A Session Subtyping Tool

2021 ◽  
pp. 90-105
Author(s):  
Lorenzo Bacchiani ◽  
Mario Bravetti ◽  
Julien Lange ◽  
Gianluigi Zavattaro
Keyword(s):  
Subtyping Tool

scholarly journals Subtype Characterization and Zoonotic Potential of Cryptosporidium felis in Cats in Guangdong and Shanghai, China

Pathogens ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 89
Author(s):  
Jiayu Li ◽  
Fuxian Yang ◽  
Ruobing Liang ◽  
Sheng Guo ◽  
Yaqiong Guo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Analysis ◽  
Genetic Characterization ◽  
Zoonotic Potential ◽  
Common Occurrence ◽  
High Genetic Diversity ◽  
Gp60 Gene ◽  
The Common ◽  
Subtyping Tool

Cryptosporidiumfelis is an important cause of feline and human cryptosporidiosis. However, the transmission of this pathogen between humans and cats remains controversial, partially due to a lack of genetic characterization of isolates from cats. The present study was conducted to examine the genetic diversity of C. felis in cats in China and to assess their potential zoonotic transmission. A newly developed subtyping tool based on a sequence analysis of the 60-kDa glycoprotein (gp60) gene was employed to identify the subtypes of 30 cat-derived C. felis isolates from Guangdong and Shanghai. Altogether, 20 C. felis isolates were successfully subtyped. The results of the sequence alignment showed a high genetic diversity, with 13 novel subtypes and 2 known subtypes of the XIXa subtype family being identified. The known subtypes were previously detected in humans, while some of the subtypes formed well-supported subclusters with human-derived subtypes from other countries in a phylogenetic analysis of the gp60 sequences. The results of this study confirmed the high genetic diversity of the XIXa subtype family of C. felis. The common occurrence of this subtype family in both humans and cats suggests that there could be cross-species transmission of C. felis.

scholarly journals Pervasive and non-random recombination in near full-length HIV genomes from Uganda

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Heather E Grant ◽  
Emma B Hodcroft ◽  
Deogratius Ssemwanga ◽  
John M Kitayimbwa ◽  
Gonzalo Yebra ◽  
...  
Keyword(s):  
Generalized Linear Model ◽  
Research Unit ◽  
Full Length ◽  
Significant Feature ◽  
Limited Evidence ◽  
Accessory Gene ◽  
Genome Sequences ◽  
Feature Characteristic ◽  
Breakpoint Location ◽  
Subtyping Tool

Abstract Recombination is an important feature of HIV evolution, occurring both within and between the major branches of diversity (subtypes). The Ugandan epidemic is primarily composed of two subtypes, A1 and D, that have been co-circulating for 50 years, frequently recombining in dually infected patients. Here, we investigate the frequency of recombinants in this population and the location of breakpoints along the genome. As part of the PANGEA-HIV consortium, 1,472 consensus genome sequences over 5 kb have been obtained from 1,857 samples collected by the MRC/UVRI & LSHTM Research unit in Uganda, 465 (31.6 per cent) of which were near full-length sequences (>8 kb). Using the subtyping tool SCUEAL, we find that of the near full-length dataset, 233 (50.1 per cent) genomes contained only one subtype, 30.8 per cent A1 (n = 143), 17.6 per cent D (n = 82), and 1.7 per cent C (n = 8), while 49.9 per cent (n = 232) contained more than one subtype (including A1/D (n = 164), A1/C (n = 13), C/D (n = 9); A1/C/D (n = 13), and 33 complex types). K-means clustering of the recombinant A1/D genomes revealed a section of envelope (C2gp120-TMgp41) is often inherited intact, whilst a generalized linear model was used to demonstrate significantly fewer breakpoints in the gag–pol and envelope C2-TM regions compared with accessory gene regions. Despite similar recombination patterns in many recombinants, no clearly supported circulating recombinant form (CRF) was found, there was limited evidence of the transmission of breakpoints, and the vast majority (153/164; 93 per cent) of the A1/D recombinants appear to be unique recombinant forms. Thus, recombination is pervasive with clear biases in breakpoint location, but CRFs are not a significant feature, characteristic of a complex, and diverse epidemic.

