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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 F1040 but also realized that minor quasispecies were also worthy of attention. Notably, some minor haplotypes (like F1040 and currently pandemic one G614) 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 x 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.
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BackgroundA 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 boxesO_ST_ABSWhat is already known on this topicC_ST_ABSAs 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.
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Acute-on-chronic liver failure (ACLF) is a common critical and severe syndrome in patients with chronic liver diseases in China and other countries in the Asia-Pacific region. In recent years, both the Eastern and Western experts have defined ACLF as a new type of liver disease manifesting as a high 28-day mortality rate (>30%) and extensive systematic inflammatory response. ACLF has become a hot topic in the field of liver diseases. This article reviews the research advances in the definition and etiological spectrum of ACLF and discusses the inspirations of such new knowledge for future research.
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AIM To observe the therapeutic effects of Shengjiang Xiexin Decoction (Zingiberis recens Rhizoma,Zingiberis Rhizoma,Coptidis Rhizoma,etc.) on irinotecan (CPT-11)-induced delayed diarrhea in colorectal carcinoma mice and to discuss its possible action mechanism.METHODS The AOM/DSS-induced female colorectal carcinoma mice were randomly divided into normal group,model group and Shengjiang Xiexin Decoction group.The Shengjiang Xiexin Decoction group was intragastrically administered with Shengjiang Xiexin Decoction,the normal group and the model group were intragastrically administered with normal saline.The diarrhea index and rectum pathologic morphology were measured,and the β-glucuronide activity,IL-15 content and UGT1A1 expression were detected.RESULTS The diarrhea index of Shengjiang Xiexin Decoction group was significantly lower than that of the model group,which might be related to the significant inhibition of β-glucuronide activity,and sig-nificant improvement of IL-15 content and UGT1A1 expression.CONCLUSION Shengjiang Xiexin Decoction shows therapeutic effects on irinotecan-induced delayed diarrhea in AOM/DSS-induced colorectal carcinoma mice.
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Objective:To observe the effects of Shexiang Baoxin Pill (SBP) on isoprenaline (Iso)-induced changes in myocardial cell volume,shape,and connexin 43 (Cx43) expression.Methods:HgC2 myocardial cells were randomly divided into a control group,a Iso group and a Iso+SBP group.After 72 h of culture,the average surface area of HgC2 cells was measured under phase contrast microscope.Bicinchoninic acid (BCA) protein assay was carried out to determine the concentration of proteins.The survival rate of myocardial cells was measured by methylthiazolyldiphenyl-tetrazolium bromide (MTT) assay,and the Cx43 expression was detected by Western blot.Results:The mean surface area and Cx43 concentration in Iso-treated myocardial cells were increased under the phase contrast microscope (P<0.05).Compared with the Iso group,the mean surface area was decreased,and the Cx43 concentration was reduced in the Iso+SBP group (both P<0.05).Compared with the control group,the Cx43 expression was obviously down-regulated in the H9C2 cells of the Iso group (P<0.05);while compared with the Iso group,the Cx43 expression was obviously up-regulated in the Iso+SBP group (P<0.05).Conclusion:Shexiang Baoxin Pills can prevent Iso-induced myocardial hypertrophy and down-regulate Cx43 expression.
