Spike substitution T813S increases Sarbecovirus fusogenicity by enhancing the usage of TMPRSS2.

SARS-CoV Spike (S) protein shares considerable homology with SARS-CoV-2 S, especially in the conserved S2 subunit (S2). S protein mediates coronavirus receptor binding and membrane fusion, and the latter activity can greatly influence coronavirus infection. We observed that SARS-CoV S is less effective in inducing membrane fusion compared with SARS-CoV-2 S. We identify that S813T mutation is sufficient in S2 interfering with the cleavage of SARS-CoV-2 S by TMPRSS2, reducing spike fusogenicity and pseudoparticle entry. Conversely, the mutation of T813S in SARS-CoV S increased fusion ability and viral replication. Our data suggested that residue 813 in the S was critical for the proteolytic activation, and the change from threonine to serine at 813 position might be an evolutionary feature adopted by SARS-2-related viruses. This finding deepened the understanding of Spike fusogenicity and could provide a new perspective for exploring Sarbecovirus' evolution.

A triple-RBD-based mucosal vaccine provides broad protection against SARS-CoV-2 variants of concern.

The rapid mutation and spread of SARS-CoV-2 variants urge the development of effective mucosal vaccines to provide broad-spectrum protection against the initial infection and thereby curb the transmission potential. Here, we designed a chimeric triple-RBD immunogen, 3Ro-NC, harboring one Delta RBD and two Omicron RBDs within a novel protein scaffold. 3Ro-NC elicits potent and broad RBD-specific neutralizing immunity against SARS-CoV-2 variants of concern. Notably, intranasal immunization with 3Ro-NC plus the mucosal adjuvant KFD (3Ro-NC + KFDi.n) elicits coordinated mucosal IgA and higher neutralizing antibody specificity (closer antigenic distance) against the Omicron variant. In Omicron-challenged human ACE2 transgenic mice, 3Ro-NC + KFDi.n immunization significantly reduces the tissue pathology in the lung and lowers the viral RNA copy numbers in both the lung (85.7-fold) and the nasal turbinate (13.6-fold). Nasal virologic control is highly correlated with RBD-specific secretory IgA antibodies. Our data show that 3Ro-NC plus KFD is a promising mucosal vaccine candidate for protection against SARS-CoV-2 Omicron infection, pathology and transmission potential.

Rational design of AAVrh10-vectored ACE2 functional domain to broadly block the cell entry of SARS-CoV-2 variants.

The frequently emerging SARS-CoV-2 variants have weakened the effectiveness of existing COVID-19 vaccines and neutralizing antibody therapy. Nevertheless, the infections of SARS-CoV-2 variants still depend on angiotensin-converting enzyme 2 (ACE2) receptor-mediated cell entry, and thus the soluble human ACE2 (shACE2) is a potential decoy for broadly blocking SARS-CoV-2 variants. In this study, we firstly generated the recombinant AAVrh10-vectored shACE2 constructs, a kind of adeno-associated virus (AAV) serotype with pulmonary tissue tropism, and then validated its inhibition capacity against SARS-CoV-2 infection. To further optimize the minimized ACE2 functional domain candidates, a comprehensive analysis was performed to clarify the interactions between the ACE2 orthologs from various species and the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein. Based on the key interface amino acids, we designed a series of truncated ACE2 orthologs, and then assessed their potential affinity to bind to SARS-CoV-2 variants RBD in silico. Of note, we found that the 24-83aa fragment of dog ACE2 (dACE224-83) had a higher affinity to the RBD of SARS-CoV-2 variants than that of human ACE2. Importantly, AAVrh10-vectored shACE2 or dACE224-83 constructs exhibited a broadly blockage breadth against SARS-CoV-2 prototype and variants in vitro and ex vivo. Collectively, these data highlighted a promising therapeutic strategy against SARS-CoV-2 variants.

