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Article ; Online: Intra-Host Diversity of SARS-Cov-2 Should Not Be Neglected: Case of the State of Victoria, Australia.

Armero, Alix / Berthet, Nicolas / Avarre, Jean-Christophe

2021 Volume 13, Issue 1

Abstract: Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the etiological agent of the current COVID-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near ...

Abstract	Since the identification of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as the etiological agent of the current COVID-19 pandemic, a rapid and massive effort has been made to obtain the genomic sequences of this virus to monitor (in near real time) the phylodynamic and diversity of this new pathogen. However, less attention has been given to the assessment of intra-host diversity. RNA viruses such as SARS-CoV-2 inhabit the host as a population of variants called quasispecies. We studied the quasispecies diversity in four of the main SARS-CoV-2 genes (ORF1a, ORF1b, S and N genes), using a dataset consisting of 210 next-generation sequencing (NGS) samples collected between January and early April of 2020 in the State of Victoria, Australia. We found evidence of quasispecies diversity in 68% of the samples, 76% of which was nonsynonymous variants with a higher density in the spike (S) glycoprotein and ORF1a genes. About one-third of the nonsynonymous intra-host variants were shared among the samples, suggesting host-to-host transmission. Quasispecies diversity changed over time. Phylogenetic analysis showed that some of the intra-host single-nucleotide variants (iSNVs) were restricted to specific lineages, highlighting their potential importance in the epidemiology of this virus. A greater effort must be made to determine the magnitude of the genetic bottleneck during transmission and the epidemiological and/or evolutionary factors that may play a role in the changes in the diversity of quasispecies over time.
MeSH term(s)	Australia ; Base Sequence ; COVID-19/virology ; Coronavirus Nucleocapsid Proteins/genetics ; Genetic Variation ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Polyproteins/genetics ; Quasispecies/genetics ; SARS-CoV-2/genetics ; Sequence Analysis, RNA ; Spike Glycoprotein, Coronavirus/genetics ; Victoria ; Viral Proteins/genetics
Chemical Substances	Coronavirus Nucleocapsid Proteins ; N protein, SARS-CoV ; ORF1ab polyprotein, SARS-CoV-2 ; Polyproteins ; Spike Glycoprotein, Coronavirus ; Viral Proteins ; spike protein, SARS-CoV-2
Language	English
Publishing date	2021-01-19
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v13010133
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Myotis fimbriatus

Armero, Alix / Li, Ruiya / Bienes, Kathrina Mae / Chen, Xing / Li, Jihao / Xu, Shiman / Chen, Yanhua / Hughes, Alice C / Berthet, Nicolas / Wong, Gary

Viruses

2022 Volume 14, Issue 9

Abstract: Significant efforts have been made to characterize viral diversity in bats from China. Many of these studies were prospective and focused mainly ... ...

Abstract	Significant efforts have been made to characterize viral diversity in bats from China. Many of these studies were prospective and focused mainly on
MeSH term(s)	Alphacoronavirus/genetics ; Animals ; China ; Chiroptera ; Coronavirus/genetics ; Ecosystem ; Genome, Viral ; Humans ; Phylogeny ; Prospective Studies ; Virome/genetics
Language	English
Publishing date	2022-08-27
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14091899
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Article: Myotis fimbriatus Virome, a Window to Virus Diversity and Evolution in the Genus Myotis

Armero, Alix / Li, Ruiya / Bienes, Kathrina Mae / Chen, Xing / Li, Jihao / Xu, Shiman / Chen, Yanhua / Hughes, Alice C. / Berthet, Nicolas / Wong, Gary

Viruses. 2022 Aug. 27, v. 14, no. 9

2022

Abstract: Significant efforts have been made to characterize viral diversity in bats from China. Many of these studies were prospective and focused mainly on Rhinolophus bats that could be related to zoonotic events. However, other species of bats that are part of ...

Abstract	Significant efforts have been made to characterize viral diversity in bats from China. Many of these studies were prospective and focused mainly on Rhinolophus bats that could be related to zoonotic events. However, other species of bats that are part of ecosystems identified as virus diversity hotspots have not been studied in-depth. We analyzed the virome of a group of Myotis fimbriatus bats collected from the Yunnan Province during 2020. The virome of M. fimbriatus revealed the presence of families of pathogenic viruses such as Coronavirus, Astrovirus, Mastadenovirus, and Picornavirus, among others. The viral sequences identified in M. fimbriatus were characterized by significant divergence from other known viral sequences of bat origin. Complex phylogenetic landscapes implying a tendency of co-specificity and relationships with viruses from other mammals characterize these groups. The most prevalent and abundant virus in M. fimbriatus individuals was an alphacoronavirus. The genome of this virus shows evidence of recombination and is likely the product of ancestral host-switch. The close phylogenetic and ecological relationship of some species of the Myotis genus in China may have played an important role in the emergence of this alphacoronavirus.
Keywords	Mastadenovirus ; Myotis ; Orthocoronavirinae ; Rhinolophus ; genome ; phylogeny ; viruses ; China
Language	English
Dates of publication	2022-0827
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v14091899
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Article ; Online: Improving transcriptome de novo assembly by using a reference genome of a related species: Translational genomics from oil palm to coconut.

