ABSTRACT
Background: A significant portion of individuals experience persistent symptoms months after SARS-CoV-2 infection, broadly referred to as Long COVID (LC). Although the frequencies of subsets of SARS-CoV-2-specific T cells have been shown to differ in individuals with LC relative to those with complete recovery, a deep dive into phenotypic and functional features of total and SARSCoV- 2-specific T cells from individuals with LC has yet to be performed. Method(s): Here, we used CyTOF to characterize the phenotypes and effector functions of T cells from LIINC cohort. The median age was 46, the cohort was 55.8% female, and 9/43 had been hospitalized. Participants were reported a median of 7 LC symptoms at 8 months. SARS-CoV-2-specific total antibody levels were also measured in concurrent sera. Manual gating was used to define T cell subsets, SPICE analyses for polyfunctionality, T cell clustering for phenotypic features, and linear regression for correlation. Permutation tests, Student's t tests, and Welch's t test were used for statistical analysis. Result(s): SARS-CoV-2 total antibody responses were elevated in the LC group (p=0.043), and correlated with frequencies of SARS-CoV-2-specific T cells in those without LC (r=0.776, p< 0.001) but not those with LC. While the frequencies of total SARS-CoV-2-specific CD4+ and CD8+ T cells were similar between individuals with and without LC, those from individuals without LC tended to be more polyfunctional (co-expressing IFNgamma, TNFalpha, IL2, and/or MIP1beta). CD4+ T cells from individuals with LC harbored higher frequencies of Tcm (p=0.003), Tfh (p=0.037), and Treg subsets (p=0.0412), and preferentially expressed a variety of tissue homing receptors including CXCR4 and CXCR5 (p=0.037). SARS-CoV-2-specific CD4+ T cells producing IL6, albeit rare, were observed exclusively among those with LC (p=0.016). In addition, participants with LC harbored significantly higher frequencies of SARS-CoV-2-specific CD8+ T cells co-expressing exhaustion markers PD1 and CTLA4 (p=0.018). Conclusion(s): Long COVID is characterized by global phenotypic differences in the CD4+ T cell compartment in ways suggesting preferential migration of these cells to inflamed mucosal tissues. Individuals with LC also harbor higher numbers of exhausted SARS-CoV-2-specific CD8+ T cells, potentially implicating viral persistence. Finally, our data additionally suggest that individuals with LC may uniquely exhibit an uncoordinated T cell and antibody response during COVID-19 convalescence.
ABSTRACT
Background: There is mounting evidence regarding the frequency and spectrum of post-acute sequelae of SARS-CoV-2 infection (PASC), but a search for causes has been elusive. Recently, a plasma-based assay for SARS-CoV-2 antigen has been developed, which in initial use revealed that a high fraction of severely affected patients with PASC had circulating antigen. It is unknown whether detectable SARS-CoV-2 antigen is specific for PASC or how the assay performs in a broader clinical spectrum of patients with PASC. Method(s): We evaluated a cohort of patients with RNA-confirmed SARS-CoV-2 infection enrolled >=3 weeks following initial symptoms. Participants, both with and without PASC at enrollment, were identified via facility- and communitybased advertising and examined every 4 months. An interviewer-administered questionnaire ascertained presence of 30 different symptoms (new or worse compared to pre-COVID) in the prior 2 days at each exam. Using the single molecule array (Simoa) assay, we measured spike, S1, and nucleocapsid SARSCoV- 2 antigens in plasma collected at time of symptom assessment. Result(s): We examined 172 participants (50% men, 46% non-white, median age 46 years) who contributed 667 timepoints from 0.7 to 15.4 months following infection, at which 66% featured report of >=1 symptom. Sixty-one of 667 timepoints (9.1%) representing 24% of persons had >=1 detectable SARSCoV- 2 antigen. Among the 437 timepoints at which >=1 symptom was present, 9.8% had >=1 detectable antigen;this compares to 7.8% of timepoints at which symptoms were absent. In comparison to those without symptoms, individuals with several specific symptom complexes (gastrointestinal, musculoskeletal, and central neurologic) more commonly had detectable antigen (Figure). Hospitalization during acute COVID-19 was strongly related to antigen detection. Conclusion(s): Among a diverse group of SARS-CoV-2-infected persons in the post-acute phase of infection, SARS-CoV-2 antigen is detectable in plasma in both those with and without symptoms but more commonly in those with gastrointestinal, musculoskeletal, and central neurologic complaints. The findings indicate that antigen persists in at least some persons and suggest (but do not prove) that antigen is causally related to symptoms. That antigen is found in only a fraction of those with PASC indicates either that not all symptoms are driven by antigen, current plasma antigen detection is insensitive relative to tissue, or nominal PASC symptoms are sometimes unrelated to SARS-CoV-2. (Figure Presented).
