Omicron BA.1 breakthrough infections in inactivated COVID-19 vaccine recipients induced distinct pattern of antibody and T cell responses to different Omicron sublineages.

The adaptive immunity against SARS-CoV-2 prototype strain and Omicron sublineages induced by BA.1 breakthrough infection in vaccinees of inactivated COVID-19 vaccines have not been well characterized. Here, we report that BA.1 breakthrough infection induced mucosal sIgA and resulted in higher IgG titers against prototype strain and Omicron sublineages in vaccinees than in vaccine naïve-infected individuals. BA.1 breakthrough infection boosted antibody-dependent cellular cytotoxicity and antibody-dependent cellular phagocytosis to prototype strain and BA.1, BA.1.1, BA.2, BA.2.12.1, and BA.2.75 but not BA.4/5 and induced neutralization against prototype strain and BA.1, BA.1.1, BA.2, BA.2.12.1, BA.2.75, and BA.4/5 but not BF.7, BQ.1, and XBB. In total, BA.1 breakthrough infection individuals produced less extensive sIgA, plasma IgG and NAb responses against Omicron sublineages compared with those against prototype strain. Further, BA.1 breakthrough infection induced recall B cell response to prototype strain and Omicron variant, primarily targeting memory B cells producing conserved epitopes. Memory T cell responses against Omicron is largely preserved. Individuals with vaccine booster did not induce more beneficial immune responses to Omicron sublineages upon BA.1 breakthrough infection than those with primary vaccine dose only. The breakthrough infection individuals produced stronger adaptive immunity than those of inactivated vaccine-healthy individuals. These data have important implications for understanding the vaccine effectiveness and adaptive immunity to breakthrough infection in individuals fully immunized with inactivated vaccines. Omicron sublineages, especially for those emerged after BA.4/5 strain, evade NAb responses induced by BA.1 breakthrough infection. It is urgent to optimize the vaccine immunogen design and formulations to SARS-CoV-2 variants.

Methodology of network pharmacology for research on Chinese herbal medicine against COVID-19: A review.

Traditional Chinese medicine, as a complementary and alternative medicine, has been practiced for thousands of years in China and possesses remarkable clinical efficacy. Thus, systematic analysis and examination of the mechanistic links between Chinese herbal medicine (CHM) and the complex human body can benefit contemporary understandings by carrying out qualitative and quantitative analysis. With increasing attention, the approach of network pharmacology has begun to unveil the mystery of CHM by constructing the heterogeneous network relationship of "herb-compound-target-pathway," which corresponds to the holistic mechanisms of CHM. By integrating computational techniques into network pharmacology, the efficiency and accuracy of active compound screening and target fishing have been improved at an unprecedented pace. This review dissects the core innovations to the network pharmacology approach that were developed in the years since 2015 and highlights how this tool has been applied to understanding the coronavirus disease 2019 and refining the clinical use of CHM to combat it.

SARS-CoV-2-specific antibody and T-cell responses 1 year after infection in people recovered from COVID-19: a longitudinal cohort study.

