Efficacy and Safety of Huashi Baidu Granules in Treating Patients with SARS-CoV-2 Omicron Variant: A Single-Center Retrospective Cohort Study.

OBJECTIVE: To evaluate the efficacy and safety of Huashi Baidu Granules (HSBD) in treating patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant. METHODS: A single-center retrospective cohort study was conducted during COVID-19 Omicron epidemic in the Mobile Cabin Hospital of Shanghai New International Expo Center from April 1st to May 23rd, 2022. All COVID-19 patients with asymptomatic or mild infection were assigned to the treatment group (HSBD users) and the control group (non-HSBD users). After propensity score matching in a 1:1 ratio, 496 HSBD users of treatment group were matched by propensity score to 496 non-HSBD users. Patients in the treatment group were administrated HSBD (5 g/bag) orally for 1 bag twice a day for 7 consecutive days. Patients in the control group received standard care and routine treatment. The primary outcomes were the negative conversion time of nucleic acid and negative conversion rate at day 7. Secondary outcomes included the hospitalized days, the time of the first nucleic acid negative conversion, and new-onset symptoms in asymptomatic patients. Adverse events (AEs) that occurred during the study were recorded. Further subgroup analysis was conducted in vaccinated (378 HSBD users and 390 non-HSBD users) and unvaccinated patients (118 HSBD users and 106 non-HSBD users). RESULTS: The median negative conversion time of nucleic acid in the treatment group was significantly shortened than the control group [3 days (IQR: 2-5 days) vs. 5 days (IQR: 4-6 days); P<0.01]. The negative conversion rate of nucleic acid in the treatment group were significantly higher than those in the control group at day 7 (91.73% vs. 86.90%, P=0.014). Compared with the control group, the hospitalized days in the treatment group were significantly reduced [10 days (IQR: 8-11 days) vs. 11 days (IQR: 10.25-12 days); P<0.01]. The time of the first nucleic acid negative conversion had significant differences between the treatment and control groups [3 days (IQR: 2-4 days) vs. 5 days (IQR: 4-6 days); P<0.01]. The incidence of new-onset symptoms including cough, pharyngalgia, expectoration and fever in the treatment group were lower than the control group (P<0.05 or P<0.01). In the vaccinated patients, the median negative conversion time and hospitalized days were significantly shorter than the control group after HSDB treatment [3 days (IQR: 2-5 days) vs. 5 days (IQR: 4-6 days), P<0.01; 10 days (IQR: 8-11 days) vs. 11 days (IQR: 10-12 days), P<0.01]. In the unvaccinated patients, HSBD treatment efficiently shorten the median negative conversion time and hospitalized days [4 days (IQR: 2-6 days) vs. 5 days (IQR: 4-7 days), P<0.01; 10.5 days (IQR: 8.75-11 days) vs. 11.0 days (IQR: 10.75-13 days); P<0.01]. No serious AEs were reported during the study. CONCLUSION: HSBD treatment significantly shortened the negative conversion time of nuclear acid, the length of hospitalization, and the time of the first nucleic acid negative conversion in patients infected with SARS-COV-2 Omicron variant (Trial registry No. ChiCTR2200060472).

Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection.

T cell responses precede antibody and may provide early control of infection. We analyzed the clonal basis of this rapid response following SARS-COV-2 infection. We applied T cell receptor (TCR) sequencing to define the trajectories of individual T cell clones immediately. In SARS-COV-2 PCR+ individuals, a wave of TCRs strongly but transiently expand, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains but not with circulating human coronaviruses. Many expanding CDR3s were present at high frequency in pre-pandemic repertoires. Early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the preinfection naive repertoire. High-frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection.

Evaluation of T cell responses to naturally processed variant SARS-CoV-2 spike antigens in individuals following infection or vaccination

Most existing studies characterising SARS-CoV-2-specific T cell responses are peptide based. This does not allow evaluation of whether tested peptides are processed and presented canonically. In this study, we use recombinant vaccinia virus (rVACV)-mediated expression of SARS-CoV-2 spike protein and SARS-CoV-2 infection of ACE-2-transduced B cell lines to evaluate overall T cell responses in a small cohort of recovered COVID-19 patients and uninfected donors vaccinated with ChAdOx1 nCoV-19. We show that rVACV expression of SARS-CoV-2 antigen can be used as an alternative to SARS-CoV-2 infection to evaluate T cell responses to naturally processed spike antigens. In addition, rVACV system can be used to evaluate the cross-reactivity of memory T cells to variants of concern (VOCs) and to identify epitope escape mutants. Finally, our data show that both natural infection and vaccination could induce multi-functional T cell responses with overall T cell responses remaining despite the identification of escape mutations. Graphical Yin et al. utilize two informative systems for evaluating overall T cell responses to SARS-CoV-2 and variants, enabling greater understanding of T cell responses to the virus, cross-reactivity to viral variants and the differences between vaccine- and infection-induced immunity to SARS-CoV-2, and other emerging viruses in the future.

