Genomic Epidemiology of SARS-CoV-2 in Guangdong Province, China.

Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2 infection and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China's most populous province, during early 2020 resulted in 1,388 reported RNA-positive cases from 1.6 million tests. In order to understand the molecular epidemiology and genetic diversity of SARS-CoV-2 in China, we generated 53 genomes from infected individuals in Guangdong using a combination of metagenomic sequencing and tiling amplicon approaches. Combined epidemiological and phylogenetic analyses indicate multiple independent introductions to Guangdong, although phylogenetic clustering is uncertain because of low virus genetic variation early in the pandemic. Our results illustrate how the timing, size, and duration of putative local transmission chains were constrained by national travel restrictions and by the province's large-scale intensive surveillance and intervention measures. Despite these successes, COVID-19 surveillance in Guangdong is still required, because the number of cases imported from other countries has increased.

Comparative efficacy and safety of Sofosbuvir/Velpatasvir and Danoprevir for the treatment of chronic hepatitis C: the real-world data in China.

BACKGROUND: Sofosbuvir/Velpatasvir (Epclusa, ECS) is the first pan-genotype direct-acting antiviral agent (DAA) for hepatitis C virus (HCV) infection, and Danoprevir (DNV) is the first DAA developed by a Chinese local enterprise, which is suitable for combined use with other drugs to treat genotype 1b chronic hepatitis C. However, previous reports have never compared the real-world data of ECS and DNV. PATIENTS AND METHODS: 178 chronic hepatitis C patients were retrospectively recruited, and 94cases were accepted with Sofosbuvir/Velpatasvir ± Ribavirin (ECS group), and others (n = 84 treated with DNV combination therapy (DNV group). The HCV genotype, virological response, adverse effects and some laboratory biochemical indexes were contrasted between above two groups in the real world study. RESULTS: DNV group had significantly lower level of alpha-fetoprotein (AFP), lower rates of decompensated cirrhosis ( P < 0.05). ECS group possessed more 6a (31.91% vs.13.10%) while DNV group was provided with more 1b (48.81% vs. 22.34%) patients. Significantly poor liver function was detected in ECS group at 4-week treatment (ALT and AST) and 12-week follow-up (AST) (all P < 0.05). The SVR12 undetectable rates of both groups were 100%, and no serious event was observed during the treatment and follow-up in both groups. CONCLUSION: In this retrospective real-world study, the efficacy of DNV combined therapy is similar to Sofosbuvir/Velpatasvir ± Ribavirin for chronic HCV infection, and the safety is comparable. DNV based therapy is a promising regimen for chronic hepatitis C.

Neural efficiency and proficiency adaptation of effective connectivity corresponding to early and advanced skill levels in athletes of racket sports.

This study explored how the neural efficiency and proficiency worked in athletes with different skill levels from the perspective of effective connectivity brain network in resting state. The deconvolved conditioned Granger causality (GC) analysis was applied to functional magnetic resonance imaging (fMRI) data of 35 elite athletes (EAs) and 42 student-athletes (SAs) of racket sports as well as 39 normal controls (NCs), to obtain the voxel-wised hemodynamic response function (HRF) parameters representing the functional segregation and effective connectivity representing the functional integration. The results showed decreased time-to-peak of HRF in the visual attention brain regions in the two athlete groups compared with NC and decreased response height in the advanced motor control brain regions in EA comparing to the nonelite groups, suggesting the neural efficiency represented by the regional HRF was different in early and advanced skill levels. GC analysis demonstrated that the GC values within the middle occipital gyrus had a linear trend from negative to positive, suggesting a stepwise "neural proficiency" of the effective connectivity from NC to SA then to EA. The GC values of the inter-lobe circuits in EA had the trend to regress to NC levels, in agreement with the neural efficiency of these circuits in EA. Further feature selection approach suggested the important role of the cerebral-brainstem GC circuit for discriminating EA. Our findings gave new insight into the complementary neural mechanisms in brain functional segregation and integration, which was associated with early and advanced skill levels in athletes of racket sports.

A reachable probability approach for the analysis of spatio-temporal dynamics in the human functional network.

