Analysis of SARS-CoV-2 mutations associated with resistance to therapeutic monoclonal antibodies that emerge after treatment

Efficient boosting of Omicron-reactive memory B cells after breakthrough infection protects from repeated exposure

Exploring the impact of persistent mutations in SARS-CoV-2 variants and reduced immunity on breakthrough infections (BTIs) is crucial, particularly in understanding how antigen-specific memory B cells (MBCs) respond to new variants. We followed 107 participants who received the ancestral inactivated vaccine and experienced one or two Omicron BTIs over six months. Using flow cytometry, SARS-CoV-2 antigen probes, single-cell RNA sequencing, and B cell receptor (BCR) profiling, we assessed MBCs and immune diversity. Our findings revealed that although neutralizing antibody levels decreased over time, the number of specific MBCs remained stable and matured progressively. Notably, pre-existing Omicron-specific MBCs played a key role in preventing secondary Omicron infections. Differential gene analysis showed enrichment in antigen processing and immune regulation pathways, while clonal lineage analysis revealed more B cell expansion and V(D)J gene-specific rearrangements in high neutralization samples. These results emphasize MBCs' critical role in long-term immunity and inform future vaccination strategies.

Potent and broadly neutralizing antibodies against sarbecoviruses elicited by single ancestral SARS-CoV-2 infection

The emergence of various SARS-CoV-2 variants presents challenges for antibody therapeutics, emphasizing the need for more potent and broadly neutralizing antibodies. Here, we employed an unbiased screening approach and successfully isolated two antibodies from individuals with only exposure to ancestral SARS-CoV-2. One of these antibodies, CYFN1006-1, exhibited robust cross-neutralization against a spectrum of SARS-CoV-2 variants, including the latest KP.2, KP.3 and XEC, with consistent IC50 values ranging from ~1 to 5 ng/mL. It also displayed broad neutralization activity against SARS-CoV and related sarbecoviruses. Structural analysis revealed that these antibodies target shared hotspot but mutation-resistant epitopes, with their Fabs locking receptor binding domains (RBDs) in the "down" conformation through interactions with adjacent Fabs and RBDs, and cross-linking Spike trimers into di-trimers. In vivo studies conducted in a JN.1-infected hamster model validated the protective efficacy of CYFN1006-1. These findings suggest that antibodies with cross-neutralization activities can be identified from individuals with exclusively ancestral virus exposure.

Development of antiviral drugs for COVID-19 in 2025: unmet needs and future challenges

INTRODUCTION

The success in the coronavirus infectious disease 2019 (COVID-19) pandemic containment largely originated from vaccine- and infection-elicited immunity, with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection only marginally mitigated by the availability of antiviral drugs. The current lack of effective antiviral prophylactic and therapeutic agents in immunocompromised patients highlights the need for a radical change in the design of both drug manufacturing and clinical trials.

AREAS COVERED

In this review, the authors summarize their suggestions for manufacturers, by reviewing classes of small molecule antivirals and passive immunotherapies and highlighting their limitations and unexploited potential.

EXPERT OPINION

Molecular and serological testing of patients can improve appropriateness. Efficacy of antivirals can be improved by combining different therapeutic classes while preserving economical sustainability. Respiratory delivery should be better investigated in clinical trials.

Production of a monoclonal antibody targeting the SARS-CoV-2 Omicron spike protein and analysis of SARS-CoV-2 Omicron mutations related to monoclonal antibody resistance

