Preliminary study on high throughput screening small molecules targeting Gram-negative bacilli outer membrane protein BamA / 中华检验医学杂志

Objective:High-throughput screening to obtain small molecular compounds against Gram-negative bacilli by targeting BamA outer membrane protein.Methods:The sybyl-X2.1 software was used to perform high-throughput virtual screening of small molecular compounds in Chemdiv compound library based on the molecular docking. The top 150 hits by high-throughput screening were re-screened through in vitro biological experiments. The top 4 small molecules with obvious antibacterial activity were selected for in-depth molecular docking analysis, and the small molecule 8308-0401 with the highest docking score was selected for further experiments. The antibacterial effect of 8308-0401 combined with rifampicin was tested by checkerboard assay. Finally, the affinity between 8308-0401 and BamA was tested by plasma surface resonance assay. Results:The docking score of the top 150 hits calculated by high-throughput virtual screening had a mean value of 5.63. In vitro biological experiments showed that small molecules 8308-0401, 8365-1335, C066-2507 and L582-0346 exhibited strong antibacterial activity. Among those molecules, 8308-0401 showed the highest molecular docking score, and synergistic antibacterial activity against both types of strains and clinical isolates when combined with rifampicin. 8308-0401 has a strong affinity to BamA with binding a constant of 182 μmol/L. Conclusion:The small molecule 8308-0401 exerts antibacterial activity against Gram negative bacilli by targeting the outer membrane protein BamA.

L007-0069 kills Staphylococcus aureus in high resistant phenotypes.

Staphylococcus aureus, a common gram-positive pathogenic bacterium, is a main cause of hospital infection. The prevalence rate of methicillin-resistant S. aureus (MRSA) has made its treatment difficult in recent decades. Moreover, S. aureus in the highly tolerant format of biofilm or persister often renders infections refractory. Thus, developing new active compounds against resistant S. aureus is urgently needed. In this study, by a high-throughput screening assay, we identified a small molecule, L007-0069, that exhibited strong and effective bactericidal activity against S. aureus and its high resistance patterns, such as biofilms and persisters, with a low probability of inducing resistance. By molecular dynamics and fluorescent probe analysis, mechanistic studies revealed that the bactericidal activity of L007-0069 was mainly mediated by membrane disruption and metabolic disorder induction. Furthermore, L007-0069 showed effective anti-MRSA effects in vivo in both a wound infection model and a peritonitis-sepsis model, with no detectable toxicity observed at the therapeutic dosage. In conclusion, L007-0069 has the potential to become an alternative for the treatment of highly resistant S. aureus-related infections.

Study on antibacterial effect of halicin (SU3327) against Enterococcus faecalis and Enterococcus faecium.

Enterococci are important pathogens of nosocomial infections and are increasingly difficult to treat due to their intrinsic and acquired resistance to a range of antibiotics. Therefore, there is an urgent need to develop novel antibacterial agents, while drug repurposing is a promising approach to address this issue. Our study aimed to determine the antimicrobial efficacy of halicin against enterococci and found that the minimum inhibitory concentrations (MIC) of halicin against different strains of Enterococcus faecalis and Enterococcus faecium ranged from 4 to 8 µg/ml. In addition, the synergistic antibacterial effect between halicin and doxycycline (DOX) against Enterococcus was observed through the checkerboard method, and it was observed that halicin and DOX could significantly synergistically inhibit biofilm formation and eradicate preformed biofilms at sub-MICs. Moreover, the electron microscope results revealed that halicin could also disrupt the bacterial cell membrane at high concentrations. Furthermore, it is also confirmed that the combination of halicin and DOX has no significant cytotoxic effect on erythrocytes and other human-derived cells. In addition, the mouse subcutaneous model and H&E staining showed that the combination of halicin and DOX could effectively reduce the bacterial load and inflammatory infiltration without obvious side effects. In nutshell, these results demonstrate the potential of halicin in combination with DOX as a novel therapy against infections by Enterococcus.

Characterization of the volatile organic compounds produced from green coffee in different years by gas chromatography ion mobility spectrometry.

