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.

Characterization of Microbial Co-infections in the Respiratory Tract of hospitalized COVID-19 patients

BackgroundSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus disease 2019 (COVID-19). However, microbial composition of the respiratory tract and other infected tissues, as well as their possible pathogenic contributions to varying degrees of disease severity in COVID-19 patients remain unclear. MethodBetween January 27 and February 26, 2020, serial clinical specimens (sputum, nasal and throat swab, anal swab and feces) were collected from a cohort of hospitalized COVID-19 patients, including 8 mildly and 15 severely ill patients (requiring ICU admission and mechanical ventilation), in the Guangdong province, China. Total RNA was extracted and ultra-deep metatranscriptomic sequencing was performed in combination with laboratory diagnostic assays. Co-infection rates, the prevalence and abundance of microbial communities in these COVID-19 patients were determined. FindingsNotably, respiratory microbial co-infections were exclusively found in 84.6% of severely ill patients (11/13), among which viral and bacterial co-infections were detected by sequencing in 30.8% (4/13) and 69.2% (9/13) of the patients, respectively. In addition, for 23.1% (3/13) of the patients, bacterial co-infections with Burkholderia cepacia complex (BCC) and Staphylococcus epidermidis were also confirmed by bacterial culture. Further, a time-dependent, secondary infection of B. cenocepacia with expressions of multiple virulence genes in one severely ill patient was demonstrated, which might be the primary cause of his disease deterioration and death one month after ICU admission. InterpretationOur findings identified distinct patterns of co-infections with SARS-CoV-2 and various respiratory pathogenic microbes in hospitalized COVID-19 patients in relation to disease severity. Detection and tracking of BCC-associated nosocomial infections are recommended to improve the pre-emptive treatment regimen and reduce fatal outcomes of hospitalized patients infected with SARS-CoV-2. FundingNational Science and Technology Major Project of China, National Major Project for Control and Prevention of Infectious Disease in China, the emergency grants for prevention and control of SARS-CoV-2 of Ministry of Science and Technology and Guangdong province, Guangdong Provincial Key Laboratory of Genome Read and Write, Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, and Shenzhen Engineering Laboratory for Innovative Molecular Diagnostics.

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.

The cytotoxicity of HIV-1 Vpr on the C8166 cells / 中华微生物学和免疫学杂志

Objective To investigate the T cell cytotoxicity induced by recombinant adenovirus carrying HIV-1 vpr gene.Methods C8166 cells infected with rAd-vpr or negative control rAd-vector,were analyzed for cell cycle distribution and cell death by flow cytometry.The discrimination of living cells,apoptotic and necrotic cells were differentiated with Hoechst-PI double staining under the confocal microscopy.Changes of mitochondrial membrane potential(△ψm)were monitored by JC-1 staining method.Results Annexin V-PI and Hoechst-PI staining indicated the death effects of HIV-1 Vpr on C8166 cells.PI flow cytometric analysis showed that cell cycle arrested in G2 phase.C8166 cell△ψm collapse mediated by Vpr was detected by JC-1 fluorescent staining.Conclusion The ability of recombinant adenovirus carrying HIV-1 vpr gene to induce mitochondria dysfunction,cell cycle G2 phase arrest and cell death was confirmed in C8166 cells.

Roles of dendritic cells treated with 17?-estradiol in immune tolerance induction in skin allograft / 中国病理生理杂志

AIM:To study the roles of bone marrow-derived dendritic cells from donor mouse treated with 17?-estradiol(E2)in immune tolerance induction in skin allograft.METHODS:Bone marrow-derived dendritic cells from C57 mouse as donor were cultured respectively treated with E2(E2 group).BALB/c mouse as recipient received respectively one injection of dendritic cells of E2 group,mature dendritic cell group and immature dendritic cell group intravenously.Skin transplantation was performed in the absence of immunosupression after 7 d.Mice that received PBS were served as control.The time of skin survival was observed after transplantation.Flow cytometry was used to analyze the percentage of CD4+CD25+ T cells in peripheral blood respectively before and after transplantation.RESULTS:Compared with immature dendritic cells and control group,the time of skin survival in E2 group was significantly longer(P