Comparative global B cell receptor repertoire difference induced by SARS-CoV-2 infection or vaccination via single-cell V(D)J sequencing.

Dynamic changes of the paired heavy and light chain B cell receptor (BCR) repertoire provide an essential insight into understanding the humoral immune response post-SARS-CoV-2 infection and vaccination. However, differences between the endogenous paired BCR repertoire kinetics in SARS-CoV-2 infection and previously recovered/naïve subjects treated with the inactivated vaccine remain largely unknown. We performed single-cell V(D)J sequencing of B cells from six healthy donors with three shots of inactivated SARS-CoV-2 vaccine (BBIBP-CorV), five people who received the BBIBP-CorV vaccine after having recovered from COVID-19, five unvaccinated COVID-19 recovered patients and then integrated with public data of B cells from four SARS-CoV-2-infected subjects. We discovered that BCR variable (V) genes were more prominently used in the SARS-CoV-2 exposed groups (both in the group with active infection and in the group that had recovered) than in the vaccinated groups. The VH gene that expanded the most after SARS-CoV-2 infection was IGHV3-33, while IGHV3-23 in the vaccinated groups. SARS-CoV-2-infected group enhanced more BCR clonal expansion and somatic hypermutation than the vaccinated healthy group. A small proportion of public clonotypes were shared between the SARS-CoV-2 infected, vaccinated healthy, and recovered groups. Moreover, several public antibodies had been identified against SARS-CoV-2 spike protein. We comprehensively characterize the paired heavy and light chain BCR repertoire from SARS-CoV-2 infection to vaccination, providing further guidance for the development of the next-generation precision vaccine.

ORF8 protein of SARS-CoV-2 reduces male fertility in mice.

As one of the most rapidly evolving proteins of the genus Betacoronavirus, open reading frames (ORF8's) function and potential pathological consequence in vivo are still obscure. In this study, we show that the secretion of ORF8 is dependent on its N-terminal signal peptide sequence and can be inhibited by reactive oxygen species scavenger and endoplasmic reticulum-Golgi transportation inhibitor in cultured cells. To trace the effect of its possible in vivo secretion, we examined the plasma samples of coronavirus disease 2019 (COVID-19) convalescent patients and found that the patients aged from 40 to 60 had higher antibody titers than those under 40. To explore ORF8's in vivo function, we administered the mice with ORF8 via tail-vein injection to simulate the circulating ORF8 in the patient. Although no apparent difference in body weight, food intake, and vitality was detected between vehicle- and ORF8-treated mice, the latter displayed morphological abnormalities of testes and epididymides, as indicated by the loss of the central ductal lumen accompanied by a decreased fertility in 5-week-old male mice. Furthermore, the analysis of gene expression in the testes between vehicle- and ORF8-treated mice identified a decreased expression of Col1a1, the loss of which is known to be associated with mice's infertility. Although whether our observation in mice could be translated to humans remains unclear, our study provides a potential mouse model that can be used to investigate the impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection on the human reproductive system.

Hospitalization, interpersonal and personal factors of social anxiety among COVID-19 survivors at the six-month follow-up after hospital treatment: the minority stress model.

Background: As a highly infectious disease with human-to-human transmission characteristics, COVID-19 has caused panic in the general public. Those who have recovered from COVID-19 may experience discrimination and internalized stigma. They may be more likely to worry about social interaction and develop social anxiety. Objectives: This study investigated the associations among hospitalization factors, social/interpersonal factors, personal factors, and social anxiety to reveal the mechanism of social anxiety in COVID-19 survivors. Methods: A cross-sectional, multicenter telephone survey was conducted from July to September 2020 in five Chinese cities (i.e. Wuhan, Nanning, Shenzhen, Zhuhai, and Dongguan); adult COVID-19 survivors were recruited 6 months after they were discharged from the hospital. Linear regressions and path analysis based on the minority stress model were conducted to test the relationships among hospitalization, social/interpersonal factors, personal factors, and social anxiety. Results: The response rate was 74.5% (N = 199, 55.3% females). Linear regression analyses showed that various hospitalization, social/interpersonal, and personal factors were statistically significantly associated with social anxiety. Path analysis showed that the proposed model fit the data well (χ2(df) = 3.196(3), p = .362, CFI = .999, NNFI = .996, RMSEA = .018). Internalized stigma fully mediated the association between perceived discrimination/social support and social anxiety, while it partially mediated the association between perceived affiliate stigma and social anxiety. Conclusions: The results suggest that social/interpersonal and personal factors have a stronger association with social anxiety than hospitalization factors and highlight the importance of internalized stigma in understanding the mechanisms of these relationships. Clinical psychologists can refer to these modifiable psychosocial factors to develop efficient interventions for mental health promotion.