SARS-CoV-2 mutations have resulted in the emergence of multiple concerning variants, with Omicron being the dominant strain presently. Therefore, we developed a monoclonal antibody (mAb) against the spike (S) protein of SARS-CoV-2 Omicron for therapeutic applications. We established the 1E3H12 mAb, recognizing the receptor binding domain (RBD) of the Omicron S protein, and found that the 1E3H12 mAb can efficiently recognize the Omicron S protein with weak affinity to the Alpha, Beta, and Mu variants, but not to the parental strain and Delta variant. Based on in vitro assays, the mAb demonstrated neutralizing activity against Omicron BA.1, BA.4/5, BQ.1.1, and XBB. A humanized antibody was further produced and proved to have neutralizing activity. To verify the potential limitations of the 1E3H12 mAb due to viral escape of SARS-CoV-2 Omicron variants, we analyzed the emergence of variants by whole genome deep sequencing after serial passage in cell culture. The results showed a few unique S protein mutations in the genome associated with resistance to the mAb. These findings suggest that this antibody not only contributes to the therapeutic arsenal against COVID-19 but also addresses the ongoing challenge of antibody resistance among the evolving subvariants of SARS-CoV-2 Omicron.

Lessons from the Use of Monoclonal Antibodies to SARS-CoV-2 Spike Protein During the COVID-19 Pandemic

Monoclonal antibodies (mAbs) targeting the SARS-CoV-2 Spike protein were deployed during the COVID-19 pandemic. While all of the clinically authorized mAbs were eventually defeated by SARS-CoV-2 variants, they were highly effective in preventing disease progression when given early in the course of the disease. The experience with mAbs to SARS-CoV-2 offers important lessons for the use of mAbs in future infectious disease emergencies, such as choosing mAbs that target conserved epitopes and designing cocktails to reduce the emergence of escape variants. Planning for future use must include the creation of infusion centers and the development of strategies to minimize the emergence of escape variants.

Using Passive Antibody Therapies in the Next Pandemic

The twenty-first century has witnessed seven human viral pandemics. Approximately once every three to four years over the past quarter-century, the world has experienced a new viral epidemic that expanded well beyond its original national borders to become a pandemic. The probability that another pandemic caused by a previously unknown agent will occur in the near future is thus very high and public health agencies must prioritize mechanisms for detecting their first signals. At the onset of these recent pandemics, no specific therapeutic agent was available for any of the newly emergent pathogens. However, convalescent plasma therapy can be available as soon as there are survivors and is likely to be effective if used early and in sufficient strength. But for the three forms of passive antibody-convalescent plasma, monoclonal antibodies, and hyperimmune globulins-to be available and effective in a pandemic situation, careful strategic planning will be necessary. In the pre-pandemic period, we must reinforce the capacities of blood banks and plasma fractionating companies in the production and storage of their products; ensure that outpatient settings can provide intravenous products; educate providers in the proper use of plasma; and create a research infrastructure to examine the effectiveness of passive antibody products. Once a pandemic is underway, regulatory bodies should simplify the approval of research and emergency use protocols and develop treatment registries. Incentives for the rapid production of monoclonal antibodies and hyperimmune globulins will likely be required. A national resource to link providers with passive antibody products and national databases to monitor pandemic progress and pandemic treatment will permit the most effective allocation of pandemic-fighting resources. We cannot afford to wait until the next pandemic is upon us to respond. The time to strengthen clinical, research, and manufacturing infrastructure to permit us to be ready to confront the next new virulent pathogen is now.

Single Monoclonal Antibodies Should Not Be Used for COVID-19 Therapy: A Call for Antiviral Stewardship

The COVID-19 pandemic witnessed the greatest deployment of monoclonal antibody (mAb) therapies for an infectious disease, but all were defeated by SARS-CoV-2 evolution. As new mAbs are developed, the infectious disease community needs stewardship practices to reduce emergence of resistance.

Impact analysis of SARS-CoV-2 vaccination in patients treated with monoclonal antibodies: A monocentric experience

BACKGROUND

Since the discovery of SARS-CoV-2, no treatment has been able to completely eradicate the virus. The study aimed to evaluate the virological and clinical impact of the vaccination in SARS-CoV-2 infected patients treated with monoclonal antibodies (mAbs).

METHODS

This single-centre, observational, retrospective, real-life study was performed on SARS-CoV-2 symptomatic outpatients and inpatients treated with mAbs from March 2021 to November 2022 includes 726 patients. Each patient received available mAbs (bamlanivimab-etesevimab or casirivimab-indevimab or sotrovimab or tixagevimab-cilgavimab) according to the circulating virus strains. Age, comorbidities, vaccination status, death rates, duration of virological clearance, average length of stay, risk factors, and hospitalization or ICU admission were recorded.