scholarly journals Development of a Subtyping Tool for Zoonotic Pathogen Cryptosporidium Canis

2020 ◽  
Author(s):  
Wen Jiang ◽  
Dawn M. Roellig ◽  
Yaqiong Guo ◽  
Na Li ◽  
Yaoyu Feng ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Zoonotic Transmission ◽  
Similar Distribution ◽  
Transmission Characteristics ◽  
Nucleotide Level ◽  
Zoonotic Pathogen ◽  
Subtyping Tool

Cryptosporidium canis is an important cause of cryptosporidiosis in canines and humans. Studies of the transmission characteristics of C. canis are currently hampered by lack of suitable subtyping tools. In this study, we conducted a genomic survey of the pathogen and developed a subtyping tool targeting the partial 60-kDa glycoprotein (gp60) gene. Seventy-six isolates previously identified as C. canis were analyzed using the new subtyping tool. Amplicons of expected size were obtained from 49 isolates, and phylogenetic analysis identified 10 subtypes clustered in five distinct groups (XXa–XXe). The largest group XXa contained 43 isolates from four subtypes that differed slightly from each other at the nucleotide level, while groups XXb–XXe contain one to three isolates each. The similar distribution of subtypes in humans and canines suggests that zoonotic transmission might play an important role in the epidemiology of C. canis. In addition, a suspected zoonotic transmission of C. canis between dogs and humans in a household was confirmed using the subtyping tool. The subtyping tool and data generated in this study might improve our understanding of the transmission of this zoonotic pathogen.

scholarly journals Covidex: an ultrafast and accurate tool for virus subtyping

2020 ◽  
Author(s):  
Marco Cacciabue ◽  
Pablo Aguilera ◽  
María Inés Gismondi ◽  
Oscar Taboga
Keyword(s):  
Open Source ◽  
Web Application ◽  
Classification Models ◽  
Genome Sequences ◽  
Link Type ◽  
Shiny App ◽  
Cross Platform ◽  
Model Generator ◽  
Free Machine ◽  
Subtyping Tool

SummaryCovidex is an open-source, alignment-free machine learning subtyping tool for viral species. It is a shiny app that allows a fast and accurate classification in pre-defined clusters for SARS-CoV-2 and FMDV genome sequences. The user can also build its own classification models with the Covidex model generator.AvailabilityCovidex is open-source, cross-platform compatible, and is available under the terms of the GNU General Public License v3 (http://www.gnu.org/licenses/gpl.txt). Covidex is available via SourceForge https://sourceforge.net/projects/covidex or the web application https://cacciabue.shinyapps.io/shiny2/[email protected]; [email protected]

scholarly journals Development and Application of a gp60-Based Subtyping Tool for Cryptosporidium bovis

2021 ◽  
Vol 9 (10) ◽  
pp. 2067
Author(s):  
Weijian Wang ◽  
Muchun Wan ◽  
Fang Yang ◽  
Na Li ◽  
Lihua Xiao ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Genetic Recombination ◽  
Transmission Characteristics ◽  
Typical Structure ◽  
Sequence Patterns ◽  
Geographic Differences ◽  
Sequence Types ◽  
Sequence Characteristics ◽  
Multiple Episodes ◽  
Subtyping Tool

Cryptosporidium bovis is a common enteric pathogen in bovine animals. The research on transmission characteristics of the pathogen is hampered by the lack of subtyping tools. In this study, we retrieve the nucleotide sequence of the 60 kDa glycoprotein (GP60) from the whole genome sequences of C. bovis we obtained previously and analyze its sequence characteristics. Despite a typical structure of the GP60 protein, the GP60 of C. bovis had only 19.3–45.3% sequence identity to those of other Cryptosporidium species. On the basis of the gene sequence, a subtype typing tool was developed for C. bovis and used in the analysis of 486 C. bovis samples from dairy cattle, yaks, beef cattle, and water buffalos from China. Sixty-eight sequence types were identified from 260 subtyped samples, forming six subtype families, namely XXVIa to XXVIf. The mosaic sequence patterns among subtype families and the 121 potential recombination events identified among the sequences both suggest the occurrence of genetic recombination at the locus. No obvious host adaptation and geographic differences in the distribution of subtype families were observed. Most farms with more extensive sampling had more than one subtype family, and the dominant subtype families on a farm appeared to differ between pre- and post-weaned calves, indicating the likely occurrence of multiple episodes of C. bovis infections. There was an association between XXVId infection and occurrence of moderate diarrhea in dairy cattle. The subtyping tool developed and the data generated in the study might improve our knowledge of the genetic diversity and transmission of C. bovis.

