Effect of inhaled interferon-β1a on SARS-CoV-2 diversity and evolution

Microbiology Spectrum · 2026-05-18

ABSTRACT Interferon resistance has been implicated in SARS-CoV-2 escape from innate immunity, but exogenous interferon’s impact on viral evolution and diversity is unknown. SNG001, an inhaled interferon-β1a treatment, was evaluated in the ACTIV-2/A5401 randomized controlled trial of therapeutics for COVID-19. We measured viral kinetics and performed whole-genome sequencing on longitudinal nasal swabs collected from ACTIV-2 participants who received either SNG001 or placebo to assess viral sequence diversity. No difference in nasal viral load decay was detected between study arms when stratifying by SARS-CoV-2 variant or by viral culture conversion. Compared to placebo participants, the SNG001-treated participants displayed significantly lower nonsynonymous amino acid average pairwise distance, indicating lower sequence diversity. Similarly, SNG001-treated individuals also developed numerically fewer nonsynonymous mutations during their infection in ORF1a, ORF1b, Spike, and Nucleocapsid. No specific emerging SARS-CoV-2 nonsynonymous amino acid changes indicating signatures of viral escape were enriched in those receiving SNG001. These in vivo data provide an intriguing signal that exogenous interferon-β1a may restrict SARS-CoV-2 viral diversity and add to growing evidence that interferon levels play a critical role in antiviral responses during COVID-19. IMPORTANCE SARS-CoV-2 encodes several genes which can antagonize the interferon signaling cascade, preventing it from activating antiviral responses and thereby facilitating viral establishment and dissemination. It is unknown how the administration of exogenous interferon might affect viral evolution and immune escape. ACTIV-2/A5401 represents a unique opportunity to study the virologic effects of interferon treatment in a rigorous randomized, placebo-controlled clinical trial setting. Our characterization of longitudinal nasal samples shows that interferon-treated individuals had lower viral diversity and no evidence of viral escape mutations. CLINICAL TRIALS This study is registered with ClinicalTrials.gov as NCT04518410 .

Quantification of pathology associated collagen in murine models of pulmonary tuberculosis with whole-slide pixel classification of stained images and localized label- free second harmonic generation imaging

Journal of Pathology Informatics · 2025-11-01

Mycobacterium tuberculosis biology, pathogenicity and interaction with the host

Nature Reviews Microbiology · 2025-06-30 · 37 citations

Rapid Elimination of Culturable SARS-CoV-2 With Intramuscular or Intravenous Administration of Antiviral Monoclonal Antibody Therapy

Open Forum Infectious Diseases · 2025-08-29 · 1 citations

We evaluated intramuscular (IM) versus intravenous (IV) administration of tixagevimab/cilgavimab in early COVID-19. Both routes achieved rapid elimination of culturable virus and minimal emergence of resistance. These results support IM delivery as a viable alternative to IV, with important implications for scalable deployment in future viral pandemics.

Cross-Neutralization of Distant Coronaviruses Strongly Correlates with Spike S2-Specific Antibodies from Immunocompetent and Immunocompromised Vaccinated SARS-CoV-2-Infected Patients

Vaccines · 2025-09-04

Background/Objectives: Despite the lifting of the COVID-19 public health emergency, SARS-CoV-2 infections continue to be recorded worldwide. The continued prevalence of infection has been attributed to the ability of the virus to evade host immune responses, including neutralizing antibody-derived immunity. The vast majority of antibody escape mutations has been associated with the S1 subunit of the spike protein. The other region of the spike, the S2 subunit, is the most conserved region amongst coronaviruses. We hypothesized that S2-specific antibody levels are modest in vaccinated and SARS-CoV-2-infected patients, resulting in suboptimal neutralization of distant coronaviruses. Methods: Here, we analyzed S1- and S2-specific antibody levels in SARS-CoV-2-infected individuals, including a mixed cohort of those with and without immunosuppression and prior vaccination. Results: We found that S2-specific antibody responses were generally lower than S1-specific antibody responses. Intriguingly, Omicron-S1-specific antibody levels were higher than Wuhan-S1-specific antibody levels despite all vaccinated participants having received Wuhan-spike-based immunogens. This emphasizes the importance of the infecting variant and vaccine immunogen in the production of spike-targeting antibodies and associated hybrid immunity. Although S1-specific antibody levels were generally higher than their S2-specific counterparts, the correlation between neutralization and binding antibody levels was mostly higher in S2- compared with S1-specific responses. Conclusions: We conclude that S2-based immunogens are suitable for the induction of antibody-based immunity against novel SARS-CoV-2 variants but also against more distant coronaviruses, which would support a better protection for the immunocompromised as well as other vulnerable populations.

