BACKGROUND:Cytomegalovirus (CMV) reactivation occurs in the context of coronavirus disease 2019 (COVID-19); however, the viral kinetics, risk factors, and clinical outcomes are poorly defined. METHODS:We examined the association of CMV DNAemia with clinical outcomes among participants of a randomized trial of remdesivir with or without baricitinib (National Institute of Allergy and Infectious Diseases [NIAID], Adaptive COVID-19 Treatment Trial 2 [ACTT-2]). Plasma CMV DNAemia from CMV-seropositive participants with COVID-19 (NIAID ordinal scale [OS] 5, 6, or 7 at entry) were assessed longitudinally by quantitative polymerase chain reaction. Factors associated with CMV DNAemia, and clinical outcomes were analyzed by Cox regression and proportional odds models. RESULTS:Of 772 trial participants with available samples, 643 (83%) were CMV seropositive. Baseline CMV serostatus was not associated with COVID-19 outcomes. The cumulative incidence of CMV DNAemia among seropositive persons by day 28 was overall 11% (baseline OS 5, 6.3%; OS 6, 16.4%; OS 7, 24.7%), and was associated with older age, baseline OS, male sex, lymphopenia, and systemic corticosteroid use, while remdesivir and baricitinib did not affect risk. CMV DNAemia was associated with a lower probability of improvement by day 29 (adjusted hazard ratio, 0.3 [95% confidence interval, .17-.56]), with a more pronounced delay of recovery with higher CMV viral load. CMV DNAemia was also associated with higher severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral load and death. CONCLUSIONS:In hospitalized adults with COVID-19 requiring oxygen, CMV viremia occurs within well-defined clinical risks and is independently associated with delayed recovery from illness, higher SARS-CoV-2 viral load, and increased mortality.

Abstract Epstein-Barr virus (EBV) reprograms B cells in autoimmune disease. Reprogrammed EBV + B cells activate nearby B and CD4 + T cells, via upregulated antigen presentation and costimulatory machinery, to drive autoimmune pathology. EBV reactivation is a known correlate of long COVID, which is a heterogeneous condition that can bear similarities to autoimmune disease. However, the mechanisms underpinning this association remain unresolved. We report on EBV metabolically reprogrammed B cells in patients with COVID-19. We find EBV + B cells provide stimulatory signals to bystander B and CD4 + T cells. SARS-CoV-2 infected participants exhibiting elevated fractions of EBV + B cells present, at convalescence, with dysregulated lipid profiles, increased autoantibody titers, and post-acute symptomology likely reflective of this metabolic reprogramming and cell-cell interactions. Enrichment of our EBV + B cell signatures seen in patients with COVID-19 is similar in patients with lupus and multiple sclerosis suggesting a potentially shared pathway of EBV-driven dysfunction across diseases.

Rapid and comprehensive detection of respiratory pathogens is essential for immunocompromised patients with suspected pneumonia. Conventional diagnostic methods are limited in scope, often slow, and lack sensitivity, leading to reduced diagnostic yield. To analytically and clinically validate a microbial cell-free DNA (mcfDNA) sequencing assay for bronchoalveolar lavage fluid (BALF) that enables broad and sensitive detection of pathogens causing pneumonia in immunocompromised patients. The BALF-mcfDNA assay detects more than 500 bacteria, DNA viruses, fungi, and parasites. Analytical validation used 324 contrived samples containing DNA from 11 representative organisms and 1,294 in-silico samples. Clinical validation compared BALF-mcfDNA sequencing with usual care (UC) testing in 118 immunocompromised adults with suspected pneumonia. An independent expert panel adjudicated the etiologic diagnoses. BALF-mcfDNA testing demonstrated high inclusivity (97

