Dynamics of early cellular responses to SARS-CoV-2 in seronegative individuals

A recent study published in the journal Nature analyzed early cellular response dynamics to SARS-CoV-2 in seronegative individuals using single-cell multi-omics profiling, identifying key cellular states and immune responses associated with different infection outcomes. COVID-19, caused by SARS-CoV-2, is a potentially fatal disease that has become a severe global health emergency. Severe outcomes are linked to disrupted antiviral and immune responses, including impaired type I interferon responses and altered T and B cell dynamics. Accurately detecting immune responses is challenging due to heterogeneous factors such as viral dose, strain, and clinical features like comorbidities. Understanding the dynamics of SARS-CoV-2 infection, particularly early phases of exposure, is crucial. Studies often miss capturing these early events in natural infections, making it difficult to pinpoint antigen-responding T cell activation and expansion. Further research is needed to accurately delineate early immune response dynamics to SARS-CoV-2 to better understand and mitigate severe COVID-19 outcomes.

Sixteen healthy adults aged 18-30 years, seronegative for SARS-CoV-2, participated in a human SARS-CoV-2 challenge study for Single-cell RNA sequencing (scRNA-seq) sample processing and analysis. This study, conducted by a government task force, Imperial College London, Royal Free London NHS Foundation Trust, University College London, and hVIVO, took place from June to August 2021. Additionally, 20 healthy adults from earlier cohorts had blood and nasal samples processed for bulk RNA-seq, with 10 receiving pre-emptive remdesivir. Volunteers were screened for anti-SARS-CoV-2 antibodies and excluded if positive. The study followed ethical guidelines, and informed consent was obtained from all volunteers.

One participant with low pre-inoculation antibody levels was classified as having an abortive infection, which did not alter the study’s conclusions. Participants were followed for one year post-inoculation, with no long-COVID symptoms reported at the final time point. Physiological observations were normal. After discharge, two participants reported receiving a vaccine or a community infection before their day 28 follow-up. ELISpot tests revealed immune responses in subsequent samples. Participants were intranasally inoculated with a wild-type pre-Alpha SARS-CoV-2 virus, and nasal and throat samples were collected to evaluate viral kinetics. Nasopharyngeal swabs and Peripheral Blood Mononuclear Cells (PBMCs) were processed for single-cell sequencing to analyze immune responses.

In the present study, 16 seronegative young adults were intranasally inoculated with a pre-Alpha SARS-CoV-2 virus strain. Extensive screening excluded participants with severe disease risk factors or comorbidities. Participants received the lowest quantifiable inoculum dose, resulting in no serious adverse events and resolved symptoms. The study analyzed local and systemic immune responses at single-cell resolution. Baseline measurements were taken before inoculation, followed by time series analyses of cellular responses in blood and nasopharynx. Six participants developed sustained infections, defined by consecutive viral load detections and symptoms. Three individuals had sporadic positive PCR tests and were classified as transient infections. Seven participants remained PCR-negative but showed early innate immune responses, termed abortive infections. The infection rate was comparable to that in a closed household of unvaccinated individuals.

scRNA-seq and single-cell T cell receptor (TCR) and B cell receptor (BCR) sequencing were performed at up to seven time points. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) quantified 123 surface proteins in PBMCs. More than 600,000 single-cell transcriptomes were generated, including 371,892 PBMCs and 234,182 nasopharyngeal cells. Predictive models and marker gene expression annotated 202 cell states, enabling detailed local and systemic response analysis.

Generalized linear mixed models (GLMMs) quantified changes in cell-type abundance over time. Immune cell types infiltrated the inoculation site after SARS-CoV-2 exposure. Sustained infections showed immune infiltration starting at day 5, while transient infections had immediate infiltration at day 1. Abortive infections showed minimal changes except for early CD4+ and CD8+ T cell infiltration. Gene expression analysis revealed that interferon response genes were the dominant infection-induced module in sustained infections. Interferon signaling was activated in all cell types in both blood and nasopharynx, peaking earlier in blood. This rapid systemic response was validated with bulk RNA-seq data. Myeloid cell redistribution between circulation and tissues was observed during early infection. MAIT cell activation was detected across all infection groups, indicating rapid viral sensing. Viral RNA peaked at day 7, with hyperinfected ciliated cells identified as major virion producers. Ciliated cells showed dynamic responses, including acute-phase and interferon-stimulated states. Activated T cells, identified through peptide-MHC staining and scRNA-seq, expanded significantly at day 10 after inoculation, resembling a typical antigen-specific adaptive immune response.