Armero, Alix / Baudouin, Luc / Bocs, Stéphanie / This, Dominique

PloS one

2017 Volume 12, Issue 3, Page(s) e0173300

Abstract: The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and ... ...

Abstract	The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions. This workflow reduces redundancy and fragmentation, two inherent problems of transcriptomic data, while preserving the functional representation of the target species. Our approach was validated in Arabidopsis thaliana using Arabidopsis lyrata and Capsella rubella as references species. This analysis showed the high sensitivity and specificity of our strategy, relatively independent of the reference proteome. The workflow increased the length of proteins products in A. thaliana by 13%, allowing, often, to recover 100% of the protein sequence length. In addition redundancy was reduced by a factor greater than 3. In coconut, the approach generated 29,366 proteins, 1,246 of these proteins deriving from new contigs obtained with the BRANCH software. The coconut proteome presented a functional profile similar to that observed in rice and an important number of metabolic pathways related to secondary metabolism. The new sequences found with BRANCH software were enriched in functions related to biotic stress. Our strategy can be used as a complementary step to de novo transcriptome assembly to get a representative proteome of a target species. The results of the current analysis are available on the website PalmComparomics (http://palm-comparomics.southgreen.fr/).
MeSH term(s)	Arecaceae/genetics ; Cocos/genetics ; Genome, Plant/genetics ; Genomics/methods ; Microsatellite Repeats/genetics ; Transcriptome/genetics
Language	English
Publishing date	2017-03-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0173300
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Article ; Online: Improving transcriptome de novo assembly by using a reference genome of a related species

Alix Armero / Luc Baudouin / Stéphanie Bocs / Dominique This

PLoS ONE, Vol 12, Iss 3, p e

Translational genomics from oil palm to coconut.

2017 Volume 0173300

Abstract	The palms are a family of tropical origin and one of the main constituents of the ecosystems of these regions around the world. The two main species of palm represent different challenges: coconut (Cocos nucifera L.) is a source of multiple goods and services in tropical communities, while oil palm (Elaeis guineensis Jacq) is the main protagonist of the oil market. In this study, we present a workflow that exploits the comparative genomics between a target species (coconut) and a reference species (oil palm) to improve the transcriptomic data, providing a proteome useful to answer functional or evolutionary questions. This workflow reduces redundancy and fragmentation, two inherent problems of transcriptomic data, while preserving the functional representation of the target species. Our approach was validated in Arabidopsis thaliana using Arabidopsis lyrata and Capsella rubella as references species. This analysis showed the high sensitivity and specificity of our strategy, relatively independent of the reference proteome. The workflow increased the length of proteins products in A. thaliana by 13%, allowing, often, to recover 100% of the protein sequence length. In addition redundancy was reduced by a factor greater than 3. In coconut, the approach generated 29,366 proteins, 1,246 of these proteins deriving from new contigs obtained with the BRANCH software. The coconut proteome presented a functional profile similar to that observed in rice and an important number of metabolic pathways related to secondary metabolism. The new sequences found with BRANCH software were enriched in functions related to biotic stress. Our strategy can be used as a complementary step to de novo transcriptome assembly to get a representative proteome of a target species. The results of the current analysis are available on the website PalmComparomics (http://palm-comparomics.southgreen.fr/).
Keywords	Medicine ; R ; Science ; Q
Subject code	580
Language	English
Publishing date	2017-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Reconstructing the genome of the most recent common ancestor of flowering plants.

Murat, Florent / Armero, Alix / Pont, Caroline / Klopp, Christophe / Salse, Jérôme

Nature genetics

2017 Volume 49, Issue 4, Page(s) 490–496

Abstract: We describe here the reconstruction of the genome of the most recent common ancestor (MRCA) of modern monocots and eudicots, accounting for 95% of extant angiosperms, with its potential repertoire of 22,899 ancestral genes conserved in present-day crops. ...