Systematic whole-protein screening and comprehensive profiling of antigen-specific CD4+ T cells are crucial for advancing vaccine design and cancer immunotherapies, yet remain technically challenging. Here, we present a high-throughput platform that utilizes large-scale class II single-chain trimer libraries to detect antigen-specific CD4+ T cells, while simultaneously profiling their antigen specificity, TCRα/β sequences, MHC restriction, whole transcriptomes, and patient/timepoint origins at single-cell resolution. Upon rigorous platform validation, we screened the full SARS-CoV-2 spike receptor binding domain in a longitudinal cohort of 22 participants, identifying 2,188 antigen-specific CD4+ T cells and showing key metrics defining the immunogenicity of class II-restricted viral antigens. We further extended the platform to whole-protein screening of HPV-16 E6/E7 in a cohort of precancerous patients, indicating HPV-specific CD4 TCRs that, upon extensive characterization, demonstrate strong therapeutic potential. By integrating high-throughput antigen screening with high-dimensional, multi-modal cellular characterization, our approach provides detailed insight into CD4+ T cell immunity, potentially guiding vaccine design and next-generation TCR-based cancer immunotherapies.

Autoantibodies (autoAbs) are linked to mortality and Long COVID, yet their cellular origins remain unclear. We analyzed the INCOV cohort and identified 12 age- and sex-matched participants with varying autoAb abundance and integrated single-cell RNA-seq and ATAC-seq data from B cells, plasma proteomics, proteome-wide autoAb profiling, clinical data, and in vitro assays. AutoAb abundance inversely correlated with neutralizing IgG and declined as infection resolved, paralleling the contraction of atypical memory B cells (AtMs). In vitro, AtMs preferentially differentiated into autoAb-producing antibody-secreting cells upon TLR7/8 stimulation. CD11c+ AtMs (double-negative 2, DN2s) in autoAb-high individuals exhibited increased TLR7 signaling, oxidative stress, and isotype switching, regulated by transcription factors T-bet and XBP1. Integrated genetic and genomic analyses showed that DN2s had the strongest enrichment for autoimmune trait heritability and inferred regulatory effects of autoimmune risk variants among B cell subsets. These findings identify DN2s as key precursors of autoAb-producing cells during SARS-CoV-2 infection.

BACKGROUND:Post-acute sequelae of SARS-CoV-2 infection, more commonly known as long COVID, has emerged as a major health problem. The pathogenesis of long COVID is unknown, but among the leading hypotheses is viral persistence. We aimed to investigate whether the use of the SARS-CoV-2 antiviral nirmatrelvir-ritonavir improved long COVID symptoms. METHODS:We conducted a double-blind, placebo-controlled, randomised trial involving adults who had developed persistent symptoms (≥12 weeks) associated with three major symptom phenotypes (cognitive, autonomic, or exercise) after acute SARS-CoV-2 infection at 69 US sites. Participants were eligible if they were 18 years or older and had a previous suspected, probable, or confirmed SARS-CoV-2 infection, as defined by the Pan American Health Organization. Eligible participants were also required to have either at least two moderate symptoms from the same phenotype or one severe phenotype-associated symptom, as identified with the Cluster Targeted COVID-19 Symptom Questions. Participants were randomly allocated in a double-blind manner in a 1:1:1 ratio using permuted blocks of size 30 to receive either 15 days of active intervention followed by 10 days of placebo (300 mg nirmatrelvir-100 mg ritonavir twice daily, then 100 mg ritonavir-placebo); 25 days of active intervention (300 mg nirmatrelvir-100 mg ritonavir twice daily); or 25 days of placebo-ritonavir (100 mg ritonavir-placebo). A clinically significant change in patient-reported outcomes at day 90 comprised the primary endpoint: Patient-Reported Outcomes Measurement Information System Cognitive Function Short Form 8a, Orthostatic Hypotension Questionnaire question 1, and a modified version of the DePaul Symptom Questionnaire Post-Exertional Malaise short form. Secondary outcomes were phenotype-specific performance measures. The study was registered at ClinicalTrials.gov (NCT05595369) and is complete. FINDINGS:Between July 27, 2023, and Sept 6, 2024, 1207 individuals were screened. Of these, 964 were randomly allocated and 959 participants, excluding four participants who were later found ineligible and one who did not initiate treatment, were enrolled in the three phenotypes: 332 to cognitive, 334 to autonomic, and 332 to exercise. In the 959 participants in the mITT population, 643 (67%) self-reported as female, 314 (33%) were male, and two participants had a sex of unknown or undifferentiated; 750 (78%) were White; and 108 (11%) were Hispanic, Latino, or Spanish. The median age was 49 years (IQR 38-59). No statistically significant benefits were observed for any phenotype for primary endpoints. For the cognitive phenotype, adjusted differences compared to placebo were 3·2% (95% CI -10·4 to 16·8, p=0·65) for the 25-day regimen and -2·2% (-15·5 to 11·1, p=0·74) for the 15-day regimen. For the autonomic phenotype, adjusted differences were -6·4% (-18·5 to 5·7, p=0·30) for the 25-day regimen compared to placebo and -0·1% (-12·5 to 12·3, p=0·99) for the 15-day regimen compared to placebo. For exercise, adjusted differences were -7·8% (-19·5 to 3·8, p=0·19) for the 25-day regimen compared to placebo and 0·9% (-11·4 to 13·2, p=0·88) for the 15-day regimen compared to placebo. There were no differences in secondary endpoints, and no safety signals were observed; there were no deaths, and 52 serious adverse events occurred in 42 (4%) of 963 participants over the course of the study. INTERPRETATION:Nirmatrelvir-ritonavir for 15 days or 25 days showed no evidence of benefit in long COVID in any of the three phenotypes studied. These findings suggest additional approaches to measuring the symptom burden and treating Long COVID are needed. FUNDING:National Institutes of Health.

