An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP).

IBD, including ulcerative colitis and Crohn's disease, is a chronic and debilitating gastrointestinal disorder that affects millions of people worldwide. Research on IBD has generated massive amounts of data, including literature, metagenomics, metabolomics, bioresources and databases. We aim to create an IBD Integrated Resources Portal (IBDIRP) that provides the most comprehensive resources for IBD. An integrated platform was developed that provides information on different aspects of IBD research resources, such as single-nucleotide polymorphisms (SNPs), genes, transcriptome, microbiota, metabolomics, single cells and other resources. Valuable and comprehensive IBD-related data were collected from PubMed, Google, GMrepo, gutMega, gutMDisorder, Single Cell Portal and other sources. Then, the data were systematically sorted, and these resources were manually curated. We systematically sorted and cataloged more than 320 unique risk SNPs associated with IBD in the SNP section. We presented over 289 IBD-related genes based on the database collection in the gene section. We also obtained 153 manually curated IBD transcriptomics data, including 12 388 samples, on the Gene Expression Omnibus database. The sorted IBD-related microbiota data from three primary microbiome databases (GMrepo, gutMega and gutMDisorder) were available for download. We selected 23 149 IBD-related taxonomic records from these databases. Additionally, we collected 24 IBD metabolomics studies with 2896 participants in the metabolomics section. We introduced two interactive single-cell data plug-in units that provided data visualization based on cells and genes. Finally, we listed 18 significant IBD web resources, such as the official European Crohn's and Colitis Organisation and International Organization for the Study of IBD websites, IBD scoring tools, IBD genetic and multi-omics resources, IBD biobanks and other useful research resources. The IBDIRP website is the first integrated resource for global IBD researchers. This portal will help researchers by providing comprehensive knowledge and enabling them to reinforce the multidimensional impression of IBD. The IBDIRP website is accessible via www.ibdirp.com Database URL: www.ibdirp.com.

Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery

Though it has been 2 years since the start of the Coronavirus Disease 19 (COVID-19) pandemic, COVID-19 continues to be a worldwide health crisis. Despite the development of preventive vaccines, very little progress has been made to identify curative therapies to treat COVID-19 and other inflammatory diseases which remain a major unmet need in medicine. Our study sought to identify drivers of disease severity and death to develop tailored immunotherapy strategies to halt disease progression. Here we assembled the Mount Sinai COVID-19 Biobank which was comprised of ~600 hospitalized patients followed longitudinally during the peak of the pandemic. Moderate disease and survival were associated with a stronger antigen (Ag) presentation and effector T cell signature, while severe disease and death were associated with an altered Ag presentation signature, increased numbers of circulating inflammatory, immature myeloid cells, and extrafollicular activated B cells associated with autoantibody formation. Strikingly, we found that in severe COVID-19 patients, lung tissue resident alveolar macrophages (AM) were not only severely depleted, but also had an altered Ag presentation signature, and were replaced by inflammatory monocytes and monocyte-derived macrophages (MoM{Phi}). Notably, the size of the AM pool correlated with recovery or death, while AM loss and functionality were restored in patients that recovered. These data therefore suggest that local and systemic myeloid cell dysregulation is a driver of COVID-19 severity and that modulation of AM numbers and functionality in the lung may be a viable therapeutic strategy for the treatment of critical lung inflammatory illnesses.

A survey of inflammatory bowel disease in China based on the Google Trends, Baidu index and WeChat index / 中华消化杂志