Change of mitochondria during apoptosis in Jurkat cells induced by arsenic trioxide / 中国病理生理杂志

AIM:To study the changes of mitochondria during apoptosis in Jurkat cells induced by arsenic oxide(As2O3).METHODS:By treated with 4?10-6 mol/L As2O3,apoptosis and necrosis of Jurkat cells were assessed by annexin V-FITC/PI double staining flowcytometry.Mitochondrial mass and its membrane potential(△?m)was measured by NAO/PI and DiOC6(3)/PI staining,respectively.Free radical formation was detected by DCFDA staining.RESULTS:After 48 h of As2O3 treatment,the rates of early apoptotic Jurkat cells in As2O3 and control groups were(18.98?1.40)% and(5.17?0.80)%,respectively(P

Murine CD200~+CK7~+ trophoblasts in poly (I∶C)-induced embryo resorption model / 中国病理生理杂志

AIM: To investigate the relationship between CD200~+CK7~+ trophoblasts and the resorption of embryos in a poly (I∶C)-induced abortion model. METHODS: The status of CD200 expression was investigated in Balb/c?C57BL/6 and Balb/c?Balb/c mice as induced model of embryo-resorption by an i.p. injection of poly (I∶C). CD200 expression on CK7~+ cells from placentas was detected with flow cytometry. CD200~+ cells in placenta were observed with immunocytochemical staining. RESULTS: Both the percentage and absolute number of CD200~+CK7~+ cells were dramatically decreased by injection of poly (I∶C) in Balb/c?C57BL/6 (6.3%?6.2% vs 36.1%?9.3%, P

Association between development of CD4~+CD25~+ regulatory T cells and thymus CD4~-CD25~+ cells / 中国病理生理杂志

AIM: To explore the correlation between development of CD4~+CD25~+ regulatory T cells (CD4~+CD25~+ Tr) and thymus CD4~-CD25~+ cells. METHODS: The ratios of CD4~+CD25~+ regulatory T cells to CD4~+ T cells in thymus, spleen, lymph node and peripheral blood of mice from birth to mature and also the ratios of CD4~-CD25~+cells to CD4~-T cells in thymus were measured by flow cytometry. Purified CD4~+CD25~+ T cells and CD4~+CD25~- T cells were labeled with CFDA-SE, and then stimulated with various kinds of stimulators. RESULTS: The percentages of CD4~+CD25~+ Tr in mouse spleen, lymph nodes and peripheral blood increased gradually, but not in thymus, from day one to week 10 of the age with rapid rising from day one to week 1. The percentages of CD4~-CD25~+ cells in mouse thymus were quite high on day one after birth, and decreased rapidly from day one to week 1. Both CD4~+CD25~+ Tr and CD4~+CD25~- T cells showed no proliferation in response to ConA, while CD4~+CD25~+ Tr showed a transient enlargement of cell size. Both CD4~+CD25~+ Tr and CD4~+CD25~- T cells underwent proliferation in response to PDB plus ionomycin. CD4~+CD25~- T cells, but not CD4~+CD25~+ Tr, showed a proliferative response to the stimulation of coated anti-CD3 plus soluble anti-CD28 antibody, however, CD4~+CD25~+ Tr showed significant proliferation and CD4~+CD25~- T cells showed a stronger response in addition of high dose of IL-2. CONCLUSION: The thymus CD4~-CD25~+ cells are probably the precursor of CD4~+CD25~+ Tr during cell development.

The mitochondrial and structural protein changes in dexamethasone-induced mouse thymocyte apoptosis / 中国病理生理杂志

AIM: To study mitochondrial mass and structural protein changes in dexamethasone (DEX)-mediated mouse thymocyte apoptosis process. METHODS: DEX-induced mouse thymocyte apoptosis model was established. Annexin V-FITC/PI double staining was used to identify apoptotic and necrotic cells by flowcytometry, JC-1 staining was adopted to test mitochondrial membrane potential (△?_m), and cellular structural protein changes were studied with CFDA-SE staining. RESULTS: By 1?10~(-6) mol/L DEX stimulation, the apoptotic rate was 51.25%?5.51% and had significantly difference from control group (12.03%?2.00%); the necrotic rate in DEX group was 30.25%?3.67% and also had significantly difference from control group (10.11%?1.11%, P

