The coronavirus disease (COVID-19) pandemic accelerated development of various vaccine platforms. Among them, mRNA vaccines played a crucial role in controlling the pandemic due to their swift development and efficacy against virus variants. Despite the success of these vaccines, recent studies highlight challenges in evaluating vaccine efficacy, especially in individuals with prior COVID-19 infection. Weakened neutralizing antibody responses after additional doses are observed in these populations, raising concerns about using neutralizing antibody titers as the sole immune correlate of protection. While neutralizing antibodies remain the primary endpoint in immunogenicity trials, they may not fully capture the immune response in populations with widespread prior infection or vaccination. This review explores reduced neutralizing antibody responses in previously infected individuals, and their impact on vaccine efficacy evaluation. It also offers recommendations for improving efficacy assessment, stressing incorporation of additional immune markers such as cell-mediated immunity to enable more comprehensive understanding of vaccine-induced immunity.

It has been five years since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and we are also approaching the five-year mark of the COVID-19 pandemic. The vaccine is a significant weapon in combating infectious diseases like SARS-CoV-2. Several vaccines were developed against SARS-CoV-2, and they demonstrated efficacy and safety during these five years. The rapid development of multiple next-generation vaccine candidates in different platforms with very little time is the success story of the vaccine development endeavor. This remarkable success of rapid vaccine development is a new paradigm for fast vaccine development that might help develop infectious diseases and fight against the pandemic. With the completion of five years since the beginning of SARS-CoV-2 origin, we are looking back on the five years and reviewing the milestones, vaccine platforms, animal models, clinical trials, successful collaborations, vaccine safety, real-world effectiveness, and challenges. Lessons learned during these five years will help us respond to public health emergencies and to fight the battle against future pandemics.

Protection against severe course of SARS-CoV-2 infection after COVID-19 vaccination or infection was extensively studied. It is unknown whether this effect also translates into shortened duration of mild infections. We assessed the duration of symptoms depending on vaccination status and previous SARS-CoV-2 infections among individuals with a mild course of infection.

For two post-pandemic winters (2022/2023 and 2023/2024), in total 13,615 participants of the German DigiHero study reported their SARS-CoV-2 infections from September to March. Via negative binomial regression adjusting for sociodemographic factors, we studied the association of infection duration (days with symptoms and in bed) with number of vaccinations, prior SARS-CoV-2 infections, and time since last vaccination/and infection.

We noted no major differences in infection duration depending on the number of vaccinations and time since last infection for short mild infections (≤21 days with symptoms). Per 6 months since the last vaccination, symptom duration and days spent in bed increased by 2 % and 4 %. The risk of long mild SARS-CoV-2 infections (>21 days with symptoms) was higher for individuals with no prior SARS-CoV-2 infection (Odds Ratio: 1.98; 95 % confidence interval [1.43; 2.76]), but not for vaccinations (OR: 0.98; 95 % CI [0.74; 1.33]).

There was no indication of reduced duration of symptoms during short mild infections depending on the number of vaccinations and time since the last SARS-CoV-2 vaccination or infection. A prior SARS-CoV-2 infection was protective against prolonged disease in mild SARS-CoV-2 infections.

The COVID-19 disease has spread rapidly across the world within just six months, affecting 169 million people and causing 3.5 million deaths globally (2021). The most affected countries include the USA, Brazil, India, and several European countries such as the UK and Russia. Healthcare professionals face new challenges in finding better ways to manage patients and save lives. In this regard, more comprehensive research is needed, including genomic and proteomic studies, personalized medicines and the design of suitable treatments. However, finding novel molecular entities (NME) using a standard or de novo strategy to drug development is a time-consuming and costly process. Another alternate strategy is discovering new therapeutic uses for old/existing/available medications, known as drug repurposing. There are a variety of computational repurposing methodologies, and some of them have been used to counter the coronavirus disease pandemic of 2019 (COVID-19). This review article compiles recently published data on the origin, transmission, pathogenesis, diagnosis, and management of the coronavirus by drug repurposing and vaccine development approach. We have attempted to screen probable drugs in clinical trials by using literature survey. This systematic review aims to create priorities for future research of drugs repurposed and vaccine development for COVID-19.

Extensive vaccination campaigns against COVID-19 have played a significant role in controlling virus spread and preventing severe illness. This study focused on breakthrough infections in vaccinated individuals, raising concerns about vaccine effectiveness against SARS-CoV-2 variant immune escape, with particular attention to lineage distribution among vaccinated and unvaccinated individuals.

A case-control study was conducted from January to April 2023, sequencing 298 samples from participants who tested positive for COVID-19 via rapid diagnostic test (RDT) from 22 health facilities, including vaccinated and unvaccinated cases. Besides clinical and epidemiological data, nasopharyngeal swabs were obtained, and reverse transcription quantitative polymerase chain reaction (RT-qPCR) was conducted to determine Cycle threshold (Ct) values, followed by whole genome sequencing of 298 samples fulfilling sequencing criteria to identify variants of concern and specific virus lineages.