The effect of storage time on green coffee volatile organic compounds (VOCs) was studied by their separation via head space solid-phase microextraction and identification via gas chromatography-ion mobility spectrometry. In total, 38 kinds of VOCs, mainly composed of alcohols, aldehydes, esters and ketones, were identified. The fingerprint showed that the VOCs produced by green coffee in different years had obvious differences, especially, acrolein, 3-methylbutyl acetate, butanoic acid, heptan-3-ol, and so on, that could be used to predict the storage time. In addition, with the increase of storage time, the contents of butanal, ethanol, dimethyl sulfide, propanal, butan-2-one had no obvious change, and could be considered as typical aroma characteristics of green coffee or special aroma components for variety identification. Meanwhile, principal component analysis (PCA) and "nearest neighbor" fingerprint analysis could also effectively distinguish green coffee with different storage times. Comprehensive analysis showed that GC-IMS technology could provide strong and favorable support for coffee storage.

Safety and efficacy of nimotuzumab combined with IMRT radiotherapy in the treatment of elderly patients with locally advanced cervical cancer / 中华放射医学与防护杂志

Objective:To investigate the safety and efficacy of nimotuzumab combined with IMRT radiotherapy in the treatment of elderly patients with locally advanced cervical cancer (LACC).Methods:A retrospective analysis was conducted for 34 elderly LACC patients treated with nimotuzumab combined with IMRT radiotherapy or concurrent chemoradiotherapy in the Zhangzhou Affiliated Hospital of Fujian Medical University from June 2020 to December 2021. The efficacy and side effects were evaluated one and two years after treatment.Results:Median follow-up time was 13.3 months (6.1-24.3 months). A total of 24 cases of complete response (CR) and eight cases of partial response (PR) were achieved after treatment, with an objective response rate (ORR) of 94.1% (32/34). The tumor diameters were (49.56 ± 19.22) mm before treatment and (19.61 ± 14.59) mm after treatment, with a tumor regression rate (TRR) of 59.22%.The 1- and 2- year progression-free survival (PFS) rates were 84.9% and 84.9%, overall survival (OS) rates 91.8% and 87.2%, respectively, disease-free survival (DFS) rates 91.8% and 87.2%, respectively, and the cancer-specific survival (CSS) rates 95.7% and 90.9%, respectively. The main adverse events included radiation enteritis, leukopenia, hypoproteinemia and anemia.Conclusions:Nimotuzumab combined with IMRT radiotherapy or concurrent chemoradiotherapy is safe and effective in the treatment of LACC.

Expression of polyphosphate kinase from Sphingobacterium siyangensis and its application in ATP regeneration system / 生物工程学报

Polyphosphate kinase plays an important role in the catalytic synthesis of ATP in vitro. In order to find a polyphosphate kinase that can efficiently synthesize ATP using short-chain polyphosphate (polyP) as substrate, the polyphosphate kinase 2 (PPK2) from Sphingobacterium siyangensis was cloned and expressed in Escherichia coli BL21(DE3). As an enzyme for ATP regeneration, PPK2 was used in combination with l-amino acid ligase (YwfE) to produce l-alanyl-l-glutamine (Ala-Gln). The length of ppk2 of S. siyangensis is 810 bp, encoding 270 amino acids. The SDS-PAGE showed that PPK2 was expressed correctly and its molecular weight was 29.7 kDa as expected. The reaction conditions of PPK2 were optimized. PPK2 could maintain good activity in the range of 22-42 ℃ and pH 7-10. The highest enzyme activity was observed at 37 ℃, pH 7, 30 mmol/L magnesium ion (Mg2+), 5 mmol/L ADP and 10 mmol/L sodium hexametaphosphate, and the yield of ATP reached 60% of the theoretical value in 0.5 hours at this condition. When used in combination with YwfE to produce Ala-Gln, the PPK2 showed a good applicability as an ATP regeneration system, and the effect was similar to that of direct addition of ATP. The PPK2 from S. siyangensis shows good performance in a wide range of temperature and pH, synthesizes ATP with cheap and readily available short chain polyP as substrate. The PPK2 thus provides a new enzyme source for ATP dependent catalytic reaction system.