Background: The memory immune response is crucial for preventing reinfection or reducing disease severity. However, the robustness and functionality of the humoral and T-cell response to SARS-CoV-2 remains unknown 12 months after initial infection. The aim of this study is to investigate the durability and functionality of the humoral and T-cell response to the original SARS-CoV-2 strain and variants in recovered patients 12 months after infection. Methods: In this longitudinal cohort study, we recruited participants who had recovered from COVID-19 and who were discharged from the Wuhan Research Center for Communicable Disease Diagnosis and Treatment at the Chinese Academy of Medical Sciences, Wuhan, China, between Jan 7 and May 29, 2020. Patients received a follow-up visit between Dec 16, 2020, and Jan 27, 2021. We evaluated the presence of IgM, IgA, and IgG antibodies against the SARS-CoV-2 nucleoprotein, Spike protein, and the receptor-binding domain 12 months after initial infection, using ELISA. Neutralising antibodies against the original SARS-CoV-2 strain, and the D614G, beta (B.1.351), and delta (B.1.617.2) variants were analysed using a microneutralisation assay in a subset of plasma samples. We analysed the magnitude and breadth of the SARS-CoV-2-specific memory T-cell responses using the interferon γ (IFNγ) enzyme-linked immune absorbent spot (ELISpot) assay and intracellular cytokine staining (ICS) assay. The antibody response and T-cell response (ie, IFN-γ, interleukin-2 [IL-2], and tumour necrosis factor α [TNFα]) were analysed by age and disease severity. Antibody titres were also analysed according to sequelae symptoms. Findings: We enrolled 1096 patients, including 289 (26·4%) patients with moderate initial disease, 734 (67·0%) with severe initial disease, and 73 (6·7%) with critical initial disease. Paired plasma samples were collected from 141 patients during the follow-up visits for the microneutralisation assay. PBMCs were collected from 92 of 141 individuals at the 12-month follow-up visit, of which 80 were analysed by ELISpot and 92 by ICS assay to detect the SARS-CoV-2-specific memory T-cell responses. N-IgG (899 [82·0%]), S-IgG (1043 [95·2%]), RBD-IgG (1032 [94·2%]), and neutralising (115 [81·6%] of 141) antibodies were detectable 12 months after initial infection in most individuals. Neutralising antibodies remained stable 6 and 12 months after initial infection in most individuals younger than 60 years. Multifunctional T-cell responses were detected for all SARS-CoV-2 viral proteins tested. There was no difference in the magnitude of T-cell responses or cytokine profiles in individuals with different symptom severity. Moreover, we evaluated both antibody and T-cell responses to the D614G, beta, and delta viral strains. The degree of reduced in-vitro neutralising antibody responses to the D614G and delta variants, but not to the beta variant, was associated with the neutralising antibody titres after SARS-CoV-2 infection. We also found poor neutralising antibody responses to the beta variant; 83 (72·2%) of 115 patients showed no response at all. Moreover, the neutralising antibody titre reduction of the recovered patient plasma against the delta variant was similar to that of the D614G variant and lower than that of the beta variant. By contrast, T-cell responses were cross-reactive to the beta variant in most individuals. Importantly, T-cell responses could be detected in all individuals who had lost the neutralising antibody response to SARS-CoV-2 12 months after the initial infection. Interpretation: SARS-CoV-2-specific neutralising antibody and T-cell responses were retained 12 months after initial infection. Neutralising antibodies to the D614G, beta, and delta viral strains were reduced compared with those for the original strain, and were diminished in general. Memory T-cell responses to the original strain were not disrupted by new variants. This study suggests that cross-reactive SARS-CoV-2-specific T-cell responses could be particularly important in the protection against severe disease caused by variants of concern whereas neutralising antibody responses seem to reduce over time. Funding: Chinese Academy of Medical Sciences, National Natural Science Foundation, and UK Medical Research Council.

Humoral responses after inactivated COVID-19 vaccination in individuals with and without prior SARS-CoV-2 infection: A prospective cohort study.

We evaluated and compared humoral immune responses after inactivated coronavirus disease 2019 (COVID-19) vaccination among naïve individuals, asymptomatically infected individuals, and recovered patients with varying severity. In this multicenter, prospective cohort study, blood samples from 666 participants were collected before and after 2 doses of inactivated COVID-19 vaccination. Among 392 severe acute respiratory syndrome coronavirus 2-naïve individuals, the seroconversion rate increased significantly from 51.8% (median antispike protein pan-immunoglobulins [S-Igs] titer: 0.8 U/ml) after the first dose to 96% (median S-Igs titer: 79.5 U/ml) after the second dose. Thirty-two percent of naïve individuals had detectable neutralizing antibodies (NAbs) against the original strain but all of them lost neutralizing activity against the Omicron variant. In 274 individuals with natural infection, humoral immunity was significantly improved after a single vaccine dose, with median S-Igs titers of 596.7, 1176, 1086.5, and 1828 U/ml for asymptomatic infections, mild cases, moderate cases, and severe/critical cases, respectively. NAb titers also improved significantly. However, the second dose did not substantially increase antibody levels. Although a booster dose is needed for those without infection, our findings indicate that recovered patients should receive only a single dose of the vaccine, regardless of the clinical severity, until there is sufficient evidence to confirm the benefits of a second dose.

Who is more likely to hesitate to accept COVID-19 vaccine: a cross-sectional survey in China.