Efficacy of Upadacitinib Dose Escalation in a Phase 3 Long-Term Extension Ulcerative Colitis Study

Introduction: Upadacitinib (UPA), an oral selective and reversible JAK inhibitor, recently demonstrated significantly greater therapeutic efficacy compared to placebo (PBO) in patients with moderate to severe ulcerative colitis (UC) during a Phase 3 program.1,2,3 We evaluated the efficacy of dose escalation to UPA 30 mg QD (UPA30) among patients who demonstrated an inadequate response to UPA 15 mg QD (UPA15) during the long-term extension (LTE) study U-ACTIVATE. Results were based on non-responder imputation (NRI-NC) with 95% confidence intervals (CI) calculated by normal approximation to binomial distribution. F020For patients enrolled from U-ACHIEVE Maintenance due to loss of response, inadequate response was defined as: SFS + RBS value that remains unchanged or has increased from wk 0 on two consecutive visits at least 7 days apart. a Non-responder imputation with no special data handling for missing due to COVID-19 was applied. 95% CI calculated by normal approximation to binomial distribution. b Clinical remission per Adapted Mayo score: SFS≤1 and not greater than baseline (of induction), RBS=0, and endoscopic subscore (ES) ≤ 1. c Clinical remission per Adapted Mayo score and CS-free clinical remission (clinical remission at wk 48 and CS-free for ≥90 days prior to wk 48 among patients with clinical remission at the end of the induction therapy). d Endoscopic improvement: ES ≤ 1 e Endoscopic remission: ES= 0.

Efficacy and Safety of Upadacitinib Maintenance Therapy in Patients With Moderately to Severely Active Ulcerative Colitis: Final Results From the Phase 3 U-ACHIEVE Maintenance Study

Introduction: Upadacitinib(UPA), has shown superior efficacy to placebo(PBO) in patients with moderate to severe active ulcerative colitis(UC) in two Phase 3 induction studies .1,2 Patients demonstrating clinical response per Adapted Mayo score with UPA 45mg once daily(QD) after 8 weeks(wks) induction were enrolled to U-ACHIEVE Maintenance. Methods: U-ACHIEVE Maintenance efficacy data from the intent-to-treat(ITT) population, defined as UPA 45mg QD 8wk induction responders enrolled per protocol for 52wk maintenance, and safety data from the safety population, defined as patients who received ≥1 dose of study therapy(ITT plus patients receiving up to 44wksmaintenanceper prior versions of protocol amendments). Non-responder imputation incorporating multiple imputations to handle missing data due to COVID-19 was used. a Based on adjusted Cochran–Mantel–Haenszel test adjusted for strata (corticosteroid use at Week 0 (yes or no), clinical remission status at Week 0 (yes or no), biologic-IR status at baseline (biologic-IR or non-biologic-IR)). b Per Adapted Mayo score ≤2: stool frequency subscore ≤1 and not greater than induction baseline, RBS=0, and ES ≤1. c Maintenance of clinical response, defined as a decrease in Adapted Mayo score ≥2 and ≥30% from induction baseline, plus a decrease in RBS ≥1 or an absolute RBS ≤1, at Week 52 among patients who achieved clinical response at the end of the induction therapy. d ES ≤1. e Maintenance of CR at Week 52 among patients with CR at the end of the induction therapy. f CR at Week 52 and corticosteroid-free for ≥90 days prior to Week 52 among patients with CR at the end of the induction therapy. g Endoscopic improvement at Week 52 among patients with endoscopic improvement at the end of the induction therapy. h ES=0. i ES ≤1 and Geboes score ≤3.1. j ES=0 and Geboes score < 2.0.