ABSTRACT
Background: Asymptomatic Cytomegalovirus (CMV) infection reshapes systemic immune responses and its replication can be both a consequence and cause of inflammation. As CMV resides in the same tissues affected by SARSCoV- 2, we hypothesized that asymptomatic CMV co-infection might modify the pathogenesis of both acute and post-acute COVID-19. Method(s): Participants had current or prior nucleic acid-confirmed SARS-CoV-2 infection in the COVID-19 Multi-Phenotyping for Effective Therapies (COMET, n=219), Immunophenotyping Assessment in a COVID-19 Cohort (IMPACC, n=244) or the Long-term Impact of Infection with Novel Coronavirus (LIINC, n=327) cohorts. We assessed the relationship between CMV serostatus and odds of hospitalization and plasma SARS-CoV-2 N antigen levels during acute COVID-19 as well as post-acute "Long COVID" symptoms, defined as >=1 of 32 COVID-19-attributed symptoms present at least 60 days following initial symptom onset. Result(s): Among 758 participants, 518 were hospitalized for their acute COVID-19 episode. CMV seropositivity was independently associated with a 1.9-fold increased odds of hospitalization for acute COVID-19, after adjustment for age, sex, race, ethnicity, HIV status, prior autoimmune disease, diabetes, and obesity (p=0.01, A). Among those hospitalized, CMV seropositivity was also associated with higher plasma SARS-CoV-2 N antigen levels (median 936 vs. 323 pg/ml, P=0.03, B), which remained significant after adjustment for potential confounders, but not with ICU admission (n=209), death (n=58), or thrombotic events (n=31). In contrast to its relationship to acute COVID-19 disease severity, CMV seropositivity was independently associated with a 48% decreased odds of having neurocognitive Long COVID symptoms such has headache and brain fog 4 months after initial COVID-19 diagnosis (P=0.036). Conversely, serologic evidence of Epstein-Barr Virus (EBV) reactivation and HIV both increased the odds of these symptoms (C). Conclusion(s): CMV seropositivity is associated with a 1.9-fold higher odds of hospitalization in people with acute COVID-19 and a nearly 3-fold higher SARS-CoV-2 antigen burden in hospitalized patients. In contrast, CMV seropositivity is associated with a decreased odds of neurocognitive Long COVID symptoms, while other chronic viral co-infections like EBV reactivation and HIV are associated with an increased odds of this complication. The biologic mechanisms mediating these relationships are unknown, but warrant further investigation. (Figure Presented).
