LIVIVO - Search results -

Search results

Result 1 - 10 of total 58

Search options

Article ; Online: The emergence and circulation of human immunodeficiency virus (HIV)-1 subtype C.

Li, Xingguang / Tamim, Sana / Trovão, Nídia S

2024 Volume 73, Issue 5

Abstract: Introduction. ...

Abstract	Introduction.
MeSH term(s)	HIV-1/genetics ; HIV-1/classification ; HIV-1/isolation & purification ; Humans ; HIV Infections/virology ; HIV Infections/epidemiology ; HIV Infections/transmission ; Phylogeny ; Evolution, Molecular
Language	English
Publishing date	2024-05-16
Publishing country	England
Document type	Journal Article
ZDB-ID	218356-0
ISSN	1473-5644 ; 0022-2615
ISSN (online)	1473-5644
ISSN	0022-2615
DOI	10.1099/jmm.0.001827
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 634: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: When Pigs Fly: Pandemic influenza enters the 21st century.

Trovão, Nídia S / Nelson, Martha I

PLoS pathogens

2020 Volume 16, Issue 3, Page(s) e1008259

MeSH term(s)	Animals ; Birds ; Evolution, Molecular ; History, 20th Century ; History, 21st Century ; Humans ; Influenza A virus/genetics ; Influenza A virus/physiology ; Influenza in Birds/epidemiology ; Influenza in Birds/history ; Influenza in Birds/transmission ; Influenza in Birds/virology ; Influenza, Human/epidemiology ; Influenza, Human/history ; Influenza, Human/transmission ; Influenza, Human/virology ; Pandemics/history ; Swine ; Swine Diseases/epidemiology ; Swine Diseases/history ; Swine Diseases/transmission ; Swine Diseases/virology
Language	English
Publishing date	2020-03-19
Publishing country	United States
Document type	Historical Article ; Journal Article ; Research Support, N.I.H., Extramural ; Review
ZDB-ID	2205412-1
ISSN	1553-7374 ; 1553-7374
ISSN (online)	1553-7374
ISSN	1553-7374
DOI	10.1371/journal.ppat.1008259
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Insect-specific viruses in the Parvoviridae family: Genetic lineage characterization and spatiotemporal dynamics of the recently established Brevihamaparvovirus genus.

Morais, Paulo / Trovão, Nídia S / Abecasis, Ana B / Parreira, Ricardo

Virus research

2022 Volume 313, Page(s) 198728

Abstract: The analysis of the viruses allocated to the recently established Brevihamaparvovirus genus (Parvoviridae family), which includes all previously known brevidensoviruses, has not yet been carried out on an extensive basis. As a result, no detailed genetic ...

Abstract	The analysis of the viruses allocated to the recently established Brevihamaparvovirus genus (Parvoviridae family), which includes all previously known brevidensoviruses, has not yet been carried out on an extensive basis. As a result, no detailed genetic lineage characterization has ever been performed for this group of insect-specific viruses. Using a wide range of molecular tools, we have explored this taxon by calculating Shannon entropy values, intra- and inter-taxon genetic distances, analysed sequence polymorphisms, and evaluated selective pressures acting on the viral genome. While the calculated Brevihamaparvovirus mutation rates were within the range of those of other parvoviruses, their genomes look to be under strong purifying selection, and are also characterized by low diversity and entropy. Furthermore, even though recombination events are quite common among parvoviruses, no evidence of recombination (either intra or intergenic) was found in the Brevihamaparvoviruses sequences analyzed. An extended taxonomic analysis and reevaluation of existing Brevihamaparvoviruses sequences, many still unclassified, was performed using cut-off values defining NS1 identity between viral sequences from the Parvovirus family. Two existing genetic lineages, Dipteran Brevihamaparvovirus 1 and Dipteran Brevihamaparvovirus 2, were rearranged and the creation of a new one, Dipteran Brevihamaparvovirus 3, was suggested. Finally, despite the uncertainties associated with both the time estimates of the most recent common ancestors, which could span from twenty thousand years before the current era to way earlier (in the last century), and the dispersal routes proposed for Brevihamaparvoviruses sequences by phylodynamic reconstruction, the analyses here presented could help define how future studies should be conducted as more isolates continue to be identified in the future, and contribute to eliminating possible analytical biases.
MeSH term(s)	Animals ; Genome, Viral ; Insect Viruses/genetics ; Insecta ; Parvoviridae/genetics ; Parvoviridae Infections ; Parvovirus/genetics ; Phylogeny
Language	English
Publishing date	2022-03-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2022.198728
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1965: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Readdressing the genetic diversity and taxonomy of the Mesoniviridae family, as well as its relationships with other nidoviruses and putative mesonivirus-like viral sequences.