Abstract	We describe here the reconstruction of the genome of the most recent common ancestor (MRCA) of modern monocots and eudicots, accounting for 95% of extant angiosperms, with its potential repertoire of 22,899 ancestral genes conserved in present-day crops. The MRCA provides a starting point for deciphering the reticulated evolutionary plasticity between species (rapidly versus slowly evolving lineages), subgenomes (pre- versus post-duplication blocks), genomic compartments (stable versus labile loci), genes (ancestral versus species-specific genes) and functions (gained versus lost ontologies), the key mutational forces driving the success of polyploidy in crops. The estimation of the timing of angiosperm evolution, based on MRCA genes, suggested that this group emerged 214 million years ago during the late Triassic era, before the oldest recorded fossil. Finally, the MRCA constitutes a unique resource for scientists to dissect major agronomic traits in translational genomics studies extending from model species to crops.
MeSH term(s)	Evolution, Molecular ; Flowers/genetics ; Genome, Plant/genetics ; Genomics ; Magnoliopsida/genetics ; Mutation/genetics ; Phylogeny
Language	English
Publishing date	2017-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	1108734-1
ISSN	1546-1718 ; 1061-4036
ISSN (online)	1546-1718
ISSN	1061-4036
DOI	10.1038/ng.3813
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Article ; Online: Characterization of HIV-1 diversity in various compartments at the time of primary infection by ultradeep sequencing.

Gaube, Géraldine / Armero, Alix / Salmona, Maud / Néré, Marie-Laure / Mahjoub, Nadia / Lascoux-Combe, Caroline / Gabassi, Audrey / Gallien, Sébastien / Amara, Ali / Molina, Jean Michel / Delaugerre, Constance / Chaix, Marie-Laure

Scientific reports

2020 Volume 10, Issue 1, Page(s) 2409

Abstract: We used next-generation sequencing to evaluate the quantity and genetic diversity of the HIV envelope gene in various compartments in eight patients with acute infection. Plasma (PL) and seminal fluid (SF) were available for all patients, whole blood (WB) ...

Abstract	We used next-generation sequencing to evaluate the quantity and genetic diversity of the HIV envelope gene in various compartments in eight patients with acute infection. Plasma (PL) and seminal fluid (SF) were available for all patients, whole blood (WB) for seven, non-spermatozoid cells (NSC) for four, and saliva (SAL) for three. Median HIV-1 RNA was 6.2 log
MeSH term(s)	Adult ; Genetic Variation ; HIV Infections/virology ; HIV-1/genetics ; Humans ; Male ; Phylogeny ; RNA, Viral/analysis ; RNA, Viral/genetics ; env Gene Products, Human Immunodeficiency Virus/genetics
Chemical Substances	RNA, Viral ; env Gene Products, Human Immunodeficiency Virus
Language	English
Publishing date	2020-02-12
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-020-59234-6
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Article ; Online: Transcriptome data from three endemic Myrtaceae species from New Caledonia displaying contrasting responses to myrtle rust (

Soewarto, Julia / Hamelin, Chantal / Bocs, Stéphanie / Mournet, Pierre / Vignes, Hélène / Berger, Angélique / Armero, Alix / Martin, Guillaume / Dereeper, Alexis / Sarah, Gautier / Carriconde, Fabian / Maggia, Laurent

Data in brief

2019 Volume 22, Page(s) 794–811

Abstract: The myrtle rust disease, caused by the ... ...

Abstract	The myrtle rust disease, caused by the fungus
Language	English
Publishing date	2019-01-03
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2786545-9
ISSN	2352-3409 ; 2352-3409
ISSN (online)	2352-3409
ISSN	2352-3409
DOI	10.1016/j.dib.2018.12.080
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Article ; Online: Effect of brincidofovir on adenovirus and A549 cells transcriptome profiles.

Salmona, Maud / Feghoul, Linda / Mercier-Delarue, Séverine / Diaz, Elise / Splitberger, Marion / Armero, Alix / Dalle, Jean-Hugues / Dutrieux, Jacques / LeGoff, Jérôme

Antiviral research

2020 Volume 182, Page(s) 104872

Abstract: Objectives: Human adenovirus (HAdV) infections are associated with a high morbidity and mortality in transplant patients requiring the use of antiviral treatments. Brincidofovir (BCV), a cytidine analog, inhibits HAdV replication through viral DNA ... ...