ABSTRACT
Background: Antigen-driven CD4+ T cell proliferation is a proposed mechanism of HIV-1 reservoir persistence. We previously reported that SARSCoV- 2 infection leads to increased detectable low-level HIV-1 plasm RNA blips months after COVID-19, but the impact of SARS-CoV-2-mediated T cell activation on expansion of HIV-1 reservoirs is not known. We sought to identify if SARSCoV- 2 infection leads to expansion of preferentially HIV-infected CD4+ T cells in people with HIV (PWH) on ART. Method(s): Five PWH with samples collected prior to and approximately two months after SARS-CoV-2 infection were identified. We performed a surface activation induced marker (AIM) assay using a CD4-optimized overlapping SARS-CoV-2 peptide pool to measure OX40/CD137 expression following peptide stimulation and sorted CD4+ T cells based on surface marker expression. ddPCR quantification of genomic HIV-1 DNA was performed on sorted subsets. Result(s): We observed an increase in the frequency of SARS-CoV-2 AIM+ non-naive CD4+ T cells following COVID-19 in samples from 4 of 5 participants (mean AIM+ % 0.13 pre- vs 0.31 post). A large percentage of non-naive AIM+ CD4+ T cells expressed PD1 compared with total non-naive cells before (76% vs 36%) and after (65% vs 19%) COVID-19;PD1 expression was lower following SARS-CoV-2 in both AIM+ and AIM- CD4+ T cell subsets (although very few cells were AIM+ prior to COVID-19). HIV-1 DNA levels in non-naive AIM- CD4+ T cells prior to COVID-19 unexpectedly decreased following infection (mean 3,522 to 766 copies/106 cells). The numbers of AIM+ cells obtained by cell sorting were overall low ( 3,863 mean) and only one participant had detectable DNA in post-COVID AIM+ CD4+ T cells. However, a large majority of this participant's post-COVID AIM+ cells harbored HIV-1 DNA (0.89 copies per cell) whereas HIV DNA in their AIM- cells decreased from 8,387 to not detected following SARSCoV- 2 infection. No HIV-1 DNA was detected in the small number of AIM+ cells obtained prior to COVID-19 in this participant. Conclusion(s): COVID-19 in PWH led to a modest SARS-CoV-2-specific CD4+ cell response approximately two months following acute presentation. One participant may have preferentially expanded HIV-1-infected, SARS-CoV-2- specific CD4+ T cells following COVID-19 but studies involving larger numbers of participants and larger numbers of cells will be needed to fully understand the impact of SARS-CoV-2 on clonal expansion and HIV persistence.
ABSTRACT
Background: The biologic mechanisms underlying neurologic post-acute-sequelae of SARS-CoV-2 infection (PASC) are incompletely understood. We measured plasma markers of neuronal injury (glial fibrillary acidic protein [GFAP], neurofilament light chain [NfL]) and inflammation among a cohort of people with prior confirmed SARS-CoV-2 infection at early and late recovery following the initial illness (defined as < and > 90 days since COVID-19 onset, respectively). We hypothesized that those experiencing persistent neurologic symptoms would have elevations in these markers. Methods: The primary clinical outcome was the presence of self-reported central nervous system (CNS) PASC symptoms during the late recovery timepoint. We compared fold-changes in marker values between those with and without CNS PASC symptoms using linear mixed effects models and examined relationships between neurologic and immunologic markers using rank linear correlations. Results: Of 121 individuals, 52 reported CNS PASC symptoms. During early recovery, those who went on to report CNS PASC symptoms had elevations in GFAP (1.3-fold higher mean ratio, 95% CI 1.04-1.63, p=0.02), but not NfL (1.06-fold higher mean ratio, 95% CI 0.89-1.26, p=0.54). During late recovery, neither GFAP nor NfL levels were elevated among those with CNS PASC symptoms. Although absolute levels of NfL did not differ, those who reported CNS PASC symptoms demonstrated a stronger downward trend over time in comparison to those who did not report CNS PASC symptoms (p=0.041). Those who went on to report CNS PASC also exhibited elevations in IL-6 (48% higher during early recovery and 38% higher during late recovery), MCP-1 (19% higher during early recovery), and TNF-alpha (19% higher during early recovery and 13% higher during late recovery). GFAP and NfL correlated with levels of several immune markers during early recovery (MCP-1, IL-6, TNF-a, IFN-g);these correlations were attenuated during late recovery. Conclusion: Self-reported neurologic symptoms present approximately four months following SARS-CoV-2 infection are associated with elevations in markers of neurologic injury and inflammation at early recovery timepoints, suggesting that early injury can result in long-term disease. The correlation of GFAP and NfL with markers of systemic immune activation suggests one possible mechanism that might contribute to these symptoms. Additional work will be needed to better characterize these processes and to identify interventions to prevent or treat this condition.
