Clinical Validation of a Novel T-cell Receptor Sequencing Assay for Identification of Recent or Prior SARS-CoV-2 Infection

Dalai, Sudeb C.; Dines, Jennifer N.; Snyder, Thomas M.; Gittelman, Rachel; Eerkes, Tera; Vaney, Pashmi; Howard, Sally; Akers, Kipp; Skewis, Lynell R.; Monteforte, Anthony; Witte, Pam; Wolf, Cristina; Nesse, Hans; Herndon, Megan; Qadeer, Jia; Duffy, Sarah Q.; Svejnoha, Emily; Taromino, Caroline; Kaplan, Ian M.; Alsobrook, John P.; Manley, Thomas; Baldo, Lance

doi:10.1101/2021.01.06.21249345

Cited by 19 publications

(30 citation statements)

References 53 publications

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“…Based on identification of public SARS-CoV-2–specific T-cell signatures shared across individuals, a classifier was developed to diagnose recent and past SARS-CoV-2 infection (17) in previously-confirmed RT-PCR-positive cases that has been validated in several independent data sets (18, 21). Optimization and application of this TCR classifier (further described in Methods) as a test for past SARS-CoV-2 infection yielded a sensitivity of 88.8% across all samples and timepoints, with a specificity of 99.8% in a control set of 1,657 pre-pandemic samples sequenced prior to 2020 (Figure 3A; Supplemental Table 2).…”

Section: Resultsmentioning

confidence: 99%

“…We also show that a SARS-CoV-2-specific TCR-based test has high sensitivity for diagnosis of prior SARS-CoV-2 infection in individuals up to at least 6 months following initial infection. We have previously described the clinical validation and performance of a TCR-based assay (T-Detect) for diagnosing past SARS-CoV-2 infection with high sensitivity, ∼100% specificity, equivalent or higher sensitivity compared to commercial serologic testing, and lack of pathogen cross-reactivity (18). In the present study, using an updated classifier that includes additional filtering of the TCR sequence list (described in Methods), we observed that performance of the TCR-based test was equivalent to serology testing in hospitalized individuals and was more sensitive than serology in non-hospitalized individuals, particularly at timepoints beyond 100 days from initial onset of symptoms.…”

Section: Resultsmentioning

confidence: 99%

“…In addition, neutralizing antibody (nAb) titers, while providing one measure of immune protection in SARS-CoV-2 infection (15), are challenging to perform, pose biohazard risks and may have limited durability over time (16). More recently, T-cell receptor (TCR) repertoire-based assays have emerged as another technology for reliable assessment of prior infection and immunity (17, 18). Such assays can be performed on standard whole blood samples of 1-2mL.…”

Section: Introductionmentioning

confidence: 99%

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T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

Elyanow

et al. 2021

Preprint

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Measuring the adaptive immune response to SARS-CoV-2 can enable the assessment of past infection as well as protective immunity and the risk of reinfection. While neutralizing antibody (nAb) titers are one measure of protection, such assays are challenging to perform at a large scale and the longevity of the SARS-CoV-2 nAb response is not fully understood. Here, we apply a T-cell receptor (TCR) sequencing assay that can be performed on a small volume standard blood sample to assess the adaptive T-cell response to SARS-CoV-2 infection. Samples were collected from a cohort of 302 individuals recovered from COVID-19 up to 6 months after infection. Previously published findings in this cohort showed that two commercially available SARS-CoV-2 serologic assays correlate well with nAb testing. We demonstrate that the magnitude of the SARS-CoV-2-specific T-cell response strongly correlates with nAb titer, as well as clinical indicators of disease severity including hospitalization, fever, or difficulty breathing. While the depth and breadth of the T-cell response declines during convalescence, the T-cell signal remains well above background with high sensitivity up to at least 6 months following initial infection. Compared to serology tests detecting binding antibodies to SARS-CoV-2 spike and nucleoprotein, the overall sensitivity of the TCR-based assay across the entire cohort and all timepoints was approximately 5% greater for identifying prior SARS-CoV-2 infection. Notably, the improved performance of T-cell testing compared to serology was most apparent in recovered individuals who were not hospitalized and were sampled beyond 150 days of their initial illness, suggesting that antibody testing may have reduced sensitivity in individuals who experienced less severe COVID-19 illness and at later timepoints. Finally, T-cell testing was able to identify SARS-CoV-2 infection in 68% (55/81) of convalescent samples having nAb titers below the lower limit of detection, as well as 37% (13/35) of samples testing negative by all three antibody assays. These results demonstrate the utility of a TCR-based assay as a scalable, reliable measure of past SARS-CoV-2 infection across a spectrum of disease severity. Additionally, the TCR repertoire may be useful as a surrogate for protective immunity with additive clinical value beyond serologic or nAb testing methods.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

Elyanow

et al. 2021

Preprint

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“…When used alongside measurements of virus-specific antibodies, T cell response readouts represent a powerful, additional measure of potential immunity from COVID-19, with a higher degree of confidence than either measurement on their own, in particular given the concern on the longevity of measurable antibody responses (21)(22)(23). In addition, the FDA's decision to issue emergency use authorisation for a SARS-CoV-2 T cell test highlights the growing acceptance and usefulness of T cell testing for the clinical management of certain patient groups (24).…”