Out of 298 samples sequenced, 281 fulfill quality for analysis with 44.8% (126) had received at least one COVID-19 vaccine dose, while 51.9% (146) were not vaccinated, and 3.2% (9) patients had no vaccination records. The analysis showed that all cases were of the Omicron variant, with the XBB.1.5 lineage being the most prevalent (38.4%), followed by FL.2 (9.3%) and XBB.1.9.1.2 (7.8%). The remaining 44.5% comprised a combination of 22 other lineages. The XBB.1.5 variant accounted for 51 (47.2%) cases among vaccinated individuals with at least one dose and 57 (52.8%) among unvaccinated, showing relatively similar prevalence across both groups. The viral load as indicated by the Ct value varied widely, with a significant appearance in the lower ranges (high viral load), suggesting active viral replication. Notably, 25% of samples exhibited high viral loads (Ct values 13-15), showing the high transmissibility of the XBB.1.5 lineage among both vaccinated and unvaccinated populations.

The findings emphasize the need for continuous genomic surveillance and regular vaccine updates to address emerging SARS-CoV-2 variants, particularly the immune-evasive XBB lineage. The high prevalence of variants like XBB.1.5 in breakthrough infection underscores the importance of adaptive vaccination strategies and next-generation vaccines to maintain efficacy. Ongoing monitoring of variant dynamics is crucial for informed public health responses, strengthening pandemic preparedness and future outbreak prevention.

The JAK family, particularly JAK3, plays a crucial role in immune signaling and inflammatory responses. Dysregulated JAK3 activation in SARS-CoV-2 infections has been associated with severe inflammation and respiratory complications, making JAK inhibitors a viable therapeutic option. However, their use raises concerns regarding immunosuppression, which could increase susceptibility to secondary infections. While long-term adverse effects are less of a concern in acute COVID-19 treatment, patient selection and monitoring remain critical. Furthermore, adverse effects associated with oral JAK3 inhibitors necessitate the exploration of alternative strategies to optimize therapeutic efficacy while minimizing risks. This review highlights the role of JAK3 in immune and epithelial cells, examines the adverse effects of oral JAK3 inhibitors in COVID-19 and other treatments, and discusses alternative therapeutic strategies for improving patient outcomes.

The decline in neutralizing antibody (nAb) titers and vaccine efficacy /effectiveness (VE) for SARS-CoV-2 vaccines has been observed over time and when confronted with emerging variants, two factors that are hard to distinguish. Despite substantial drop in nAb titers against Omicron, VE remains high for severe cases and fatalities, raising questions about the utility of detected nAbs as a correlate of protection for COVID-19 vaccines for varying disease severity. Here, we conducted a systematic comparison of waning dynamics of nAb and VE over time and against variants with varying levels of disease severity. Using Bayesian linear regression models, we found that antigenically-shifted variants, like Omicron, could potentially lead to greater reductions in nAb titers and primary VE against mild infections than associated immunity waning observed over a 180-day period. By comparing model predicted nAb titers and VE on the same time scales, we found that VE against severe and fatal outcomes remained above 75% even when nAb titers reached the detectable limit of assays, despite strong correlations with nAb titers (spearman correlations ≥0.7) across variants over time. This finding suggested detectable nAb titers are not always sensitive enough to fully predict protection against severe disease and death from SARS-CoV-2.

Understanding COVID-19 vaccine effectiveness (VE) in healthcare workers (HCWs) is critical to inform vaccination policies. We measured COVID-19 VE against laboratory-confirmed symptomatic infection in HCWs in the country of Georgia from January - June 2022, during a period of Omicron circulation.

We conducted a cohort study of HCWs in six hospitals in Georgia. HCWs were enrolled in early 2021. Participants completed weekly symptom questionnaires. Symptomatic HCWs were tested by RT-PCR and/or rapid antigen test (RAT). Participants were also routinely tested, at varying frequencies during the study period, for SARS-CoV-2 by RT-PCR or RAT, regardless of symptoms. Serology was collected quarterly throughout the study and tested by electrochemiluminescence immunoassay for SARS-CoV-2 antibodies. We estimated absolute and relative VE of a first booster dose compared to a primary vaccine series as (1-hazard ratio)*100 using Cox proportional hazards models.

Among 1253 HCWs, 141 (11%) received a primary vaccine series (PVS) and a first booster, 855 (68%) received PVS only, and 248 (20%) were unvaccinated. Most boosters were BNT162b2 (Comirnaty original monovalent) vaccine (90%) and BBIBP-CorV vaccine (Sinopharm) (9%). Most PVS were BNT162b2 vaccine (68%) and BBIBP-CorV vaccine (24%). Absolute VE for a first booster was 40% (95% Confidence Interval (CI) -56-77) at 7-29 days following vaccination, -9% (95% CI -104-42) at 30-59 days following vaccination, and -46% (95% CI -156-17) at ≥ 60 days following vaccination. Relative VE of first booster dose compared to PVS was 58% (95% CI 1-82) at 7-29 days following vaccination, 21% (95% CI -33-54) at 30-59 days following vaccination, and -9% (95% CI -82-34) at ≥ 60 days following vaccination.

In Georgia, first booster dose VE against symptomatic SARS-CoV-2 infection among HCWs was moderately effective but waned very quickly during Omicron. Increased efforts to vaccinate priority groups in Georgia, such as healthcare workers, prior to periods of anticipated high COVID-19 incidence are essential.