Objective:To analyze the epidemiological trends and population characteristics of inflammatory bowel disease(IBD)in China by searching keywords related to IBD through Google Trends, Baidu index, and WeChat index, so as to provide a reference for national epidemiological studies on IBD.Methods:IBD-related hot words such as "inflammatory bowel disease" , "Crohn′s disease" , "ulcerative colitis" , "gastroesophageal reflux disease (GERD)" , "irritable bowel syndrome (IBS)" and " Helicobacter pylori ( H. pylori)" were selected. The search volume and trends of the above keywords in the world and China were analyzed through Google Trends, Baidu index and WeChat index. The epidemiological characteristics of IBD in China were summarized. Descriptive methods were used for statistical analysis. Results:The results of Google Trends analysis showed that among 5 common digestive diseases (GERD, IBS, H. pylori infection, IBD and peptic ulcer), GERD was the most concerned disease, while IBD was not the focus among the common digestive diseases. When the global searching scope was limited to IBD related hot words, Crohn′s disease was the disease of primary concern among IBD-related diseases. In South America, South Asia, and parts of Africa, ulcerative colitis was mainly concerned, and in China and countries of Southeast Asia, IBD was more concerned. The searching results of Baidu index indicated that among the national search for IBD-related hot words, the 3 keywords of "inflammatory bowel disease" , "ulcerative colitis" and "Crohn′s disease" were all highly searched, the overall daily average of the search indexes of the 3 keywords were 325, 1 320 and 2 559, respectively, and the searching volume of "Crohn′s disease" was higher than "inflammatory bowel disease" and "ulcerative colitis" . The national wide trends of search volume for "inflammatory bowel disease" , "ulcerative colitis" and "Crohn′s disease" were similar, the search heat gradually decreased from the east coast to the northwest of China, which basically coincided with the three-level ladder trend of China′s economic development, suggesting that the level of economic development was related to the incidence of IBD. The results of Baidu index analysis showed that the main populations who searched IBD-related keywords were young adults and women aged from 20 to 39 years old. The results of WeChat index analysis revealed that the searching volume of "inflammatory bowel disease" , "ulcerative colitis" and "Crohn′s disease" were 205 000, 195 000 and 120 000, respectively, and the search volume for " inflammatory bowel disease" was the highest. The official account (90.27%) and the video account (7.43%) occupied the main sources of IBD-related information on mobile terminals. Conclusions:The IBD-associated internet activities reveal a global lack of public awareness of IBD. China also faces the same problem. The search trend is consistent with the epidemiology of IBD, which may be helpful for future epidemiological research of IBD in China. Mobile media will be a potential force in promoting the patient education and disease management of IBD in China.

Efficacy of transcatheter arterial embolization and laparotomy in the treatment of severe liver injury: a comparative study / 中华创伤杂志

Objective:To compare the efficacy of transcatheter arterial embolization (TAE) with laparotomy in the treatment of severe liver injury.Methods:A retrospective cohort study was conducted to analyze the clinical data of 48 patients with severe liver injury admitted to 909th Hospital of Joint Logistics Support Force (Affiliated Dongnan Hospital of Xianmen University Medical College) from December 2013 to June 2020, including 28 males and 20 females; aged 16-75 years [(45.7±6.2)years]. There were 25 patients with grade III, 15 grade IV and 8 grade V according to the American Association for the Surgery of Trauma (AAST) classification. After general treatments such as infusion and hemostasis, TAE was performed in 26 patients (TAE group) and laparotomy in 22 patients (laparotomy group). The operation time and length of hospital stay were compared between the two groups. Erythrocyte, hemoglobin and serum creatinine were compared before operation and at postoperative 1 day. Alanine aminotransferase (ALT) and aspartate aminotransferase (AST) were analyzed before operation and at postoperative 1, 3, 7 days. Complications were observed.Results:All patients were followed up for 12-60 months [(17.1±9.1)months]. The operation time and length of hospital stay were (65.7±9.2)minutes and (21.6±6.6)days in TAE group, significantly shorter than (162.5±28.1)minutes and (31.5±7.4)days in laparotomy group ( P<0.05 or 0.01). There was no significant difference between the two groups referring to erythrocyte, hemoglobin and serum creatinine before operation and at postoperative 1 day (all P>0.05). There was no significant difference in ALT and AST between the two groups before operation (all P>0.05). TAE group showed ALT level of 1 154(884, 1 698)U/L, (975.3±400.9)U/L and (403.4±232.9)U/L at postoperative 1, 3, 7 days, significantly lower than 2 053(1 965, 2 132)U/L, (1 604.1±188.2)U/L and (915.3±160.5)U/L in laparotomy group (all P<0.05). TAE group showed AST level of (1 313.2±542.0)U/L, 525(302, 971)U/L and 174(84, 324)U/L at postoperative 1, 3, 7 days, significantly lower than (1 962.9±245.4)U/L, 1 478(1 089, 1 677)U/L and 837(674, 1 006)U/L in laparotomy group ( P<0.05 or 0.01). The complication rate was 26.9% (7/26) in TAE group, significantly lower than 59.1% (13/22) in laparotomy group ( P<0.05). Conclusion:For severe liver injury, TAE can significantly shorten operation time and length of hospital stay, accelerate the recovery of liver function and reduce the complication rate in comparison with laparotomy.