RESULTS

Of 726 patients with complete data analyzed (median age 64), 516 outpatients and 210 inpatients were included. Vaccination status was known for all participants: 74.4 % and 51.7 % were vaccinated against SARS-CoV-2 among inpatients and outpatients, respectively. A shorter duration of virological clearance was observed in the vaccinated group, with a median of 16 days (IQR 15-17), compared to 19 days (IQR 18-21) in the unvaccinated group [HR 1.21; p < 0.032]. Multivariate analysis of virological clearance also showed statistical significance with tixagevimab cilgavimab 300 mg/300 mg (HR 2.73, p value < 0.001). No significant difference was found in worsening [OR 1,29; p = 0.57] and mortality [OR 0.65; p = 0.81] rates between vaccinated and unvaccinated patients treated with mAbs.

CONCLUSIONS

Key findings include a shorter duration of virological clearance in vaccinated outpatients but no significant differences in worsening or mortality rates between vaccinated and unvaccinated patients treated with mAbs. The study suggests a potential synergistic role of mAbs in accelerating virological clearance in vaccinated patients with mild to moderate COVID-19, with differing effects in hospitalized patients. Therefore, it is essential to implement health surveillance in high-risk patients with comorbidities in order to identify early any variants that might otherwise escape neutralizing antibodies.

Molecular and phenotypic characteristics of respiratory syncytial virus isolates recovered from medically vulnerable children: An exploratory analysis of a phase 2/3 randomized, double-blind, palivizumab-controlled trial of nirsevimab (MEDLEY)

BACKGROUND

Nirsevimab is an extended half-life monoclonal antibody (mAb) licensed for the prevention of respiratory syncytial virus (RSV)-associated lower respiratory tract disease in neonates, infants and medically vulnerable children. We characterized RSV isolates recovered from participants enrolled in MEDLEY: a randomized, palivizumab-controlled phase 2/3 trial of nirsevimab in infants born preterm and/or with congenital heart disease or chronic lung disease of prematurity.

METHODS

Participants were assessed in two RSV seasons (Season 1 and 2). Season 1 participants were randomized (2:1) to receive a single dose of nirsevimab (50 mg if weight <5 kg or 100 mg if weight ≥5 kg in Season 1; 200 mg in Season 2) followed by four monthly doses of placebo, or five once-monthly doses of palivizumab (15 mg/kg weight per dose). Season 2 participants continued nirsevimab and placebo (nirsevimab/nirsevimab) or were re-randomized (1:1) to switch to nirsevimab (palivizumab/nirsevimab) or continue palivizumab (palivizumab/palivizumab). Cases of RSV infection were identified by central testing of nasal swabs from participants seeking medical attention for respiratory illnesses. Nirsevimab and palivizumab binding site substitutions were assessed via microneutralization assay.

RESULTS

Twenty-five cases of confirmed RSV infection were observed during the trial and sequenced: 12 in nirsevimab recipients and 10 in palivizumab recipients during Season 1, and 1 case in each Season 2 group. Molecular sequencing of RSV A (n = 14) isolates detected no nirsevimab binding site substitutions, and 3 palivizumab neutralization-resistant substitutions (Lys272Met, Lys272Thr, Ser275Leu). The nirsevimab binding site Ile206Met:Gln209Arg and Ile206Met:Gln209Arg:Ser211Asn substitutions were the only anti-RSV mAb binding site substitutions detected among RSV B isolates (n = 11). Nirsevimab neutralized all nirsevimab and palivizumab binding site substitutions in RSV A and B isolates recovered from MEDLEY participants.

CONCLUSION

No binding site substitution detected during MEDLEY affected RSV susceptibility to nirsevimab neutralization.