Effect of activation of stimulator cells on expression of CD69 by responder T cells in mixed lymphocyte reaction / 中国病理生理杂志

AIM: To study the influence of status of stimulator cells on activation of responder T cells in mixed lymphocyte reaction (MLR), so as to provide some basis for clinical transplantation. METHODS: Stimulator cells were pretreated differently before mixed lymphocyte culture (MLC) to change their functional status, fluorescence conjugated antibodies and flow cytometry were used to detect expression of CD69 by responder T cells at several different time points. RESULTS: The expression percentages of CD69 by responder T cells in MLCa group (stimulator cells were pre-activated) were significantly higher than those in MLC group (stimulator cells were not pre-activated) at 24, 48 and 72 hours of culture, respectively (5 21%?0 24% vs 1 98%?0 33%, 29 81%?0 85% vs 20 65%?1 00% and 39 61%?1 62% vs 13 49%?0 60%, P

Effect of isoflavone and genistein on expression of CD69 by activated T lymphocytes in vitro / 中国免疫学杂志

Objective:To study the effect of isoflavone and genistein on activation of T lymphocytes in order to develope new immuno intervention reagent.Methods:Fluorescence conjugated monoclonal antibodies and flow cytometer were used to detect the expression rate of CD69 by activated T cells in vitro in response to Phytohemagglutinin(PHA) and Phorbol 12,13 dibutyrate(PDB),with some samples pre incubated with 10,50 or 100 ?mol/L of genistein,after 2 h and 6 h of incubation in whole blood culture system.Results:After 2 h of culture,the inhibitory effect in PHA group was stronger than PDB group(P

Effects of progesterone on the maturation and immunologic function of dendritic cells from human peripheral blood / 中国病理生理杂志

AIM:To study the effects of progesterone(P4) on the maturation and immunologic function of dendritic cells(DCs) from human peripheral blood.METHODS:Cultured DCs were treated with P4 at doses of 10-7 mol/L and 10-6 mol/L.The morphologic changes were observed under the scanning electronic microscope.The immunophenotypes of DCs in control and treated groups were analyzed by flow cytometry.IL-10 and IL-12 production in culture supernatant was examined by ELISA assay.The capability of the stimulatory activity of the DCs on allogeneic T cells in mixed reaction was tested by incorporation of [3H]-TdR.RESULTS:Compared with control group,cultured DCs in the presence of P4 displayed less dendritic pseudopod,expressed low levels of MHC-II,CD40,CD80 and CD86,and exhibited weakly activity in stimulating the proliferation of allogeneic T cells.Increase in IL-10 production and decrease in IL-12 production were observed.CONCLUSION:P4 exerts negative effect on the maturation and immunologic function in dendritic cells from human peripheral blood.

Mechanisms underlying the induction of IL-2 secretion by PDB plus ionomycin in CD4~+CD25~+ T cells from cord blood and adult peripheral blood / 中国病理生理杂志

AIM: To confirm that CD4~+CD25~+ regulatory T cells don't have an instinctive defection in IL-2 secretion, and to have an insight into the maturation state of CD4~+CD25~+ T cells in cord blood. METHODS: CD4~+CD25~+ and CD4~+CD25~- T cells were purified from cord blood of term infants (CB) and adult peripheral blood (PB) by autoMACS, and stimulated with PDB plus ionomycin. After 45 hours of culture, cells were detected for expression of CD69 and CD25 by flow cytometry, and the supernatants were measured for 7 kinds of cytokines by Luminex. RESULTS: CD4~+CD25~+ T cells from both CB and PB proliferated comparably with CD4~+CD25~- T cells when stimulated with PDB plus ionomycin. After 45 hours of culture, however, the CD4~+CD25~+ T cells underwent a tendency of cell death. Expression of CD25 was further upregulated when CD25~+ cells were activated. Under stimulation of PDB plus ionomycin, both CD4~+CD25~+ and CD4~+CD25~- T cells in PB secreted high levels of IFN-?, IL-2 and TNF-?, with CD25~+ cells secreted much higher level of IL-5, IL-4 and IL-10 than those in CD25~- cells; CD4~+CD25~+ and CD4~+CD25~- T cells in CB also secreted high level of IL-2 and TNF-? but much lower level of IFN-? than those in PB, and no secretion of IL-5, IL-4 and IL-10 was observed. CONCLUSION: CD4~+CD25~+ regulatory T cells don't have an instinctive defection in IL-2 secretion, otherwise there may be a different TCR signaling pattern in CD4~+CD25~+ T cells from traditional T cells. The CD4~+CD25~+ T cells in cord blood have not fully matured in function.