ABSTRACT
Background: SARS-CoV-2 produces variable immune responses leading to different levels of immune protection. The relationship between neutralizing antibody level (NAb) and protective immunity has been well characterized after infection and vaccination. While comparatively specific T cell responses tend to be more variable, the impacts of these responses have broad implications on long-term immunity and their role in protective immunity has not been as clearly defined. Using data from our prospective cohort study and studies of clinical protective immunity/efficacy (from vaccines), we predicted protective immunity over time in relation to SARS-CoV-2-specific T cell dynamics. Methods: With linear mixed-effects models from our published immune data from people recovering from COVID-19, we simulated the Spike (S)-specific interferon-γ (IFNγ)+ CD4+, S-specific IFNγ+ CD8+, and nucleocapsid (N)-specific IFNγ+ CD8+ T cells over time (n=500 individuals). We then predicted NAbs from linear regression models developed from the same cohort. Finally, protective immunity from NAb titers was simulated from a published model. We similarly simulated 25, 50, and 75% lower T cell responses than those observed post-COVID-19 to understand how immune response variation may impact protective immunity. Results: Virus-specific T cell responses resulted in similar protective immunity across T cell subsets, but with differences in variability over time. Protective immunity for IFNγ+ S CD8 T cells spanned from 86-95%, while for IFNγ+ S CD4 T cells and IFNγ+ N CD4 T cells it ranged from 81-96% and 84-95% respectively. Further, based on simulated dampened T cell responses, protective immunity overall did not drop below 81% less than nine months after infection even with a 75% reduction in specific T cell immunity. Conclusion: NAbs are often the singular focus to predict protective immunity and the role of virus-specific T cell immunity has often been discussed as a secondary immune response. Our analysis demonstrates that for SARS-CoV-2, certain T cells responses can reliably predict protective immunity and may be intrinsically linked. Simulating dampened T cell response to mimic a more virulent strain or inadequate immune response, demonstrated that dampened T cell response may not be responsible for inadequate protective immunity in these scenarios. In the absence of prospective clinical data, similar models may be utilized to explore the impact of potential therapeutics on immune responses and resulting protective immunity.
ABSTRACT
Background. Limited data are available on whether there are differences in the immune response to SARS-CoV-2 vaccination by HIV status or by mRNA vaccine type. Methods. We saved residual outpatient laboratory samples of all previously mRNA-vaccinated individuals in the adult medicine clinics of a public hospital with a large outpatient HIV clinic during May 2021, and then excluded individuals with prior SARS-CoV-2 infection. We next 1:1 matched 100 PLWH to 100 outpatient HIVnegative adult medicine patients receiving care for chronic medical conditions on days since completion of second vaccination (minimum 10), sex, age +/-5 years, and the type of mRNA vaccine received. We defined a non-response as reciprocal pseudovirus neutralizing titer< 10 and anti-RBD IgG< 10 relative fluorescent units, and compared non-response by HIV status using mixed models. Results. In each matched group there were 13 women;25 received the mRNA-1273 vaccine and 75 received the BNT162b2 vaccine;the median age was 59. The median time from second vaccination was 35 days (IQR: 20-63). Among PLWH, the median CD4+ T-cell count was 511 (IQR: 351-796) and 5 individuals had HIV RNA > 200. We found 2.4-fold greater odds of pseudovirus neutralizing antibody non-response among PLWH compared to people without HIV (95% CI=1.1-5.4). Although few individuals in each group did not mount an IgG response (12 among PLWH vs. 5;p=0.08), continuous anti-RBD IgG concentrations were 43% lower among PLWH (95% CI=0.36-0.88). Among PLWH, when adjusting for age, sex, and days post-vaccination, each 100-cell increase in CD4+T-cell count was associated with 22% higher neutralizing antibody titers (GMR 1.22;95% CI=1.09-1.37). Unsuppressed HIV RNA >200 was associated with 89% lower neutralizing antibody titers (GMR 0.11;95% CI=0.01-0.84). Receipt of the BNT162b2 vs. mRNA-1273 vaccine was associated with 77% lower neutralizing titers (GMR 0.23;95% CI=0.08-0.65) among PLWH. Post-mRNA Vaccination SARS-CoV-2 IgG Concentrations and Pseudovirus Neutralizing Titers by HIV Status and Vaccine Conclusion. PLWH had lower than expected response to mRNA SARS-CoV-2 vaccines, with the highest non-response among those with low CD4+ counts, unsuppressed HIV RNA, and those who received the BNT162b2 vaccine. Immunization strategies to improve immune responses among PLWH should be studied, and may include booster vaccination or preference of the mRNA-1273 vaccine in this group.