Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection.

Although host responses to the ancestral SARS-CoV-2 strain are well described, those to the new Omicron variants are less resolved. We profiled the clinical phenomes, transcriptomes, proteomes, metabolomes, and immune repertoires of >1,000 blood cell or plasma specimens from SARS-CoV-2 Omicron patients. Using in-depth integrated multi-omics, we dissected the host response dynamics during multiple disease phases to reveal the molecular and cellular landscapes in the blood. Specifically, we detected enhanced interferon-mediated antiviral signatures of platelets in Omicron-infected patients, and platelets preferentially formed widespread aggregates with leukocytes to modulate immune cell functions. In addition, patients who were re-tested positive for viral RNA showed marked reductions in B cell receptor clones, antibody generation, and neutralizing capacity against Omicron. Finally, we developed a machine learning model that accurately predicted the probability of re-positivity in Omicron patients. Our study may inspire a paradigm shift in studying systemic diseases and emerging public health concerns.

The relationships of preventive behaviors and psychological resilience with depression, anxiety, and stress among university students during the COVID-19 pandemic: A two-wave longitudinal study in Shandong Province, China.

Introduction: Studies have shown that the psychological impact of the COVID-19 pandemic may lead to long-term health problems; therefore, more attention should be paid to the mental health of university students. This study aimed to explore the longitudinal effects of preventive behaviors and psychological resilience on the mental health of Chinese college students during COVID-19. Methods: We recruited 2,948 university students from five universities in Shandong Province. We used a generalized estimating equation (GEE) model to estimate the impact of preventive behaviors and psychological resilience on mental health. Results: In the follow-up survey, the prevalence of anxiety (44.8% at T1 vs 41.2% at T2) and stress (23.0% at T1 vs 19.6% at T2) decreased over time, whereas the prevalence of depression (35.2% at T1 vs 36.9% at T2) increased significantly (P < 0.001). Senior students were more likely to report depression (OR = 1.710, P < 0.001), anxiety (OR = 0.815, P = 0.019), and stress (OR = 1.385, P = 0.011). Among all majors, medical students were most likely to report depression (OR = 1.373, P = 0.021), anxiety (OR = 1.310, P = 0.040), and stress (OR = 1.775, P < 0.001). Students who wore a mask outside were less likely to report depression (OR = 0.761, P = 0.027) and anxiety (OR = 0.686, P = 0.002) compared to those who did not wear masks. Students who complied with the standard hand-washing technique were less likely to report depression (OR = 0.628, P < 0.001), anxiety (OR = 0.701, P < 0.001), and stress (OR = 0.638, P < 0.001). Students who maintained a distance of one meter in queues were less likely to report depression (OR = 0.668, P < 0.001), anxiety (OR = 0.634, P < 0.001), and stress (OR = 0.638, P < 0.001). Psychological resilience was a protective factor against depression (OR = 0.973, P < 0.001), anxiety (OR = 0.980, P < 0.001), and stress (OR = 0.976, P < 0.001). Discussion: The prevalence of depression among university students increased at follow-up, while the prevalence of anxiety and stress decreased. Senior students and medical students are vulnerable groups. University students should continue to follow relevant preventive behaviors to protect their mental health. Improving psychological resilience may help maintain and promote university students' mental health.

CoV2-TCR: A web server for screening TCR CDR3 from TCR immune repertoire of COVID-19 patients and their recognized SARS-CoV-2 epitopes.

Although multiple vaccines have been developed and widely administered, several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants have been reported to evade immune responses and spread diffusely. Here, 108 RNA-seq files from coronavirus disease 2019 (COVID-19) patients and healthy donors (HD) were downloaded to extract their TCR immune repertoire by MiXCR. Those extracted TCR repertoire were compared and it was found that disease progression was related negatively with diversity and positively with clonality. Specifically, greater proportions of high-abundance clonotypes were observed in active and severe COVID-19 samples, probably resulting from strong stimulation of SARS-CoV-2 epitopes and a continued immune response in host. To investigate the specific recognition between TCR CDR3 and SARS-CoV-2 epitopes, we constructed an accurate classifier CoV2-TCR with an AUC of 0.967 in an independent dataset, which outperformed several similar tools. Based on this model, we observed a huge range in the number of those TCR CDR3 recognizing those different peptides, including 28 MHC-I epitopes from SARS-CoV-2 and 22 immunogenic peptides from SARS-CoV-2 variants. Interestingly, their proportions of high-abundance, low-abundance and rare clonotypes were close for each peptide. To expand the potential application of this model, we established the webserver, CoV2-TCR, in which users can obtain those recognizing CDR3 sequences from the TCR repertoire of COVID-19 patients based on the 9-mer peptides containing mutation site(s) on the four main proteins of SARS-CoV-2 variants. Overall, this study provides preliminary screening for candidate antigen epitopes and the TCR CDR3 that recognizes them, and should be helpful for vaccine design on SARS-CoV-2 variants.