The dynamic architecture of the human brain has been consistently observed. However, there is still limited modeling work to elucidate how neuronal circuits are hierarchically and flexibly organized in functional systems. Here we proposed a reachable probability approach based on non-homogeneous Markov chains, to characterize all possible connectivity flows and the hierarchical structure of brain functional systems at the dynamic level. We proved at the theoretical level the convergence of the functional brain network system, and demonstrated that this approach is able to detect network steady states across connectivity structure, particularly in areas of the default mode network. We further explored the dynamically hierarchical functional organization centered at the primary sensory cortices. We observed smaller optimal reachable steps to their local functional regions, and differentiated patterns in larger optimal reachable steps for primary perceptual modalities. The reachable paths with the largest and second largest transition probabilities between primary sensory seeds via multisensory integration regions were also tracked to explore the flexibility and plasticity of the multisensory integration. The present work provides a novel approach to depict both the stable and flexible hierarchical connectivity organization of the human brain.

Cell-free DNA testing for early hepatocellular carcinoma surveillance.

BACKGROUND: Liver cirrhosis (LC) is the highest risk factor for hepatocellular carcinoma (HCC) development worldwide. The efficacy of the guideline-recommended surveillance methods for patients with LC remains unpromising. METHODS: A total of 4367 LCs not previously known to have HCC and 510 HCCs from 16 hospitals across 11 provinces of China were recruited in this multi-center, large-scale, cross-sectional study. Participants were divided into Stage Ⅰ cohort (510 HCCs and 2074 LCs) and Stage Ⅱ cohort (2293 LCs) according to their enrollment time and underwent Tri-phasic CT/enhanced MRI, US, AFP, and cell-free DNA (cfDNA). A screening model called PreCar Score was established based on five features of cfDNA using Stage Ⅰ cohort. Surveillance performance of PreCar Score alone or in combination with US/AFP was evaluated in Stage Ⅱ cohort. FINDINGS: PreCar Score showed a significantly higher sensitivity for the detection of early/very early HCC (Barcelona stage A/0) in contrast to US (sensitivity of 51.32% [95% CI: 39.66%-62.84%] at 95.53% [95% CI: 94.62%-96.38%] specificity for PreCar Score; sensitivity of 23.68% [95% CI: 14.99%-35.07%] at 99.37% [95% CI: 98.91%-99.64%] specificity for US) (P < 0.01, Fisher's exact test). PreCar Score plus US further achieved a higher sensitivity of 60.53% at 95.08% specificity for early/very early HCC screening. INTERPRETATION: Our study developed and validated a cfDNA-based screening tool (PreCar Score) for HCC in cohorts at high risk. The combination of PreCar Score and US can serve as a promising and practical strategy for routine HCC care. FUNDING: A full list of funding bodies that contributed to this study can be found in Acknowledgments section.

The development of a cSMART-based integrated model for hepatocellular carcinoma diagnosis.

BACKGROUND: Hepatocellular carcinoma (HCC) generally arises from a background of liver cirrhosis (LC). Patients with cirrhosis and suspected HCC are recommended to undergo serum biomarker tests and imaging diagnostic evaluation. However, the performance of routine diagnostic methods in detecting early HCC remains unpromising. METHODS: Here, we conducted a large-scale, multicenter study of 1675 participants including 490 healthy controls, 577 LC patients, and 608 HCC patients from nine clinical centers across nine provinces of China, profiled gene mutation signatures of cell-free DNA (cfDNA) using Circulating Single-Molecule Amplification and Resequencing Technology (cSMART) through detecting 931 mutation sites across 21 genes. RESULTS: An integrated diagnostic model called "Combined method" was developed by combining three mutation sites and three serum biomarkers. Combined method outperformed AFP in the diagnosis of HCC, especially early HCC, with sensitivities of 81.25% for all stages and 66.67% for early HCC, respectively. Importantly, the integrated model exhibited high accuracy in differentiating AFP-negative, AFP-L3-negative, and PIVKA-II-negative HCCs from LCs.

A Stepwise Multivariate Granger Causality Method for Constructing Hierarchical Directed Brain Functional Network.