Proteomic Characterization of Acute Kidney Injury in Patients Hospitalized with SARS-CoV2 Infection

Acute kidney injury (AKI) is a known complication of COVID-19 and is associated with an increased risk of in-hospital mortality. Unbiased proteomics using biological specimens can lead to improved risk stratification and discover pathophysiological mechanisms. Using measurements of [~]4000 plasma proteins in two cohorts of patients hospitalized with COVID-19, we discovered and validated markers of COVID-associated AKI (stage 2 or 3) and long-term kidney dysfunction. In the discovery cohort (N= 437), we identified 413 higher plasma abundances of protein targets and 40 lower plasma abundances of protein targets associated with COVID-AKI (adjusted p <0.05). Of these, 62 proteins were validated in an external cohort (p <0.05, N =261). We demonstrate that COVID-AKI is associated with increased markers of tubular injury (NGAL) and myocardial injury. Using estimated glomerular filtration (eGFR) measurements taken after discharge, we also find that 25 of the 62 AKI-associated proteins are significantly associated with decreased post-discharge eGFR (adjusted p <0.05). Proteins most strongly associated with decreased post-discharge eGFR included desmocollin-2, trefoil factor 3, transmembrane emp24 domain-containing protein 10, and cystatin-C indicating tubular dysfunction and injury. Using clinical and proteomic data, our results suggest that while both acute and long-term COVID-associated kidney dysfunction are associated with markers of tubular dysfunction, AKI is driven by a largely multifactorial process involving hemodynamic instability and myocardial damage.

Circulating proteins to predict adverse COVID-19 outcomes

Predicting COVID-19 severity is difficult, and the biological pathways involved are not fully understood. To approach this problem, we measured 4,701 circulating human protein abundances in two independent cohorts totaling 986 individuals. We then trained prediction models including protein abundances and clinical risk factors to predict adverse COVID-19 outcomes in 417 subjects and tested these models in a separate cohort of 569 individuals. For severe COVID-19, a baseline model including age and sex provided an area under the receiver operator curve (AUC) of 65% in the test cohort. Selecting 92 proteins from the 4,701 unique protein abundances improved the AUC to 88% in the training cohort, which remained relatively stable in the testing cohort at 86%, suggesting good generalizability. Proteins selected from different adverse COVID-19 outcomes were enriched for cytokine and cytokine receptors, but more than half of the enriched pathways were not immune-related. Taken together, these findings suggest that circulating proteins measured at early stages of disease progression are reasonably accurate predictors of adverse COVID-19 outcomes. Further research is needed to understand how to incorporate protein measurement into clinical care.

Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae

Summary ParagraphTwo years into the SARS-CoV-2 pandemic, the post-acute sequelae of infection are compounding the global health crisis. Often debilitating, these sequelae are clinically heterogeneous and of unknown molecular etiology. Here, a transcriptome-wide investigation of this new condition was performed in a large cohort of acutely infected patients followed clinically into the post-acute period. Gene expression signatures of post-acute sequelae were already present in whole blood during the acute phase of infection, with both innate and adaptive immune cells involved. Plasma cells stood out as driving at least two distinct clusters of sequelae, one largely dependent on circulating antibodies against the SARS-CoV-2 spike protein and the other antibody-independent. Altogether, multiple etiologies of post-acute sequelae were found concomitant with SARS-CoV-2 infection, directly linking the emergence of these sequelae with the host response to the virus.