Sequence difference of angiotensin-converting enzyme 2 between nonhuman primates affects its binding-affinity with SARS-CoV-2 S receptor binding domain.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused many deaths and contributed to a tremendous public health concern worldwide since 2020. Angiotensin-converting enzyme 2 (ACE2) binds to the SARS-CoV-2 virus as a receptor. The challenge of different nonhuman primate (NHP) species by SARS-CoV-2 virus demonstrated different effects on virus replication and disease pathology. This study characterizes differences between host ACE2 sequences of three NHP species: Macaca mulatta, Macaca fascicularis, and Chlorocebus sabaeus. In addition, the binding affinity between the ACE2 ectodomain and the SARS-CoV-2 S receptor-binding domain (RBD) was analyzed. Variation of ACE2 sequence among NHP species and the binding affinity may account for different susceptibility and responses to SARS-CoV-2 infection.

Changing Social Mentality among University Students in the COVID-19 Pandemic: A Five-Wave Longitudinal Study in China.

(1) Background: The COVID-19 pandemic has led to significant shifts in university students' lives, which could be displayed by social mentality, a psychosocial conception at the individual and social levels. This five-wave longitudinal study aims to evaluate the changing social mentality of university students during the peak and preventive-order phases of the pandemic in China and investigate the trends and differences in social-demographic variables. (2) Methods: The Bi-Dimensional Structure Questionnaire of Social Mentality (B-DSMQ) was used to collect data from March 2020 to January 2021. Five-wave surveys were administered to 1319 students from five universities using online questionnaires. Analysis of variance (ANOVA) was used to compare the changes in social mentality over time and covariate groups. Linear mixed models were used to explore the associations of overall social mentality with time and covariates. Post hoc analysis was implemented within subgroups, including university, major, grade, parenting style, and the harmonious degree of parents. (3) Results: Students' social mentality changed significantly from Waves 1 to 5 (p < 0.001). It fell to its lowest in the third survey, increased in the fourth survey, and peaked in the fifth survey. In all of the subgroups, the changing social mentality differed significantly over time (p < 0.001). The p-values between groups suggested that changing social mentality was significantly different regarding gender, residence, university, major, grade, student cadre, graduates, nuclear family, economic status, parenting styles, and the harmonious degree of parents' relationship (p < 0.001). (4) Conclusions: Social mentality among university students decreased during the peak of the pandemic before increasing in the contained-risk period. It was the lowest in June when students began to return to the pandemic-preventive campus from quarantined homes. Students living in provinces (except for Shandong) who were from high-level universities in 2016 and 2017 and who majored in medicine displayed a more negative social mentality. Students who were female, student cadres, non-graduates, and enjoying high socioeconomic status displayed a more positive social mentality. Further research is needed on the relationship between mental health and social mentality, specifically the associates and interventions for positive social mentality.

The Prevalence and Determinant of PTSD Symptoms among Home-Quarantined Chinese University Students during the COVID-19 Pandemic.

BACKGROUND: When COVID-19 emerged in China in late 2019, most Chinese university students were home-quarantined to prevent the spread of the virus, considering the great impact of the lockdown on young people habits and their psychological well-being. This study explored the prevalence of post-traumatic stress disorder (PTSD) and its associated factors among Chinese university students who are isolated at home during the COVID-19 pandemic. METHOD: 4520 participants from five universities in China were surveyed by online questionnaire and the PTSD Checklist-Civilian Version (PCL-C) was adopted as a screening instrument. RESULTS: Exposure to virus was significantly related to PTSD outcomes. The most important predictors for PTSD outcomes were parents' relationship and the way parents educated, and university-provided psychological counseling was a protective factor against developing PTSD. CONCLUSIONS: The COVID-19 pandemic had adverse psychological consequences on Chinese university students who were isolated at home due to the relatively high prevalence rate of PTSD which was reported. Adverse parental relationships and the extreme way parents educate their children could be the major risk factors for PTSD outcomes. Psychological interventions need to be made available to home-quarantined university students, and those in the worst-hit and exposed areas to virus should be given priority focus.