The directed brain functional network construction gives us the new insights into the relationships between brain regions from the causality point of view. The Granger causality analysis is one of the powerful methods to model the directed network. The complex brain network is also hierarchically constructed, which is particularly suited to facilitate segregated functions and the global integration of the segregated functions. Therefore, it is of great interest to explore new approach to model the hierarchical architecture of the directed network. In the present study, we proposed a new approach, namely, stepwise multivariate Granger causality (SMGC), considering both the directed and hierarchical features of brain functional network to explore the stepwise causal relationship in the network. The simulation study demonstrated that the diverse and complex hierarchical organization could be embedded in the apparently simple directed network. The proposed SMGC method could capture the multiple hierarchy of the directed network. When applying to the real functional magnetic resonance imaging (fMRI) datasets, the core triple resting-state networks in human brain showed within-network directed connections in the first-level directed network and rich and diverse between-network pathways in the second-level hierarchical network. The default mode network (DMN) had a prominent role in the resting-state acting as both the causal source and the important relay station. Further exploratory research on the adaption of directed hierarchical network in athletes suggested the enhanced bidirectional communication between the DMN and the central executive network (CEN) and the enhanced directed connections from the salience network (SN) to the CEN in the athlete group. The SMGC approach is capable of capturing the hierarchical architecture of the brain directed functional network, which refreshes the new stepwise causal relationship in the directed network. This might shed light on the potential application for exploring the altered hierarchical organization of brain directed network in neuropsychiatric disorders.

Cellular immune responses in patients with hepatitis B surface antigen seroclearance induced by antiviral therapy.

BACKGROUND: The mechanisms by which chronic hepatitis B is completely resolved through antiviral therapy are unknown, and the contribution of acquired T cell immunity to hepatitis B surface antigen (HBsAg) seroclearance has not been investigated. Therefore, we measured the T-cell responses to core and envelope antigens in patients with HBsAg seroclearance. METHODS: Fourteen subjects with HBsAg seroclearance following antiviral treatment for chronic hepatitis B, 7 HBeAg-positive immunotolerant HBV carriers and 9 HBeAg-negative inactive HBsAg carriers were recruited. HBV-specific T-cell responses to recombinant HBV core (rHBcAg) and envelope (rHBsAg) proteins and pools of core and envelope peptides were measured using an ELISPOT assay detecting interferon-gamma and intracellular cytokine staining (ICS) assays detecting interferon-gamma or interleukin 2. RESULTS: Interferon-gamma ELISPOT assays showed a low frequency of weak responses to the rHBsAg and S peptide pool in the HBsAg seroclearance group, and the response frequency to the rHBcAg and the C peptide pool was higher than to the rHBsAg (P < 0.001) and S peptide pool (P = 0.001) respectively. A higher response frequency to C than S peptide pools was confirmed in the interferon-gamma ICS assays for both CD4+ (P = 0.033) and CD8+ (P = 0.040) T cells in the HBsAg seroclearance group. The responses to C and S antigens in the inactive carriers were similar. CONCLUSIONS: There was a low frequency of CD4+ and CD8+ T cell immune responses to envelope antigens in Chinese subjects with HBsAg seroclearance following antiviral therapy. It is unlikely that these immune responses are responsible for HBsAg seroclearance in these subjects.

Liver injury in COVID-19 patients with metabolic syndrome-a narrative review.

OBJECTIVE: To comprehensively analyze that how liver injury in patients with metabolic syndrome is affected by coronavirus disease 2019 (COVID-19) and provide clinical reference to their prevention and treatment. BACKGROUND: The current COVID-19 pandemic poses a major threat to human life and health. Metabolic syndrome is also a major global health problem, and evidence suggests that patients with metabolic syndrome are at an increased risk of COVID-19 complications. Liver injury is one of the main manifestations of extra-pulmonary organ injury in patients with COVID-19. Currently, the effects of metabolic syndrome on liver injury in patients with COVID-19 are unclear. METHODS: In this study, we searched the PubMed, Embase, and China National Knowledge Infrastructure (CNKI) databases for articles on the latest developments of liver injury in COVID-19 patients with metabolic syndrome from 2019 to comprehensively analyze the current knowledge of how liver injury in patients with metabolic syndrome is affected by COVID-19. We used the free key words "metabolic syndrome" OR "hypertension" OR "obesity" OR "diabetes" OR "dyslipidemia" OR "liver injury" OR "SARS-CoV-2" OR "COVID-19" in all fields. We imposed no language restrictions. CONCLUSIONS: Both COVID-19 and metabolic syndrome and its components are closely related to liver injury, may induce liver injury through direct or indirect mechanisms. Therefore, when COVID-19 is combined with metabolic syndrome, it may increase the risk of liver injury, and it cannot be ruled out that the two diseases have a superimposed effect on liver injury.