SARS-CoV-2 vaccines are highly effective in preventing severe COVID-19 but require boosting to maintain protection. Changes to circulating variants and prevalent natural immunity may impact on real-world effectiveness of boosters. With NHS England approval, we used linked routine clinical data from >24 million patients to evaluate the effectiveness of the 2022 combined COVID-19 autumn booster and influenza vaccine campaign in non-clinically vulnerable 50-year-olds in England using a regression discontinuity design. Our primary outcome was a composite of 6-week COVID-19 emergency attendance, COVID-19 unplanned hospitalisation, or death. By 26 November 2022, booster vaccine coverage was 11.1 % at age 49.75 years increasing to 39.7 % at age 50.25 years. The estimated effect of the campaign on the risk of the primary outcome in 50-year-olds during weeks 7-12 after the start of the campaign was -0.4 per 100,000 (95 % CI -7.8, 7.1). The results were similar when using different follow-up start dates or when estimating the effect of vaccination (rather than the campaign). This study found little evidence that the autumn 2022 vaccination campaign in England was associated with a reduction in severe COVID-19-related outcomes among non-clinically vulnerable 50-year-olds. Possible explanations include the low risk of severe outcomes and substantial pre-existing vaccine- and infection-induced immunity. The booster campaign may have had effects beyond those we estimated, including reducing virus transmission and incidence of mild or moderate COVID-19.

Wastewater-based epidemiology (WBE) can provide critical early warnings to aid public health, which can be particularly beneficial in rural communities with limited access to health care. Spikes of SARS-CoV-2 RNA concentration in wastewater have been used to represent infections in a community, but wastewater holds a wealth of information that has not been explored yet. The objectives of this research were to expand the use of WBE to 1) determine the dynamic of SARS-CoV-2 variants in rural communities, and 2) evaluate the relationship between community vaccination status and the outbreak of a variant. We quantified the concentration of SARS-CoV-2 RNA, as well as specific mutations that are consistent with Delta and Omicron in influent raw wastewater samples collected from wastewater treatment facilities (WWTFs) for five populations with <1000 residents and one larger population in Latah County, ID. A binomial generalized linear model using the percent of the population with protection against Omicron from the initial vaccines and the booster shot was able to predict the probability of an uptick in Omicron concentration in wastewater with an accuracy of 0.96. Evaluation of vaccination data indicate that the spike in Omicron infections in December 2021 in the studied towns was linked to low levels of population protection from the initial shots of the COVID-19 vaccine against Omicron infection and limited uptake of booster shots in these communities. Despite difficulties with applying WBE in rural regions, this study shows that beyond evaluating spikes of viral infections, WBE can be used to evaluate the effect of a population's vaccine coverage on SARS-CoV-2 variant dynamics.

Quantifying the extent to which previous infections and vaccinations confer protection against future infection or disease outcomes is critical to managing the transmission and consequences of infectious diseases. We present a general statistical model for predicting the strength of protection conferred by different immunising exposures (numbers, types, and strains of both vaccines and infections), against multiple outcomes of interest, whilst accounting for immune waning. We predict immune protection against key clinical outcomes: developing symptoms, hospitalisation, and death. We also predict transmission-related outcomes: acquisition of infection and onward transmission in breakthrough infections. These enable quantification of the impact of immunity on population-level transmission dynamics. Our model calibrates the level of immune protection, drawing on both population-level data, such as vaccine effectiveness estimates, and neutralising antibody levels as a correlate of protection. This enables the model to learn realised immunity levels beyond those which can be predicted by antibody kinetics or other correlates alone. We demonstrate an application of the model for SARS-CoV-2, and predict the individual-level protective effectiveness conferred by natural infections with the Delta and the Omicron B.1.1.529 variants, and by the BioNTech-Pfizer (BNT162b2), Oxford-AstraZeneca (ChAdOx1), and 3rd-dose mRNA booster vaccines, against outcomes for both Delta and Omicron. We also demonstrate a use case of the model in late 2021 during the emergence of Omicron, showing how the model can be rapidly updated with emerging epidemiological data on multiple variants in the same population, to infer key immunogenicity and intrinsic transmissibility characteristics of the new variant, before the former can be more directly observed via vaccine effectiveness data. This model provided timely inference on rapidly evolving epidemic situations of significant concern during the early stages of the COVID-19 pandemic. The general nature of the model enables it to be used to support management of a range of infectious diseases.

This large-scale cohort study conducted in Hong Kong examined the time-varying protective effects of various COVID-19 vaccines and dosing regimens against the Omicron BA.1/BA.2 variants. An innovative pharmacokinetic/pharmacodynamic model was employed to estimate the trajectory of vaccine effectiveness over time. Results indicated that the maximum protection for a single dose reached 0.120 for CoronaVac and 0.171 for Comirnaty. The peak protective effectiveness for the second and third doses were observed at 0.348 and 0.522, respectively. In a 4-dose regimen, CoronaVac demonstrated a maximum protective effectiveness of 0.548, stabilizing at 0.487, while Comirnaty achieved a maximum effectiveness of 0.784, stabilizing at 0.714 six months after the administration of the last dose. The vaccine effectiveness exhibited a rising and then declining pattern, peaking approximately 1-2 months post-vaccination. Understanding waning immunity is crucial for optimizing vaccination strategies and policies as viral evolution continues. This real-world study captured changing dynamics that may differ from clinical trials with limited follow-up, providing essential evidence to guide the optimization of vaccination efforts. Ongoing monitoring of vaccine effectiveness remains critical as the viral landscape evolves.