scholarly journals TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer

2012 ◽  
Vol 11 ◽  
pp. CIN.S9983 ◽  
Author(s):  
Xi Chen ◽  
Jiang Li ◽  
William H. Gray ◽  
Brian D. Lehmann ◽  
Joshua A. Bauer ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Triple Negative Breast Cancer ◽  
Triple Negative ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Genomic Research ◽  
Data Matrix ◽  
Cancer Data ◽  
Subtyping Tool

Motivation Triple-negative breast cancer (TNBC) is a heterogeneous breast cancer group, and identification of molecular subtypes is essential for understanding the biological characteristics and clinical behaviors of TNBC as well as for developing personalized treatments. Based on 3,247 gene expression profiles from 21 breast cancer data sets, we discovered six TNBC subtypes from 587 TNBC samples with unique gene expression patterns and ontologies. Cell line models representing each of the TNBC subtypes also displayed different sensitivities to targeted therapeutic agents. Classification of TNBC into subtypes will advance further genomic research and clinical applications. Result We developed a web-based subtyping tool TNBCtype for candidate TNBC samples using our gene expression meta data and classification methods. Given a gene expression data matrix, this tool will display for each candidate sample the predicted subtype, the corresponding correlation coefficient, and the permutation P-value. We offer a user-friendly web interface to predict the subtypes for new TNBC samples that may facilitate diagnostics, biomarker selection, drug discovery, and the more tailored treatment of breast cancer.

Comparative performance of the REGA subtyping tool version 2 versus version 1

2010 ◽  
Vol 10 (3) ◽  
pp. 380-385 ◽  
Author(s):  
Ana B. Abecasis ◽  
Yunpeng Wang ◽  
Pieter Libin ◽  
Stijn Imbrechts ◽  
Tulio de Oliveira ◽  
...  
Keyword(s):  
Comparative Performance ◽  
Subtyping Tool

scholarly journals Subtyping Cryptosporidium xiaoi, a Common Pathogen in Sheep and Goats

Pathogens ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 800
Author(s):  
Yingying Fan ◽  
Xitong Huang ◽  
Sheng Guo ◽  
Fang Yang ◽  
Xin Yang ◽  
...  
Keyword(s):  
Genetic Recombination ◽  
Furin Cleavage ◽  
Sheep And Goats ◽  
Gp60 Gene ◽  
Furin Cleavage Site ◽  
Glycosylation Sites ◽  
Sequence Patterns ◽  
Established Species ◽  
Sequence Types ◽  
Subtyping Tool

Cryptosporidiosis is a significant cause of diarrhea in sheep and goats. Among the over 40 established species of Cryptosporidium, Cryptosporidium xiaoi is one of the dominant species infecting ovine and caprine animals. The lack of subtyping tools makes it impossible to examine the transmission of this pathogen. In the present study, we identified and characterized the 60-kDa glycoprotein (gp60) gene by sequencing the genome of C. xiaoi. The GP60 protein of C. xiaoi had a signal peptide, a furin cleavage site of RSRR, a glycosylphosphatidylinositol anchor, and over 100 O-glycosylation sites. Based on the gp60 sequence, a subtyping tool was developed and used in characterizing C. xiaoi in 355 positive samples from sheep and goats in China. A high sequence heterogeneity was observed in the gp60 gene, with 94 sequence types in 12 subtype families, namely XXIIIa to XXIIIl. Co-infections with multiple subtypes were common in these animals, suggesting that genetic recombination might be responsible for the high diversity within C. xiaoi. This was supported by the mosaic sequence patterns among the subtype families. In addition, a potential host adaptation was identified within this species, reflected by the exclusive occurrence of XXIIIa, XXIIIc, XXIIIg, and XXIIIj in goats. This subtyping tool should be useful in studies of the genetic diversity and transmission dynamics of C. xiaoi.

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