The study revealed multiple immune response states that precede clinical symptoms, including MAIT cell activation and a decrease in inflammatory monocytes. These responses emerged even when SARS-CoV-2 exposure did not lead to COVID-19, suggesting their potential as biomarkers of immediate immune response. In sustained infections, a new acute phase response (APR) in ciliated cells and a distinct state for activated T cells with SARS-CoV-2-specific TCRs were identified. Interferon signaling was activated globally in circulating immune cells before the site of infection. These findings provide a detailed time-resolved description of early immune responses to SARS-CoV-2.

hVIVO plc (formerly Open Orphan plc), led by Cathal Friel, is a rapidly growing specialist contract research organisation (CRO) and the world leader in testing infectious and respiratory disease vaccines and antivirals using human challenge clinical trials, providing end-to-end early clinical development services for its broad and long-standing client base of biopharma companies.

Click to view all articles for the EPIC:
Or click to view the full company profile:
    Facebook
    X
    LinkedIn
    hVIVO plc

    More articles like this

    hVIVO plc

    Exploring the human viral challenge model for influenza research

    This study evaluates the human viral challenge model using the A/Perth/16/2009 H3N2 influenza virus, involving 216 volunteers across five clinical studies. Administered intranasally under controlled conditions, the research aimed to improve the understanding of influenza infection

    hVIVO plc

    Advancing influenza research with new challenge agents

    Controlled Human Infection Studies (CHIS) have proven to be essential in exploring human responses to respiratory infections and testing the effectiveness of vaccines and treatments. These studies hinge on selecting an appropriate challenge virus, making a

    hVIVO plc

    hVIVO’s patient enrolment & retention at Canary Wharf

    hVIVO plc (formerly Open Orphan plc), led by Cathal Friel, is a rapidly growing specialist contract research organisation (CRO) and the world leader in testing infectious and respiratory disease vaccines and antivirals using human challenge clinical trials,

    hVIVO plc

    Inside hVIVO’s cutting-edge QA facility at Canary Wharf

    hVIVO plc (formerly Open Orphan plc), led by Cathal Friel, is a rapidly growing specialist contract research organisation (CRO) and the world leader in testing infectious and respiratory disease vaccines and antivirals using human challenge clinical trials,

    hVIVO plc

    Virus portfolio for RSV research and development

    Respiratory Syncytial Virus (RSV), discovered in 1956, is a common and contagious RNA virus responsible for a range of respiratory illnesses worldwide. Initially identified by Dr. Robert Chanock and colleagues in chimpanzees, RSV belongs to the

    hVIVO plc

    Clinical trial eligibility: Pre-screening and Screening

    In clinical trials, ensuring patient safety is paramount, and researchers must identify suitable participants who meet specific requirements. To this end, there are distinct processes involved, known as pre-screening and screening, which help determine whether a

    hVIVO plc

    Connecting Airway Epithelial Cell Models with Human Challenge Studies

    Airway epithelial cells cultured in Air–Liquid Interface (ALI) conditions provide an environment that closely resembles the human airway system. This method facilitates improved oxygen availability and supports cellular differentiation, replicating the physiological conditions of the human

    hVIVO plc

    Esmée shares her FluCamp clinical trial volunteer experience

    hVIVO plc (formerly Open Orphan plc), led by Cathal Friel, is a rapidly growing specialist contract research organisation (CRO) and the world leader in testing infectious and respiratory disease vaccines and antivirals using human challenge clinical trials,

    hVIVO plc

    Overcoming challenges in high-growth regulated industries

    The Navigating Risk podcast recently explored the challenges faced by high-growth businesses operating in highly regulated industries, particularly life sciences. Helen Yates, the Editor of Global Thought Leadership, engaged in a conversation with Mo Khan, the

    hVIVO plc

    Take a 360° interactive tour of a FluCamp Volunteer Room

    hVIVO plc (formerly Open Orphan plc), led by Cathal Friel, is a rapidly growing specialist contract research organisation (CRO) and the world leader in testing infectious and respiratory disease vaccines and antivirals using human challenge clinical trials,

    hVIVO plc

    Clinical trial approval process in the UK

    The process of obtaining approval for clinical trials is comprehensive, as it involves multiple regulatory bodies that ensure the safety and efficacy of the medical interventions being tested. Researchers begin by meticulously planning the trial, outlining

    hVIVO plc

    hVIVO reports positive results from RSV antiviral human challenge trial

    hVIVO plc (LON:HVO), a fast-growing specialist contract research organisation (CRO) and world leader in testing infectious and respiratory disease products using human challenge clinical trials, has noted the announcement by Enanta Pharmaceuticals, reporting positive topline results from

    hVIVO plc

    The importance of Clinical Trial Monitoring

    Monitoring is essential from the moment a clinical trial is planned until it concludes. This ensures that the study remains unbiased, patient safety is prioritised, and accurate results are achieved. The process of clinical trial monitoring

    hVIVO plc

    The future of vaccine development through human challenge trials

    Testing new treatments and vaccines often requires years, if not decades, to gather sufficient data. In response, scientists are turning to a more direct approach that involves deliberately infecting volunteers with potentially deadly pathogens. A notable