Antecedentes: Como una enfermedad altamente infecciosa con características de transmisión de persona a persona, el COVID-19 ha causado pánico en el público en general. Aquellos que se han recuperado del COVID-19 pueden experimentar discriminación y estigma internalizado. Es más probable que se preocupen por la interacción social y desarrollen ansiedad social.Objetivos: Este estudio investigó las asociaciones entre factores de hospitalización, factores sociales /interpersonales, factores personales y ansiedad social para revelar el mecanismo de ansiedad social en sobrevivientes de COVID-19.Métodos: Se realizó una encuesta telefónica transversal multicentro de julio a septiembre de 2020 en cinco ciudades chinas (es decir, Wuhan, Nanning, Shenzhen, Zhuhai y Dongguan). Se reclutaron sobrevivientes adultos de COVID-19 seis meses después de ser dados de alta del hospital. Se realizaron regresiones lineales y análisis de ruta basados en el modelo de estrés de minoría para probar las relaciones entre la hospitalización, los factores sociales/interpersonales, los factores personales y la ansiedad social.Resultados: La tasa de respuesta fue del 74,5% (N = 199, 55,3% mujeres). Los análisis de regresión lineal mostraron que varios factores de hospitalización, sociales/interpersonales y personales se asociaron de manera estadísticamente significativa con la ansiedad social. El análisis de ruta mostró que el modelo propuesto se ajustaba bien a los datos (χ2 (df) = 3.196 (3), p = .362, CFI = .999, NNFI = .996, RMSEA = .018). El estigma internalizado medió completamente la asociación entre discriminación/apoyo social percibido y ansiedad social, mientras que medió parcialmente la asociación entre el estigma percibido de afiliados y ansiedad social.Conclusiones: Los resultados sugieren que los factores sociales/interpersonales y personales tienen una asociación más fuerte con la ansiedad social que los factores de hospitalización y resaltan la importancia del estigma internalizado en la comprensión de los mecanismos de estas relaciones. Los psicólogos clínicos pueden referirse a estos factores psicosociales modificables para desarrollar intervenciones eficientes para la promoción de la salud mental.

Hospitalization, interpersonal and personal factors of social anxiety among COVID-19 survivors at the six-month follow-up after hospital treatment: the minority stress model Hospitalización, factores interpersonales y personales de ansiedad social entre los sobrevivientes de COVID-19 en el seguimiento seis meses después del tratamiento hospitalario: el modelo de estrés de minoría 基于少数群体压力模型的新冠康复者住院经历, 出院后六个月人际及个人因素与社交焦虑之间的关联分析