Modeling suggests SARS-CoV-2 rebound after nirmatrelvir-ritonavir treatment is driven by target cell preservation coupled with incomplete viral clearance

Journal of Virology · 2025-02-04 · 14 citations

In a subset of SARS-CoV-2-infected individuals treated with the antiviral nirmatrelvir-ritonavir, the virus rebounds following treatment. The mechanisms driving this rebound are not well understood. We used a mathematical model to describe the longitudinal viral load dynamics of 51 individuals treated with nirmatrelvir-ritonavir, 20 of whom rebounded. Target cell preservation, either by a robust innate immune response or initiation of N-R near the time of symptom onset, coupled with incomplete viral clearance, appears to be the main factor leading to viral rebound. Moreover, the occurrence of viral rebound is likely influenced by the time of treatment initiation relative to the progression of the infection, with earlier treatments leading to a higher chance of rebound. A comparison with an untreated cohort suggests that early treatments with nirmatrelvir-ritonavir may be associated with a delay in the onset of an adaptive immune response. Nevertheless, our model demonstrates that extending the course of nirmatrelvir-ritonavir treatment to a 10-day regimen may greatly diminish the chance of rebound in people with mild-to-moderate COVID-19 and who are at high risk of progression to severe disease. Altogether, our results suggest that in some individuals, a standard 5-day course of nirmatrelvir-ritonavir starting around the time of symptom onset may not completely eliminate the virus. Thus, after treatment ends, the virus can rebound if an effective adaptive immune response has not fully developed. These findings on the role of target cell preservation and incomplete viral clearance also offer a possible explanation for viral rebounds following other antiviral treatments for SARS-CoV-2. IMPORTANCE: Nirmatrelvir-ritonavir is an effective treatment for SARS-CoV-2. In a subset of individuals treated with nirmatrelvir-ritonavir, the initial reduction in viral load is followed by viral rebound once treatment is stopped. We show that the timing of treatment initiation with nirmatrelvir-ritonavir may influence the risk of viral rebound. Nirmatrelvir-ritonavir stops viral growth and preserves target cells but may not lead to full clearance of the virus. Thus, once treatment ends, if an effective adaptive immune response has not adequately developed, the remaining virus can lead to rebound. Our results provide insights into the mechanisms of rebound and can help develop better treatment strategies to minimize this possibility.

Inflammatory Macrophages Associate With Tissue Injury and Fibrosis in a Mouse Model of Tuberculosis

The Journal of Infectious Diseases · 2025-07-07 · 1 citations

BACKGROUND: Post-tuberculosis lung disease causes a significant burden of global disease. While a consensus definition of post-tuberculosis lung disease is still in development, parenchymal cavitation, bronchiectasis, and fibrosis are recognized pathologic features. The molecular mechanisms driving development of each feature are largely unknown. METHODS: To facilitate the mechanistic study of tuberculosis-associated pathologic tissue remodeling and fibrosis, we adapted a mouse model of infection. RESULTS: The morphologies of fibrosis observed in mice were similar to those observed in human tissue samples, and fibrillar collagen deposition did not resolve with antituberculosis antibiotics. Inflammatory transcriptional signatures were persistently upregulated during chronic infection and did not fully resolve after weeks of antibiotics. Inflammatory and fibrosis-associated macrophages similarly persisted during treatment. Immunofluorescence microscopy revealed persistent macrophage populations and shifts in abundance and distribution of type 2 alveolar cells at sites of fibrogenesis. CONCLUSIONS: A mouse model recapitulates key aspects of tuberculosis-assocaiated fibrosis. Transcriptional and cellular markers of inflammation persist through weeks of antibiotic treatment.