This study aims to investigate the time-varying protective effects of various COVID-19 vaccines and dosing regimens against infections caused by the Omicron BA.1/BA.2 in Hong Kong.

This territory-wide cohort study from Hong Kong combined vaccination records, confirmed COVID-19 cases, and census data from January 2022 to May 2022 to comprehensively analyze the time-varying protective effects of different COVID-19 vaccines and dosing regimens against Omicron BA.1 and BA.2 infections. A 4-parameter pharmacokinetic/pharmacodynamic model was used to estimate the trajectory of vaccine effectiveness over time.

Among 6.2 million adults, the maximum protective effectiveness for a single vaccine dose reached 0.120 for CoronaVac and 0.171 for Comirnaty. For the second and third doses, peak effectiveness were observed at 0.348 for CoronaVac and 0.522 for Comirnaty. Notably, a 4-dose regimen resulted in maximum protections of 0.548 for CoronaVac and 0.785 for Comirnaty, which stabilized at 0.487 and 0.714, respectively, six months following the last doses. The vaccine effectiveness exhibited a rising then declining pattern, peaking around 1-2 months post-vaccination, underscoring the importance of ongoing vaccination strategies.

Understanding the waning of vaccine protection over time is critical for informing optimal vaccination strategies, booster schedules, and public health policies. This real-world study can capture changing dynamics that may differ from clinical trials which have more limited follow-up periods, and can provide crucial evidence to guide optimization of vaccination strategies. Ongoing monitoring of vaccine effectiveness remains crucial as the viral evolution continues.

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in millions of deaths and continues to pose serious threats to global public health. The main protease (Mpro) of SARS-CoV-2 is crucial for viral replication and its conservation, making it an attractive drug target. Here, we employed a structure-based drug design strategy to develop and optimize novel inhibitors targeting SARS-CoV-2 Mpro. By fully exploring occupation of the S1, S2, and S3/S4 binding pockets, we identified eight promising inhibitors with half-maximal inhibitory concentration (IC50) values below 20 nM. The cocrystal structure of Mpro with compound 10 highlighted the crucial roles of the interactions within the S3/S4 pockets in inhibitor potency enhancement. These findings demonstrated that expanding the utilization of these binding pockets was an effective strategy for developing noncovalent small molecule inhibitors that target SARS-CoV-2 Mpro. Compound 4 demonstrated outstanding in vitro antiviral activity against wild-type SARS-CoV-2 with an EC50 of 9.4 nM. Moreover, oral treatment with compounds 1 and 9 exhibited excellent antiviral potency and substantially ameliorated virus-induced tissue damage in the lungs of Omicron BA.5-infected K18-human ACE2 (K18-hACE2) transgenic mice, indicating that these novel noncovalent inhibitors could be potential oral agents for the treatment of COVID-19.

SARS-CoV-2 high transmission and genomic mutations result in the emergence of new variants that impact COVID-19 vaccine efficacy and virus transmission by evading the host immune system. Wastewater-based epidemiology is an effective approach to monitor SARS-CoV-2 variants circulation in the population but is a challenge due to the presence of reaction inhibitors and the low concentrations of SARS-CoV-2 in this environment. Here, we aim to improve SARS-CoV-2 variant detection in wastewater by employing nested PCR followed by next-generation sequencing (NGS) of small amplicons of the S gene. Eight SARS-CoV-2 wastewater samples from Alegria Wastewater Treatment Plant, in Rio de Janeiro, Brazil, were collected monthly from February to September 2021. Samples were submitted to virus concentration, RNA extraction and nested PCR followed by NGS. The small amplicons were used to prepare libraries for sequencing without the need to perform any fragmentation step. We identified and calculated the frequencies of 29 mutations matching the Alpha, Beta, Gamma, Delta, Omicron, and P.2 variants. Omicron matching-mutations were detected before the lineage was classified as a variant of concern. SARS-CoV-2 wastewater sequences clustered with SARS-CoV-2 variants detected in clinical samples that circulated in 2021 in Rio de Janeiro. We show that sequencing of selected small amplicons of SARS-CoV-2 S gene allows the identification of SARS-CoV-2 variants matching mutations and their frequencies' calculation. This approach may be expanded using customizing primers for additional genomic regions, in order to differentiate current variants. Approaches that allow us to learn how variants emerge and how they relate to clinical outcomes are crucial for our understanding of the dynamics of virus variants circulation, providing valuable data for public health management.

The use of modified nucleotides to suppress the interferon response and maintain translation of self-amplifying RNA (saRNA), which has been achieved for mRNA, has not yet succeeded. We identify modified nucleotides that, when substituted at 100% in saRNA, confer innate immune evasion and robust long-term protein expression, and when formulated as a vaccine, protect against lethal SARS-CoV-2 challenge in mice. This discovery advances saRNA therapeutics by enabling prolonged protein expression at low doses.

Amid changing variant and immunity landscapes since early in the coronavirus disease 2019 (COVID-19) pandemic, common COVID-19 symptoms need better understanding in relation to prior immunity or infecting variant.

