding duration and immune-related indicators, such as WBC, Hb, PLT, Neu, Lym, CRP, allergy, fever, and vaccination status (p > 0.05). Furthermore, viral shedding duration was not associated with vaccination status, intervals between vaccinations, or vaccine types (p > 0.05).

Conclusion

The duration of viral shedding in patients infected with Omicron variants BA.4/5 and BF.7 is not associated with WBC, Hb, Lym, CRP, fever, allergy, or vaccine-related indicators. This lack of association may be attributed to immune escape mechanisms.

Ultra-Sensitive Aptamer-Based Diagnostic Systems for Rapid Detection of All SARS-CoV-2 Variants

The emergence of numerous SARS-CoV-2 variants, characterized by mutations in the viral RNA genome and target proteins, has presented challenges for accurate COVID-19 diagnosis. To address this, we developed universal aptamer probes capable of binding to the spike proteins of SARS-CoV-2 variants, including highly mutated strains like Omicron. These aptamers were identified through protein-based SELEX using spike proteins from three key variants (D614G-substituted Wuhan-Hu-1, Delta, and Omicron) and virus-based SELEX, known as viro-SELEX. Leveraging these universal aptamers, we created a highly sensitive lateral flow assay (LFA) and an ultra-sensitive molecular diagnostic platform that integrates a novel rapid PCR technique, enabling fast and reliable detection across all SARS-CoV-2 variants.

Phenotypic evolution of SARS-CoV-2 spike during the COVID-19 pandemic

SARS-CoV-2 variants are mainly defined by mutations in their spike. It is therefore critical to understand how the evolutionary trajectories of spike affect virus phenotypes. So far, it has been challenging to comprehensively compare the many spikes that emerged during the pandemic in a single experimental platform. Here we generated a panel of recombinant viruses carrying different spike proteins from 27 variants circulating between 2020 and 2024 in the same genomic background. We then assessed several of their phenotypic traits both in vitro and in vivo. We found distinct phenotypic trajectories of spike among and between variants circulating before and after the emergence of Omicron variants. Spike of post-Omicron variants maintained enhanced tropism for the nasal epithelium and large airways but displayed, over time, several phenotypic traits typical of the pre-Omicron variants. Hence, spike with phenotypic features of both pre- and post-Omicron variants may continue to emerge in the future.

Passive infusion of an S2-Stem broadly neutralizing antibody protects against SARS-CoV-2 infection and lower airway inflammation in rhesus macaques

The continued evolution of SARS-CoV-2 variants capable of subverting vaccine and infection-induced immunity suggests the advantage of a broadly protective vaccine against betacoronaviruses (β-CoVs). Recent studies have isolated monoclonal antibodies (mAbs) from SARS-CoV-2 recovered-vaccinated donors capable of neutralizing many variants of SARS-CoV-2 and other β-CoVs. Many of these mAbs target the conserved S2 stem region of the SARS-CoV-2 spike protein, rather than the receptor binding domain contained within S1 primarily targeted by current SARS-CoV-2 vaccines. One of these S2-directed mAbs, CC40.8, has demonstrated protective efficacy in small animal models against SARS-CoV-2 challenge. As the next step in the pre-clinical testing of S2-directed antibodies as a strategy to protect from SARS-CoV-2 infection, we evaluated the in vivo efficacy of CC40.8 in a clinically relevant non-human primate model by conducting passive antibody transfer to rhesus macaques (RM) followed by SARS-CoV-2 challenge. CC40.8 mAb was intravenously infused at 10mg/kg, 1mg/kg, or 0.1 mg/kg into groups (n = 6) of RM, alongside one group that received a control antibody (PGT121). Viral loads in the lower airway were significantly reduced in animals receiving higher doses of CC40.8. We observed a significant reduction in inflammatory cytokines and macrophages within the lower airway of animals infused with 10mg/kg and 1mg/kg doses of CC40.8. Viral genome sequencing demonstrated a lack of escape mutations in the CC40.8 epitope. Collectively, these data demonstrate the protective efficiency of broadly neutralizing S2-targeting antibodies against SARS-CoV-2 infection within the lower airway while providing critical preclinical work necessary for the development of pan-β-CoV vaccines.

Kaposi's sarcoma-associated herpesvirus (KSHV) gB dictates a low-pH endocytotic entry pathway as revealed by a dual-fluorescent virus system and a rhesus monkey rhadinovirus expressing KSHV gB