Background: Long COVID presents with one or multiple symptoms or diagnosable conditions after SARS-CoV-2 infection. To study whether use of the antiviral remdesivir in persons hospitalized with acute COVID-19 is associated with reduced Long COVID, we created a computational phenotype for Long COVID. Methods: In electronic health records (EHR) from a multistate healthcare system (US), hospital admissions from 5/1/20 - 9/30/22 were reviewed. The study group was hospitalized with acute COVID-19 and the control group was hospitalized for other reasons without prior SARS-CoV-2 infection. The populations were balanced with overlap weights based on a high-dimensional propensity score of pre-specified variables and the top 100 comorbidities differing between the groups. Hazard ratios (HR) were calculated for the combined primary outcome: U09.9 (Post-Covid Conditions) or any incident secondary outcome from 90 to 365 days after admission. Secondary outcomes included 27 individual incident diagnoses, corrected for multiplicity with Holm-Bonferroni. Results: Admissions included 45,540 with, and 409,186 without COVID-19 during the study period, evaluable for the primary outcome. After weighting, standardized difference was < 0.01 for all measured confounders including demographic and clinical features. In the COVID+ and non-COVID groups 38.0% and 29.3% met the combined primary outcome, respectively. Weighted HR (95%CI) for the primary outcome was 1.37 (1.35, 1.40), p < 0.0001. All secondary outcomes were associated with the COVID+ group, when adjusted for multiplicity. Incident diagnoses with strong associations (HR > 2) included thromboembolism, hair loss, diabetes mellitus, obesity, and hypoxia. Anosmia/dysgeusia was associated with COVID, but wide confidence intervals reflected few charted diagnoses. Conclusions: Manifestations of Long COVID at population scale are detectable as part of routine symptoms and clinical diagnoses in the EHR after admissions for COVID-19, compared with all other hospital admissions. This a prior computational phenotype for Long COVID will be used to assess whether remdesivir use is associated with decreased Long COVID. ### Competing Interest Statement JDG reports a grant from Gilead for the conduct of the current work; contracted research from Gilead. Pfizer and BioVie, and serving as a speaker, consultant or advisory board member for Gilead, Merck and Invivyd related to Long COVID, outside the submitted work. MB and EM were employees of Gilead. All other authors have no disclosures. ### Funding Statement The study was funded by an investigator-initiated grant from Gilead Sciences, Inc. to Dr. Goldman. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All procedures were reviewed and approved by the Providence Institutional Review Board (Providence IRB STUDY2023000049). Patient consent was waived because disclosure of protected health information for the study was determined to involve no more than a minimal risk to the privacy of individuals. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.