An Easy-to-Understand Method to Construct Desired Distance-Like Measures

Metrics and their weaker forms are used to measure the difference between two data (or other things). There are many metrics that are available but not desired by a practitioner. This paper recommends in a plausible reasoning manner an easy-to-understand method to construct desired distance-like measures: to fuse easy-to-obtain (or easy to be coined by practitioners) pseudo-semi-metrics, pseudo-metrics, or metrics by making full use of well-known t-norms, t-conorms, aggregation operators, and similar operators (easy to be coined by practitioners). The simple reason to do this is that data for a real world problem are sometimes from multiagents. A distance-like notion, called weak interval-valued pseudo-metrics (briefly, WIVP-metrics), is defined by using known notions of pseudo-semi-metrics, pseudo-metrics, and metrics;this notion is topologically good and shows precision, flexibility, and compatibility than single pseudo-semi-metrics, pseudo-metrics, or metrics. Propositions and detailed examples are given to illustrate how to fabricate (including using what “material”) an expected or demanded WIVP-metric (even interval-valued metric) in practical problems, and WIVP-metric and its special cases are characterized by using axioms. Moreover, some WIVP-metrics pertinent to quantitative logic theory or interval-valued fuzzy graphs are constructed, and fixed point theorems and common fixed point theorems in weak interval-valued metric spaces are also presented. Topics and strategies for further study are also put forward concretely and clearly.

How does COVID-19 emergency cognition influence public pro-environmental behavioral intentions? An affective event perspective.

Social impacts and serious damages caused by the COVID-19 pandemic have resulted in public introspection on the issue of ecological environmental protection. However, whether the public cognition of COVID-19 can promote pro-environmental behavioral intentions (PEBI) has not yet been determined; this is crucial for studying the ecological significance of the pandemic. Based on the affective events theory (AET), this study investigated the mechanism by which COVID-19 emergency cognition influences public PEBI. Following an analysis of 873 public questionnaires, the results reveal that public cognition of COVID-19 emergency can significantly promote PEBI. Among them, the effect of emergency coping is stronger than that of emergency relevance. Besides, the positive and negative environmental affective reactions aroused by COVID-19 pandemic play a mediating role between the emergency cognition and PEBI. Moreover, the positive environmental affective reactions show a stronger positive effect on household-sphere PEBI. However, the negative environmental affective reactions are more prominent in promoting public-sphere PEBI. This research aims to bridge a research gap by establishing a link between COVID-19 pandemic and PEBI. The findings can provide useful recommendations for policymakers to find the opportunity behind the COVID-19 emergency to promote public PEBI.

Understanding and changing wildlife consumption behavior from a multidisciplinary perspective

Escalating global demand for wildlife products and consequential illegal wildlife trade has become one of the major threats to biodiversity conservation. In the recent COVID-19 pandemic, growing public health risks of wildlife trade and consumption have triggered widespread public concern. In this review, we adopt a multidisciplinary perspective, including sociology, psychology, behavioral science and other disciplines, to understand the motivations for wildlife consumption in China, and to propose scientifically guided behavioral change countermeasures. The current state of wildlife consumption in China reveals certain functional, social, experiential and other non-essential needs of wildlife as major drivers of consumption, which are affected by a host of complex factors. Based on our understanding of the drivers of demand, we suggest using behavioral change frameworks, and a variety of behavioral change methods, including education, social influence, regulation and nudging, to effectively influence and change wildlife consumption behavior. For effective implementation of behavioral change strategies, collaboration needs to be strengthened, both among and across diverse disciplines, actors and scales of interest.

Survey of COVID-19 Disease Among Orthopaedic Surgeons in Wuhan, People's Republic of China.