Impact of Inflammatory Burden on Efficacy of Upadacitinib Maintenance Therapy in Ulcerative Colitis: Results From the Phase 3 U-ACHIEVE Study

Introduction: Upadacitinib (UPA) has demonstrated superior efficacy to placebo (PBO) and a favorable safety profile in patients with moderately to severely active ulcerative colitis (UC) in trial U-ACHIEVE Maintenance, in which two maintenance doses of UPA (30mg and 15mg once daily [QD]) were evaluated.1–3 However, data are limited on the impact of inflammatory burden on the efficacy of the two maintenance doses. Endoscopic improvement c at Week 52 BL Full Mayo score ≤9 BL Full Mayo score >9 8/74 (10.8) 14/75 (18.1) 45/75 (60.4) 27/73 (36.7) 44/73 (60.6) 50/79 (62.8) 0.2 26.1 Pancolitis at BL, no Pancolitis at BL, yes 16/79 (20.3) 6/70 (8.0) 33/66 (49.6) 39/82 (47.9) 43/68 (63.7) 52/86 (59.9) 14.1 12.0 EIM at BL, no EIM at BL, yes 15/112 (13.7) 6/37 (16.9) 57/112 (50.9) 15/36 (41.7) 68/113 (60.2) 27/41 (65.4) 9.3 23.7 Data are from the ITT population, defined as the first 450 randomized and treated patients with 8-week UPA 45 mg QD induction treatment who were enrolled in Cohort 1 under the protocol for the 52-week maintenance treatment period. Non-responder imputation incorporating multiple imputations was performed to handle missing data due to COVID-19 incidence. a Not part of the predefined statistical analyses. b Adapted Mayo score ≤2, with stool frequency subscore ≤1 (and not greater than induction baseline), rectal bleeding subscore of 0, and endoscopic subscore ≤1. c Endoscopic subscore ≤1.

Pandemic Control, Game Theory and Machine Learning (preprint)

Game theory has been an effective tool in the control of disease spread and in suggesting optimal policies at both individual and area levels. In this AMS Notices article, we focus on the decision-making development for the intervention of COVID-19, aiming to provide mathematical models and efficient machine learning methods, and justifications for related policies that have been implemented in the past and explain how the authorities' decisions affect their neighboring regions from a game theory viewpoint.

An immunodominant NP105-113-B*07:02 cytotoxic T cell response controls viral replication and is associated with less severe COVID-19 disease.

NP105-113-B*07:02-specific CD8+ T cell responses are considered among the most dominant in SARS-CoV-2-infected individuals. We found strong association of this response with mild disease. Analysis of NP105-113-B*07:02-specific T cell clones and single-cell sequencing were performed concurrently, with functional avidity and antiviral efficacy assessed using an in vitro SARS-CoV-2 infection system, and were correlated with T cell receptor usage, transcriptome signature and disease severity (acute n = 77, convalescent n = 52). We demonstrated a beneficial association of NP105-113-B*07:02-specific T cells in COVID-19 disease progression, linked with expansion of T cell precursors, high functional avidity and antiviral effector function. Broad immune memory pools were narrowed postinfection but NP105-113-B*07:02-specific T cells were maintained 6 months after infection with preserved antiviral efficacy to the SARS-CoV-2 Victoria strain, as well as Alpha, Beta, Gamma and Delta variants. Our data show that NP105-113-B*07:02-specific T cell responses associate with mild disease and high antiviral efficacy, pointing to inclusion for future vaccine design.

The impact of viral mutations on recognition by SARS-CoV-2 specific T cells.

We identify amino acid variants within dominant SARS-CoV-2 T cell epitopes by interrogating global sequence data. Several variants within nucleocapsid and ORF3a epitopes have arisen independently in multiple lineages and result in loss of recognition by epitope-specific T cells assessed by IFN-γ and cytotoxic killing assays. Complete loss of T cell responsiveness was seen due to Q213K in the A∗01:01-restricted CD8+ ORF3a epitope FTSDYYQLY207-215; due to P13L, P13S, and P13T in the B∗27:05-restricted CD8+ nucleocapsid epitope QRNAPRITF9-17; and due to T362I and P365S in the A∗03:01/A∗11:01-restricted CD8+ nucleocapsid epitope KTFPPTEPK361-369. CD8+ T cell lines unable to recognize variant epitopes have diverse T cell receptor repertoires. These data demonstrate the potential for T cell evasion and highlight the need for ongoing surveillance for variants capable of escaping T cell as well as humoral immunity.