American Red Cross blood donors were surveyed during February-April 2022 about prior COVID-19 vaccinations and symptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections. Donations were tested for anti-nucleocapsid antibodies to inform infection history. Restricting analysis to donors with survey-reported infections during the Omicron BA.1-predominant period (19 December 2021 through 19 March 2022), we used multivariable logistic regression to compare symptoms by existing immunity from prior infection or vaccination. Restricting analysis to those with no existing immunity, we compared symptoms by variant-predominant period of their first reported infection (BA.1 vs before).

Among 9505 donors with a BA.1-predominant period infection, donors with prior infection (n = 1115), vaccination (n = 5888), or both (n = 1738) were less likely than those without prior immunity (n = 764) to report loss of taste or smell, lower respiratory tract, constitutional, or gastrointestinal symptoms and more likely to report upper respiratory tract symptoms. Stronger associations followed recent prior infection, vaccination, or more vaccine doses. Among 8539 donors without prior immunity, those with survey-reported infections during the BA.1-predominant period (n = 764) were less likely to report loss of taste or smell, or lower respiratory tract symptoms than those with infections before this period (n = 7775).

Our data suggest that both prior immunity and Omicron predominance redistributed COVID-19 symptoms toward upper respiratory tract presentations and likely both contributed to a decrease in COVID-19 severity over time. These findings may better inform COVID-19 identification in high-immunity settings and demonstrate additional benefits of vaccination.

The SARS-CoV-2 pandemic necessitated effective vaccines that can endure antigenic mutations. Here we demonstrate highly immunogenic conjugate vaccines that elicit broad cross-neutralization to variants of concern (VOC) in animal studies. By utilizing protein-protein conjugation and Toll-Like Receptor (TLR) agonist adjuvants we achieve enhanced immunogenicity compared to unconjugated equivalents. These vaccine candidates induced broad cross-protection against several VOC, a characteristic lacking in early COVID-19 vaccines. Murine neutralizing antibody (nAb) titers from animals vaccinated with Beta-only conjugates were equivalent between Beta, Delta, Omicron BA.1, BA.2, and BA.4/BA.5 variants, which were circulating up to three years after the antigenic Beta strain. Additionally, Beta-Delta bivalent conjugate vaccines readily prevented disease in hamster challenge. Together this demonstrates a vaccine with remarkably broad cross-protection and potential to protect for extended periods despite mutations, without requiring modified boosters or antigen adaption. These techniques can be applied to more recent SARS-CoV-2 strains, and other viruses, highlighting the benefits of protein-protein conjugation coupled with TLR agonist secondary adjuvants.

To control COVID-19 mutations and prevent further spread, periodic revaccination is essential. Despite the substantial evidence supporting vaccine efficacy, hesitancy towards COVID-19 booster doses persists.

We examined factors associated with the booster vaccine uptake and the intention to receive a booster among fully vaccinated adults in Texas (N = 14,543), using a weighted telephone survey in 2022. We employed multiple logistic regression with Lasso-selected variables to identify sociodemographic, geographic, and health-related predictors of booster uptake and intentions.

Of the respondents, 9989 (70 %) respondents reported having received a booster dose. Booster uptake was higher among older (65 years and older), White, publicly insured, and financially stable individuals. It was also higher among those without a history of COVID-19 infection and those with comorbidities and concerns about the virus. Higher odds of being boosted were associated with older age, Asian race, Spanish language, three public health regions (PHR 11, 7, 9/10), and diabetes and HIV diagnoses. Lower odds were observed among smokers, the uninsured, and those experiencing financial struggles. Among those who had not received the booster, greater intentions to receive a booster were observed across all racial/ethnic groups compared to White individuals, Spanish speakers, and the uninsured. Those with diabetes expressed stronger intentions to receive a booster, while individuals previously infected with COVID-19 and males were less inclined to seek a booster. However, individuals expressing concerns about the infection had higher intention to be boosted.

The findings highlighted disparities in booster vaccinations across geographic regions, racial/ethnic groups, and insurance status. Targeted educational initiatives about the importance of booster vaccination are needed, especially for underserved populations with limited access to healthcare. Public health efforts should also focus on countering misinformation and promoting the benefits of boosters through gain-framed messages to motivate vaccine uptake and mitigate the spread of COVID-19.

The coronavirus disease 2019 (COVID-19) pandemic has exerted a catastrophic impact on public health. Meanwhile, the seasonal influenza outbreak overlaps with the current pandemic wave. There is still an urgent need to develop effective therapeutic agents for the treatment of co-infection of multiple respiratory viruses. This study aimed to investigate antiviral effects of EIDD-2801, an orally bioavailable ribonucleoside analog, and its potent therapeutic effects in co-infection of multiple respiratory viruses.

BALB/c mice and hamsters were infected with IFV or SARS-CoV-2, then were dosed orally with EIDD-2801 to measure the antiviral effects of EIDD-2801. Viral replication and mRNA transcription were evaluated by quantitative polymerase chain reaction (qPCR) and protein expression by Western Blot. Influenza viral titer was assessed using EID50 assay.