TaqMan Real-time RT-PCR Assay for Detecting and Differentiating Japanese Encephalitis Virus / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>To detect Japanese encephalitis virus (JEV) rapidly and distinguish its genotypes, a TaqMan-based reverse transcriptase quantitative polymerase chain reaction (RT-PCR) detection system was developed.</p><p><b>METHODS</b>By aligning the full-length sequences of JEV (G1-G5), six sets of highly specific TaqMan real-time RT-PCR primers and probes were designed based on the highly conserved NS1, NS2, and M genes of JEV, which included one set for non-specific JEV detection and five sets for the detection of specific JEV genotypes. Twenty batches of mosquito samples were used to evaluate our quantitative PCR assay.</p><p><b>RESULTS</b>With the specific assay, no other flavivirus were detected. The lower limits of detection of the system were 1 pfu/mL for JEV titers and 100 RNA copies/µL. The coefficients of variation of this real-time RT-PCR were all < 2.8%. The amplification efficiency of this method was between 90% and 103%.</p><p><b>CONCLUSION</b>A TaqMan real-time RT-PCR detection system was successfully established to detect and differentiate all five JEV genotypes.</p>

Value of PET/CT in staging and treatment of small cell lung cancer / 中国医学影像技术

Small cell lung cancer is the most common primary neuroendocrine malignancy of the lung and is characterized by high malignant degree,rapid doubling time,easy metastasis in early stage and poor prognosis.Accurate staging of small cell lung cancer can formulate personalized therapeutic plans and improve the prognosis of patients.PET/CT can obtain metabolism and anatomical images of the whole body in one scan and improve the diagnostic accuracy and integrity.PET/CT has been widely applied to clinical practice now.PET/CT will play a more and more important role in diagnosis,staging,treatment and prognosis assessment of patients with small cell lung cancer.The value of PET/CT in staging and treatment of small cell lung cancer was reviewed in this article.

CT signs of peripheral small cell lung cancer / 实用放射学杂志

Objective To investigate CT signs of peripheral small cell lung cancer (SCLC).Methods The CT signs of 78 patients with SCLC confirmed by pathology were retrospectively reviewed.According to the presence of mediastinal lymph node metastasis and its size, 78 cases of peripheral SCLC were divided into two types: typeⅠ(isolated lesion) and typeⅡ(lung lesion + lymph nodes).Type Ⅱwere divided into two subtypes:type Ⅱa (short diameter of lymph nodes of pulmonary hilar and mediastinum less than 10 mm) and type Ⅱ b (short diameter of lymph nodes of pulmonary hilar and mediastinum greater than or equal to 10 mm).Results Of the 78 SCLCs, typeⅠwas 7 cases, and typeⅡwas 71 cases,including 8 cases of typeⅡa and 63 cases of typeⅡb.All of the lesions were soild density.The shape were round or oval in 52 cases, vermicular or spindlein 9 cases, and other shapes in 17 cases.Among 71 cases performed CT enhancement, there were 9 cases with homogeneous enhancement, 58 cases with heterogeneous enhancement, 4 cases with non-enhancement large necrosis area.These cases showed the following CT signs: smooth edge in 65 cases, coarse edge in 12 cases, blurred edge in 1 case;air bronchogram in 3 cases, vacuole sign in 4 cases, calcification in 4 cases;lobulation sign in 46 cases, spiculated sign in 5 cases;thickening of the bronchovascular bundle in 41 cases, pleural indentation in 6 cases, marginal ground-glass opacity in 5 cases, vascular convergence sign in 1 case;emphysema in 42 cases;obstructive pneumonia in 4 cases;bronchus abruptly interruption on the edge of the nodules in 18 cases;enlargement of mediastinal lymph nodes in 63 cases, the diameter of mediastinal lymph nodes larger than the primary lesions in 42 cases;and a little pleural effusion in 9 cases.Conclusion Solid density, smooth margin with lobulation,and significantly enlarged mediastinal lymph nodes are common signs in peripheral SCLC.Thickening of the bronchovascular bundle indicates reletively advanced stage.