Background As a highly infectious disease with human-to-human transmission characteristics, COVID-19 has caused panic in the general public. Those who have recovered from COVID-19 may experience discrimination and internalized stigma. They may be more likely to worry about social interaction and develop social anxiety. Objectives This study investigated the associations among hospitalization factors, social/interpersonal factors, personal factors, and social anxiety to reveal the mechanism of social anxiety in COVID-19 survivors. Methods A cross-sectional, multicenter telephone survey was conducted from July to September 2020 in five Chinese cities (i.e. Wuhan, Nanning, Shenzhen, Zhuhai, and Dongguan);adult COVID-19 survivors were recruited 6 months after they were discharged from the hospital. Linear regressions and path analysis based on the minority stress model were conducted to test the relationships among hospitalization, social/interpersonal factors, personal factors, and social anxiety. Results The response rate was 74.5% (N = 199, 55.3% females). Linear regression analyses showed that various hospitalization, social/interpersonal, and personal factors were statistically significantly associated with social anxiety. Path analysis showed that the proposed model fit the data well (χ2(df) = 3.196(3), p = .362, CFI = .999, NNFI = .996, RMSEA = .018). Internalized stigma fully mediated the association between perceived discrimination/social support and social anxiety, while it partially mediated the association between perceived affiliate stigma and social anxiety. Conclusions The results suggest that social/interpersonal and personal factors have a stronger association with social anxiety than hospitalization factors and highlight the importance of internalized stigma in understanding the mechanisms of these relationships. Clinical psychologists can refer to these modifiable psychosocial factors to develop efficient interventions for mental health promotion. HIGHLIGHTS Internalized stigma fully mediated the effects of perceived discrimination and social support on social anxiety and partially mediated the effect of perceived affiliate stigma on social anxiety.

Post-traumatic Stress Disorder Symptoms in COVID-19 Survivors 6 Months After Hospital Discharge: An Application of the Conservation of Resource Theory.

COVID-19 survivors who had acute respiratory symptoms might experience prolonged post-traumatic stress disorder (PTSD) due to further rehabilitation, somatic symptoms and related distress. The conservation of resource (COR) theory is a well-developed theory to understand how people develop PTSD symptoms in traumatic events. The current study aimed to examine the potential factors of PTSD symptoms and interrelationships among this factors among COVID-19 survivors based on the COR theory. This cross-sectional telephone survey enrolled 199 COVID-19 patients (Mean age = 42.7; 53.3% females) 6 months after their hospital discharge in five Chinese cities (i.e., Wuhan, Shenzhen, Zhuhai, Dongguan, and Nanning). The results showed that 7% of participants were classified as having probable PTSD. The significant potential factors relating to PTSD symptoms included socio-demographic status, hospitalization experiences, post-hospitalization experiences, and psychological status. Besides, the proposed statistical mediation model based on the COR framework showed good model fit, χ2(df) = 17.286 (5), p = 0.004, CFI = 0.962, NNFI = 0.951, RMSEA = 0.077. Perceived resource loss/gain fully mediated the association between exposure to other patients' suffering during hospitalization and PTSD symptoms, and partially mediated the relationships from somatic symptoms/perceived impact of being infected with COVID-19 after discharge to PTSD symptoms. On the other hand, resilience was a full mediator in the relationship from ICU experience to PTSD symptoms and a partial mediator in the relationship from perceived impact to PTSD symptoms. The results provide preliminary support on applying the COR theory to understand the factors of PTSD symptoms among COVID-19 survivors. Interventions to reduce PTSD symptoms in this population can be developed based on the modifiable psychosocial mediators.

Associations between COVID-19 related stigma and sleep quality among COVID-19 survivors six months after hospital discharge.

BACKGROUND: Many COVID-19 survivors reported stigmatization after recovery. This study investigated the association between stigma (discrimination experiences, self-stigma and perceived affiliate stigma) and sleep quality among COVID-19 survivors six months after hospital discharge. METHODS: Participants were recovered adult COVID-19 survivors discharged between February 1 and April 30, 2020. Medical staff of five participating hospitals approached all discharged COVID-19 period during this period. A total of 199 participants completed the telephone interview during July to September, 2020. Structural equation modeling was performed to test the hypothesize that resilience and social support would mediate the associations between stigma and sleep quality. RESULTS: The results showed that 10.1% of the participants reported terrible/poor sleep quality, 26.1% reported worse sleep quality in the past week when comparing their current status versus the time before COVID-19. After adjusting for significant background characteristics, participants who had higher number of discrimination experience, perceived stronger self-stigma and stronger perceived affiliate stigma reported poorer sleep quality. Resilience and social support were positively and significantly associated with sleep quality. The indirect effect of self-stigma on sleep quality through social support and resilience was significant and negative. Perceived affiliate stigma also had a significant and negative indirect effect on sleep quality through social support and resilience. CONCLUSIONS: Various types of stigma after recovery were associated with poor sleep quality among COVID-19 survivors, while social support and resilience were protective factors. Resilience and social support mediated the associations between self-stigma/perceived affiliate stigma and sleep quality.