Quality of life in patients with early-stage extra-nodal NK/T cell lymphoma of nasal type after definitive radiation therapy / 中华放射肿瘤学杂志

Objective:To investigate the quality of life in patients with early-stage extra-nodal NK/T cell lymphoma of nasal type (ENKTL) arising from the upper aerodigestive tract, who had remained progression-free survival (PFS) for over 3 months after definitive intensity-modulated radiation therapy (IMRT), and to analyze the factors related to main adverse symptoms.Methods:276 patients who received IMRT from March, 2012 to June, 2021 were included. There were 201 males and 75 females with a median age of 41.5 years (range: 13-81 years) upon diagnosis. Consistent target delineation schemes and similar dose gradients were adopted for IMRT, with a median prescribed dose of 54.6 Gy/26F. Cross-sectional investigation was performed with a modified EORTC QLQ-H&N35 questionnaire, the incidence and severity of adverse symptoms, severity of disease and their influencing factors at each time-point during their survival were statistically analyzed.Results:The median age of patients at the investigation was 46.2 years, and the median PFS after IMRT was 47.2 months (range: 3.1-115.7 months). The most common adverse symptoms included nasal symptoms (incidence rate 63.8%), dry mouth (50%), tooth diseases (47.1%), smell and taste alteration, and sexual apathy, etc. Most symptoms were mild (the average standardized score was 5.50, the full score of 100 indicating the most severe), and could be relieved remarkably over survival time, but some symptoms, such as tooth diseases and sexual apathy, were more obvious and recurred for several years. Age and anti-PD-1 immune therapy influenced the symptom scores, and tooth diseases were closely correlated with dry mouth. Conclusion:The quality of life in patients with early-stage ENKTL after definitive IMRT is high, and the most significant symptoms include nasal symptoms, tooth diseases, and sexual apathy, etc. , which need to be mitigated with more studies.

Clinical characteristics of imported patients infected with 2019 novel coronavirus Omicron variants and Delta variants in Guangzhou City / 中华传染病杂志

Objective:To analyze and compare the clinical characteristics and prognosis of imported patients infected with 2019 novel coronavirus (2019-nCoV) Omicron variants and Delta variants, so as to provide references for clinical diagnosis, treatment and epidemic prevention strategies.Methods:The patients with imported 2019-nCoV infection from August 1, 2021 to January 18, 2022 in Guangzhou Eighth People′s Hospital, Guangzhou Medical University were retrospectively analyzed. According to the whole genome sequencing of 2019-nCoV in nasal or throat swabs, they were divided into Omicron group and Delta group. The clinical characteristics, laboratory tests, antibody levels, viral nucleic acid (the cycle threshold (Ct) of N gene and open reading frame ( ORF) 1 ab), main treatment measures and clinical prognosis were analyzed in the two groups. Statistical analysis was performed using the rank sum test, chi-square test or Fisher′s exact test. Results:A total of 344 cases were enrolled, including 152 cases in the Delta group and 192 cases in the Omicron group, and there were 240 males (69.8%), with a median age of 33 years old. One hundred and two (29.7%) of those patients had underlying disease.Two hundred and seventy-one had completed full or booster vaccination. The overall full vaccination rate in Omicron group was 70.8%(136/192), which was higher than 51.3%(78/152) in Delta group. The proportion of mild patients in Omicron group was higher than that in Delta group (57.3%(110/192) vs 24.3%(37/152), respectively), and the proportions of common type and severe type were lower than those of the Delta group (33.9%(65/192) vs 55.3%(84/152) and 0(0/192) vs 10.5%(16/152)), the differences were all statistically significant ( χ2=37.64 and 15.84, respectively, Fisher′s exact test; all P<0.001). The duration and peak of fever in Omicron group were 1.5(1.0, 2.0) d and 38.1(37.8, 38.5) ℃, respectively, which were lower than those in Delta group (3.0(1.0, 4.8) d and 38.5(38.1, 39.0) ℃, respectively), and the differences were both statistically significant ( Z=-4.14 and -3.85, respectively, both P<0.001). The 2019-nCoV antibody IgG and the Ct values of virus nucleic acid N gene and ORF1 ab gene in the vaccinated Omicron group at admission were higher than those in the Delta group ( Z=-3.25, -2.18 and -2.82, respectively, all P<0.050). Compared with patients in Delta group, patients in Omicron group had lower proportion of receiving respiratory therapy support, shorter oxygen therapy time, shorter reversion time from admission to nucleic acid Ct value≥35 and shorter hospitalization time. The differences were all statistically significant ( χ2=47.86, Z=-5.41, -5.60 and -4.71, respectively, all P<0.001). There was no critical illness or 28-day death case in both groups. Conclusions:The severity of patients infected with Omicron variants is lighter than that of patients with Delta variants, and the viral nucleic acid has shorter conversion time, which is mainly related to the virulence of variant strain and vaccination.

