Mycoplasma pneumoniae infections resurged globally in 2023-2024 following a significant decline during the coronavirus disease 2019 (COVID-19) pandemic. To understand the genomic epidemiology of this resurgence in China, a nationwide 1-year genomic surveillance identified 9907 patients infected with M. pneumoniae, resulting in an overall positive rate of 10.05%. We developed a hybrid capture-based targeted next-generation sequencing (hc-tNGS) assay, obtaining 271 high-quality genomes directly from clinical samples. Phylogenetic analysis of a global collection of 562 M. pneumoniae genomes identified six distinct lineages, including three newly emerged main Chinese clades (MCCs) that co-circulated across various regions of China. Among these MCCs, one clade, comprising P1-1, ST17, and L4, was localized in Taiwan, while two others-P1-1, ST3, and L6 clade, and P1-2, ST14 and L2 clade-co-circulated in different regions of China during the 2023-2024 epidemic season. Notably, 96.31% of the isolates identified in this study exhibited a point mutation, primarily A2063G (95.94%). This study offers a comprehensive genomic characterization of the post-pandemic M. pneumoniae resurgence in China, highlighting the emergence and spread of resistant clades. These findings emphasize the importance of adopting a One Health approach to address the potential global public health threats posed by this resurgent pathogen.

Acute exacerbation (AE) is common for patients with chronic hepatitis B (CHB). The aim of the study is to investigate the values of hepatitis B core antibody (anti-HBc) IgM in CHB-AE. Patients were screened from a prospective sub-cohort, 419 CHB patients with AE were enrolled and divided into groups according to antiviral treatment history, treatment naïve, withdrawal above or within 6 months, and on-treatment. The prevalence, clinical characteristics of anti-HBc IgM, and its relationship with the outcomes of CHB were assessed. A total of 157 patients (37.5%) were tested positive for anti-HBc IgM, of which patients with antiviral-withdrawal more than 6 months had the highest prevalence (49.3%). Anti-HBc IgM was significantly associated with HBV DNA and ALT, regarding to its prevalence and serum level. Furthermore, serum anti-HBc IgM values varied in different phases of CHB, of which immune active and HBeAg-negative chronic hepatitis phases were significantly higher than that in inactive carriers (p = 0.017 and p = 0.0097, respectively). Anti-HBc IgM could distinguish hepatitis from inactive infection phases in HBeAg-negative patients (AUC 0.841). Anti-HBc IgM levels were significantly higher in subgroup who developed ACLF (p < 0.05), but had no relationship with short-term mortality. Finally, anti-HBc IgM seropositivity was the only predictor of HBeAg seroclearance (OR 3.18, 95% CI 1.30-7.73) and all patients who achieved HBsAg seroclearance within 1-year had a markedly elevated anti-HBc IgM level. In conclusion, our study shows anti-HBc IgM is highly prevalent in CHB patients with AE and would be a new predictor of HBeAg and HBsAg loss in this population.

Background and AimsHepatitis B virus (HBV) reactivation is a serious condition and has been extensively described in chemotherapeutic immunosuppressive population. However, little is known about HBV reactivation in immunocompetent patients with chronic hepatitis B (CHB). In this study, we evaluated the prevalence and the clinical significance of HBV reactivation in CHB patients with acute exacerbations.MethodPatients were screened from two prospective multicenter observational cohorts (CATCH-LIFE cohort). A total of 1,020 CHB patients with previous antiviral treatment history were included to assess the prevalence, risk factors, clinical characteristics of HBV reactivation, and its influence on the progression of chronic liver disease.ResultsThe prevalence of HBV reactivation was 51.9% in CHB patients with acute exacerbations who had antiviral treatment history in our study. Among the 529 patients with HBV reactivation, 70.9% of them were triggered by discontinued antiviral treatment and 5.9% by nucleos(t)ide analogs (NUCs) resistance. The prevalence of antiviral treatment disruption and NUCs resistance in patients with HBV reactivation is much higher than that in the patients without (70.9% vs. 0.2%, and 5.9% vs. 0, respectively, both p < 0.001). Stratified and interaction analysis showed that HBV reactivation was correlated with high short-term mortality in cirrhosis subgroup (HR = 2.1, p < 0.001). Cirrhotic patients with HBV reactivation had a significantly higher proportion of developing hepatic failure (45.0% vs. 20.3%, p < 0.001), acute-on-chronic liver failure (ACLF; 31.4% vs. 21.8%, p = 0.005), and short-term death (14.0% vs. 5.9% for 28-day, and 23.3% vs. 12.4% for 90-day, both p < 0.001) than those without. HBV reactivation is an independent risk factor of 90-day mortality for cirrhosis patients (OR = 1.70, p = 0.005), as well as hepatic encephalopathy, ascites, and bacterial infection.ConclusionThis study clearly demonstrated that there was a high prevalence of HBV reactivation in CHB patients, which was mainly triggered by discontinued antiviral treatment. The HBV reactivation strongly increased the risk of developing hepatic failure, ACLF and short-term death in HBV-related cirrhotic patients, which may suggest that HBV reactivation would be a new challenge in achieving the WHO target of 65% reduction in mortality from hepatitis B by 2030.