BACKGROUND:Obeldesivir is an oral nucleoside analogue prodrug antiviral that inhibits SARS-CoV-2 replication. We aimed to assess the efficacy, safety, and tolerability of obeldesivir for the treatment of COVID-19 in non-hospitalised individuals at low risk of progression to severe disease. METHODS:OAKTREE was a phase 3, randomised, double-blind, placebo-controlled trial in 107 centres (including research centres, primary care centres, and hospitals) in Japan and the USA. Low-risk, non-hospitalised adults and adolescents with mild-to-moderate COVID-19 were enrolled within 3 days of symptom onset. Eligible participants were randomly assigned 1:1 using permuted block randomisation (block size of four), stratified by historical completion of a primary COVID-19 vaccination series, to receive either oral obeldesivir 350 mg or matched placebo twice daily for 5 days. The primary efficacy endpoint was time to COVID-19 symptom alleviation by day 29, which was assessed in all randomly assigned participants who received one or more doses of study drug, had positive SARS-CoV-2 RT-PCR (per central laboratory testing) at baseline, and had COVID-19 symptom data (full analysis positive set). The primary safety endpoint was the incidence of adverse events and laboratory abnormalities and was assessed in all randomly assigned participants who received one or more doses of study drug. As a secondary endpoint we assessed change from baseline in nasal swab viral RNA copy number at day 5 in all randomly assigned participants who received one or more doses of study drug and had a quantifiable baseline value. This trial is registered with ClinicalTrials.gov, NCT05715528, and is complete. FINDINGS:Between Feb 13, 2023 and Oct 31, 2023, 1955 participants (1155 female and 800 male; 1698 White, 207 Black, 42 Asian, and eight Other) were randomly assigned and received at least one dose of either obeldesivir (n=979) or placebo (n=976). Overall, 1368 (70·0%) participants had completed a primary COVID-19 vaccination series and 1938 (99·6%) were seropositive for SARS-CoV-2 antibodies. There were 884 participants in each group in the full analysis positive set. Among those in the full analysis positive set who completed the symptom questionnaire (ie, who had COVID-19 symptom data; 879 obeldesivir, 882 placebo), median time to COVID-19 symptom alleviation was 5·9 days (95% CI 5·4-6·1) in the obeldesivir group and 6·0 days (5·8-6·3) in the placebo group (hazard ratio 1·099 [95% CI 0·997-1·211], p=0·068). The least-squares mean change from baseline in viral RNA copy number at day 5 was -2·13 log10 copies per mL (SE 0·04) and -1·95 log10 copies per mL (0·04) for the obeldesivir group (n=637) and placebo group (n=622), respectively, with a least-squares mean difference of -0·18 (95% CI -0·30 to -0·06) log10 copies per mL (p=0·0037). The safety profile was comparable between groups. 53 (5·4%) of 979 participants in the obeldesivir group and 56 (5·7%) of 976 participants in the placebo group had one or more treatment-emergent adverse events. 753 (77·5%) participants in the obeldesivir group and 757 (78·5%) participants in the placebo group had one or more graded laboratory abnormalities, most of which were grade 1 or 2. INTERPRETATION:Obeldesivir was generally safe and well tolerated, with greater reduction of SARS-CoV-2 viral RNA copy number versus placebo at day 5. However, obeldesivir did not significantly reduce time to symptom alleviation, possibly reflecting the challenges of assessing efficacy in this population in an era of high rates of vaccine-induced and natural immunity. FUNDING:Gilead Sciences.