Plasma cell-free DNA promise disease monitoring and tissue injury assessment of COVID-19

COVID-19 is a huge threat to global health. Due to the lack of definitive etiological therapeutics currently, effective disease monitoring is of high clinical value for better healthcare and management of the large number of COVID-19 patients. In this study, we recruited 37 COVID-19 patients, collected 176 blood samples upon diagnosis and during treatment, and analyzed cell-free DNA (cfDNA) in these samples. We report gross abnormalities in cfDNA of COVID-19 patients, including elevated GC content, altered molecule size and end motif patterns. More importantly, such cfDNA characteristics reflect patient-specific physiological conditions during treatment. Further analysis on tissue origin tracing of cfDNA reveals frequent tissue injuries in COVID-19 patients, which is supported by clinical diagnoses. Hence, we demonstrate the translational merit of cfDNA as valuable analyte for effective disease monitoring, as well as tissue injury assessment in COVID-19 patients.

Enhanced effect of pyrite on the removal of metronidazole by zero valent iron.

The abuse and improper disposal of antibiotics including metronidazole (MNZ) result in serious contamination in aquatic environments. In this study, pyrite, which was not reactive for MNZ removal, was simply mixed with zero valent iron (ZVI) to efficiently remove MNZ in anaerobic aqueous solutions. A dual ZVI/pyrite system consisting of ZVI (1.0 g/L) and pyrite (4.0 g/L) removed MNZ completely in 360 min within a broad pH0 range (5.0-9.0), and it still maintained a high removal efficiency (~80%) even at a high pH0 of 10.0. By contrast, single ZVI (1.0 g/L) showed much lower efficiency (4.8%-22.0%) within the same pH0 range (5.0-10.0). On investigating the mechanism of MNZ removal, the cooperation between ZVI and pyrite enhanced the surface corrosion of ZVI and facilitated the redox cycle of Fe(III)/Fe(II) to generate more sorbed Fe(II), which was a dominant reactive species for MNZ removal. Pyrite also activated the ZVI surface to form FeS@Fe in situ, accelerating the electron transfer from Fe0 core to the surface-enriched MNZ, and stimulated the formation of green rust sulfate on the ZVI surface to further promote MNZ removal. LC-MS analysis confirmed ZVI/pyrite reductively transformed MNZ into readily biodegradable products by denitration and cleavage of hydroxyethyl.

A multicenter prospective cohort study of Xuebijing injection in the treatment of severe coronavirus disease 2019 / 中华危重病急救医学

Objective:To evaluate the effect of Xuebijing injection on the improvement of pneumonia severity index (PSI) and prognosis in patients with severe coronavirus disease 2019 (COVID-19).Methods:A multicenter prospective cohort study was designed. Adult patients with COVID-19 admitted to the intensive care unit (ICU) of 28 designated COVID-19 hospitals in 15 provinces and cities of China from January to March 2020 were enrolled. All patients were treated according to the standard treatment plan of COVID-19 issued by the National Health Commission of the People's Republic of China. They were divided into Xuebijing group and standard treatment group according to whether they received Xuebijing injection or not. In the standard treatment group, routine medical care measures such as antiviral, respiratory support, circulatory support and symptomatic treatment were taken. In the Xuebijing group, on the basis of standard treatment, Xuebijing was used within 12 hours of admission to the ICU, 100 mL each time, twice daily. The minimum duration of Xuebijing administration was 1 day. The improvement rate of PSI risk rating on the 8th day and clinical outcome on the 28th day were recorded.Results:A total of 276 COVID-19 patients were screened continuously, and the data of 144 severe patients who met PSI risk rating Ⅲ-Ⅴ were analyzed. Seventy-two cases were involved each in standard treatment group and Xuebijing group. The average age of the standard treatment group and Xuebijing group were (65.7±7.9) years old and (63.5±10.9) years old, and male accounted for 75.0% (54/72) and 70.8% (51/72), respectively. There were no significant differences in general conditions, comorbidities, PSI risk rating and score, sequential organ failure assessment (SOFA) score, oxygenation index (PaO 2/FiO 2), respiratory support mode and other baseline indicators between the two groups. Compared with the standard treatment group, the improvement rate of PSI risk rating in Xuebijing group on the 8th day after admission was significantly improved [56.9% (41/72) vs. 20.8% (15/72), between-group difference and 95% confidence interval (95% CI) was 36.1% (21.3% to 50.9%), P < 0.01], PSI score, SOFA score and PaO 2/FiO 2 were significantly improved [PSI score: 83.7±34.8 vs. 108.2±25.6, between-group difference (95% CI) was -24.5 (-34.9 to -14.1); SOFA score: 2.0 (1.0, 4.0) vs. 7.0 (4.0, 10.0), between-group difference (95% CI) was -3.5 (-5.0 to -2.0); PaO 2/FiO 2 (mmHg, 1 mmHg = 0.133 kPa): 289.4±111.6 vs. 188.5±98.1, between-group difference (95% CI) was 100.9 (65.3 to 136.5); all P < 0.01]. The 28-day discharge rate of Xuebijing group was 44.5% higher than that of standard treatment group [66.7% (48/72) vs. 22.2% (16/72), P < 0.01], and the 28-day survival rate was 9.8% [91.7% (66/72) vs. 81.9% (59/72), P < 0.01]. There was no significant difference in the combination of antiviral drugs, antibiotics, anticoagulants and vasopressor drugs between the two groups. There was no significant difference in the incidence of adverse events between the Xuebijing group and standard treatment group [41.7% (30/72) vs. 43.1% (31/72), P > 0.05], and no serious adverse events and adverse reactions of Xuebijing were reported. Conclusion:Standard treatment combined with Xuebijing injection can significantly improve the PSI risk score and clinical prognosis of patients with severe COVID-19 without increasing drug safety risk.