Diagnostic value of string beads sign in peripheral small cell lung cancer / 实用放射学杂志

Objective To investigate the formation mechanism of string beads sign in peripheral small cell lung cancer (SCLC) and evaluate the significance of it in differential diagnosis among SCLC,peripheral lung adenocarcinoma and peripheral lung squa-mous cell carcinoma.Methods 78 cases of SCLC,69 cases of peripheral lung adenocarcinoma and 33 cases of peripheral lung squa-mous cell carcinoma,confirmed pathologically were included in this study.The positive rates of string beads sign,mediastinal lymph node metastasis and mediastinal lymph nodes larger than primary lung lesions were calculated and analyzed in these three groups.Results 10 out of SCLC cases (12.8%)have string beads sign,in which all mediastinal lymph nodes were larger than lung lesions.Mediasti-nal lymph node metastases were observed in 63(80.8%)of 78 cases,and 42 (53.8%)cases had larger mediastinal lymph nodes than lung lesions.No string beads sign was observed in patients with peripheral solid lung adenocarcinomas,but 25 of 69 cases (36.2%) have mediastinal lymph node metastasis and 2 cases (2.9%)had larger mediastinal lymph nodes than lung lesions.13 cases(39.4%) of 33 patients with peripheral lung squamous cell carcinomas had mediastinal lymph node metastasis,and 6 cases (16.7%)had larger mediastinal lymph nodes than lung lesions.The statistical results showed the positive rate of string beads sign was not significantly different between peripheral SCLC group and peripheral lung squamous cell carcinoma group,but that of mediastinal lymph node and larger mediastinal lymph nodes than lung lesions were statistically different among these three groups.Conclusion To some extent, string beads sign on CT could reflect the biologic character of SCLC.It played an important role in differential diagnosis of peripheral SCLC,peripheral lung adenocarcinoma and periph-eral lung squamous cell carcinoma,but it should be combined with mediastinal lymph node size.

CT findings of abnormal bronchovascular bundle in peripheral small cell lung cancer / 实用放射学杂志

Objective To investigate CT findings of abnormal bronchovascular bundle in patients with peripheral small cell lung cancer (SCLC).Methods The CT findings of abnormal bronchovascular bundle in 78 peripheral SCLC patients confirmed by pathology were retrospectively reviewed.Abnormal bronchovascular bundle of peripheral SCLC was divided into three types:type Ⅰ (thickening of the bronchovascular bundle),type Ⅱ (string beads of bronchovascular bundle) and type Ⅲ (bronchial cast with bronchus cut-off).Results 41 of 78 patients had abnormal bronchovascular bundle,in which 26 cases were in type Ⅰ,10 in type Ⅱ,5 in type Ⅲ.Except for 1 case with no mediastinal lymph node metastasis among 41 cases with abnormal bronchovascular bundle,all other 40 cases had mediastinal lymph node metastasis.Conclusion The abnormal bronchovascular bundle could reflect the biologic character of SCLC.Abnormal bronchovascular bundle is associated with advanced patients.

Early diagnosis and surgery timing of strangulated intestinal obstruction / 局解手术学杂志

Objective To investigate the early diagnosis and surgery timing of strangulated intestinal obstruction.Methods The clinical data of 90 patients with strangulated intestinal obstruction who were admitted into our hospital from January 2013 and January 2016 were retrospectively analyzed.And these patients were divided into the early stage group (28 cases) and the later stage group (62 cases).The rate of mortality and the rate of necrotic bowel resection of the two groups were analyzed.Results Among the 90 patients underwent emergency surgery,there were 88 cases cured and 2 cases died,and there were 10 cases (11.11％) of necrotic bowel resection among the survivor.In the early stage group,there were 8 cases of necrotic bowel resection and 1 case of death.In the later stage group,there were 2 cases of necrotic bowel resection and 1 case of death.Conclusion Early diagnosis and prompt surgical treatment can reduce the mortality of strangulation obstruction and necrosis of bowel resection.