In patients coinfected with SARS-CoV-2 and HBV, liver injury was common. However, the interactions between SARS-CoV-2 and HBV coinfection remained unknown. Sixty-seven COVID-19 patients from the previous cohort were enrolled and classified into 2 groups (7 with HBsAg+ and 60 with HBsAg-). The association of HBV- and SARS-CoV-2-related markers were analyzed. During the acute course of SARS-CoV-2 infection, markers of HBV replication did not extensively fluctuate during SARS-CoV-2 infection. Coinfection with HBV did not extend the viral shedding cycle or incubation periods of SARS-CoV-2. Effects of SARS-CoV-2 on the dynamics of chronic HBV infection seemed not apparent. SARS-CoV-2 infection would not be the source of HBV reactivation in these individuals.

Background: HBV-related acute-on-chronic liver failure (HBV-ACLF) has a high short-term mortality and urgently needs an early warning system with simplicity and high accuracy. Previous studies show that sex hormones play potential roles in the progression of HBV-related liver diseases. Aims: To explore the effect of testosterone and estradiol on the occurrence and prognosis of HBV-ACLF. Methods: A prospective cohort of 300 chronic hepatitis B (CHB) patients was enrolled among which 108 were diagnosed with HBV-ACLF at admission and 20 developed to HBV-ACLF during hospitalization. We compared the level of serum testosterone and estradiol of patients with varied ACLF background, disease severity and cirrhosis conditions and analyzed the predictive ability of short-term prognosis. A novel prognostic model involving testosterone was developed and further validated in the HBV-ACLF group. Results: The baseline estradiol level of HBV-ACLF group was significantly higher while testosterone was lower than that of non-ACLF group. The estradiol level increased while the testosterone level decreased as the number of organ failures increased. Testosterone had high accuracy in predicting the short-term mortality in HBV-ACLF (AUROC = 0.726) and estradiol did better in predicting the occurrence of ACLF during hospitalization (AUROC = 0.695). The novel prognostic model involving testosterone (TATIM model) was proved to have considerable prediction efficiency in HBV-ACLF cohort with or without cirrhosis. Conclusion: Testosterone could be utilized as short-term prognostic indicator for HBV-related ACLF and estradiol can help to predict its occurrence. TATIM model is a novel prognostic model for HBV-related ACLF with simplicity and good performance irrespectively of liver cirrhosis. Clinical Trial Registration Number: This study was based on a sub-cohort from the prospective multicenter cohort (NCT02457637).

RNA virus population in a host does not consist of a consensus single haplotype but rather an ensemble of related sequences termed quasispecies. The dynamics of quasispecies afford SARS-CoV-2 a great ability on genetic fitness during intrahost evolution.