Estimates of actual and potential lives saved in the United States from the use of COVID-19 convalescent plasma

In the Spring of 2020, the United States of America (USA) deployed COVID-19 convalescent plasma (CCP) to treat hospitalized patients. Over 500,000 patients were treated with CCP during the first year of the pandemic. In this study, we estimated the number of actual inpatient lives saved by CCP treatment in the United States of America based on CCP weekly use, weekly national mortality data, and CCP mortality reduction data from meta-analyses of randomized controlled trials and real-world data. We also estimate the potential number of lives saved if CCP had been deployed for 100% of hospitalized patients or used in 15 to 75% of outpatients. Depending on the assumptions modeled in stratified analyses, we estimated that CCP saved between 16,476 and 66,296 lives. The CCP ideal use might have saved as many as 234,869 lives and prevented 1,136,133 hospitalizations. CCP deployment was a successful strategy for ameliorating the impact of the COVID-19 pandemic in the USA. This experience has important implications for convalescent plasma use in future infectious disease emergencies.

Comparison of Dual Monoclonal Antibody Therapies for COVID-19 Evolution: A Multicentric Retrospective Study

BACKGROUND

Neutralizing antibodies targeting the SARS-CoV-2 Spike protein reduce COVID-19-related risk of hospitalization, particularly in high-risk individuals. The COCOPREV-R study aimed to evaluate and compare clinical outcomes in high-risk SARS-CoV-2 patients treated with dual monoclonal antibody therapies and to identify associated virological factors.

METHODS

The COCOPREV-R study retrospectively collected real-world data from high-risk patients receiving Bamlanivimab/Etesevimab or Casirivimab/Imdevimab dual monoclonal antibody therapies (22 February 2021 to 15 June 2021).

RESULTS

The study included 1004 patients with COVID-19, of whom 691 received Bamlanivimab/Etesevimab and 313 received Casirivimab/Imdevimab. The alpha variant represented 90.1% of those for whom data were available. The risk of hospitalization within 30 days was lower with Bamlanivimab/Etesevimab (12.7%, CI 95% [9.9-16.3%]) compared to Casirivimab/Imdevimab (28.4%, CI 95% [22.7-35.1%) (p < 0.001). The 30-day mortality rates were comparable between both groups (p = 0.982). Analysis of SARS-CoV-2 PCR negativity showed no difference between the two treatment groups (95.2% [93.0-96.9%] and 93.5% [89.1-96.6%] until day 30, p = 0.851 for Bamlanivimab/Etesevimab and Casirivimab/Imdevimab, respectively). Among persistently positive samples with available sequencing results (n = 43), Spike protein changes occurred only in Bamlanivimab/Etesevimab (42.9%) vs. Casirivimab/Imdevimab (0.0%) groups. Q493R (25.0%) and E484K (12.5%) were the most common mutations selected by Bamlanivimab/Etesevimab in follow-up samples. Other factors (immunodepression, comorbidities, and age) did not appear to be associated with the occurrence of Spike protein mutations.

CONCLUSIONS

A higher rate of hospitalization was seen with Casirivimab/Imdevimab (RONAPREVE®) in comparison with Bamlanivimab/Etesevimab treatment, but with the emergence of Spike mutations only in the Bamlanivimab/Etesevimab group.

Deep mutational scanning reveals functional constraints and antibody-escape potential of Lassa virus glycoprotein complex

Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of the Lassa virus's glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we used pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affected cell entry and antibody neutralization. Our experiments defined functional constraints throughout GPC. We quantified how GPC mutations affected neutralization with a panel of monoclonal antibodies. All antibodies tested were escaped by mutations that existed among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid the design of therapeutics and vaccines.

Monoclonal Antibody Therapies Against SARS-CoV-2: Promises and Realities

Monoclonal antibodies targeting the Spike protein of SARS-CoV-2 have been widely deployed in the ongoing COVID-19 pandemic. I review here the impact of those therapeutics in the early pandemic, ranging from structural classification to outcomes in clinical trials to in vitro and in vivo evidence of basal and treatment-emergent immune escape. Unfortunately, the Omicron variant of concern has completely reset all achievements so far in mAb therapy for COVID-19. Despite the intrinsic limitations of this strategy, future developments such as respiratory delivery of further engineered mAb cocktails could lead to improved outcomes.

