An Unsupervised Algorithm for Host Identification in Flaviviruses

Early characterization of emerging viruses is essential to control their spread, such as the Zika Virus outbreak in 2014. Among other non-viral factors, host information is essential for the surveillance and control of virus spread. Flaviviruses (genus Flavivirus), akin to other viruses, are modulated by high mutation rates and selective forces to adapt their codon usage to that of their hosts. However, a major challenge is the identification of potential hosts for novel viruses. Usually, potential hosts of emerging zoonotic viruses are identified after several confirmed cases. This is inefficient for deterring future outbreaks. In this paper, we introduce an algorithm to identify the host range of a virus from its raw genome sequences. The proposed strategy relies on comparing codon usage frequencies across viruses and hosts, by means of a normalized Codon Adaptation Index (CAI). We have tested our algorithm on 94 flaviviruses and 16 potential hosts. This novel method is able to distinguish between arthropod and vertebrate hosts for several flaviviruses with high values of accuracy (virus group 91.9% and host type 86.1%) and specificity (virus group 94.9% and host type 79.6%), in comparison to empirical observations. Overall, this algorithm may be useful as a complementary tool to current phylogenetic methods in monitoring current and future viral outbreaks by understanding host–virus relationships.

Correlation Between Portal Pressure and Indocyanine Green Retention Rate is Unaffected by the Cause of Cirrhosis: A Prospective Study

Background Accurate estimation of the hepatic functional reserve before liver resection is important to avoid post-hepatectomy liver failure (PHLF). The aim of the present study was to evaluate the association of indocyanine green retention test with portal pressure by the cause of cirrhosis (non-viral vs. viral) and assessed postoperative outcomes including incidence of PHLF in patients with viral and non-viral cirrhosis. Methods The cohort includes 50 consecutive patients with liver cirrhosis scheduled for liver resection for primary liver tumors at the Lausanne University Hospital between 2009 and 2018. Results There were 31 patients with non-viral liver cirrhosis (Non-virus group) and 19 with viral liver cirrhosis (virus group). The indocyanine green retention rate at 15 min (ICG-R15) (p = 0.276), Hepatic Venous Portal Gradient (HVPG; p = 0.301), and postoperative outcomes did not differ between the non-virus group and viral group. ICG-R15 and HVPG showed a significant linear correlation in all patients (Spearman’s rank correlation coefficient, ρ = 0.599, p < 0.001), the non-virus group (ρ = 0.555, p = 0.026), and the virus group (ρ = 0.534, p = 0.007). A receiver operating characteristic curve analysis showed that ICG-R15 was a predictor for presence of portal hypertension (PH; HVPG ≥ 12 mmHg) (area under the curve [AUC] = 0.780). The cut-off value of ICG-R15 for predicting the presence of PH was 16.0% with 72.3% of sensitivity and 79.0% of specificity. Conclusions The ICG-R15 level was associated with portal pressure in both patients with non-virus cirrhosis and patients with virus cirrhosis and predicts the incidence of PH with relatively good discriminatory ability. Clinical trial number https://clinicalTrials.gov(ID:NCT00827723) Local ethics committee number CER-VD 251.08

Usefulness of the New Hematological Parameter: Reactive Lymphocytes RE-LYMP with Flow Cytometry Markers of Inflammation in COVID-19

Identification of patients with activation of the immune system which indicates the presence of infection is essential, especially in the times of the global coronavirus 2019 (COVID-19) pandemic. The aim of the present study was to evaluate the reactive lymphocytes (RE-LYMP) parameter in COVID-19 and to correlate it with activation lymphocytes markers by flow cytometry. The study group consisted of 40 patients: with COVID-19 infection (n = 20) and with others virus infections without COVID-19 (COVID-19(−) virus (n = 20)) and 20 healthy donors (HC). Blood count and flow cytometry were performed. The COVID-19(+) group had significantly lower RE-LYMP parameter than the COVID-19(−) virus group (5.45 vs. 11.05, p < 0.05). We observed higher proportion of plasmablasts in the COVID-19(+) and COVID-19(−) virus groups than HC (8.8 vs. 11.1 vs. 2.7, p < 0.05). In the COVID-19(+) there was a lower proportion of CD4+ CD38+ cells than in the other groups (significant differences between COVID-19(+) and COVID-19(−) virus groups). RE-LYMP correlated with activated T lymphocytes CD38+ and HLA-DR+ in the COVID-19(−) virus group, however in the COVID-19(+) group correlations with T lymphocytes CD25+ and CD45RO+ were observed. In summary the analysis of the RE-LYMP together with flow cytometric activation markers can be helpful in identifying and distinguishing patients with COVID-19(+) from other viruses and HC.