Changes of mitochondrial membrane potential and mitochondrial mass in camptothecin-induced Jurkat cells / 中国病理生理杂志

AIM: To study the changes of mitochondrial membrane potential(△?m) and mitochondrial mass in apoptosis of Jurkat cells induced by camptothecin(CPT).METHODS: Jurkat cells were treated with CPT.Annexin V-FITC/propidium iodine(PI) double stainig was used to detected early stage of apoptosis and PI staining for analyzing the cell cycle.Jurkat cells were stained by annexin V-PE/DiOC_6(3) to detect changes of △?m.The mitochondrial mass was measured by cytometry with NAO staining.RESULTS: 6 h after treated with 10 ?mol/L CPT,the rate of early apoptotic cells(22.59?1.04)% had significantly difference compared with control group(3.93?0.73)%(P0.05).Apoptotic peak appeared obviously after treated with CPT,the percentage of late apoptotic cells(13.58?0.97)% had distinctly difference compared with control group(3.18?0.51)%(P

Effects of ultraviolet on mitochondrial functions and apoptosis in HaCaT cells / 中国病理生理杂志

AIM: To study the effects of ultraviolet (UV) on mitochondrial functions and apoptosis in HaCaT cells.METHODS: After irradiation by UV at low dose(UVA 2 J/cm~2,UVB 10 mJ/cm~2) and high dose(UVA 6 J/cm~2,UVB(30 mJ/cm~2),) HaCaT cells were cultured for 15 hours.Flow cytometry was used to measure mitochondrial membrane potential,mitochondrial mass and apoptotic rate.Annexin V-FITC/PI staining of apoptotic cells was analyzed by laser confocal microscopy.RESULTS: After UV irradiation,cell proportion with low mitochondrial membrane potential increased with irradiation doses.The proportion of control group,low dose group and high dose group were 7.94%?1.02%,25.87%?4.55% and 39.27%?5.32%,respectively.Cells proportion with low mitochondrial mass increased with irradiation doses.The proportion of control group,low dose group and high dose group were 15.19%?1.58%,40.36%?4.41% and 68.79%?5.46%,respectively.The hypodiploid peaks of DNA content analysis represented the apoptotic rate of HaCaT cells.The apoptotic rate of control group,low dose group and high dose group were 1.82%?0.51%,30.16%?5.47% and 58.49%?5.98%,respectively.To analyze the cells apoptosis by staining with annexin V-FITC and PI,the results were consistent with those of DNA content analysis.Cells in control group showed almost no positive staining cells.Single annexin V-FITC positive cells in low dose group and double positive cells in high dose group were predominant,respectively.CONCLUSION: UV irradiation induces HaCaT cell mitochondrial depolarization,as well as mitochondrial mass loss.These changes are related to cell apoptosis.