SummaryBACKGROUNDNucleic acid test and antibody assay have been employed in the diagnosis for SARS-CoV-2 infection, but the use of viral antigen for diagnosis has not been successfully developed. Theoretically, viral antigen is the specific marker of the virus and precedes antibody appearance within the infected population. There is a clear need of detection of viral antigen for rapid and early diagnosis.METHODSWe included a cohort of 239 participants with suspected SARS-CoV-2 infection from 7 centers for the study. We measured nucleocapsid protein in nasopharyngeal swab samples in parallel with the nucleic acid test. Nucleic acid test was taken as the reference standard, and statistical evaluation was taken in blind. We detected nucleocapsid protein in 20 urine samples in another center, employing nasopharyngeal swab nucleic acid test as reference standard.RESULTSWe developed a fluorescence immunochromatographic assay for detecting nucleocapsid protein of SARS-CoV-2 in nasopharyngeal swab sample and urine within 10 minutes. 100% of nucleocapsid protein positive and negative participants accord with nucleic acid test for same samples. Further, earliest participant after 3 days of fever can be identified by the method. In an additional preliminary study, we detected nucleocapsid protein in urine in 73.6% of diagnosed COVID-19 patients.CONCLUSIONSThose findings indicate that nucleocapsid protein assay is an accurate, rapid, early and simple method for diagnosis of COVID-19. Appearance of nucleocapsid protein in urine coincides our finding of the SARS-CoV-2 invading kidney and might be of diagnostic value.

A novel coronavirus disease (COVID-19) caused by SARS-CoV-2 has been pandemic worldwide. The genetic dynamics of quasispecies afford RNA viruses a great fitness on cell tropism and host range. However, no quasispecies data of SARS-CoV-2 have been reported yet. To explore quasispecies haplotypes and its transmission characteristics, we carried out single-molecule real-time (SMRT) sequencing of the full-length of SARS-CoV-2 spike gene within 14 RNA samples from 2 infection clusters, covering first-to third-generation infected-patients. We observed a special quasispecies structure of SARS-CoV-2 (modeled as ‘One-King’): one dominant haplotype (mean abundance ~70.15%) followed by numerous minor haplotypes (mean abundance < 0.10%). We not only discovered a novel dominant haplotype of F 1040 but also realized that minor quasispecies were also worthy of attention. Notably, some minor haplotypes (like F 1040 and currently pandemic one G 614 ) could potentially reveal adaptive and converse into the dominant one. However, minor haplotypes exhibited a high transmission bottleneck (~6% could be stably transmitted), and the new adaptive/dominant haplotypes were likely originated from genetic variations within a host rather than transmission. The evolutionary rate was estimated as 2.68-3.86 × 10 −3 per site per year, which was larger than the estimation at consensus genome level. The ‘One-King’ model and conversion event expanded our understanding of the genetic dynamics of SARS-CoV-2, and explained the incomprehensible phenomenon at the consensus genome level, such as limited cumulative mutations and low evolutionary rate. Moreover, our findings suggested the epidemic strains may be multi-host origin and future traceability would face huge difficulties.