As part of a multi-state viral genomic surveillance program, we conducted a case-only analysis to evaluate the effectiveness of XBB.1.5-adapated mRNA vaccines in preventing severe illness among individuals with medically attended SARS-CoV-2 infection. We compared prior receipt of an XBB.1.5-adapted mRNA vaccine between SARS-CoV-2-infected adults with inpatient or emergency department (ED) visits (as a proxy for severe illness) vs those with outpatient visits (as a proxy for mild illness). Among 6,551 patients between September 2023 and January 2024, 6.1% with inpatient or ED visits vs 12.0% with outpatient visits had received XBB.1.5 vaccination (adjusted odds ratio [aOR]=0.41; 95% confidence interval [CI]: 0.32-0.53). This protective association was weaker among JN.1 (aOR=0.62; 95% CI: 0.40-0.96) vs XBB-lineage (aOR=0.28; 95% CI: 0.18-0.43) variant infections (interaction, p=0.003). XBB.1.5 vaccines protect against severe illness, but protection may be weaker against JN.1 vs XBB-lineage variants. This study highlights the need for COVID-19 vaccines to be routinely updated to align with circulating strains and for individuals to stay up to date with recommended vaccines.

Long COVID comprises a multisystem syndrome occurring after COVID-19. This retrospective cohort study investigated whether remdesivir given during acute COVID-19 is associated with reduced incidence of Long COVID, including in immunocompromised subgroups. The HealthVerity database of hospital chargemaster data linked to closed claims was queried for patients aged ≥ 12 years hospitalized for ≥ 2 days with COVID-19 between May 1, 2020, and September 30, 2021. Relative risk between remdesivir-exposed and unexposed patients was calculated for 16 individual Long COVID outcomes and a composite of any Long COVID outcome, occurring 90–270 days after hospital admission. Subgroup analyses occurred in immunocompromised patients. Regression models accounted for censoring, competing risks, and treatment assignment weights; statistical inferences were adjusted for multiple comparisons. Among 3,661,303 hospitalized patients, 52,006 with COVID-19 were included; 20,246 (38.9%) were immunocompromised. In the overall and immunocompromised populations, respectively, 33.0% and 29.5% received remdesivir; the composite of ≥ 1 Long COVID outcome occurred in 55.5% and 62.9%. Patients administered remdesivir experienced lower risk of any Long COVID outcome (risk ratio, 0.96; 95% CI 0.94–0.97; adjusted P < 0.001). Risk for several individual Long COVID outcomes was lower in those receiving remdesivir in the overall and immunocompromised populations. In conclusion, exposure to remdesivir was associated with a lower risk of Long COVID.

Importance Classification of persons with long COVID (LC) or post-COVID-19 condition must encompass the complexity and heterogeneity of the condition. Iterative refinement of the classification index for research is needed to incorporate newly available data as the field rapidly evolves. Objective To update the 2023 research index for adults with LC using additional participant data from the Researching COVID to Enhance Recovery (RECOVER-Adult) study and an expanded symptom list based on input from patient communities. Design, Setting, and Participants Prospective, observational cohort study including adults 18 years or older with or without known prior SARS-CoV-2 infection who were enrolled at 83 sites in the US and Puerto Rico. Included participants had at least 1 study visit taking place 4.5 months after first SARS-CoV-2 infection or later, and not within 30 days of a reinfection. The study visits took place between October 2021 and March 2024. Exposure SARS-CoV-2 infection. Main Outcomes and Measures Presence of LC and participant-reported symptoms. Results A total of 13 647 participants (11 743 with known SARS-CoV-2 infection and 1904 without known prior SARS-CoV-2 infection; median age, 45 years [IQR, 34-69 years]; and 73% were female) were included. Using the least absolute shrinkage and selection operator analysis regression approach from the 2023 model, symptoms contributing to the updated 2024 index included postexertional malaise, fatigue, brain fog, dizziness, palpitations, change in smell or taste, thirst, chronic cough, chest pain, shortness of breath, and sleep apnea. For the 2024 LC research index, the optimal threshold to identify participants with highly symptomatic LC was a score of 11 or greater. The 2024 index classified 20% of participants with known prior SARS-CoV-2 infection and 4% of those without known prior SARS-CoV-2 infection as having likely LC (vs 21% and 5%, respectively, using the 2023 index) and 39% of participants with known prior SARS-CoV-2 infection as having possible LC, which is a new category for the 2024 model. Cluster analysis identified 5 LC subtypes that tracked quality-of-life measures. Conclusions and Relevance The 2024 LC research index for adults builds on the 2023 index with additional data and symptoms to help researchers classify symptomatic LC and its symptom subtypes. Continued future refinement of the index will be needed as the understanding of LC evolves.