Research on Influencing Factors and Classification of Patients With Mild and Severe COVID-19 Symptoms.

Objective: To analyze the epidemiological history, clinical symptoms, laboratory testing parameters of patients with mild and severe COVID-19 infection, and provide a reference for timely judgment of changes in the patients' conditions and the formulation of epidemic prevention and control strategies. Methods: A retrospective study was conducted in this research, a total of 90 patients with COVID-19 infection who received treatment from January 21 to March 31, 2020 in the Ninth People's Hospital of Dongguan City were selected as study subject. We analyzed the clinical characteristics of laboratory-confirmed patients with COVID-19, used the oversampling method (SMOTE) to solve the imbalance of categories, and established Lasso-logistic regression and random forest models. Results: Among the 90 confirmed COVID-19 cases, 79 were mild and 11 were severe. The average age of the patients was 36.1 years old, including 49 males and 41 females. The average age of severe patients is significantly older than that of mild patients (53.2 years old vs 33.7 years old). The average time from illness onset to hospital admission was 4.1 days and the average actual hospital stay was 18.7 days, both of these time actors were longer for severe patients than for mild patients. Forty-eight of the 90 patients (53.3%) had family cluster infections, which was similar among mild and severe patients. Comorbidities of underlying diseases were more common in severe patients, including hypertension, diabetes and other diseases. The most common symptom was cough [45 (50%)], followed by fever [43 (47.8%)], headache [7 (7.8%)], vomiting [3 (3.3%)], diarrhea [3 (3.3%)], and dyspnea [1 (1.1%)]. The laboratory findings of patients also included leukopenia [13(14.4%)] and lymphopenia (17.8%). Severe patients had a low level of creatine kinase (median 40.9) and a high level of D-dimer. The median NLR of severe patients was 2.82, which was higher than that of mild patients. Logistic regression showed that age, phosphocreatine kinase, procalcitonin, the lymphocyte count of the patient on admission, cough, fatigue, and pharynx dryness were independent predictors of COVID-19 severity. The classification of random forest was predicted and the importance of each variable was displayed. The variable importance of random forest indicates that age, D-dimer, NLR (neutrophil to lymphocyte ratio) and other top-ranked variables are risk factors. Conclusion: The clinical symptoms of COVID-19 patients are non-specific and complicated. Age and the time from onset to admission are important factors that determine the severity of the patient's condition. Patients with mild illness should be closely monitored to identify those who may become severe. Variables such as age and creatine phosphate kinase selected by logistic regression can be used as important indicators to assess the disease severity of COVID-19 patients. The importance of variables in the random forest further complements the variable feature information.

Rapid isolation and immune profiling of SARS-CoV-2 specific memory B cell in convalescent COVID-19 patients via LIBRA-seq.