BACKGROUND: Coronavirus disease 2019 (COVID-19) broke out in Wuhan, the People's Republic of China, in December 2019 and now is a pandemic all around the world. Some orthopaedic surgeons in Wuhan were infected with COVID-19. METHODS: We conducted a survey to identify the orthopaedic surgeons who were infected with COVID-19 in Wuhan. A self-administered questionnaire was distributed to collect information such as social demographic variables, clinical manifestations, exposure history, awareness of the outbreak, infection control training provided by hospitals, and individual protection practices. To further explore the possible risk factors at the individual level, a 1:2 matched case-control study was conducted. RESULTS: A total of 26 orthopaedic surgeons from 8 hospitals in Wuhan were identified as having COVID-19. The incidence in each hospital varied from 1.5% to 20.7%. The onset of symptoms was from January 13 to February 5, 2020, and peaked on January 23, 8 days prior to the peak of the public epidemic. The suspected sites of exposure were general wards (79.2%), public places at the hospital (20.8%), operating rooms (12.5%), the intensive care unit (4.2%), and the outpatient clinic (4.2%). There was transmission from these doctors to others in 25% of cases, including to family members (20.8%), to colleagues (4.2%), to patients (4.2%), and to friends (4.2%). Participation in real-time training on prevention measures was found to have a protective effect against COVID-19 (odds ratio [OR], 0.12). Not wearing an N95 respirator was found to be a risk factor (OR, 5.20 [95% confidence interval (CI), 1.09 to 25.00]). Wearing respirators or masks all of the time was found to be protective (OR, 0.15). Severe fatigue was found to be a risk factor (OR, 4 [95% CI, 1 to 16]) for infection with COVID-19. CONCLUSIONS: Orthopaedic surgeons are at risk during the COVID-19 pandemic. Common places of work could be contaminated. Orthopaedic surgeons have to be more vigilant and take more precautions to avoid infection with COVID-19. LEVEL OF EVIDENCE: Diagnostic Level IV. See Instructions for Authors for a complete description of levels of evidence.

Risk factors of critical & mortal COVID-19 cases: A systematic literature review and meta-analysis.

BACKGROUND: An epidemic of Coronavirus Disease 2019 (COVID-19) began in December 2019 and triggered a Public Health Emergency of International Concern (PHEIC). We aimed to find risk factors for the progression of COVID-19 to help reducing the risk of critical illness and death for clinical help. METHODS: The data of COVID-19 patients until March 20, 2020 were retrieved from four databases. We statistically analyzed the risk factors of critical/mortal and non-critical COVID-19 patients with meta-analysis. RESULTS: Thirteen studies were included in Meta-analysis, including a total number of 3027 patients with SARS-CoV-2 infection. Male, older than 65, and smoking were risk factors for disease progression in patients with COVID-19 (male: OR = 1.76, 95% CI (1.41, 2.18), P < 0.00001; age over 65 years old: OR =6.06, 95% CI(3.98, 9.22), P < 0.00001; current smoking: OR =2.51, 95% CI(1.39, 3.32), P = 0.0006). The proportion of underlying diseases such as hypertension, diabetes, cardiovascular disease, and respiratory disease were statistically significant higher in critical/mortal patients compared to the non-critical patients (diabetes: OR=3.68, 95% CI (2.68, 5.03), P < 0.00001; hypertension: OR = 2.72, 95% CI (1.60,4.64), P = 0.0002; cardiovascular disease: OR = 5.19, 95% CI(3.25, 8.29), P < 0.00001; respiratory disease: OR = 5.15, 95% CI(2.51, 10.57), P < 0.00001). Clinical manifestations such as fever, shortness of breath or dyspnea were associated with the progression of disease [fever: 0R = 0.56, 95% CI (0.38, 0.82), P = 0.003;shortness of breath or dyspnea: 0R=4.16, 95% CI (3.13, 5.53), P < 0.00001]. Laboratory examination such as aspartate amino transferase(AST) > 40U/L, creatinine(Cr) ≥ 133mol/L, hypersensitive cardiac troponin I(hs-cTnI) > 28pg/mL, procalcitonin(PCT) > 0.5ng/mL, lactatede hydrogenase(LDH) > 245U/L, and D-dimer > 0.5mg/L predicted the deterioration of disease while white blood cells(WBC)<4 × 109/L meant a better clinical status[AST > 40U/L:OR=4.00, 95% CI (2.46, 6.52), P < 0.00001; Cr ≥ 133µmol/L: OR = 5.30, 95% CI (2.19, 12.83), P = 0.0002; hs-cTnI > 28 pg/mL: OR = 43.24, 95% CI (9.92, 188.49), P < 0.00001; PCT > 0.5 ng/mL: OR = 43.24, 95% CI (9.92, 188.49), P < 0.00001;LDH > 245U/L: OR = 43.24, 95% CI (9.92, 188.49), P < 0.00001; D-dimer > 0.5mg/L: OR = 43.24, 95% CI (9.92, 188.49), P < 0.00001; WBC < 4 × 109/L: OR = 0.30, 95% CI (0.17, 0.51), P < 0.00001]. CONCLUSION: Male, aged over 65, smoking patients might face a greater risk of developing into the critical or mortal condition and the comorbidities such as hypertension, diabetes, cardiovascular disease, and respiratory diseases could also greatly affect the prognosis of the COVID-19. Clinical manifestation such as fever, shortness of breath or dyspnea and laboratory examination such as WBC, AST, Cr, PCT, LDH, hs-cTnI and D-dimer could imply the progression of COVID-19.