Longitudinal trajectories of Long COVID remain ill-defined, yet are critically needed to advance clinical trials, patient care, and public health initiatives for millions of individuals with this condition. Long COVID trajectories were determined prospectively among 3,659 participants (69% female; 99.6% Omicron era) in the National Institutes of Health Researching COVID to Enhance Recovery (RECOVER) Adult Cohort. Finite mixture modeling was used to identify distinct longitudinal profiles based on a Long COVID research index measured 3 to 15 months after infection. Eight longitudinal profiles were identified. Overall, 195 (5%) had persistently high Long COVID symptom burden, 443 (12%) had non-resolving, intermittently high symptom burden, and 526 (14%) did not meet criteria for Long COVID at 3 months but had increasing symptoms by 15 months, suggestive of distinct pathophysiologic features. At 3 months, 377 (10%) met the research index threshold for Long COVID. Of these, 175 (46%) had persistent Long COVID, 132 (35%) had moderate symptoms, and 70 (19%) appeared to recover. Identification of these Long COVID symptom trajectories is critically important for targeting enrollment for future studies of pathophysiologic mechanisms, preventive strategies, clinical trials and treatments.

Importance Olfactory dysfunction is common after SARS-CoV-2 infection and has been associated with cognitive loss in other conditions. Formal testing is needed to characterize the presence, severity, and patterns of olfactory dysfunction. ObjectiveTo characterize long-term olfactory dysfunction after SARS-CoV-2 infection. Design, Setting, and Participants This prospective cohort study included adults enrolled in the Researching COVID to Enhance Recovery (RECOVER)-Adult study. All those with and a random sample of those without self-reported change or loss in smell or taste were offered olfactory testing, performed at 83 sites in 35 US states and territories. Participants included 2956 enrollees with prior infection (1393 with and 1563 without self-reported change or loss) and 569 without prior infection (9 with and 560 without self-reported change or loss in taste) who underwent olfactory testing a mean (SD) of 671.6 (417.8) days after the index date. Data were collected from October 29, 2021, to June 6, 2025.ExposureSARS-CoV-2 infection.Main Outcomes and Measures Olfactory function, as defined by age- and sex-standardized performance on the University of Pennsylvania Smell Identification Test (UPSIT), a well-validated test comprising 40 unique odors. ResultsThe study included 3525 participants with a mean (SD) age of 47.6 (15.2) years; of 3520 with data available, 2548 (72.4%) were female or intersex. Among 1393 infected participants with self-reported change or loss, 1111 (79.8%) had hyposmia on the UPSIT, including 321 (23.0%) with severe microsmia or anosmia. Among 1563 infected participants without self-reported change or loss, 1031 (66.0%) had hyposmia, including 128 (8.2%) with severe microsmia or anosmia. Participants with prior infection and self-reported change or loss scored at the 16th age- and sex-standardized UPSIT percentile, compared with the 23rd and 28th percentiles for those without self-reported change or loss with and without prior known infection, respectively. Younger women had scores corresponding to lower mean age- and sex-standardized percentiles. Among participants who self-reported change or loss in smell, those with abnormal UPSIT scores more often reported cognitive problems (742 of 1111 [66.8%]) than those with normal UPSIT scores (179 of 282 [63.5%]).Conclusions and RelevanceIn this cohort study of RECOVER-Adult participants, self-reported change or loss in smell or taste was an accurate signal of verified hyposmia, but a high rate of hyposmia among those with no reported change or loss was also observed. Formal smell testing may be considered in those with prior SARS-CoV-2 infection to diagnose occult hyposmia and counsel patients about risks.

Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system's own record of antigen exposures encoded by receptors on B cells and T cells. We analyzed immune receptor datasets from 593 individuals to develop MAchine Learning for Immunological Diagnosis, an interpretive framework to screen for multiple illnesses simultaneously or precisely test for one condition. This approach detects specific infections, autoimmune disorders, vaccine responses, and disease severity differences. Human-interpretable features of the model recapitulate known immune responses to severe acute respiratory syndrome coronavirus 2, influenza, and human immunodeficiency virus, highlight antigen-specific receptors, and reveal distinct characteristics of systemic lupus erythematosus and type-1 diabetes autoreactivity. This analysis framework has broad potential for scientific and clinical interpretation of immune responses.

CD16A is an activating Fc receptor on NK cells that mediates antibody-dependent cellular cytotoxicity (ADCC), a key mechanism in antiviral immunity. However, the role of NK cell-mediated ADCC in SARS-CoV-2 infection remains unclear, particularly whether it limits viral spread and disease severity or contributes to the immunopathogenesis of COVID-19. We hypothesized that the high-affinity CD16AV176 polymorphism influences these outcomes. Using an in vitro reporter system, we demonstrated that CD16AV176 is a more potent and sensitive activator than the common CD16AF176 allele. To assess its clinical relevance, we analyzed 1,027 patients hospitalized with COVID-19 from the Immunophenotyping Assessment in a COVID-19 cohort (IMPACC), a comprehensive longitudinal dataset with extensive transcriptomic, proteomic, and clinical data. The high-affinity CD16AV176 allele was associated with a significantly reduced risk of ICU admission, mechanical ventilation, and severe disease trajectories. Lower anti-SARS-CoV-2 IgG titers were correlated to CD16AV176; however, there was no difference in viral load across CD16A genotypes. Proteomic analysis revealed that participants homozygous for CD16AV176 had lower levels of inflammatory mediators. These findings suggest that CD16AV176 enhances early NK cell-mediated immune responses, limiting severe respiratory complications in COVID-19. This study identifies a protective genetic factor against severe COVID-19, informing future host-directed therapeutic strategies.

Elucidating the relationships between a class I peptide antigen, a CD8 T cell receptor (TCR) specific to that antigen, and the T cell phenotype that emerges following antigen stimulation, remains a mostly unsolved problem, largely due to the lack of large data sets that can be mined to resolve such relationships. Here, we describe Antigen-TCR Pairing and Multiomic Analysis of T-cells (APMAT), an integrated experimental-computational framework designed for the high-throughput capture and analysis of CD8 T cells, with paired antigen, TCR sequence, and single-cell transcriptome. Starting with 951 putative antigens representing a comprehensive survey of the SARS-CoV-2 viral proteome, we utilize APMAT for the capture and single cell analysis of CD8 T cells from 62 HLA A*02:01 COVID-19 participants. We leverage this comprehensive dataset to integrate with peptide antigen properties, TCR CDR3 sequences, and T cell phenotypes to show that distinct physicochemical features of the antigen-TCR pairs strongly associate with both T cell phenotype and T cell persistence. This analysis suggests that CD8 T cell phenotype following antigen stimulation is at least partially deterministic, rather than the result of stochastic biological properties. Combinatorial experimental and bioinformatics methods can be used to analyse function and specificity of CD8 T cells. Here the authors propose a multiomic analysis framework Antigen-TCR Pairing and Multiomic Analysis of T cell (APMAT) to relate TCR specificity to transcriptomic phenotype indicating associations with physicochemical features.