The Study of Proliferation Relative Long Non-Coding RNA FAM157C in CD59- cell from Paroxysmal Nocturnal Hemoglobinuria Patients

Background: Paroxysmal nocturnal hemoglobinuria (PNH) is a rare clonogenic disease of hematopoietic stem cells. LncRNAs has a wide range of biological functions, including cell differentiation, cell proliferation and substance metabolism. LncRNAs maybe contribute to the proliferation of PNH clones. Methods: CD59- and CD59+ granulocytes and monocytes cells were sorted by FCM and analyzed by RNA sequencing in 5 PNH patients. We focus on the proliferation relative pathway-NF-κB pathway. The mRNAs which FPKM&gt;10 and over 3 patients were chosen to search out the upstream regulation LncRNAs. Then the expression of LncRNAs were detected by qRT-PCR in 30 PNH patients. The highly expressed LncRNA FAM157C was screened out, and analyzed the correlation with clinical index. Finally, we knock-down FAM157C gene in the PIGA knocked out THP-1 cells by lentivirus transfection technique, and observe the cell proliferation, apoptosis to verify its function. Results: Transcription analysis revealed that 742 upregulation LncRNAs and 3276 upregulation mRNAs were identified in CD59- cells (Figure A). The highly expressed NF-κB pathway (Figure B) mRNAs were analysed by co-expression, after that MALAT1, LINC01002, FAM157C, CTD-2530H12.2, XLOC-064331 and XLOC-106677 were concerned with the 8 mRNAs (Figure C). The results showed that the levels of MALAT1 and FAM157C in CD59- cells expression were significantly higher than that of the CD59+ cell in 30 PNH patients (p&lt;0.05). The expression level of MALAT1 and FAM157C were positive correlation with LDH level and CD59- granulated and monocytes cells ratio (Figure D). Lentivirus FAM157C transfection knock-down FAM157C gene expression (90%) in the PIGA knocked out THP-1 cells. The cell proliferation assay results showed that there was no significant change in the cell viability at 24h after transfection. But with the transfection time, the cell proliferation activity showed a decreasing trend. The cell viability of the control group, empty virus group and FAM157C knock-down group were (100±0), (93.75±5.995), (77.49±6.597) and (100±0), (92.795±5.802), (60.47±2.059) after 48h, 72h transfection respectively (p=0.0069, 0.0002) (Figure E). The apoptosis rate of control group, empty virus group and FAM157C knock-down group were (2.483±0.3083)%, (2.926±0.5517)%, (6.256±0.5453)% and (5.593±0.6400)%, (6.723±0.3256)%, (11.30±1.075)% and (9.797±0.3235)%, (10.21±0.3005)%, (18.81±0.5363)% after 24h, 48h, 72h transfection respectively (p=0.0006, 0.0005, &lt; 0.0001). The cell apoptosis experiment showed that apoptosis rate increased after transfection of lentivirus FAM157C (Figure F). The results of cell cycle test showed that the G0/G1 phase of the control group, empty virus group and FAM157C knockdown group were (62.98±1.513)%, (65.95±1.174)% and (70.00±0.2404)%, S phase were (3.825±0.7849)%, (5.920±0.9192)% and (13.47±1.039)%, G2 phase were (32.81±1.612)%, (27.47±1.160)% and (16.54±0.7990)% after transfection of lentivirus FAM157C (p=0.0269, 0.0198, 0.0145) (Figure G). Conclusion: High expressed FAM157C was associated with hemolysis index in PNH, and knock-down it can decrease proliferation ability, induce the apoptosis and the cells were blocked in G0/G1 phase and S phase, indicating FAM157C may be involved in the proliferation of PNH clones. Key words: Paroxysmal Nocturnal Hemoglobinuria, LncRNAs, clone proliferation NF-κB pathway, LncRNA FAM157C Figure Legends Figure A: Volcanic map of differentially expressed LncRNAs and mRNAs, C2 represents CD59- cells, and C1 represents CD59+ cells. Figure B: Scatter plot is a graphical representation of KEGG enrichment analysis results. Figure C: Screening of mRNAs and LncRNAs from NF-κB pathway. Figure D: Correlation analysis between MALAT1 and FAM157C expression and clinical date. Figure E: The cell proliferation assay was examined by CCK-8 kit. Figure F: The Cell apoptosis rate was examined by flow cytometry. Figure G: After FAM157C knockdown, the proportion of cells in G0/G1 phase and S phase increased, while the proportion of cells in G2 phase decreased, and the cells were blocked in G0/G1 phase and S phase. Figure Disclosures No relevant conflicts of interest to declare.