Abstract	Objectives: Human adenovirus (HAdV) infections are associated with a high morbidity and mortality in transplant patients requiring the use of antiviral treatments. Brincidofovir (BCV), a cytidine analog, inhibits HAdV replication through viral DNA elongation termination and likely through other mechanisms. To elucidate if BCV regulates cellular antiviral pathways, we analyzed its impact on HAdV-infected and non-HAdV-infected lung epithelial cells. Methods: We assessed the cellular and viral transcriptome of A549 cells infected and non-infected with HAdV C5 and treated or non-treated with BCV by RNAseq after 72 h. Results: BCV treatment of HAdV infected cells resulted in a profound decrease of viral transcription associated with a relative overexpression of the early genes E1A and E4 and of the late gene L1. BCV had also a profound impact on A549 cells' transcriptome. Ontologic analysis revealed an effect of BCV on several pathways known to interact with adenovirus replication as mTor signalling and Wnt pathways. A549 cells treated with BCV demonstrated a significant inhibition of the biological function of "viral replication" including 25 dysregulated genes involved in inflammation pathways. Conclusion: We demonstrated that BCV alters viral gene expression and promotes the expression of antiviral cellular pathways in A549 cells. These results provide new insights how to interfere with cellular pathways to control HAdV infections.
Language	English
Publishing date	2020-08-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	306628-9
ISSN	1872-9096 ; 0166-3542
ISSN (online)	1872-9096
ISSN	0166-3542
DOI	10.1016/j.antiviral.2020.104872
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Article ; Online: Deep sequencing analysis of M184V/I mutation at the switch and at the time of virological failure of boosted protease inhibitor plus lamivudine or boosted protease inhibitor maintenance strategy (substudy of the ANRS-MOBIDIP trial).

Delaugerre, Constance / Nere, Marie-Laure / Eymard-Duvernay, Sabrina / Armero, Alix / Ciaffi, Laura / Koulla-Shiro, Sinata / Sawadogo, Adrien / Ngom Gueye, Ndaye Fatou / Ndour, Cheik Tidiane / Mpoudi Ngolle, Mireille / Amara, Ali / Chaix, Marie-Laure / Reynes, Jacques

The Journal of antimicrobial chemotherapy

2020 Volume 76, Issue 5, Page(s) 1286–1293

Abstract: Background: The ANRS12286/MOBIDIP trial showed that boosted protease inhibitor (bPI) plus lamivudine dual therapy was superior to bPI monotherapy as maintenance treatment in subjects with a history of M184V mutation.: Objectives: We aimed to deep ... ...

Abstract	Background: The ANRS12286/MOBIDIP trial showed that boosted protease inhibitor (bPI) plus lamivudine dual therapy was superior to bPI monotherapy as maintenance treatment in subjects with a history of M184V mutation. Objectives: We aimed to deep analyse the detection of M184V/I variants at time of switch and at the time of virological failure (VF). Methods: Ultra-deep sequencing (UDS) was performed on proviral HIV-DNA at inclusion among 265 patients enrolled in the ANRS 12026/MOBIDIP trial, and on plasma from 31 patients experiencing VF. The proportion of M184V/I variants was described and the association between the M184V/I mutation at 1% of threshold and VF was explored with logistic regression models. Results: M184V and I mutations were detected in HIV-DNA for 173/252 (69%) and 31/252 (12%) of participants, respectively. Longer duration of first-line treatment, higher plasma viral load at first-line treatment failure and higher baseline HIV-DNA load were associated with the archived M184V. M184I mutation was always associated with a STOP codon, suggesting defective virus. The 48 week estimated probability of remaining free from VF was comparable with or without the M184V/I mutation for dual therapy. At failure, M184V and major PI mutations were detected in 1/17 and 5/15 patients in the bPI arm and in 2/2 and 0/3 in the bPI+lamivudine arm, respectively. Conclusions: Using UDS evidenced that archiving of M184V in HIV-DNA is heterogeneous despite past historical M184V in 96% of cases. The antiviral efficacy of lamivudine-based dual therapy regimens is mainly due to the residual lamivudine activity.
MeSH term(s)	Anti-HIV Agents/pharmacology ; Anti-HIV Agents/therapeutic use ; Drug Resistance, Viral ; HIV Infections/drug therapy ; HIV-1/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Lamivudine/therapeutic use ; Mutation ; Protease Inhibitors/therapeutic use ; Viral Load
Chemical Substances	Anti-HIV Agents ; Protease Inhibitors ; Lamivudine (2T8Q726O95)
Language	English
Publishing date	2020-12-09
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	191709-2
ISSN	1460-2091 ; 0305-7453
ISSN (online)	1460-2091
ISSN	0305-7453
DOI	10.1093/jac/dkab002
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