BACKGROUND: The aim of our study was to identify factors associated with coronavirus disease 2019 (COVID-19)vaccine willingness in China to aid future public health actions to improve vaccination. RESEARCH DESIGN AND METHODS: This study was conducted in August 2020 using a mixed-method approach, including a cross-sectional self-administered anonymous questionnaire survey and in-depth interviews with community residents in China. RESULTS: Of the participants, 30.9% showedCOVID-19 vaccine hesitancy. Being female(OR = 1.297), having poor health(OR = 1.312), having non-health or medical-related occupations (OR = 1.129), no COVID-19 infection experience(OR = 1.523), living with vulnerable family members(OR = 1.294), less knowledge(OR = 1.371), less attention to COVID-19 information(OR = 1.430), less trust in official media(OR = 1.336), less perceived susceptibility to COVID-19(OR = 1.367), and less protective behavior(OR = 1.195) were more likely to hesitate. Qualitative research has shown that they doubt the importance and necessity, as well as the effectiveness and safety of the vaccination. The economic and service accessibility of the vaccination was an impediment to their vaccine acceptance. CONCLUSION: Nearly one-thirdof people showed hesitancy to accept COVID-19 vaccination in China. Our findings highlight that health communication and publicity should be performed for the targeted population, and immunization programs should be designed to remove underlying barriers to vaccine uptake.

Risk Culture and COVID-19 Protective Behaviors: A Cross-Sectional Survey of Residents in China.

The COVID-19 outbreak caused by the Severe Acute Respiratory Syndrome CoronaVirus type 2 (SARS-CoV-2) has spread across the world. However, our understanding of the public responses, in particular in adopting protective behaviors, has been limited. The current study aimed to determine the level of protective behaviors adopted by the residents in China and its association with their cultural attributes. A national cross-sectional online survey was conducted in mainland China from 4th to 13th August 2020. Protective behaviors were assessed as a summed score (ranging from 0 to 40) measured by ten items. The self-report tendency of study participants toward the four cultural attributes (individualism, egalitarianism, fatalism, hierarchy) was rated on a seven-point Likert scale. A total of 17651 respondents returned a valid questionnaire, representing 47.9% of those who accessed the online survey. Most (89.8%) respondents aged between 18 and 45 years in the age range of and 47.7% were male. High levels of protective behaviors (34.04 ± 5.78) were reported. The respondents had high scores in the cultural attributes of hierarchy (Median = 5) and egalitarianism (Median = 5), compared with low scores in individualism (Median = 1) and fatalism (Median = 1). High levels of protective behaviors were associated a higher tendency toward egalitarianism (AOR = 2.90, 95% CI 2.67-3.15) and hierarchy (AOR = 1.66, 95% CI 1.53-1.81) and a low tendency toward fatalism (AOR = 1.79, 95% CI 1.63-1.97) and individualism (AOR = 2.62, 95% CI 2.41-2.85). The cultural attributes explained 17.3% of the variations in the protective behavioral scores. In conclusion, the adoption of protective behaviors is associated a risk culture characterized by high levels of hierarchy and egalitarianism and low levels of individualism and fatalism. Government actions and communication strategies need to adapt to the cultural characteristics of their target audience.

The sum of root-leaf distance interdiction problem by upgrading edges/nodes on trees.

Network interdiction problems by upgading critical edges/nodes have important applications to reduce the infectivity of the COVID-19. A network of confirmed cases can be described as a rooted tree that has a weight of infectious intensity for each edge. Upgrading edges (nodes) can reduce the infectious intensity with contacts by taking prevention measures such as disinfection (treating the confirmed cases, isolating their close contacts or vaccinating the uninfected people). We take the sum of root-leaf distance on a rooted tree as the whole infectious intensity of the tree. Hence, we consider the sum of root-leaf distance interdiction problem by upgrading edges/nodes on trees (SDIPT-UE/N). The problem (SDIPT-UE) aims to minimize the sum of root-leaf distance by reducing the weights of some critical edges such that the upgrade cost under some measurement is upper-bounded by a given value. Different from the problem (SDIPT-UE), the problem (SDIPT-UN) aims to upgrade a set of critical nodes to reduce the weights of the edges adjacent to the nodes. The relevant minimum cost problem (MCSDIPT-UE/N) aims to minimize the upgrade cost on the premise that the sum of root-leaf distance is upper-bounded by a given value. We develop different norms to measure the upgrade cost. Under weighted Hamming distance, we show the problems (SDIPT-UE/N) and (MCSDIPT-UE/N) are NP-hard by showing the equivalence of the two problems and the 0-1 knapsack problem. Under weighted l 1 norm, we solve the problems (SDIPT-UE) and (MCSDIPT-UE) in O(n) time by transforimg them into continuous knapsack problems. We propose two linear time greedy algorithms to solve the problem (SDIPT-UE) under unit Hamming distance and the problem (SDIPT-UN) with unit cost, respectively. Furthermore, for the the minimum cost problem (MCSDIPT-UE) under unit Hamming distance and the problem (MCSDIPT-UN) with unit cost, we provide two O ( n log n ) time algorithms by the binary search methods. Finally, we perform some numerical experiments to compare the results obtained by these algorithms.