AbstractBackgroundA pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading over the world. However, the viral dynamics, host serologic responses, and their associations with clinical manifestations, have not been well described in prospective cohort.MethodsWe conducted a prospective cohort and enrolled 67 COVID-19 patients admitting between Jan 26 and Feb 5, 2020. Clinical specimens including nasopharyngeal swab, sputum, blood, urine and stool were tested periodically according to standardized case report form with final follow-up on February 27. The routes and duration of viral shedding, antibody response, and their associations with disease severity and clinical manifestations were systematically evaluated. Coronaviral particles in clinical specimens were observed by transmission electron microscopy (TEM).ResultsThe median duration of SARS-CoV-2 RNA shedding were 12 (3-38), 19 (5-37), and 18 (7-26) days in nasopharyngeal swabs, sputum and stools, respectively. Only 13 urines (5.6%) and 12 plasmas (5.7%) were viral positive. Prolonged viral shedding was observed in severe patients than that of non-severe patients. Cough but not fever, aligned with viral shedding in clinical respiratory specimens, meanwhile the positive stool-RNA appeared to align with the proportion who concurrently had cough and sputum production, but not diarrhea. Typical coronaviral particles could be found directly in sputum by TEM. The anti-nucleocapsid-protein IgM started on day 7 and positive rate peaked on day 28, while that of IgG was on day 10 and day 49 after illness onset. IgM and IgG appear earlier, and their titers are significantly higher in severe patients than non-severe patients (p<0.05). The weak responders for IgG had a significantly higher viral clearance rate than that of strong responders (p= 0.011).ConclusionsNasopharyngeal, sputum and stools rather than blood and urine, were the major shedding routes for SARS-CoV-2, and meanwhile sputum had a prolonged viral shedding. Symptom cough seems to be aligned with viral shedding in clinical respiratory and fecal specimens. Stronger antibody response was associated with delayed viral clearance and disease severity.Summary boxesWhat is already known on this topicAs a newly appearing infectious disease, early efforts have focused on virus identification, describing the epidemiologic characteristics, clinical course, prognostics for critically illed cases and mortality. Among COVID-19 cases reported in mainland China (72 314 cases, updated through February 11, 2020), 81% are mild, 14% are severe, and 5% are critical. The estimated overall case fatality rate (CFR) is 2.3%.Some case series reported had shown that SARS-CoV-2 could shed in upper/lower respiratory specimens, stools, blood and urines of patients. However, important knowledge gaps remain, particularly regarding full kinetics of viral shedding and host serologic responses in association with clinical manifestations and host factors.What this study addsThe incubation period has no change after spreading out of Wuhan, and has no sex or age differences, however, children had prolonged incubation period. Due to early recognition and intervention, COVID-19 illness of Chongqing cohort is milder than that of Wuhan patients reported.This prospective cohort study on SARS-CoV-2 infection shows clearly that the viral and serological kinetics were related in duration of infection, disease severity, and clinical manifestations of COVID-19. Our data demonstrate that nasopharyngeal, sputum and stools are major shedding routes for SARS-CoV-2, and stronger NP antibody response is associated with delayed viral clearance and disease severity.

Objective To investigate the quasispecies variation characteristics of HBV in Tibetan population based on the third-generation sequencing. Methods An epidemiological investigation of hepatitis B virus was conducted by our department of infectious disease in southern Tibet from May 2016 to July 2017. A total of 24 HBsAg positive subjects were obtained in this investigation and were assignd into the plateau Tibetan group, and then another 24 cases subjected from our outpatient department were recruited and served as the plain Han control group. Their HBV DNA was extracted, and the full virus sequence was amplified to build a whole genome sequencing library, and then sequenced on the third-generation sequencing platform PacBio RSⅡ. Biological information tools such as ClustalW, MEGA and SimPlot were used to analyze the quasispecies characteristics. Results Totally 29 samples were successfully amplified and sequenced finally, including 9 cases from the Tibetan group with an average of 65 quasispecies sequences per sample, and 20 cases from the control group with an average of 124 quasispecies sequences per sample. After comparative analysis, 7 cases (7/9, 77.8%) of typeC/D1 HBV were found in the Tibetan group with recombining at 750 nt by type D4 and type C2 HBV, 1 case of type C/D2 HBV was recombined by type D3 and type C2 HBV at 1 500 nt, and the rest 1 was type C2. The quasispecies complexity and nonsynonymous mutation ratio of HBV preC/C gen was highere in the Tibetan group than the control group. Variation spectrums of nucleic acid were different between the recombinant HBV and the control. The nucleic acid mutation of the C/D recombinant HBV was mainly in EnhⅡ, BCP, and preS regions, while the HBV sequences in the control group were dominated by mutations in preC, S, and X regions besides BCP and preS regions. Conclusion The C/D recombinant strain is the dominant strain of HBV in Tibetans, and C/D1 HBV is more common. The quasispecies complexity and nonsynonymous mutation ratio of HBV preC/C in Tibetans are higher than those of the Han, While the variants of nucleotide mainly occur in the Enh Ⅱ, BCP, and preS regions