Editorial: Tuberculosis: host immunity, diagnostics and therapeutics

Frontiers in Molecular Medicine · 2025-02-18

This Research Topic aimed to attract studies that would enhance our understanding of host immunity against TB and its role in both pathogenesis and protection. The submitted papers represent diverse approaches to understanding TB, from biomarker discovery and drug resistance surveillance to host genetic factors and immune cell responses in both human and bovine TB.Rapulana et al. addressed a critical need in TB control: the accurate diagnosis of LTBI [1]. While current diagnostic tools like the Tuberculin Skin Test (TST) and interferon-gamma release assays (IGRAs) have served as cornerstones of LTBI diagnosis, their limitation, particularly the frequency of indeterminate results in immunosuppressed patients, highlights the need for more reliable biomarkers. Their study identified several promising candidates, with IL-2 and IP-10 showing particularly strong potential as complementary markers to existing IFN-γ assays. The high positive and negative predictive values of these markers in ESAT-6/CFP-10 stimulated plasma suggest a possible path toward more reliable LTBI diagnosis.The growing challenge of drug resistance in TB is highlighted by Otchere et al. in their study of difficult-to-treat TB patients in Ghana [2]. Their identification of pre-extensively drug-resistant (pre-XDR) TB cases is particularly concerning, as it signals the potential for even more challenging treatment scenarios in the future. Their finding that 58.7% of samples showed resistance to at least one drug, with 25.2% being multidrug-resistant (MDR), underscores the urgent need for enhanced surveillance and monitoring systems. This work provides valuable insights into the molecular basis of drug resistance, particularly the distribution of mutations in key resistance-associated genes.Fang et al. contributed to our understanding of genetic susceptibility to TB by investigating polymorphisms in the Notch4 gene [3]. Their identification of specific SNPs associated with TB susceptibility, validated across two independent cohorts, represents a significant advance in understanding host genetic factors that influence TB risk. The demonstration that Notch4 expression increases in TB patients and correlates with disease severity, coupled with their mechanistic studies showing Mtb-induced Notch4 expression through TLR2/P38 signalling, opens new possibilities for host-directed therapeutic approaches.The fourth paper, by Bhat et al., provides important insights into the immune response to bovine TB, focusing on γδ T cells-a crucial bridge between innate and adaptive immunity [4]. Their RNA-seq analysis of different γδ T cell subsets revealed preferential activation of the WC1.1+ compartment during natural Mycobacterium bovis infection, characterized by upregulation of genes involved in cytotoxicity, cell activation, and chemotaxis. This work enhances our understanding of the cellular immune response to mycobacterial infection and may have implications for both bovine and human TB.Collectively, these papers advance our knowledge of TB in several key areas (Figure 1). First, they contribute to the development of improved diagnostic approaches, particularly for LTBI, which remains a major challenge in TB control. Second, they highlight the evolving landscape of drug resistance and the urgent need for enhanced surveillance and monitoring systems. Third, they provide new insights into host genetic factors and immune responses that influence TB susceptibility and progression, potentially opening new avenues for therapeutic intervention.However, these studies also highlight significant gaps in our understanding. The emergence of pre-XDR TB cases emphasizes the need for new therapeutic approaches and more effective means of preventing resistance development. The complex interplay between host genetic factors and immune responses, particularly in the context of LTBI, requires further investigation. Additionally, while the study of bovine TB provides valuable insights, more research is needed to understand the similarities and differences between human and bovine immune responses to mycobacterial infection.Looking ahead, several priorities emerge from these studies. There is a clear need for:1. Development and validation of multi-marker diagnostic approaches for more accurate diagnosis of LTBI and stratification by likelihood to progress to active TB.2. Enhanced global surveillance systems for drug-resistant TB that both build upon and advance our molecular understanding of resistance mechanisms.3. Development of host-directed therapeutic approaches based on our growing understanding of genetic and immunological factors that drive progression to active disease.As we continue to face the challenge of TB control globally, research that bridges basic science and clinical applications, as exemplified by the papers in this Research Topic, will be crucial for developing more effective diagnostic approaches and therapeutic interventions against this persistent pathogen.

Case 5-2025: A 30-Year-Old Woman with Headache and Dysesthesia

New England Journal of Medicine · 2025-02-12

Virologic characteristics of SARS-CoV-2 infection across evolving Omicron subvariants

JCI Insight · 2025-09-09 · 1 citations

BACKGROUNDSARS-CoV-2 has evolved subvariants since the emergence of the Omicron variant in 2021. Whether these changes impact viral shedding and transmissibility is not known.METHODSPOSITIVES is a prospective longitudinal cohort of individuals with mild SARS-CoV-2 infection. Ambulatory, immunocompetent participants who did not receive antivirals self-administered 6 anterior nasal swabs over 15 days. Samples were analyzed by qPCR to quantify viral RNA, semiquantitative viral culture to detect shedding of replication-competent virus, and whole-genome sequencing to classify subvariants. Our predictor of interest was Omicron subvariants: BA.1x, BA.2x, BA.4/5x, XBB.x, and JN.x. Outcomes included RNA levels and duration of shedding replication-competent virus. We additionally explored whether symptoms are a valid marker for ending isolation.RESULTSThe median peak nasal SARS-CoV-2 RNA (6.0-6.3 log10 RNA copies/mL), median days to peak RNA (4-5 days), median days to undetectable viral RNA (12-14 days), and median days to negative viral culture (4-8 days) were similar across Omicron subvariants. Number and duration of symptoms were also similar. For all subvariants, a sizeable percentage (range 27.5%-56.0%) shed replication-competent virus after fever resolution and improvement of symptoms.CONCLUSIONDespite ongoing viral evolution, key aspects of viral dynamics of SARS-CoV-2 infection, including the duration of shedding replication-competent virus, have not substantially changed across Omicron subvariants. Replication-competent shedding of these subvariants is detected for a large proportion of people who meet criteria for ending isolation.FUNDINGNIH (U19 AI110818, R01 AI176287, K24 HL166024), the Massachusetts Consortium on Pathogen Readiness, and the Massachusetts General Hospital Department of Medicine.