Convalescent Plasma and Other Antibody Therapies for Infectious Diseases-Lessons Learned from COVID-19 and Future Prospects

Antiviral passive antibody therapy includes convalescent plasma, hyperimmune globulin, and monoclonal antibodies. Passive antibodies have proven effective in reducing morbidity and mortality for SARS-CoV-2 and other infectious diseases when given early in the disease course with sufficiently high specific total and neutralizing antibody levels. Convalescent plasma can be delivered to patients before vaccination implementation or novel drug production. Carefully designed and executed randomized controlled trials near the pandemic outset are important for regulatory bodies, healthcare workers, guideline committees, the public, and the government. Unfortunately, many otherwise well-designed antibody-based clinical trials in COVID-19 were futile, either because they intervened too late in the disease or provided plasma with insufficient antibodies. The need for early treatment mandates outpatient clinical trials in parallel with inpatient trials. Early outpatient COVID-19 convalescent plasma transfusion with high antibody content within 9 days of symptom onset has proven effective in blunting disease progression and reducing hospitalization, thus reducing hospital overcrowding in a pandemic. Convalescent plasma offers the opportunity for hope by enabling community participation in outpatient curative therapy while monoclonal therapies, vaccines, and drugs are being developed. Maintaining the appropriate infrastructure for antibody infusion in both outpatient and inpatient facilities is critical for future pandemic readiness.

An update on the anti-spike monoclonal antibody pipeline for SARS-CoV-2

BACKGROUND

Anti-spike monoclonal antibodies represent one of the most tolerable prophylaxis and therapies for COVID-19 in frail and immunocompromised patients. Unfortunately, viral evolution in Omicron has led all of them to failure.

OBJECTIVES

We review here the current pipeline of anti-spike mAb's, discussing in detail the most promising candidates.

SOURCES

We scanned PubMed, ClinicalTrials.gov and manufacturers' press releases for clinical studies on anti-spike monoclonal antibodies.

CONTENT

We present state-of-art data clinical progress for AstraZeneca's AZD3152, Invivyd's VYD222, Regeneron's REGN-17092 and Aerium Therapeutics' AER-800.

IMPLICATIONS

The anti-spike monoclonal antibody clinical pipeline is currently limited to few agents (most being single antibodies) with unknown efficacy against the dominant JN.1 sublineage. The field of antibody-based therapies requires boosting by both manufacturers and institutions.

Comprehensive procedure for injecting Evusheld® for hematological diseases in a single institute

Tixagevimab and cilgavimab (EVA, Evusheld®), monoclonal antibody combination treatments, consisted of two neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). EVA showed prophylactic and therapeutic effects against coronavirus disease 2019. The Japanese Society of Hematology recommended EVA for such patients with active treatment, but each institution decided on comprehensive administration. We develop a systematic procedure for comprehensive EVA injection prophylactically in patients with hematological malignancies without any over/under-indication. We listed all patients with the required indications from November 2022 to March 2023. We included 178 cases, 84 females and 94 males, with a median age of 70 (range: 19-90) years. Underlying diseases are myeloid neoplasms in 36 (20%), lymphoid neoplasms in 75 (73%), and others. Indications were intensively hematological malignancy treatment, rituximab treatment within 12 months, burton kinase inhibitor treatment, after chimeric antigen receptor T cell immunotherapy, and after stem cell transplantation in 74 (41%), 73 (41%), 3 (2%), 5 (3%), and 23 (13%) cases, respectively. Of the 178 cases, 22 (12.4%) refused EVA injection. Further, 42 and 136 cases were administered outpatient and inpatient, respectively. Over 95% of the listed cases received EVA injection within 3 months. No severe toxicities were observed among them (N = 156), and 8 (5.2%) cases had breakthrough SARS-CoV-2 infection, which was significantly lower (P = 0.02) than those without EVA (4 [18.2%] of 22 cases). Both groups showed no moderate or severe infection cases. This single-center experience showed that comprehensive EVA injection management effectively generated safer completion with preferable clinical impact.