B cell response plays a critical role against SARS-CoV-2 infection. However, little is known about the diversity and frequency of the paired SARS-CoV-2 antigen-specific BCR repertoire after SARS-CoV-2 infection. Here, we performed single-cell RNA sequencing and VDJ sequencing using the memory and plasma B cells isolated from five convalescent COVID-19 patients, and analyzed the spectrum and transcriptional heterogeneity of antibody immune responses. Via linking BCR to antigen specificity through sequencing (LIBRA-seq), we identified a distinct activated memory B cell subgroup (CD11chigh CD95high) had a higher proportion of SARS-CoV-2 antigen-labeled cells compared with memory B cells. Our results revealed the diversity of paired BCR repertoire and the non-stochastic pairing of SARS-CoV-2 antigen-specific immunoglobulin heavy and light chains after SARS-CoV-2 infection. The public antibody clonotypes were shared by distinct convalescent individuals. Moreover, several antibodies isolated by LIBRA-seq showed high binding affinity against SARS-CoV-2 receptor-binding domain (RBD) or nucleoprotein (NP) via ELISA assay. Two RBD-reactive antibodies C14646P3S and C2767P3S isolated by LIBRA-seq exhibited high neutralizing activities against both pseudotyped and authentic SARS-CoV-2 viruses in vitro. Our study provides fundamental insights into B cell response following SARS-CoV-2 infection at the single-cell level.

A SARS-CoV-2 antibody curbs viral nucleocapsid protein-induced complement hyperactivation.

Although human antibodies elicited by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid (N) protein are profoundly boosted upon infection, little is known about the function of N-reactive antibodies. Herein, we isolate and profile a panel of 32 N protein-specific monoclonal antibodies (mAbs) from a quick recovery coronavirus disease-19 (COVID-19) convalescent patient who has dominant antibody responses to the SARS-CoV-2 N protein rather than to the SARS-CoV-2 spike (S) protein. The complex structure of the N protein RNA binding domain with the highest binding affinity mAb (nCoV396) reveals changes in the epitopes and antigen's allosteric regulation. Functionally, a virus-free complement hyperactivation analysis demonstrates that nCoV396 specifically compromises the N protein-induced complement hyperactivation, which is a risk factor for the morbidity and mortality of COVID-19 patients, thus laying the foundation for the identification of functional anti-N protein mAbs.

New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2.

The 2019 novel coronavirus (SARS-CoV-2) has spread rapidly worldwide and was declared a pandemic by the WHO in March 2020. The evolution of SARS-CoV-2, either in its natural reservoir or in the human population, is still unclear, but this knowledge is essential for effective prevention and control. We propose a new framework to systematically identify recombination events, excluding those due to noise and convergent evolution. We found that several recombination events occurred for SARS-CoV-2 before its transfer to humans, including a more recent recombination event in the receptor-binding domain. We also constructed a probabilistic mutation network to explore the diversity and evolution of SARS-CoV-2 after human infection. Clustering results show that the novel coronavirus has diverged into several clusters that cocirculate over time in various regions and that several mutations across the genome are fixed during transmission throughout the human population, including D614G in the S gene and two accompanied mutations in ORF1ab. Together, these findings suggest that SARS-CoV-2 experienced a complicated evolution process in the natural environment and point to its continuous adaptation to humans. The new framework proposed in this study can help our understanding of and response to other emerging pathogens.

The Characterization of Disease Severity Associated IgG Subclasses Response in COVID-19 Patients.

Increasing evidence suggests that dysregulated immune responses are associated with the clinical outcome of coronavirus disease 2019 (COVID-19). Nucleocapsid protein (NP)-, spike (S)-, receptor binding domain (RBD)- specific immunoglobulin (Ig) isotypes, IgG subclasses and neutralizing antibody (NAb) were analyzed in 123 serum from 63 hospitalized patients with severe, moderate, mild or asymptomatic COVID-19. Mild to modest correlations were found between disease severity and antigen specific IgG subclasses in serum, of which IgG1 and IgG3 were negatively associated with viral load in nasopharyngeal swab. Multiple cytokines were significantly related with antigen-specific Ig isotypes and IgG subclasses, and IL-1ß was positively correlated with most antibodies. Furthermore, the old patients (≥ 60 years old) had higher levels of chemokines, increased NAb activities and SARS-CoV-2 specific IgG1, and IgG3 responses and compromised T cell responses compared to the young patients (≤ 18 years old), which are related with more severe cases. Higher IgG1 and IgG3 were found in COVID-19 patients with comorbidities while biological sex had no effect on IgG subclasses. Overall, we have identified diseases severity was related to higher antibodies, of which IgG subclasses had weakly negative correlation with viral load, and cytokines were significantly associated with antibody response. Further, advancing age and comorbidities had obvious effect on IgG1 and IgG3.