Effect of oxidative stress response in acute respiratory distress syndrome caused by influenza / 中华危重病急救医学

Influenza virus is one of the common pathogens causing acute respiratory infectious diseases, and is easy to cause acute respiratory distress syndrome (ARDS) after infecting human body, which is an important cause of death of influenza patients. Influenza-induced ARDS results from a combination of overwhelming inflammation and immune response, causing tissue damage and apoptosis. Furthermore, virus-mediated oxidative stress is another important mechanism. Viral infection can produce excessive reactive oxygen species, which damage the epithelial-endothelial barrier with pulmonary edema. In this content, numerous studies have highlighted the importance of antioxidants as a new therapy aimed at blocking both viral replication and virus-induced inflammation. Therefore, this paper summarizes the epidemiology and mechanisms of influenza-induced ARDS, the role of oxidative stress in the occurrence and development of influenza-related ARDS and the role of antioxidants in anti influenza virus infection, in order to provide reference for effective treatment of influenza patients, reducing mortality, developing new anti influenza drugs and preventing and controlling influenza epidemic.

Incidence and prognoses of human cytomegalovirus reactivation in immunocompetent severe pneumonia patients with mechanical ventilation / 中华危重病急救医学

Objective:To investigate the incidence and risk factors of human cytomegalovirus (HCMV) reactivation in immunocompetent severe pneumonia patients with mechanical ventilation and their effects on clinical outcomes.Methods:A prospective observational study was conducted. Forty-eight immunocompetent patients requiring invasive mechanical ventilation due to severe pneumonia in the department of critical care medicine of the First Affiliated Hospital of Guangzhou Medical University from June 30th, 2017 to July 1st, 2018 were enrolled. Meanwhile, all cases were followed up until 90 days after inclusion and were required to quantitatively detect HCMV DNA in serum at regular weekly intervals until 28 days after transferring to intensive care unit (ICU). Patients were divided into HCMV reactivation group (≥5×10 5 copies/L) and non-reactivation group (<5×10 5 copies/L) based on HCMV DNA at any time point within 28 days. Demographic data, basic indicators, respiratory indicators, disease severity scores, laboratory indicators, complication and clinical outcomes of the two groups were collected and analyzed. Multivariate Logistic regression analysis was performed to screen independent risk factors for HCMV reactivation. Results:All 48 subjects were tested positive for HCMV immunoglobulin G (IgG), so HCMV seropositive rate was 100%. HCMV reactivation occurred in 10 patients within 28 days after admission to ICU, and the reactivation incidence of HCMV was 20.83%. There was no significant difference in gender, age, body mass index (BMI), underling disease reasons for ICU transfer (except sepsis), basic vital signs, disease severity scores, or laboratory findings including infection, immune, blood routine, liver, kidney and circulatory indicators except neutrophils count (NEU), hypersensitivity C-reactive protein(hs-CRP), hemoglobin (Hb), blood urea nitrogen (BUN), N-terminal pro-brain natriuretic peptide (NT-proBNP) between the two groups. The height (cm: 160±6 vs. 166±8), body weight (kg: 49.4±11.2 vs. 57.6±10.5), Hb (g/L: 87±18 vs. 104±24) in HCMV reactivation group were significantly lower than non-reactivation group, as well as NEU [×10 9/L:12.7 (9.9, 22.5) vs. 8.9 (6.2, 13.8)], hs-CRP [mg/L: 115.5 (85.2, 136.6) vs. 39.9 (17.5, 130.2)], BUN [mmol/L:13.7 (8.9, 21.5) vs. 7.1 (4.9, 10.5)] and NT-proBNP [ng/L: 6 751 (2 222, 25 449) vs. 1 469 (419, 4 571)] within 24 hours of admission to ICU. The prevalence of sepsis [60.0% (6/10) vs. 15.8% (6/38)], blood transfusion [100.0% (10/10) vs. 60.5% (23/38)], hospitalization expense [ten thousand yuan: 35.7 (25.3, 67.1) vs. 15.2 (10.4, 22.0)], 90-day all-cause mortality [70.0% (7/10) vs. 21.1% (8/38)], length of ICU stay [days: 26 (16, 66) vs. 14 (9, 19)], the duration of mechanical ventilation [days: 26 (19, 66) vs. 13 (8, 18)] in HCMV reactivation group were