Prediction of Disease Progression of COVID-19 Based upon Machine Learning.

BACKGROUND: Since December 2019, COVID-19 has spread throughout the world. Clinical outcomes of COVID-19 patients vary among infected individuals. Therefore, it is vital to identify patients at high risk of disease progression. METHODS: In this retrospective, multicenter cohort study, COVID-19 patients from Huoshenshan Hospital and Taikang Tongji Hospital (Wuhan, China) were included. Clinical features showing significant differences between the severe and nonsevere groups were screened out by univariate analysis. Then, these features were used to generate classifier models to predict whether a COVID-19 case would be severe or nonsevere based on machine learning. Two test sets of data from the two hospitals were gathered to evaluate the predictive performance of the models. RESULTS: A total of 455 patients were included, and 21 features showing significant differences between the severe and nonsevere groups were selected for the training and validation set. The optimal subset, with eleven features in the k-nearest neighbor model, obtained the highest area under the curve (AUC) value among the four models in the validation set. D-dimer, CRP, and age were the three most important features in the optimal-feature subsets. The highest AUC value was obtained using a support vector-machine model for a test set from Huoshenshan Hospital. Software for predicting disease progression based on machine learning was developed. CONCLUSION: The predictive models were successfully established based on machine learning, and achieved satisfactory predictive performance of disease progression with optimal-feature subsets.

Potential Role of Gut Microbiota in Traditional Chinese Medicine against COVID-19.

The coronavirus disease 2019 (COVID-19) spreads and rages around the world and threatens human life. It is disappointing that there are no specific drugs until now. The combination of traditional Chinese medicine (TCM) and western medication seems to be the current more effective treatment strategy for COVID-19 patients in China. In this review, we mainly discussed the relationship between COVID-19 and gut microbiota (GM), as well as the possible impact of TCM combined with western medication on GM in the treatment of COVID-19 patients, aiming to provide references for the possible role of GM in TCM against COVID-19. The available data suggest that GM dysbiosis did occur in COVID-19 patients, and the intervention of GM could ameliorate the clinical condition of COVID-19 patients. In addition, TCMs (e.g., Jinhua Qinggan granule, Lianhua Qingwen capsule, Qingfei Paidu decoction, Shufeng Jiedu capsule, Qingjin Jianghuo decoction, Toujie Quwen granules, and MaxingShigan) have been proven to be safe and effective for the treatment of COVID-19 in Chinese clinic. Among them, Ephedra sinica, Glycyrrhiza uralensis, Bupleurum chinense, Lonicera japonica,Scutellaria baicalensi, and Astragalus membranaceus are common herbs and have a certain regulation on GM, immunity, and angiotensin converting enzyme 2 (ACE2). Notably, Qingfei Paidu decoction and MaxingShigan have been demonstrated to modulate GM. Finally, the hypothesis of GM-mediated TCM treatment of COVID-19 is proposed, and more clinical trials and basic experiments need to be initiated to confirm this hypothesis.

Risk Factors and Prognosis in Patients with COVID-19 and Liver Injury: A Retrospective Analysis.

PURPOSE: COVID-19 is a new infectious disease with global spread. The aim of the present study was to explore possible risk factors and evaluate prognosis in COVID-19 with liver injury. METHODS: A retrospective study was conducted on 356 COVID-19 patients in the Third People's Hospital of Yichang, Hubei, China. Clinical characteristics and laboratory tests between patients with and without liver injury were compared, while risk factors of COVID-19-related liver injury were analyzed. Univariate and multivariate Cox regression analyses were conducted to identify risk factors of in-hospital death. RESULTS: Of the patients with liver injury, severe and critical types of COVID-19 comprised 12.43% and 14.69%, respectively, higher than in patients without liver injury (both P<0.05). CRP and male sex were independent risk factors for for patients with liver injury, while decreased lymphocyte count (HR 0.024, 95% CI 0.001-0.821) and elevated monocytes (HR 1.951, 95% CI 1.040-3.662) and CRP (HR 1.028, 95% CI 1.010-1.045) were independent risk factors of prognosis of death in COVID-19 patients with liver injury. CONCLUSION: Liver injury is a common complication in severe COVID-19 patients. Male sex and elevated CRP were independent risk factors in COVID-19 complicated by liver damage. Liver damage with increased CRP and monocyte count and decreased lymphocyte count may imply a poor prognosis.