Effect of EGFP gene transfection on the cell cycle distribution of primary cultured human chondrocytes / 中国病理生理杂志

AIM: To investigate the effect of enhanced green fluorescence protein (EGFP) gene transfection on the cell cycle distribution of primary cultured human chondrocytes in order to establish a tracking method of cultured human nasoseptal chondrocytes. METHODS: pEGFP-N1 plasmid was amplified in E.coli, and purified by high purity kit. Primary cultured human chondrocytes,which were initially obtained from the nasoseptal cartilage, were cultured in vitro and transferred with pEGFP-N1 by means of electroporation with Amaxa nucleofector device. Transfering process and transient expression were evaluated by laser scanning confocal microscope (LSCM), the transfer efficiency and the cell cycle distribution were evaluated by flow cytometry. RESULTS: There was significant expression of EGFP at 24 h after transferring. The transfection efficiency of pEGFP-N1 into primary cultured human chondrocytes reached 35 37% at 48 h. It didn't affect the process of cell adherance and had no effect on the cell cycle distribution. CONCLUSION: Primary cultured human chondrocytes, which were transfected with pEGFP, are alive in vitro, and the transferring process doesn't affect the cell cycle distribution. These results suggest that pEGFP-N1 is an ideal transient expression vector for primary cultured human chondrocytes and it might be a well tracer in construction tissue engineered cartilage.

Serum immunopharmacological assessment:effects of cycloheximide on the activation of T lymphocytes of mouse / 中国病理生理杂志

AIM: To investigate the effect of cycloheximide on the T cells activation by mitogen in vitro with CD69 expression as activation marker for the application of this drug clinically. METHODS:Lymphocytes were isolated from lymphoid nodes of C57BL/6 mouse. The cells were preincubated with cycloheximide(CHX), 5% serum containing CHX respectively for an hour, then further incubated with polyclonal activators (Con A or PDB). Harvesting the cells after whole incubation for 24 h, we estimated the expression rates of CD69 on T cells by flow cytometry following two-color immunofluorescent staining. RESULTS: The expression rates of CD69 on the T cells preincubated with CHX, serum containing CHX after the stimulation in response to Con A or PDB all showed significant difference with the expression rates of control group, respectively ( P

CD45~+CD86~+ cells isolated from para-aortic lymph nodes in a murine abortion-prone model / 中国病理生理杂志

AIM: To address whether the analysis of CD45~+CD86~+ cells isolated from para-aortic lymph nodes (PLNs) is valuable in assessment of the status of local immunity at the feto-maternal interface. METHODS: CBA/J?DBA/2, virgin CBA/J, and CBA/J?BALB/c mice were used as an abortion-prone model (group A), non-pregnant controls (group N), and fertile controls (group F), respectively. The percentage of CD45~+CD86~+ cell in the CD45~+ cell group (CD45~+CD86~+ percentage for short) and the absolute number of these cells were determined with flow cytometry (FCM), using mononuclear cells isolated from PLNs collected on day 5.5, 9.5, and 13.5 of gestation, respectively, and mononuclear cells from placentas on day 13.5 of gestation. To clarify the identity of these CD86~+ cells, FCM was also performed with CD3, CD19 and DX5 as markers for T cells, B cells, and NK cells, respectively. RESULTS: Both resorption rate and absolute number of resorption were significantly higher in group A (29.3%, 1.8?1.0) than those in group F (4.8%, 0.3?0.5, P

Effect of oxymatrine on mouse allergic contact dermatitis induced by DNFB and lymphocyte proliferation stimulated by Con A / 中国病理生理杂志

AIM: To explore the inhibitory effect of oxymatrine (OMT) on the allergic contact dermatitis (ACD) stimulated by dinitrofluorobenzene (DNFB) and its effects on the proliferation of the lymphocytes. METHODS: ① An ACD mouse model was established by stimulation with DNFB, and then the mice were injected intraperitoneally with different dosages of OMT, PBS and hydrocortisone (HCT) respectively, the swelling degree of their auricles was examined. ② Carboxyfluorescein diacetate, succinimidyl ester (CFDA-SE) dye and flow cytometer were used to examine the fluorescence intensity changes of lymphocytes stimulated by polyclonal stimulator ConA and OMT. RESULTS: ① compared with PBS group, OMT possessed the strong inhibitory effect on the ACD caused by DNFB in a dose-dependent manner, and its inhibitory effect was equivalent to the HCT of the same dosage with fewer side effects. ② In vitro experiments proved that OMT (500, 125 and 31 mg/L) had the ability to restrain the proliferation of lymphocytes of mouse. CONCLUSION: OMT possesses an inhibitory effect on the ACD induced by DNFB, and OMT is a kind of immunosuppressor.