An Improved Barcoded Oligonucleotide Primers-based Next-generation Sequencing Approach for Direct Identification of Viral Pathogens in Clinical Specimens / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>To provide a feasible and cost-effective next-generation sequencing (NGS) method for accurate identification of viral pathogens in clinical specimens, because enormous limitations impede the clinical use of common NGS, such as high cost, complicated procedures, tremendous data analysis, and high background noise in clinical samples.</p><p><b>METHODS</b>Viruses from cell culture materials or clinical specimens were identified following an improved NGS procedure: reduction of background noise by sample preprocessing, viral enrichment by barcoded oligonucleotide (random hexamer or non-ribosomal hexanucleotide) primer-based amplification, fragmentation-free library construction and sequencing of one-tube mixtures, as well as rapid data analysis using an in-house pipeline.</p><p><b>RESULTS</b>NGS data demonstrated that both barcoded primer sets were useful to simultaneously capture multiple viral pathogens in cell culture materials or clinical specimens and verified that hexanucleotide primers captured as many viral sequences as hexamers did. Moreover, direct testing of clinical specimens using this improved hexanucleotide primer-based NGS approach provided further detailed genotypes of enteroviruses causing hand, foot, and mouth disease (HFMD) and identified other potential viruses or differentiated misdiagnosis events.</p><p><b>CONCLUSION</b>The improved barcoded oligonucleotide primer-based NGS approach is simplified, time saving, cost effective, and appropriate for direct identification of viral pathogens in clinical practice.</p>

Comparison of surgical site infection between laparoscopic distal gastrectomy and open distal gastrectomy for gastric cancer:A Meta-analysis / 中国内镜杂志

Objective To compare the differences of surgical site infection (SSI) between laparoscopic distal gas-trectomy (LDG) and open distal gastrectomy (ODG) for gastric cancer. Methods We set up strict inclusion and ex-clusion criteria. All the randomized controlled trials (RCT) on LDG and ODG for gastric cancer were collected. Meta-analysis was performed according to the recommendation by the Cochrane handbook. Results Six RCTs in-cluding 767 patients were analyzed, who were divided into LDG group (n =394) and ODG group ( n=373). Postop-erative wound infection and SSI were significantly lower in LDG than in ODG [RR=0.32, 95 %Cl (0.11, 0.91).P =0.03; RR= 0.28, 95 %Cl (0.12, 0.70),P =0.006]. There was no significant difference in intra-abdominal abscess between the two groups [RR=0.35, 95 % Cl (0.09, 1.31), P=0.12]. Conclusions LDG was associated with a lower incidence of SSI, especially wound infection, as compared with ODG in the meta-analysis.

Detection of the Zaire Subtype of the Ebola Virus by Isothermal Multiple Self-matching Initiated Amplification / 病毒学报

Given the Ebola outbreak in West Africa and the risks of spread to other regions, a rapid, sensitive and simple method for the detection of the Ebola virus (EBOV) is of great significance for the prevention and control of Ebola. We developed a simple colorimetric isothermal multiple self-matching initiated amplification (IMSA) for rapid detection of the Zaire subtype of the Ebola virus (EBOV-Z). This method employed six primers that recognized seven sites of the EBOV-Z nucleoprotein gene for amplification of nucleic acids under isothermal conditions at 63 degrees C for 1 h. Amplification products were detected through visual inspection of color change by pre-addition of hydroxyl naphthol blue dye. Relative sensitivity was validated by detection of serial tenfold dilutions of virus-like particles containing the partial EBOV-Z nucleoprotein gene and mock clinical sample. Specificity of IMSA was validated by detection of the plasma of 30 healthy volunteers, the dengue virus, and Japanese encephalitis virus. IMSA had comparable sensitivity to Reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and cross-reaction with human plasma or other viruses was not observed. Reverse transcription-isothermal multiple self-matching initiated amplification (RT-IMSA) was also evaluated and compared in parallel with the commercial RT-qPCR kit for detection of EBOV-suspected samples of human blood in Sierra Leone. Sensitivity and specificity of the RT-IMSA was 91.4% and 100%, respectively. These data suggest that RT-IMSA is a valuable tool for the detection of the EBOV with the distinct advantages of simplicity and low cost compared with RT-qPCR.

Establishment of Quality Control System of Nucleic Acid Detection for Ebola Virus in Sierra Leone-China Friendship Biological Safety Laboratory / 病毒学报

The quality control process throughout the Ebola virus nucleic acid detection in Sierra Leone-China Friendship Biological Safety Laboratory (SLE-CHN Biosafety Lab) was described in detail, in order to comprehensively display the scientific, rigorous, accurate and efficient practice in detection of Ebola virus of first batch detection team in SLE-CHN Biosafety Lab. Firstly, the key points of laboratory quality control system was described, including the managements and organizing, quality control documents and information management, instrument, reagents and supplies, assessment, facilities design and space allocation, laboratory maintenance and biosecurity. Secondly, the application of quality control methods in the whole process of the Ebola virus detection, including before the test, during the test and after the test, was analyzed. The excellent and professional laboratory staffs, the implementation of humanized management are the cornerstone of the success; High-level biological safety protection is the premise for effective quality control and completion of Ebola virus detection tasks. And professional logistics is prerequisite for launching the laboratory diagnosis of Ebola virus. The establishment and running of SLE-CHN Biosafety Lab has landmark significance for the friendship between Sierra Leone and China, and the lab becomes the most important base for Ebola virus laboratory testing in Sierra Leone.