Considerations for the development of monoclonal antibodies to address new viral variants in COVID-19

INTRODUCTION

Monoclonal antibody (mAb) therapies proved safe and effective in preventing progression of COVID-19 to hospitalization, but most were eventually defeated by continued viral evolution. mAb combinations and those mAbs that were deliberatively selected to target conserved regions of the SARS-CoV-2 spike protein proved more resilient to viral escape variants as evident by longer clinical useful lives.

AREAS COVERED

We searched PubMed for literature covering the need, development, and use of mAb therapies for COVID-19. As much of humanity now has immunity to SARS-CoV-2, the population at most risk is that of immunocompromised individuals. Hence, there continues to be a need for mAb therapies for immunocompromised patients. However, mAb use in this population carries the risk for selecting mAb-resistant variants, which could pose a public health concern if they disseminate to the general population.

EXPERT OPINION

Going forward, structural knowledge of the interactions of Spike with its cellular receptor has identified several regions that may be good targets for future mAb therapeutics. A focus on designing variant-resistant mAbs together with cocktails that target several epitopes and the use of other variant mitigating strategies such as the concomitant use of small molecule antivirals and polyclonal preparations could extend the clinical usefulness of future preparations.

Antibody drugs targeting SARS-CoV-2: Time for a rethink?

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) heavily burdens human health. Multiple neutralizing antibodies (nAbs) have been issued for emergency use or tested for treating infected patients in the clinic. However, SARS-CoV-2 variants of concern (VOC) carrying mutations reduce the effectiveness of nAbs by preventing neutralization. Uncoding the mutation profile and immune evasion mechanism of SARS-CoV-2 can improve the outcome of Ab-mediated therapies. In this review, we first outline the development status of anti-SARS-CoV-2 Ab drugs and provide an overview of SARS-CoV-2 variants and their prevalence. We next focus on the failure causes of anti-SARS-CoV-2 Ab drugs and rethink the design strategy for developing new Ab drugs against COVID-19. This review provides updated information for the development of therapeutic Ab drugs against SARS-CoV-2 variants.

Monoclonal Antibody Therapies for Infectious Diseases

In contrast to therapy in oncology and immune-related diseases, where dozens of monoclonal antibodies (mAbs) have been introduced, often in transformative fashion, the use of mAbs for infectious diseases is generally underdeveloped, with fewer than a dozen mAbs currently licensed for the treatment of microbial diseases. This situation is paradoxical given that antibodies are major products of the immune system for protecting against infectious diseases. The underdevelopment of mAbs for infectious diseases has several causes including the availability of effective therapy against many microbial diseases, the fact that many pathogenic microbes are antigenically diverse and thus all strains are not covered by a single mAb, and the high expense of mAb therapies. Despite these hurdles the number of mAbs licensed for infectious disease indications is slowly increasing and there are numerous opportunities for the development of mAbs in the prevention and treatment of microbial diseases.

COVID-19 therapeutics

SUMMARYSince the emergence of COVID-19 in 2020, an unprecedented range of therapeutic options has been studied and deployed. Healthcare providers have multiple treatment approaches to choose from, but efficacy of those approaches often remains controversial or compromised by viral evolution. Uncertainties still persist regarding the best therapies for high-risk patients, and the drug pipeline is suffering fatigue and shortage of funding. In this article, we review the antiviral activity, mechanism of action, pharmacokinetics, and safety of COVID-19 antiviral therapies. Additionally, we summarize the evidence from randomized controlled trials on efficacy and safety of the various COVID-19 antivirals and discuss unmet needs which should be addressed.