Section: Discussionmentioning

confidence: 99%

Whole blood-based measurement of SARS-CoV-2-specific T cell responses reveals asymptomatic infection and vaccine efficacy in healthy subjects and patients with solid organ cancers

Scurr

Zelek

Lippiatt³

et al. 2021

Preprint

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Accurate assessment of SARS-CoV-2 immunity in the population is critical to evaluating vaccine efficacy and devising public health policies. Whilst the exact nature of effective immunity remains incompletely defined, SARS-CoV-2-specific T cell responses are a critical feature of the immune response that will likely form a key correlate of protection against COVID-19. Here, we developed and optimised a high-throughput whole blood-based assay to determine the T cell response associated with prior SARS-CoV-2 infection and/or vaccination amongst 156 healthy donors and 67 cancer patients. Following overnight in vitro stimulation with SARS-CoV-2-specific peptides, blood plasma samples were harvested and analysed for Th1-type effector cytokines (IFN-γ and IL-2). Amongst healthy donors, highly significant differential IFN-γ+/IL-2+ SARS-CoV-2-specific T cell responses were seen amongst vaccinated or previously infected COVID-19-positive individuals in comparison to unknown/naïve individuals (P < 0.0001). IL-2 production from T cells in response to SARS-CoV-2 derived antigens was a highly predictive diagnostic assay (P < 0.0001; 96.0% sensitivity, 93.9% specificity); measurement of IFN-γ+ SARS-CoV-2 specific T cell responses was equally effective at identifying asymptomatic (antibody and T cell positive) participants. A single dose of COVID-19 vaccine induced IFN-γ and/or IL-2 SARS-CoV-2-specific T cell responses in 28/29 (96.6%) of healthy donors, reducing significantly to 27/56 (48.2%) when measured in cancer patients (P = 0.0003). Overall, this cost-effective standardisable test ensures accurate and comparable assessments of SARS-CoV-2-specific T cell responses amenable to widespread population immunity testing.

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“…Such classifiers leverage the relative frequency of disease-associated sequences within the repertoire, measures that have been shown to be associated with disease severity in the setting of SARS-CoV-2 (45,46). Clinical validation of a T-cell assay for SARS-CoV-2 utilizing a similar methodology demonstrated high positive percent agreement (>94.5%) and negative percent agreement (~100%) with reverse transcriptase PCR (RT-PCR) for detection of past SARS-CoV-2 infection (46,47). However, this approach has not previously been applied to bacterial disease.…”

Section: Introductionmentioning

confidence: 99%

Immunosequencing of the T-cell receptor repertoire reveals signatures specific for diagnosis and characterization of early Lyme disease

Greissl

Pesesky

Dalai

et al. 2021

Preprint

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Lyme disease, the most common tick-borne illness in the United States, is most frequently caused by infection with Borrelia burgdorferi. Although early antibiotic treatment can prevent development of severe illness and late manifestations, diagnosis is challenging in patients who do not present with a typical erythema migrans rash. To support a diagnosis of Lyme disease in such cases, guidelines recommend 2-tiered serologic testing. However, 2-tiered testing has numerous limitations, including ambiguity in interpretation and lower sensitivity in early disease. We developed a diagnostic approach for Lyme disease based on the T-cell response to B. burgdorferi infection by immunosequencing T-cell receptor (TCR) repertoires in blood samples from 3 independent cohorts of patients with laboratory-confirmed or clinically diagnosed early Lyme disease, as well as endemic and non-endemic controls. We identified 251 public, Lyme-associated TCRs that were used to train a classifier for detection of early Lyme disease with 99% specificity. In a validation cohort of individuals with early Lyme disease, TCR testing demonstrated a 1.9-fold increase in sensitivity compared to standard 2-tiered testing (STTT; 56% versus 30%), with a 3.1-fold increase <=4 days from the onset of symptoms (44% versus 14%). TCR positivity predicted subsequent seroconversion in 37% of initially STTT-negative patients, suggesting that the T-cell response is detectable before the humoral response. While positivity for both tests declined after treatment, greater declines in posttreatment sensitivity were observed for STTT compared to TCR testing. Higher TCR scores were associated with clinical measures of disease severity, including abnormal liver function test results, disseminated rash, and number of symptoms. A subset of Lyme-associated TCRs mapped to B. burgdorferi antigens, demonstrating high specificity of a TCR immunosequencing approach. These results support the clinical utility of T-cell-based testing as a sensitive and specific diagnostic for early Lyme disease, particularly in the initial days of illness.

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Clinical Validation of a Novel T-cell Receptor Sequencing Assay for Identification of Recent or Prior SARS-CoV-2 Infection

Cited by 19 publications

References 53 publications

T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

Whole blood-based measurement of SARS-CoV-2-specific T cell responses reveals asymptomatic infection and vaccine efficacy in healthy subjects and patients with solid organ cancers

Immunosequencing of the T-cell receptor repertoire reveals signatures specific for diagnosis and characterization of early Lyme disease

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