significantly higher than non-reactivation group, and there were significant statistical differences between the two groups (all P < 0.05). Logistic regression analysis showed that sepsis was an independent risk factor for HCMV reactivation in immunocompetent mechanical ventilation severe pneumonia patients with mechanical ventilation [odds ratio ( OR) = 9.35, 95% confidence interval (95% CI) was 1.72-50.86, P = 0.010]. Conclusions:HCMV infection is very common in immunocompetent severe pneumonia patients on mechanical ventilation and incidence of HCMV reactivation is high. Moreover, HCMV reactivation could adversely affect clinical prognoses, and sepsis may be a risk factor for HCMV reactivation.

Clinical characteristics of coronavirus disease 2019 infected with Delta variant in Guangzhou:A real-world study / 中华急诊医学杂志

Objective:To summarize the clinical characteristics of patients with coronavirus disease 2019 (COVID-19) infected with Delta variant, so as to provide further references for clinical diagnosis and treatment.Methods:A real-world study was conducted to analyze the characteristics of 166 COVID-19 patients infected with Delta variant at Guangzhou Eighth People’s Hospital, Guangzhou Medical University.Results:The study enrolled 5 asymptomatic cases, 123 non-severe cases (mild and moderate type), and 38 severe cases (severe and critical type). Among these patients, 69 (41.6%) were male and 97 (58.4%) were female, with a mean age of 47.0±23.5 years. Thirty-nine cases (23.5%) had received 1 or 2 doses of inactivated vaccine. The incidence of severe COVID-19 cases was 7.7% in 2-doses vaccinated patients, which was lower than that of 11.5% in 1-dose and 26.8% in unvaccinated patients. The proportion of severe cases in 2 dose-vaccinated patients was 7.7%, which was lower than that of 11.5% in 1-dose vaccinated patients and 26.8% in unvaccinated patients, but the difference was not significant ( P>0.05). The most common clinical symptom was fever (134 cases, 83.2%), and 39.1% of cases presented with high-grade fever (≥39 °C); other symptoms were cough, sputum, fatigue, and xerostomia. The proportion of fever in severe cases was significantly higher than that of non-severe cases (97.4% vs. 76.4%, P<0.01). Similarly, the proportion of severe cases with high peak temperature (≥39 ℃) () was also higher than that of non-severe cases (65.8% vs. 30.9%, P<0.01). The median minimal Cycle threshold (Ct) values of viral nucleic acid N gene and ORFlab gene were 20.3 and 21.5, respectively, and the minimum Ct values were 11.9 and 13.5, respectively. Within 48 h of admission, 9.0% of cases presented with decreased white blood cell counts, and 52.4% with decreased lymphocyte counts. The proportions of increased C-reactive protein, serum amyloid A, interleukin 6, and interleukin 10 were 32.5%, 57.4%, 65.3%, and 35.7%, respectively. The proportions of elevated C-reactive protein, serum amyloid A and interleukin-6 in severe cases were significantly higher than those in non-severe cases ( P<0.01). Logistic regression analysis showed that older age and higher peak temperature were associated with a higher likelihood of severe cases ( OR>3, 95% CI: 2-7, P<0.01). In terms of treatment, traditional Chinese medicine (TCM) was used in 97.6% of non-severe cases and 100% in severe cases. Other treatments included respiratory and nutritional support, immunotherapy (such as neutralizing antibodies and plasma of recovered patients). The median times from admission to progression to severe cases, of fever clearance, and of nucleic acid conversion were 5 days, 6 days and 19 days, respectively. No deaths were reported within 28 days. Conclusions:The symptoms of Delta variant infection in Guangzhou are characterized by a high proportion of fever, high peak temperature, long duration of fever, high viral load, a long time to nucleic acid conversion, and a high incidence of severe cases. The severe cases exhibit a higher percentage of elderly patients, a longer duration of fever and have a higher fever rate and a higher hyperthermia rate than non-severe cases. Age and hyperthermia are independent risk factors for progression to severe disease. The combination of TCM and Western medicine can control the progression of the disease effectively.

Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2

The emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions. Author summaryIn this study, we compared SARS-CoV-2 populations of 13 Chinese COVID-19 patients. Those viral populations contained a considerable proportion of viral sub-genomic messenger RNAs (sgmRNA), reflecting an active viral replication activity in the respiratory tract tissues. The comparison of 66 identified intra-host variants further showed a low viral genetic distance between intra-household patients and a narrow transmission bottleneck size. Despite the co-existence of genetically distinct viruses within the same host, most intra-host minor variants were not shared between transmission pairs, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions. Furthermore, the narrow bottleneck and active viral activity in the respiratory tract show that the passage of a small number of virions can cause infection. Our data have therefore delivered a key genomic resource for the SARS-CoV-2 transmission research and enhanced our understanding of the evolutionary dynamics of SARS-CoV-2.

Intra-host Variation and Evolutionary Dynamics of SARS-CoV-2 Population in COVID-19 Patients

As of middle May 2020, the causative agent of COVID-19, SARS-CoV-2, has infected over 4 million people with more than 300 thousand death as official reports1,2. The key to understanding the biology and virus-host interactions of SARS-CoV-2 requires the knowledge of mutation and evolution of this virus at both inter- and intra-host levels. However, despite quite a few polymorphic sites identified among SARS-CoV-2 populations, intra-host variant spectra and their evolutionary dynamics remain mostly unknown. Here, using deep sequencing data, we achieved and characterized consensus genomes and intra-host genomic variants from 32 serial samples collected from eight patients with COVID-19. The 32 consensus genomes revealed the coexistence of different genotypes within the same patient. We further identified 40 intra-host single nucleotide variants (iSNVs). Most (30/40) iSNVs presented in single patient, while ten iSNVs were found in at least two patients or identical to consensus variants. Comparison of allele frequencies of the iSNVs revealed genetic divergence between intra-host populations of the respiratory tract (RT) and gastrointestinal tract (GIT), mostly driven by bottleneck events among intra-host transmissions. Nonetheless, we observed a maintained viral genetic diversity within GIT, showing an increased population with accumulated mutations developed in the tissue-specific environments. The iSNVs identified here not only show spatial divergence of intra-host viral populations, but also provide new insights into the complex virus-host interactions.

Single-Cell Analysis Reveals Macrophage-Driven T Cell Dysfunction in Severe COVID-19 Patients

The vastly spreading COVID-19 pneumonia is caused by SARS-CoV-2. Lymphopenia and cytokine levels are tightly associated with disease severity. However, virus-induced immune dysregulation at cellular and molecular levels remains largely undefined. Here, the leukocytes in the pleural effusion, sputum, and peripheral blood biopsies from severe and mild patients were analyzed at single-cell resolution. Drastic T cell hyperactivation accompanying elevated T cell exhaustion was observed, predominantly in pleural effusion. The mechanistic investigation identified a group of CD14+ monocytes and macrophages highly expressing CD163 and MRC1 in the biopsies from severe patients, suggesting M2 macrophage polarization. These M2-like cells exhibited up-regulated IL10, CCL18, APOE, CSF1 (M-CSF), and CCL2 signaling pathways. Further, SARS-CoV-2-specific T cells were observed in pleural effusion earlier than in peripheral blood. Together, our results suggest that severe SARS-CoV-2 infection causes immune dysregulation by inducing M2 polarization and subsequent T cell exhaustion. This study improves our understanding of COVID-19 pathogenesis.