BackgroundGlycogen storage disease type I (GSD I), also known as von Gierk disease, is a metabolic disorder leading to the excessive accumulation of glycogen and fat in organs, characterized by hepatomegaly, hypoglycemia, lactic acidemia, hyperlipidemia, hyperuricemia, puberty delay and growth retardation, which can be indicated by height, weight, blood glucose and blood lipids.Case presentationHere we present a 16-year-old male patient with GSD Ia complicated with hepatic adenoma and combined with hepatitis B. As a chronic hepatitis B patient, the patient was admitted to hospital in order to further clarify the nature of hepatic space occupancy because of suspicion of hepatocellular carcinoma. However, the imaging studies did not support hepatocellular carcinoma certainly. And by tracing his clinical history, we suggested that he might suffer from GSD I. Finally the diagnosis was confirmed by MRI (Gd-EOB-DTPA), liver biopsy and whole exome sequencing (WES).The WES discovered a homozygous point mutation at the exon 5 of G6PC gene at 17th chromosome, c.G648T (p.L216L, NM_000151, rs80356484). This pathogenic mutation causes CTG changing to CTT at protein 216. Though both codons encode leucine, this silent mutation creates a new splicing site 91bp downstream of the authentic splice site. According to previous research, this mutation is a disease causal variant for GSD Ia, and has a high frequency among GSD patients in China and Japan.This patient was finally diagnosed as GSD Ia complicated with hepatic adenoma and combined with chronic hepatitis B, and received corn starch therapy immediately after GSD was suspected.After receiving corn starch therapy, the height and weight of the patient were increased, and the secondary sexual characteristics were developed, including beard, pubic hair and seminal emission. Unexpectedly, the liver adenomas were still increasing, and we did not find any cause to explain this phenomenon.ConclusionThis patient was diagnosed as GSD Ia combined with chronic hepatitis B, who responded to corn starch intervention. For childhood patients with hypoglycaemia, hyperlipidemia, puberty delay and growth retardation, GSD should be considered. Gene sequencing is valuable for the quick identification of GSD subtypes.

目的 探讨肝豆状核变性的临床特征及其致病基因ATP7B的中国人群变异谱.方法 收集2011年1月-2017年10月我院肝豆状核变性119例,随访至2018年4月,分析发病年龄、临床特征、生化指标、ATP7B基因变异谱及转归,比较肝型和脑型患者的差异.结果 119例患者中肝型占57.1％,脑型占27.7％,混合型占15.1％.肝型与脑型患者发病年龄差异有统计学意义(P=0.0036),脑型患者全部集中在儿童青少年期起病,肝型患者各年龄段均有发病.本组患者肝损害主要表现为肝功能异常(53.8％)、肝硬化(50.4％)、肝脾肿大(47.9％)和皮肤巩膜黄染(40.3％);神经系统损伤主要表现为口下颌肌张力障碍(31.9％)、精神症状(24.4％)和不自主运动(23.5％);成年患者的肝硬化、腹水、不自主运动等症状显著多于未成年患者(分别为:P=0.005、0.008、0.026).对诊断时效进行分析,从首次发病至明确诊断中位病程为5个月,最长82个月,52.1％的患者在起病5个月之后才得以明确诊断,肝型患者确诊所用时间显著少于脑型和混合型患者(分别为:Z=-2.233,P=0.026;Z=-2.424,P=0.015).31例患者进行ATP7B基因检测,阳性率83.9％,最常见致病变异位点是Arg778Leu,等位频率17.4％,其次是Pro992Leu、Met769 HisfsX26、Ala874Val和Ile1148Thr.生存分析结果显示,有肝硬化的肝豆状核变性患者的生存率显著低于非肝硬化患者(x2=4.202,P=0.04).结论 婴幼儿及中老年人发病并不少见,应重视年幼和年老患者的诊治;进展为肝硬化的患者因铜沉积久、肝损伤重,其生存率显著低于非肝硬化患者,而基因检测有助于提高早期诊断率.

Butyrylcholinesterase (BChE), an ester hydrolase produced mainly by the liver, hydrolyzes certain short-acting neuromuscular blocking agents, like succinylcholine and mivacurium that are widely used during anesthesia. Patients with BChE deficiency are possibly in danger of postanesthetic apnea. Hereditary BChE deficiency results from the mutations of BCHE gene located on chromosome 3, 3q26.1-q26.2, between nucleotides 165,490,692–165,555,260.