The Landscape of Cell-Free HBV Integrations and Mutations in Cirrhosis and Hepatocellular Carcinoma Patients.

PURPOSE: Intratumoral hepatitis B virus (HBV) integrations and mutations are related to hepatocellular carcinoma (HCC) progression. Circulating cell-free DNA (cfDNA) has shown itself as a powerful noninvasive biomarker for cancer. However, the HBV integration and mutation landscape on cfDNA remains unclear. EXPERIMENTAL DESIGN: A cSMART (Circulating Single-Molecule Amplification and Resequencing Technology)-based method (SIM) was developed to simultaneously investigate HBV integration and mutation landscapes on cfDNA with HBV-specific primers covering the whole HBV genome. Patients with HCC (n = 481) and liver cirrhosis (LC; n = 517) were recruited in the study. RESULTS: A total of 6,861 integration breakpoints including TERT and KMT2B were discovered in HCC cfDNA, more than in LC. The concentration of circulating tumor DNA (ctDNA) was positively correlated with the detection rate of these integration hotspots and total HBV integration events in cfDNA. To track the origin of HBV integrations in cfDNA, whole-genome sequencing (WGS) was performed on their paired tumor tissues. The paired comparison of WGS data from tumor tissues and SIM data from cfDNA confirmed most recurrent integration events in cfDNA originated from tumor tissue. The mutational landscape across the whole HBV genome was first generated for both HBV genotype C and B. A region from nt1100 to nt1500 containing multiple HCC risk mutation sites (OR > 1) was identified as a potential HCC-related mutational hot zone. CONCLUSIONS: Our study provides an in-depth delineation of HBV integration/mutation landscapes at cfDNA level and did a comparative analysis with their paired tissues. These findings shed light on the possibilities of noninvasive detection of virus insertion/mutation.

Altered Brain Functional Connectivity Density in Fast-Ball Sports Athletes With Early Stage of Motor Training.

The human brain shows neuroplastic adaptations caused by motor skill training. Of note, there is little known about the plastic architecture of the whole-brain network in resting state. The purpose of the present study was to detect how motor training affected the density distribution of whole-brain resting-state functional connectivity (FC). Resting-state functional magnetic resonance imaging data was assessed based on a comparison of fast-ball student athletes (SA) and non-athlete healthy controls (NC). The voxel-wise data-driven graph theory approach, global functional connectivity density (gFCD) mapping, was applied. Results showed that the SA group exhibited significantly decreased gFCD in brain regions centered at the left triangular part of the inferior frontal gyrus (IFG), extending to the opercular part of the left IFG and middle frontal gyrus compared to the NC group. In addition, findings suggested the idea of an increased neural efficiency of athletes' brain regions associated with attentional-motor modulation and executive control. Furthermore, behavioral results showed that in the SA group, faster executive control reaction time relates to smaller gFCD values in the left IFG. These findings suggested that the motor training would decrease the numbers of FC in IFG to accelerate the executive control with high attentional demands and enable SA to rapidly focus the attention to detect the intriguing target.

SARS-CoV-2: minireview and review of first case in Foshan, China.

The first case of #COVID19 in Foshan provides a reference for the treatment of severe #SARSCoV2 pneumonia https://bit.ly/3eD81qj.

[Characteristics of HBcAg(18-27) CTL epitopes of the main epidemic HBV strains in China].