Clinical findings in critical ill patients infected with SARS-Cov-2 in Guangdong Province, China: a multi-center, retrospective, observational study

BackgroundIn December 2019, human infection with a novel coronavirus, known as SARS-CoV-2, was identified in Wuhan, China. The mortality of critical illness was high in Wuhan. Information about critically ill patients with SARS-CoV-2 infection outside of Wuhan is scarce. We aimed to provide the clinical features, treatment, and prognosis of the critically ill patients with SARS-CoV-2 infection in Guangdong Province. MethodsIn this multi-centered, retrospective, observational study, we enrolled critically ill patients with SARS-CoV-2 pneumonia who were admitted to the intensive care unit (ICU) in Guangdong Province. Demographic data, symptoms, laboratory findings, comorbidities, treatments, and prognosis were collected. Data were compared between patients with and without intubation. ResultsForty-five critically ill patients with SARS-CoV-2 pneumonia were identified in 7 ICUs in Guangdong Province. The mean age was 56.7 years, and 29 patients (64.4%) were men. The most common symptoms at the onset of illness were high fever and cough. Majority of patients presented with lymphopenia and elevated lactate dehydrogenase. Treatment with antiviral drugs was initiated in all the patients. Thirty-seven patients (82.2%) had developed acute respiratory distress syndrome, and 13 (28.9%) septic shock. A total of 20 (44.4%) patients required intubation and 9 (20%) required extracorporeal membrane oxygenation. As of February 28th 2020, only one patient (2.2%) had died and half of them had discharged of ICU. ConclusionsInfection with SARS-CoV-2 in critical illness is characterized by fever, lymphopenia, acute respiratory failure and multiple organ dysfunction. Compared with critically ill patients infected with SARS-CoV-2 in Wuhan, the mortality of critically ill patients in Guangdong Province was relatively low. These data provide some general understandings and experience for the critical patients with SARS-CoV-2 outside of Wuhan.

Multiple approaches for massively parallel sequencing of HCoV-19 genomes directly from clinical samples

COVID-19 has caused a major epidemic worldwide, however, much is yet to be known about the epidemiology and evolution of the virus. One reason is that the challenges underneath sequencing HCoV-19 directly from clinical samples have not been completely tackled. Here we illustrate the application of amplicon and hybrid capture (capture)-based sequencing, as well as ultra-high-throughput metatranscriptomic (meta) sequencing in retrieving complete genomes, inter-individual and intra-individual variations of HCoV-19 from clinical samples covering a range of sample types and viral load. We also examine and compare the bias, sensitivity, accuracy, and other characteristics of these approaches in a comprehensive manner. This is, to date, the first work systematically implements amplicon and capture approaches in sequencing HCoV-19, as well as the first comparative study across methods. Our work offers practical solutions for genome sequencing and analyses of HCoV-19 and other emerging viruses.

The efficacy of convalescent plasma for the treatment of severe influenza

BackgroundAdministration of convalescent plasma may be of clinical benefit for treatment of severe acute viral respiratory infections. However, no clear evidence exists to support or oppose convalescent plasma use in clinical practice. We conducted a systematic review and meta-analysis to assess the evidence of randomized controlled trials (RCTs) in the convalescent plasma for the treatment of severe influenza. MethodsHealthcare databases were searched in February 2020. All records were screened against the eligibility criteria. Data extraction and risk of bias assessments were undertaken. The primary outcome was case-fatality rates by influenza. ResultsWe identified 5 RCTs of severe influenza. The pooled analyses showed no evidence for a reduction in mortality (Odds Ratio (OR) 1.06; 95% confidence interval (CI) 0.51-2.23; p = 0.87; I2 = 35%). We also found non-significant reductions in days in ICU and hospital, and days on mechanical ventilation. There seemed to have a biological benefit of increasing HAI titer levels and decreasing influenza B virus loads and cytokines after convalescent plasma treatment. No serious adverse events was reported between two groups. Studies were commonly of low risk of bias with high quality. ConclusionsConvalescent plasma appears safe but may not reduce mortality in severe influenza. This therapy should be studied within the context of a well-designed clinical trial for treatment of SARS-Cov-2 infection.