Research Progress on Spike-Dependent SARS-CoV-2 Fusion Inhibitors and Small Molecules Targeting the S2 Subunit of Spike

Since the beginning of the COVID-19 pandemic, extensive drug repurposing efforts have sought to identify small-molecule antivirals with various mechanisms of action. Here, we aim to review research progress on small-molecule viral entry and fusion inhibitors that directly bind to the SARS-CoV-2 Spike protein. Early in the pandemic, numerous small molecules were identified in drug repurposing screens and reported to be effective in in vitro SARS-CoV-2 viral entry or fusion inhibitors. However, given minimal experimental information regarding the exact location of small-molecule binding sites on Spike, it was unclear what the specific mechanism of action was or where the exact binding sites were on Spike for some inhibitor candidates. The work of countless researchers has yielded great progress, with the identification of many viral entry inhibitors that target elements on the S1 receptor-binding domain (RBD) or N-terminal domain (NTD) and disrupt the S1 receptor-binding function. In this review, we will also focus on highlighting fusion inhibitors that target inhibition of the S2 fusion function, either by disrupting the formation of the postfusion S2 conformation or alternatively by stabilizing structural elements of the prefusion S2 conformation to prevent conformational changes associated with S2 function. We highlight experimentally validated binding sites on the S1/S2 interface and on the S2 subunit. While most substitutions to the Spike protein to date in variants of concern (VOCs) have been localized to the S1 subunit, the S2 subunit sequence is more conserved, with only a few observed substitutions in proximity to S2 binding sites. Several recent small molecules targeting S2 have been shown to have robust activity over recent VOC mutant strains and/or greater broad-spectrum antiviral activity for other more distantly related coronaviruses.

SARS-CoV-2 evolution during prolonged infection in immunocompromised patients

Prolonged infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in immunocompromised patients provides an opportunity for viral evolution, potentially leading to the generation of new pathogenic variants. To investigate the pathways of viral evolution, we carried out a study on five patients experiencing prolonged SARS-CoV-2 infection (quantitative polymerase chain reaction-positive for 79-203 days) who were immunocompromised due to treatment for lymphoma or solid organ transplantation. For each timepoint analyzed, we generated at least two independent viral genome sequences to assess the heterogeneity and control for sequencing error. Four of the five patients likely had prolonged infection; the fifth apparently experienced a reinfection. The rates of accumulation of substitutions in the viral genome per day were higher in hospitalized patients with prolonged infection than those estimated for the community background. The spike coding region accumulated a significantly greater number of unique mutations than other viral coding regions, and the mutation density was higher. Two patients were treated with monoclonal antibodies (bebtelovimab and sotrovimab); by the next sampled timepoint, each virus population showed substitutions associated with monoclonal antibody resistance as the dominant forms (spike K444N and spike E340D). All patients received remdesivir, but remdesivir-resistant substitutions were not detected. These data thus help elucidate the trends of emergence, evolution, and selection of mutational variants within long-term infected immunocompromised individuals.

IMPORTANCE

SARS-CoV-2 is responsible for a global pandemic, driven in part by the emergence of new viral variants. Where do these new variants come from? One model is that long-term viral persistence in infected individuals allows for viral evolution in response to host pressures, resulting in viruses more likely to replicate efficiently in humans. In this study, we characterize replication in several hospitalized and long-term infected individuals, documenting efficient pathways of viral evolution.

Target-based drug design strategies to overcome resistance to antiviral agents: opportunities and challenges

Viral infections have a major impact in human health. Ongoing viral transmission and escalating selective pressure have the potential to favor the emergence of vaccine- and antiviral drug-resistant viruses. Target-based approaches for the design of antiviral drugs can play a pivotal role in combating drug-resistant challenges. Drug design computational tools facilitate the discovery of novel drugs. This review provides a comprehensive overview of current drug design strategies employed in the field of antiviral drug resistance, illustrated through the description of a series of successful applications. These strategies include technologies that enhance compound-target affinity while minimizing interactions with mutated binding pockets. Furthermore, emerging approaches such as virtual screening, targeted protein/RNA degradation, and resistance analysis during drug design have been harnessed to curtail the emergence of drug resistance. Additionally, host targeting antiviral drugs offer a promising avenue for circumventing viral mutation. The widespread adoption of these refined drug design strategies will effectively address the prevailing challenge posed by antiviral drug resistance.