3-Hydroxyphthalic Anhydride-Modified Chicken Ovalbumin as a Potential Candidate Inhibits SARS-CoV-2 Infection by Disrupting the Interaction of Spike Protein With Host ACE2 Receptor.

The global spread of the novel coronavirus SARS-CoV-2 urgently requires discovery of effective therapeutics for the treatment of COVID-19. The spike (S) protein of SARS-CoV-2 plays a key role in receptor recognition, virus-cell membrane fusion and virus entry. Our previous studies have reported that 3-hydroxyphthalic anhydride-modified chicken ovalbumin (HP-OVA) serves as a viral entry inhibitor to prevent several kinds of virus infection. Here, our results reveal that HP-OVA can effectively inhibit SARS-CoV-2 replication and S protein-mediated cell-cell fusion in a dose-dependent manner without obvious cytopathic effects. Further analysis suggests that HP-OVA can bind to both the S protein of SARS-CoV-2 and host angiotensin-converting enzyme 2 (ACE2), the functional receptor of SARS-CoV-2, and disrupt the S protein-ACE2 interaction, thereby exhibiting inhibitory activity against SARS-CoV-2 infection. In summary, our findings suggest that HP-OVA can serve as a potential therapeutic agent for the treatment of deadly COVID-19.

Epithelial cell-specific loss of function of Miz1 causes a spontaneous COPD-like phenotype and up-regulates Ace2 expression in mice.

Cigarette smoking, the leading cause of chronic obstructive pulmonary disease (COPD), has been implicated as a risk factor for severe disease in patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Here we show that mice with lung epithelial cell-specific loss of function of Miz1, which we identified as a negative regulator of nuclear factor κB (NF-κB) signaling, spontaneously develop progressive age-related changes resembling COPD. Furthermore, loss of Miz1 up-regulates the expression of Ace2, the receptor for SARS-CoV-2. Concomitant partial loss of NF-κB/RelA prevented the development of COPD-like phenotype in Miz1-deficient mice. Miz1 protein levels are reduced in the lungs from patients with COPD, and in the lungs of mice exposed to chronic cigarette smoke. Our data suggest that Miz1 down-regulation-induced sustained activation of NF-κB-dependent inflammation in the lung epithelium is sufficient to induce progressive lung and airway destruction that recapitulates features of COPD, with implications for COVID-19.

Containing the spread of coronavirus disease 2019 (COVID-19): Meteorological factors and control strategies.

The novel coronavirus disease 2019 (COVID-19) has spread globally and the meteorological factors vary greatly across the world. Understanding the effect of meteorological factors and control strategies on COVID-19 transmission is critical to contain the epidemic. Using individual-level data in mainland China, Hong Kong, and Singapore, and the number of confirmed cases in other regions, we explore the effect of temperature, relative humidity, and control measures on the spread of COVID-19. We find that high temperature mitigates the transmission of the disease. High relative humidity promotes COVID-19 transmission when temperature is low, but tends to reduce transmission when temperature is high. Implementing classical control measures can dramatically slow the spread of the disease. However, due to the occurrence of pre-symptomatic infections, the effect of the measures to shorten treatment time is markedly reduced and the importance of contact quarantine and social distancing increases.

Ultrafast physical bacterial inactivation and photocatalytic self-cleaning of ZnO nanoarrays for rapid and sustainable bactericidal applications.

Various nanostructured surfaces have been developed recently to physically inactivate bacteria, for reducing the rapidly spreading threat of pathogenic bacteria. However, it generally takes several hours for these surfaces to inactivate most of the bacteria, which greatly limits their application in the fields favoring rapid bactericidal performance. Besides, the accumulated bacteria debris left on these surfaces is rarely discussed in the previous reports. Herein we report the nanotip-engineered ZnO nanoarrays (NAs) with ultrafast physical bactericidal rate and the ability to photocatalytically remove the bacteria debris. Neither chemical (Zn2+ or reactive oxygen species) nor photocatalytic effect leads to the ultrafast bactericidal rate, where 97.5% of E. coli and 94.9% of S. aureus are inactivated within only 1 min. The simulation analysis further supported our proposed mechanism attributing the ultrafast bactericidal activity to the great stress enabled by the uneven topography. Moreover, the re-exposure of the ZnO NAs nanotips can be achieved in only 10 min under a mild UV light source. This study not only presents an ultrafast physical bactericidal activity, but also demonstrates the potential of the recyclable and photocatalytic self-cleaning functions of theses surfaces for applications that desire rapid and sustainable bactericidal performance.