Establishment of TaqMan RT-PCR assay for Flanders virus / 中国人兽共患病学报

The Flanders virus (FLAV) is a number of family Rhabdoviridae ,contains a single‐stranded ,negative‐sense vi‐ral RNA .Here we describe a molecular detection method developed for fast measurement of FLAV based on Taqman RT‐PCR method .In this study ,FLAV specific primers and probe were designed based on the FLAV L gene sequences published in GeneBank .Quantitative standard curve of FLAV TaqMan PCR was also successfully established .The specificity and stability test showed that the system is specific and the coefficient variables were all less than 1 .7% .Quantitative standard curve based on the genomic copy was drawn ,and the lowest detectable limit (LOD) of system was 100 copies/PCR ,with higher sensitivity and stability than that of the conventional RT‐PCR assay targeting the same gene .

Colorimetric detection of coxsackievirus A6 by reverse transcription loop mediated isothermal amplification / 中华预防医学杂志

<p><b>OBJECTIVE</b>To develop a simple, rapid and sensitive colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of coxsackievirus A6 (CV-A6) based on the colour chang of hydroxy naphthol blue (HNB).</p><p><b>METHODS</b>The method employed a set of six primers that recognized sequences of VP1 gene for amplification of nucleic acid under isothermal conditions at 63 °C for 50 min. The products were detected through visual inspection of color change by the pre-addition of HNB dye. The specificity was validated by detecting a collection of different human enteroviruses. The sensitivity of this assay was evaluated by serial dilutions of RNA molecules from in vitro transcription of CV-A6 VP1 gene, and compared with real-time RT-PCR (rRT-PCR) in parallel. This assay was evaluated with 92 clinical specimens from patients with hand-foot-mouth disease.</p><p><b>RESULTS</b>A positive color (sky blue) was only observed in the preparation of CV-A6, whereas none of the other 23 kinds of human enteroviruses showed a color change. The HNB based RT-LAMP showed a sensitivity of 100 copies/reaction, which was at the same level as that of the rRT-PCR. The result of RT-LAMP in analysis of 92 clinical specimens was consistent with that of the rRT-PCR. The kappa correlation between the two methods was 1 and both of the sensitivity and specificity of the RT-LAMP assay were 100%.</p><p><b>CONCLUSION</b>The established RT-LAMP assay had good specificity and sensitivity and thus demonstrated to be a promising screening tool for CV-A6 infection. It also has the potential to be used in resource-limited clinical sites and field study.</p>

Detection of Middle East Respiratory Syndrome Coronavirus by Reverse-transcription Loop-Mediated Isothermal Amplification / 病毒学报

A simple, rapid and sensitive colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) was developed for rapid detection of Middle East respiratory syndrome coronavirus (MERS-CoV). The method employed six primers that recognized sequences of a nucleocapsid gene for amplification of nucleic acids under isothermal conditions at 63 degrees C for 60 min. Products were detected through a LA-320c Loopamp Turbidimeter (real-time RT-LAMP) or visual inspection of color change by pre-addition of Hydroxynaphthol Blue dye (visual RT-LAMP). Specificity of RT-LAMP was validated by detection of several human coronaviruses and common respiratory viruses. MERS-CoV real-time RT-LAMP had a linear correlation (R2) of 0.995 at 10(3)-10(6) copies. The limit of detection of real-time RT-LAMP, visual RT-LAMP and quantitative real-time PCR was 500, 1000 and 100 copies/reaction, respectively. The established RT-LAMP assay was demonstrated to be a rapid screening tool for MERS-CoV infection, and could be suitable in resource-limited clinical sites and for field studies.