Genotypic Tropism Prediction from Paired Cell and Plasma Using Single and Replicate Sequences

2014 ◽  
Vol 30 (7) ◽  
pp. 711-716 ◽  
Author(s):  
Luana Portes Ozório Coelho ◽  
João Leandro de Paula Ferreira ◽  
Gabriela Bastos Cabral ◽  
Paula Morena de Souza Guimarães ◽  
Luis Fernando de Macedo Brigido
2018 ◽  
Vol 71 (11) ◽  
pp. A158
Author(s):  
Kathryn Arnold ◽  
John Blair ◽  
Jonathan Paul ◽  
Atman Shah ◽  
Sandeep Nathan ◽  
...  

2020 ◽  
Author(s):  
Zhong Peng ◽  
Junyang Liu ◽  
Wan Liang ◽  
Fei Wang ◽  
Li Wang ◽  
...  

Abstract Background: Different typing systems including capsular genotyping, lipopolysaccharide (LPS) genotyping, multilocus sequence typing (MLST), and virulence genotyping based on the detection of different virulence factor-encoding gene (VFG) profiles have been applied to characterize Pasteurella multocida strains from different host species. However, these methods require much time and effort in laboratories. Particularly, relying on one of these methods is difficult to address the biology of P. multocida from host species. Recently, we found that assigning P. multocida strains according to the combination of their capsular, LPS, and MLST genotypes (marked as capsular genotype: LPS genotype: MLST genotype) could help address the biological characteristics of P. multocida circulation in multiple hosts. However, it is still lack of a rapid, efficient, intelligent and cost-saving tool to diagnose P. multocida according to this system. Results: We have developed an intelligent genotyping and host tropism prediction tool PmGT for P. multocida strains according to their whole genome sequences by using machine learning and web 2.0 technologies. By using this tool, the capsular genotypes, LPS genotypes, and MLST genotypes as well as the main VFGs of P. multocida isolates in different host species were determined based on whole genome sequences. The results revealed a closer association between the genotypes and pasteurellosis rather than between genotypes and host species. Finally, we also used PmGT to predict the host species of P. multocida strains with the same capsular: lipopolysaccharide: MLST genotypes. Conclusions: With the advent of high-quality, inexpensive DNA sequencing, this platform represents a more efficient and cost-saving tool for P. multocida diagnosis in both epidemiological studies and clinical settings.


2008 ◽  
Vol E91-C (5) ◽  
pp. 731-735 ◽  
Author(s):  
S. CHO ◽  
I. H. PARK ◽  
J. H. LEE ◽  
J.-G. YUN ◽  
D.-H. KIM ◽  
...  

2014 ◽  
Vol 30 (12) ◽  
pp. 1203-1212 ◽  
Author(s):  
Claudia Montagna ◽  
Elisa De Crignis ◽  
Isabella Bon ◽  
Maria Carla Re ◽  
Ivano Mezzaroma ◽  
...  

Intervirology ◽  
2015 ◽  
Vol 58 (3) ◽  
pp. 155-159 ◽  
Author(s):  
Matthieu Sechet ◽  
Catherine Roussel ◽  
Jean-Luc Schmit ◽  
Carlo Saroufim ◽  
Kamel Ghomari ◽  
...  

Objective: The aim of this study was to evaluate tropism prediction performances of three algorithms [geno2pheno false-positive rate 10% (G2P10), position-specific scoring matrix (PSSM) and a combination of the 11/25 and net charge rules] and to investigate the viral and host factors potentially involved in the X4 or R5 prediction in human immunodeficiency virus-1 (HIV-1) patients. Methods: Viral tropism was determined in 179 HIV-1-infected patients eligible for CCR5 antagonist therapy. HIV-1 RNA or DNA was extracted and amplified for env gp120 sequencing. In parallel, demographic, viral, immunological and clinical determinants were analyzed. Results: According to the G2P10 algorithm, 48 patients harbored X4 or X4R5 virus. The tropism prediction was concordant for 87.7 and 88.2% of samples when comparing G2P10 with PSSM or with a combination of the 11/25 and net charge rules, respectively. X4 prediction was significantly associated with more than 35 amino acids in the V3 domain (p < 0.0001) and loss of an N-linked glycosylation site (p < 0.0001). Of the factors studied, only the nadir CD4 T-cell count was significantly associated with X4 tropism (p = 0.01). Conclusion: We determined that the X4 virus detection is closely linked to the nadir CD4 T-cell count below 100 cells/mm3 that must be taken into account when considering a CCR5 antagonist therapy switch.


1994 ◽  
Vol 34 (2) ◽  
pp. 199-202 ◽  
Author(s):  
Norio Matsumoto ◽  
Tomokazu Matsue ◽  
Isamu Uchida
Keyword(s):  

2013 ◽  
Vol 68 (7) ◽  
pp. 1471-1485 ◽  
Author(s):  
Francisco Díez-Fuertes ◽  
Elena Delgado ◽  
Yolanda Vega ◽  
Aurora Fernández-García ◽  
María Teresa Cuevas ◽  
...  

2019 ◽  
Vol 7 (3) ◽  
pp. 938-950 ◽  
Author(s):  
Chang Yang ◽  
Yun Wang ◽  
Ming Hua Ge ◽  
Yu Jie Fu ◽  
Rui Hao ◽  
...  

Aptamer S30 selected using modified paired cell-based approach can precisely target CD33-positive cancer cells and deliver anticancer drugs.


2018 ◽  
Vol 16 (2) ◽  
pp. 113-120
Author(s):  
Amare Worku Kalu ◽  
Nigus Fikrie Telele ◽  
Shambhu G Aralaguppe ◽  
Solomon Gebre-Selassie ◽  
Daniel Fekade ◽  
...  

Objectives:Genotypic Tropism Testing (GTT) tools are generally developed based on HIV-1 subtype B (HIV-1B) and used for HIV-1C as well but with a large discordance of prediction between different methods. We used an established phenotypic assay for comparison with GTT methods and for the determination of in vitro maraviroc sensitivity of pure R5-tropic and dual-tropic HIV-1C.Methods:Plasma was obtained from 58 HIV-1C infected Ethiopians. Envgp120 was cloned into a luciferase tagged NL4-3 plasmid. Phenotypic tropism was determined by in house method and the V3 sequences were analysed by five GTT methods. In vitro maraviroc sensitivity of R5-tropic and dual-tropic isolates were compared in the TZMbl cell-line.Results:The phenotypes were classified as R5 in 92.4% and dual tropic (R5X4) in 7.6% of 79 clones. The concordance between phenotype and genotype ranged from 64.7% to 84.3% depending on the GTT method. Only 46.9% of the R5 phenotypes were predicted as R5 by all GTT tools while R5X4 phenotypes were predicted as X4 by four methods, but not by Raymond’s method. All six tested phenotypic R5 clones, as well as five of six of dual tropic clones, showed a dose response to maraviroc.Conclusion:There is a high discordance between GTT methods, which underestimates the presence of R5 and overestimates X4 strains compared to a phenotypic assay. Currently available GTT algorithms should be further improved for tropism prediction in HIV-1C. Maraviroc has an in vitro activity against most HIV-1C viruses and could be considered as an alternative regimen in individuals infected with CCR5-tropic HIV-1C viruses.


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