EIDD-2801 was found to be significantly effective against influenza A virus and influenza B virus. The antiviral activity against SARS-CoV-2 and further co-infection with influenza virus was also distinct. EIDD-2801 had potent antiviral effects against multiple respiratory viruses both in vitro and in vivo.

This study demonstrated that the small-molecule compound EIDD-2801, an orally available broad-spectrum antiviral agent, significantly inhibited the infection of influenza virus and SARS-CoV-2 and effectively protected animals from lethal influenza virus co-infection.

The Coronavirus Immunotherapeutic Consortium (CoVIC) conducted side-by-side comparisons of over 400 anti-SARS-CoV-2 spike therapeutic antibody candidates contributed by large and small companies as well as academic groups on multiple continents. Nine reference labs analyzed antibody features, including in vivo protection in a mouse model of infection, spike protein affinity, high-resolution epitope binning, ACE-2 binding blockage, structures, and neutralization of pseudovirus and authentic virus infection, to build a publicly accessible dataset in the database CoVIC-DB. High-throughput, high-resolution binning of CoVIC antibodies defines a broad and predictive landscape of antibody epitopes on the SARS-CoV-2 spike protein and identifies features associated with durable potency against multiple SARS-CoV-2 variants of concern and high in vivo efficacy. Results of the CoVIC studies provide a guide for selecting effective and durable antibody therapeutics and for immunogen design as well as providing a framework for rapid response to future viral disease outbreaks.

In England, and many other countries, immunity to SARS-CoV-2 infection and COVID-19 disease is highly heterogeneous. Immunity has been acquired through natural infection, primary and booster vaccination, while protection has been lost through waning immunity and viral mutation. During the height of the pandemic in England, the main aim was to rapidly protect the population and large supplies of vaccine were pre-purchased, eliminating the need for cost-effective calculations. As we move to an era where for the majority of the population SARS-CoV-2 infections cause relatively mild disease, and vaccine stocks need to be re-purchased, it is important we consider the cost-effectiveness and economic value of COVID-19 vaccination programmes. Here using data from 2023 and 2024 in England on COVID-19 hospital admissions, ICU admissions and deaths, coupled with bespoke health economic costs, we consider the willingness to pay threshold for COVID-19 vaccines in different age and risk groups. Willingness to pay thresholds vary from less than £1 for younger age-groups without any risk factors, to over £100 for older age-groups with comorbidities that place them at risk. This extreme non-linear dependence on age, means that despite the different method of estimating vaccine effectiveness, there is considerable qualitative agreement on the willingness to pay threshold, and therefore which ages it is cost-effective to vaccinate. The historic offer of COVID-19 vaccination to those 65 and over for the autumn 2023 programme and those over 75 for the spring 2023 programme, aligns with our cost- effective threshold for pre-purchased vaccine when the only cost was administration. However, for future programmes, when vaccine costs are included, the age-thresholds slowly increase thereby demonstrating the continued importance of protecting the eldest and most vulnerable in the population.

Timely and complete administration of multiple-dose vaccines is essential to guarantee the efficacy. Our study aimed to investigate how people's vaccination attitudes changed over the course of the multi-dose vaccination schedule and comprehensively reported a phenomenon of vaccination burnout. The participants' vaccination burnout levels were quantified by our designed vaccination burnout scale. This study is a retrospective cross-sectional study. Among 3068 valid participants, 2991 had finished the routine two shots of COVID-19 vaccine, and 2367 had a positive attitude towards the primary doses of vaccination. Notably, 232 participants who previously had a positive attitude towards primary doses of vaccination refused to take additional multiple shots, and another 83 had changed their positive attitudes to negative, despite having taken the third shot. Participants whose attitudes or behaviors had changed had higher scores of vaccination burnout than those who still maintained a positive attitude (Z=-8.491, P < .001). The frequency of actively paying attention to the related disease news, occupation, monthly income, and residence of the participants were key factors associated with the vaccination burnout. Interventions should be implemented to alleviate the exhausted attitudes and improve people's compliance with vaccination schedules against the future pandemic.

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.

Since 2020, numerous compounds have been investigated for their potential use in treating SARS-CoV-2 infections. By identifying the molecular targets during the virus replication process, rationally designed anti-SARS-CoV-2 agents are developed. Among these targets, the main protease (Mpro) is a crucial enzyme required for virus replication, and its highly conserved characteristic make it an important drug target for the development of anti-SARS-CoV-2 drugs. Herein, we utilized warhead-based design strategy to conduct the structural optimization of M-1 developed through virtual screening, leading to a series of novel Mpro inhibitors with 4-(quinolin-2-yl)aniline scaffold. Among them, M-32 exhibited good SARS-CoV-2 Mpro inhibitory activity (IC50 = 5.2 μM) with a nearly 25-fold increase. Isothermal titration calorimetry (ITC) directly proved that M-32 binds directly to SARS-CoV-2 Mpro in an entropy-driven manner. Mass spectrometry (MS) further confirmed the covalent binding ability of M-32 to Mpro. Meanwhile, M-32 effectively inhibited the replication of SARS-CoV-2 in Vero E6 cells (EC50 = 5.29 μM).