Effects of Xinjiaxiangruyin on the TLR7 pathway in influenza virus-infected lungs of mice housed in a hygrothermal environment

Background To investigate the effects and immunological mechanisms of the traditional Chinese medicine Xinjiaxiangruyin on controlling influenza virus (FM1 strain) infection in mice housed in a hygrothermal environment. Methods Mice were housed in normal and hygrothermal environments, and intranasally infected with influenza virus (FM1). A high-performance liquid chromatography fingerprint of Xinjiaxiangruyin was used to provide an analytical method for quality control. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to measure messenger RNA expression of Toll-like receptor 7 (TLR7), myeloid differentiation primary response 88 (MyD88), and nuclear factor-kappa B (NF-κB) p65 in the TLR7 signaling pathway and virus replication in the lungs. Western blotting was used to measure the expression levels of TLR7, MyD88, and NF-κB p65 proteins. Flow cytometry was used to detect the proportion of Th17/T-regulatory cells. Results Xinjiaxiangruyin effectively alleviated lung inflammation in C57BL/6 mice in hot and humid environments. Guizhimahuanggebantang significantly reduced lung inflammation in C57BL/6 mice. The expression of TLR7, MyD88, and NF-κB p65 mRNA in lung tissue of WT mice in the normal environment, GZMHGBT group was significantly lower than that in the model group (P < 0.05). In WT mice exposed to the hot and humid environment, the expression levels of TLR7, MyD88, and NF-κB p65 mRNA in the XJXRY group were significantly different from those in the virus group. The expression levels of TLR7, MyD88, and NF-κB p65 protein in lung tissue of WT mice exposed to the normal environment, GZMHGBT group was significantly lower than those in the model group. In WT mice exposed to hot and humid environments, the expression levels of TLR7, MyD88, and NF-κB p65 protein in XJXRY group were significantly different from those in the virus group. Conclusion Guizhimahuanggebantang demonstrated a satisfactory therapeutic effect on mice infected with the influenza A virus (FM1 strain) in a normal environment, and Xinjiaxiangruyin demonstrated a clear therapeutic effect in damp and hot environments and may play a protective role against influenza through downregulation of the TLR7 signal pathway.

Detection of novel tick-borne pathogen, Alongshan virus, in Ixodes ricinus ticks, south-eastern Finland, 2019

The newly identified tick-borne Alongshan virus (ALSV), a segmented Jingmen virus group flavivirus, was recently associated with human disease in China. We report the detection of ALSV RNA in Ixodes ricinus ticks in south-eastern Finland. Screening of sera from patients suspected for tick-borne encephalitis for Jingmen tick virus-like virus RNA and antibodies revealed no human cases. The presence of ALSV in common European ticks warrants further investigations on its role as a human pathogen.