Broad phenotypic alterations and potential dysfunction of lymphocytes in individuals clinically recovered from COVID-19.

Although millions of patients have clinically recovered from COVID-19, little is known about the immune status of lymphocytes in these individuals. In this study, the peripheral blood mononuclear cells of a clinically recovered (CR) cohort were comparatively analyzed with those of an age- and sex-matched healthy donor cohort. We found that CD8+ T cells in the CR cohort had higher numbers of effector T cells and effector memory T cells but lower Tc1 (IFN-γ+), Tc2 (IL-4+), and Tc17 (IL-17A+) cell frequencies. The CD4+ T cells of the CR cohort were decreased in frequency, especially the central memory T cell subset. Moreover, CD4+ T cells in the CR cohort showed lower programmed cell death protein 1 (PD-1) expression and had lower frequencies of Th1 (IFN-γ+), Th2 (IL-4+), Th17 (IL-17A+), and circulating follicular helper T (CXCR5+PD-1+) cells. Accordingly, the proportion of isotype-switched memory B cells (IgM-CD20hi) among B cells in the CR cohort showed a significantly lower proportion, although the level of the activation marker CD71 was elevated. For CD3-HLA-DR- lymphocytes in the CR cohort, in addition to lower levels of IFN-γ, granzyme B and T-bet, the correlation between T-bet and IFN-γ was not observed. Additionally, by taking into account the number of days after discharge, all the phenotypes associated with reduced function did not show a tendency toward recovery within 4‒11 weeks. The remarkable phenotypic alterations in lymphocytes in the CR cohort suggest that  severe acute respiratory syndrome coronavirus 2 infection profoundly affects lymphocytes and potentially results in dysfunction even after clinical recovery.

Characteristics of T-cell responses in COVID-19 patients with prolonged SARS-CoV-2 positivity - a cohort study.

OBJECTIVE: SARS-CoV-2 has caused a worldwide pandemic of COVID-19. The existence of prolonged SARS-CoV-2 positivity (PP) has further increased the burden on the health system. Since T cells are vital for viral control, we aimed to evaluate the characteristics of T-cell responses associated with PP. METHODS: We established a PP cohort and two age- and sex-matched control cohorts: a regular clinical recovery (CR) cohort and a healthy donor (HD) cohort. The mean time for RNA negativity conversion in the PP cohort was markedly longer than that in the CR cohort (66.2 vs 25.3 days), while the time from illness onset to sampling was not significantly different. T-cell responses in the PP cohort were assayed, analysed and compared with those in the CR and HD cohorts by flow cytometry and ELISpot analysis of peripheral blood mononuclear cells. RESULTS: Compared with the CR cohort, the proliferation, activation and functional potential of CD8+ and CD4+ T cells in the PP cohort were not significantly different. However, the frequencies and counts of Teff and Tem in CD8+ but not in CD4+ T cells of the PP cohort were prominently lower. Moreover, a weaker SARS-CoV-2 N protein-specific IFN-γ+ T-cell response and a higher frequency of Tregs were detected in the PP cohort. CONCLUSION: Suppressed CD8+ T-cell differentiation is associated with PP and may be an indicator for the prediction of prolonged SARS-CoV-2 positivity in COVID-19 patients. The association between suppressed CD8+ T-cell differentiation and elevated Tregs warrants studies in the future.

Alterations in Phenotypes and Responses of T Cells Within 6 Months of Recovery from COVID-19: A Cohort Study.