Upadacitinib Is Effective at Inducing Clinical Remission and Response in Ulcerative Colitis Patients Regardless of Baseline Corticosteroid Use: Results From Two Phase 3 Studies

Endpoints presented here are the percentage of patients in clinical remission at wk 8, per Adapted Mayo score, and the percentage of patients with a clinical response at wk 2, per partial Adapted Mayo score (both defined in Table footnotes), respectively, in patients who were on concomitant CS at baseline, at a dose maintained to the end of induction and in those treated with UPA without concomitant CS. Similar results were found with the clinical response rate at wk 2, with no difference between UPA-treated patients who received baseline CS (U-ACHIEVE: 58.1%;U-ACCOMPLISH: 55.1%) and those that received UPA without CS (U-ACHIEVE: 61.4%;U-ACCOMPLISH: 67.7%). Subjects were considered "non-responder" for binary endpoints at and after the UC-related corticosteroids censoring time point through the end of the Induction Study. † Dosing for main corticosteroids were as follows: prednisone. 10-40 mg QD, budesonide, 9 mg QD;or beclomethasone, 5 mg QD. § 95% CI for response rate is the synthetic result based on Student's t-distribution from PROC MIANALYZE procedure if there were missing data due to COVID-19 or is based on the normal approximation to the binomial distribution if there are no missing data due to COVID-19. ‡ 95% CI for response rate difference was calculated based on normal approximation to the binomial distribution.

Applicability of MuLBSTA scoring system as diagnostic and prognostic role in early warning of severe COVID-19.

To explore the applicability of MuLBSTA Score in COVID-19 patients, a retrospective analysis was performed on 330 cases of COVID-19 patients in Southeast Hospital of Xiaogan City, Hubei Province. The clinical characteristics of COVID-19 patients were described and multilobe infiltrate in CT, bacterial infection, lymphocyte count, smoke in history, history of hypertension, and age distribution in the population of mild and severe patients were analyzed. All included patients were scored according to the MuLBSTA early warning scoring system and its efficacy in early warning of severe symptoms was analyzed. CT feature of infiltration changes on multiple lobes, the absolute value of lymphocyte count of less than 0.8 × 109, accompanied by bacterial infection, history of smoking, history of hypertension, and an age of greater than 60 years old were all statistically significant factors in patients with severe COVID-19. ROC curve analysis indicated that the sensitivity, specificity and accuracy of the early warning system were 0.651, 0.954 and 0.93, respectively. The MuLBSTA Score has a good early warning effect on severe COVID-19 patients.

Optimal Policies for a Pandemic: A Stochastic Game Approach and a Deep Learning Algorithm (preprint)

Game theory has been an effective tool in the control of disease spread and in suggesting optimal policies at both individual and area levels. In this paper, we propose a multi-region SEIR model based on stochastic differential game theory, aiming to formulate optimal regional policies for infectious diseases. Specifically, we enhance the standard epidemic SEIR model by taking into account the social and health policies issued by multiple region planners. This enhancement makes the model more realistic and powerful. However, it also introduces a formidable computational challenge due to the high dimensionality of the solution space brought by the presence of multiple regions. This significant numerical difficulty of the model structure motivates us to generalize the deep fictitious algorithm introduced in [Han and Hu, MSML2020, pp.221--245, PMLR, 2020] and develop an improved algorithm to overcome the curse of dimensionality. We apply the proposed model and algorithm to study the COVID-19 pandemic in three states: New York, New Jersey, and Pennsylvania. The model parameters are estimated from real data posted by the Centers for Disease Control and Prevention (CDC). We are able to show the effects of the lockdown/travel ban policy on the spread of COVID-19 for each state and how their policies affect each other.

Broad and strong memory CD4+ and CD8+ T cells induced by SARS-CoV-2 in UK convalescent individuals following COVID-19.

The development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccines and therapeutics will depend on understanding viral immunity. We studied T cell memory in 42 patients following recovery from COVID-19 (28 with mild disease and 14 with severe disease) and 16 unexposed donors, using interferon-γ-based assays with peptides spanning SARS-CoV-2 except ORF1. The breadth and magnitude of T cell responses were significantly higher in severe as compared with mild cases. Total and spike-specific T cell responses correlated with spike-specific antibody responses. We identified 41 peptides containing CD4+ and/or CD8+ epitopes, including six immunodominant regions. Six optimized CD8+ epitopes were defined, with peptide-MHC pentamer-positive cells displaying the central and effector memory phenotype. In mild cases, higher proportions of SARS-CoV-2-specific CD8+ T cells were observed. The identification of T cell responses associated with milder disease will support an understanding of protective immunity and highlights the potential of including non-spike proteins within future COVID-19 vaccine design.