Adenovirus (Ad) vectors are widely used for gene delivery, and some of them have been approved for vaccine development. In particular, the recombinant COVID-19 vaccine for inhalation, which was developed using adenovirus type 5 (Ad5), represents a milestone in respiratory immunization. Owing to the high pre-existing immunity (PEI) to Ad5, the development of an adenoviral vector with lower PEI and higher immunogenicity has been explored. However, the majority of the developed novel Ad vectors showed suboptimal immunogenicity compared to Ad5 in animal models.

In this study, we constructed a novel replication-deficient viral vector based on human adenovirus type 4 (Ad4), which has long been used as a live virus vaccine with a favorable safety profile in the U.S. military. The mice were immunized intramuscularly or intranasally with an Ad4-vectored vaccine to verify immune responses and protective efficacy.

Compared with Ad5, the novel Ad4 vector showed comparable viral growth kinetics and transgene expression in cells and similar exogenous protein expression and distribution in mice. Furthermore, the Ad4-vectored vaccine elicited superior humoral and cellular responses and protective effects when vaccinated intranasally than those triggered by the Ad5-vectored vaccine. Finally, the heterologous Ad5 prime and Ad4 boost immunization showed better immunogenicity and protective efficacy.

This study broadens the research trajectory of adenovirus-vectored vaccines and offers a new option for the development of recombinant viral-vectored vaccines.

Vaccination has played a key role in limiting the impacts of COVID-19. Even though the acute phase of the COVID-19 pandemic is now over, the potential for substantial numbers of cases and deaths due to novel SARS-CoV-2 variants remains. In the Republic of Korea, a strategy of vaccinating individuals in high-risk groups annually began in October 2023.

We used mathematical modeling to assess the effectiveness of alternative vaccination strategies under different assumptions about the number of available vaccine doses. An age-structured transmission model was developed using vaccination and seropositivity data. Various vaccination scenarios were considered, taking into account the effect of undetected or unreported cases (with different levels of reporting by age group): S1: prioritizing vaccination towards the oldest individuals; S2: prioritizing vaccination towards the youngest individuals; and S3: spreading vaccines among all age groups.

Our analysis reveals three key findings. First, administering vaccines to older age groups reduces the number of deaths, while instead targeting younger individuals reduces the number of infections. Second, with approximately 6,000,000 doses available annually, it is recommended that older age groups are prioritized for vaccination, achieving a substantial reduction in the number of deaths compared to a scenario without vaccination. Finally, since case detection (and subsequent isolation) affects transmission, the number of cumulative cases was found to be affected substantially by changes in the reporting rate.

In conclusion, vaccination and case detection (facilitated by contact tracing) both play important roles in limiting the impacts of COVID-19. The mathematical modeling approach presented here provides a framework for assessing the effectiveness of different vaccination strategies in scenarios with limited vaccine supply.

SARS-CoV-2 has undergone repeated and rapid evolution to circumvent host immunity. However, outside of prolonged infections in immunocompromised hosts, within-host positive selection has rarely been detected. Here we combine daily longitudinal sampling of individuals with replicate sequencing to increase the accuracy of and lower the threshold for variant calling. We sequenced 577 specimens from 105 individuals in a household cohort during the BA.1/BA.2 variant period. Individuals exhibited extremely low viral diversity, and we estimated a low within-host evolutionary rate. Within-host dynamics were dominated by genetic drift and purifying selection. Positive selection was rare but highly concentrated in spike. A Wright Fisher Approximate Bayesian Computational model identified positive selection at 14 loci with 7 in spike, including S:448 and S:339. This detectable immune-mediated selection is unusual in acute respiratory infections and may be caused by the relatively narrow antibody repertoire in individuals during the early Omicron phase of the SARS-CoV-2 pandemic.

The effect of the COVID-19 booster vaccination and the long-term consequences concerning preventing post-COVID-19 condition (PCC) remains unclear. We aimed to investigate the association of COVID-19 booster vaccination dose and vaccination timing before infection with the risk of PCC during the Omicron variant-dominant wave.

This population-based study included patients confirmed with COVID-19 (extracted from the Health Center Real-time Information-sharing System) aged 20-69 years, who were infected between 1 July and 31 August 2022. We used a self-report questionnaire to evaluate PCC and extracted information on vaccination from the municipal vaccine registry system. We calculated multiple propensity scores for COVID-19 vaccination status (unvaccinated, 1-2 doses and ≥3 doses) to control for baseline population differences. We then used a logistic regression model with inverse probability weighting to analyse the associations between the number of vaccine doses and the risk of PCC. Additionally, we conducted stratified analysis by gender and subgroup analysis for respiratory and neurological symptoms. Multivariable logistic regression was used to analyse the association between vaccination timing and PCC risk, adjusting for vaccination doses.

Of the 7936 participants with COVID-19 (mean age 42.9 years, 4553 women), 940 (11.8%) had at least 1 PCC. Compared with people unvaccinated, those vaccinated ≥3 times before the infection had a lower probability of PCC with the OR of 0.69 (95% CI: 0.53-0.90), although we detected no association with one or two doses. This association was present in women (≥3 doses vs. unvaccinated OR: 0.70, 95% CI: 0.51-0.95) but not in men. Those vaccinated ≥3 times had fewer neurological symptoms compared with those unvaccinated (OR: 0.61, 95% CI: 0.45-0.83); however, no significant association was found for respiratory symptoms.