The COVID-19 pandemic, caused by the SARS-CoV-2 infection, is a global health crisis. While many patients have clinically recovered, little is known about long-term alterations in T cell responses of COVID-19 convalescents. In this study, T cell responses in peripheral blood mononuclear cells of a long-time COVID-19 clinically recovered (20-26 weeks) cohort (LCR) were measured via flow cytometry and ELISpot. The T cell responses of LCR were comparatively analyzed against an age and sex matched short-time clinically recovered (4-9 weeks) cohort (SCR) and a healthy donor cohort (HD). All volunteers were recruited from Wuhan Jinyintan Hospital, China. Phenotypic analysis showed that activation marker PD-1 expressing on CD4+ T cells of LCR was still significantly lower than that of HD. Functional analysis indicated that frequencies of Tc2, Th2 and Th17 in LCR were comparable to those of HD, but Tc17 was higher than that of HD. In LCR, compared to the HD, there were fewer IFN-γ producing T cells but more IL-2 secreting T cells. In addition, the circulating Tfh cells in LCR were still slightly lower compared to HD, though the subsets composition had recovered. Remarkably, SARS-CoV-2 specific T cell responses in LCR were comparable to that of SCR. Collectively, T cell responses experienced long-term alterations in phenotype and functional potential of LCR cohort. However, after clinical recovery, SARS-CoV-2 specific T cell responses could be sustained at least for six months, which may be helpful in resisting re-infection.

Impact of Systematic Factors on the Outbreak Outcomes of the Novel COVID-19 Disease in China: Factor Analysis Study.

BACKGROUND: The novel COVID-19 disease has spread worldwide, resulting in a new pandemic. The Chinese government implemented strong intervention measures in the early stage of the epidemic, including strict travel bans and social distancing policies. Prioritizing the analysis of different contributing factors to outbreak outcomes is important for the precise prevention and control of infectious diseases. We proposed a novel framework for resolving this issue and applied it to data from China. OBJECTIVE: This study aimed to systematically identify national-level and city-level contributing factors to the control of COVID-19 in China. METHODS: Daily COVID-19 case data and related multidimensional data, including travel-related, medical, socioeconomic, environmental, and influenza-like illness factors, from 343 cities in China were collected. A correlation analysis and interpretable machine learning algorithm were used to evaluate the quantitative contribution of factors to new cases and COVID-19 growth rates during the epidemic period (ie, January 17 to February 29, 2020). RESULTS: Many factors correlated with the spread of COVID-19 in China. Travel-related population movement was the main contributing factor for new cases and COVID-19 growth rates in China, and its contributions were as high as 77% and 41%, respectively. There was a clear lag effect for travel-related factors (previous vs current week: new cases, 45% vs 32%; COVID-19 growth rates, 21% vs 20%). Travel from non-Wuhan regions was the single factor with the most significant impact on COVID-19 growth rates (contribution: new cases, 12%; COVID-19 growth rate, 26%), and its contribution could not be ignored. City flow, a measure of outbreak control strength, contributed 16% and 7% to new cases and COVID-19 growth rates, respectively. Socioeconomic factors also played important roles in COVID-19 growth rates in China (contribution, 28%). Other factors, including medical, environmental, and influenza-like illness factors, also contributed to new cases and COVID-19 growth rates in China. Based on our analysis of individual cities, compared to Beijing, population flow from Wuhan and internal flow within Wenzhou were driving factors for increasing the number of new cases in Wenzhou. For Chongqing, the main contributing factor for new cases was population flow from Hubei, beyond Wuhan. The high COVID-19 growth rates in Wenzhou were driven by population-related factors. CONCLUSIONS: Many factors contributed to the COVID-19 outbreak outcomes in China. The differential effects of various factors, including specific city-level factors, emphasize the importance of precise, targeted strategies for controlling the COVID-19 outbreak and future infectious disease outbreaks.