Interaction with host cell receptors initiates internalization of Kaposi's sarcoma-associated herpesvirus (KSHV) particles. Fusion of viral and host cell membranes, which is followed by release of the viral capsid into the cytoplasm, is executed by the core fusion machinery composed of glycoproteins H (gH), L (gL), and B (gB), that is common to all herpesviruses. KSHV infection has been shown to be sensitive to inhibitors of vacuolar acidification, suggestive of low pH as a fusion trigger. To analyze KSHV entry at the single particle level we developed dual-fluorescent recombinant KSHV strains that incorporate fluorescent protein-tagged glycoproteins and capsid proteins. In addition, we generated a hybrid rhesus monkey rhadinovirus (RRV) that expresses KSHV gB in place of RRV gB to analyze gB-dependent differences in infection pathways. We demonstrated lytic reactivation and infectivity of dual-fluorescent KSHV. Confocal microscopy was used to quantify co-localization of fluorescently-tagged glycoproteins and capsid proteins. Using the ratio of dual-positive KSHV particles to single-positive capsids as an indicator of fusion events we established KSHV fusion kinetics upon infection of different target cells with marked differences in the "time-to-fusion" between cell types. Inhibition of vesicle acidification prevented KSHV particle-cell fusion, implicating low vesicle pH as a requirement. These findings were corroborated by comparison of RRV-YFP wildtype reporter virus and RRV-YFP encoding KSHV gB in place of RRV gB. While RRV wt infection of receptor-overexpressing cells was unaffected by inhibition of vesicle acidification, RRV-YFP expressing KSHV gB was sensitive to Bafilomycin A1, an inhibitor of vacuolar acidification. Single- and dual-fluorescent KSHV strains eliminate the need for virus-specific antibodies and enable the tracking of single viral particles during entry and fusion. Together with a hybrid RRV expressing KSHV gB and classical fusion assays, these novel tools identify low vesicle pH as an endocytotic trigger for KSHV membrane fusion.

Effectiveness of COVID-19 vaccines against SARS-CoV-2 infection and severe outcomes in adults: a systematic review and meta-analysis of European studies published up to 22 January 2024

BACKGROUND

Up-to-date evidence from European studies on long-term vaccine effectiveness (VE) of COVID-19 vaccines is lacking. This review aimed to evaluate effectiveness and durability of primary vaccine series and boosters in preventing infection and severe outcomes in the European population.

METHODS

We conducted systematic searches of PubMed and Embase up to 22 January 2024. We included observational studies that evaluated VE against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection or severe disease (hospitalisation, intensive care unit admission or death) for primary series and boosters in Europe. We applied a random-effects meta-analysis model.

RESULTS

We included 33 studies and over 56 million participants. The overall VE of the complete primary series against infection with any SARS-CoV-2 variant was 70.7%. VE was lower for Omicron, at 26.1%, than for pre-Omicron strains, at 77.0%. Over time, VE against infection by any variant decreased from 68.9% to 38.9% after 6 months. Boosters restored VE to 76.4% and maintained at 58.4% after 3 months. The overall VE of a complete primary series for severe outcomes due to any variant was 87.4%, with 93.3% for pre-Omicron and 62.8% for Omicron strains. Protection against severe outcomes declined less than for infection. 6 months after the primary series, the vaccine still provided over 50% protection against severe outcomes caused by Omicron. Boosters restored VE to 87.9% and maintained at 78.5% after 3 months.

CONCLUSION

VE against SARS-CoV-2 infection declines markedly with time and Omicron variants. Protection against severe outcomes was more durable and resistant to viral mutation. Boosters restored protection, emphasising the need for timely booster vaccination for vulnerable populations.

Emergence of SARS-CoV-2 subgenomic RNAs that enhance viral fitness and immune evasion

Coronaviruses express their structural and accessory genes via a set of subgenomic RNAs, whose synthesis is directed by transcription regulatory sequences (TRSs) in the 5' genomic leader and upstream of each body open reading frame. In SARS-CoV-2, the TRS has the consensus AAACGAAC; upon searching for emergence of this motif in the global SARS-CoV-2 sequences, we find that it evolves frequently, especially in the 3' end of the genome. We show well-supported examples upstream of the Spike gene-within the nsp16 coding region of ORF1b-which is expressed during human infection, and upstream of the canonical Envelope gene TRS, both of which have evolved convergently in multiple lineages. The most frequent neo-TRS is within the coding region of the Nucleocapsid gene, and is present in virtually all viruses from the B.1.1 lineage, including the variants of concern Alpha, Gamma, Omicron and descendants thereof. Here, we demonstrate that this TRS leads to the expression of a novel subgenomic mRNA encoding a truncated C-terminal portion of Nucleocapsid, which is an antagonist of type I interferon production and contributes to viral fitness during infection. We observe distinct phenotypes when the Nucleocapsid coding sequence is mutated compared to when the TRS alone is ablated. Our findings demonstrate that SARS-CoV-2 is undergoing evolutionary changes at the functional RNA level in addition to the amino acid level.

Immune imprinting: The persisting influence of the first antigenic encounter with rapidly evolving viruses

Immune imprinting is a phenomenon that stems from the fundamentals of immunological memory. Upon recurrent exposures to an evolving pathogen, the immune system must weigh the benefits of rapidly recalling established antibody repertoires with greater affinity to the initial variant or invest additional time and energy in producing de novo responses specific to the emerging variant. In this review, we delve into the mechanistic complexities of immune imprinting and its role in shaping subsequent immune responses, both de novo and recall, against rapidly evolving respiratory viruses such as influenza and coronaviruses. By exploring the duality of immune imprinting, we examine its potential to both enhance or hinder immune protection against disease, while emphasizing the role of host and viral factors. Finally, we explore how different vaccine platforms may affect immune imprinting and comment on vaccine strategies that can favor de novo variant-specific antibody responses.