This study suggests that booster vaccination could lower the risk of PCC.

In May 2023 the World Health Organization (WHO) declared the end of COVID-19 as a public health emergency. Seroprevalence studies performed in African countries, such as Cameroon, depicted a much higher COVID-19 burden than reported by the WHO. To better understand humoral responses kinetics following infection, we enrolled 333 participants from Yaoundé, Cameroon between March 2020 and January 2022. We measured the levels of antibodies targeting the SARS-CoV-2 receptor-binding-domain (RBD) and the Spike glycoproteins of Delta, Omicron BA.1 and BA.4/5 and the common cold coronavirus HCoV-OC43. We also evaluated plasma capacity to neutralize authentic SARS-CoV-2 virus and to mediate Antibody-Dependent Cellular Cytotoxicity (ADCC). Most individuals mounted a strong antibody response against SARS-CoV-2 Spike. Plasma neutralization waned faster than anti-Spike binding and ADCC. We observed differences in humoral responses by age and circulating variants. Altogether, we show a global overview of antibody dynamics and functionality against SARS-CoV-2 in Cameroon.

Live attenuated vaccines against SARS-CoV-2 activate all phases of host immunity resembling a natural infection and they block viral transmission more efficiently than existing vaccines in human use. In our prior work, we characterised an attenuated SARS-CoV-2 variant, designated d16, which harbours a D130A mutation in the NSP16 protein, inactivating its 2'-O-methyltransferase function. The d16 variant has demonstrated an ability to induce both mucosal and sterilising immunity in animal models. However, further investigation is required to identify any additional modifications to d16 that could mitigate concerns regarding potential virulence reversion and the suboptimal regulation of the proinflammatory response.

Mutations were introduced into molecular clone of SARS-CoV-2 and live attenuated virus was recovered from cultured cells. Virological, biochemical and immunological assays were performed in vitro and in two animal models to access the protective efficacies of the candidate vaccine strain.

Here we describe evaluation of a derivative of d16. We further modified the d16 variant by inverting the open reading frame of the ORF3a accessory protein, resulting in the d16i3a strain. This modification is anticipated to enhance safety and reduce pathogenicity. d16i3a appeared to be further attenuated in hamsters and transgenic mice compared to d16. Intranasal vaccination with d16i3a stimulated humoural, cell-mediated and mucosal immune responses, conferring sterilising protection against SARS-CoV-2 Delta and Omicron variants in animals. A version of d16i3a expressing the XBB.1.16 spike protein further expanded the vaccine's protection spectrum against circulating variants. Notably, this version has demonstrated efficacy as a booster in hamsters, providing protection against Omicron subvariants and achieving inhibition of viral transmission.

Our work established a platform for generating safe and effective live attenuated vaccines by dual inactivation of NSP16 and ORF3a of SARS-CoV-2.

This work was supported by National Key Research and Development Program of China (2021YFC0866100, 2023YFC3041600, and 2023YFE0203400), Hong Kong Health and Medical Research Fund (COVID190114, CID-HKU1-9, and 23220712), Hong Kong Research Grants Council (C7142-20GF and T11-709/21-N), Hong Kong Innovation and Technology Commission grant (MHP/128/22), Guangzhou Laboratory (EKPG22-01) and Health@InnoHK (CVVT). Funding sources had no role in the writing of the manuscript or the decision to submit it for publication.

The impact of treatment-emergent amino acid substitutions (TEAASs) in severe acute respiratory syndome coronavirus 2 (SARS-CoV-2) 3C-like protease (3CLpro) on clinical and virologic outcomes was evaluated in patients with mild-to-moderate coronavirus disease 2019 (COVID-19) who received ensitrelvir 125 mg in the SCORPIO-SR trial. Individuals were randomised to ensitrelvir or matched placebo once daily for 5 days (first dose <72 h after disease onset). 3CLpro-TEAASs were identified by sequencing nsp5 encoding 3CLpro from pre- and post-treatment nasopharyngeal swabs. Time to resolution of a composite of five characteristic COVID-19 symptoms (TTR) was compared between patients with and without the most common 3CLpro-TEAASs in the ensitrelvir arm. The ensitrelvir and placebo intention-to-treat populations comprised 345 and 341 patients, respectively. 3CLpro-TEAASs were detected in 19/204 (9.3%) ensitrelvir-treated and 3/137 (2.2%) placebo-treated patients with paired sequence data. The most common 3CLpro-TEAASs in the ensitrelvir arm were M49L (n = 12), M49I (n = 3) and S144A (n = 2). In the placebo arm, all 3CLpro-TEAASs occurred in ≤1 patient. Median (95% confidence interval) TTR was comparable between patients with and without those TEAASs (158.8 h [112.1-281.9] vs 189.7 h [151.4-234.4]). Mean viral RNA levels declined more slowly in patients with M49L/I or S144A versus those without. Reductions in viral titre were unaffected by these TEAASs. The characteristics of recombinant SARS-CoV-2 with 3CLpro mutations were explored in vitro. Recombinant viruses with some 3CLpro mutations had reduced susceptibility to ensitrelvir in vitro, with limited effects on viral and competitive fitness. Continued surveillance is warranted to monitor the spread of viruses with 3CLpro mutations.

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.