Background Improved diagnostic testing (DT) of infections may optimize outcomes for solid organ transplant recipients (SOTR), but a comprehensive analysis is lacking.Methods We conducted a systematic literature review across multiple databases, including EMBASE and MEDLINE(R), of studies published between 1 January 2012-11 June 2022, to examine the evidence behind DT in SOTR. Eligibility criteria included the use of conventional diagnostic methods (culture, biomarkers, directed-polymerase chain reaction [PCR]) or advanced molecular diagnostics (broad-range PCR, metagenomics) to diagnose infections in hospitalized SOTR. Bias was assessed using tools such as the Cochrane Handbook and PRISMA 2020.Results Of 2362 studies, 72 were eligible and evaluated heterogeneous SOT populations, infections, biospecimens, DT, and outcomes. All studies exhibited bias, mainly in reporting quality. Median study sample size was 102 (range, 11-1307). Culture was the most common DT studied (N = 45 studies, 62.5%), with positive results in a median of 27.7% (range, 0%-88.3%). Biomarkers, PCR, and metagenomics were evaluated in 7, 19, and 3 studies, respectively; only 6 reported sensitivity, specificity, and positive/negative predictive values. Directed-PCR performed well for targeted pathogens, but only 1 study evaluated broad-range PCR. Metagenomics approaches detected numerous organisms but required clinical adjudication, with too few studies (N = 3) to draw conclusions. Turnaround time was shorter for PCR/metagenomics than conventional diagnostic methods (N = 4 studies, 5.6%). Only 6 studies reported the impact of DT on outcomes like antimicrobial use and length of stay.Conclusions We identified considerable evidence gaps in infection-related DT among SOT, particularly molecular DT, highlighting the need for further research. This systematic literature review (2012-2022) assessed infection diagnostic testing in solid organ transplant recipients. Studies demonstrated wide heterogeneity, lacking data on accuracy and impact on clinical outcomes. Additional studies on novel infection diagnostic testing in solid organ transplant recipients are greatly needed.

SARS-CoV-2 infection has been associated with increased autoimmune disease risk. Past studies have not aligned regarding the most prevalent autoimmune diseases after infection, however. Furthermore, the relationship between infection severity and new autoimmune disease risk has not been well examined. We used RECOVER's electronic health record (EHR) networks, N3C, PCORnet, and PEDSnet, to estimate types and frequency of autoimmune diseases arising after SARS-CoV-2 infection and assessed how infection severity related to autoimmune disease risk. We identified patients of any age with SARS-CoV-2 infection between April 1, 2020 and April 1, 2021, and assigned them to a World Health Organization COVID-19 severity category for adults or the PEDSnet acute COVID-19 illness severity classification system for children (30 days after SARS-CoV-2 infection index date and occurring ≥1 day apart. We calculated overall and infection severity-stratified incidence ratesper 1000 person-years for all autoimmune diseases. With least severe COVID-19 severity as reference, survival analyses examined incident autoimmune disease risk. The most common new-onset autoimmune diseases in all networks were thyroid disease, psoriasis/psoriatic arthritis, and inflammatory bowel disease. Among adults, inflammatory arthritis was the most common, and Sjögren's disease also had high incidence. Incident type 1 diabetes and hematological autoimmune diseases were specifically found in children. Across networks, after adjustment, patients with highest COVID-19 severity had highest risk for new autoimmune disease vs. those with least severe disease (N3C: adjusted Hazard Ratio, (aHR) 1.47 (95%CI 1.33-1.66); PCORnet aHR 1.14 (95%CI 1.02-1.26); PEDSnet: aHR 3.14 (95%CI 2.42-4.07)]. Overall, severe acute COVID-19 was most strongly associated with autoimmune disease risk in three EHR networks.