Compositional features analysis by machine learning in genome represents linear adaptation of monkeypox virus

Introduction: The global headlines have been dominated by the sudden and widespread outbreak of monkeypox, a rare and endemic zoonotic disease caused by the monkeypox virus (MPXV). Genomic composition based machine learning (ML) methods have recently shown promise in identifying host adaptability and evolutionary patterns of virus. Our study aimed to analyze the genomic characteristics and evolutionary patterns of MPXV using ML methods. Methods: The open reading frame (ORF) regions of full-length MPXV genomes were filtered and 165 ORFs were selected as clusters with the highest homology. Unsupervised machine learning methods of t-distributed stochastic neighbor embedding (t-SNE), Principal Component Analysis (PCA), and hierarchical clustering were performed to observe the DCR characteristics of the selected ORF clusters. Results: The results showed that MPXV sequences post-2022 showed an obvious linear adaptive evolution, indicating that it has become more adapted to the human host after accumulating mutations. For further accurate analysis, the ORF regions with larger variations were filtered out based on the ranking of homology difference to narrow down the key ORF clusters, which drew the same conclusion of linear adaptability. Then key differential protein structures were predicted by AlphaFold 2, which meant that difference in main domains might be one of the internal reasons for linear adaptive evolution. Discussion: Understanding the process of linear adaptation is critical in the constant evolutionary struggle between viruses and their hosts, playing a significant role in crafting effective measures to tackle viral diseases. Therefore, the present study provides valuable insights into the evolutionary patterns of the MPXV in 2022 from the perspective of genomic composition characteristics analysis through ML methods.

Deep mutational scanning reveals functional constraints and antigenic variability of Lassa virus glycoprotein complex

Lassa virus is estimated to cause thousands of human deaths per year, primarily due to spillovers from its natural host, Mastomys rodents. Efforts to create vaccines and antibody therapeutics must account for the evolutionary variability of Lassa virus's glycoprotein complex (GPC), which mediates viral entry into cells and is the target of neutralizing antibodies. To map the evolutionary space accessible to GPC, we use pseudovirus deep mutational scanning to measure how nearly all GPC amino-acid mutations affect cell entry and antibody neutralization. Our experiments define functional constraints throughout GPC. We quantify how GPC mutations affect neutralization by a panel of monoclonal antibodies and show that all antibodies are escaped by mutations that exist among natural Lassa virus lineages. Overall, our work describes a biosafety-level-2 method to elucidate the mutational space accessible to GPC and shows how prospective characterization of antigenic variation could aid design of therapeutics and vaccines.

The Role of Convalescent Plasma in COVID-19: A Conclusive Post-Pandemic Review

COVID-19 convalescent plasma (CCP) has represented the frontline response to the COVID-19 pandemic, largely because of encouraging historical evidences in previous pandemics, biological plausibility, and the initial unavailability of targeted antivirals. Unfortunately, investigator-initiated randomized clinical trials in 2020, launched during a stressful pandemic peak, were designed mostly at addressing the main unmet need, i.e., treating critically ill hospitalized patients who were unlikely to benefit from any antiviral therapy. The failure of most of these drugs, in combination with the lack of any sponsor, led to the false belief that convalescent plasma was useless. With the relaxing pandemic stages, evidences have instead mounted that, when administered properly (i.e., within 5 days from onset of symptoms and at high titers of neutralizing antibodies), CCP is as effective as other antivirals at preventing disease progression in outpatients, and also reduces mortality in hospitalized patients. Recently, the focus of clinical use has been on immunosuppressed patients with persistent seronegativity and infection, where a randomized clinical trial has shown a reduction in mortality. Lessons learnt during the COVID-19 pandemic will be of utmost importance for future pandemics.