OBJECTIVE: To study the characteristics of the virology background of HLA-A2 restricted HBcAg(18-27) epitope mutations in HBV infected patients in China. METHOD: 30 HBV sequences with different genotypes from Genbank were analyzed by bioinformatics and the mismatched primers were designed for constructing a PCR-RFLP method to screen HBcAg(18-27)V/I in China. The distributions of HBcAg(18-27)V/I of 160 samples with HBV genotype B/C infection from 8 areas in China were screened and analyzed by PCR-RFLP and sequencing. The affinity of HBcAg(18-27)V/I to HLA-A0201 was analyzed through referencing the bioinformatics websites. RESULTS: We successfully constructed a PCR-RFLP method for screening HBcAg(18-27)V/I from genotype B/C, and only 3 samples with HBcAg(18-27)V sequence were found in the 160 samples (3/160, 1.88%). The affinity of HBcAg(18-27)I to HLA-A 0201 was lower than the one of HBcAg(18-27)V through bioinformatic analysis (HLA ligand score was 123 vs 156, and the SYFPEITHI score was 22 vs 24). CONCLUSION: The last amino acid of most HBcAg(18-27) sequences of epidemic HBV strains in China is isoleucine, and not valine. Therefore HBcAg(18-27) sequence background in different HBV genotypes should be thoroughly considered when using it as a reference or control in immunological research about HBV.

Analysis of the CDR3 length of TCR alphabeta T cells in the peripheral blood of patients with chronic hepatitis B.

To clarify the characteristics of TCR alphabeta T cells in the peripheral blood of patients with chronic hepatitis B (CHB), we investigated the patterns of Complementarity Determining Region3 (CDR3) length distribution for all 24 TCR BV gene families and 32 TCR AV gene family in the peripheral blood lymphocytes of two patients with CHB and two healthy controls by immunoscope spectratyping technique. We found that the profiles of CDR3 length distribution for all TCR AV and TCR BV family showed Gaussian distribution (the polyclonal TCR alphabeta T cells) in healthy controls, however, the restricted usage of TCR BV and TCR AV family (the oligoclonal TCR alphabeta T cells) has been monitored in two CHB patients, furthermore, the oligoclonal TCR alphabeta T cells showed the different CDR3 sequences and length, it might be correlated to the different epitope of hepatitis B virus (HBV) or the different HLA type of the patients. Detailed analysis of the CDR3 length of TCR alphabeta T cells might be interesting to light on the further study of the individualized immunotherapy of CHB and the further research of the new T lymphocyte epitope vaccine of HBV.

[Adenovirus-mediated transduction of HBV/C genome into HepG2 cell line].

OBJECTIVE: To establish a method for efficient transfer of 1.3-fold HBV/C genome into HepG2 cell line using adenoviral vector system for studying the replication and antigen expression of HBV. METHODS: The 1.3-copy overlength genome of HBV genotype C was constructed and cloned into the shuttle vector pAdTrack. After confirmation of the constructed HBV genome by sequencing, the resultant plasmid linearized by digestion with Pme I was transformed into competent E.coli Adeasier-1 cells. The recombinants of pAdEasy-HBV/C were linearized by digestion with Pac I and transfected into the packaging cells (293 cells) via liposome. HepG2 cells were then infected with a proper quantity of the recombinant adenoviruses. The HBV DNA level and HBeAg and HBsAg titers were detected in the cell medium. RESULTS: The 1.3-fold overlength HBV/C genome was efficiently transferred into HepG2 cells via the adenoviral vector system, which resulted in initiation of the virus replication and protein expression in the cells using the viral replication mechanism. CONCLUSION: The adenovirus vector system (AdEasy) allows convenient and effective transfer of HBV genome into HepG2 cells, and provides a convenient means for screening therapeutic drugs against HBV.

[Distribution of hepatitis B virus genotype B subgenotype in China].

OBJECTIVE: To investigate the distribution of hepatitis B virus (HBV) genotype B subgenotype in China. METHODS: A cohort of 511 patients with chronic HBV genotype B infection, collected from 7 centers across China, were analyzed by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) or nucleotide sequencing. RESULTS: For the 511 patients, only subgenotype Ba was identified and subgenotype Bj was not found. CONCLUSION: In China, subgenotype Ba was the most prevalent HBV strains, while subgenotype Bj was very rarely found.