Morais, Paulo / Trovão, Nídia S / Abecasis, Ana B / Parreira, Ricardo

Virus research

2022 Volume 313, Page(s) 198727

Abstract: Research on the recently established Mesoniviridae family (Order Nidovirales), RNA genome insect-specific viruses, has been steadily growing in the last decade. However, after the last detailed phylogenetic characterization of mesoniviruses in 2014, ... ...

Abstract	Research on the recently established Mesoniviridae family (Order Nidovirales), RNA genome insect-specific viruses, has been steadily growing in the last decade. However, after the last detailed phylogenetic characterization of mesoniviruses in 2014, numerous new sequences, even in organisms other than mosquitos, have been identified and characterized. In this study, we analyzed nucleotide and protein sequences of mesoniviruses with a wide range of molecular tools including genetic distance, Shannon entropy, selective pressure analysis, polymorphism identification, principal coordinate analysis, likelihood mapping and phylodynamic reconstruction. We also sought to revaluate new mesoniviruses sequence positions within the family, proposing a taxonomic revision. The different sub-lineages of mosquito mesoniviruses sequences presented low sequence diversity and entropy, with incongruences to the existing taxonomy being found after an extensive phylogenetic characterization. High sequence discrepancy and differences in genome organization were found between mosquito mesoniviruses and other mesoniviruses, so their future classification, as other meso-like viruses that are found in other organisms, should be approached with caution. No evidence of frequent recombination was found, and mesonivirus genomes seem to evolve under strong purifying selection. Insufficient data by root-to-tip analysis did not yet allow for an adequate phylogeographic reconstruction.
MeSH term(s)	Amino Acid Sequence ; Animals ; Culicidae ; Genetic Variation ; Genome, Viral ; Nidovirales/genetics ; Phylogeny
Language	English
Publishing date	2022-03-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2022.198727
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1965: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article: Optimizing ancestral trait reconstruction of large HIV Subtype C datasets through multiple-trait subsampling.

Li, Xingguang / Trovão, Nídia S / Wertheim, Joel O / Baele, Guy / de Bernardi Schneider, Adriano

Virus evolution

2023 Volume 9, Issue 2, Page(s) vead069

Abstract: Large datasets along with sampling bias represent a challenge for phylodynamic reconstructions, particularly when the study data are obtained from various heterogeneous sources and/or through convenience sampling. In this study, we evaluate the presence ... ...

Abstract	Large datasets along with sampling bias represent a challenge for phylodynamic reconstructions, particularly when the study data are obtained from various heterogeneous sources and/or through convenience sampling. In this study, we evaluate the presence of unbalanced sampled distribution by collection date, location, and risk group of human immunodeficiency virus Type 1 Subtype C using a comprehensive subsampling strategy and assess their impact on the reconstruction of the viral spatial and risk group dynamics using phylogenetic comparative methods. Our study shows that a most suitable dataset for ancestral trait reconstruction can be obtained through subsampling by all available traits, particularly using multigene datasets. We also demonstrate that sampling bias is inflated when considerable information for a given trait is unavailable or of poor quality, as we observed for the trait risk group. In conclusion, we suggest that, even if traits are not well recorded, including them deliberately optimizes the representativeness of the original dataset rather than completely excluding them. Therefore, we advise the inclusion of as many traits as possible with the aid of subsampling approaches in order to optimize the dataset for phylodynamic analysis while reducing the computational burden. This will benefit research communities investigating the evolutionary and spatio-temporal patterns of infectious diseases.
Language	English
Publishing date	2023-11-22
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/vead069
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Comparative evolution of influenza A virus H1 and H3 head and stalk domains across host species.

Trovão, Nidia S / Khan, Sairah M / Lemey, Philippe / Nelson, Martha I / Cherry, Joshua L

mBio

2023 Volume 15, Issue 1, Page(s) e0264923

Abstract: Importance: For decades, researchers have studied the rapid evolution of influenza A viruses for vaccine design and as a useful model system for the study of host/parasite evolution. By performing an exhaustive analysis of hemagglutinin protein (HA) ... ...

Abstract	Importance: For decades, researchers have studied the rapid evolution of influenza A viruses for vaccine design and as a useful model system for the study of host/parasite evolution. By performing an exhaustive analysis of hemagglutinin protein (HA) sequences from 49 lineages independently evolving in birds, swine, canines, equines, and humans over the last century, our work uncovers surprising features of HA evolution. In particular, the canine H3 stalk, unlike human H3 and H1 stalk domains, is not evolving slowly, suggesting that evolution in the stalk domain is not universally constrained across all host species. Therefore, a broader multi-host perspective on HA evolution may be useful during the evaluation and design of stalk-targeted vaccine candidates.
MeSH term(s)	Animals ; Dogs ; Humans ; Swine ; Horses ; Influenza A virus/genetics ; Hemagglutinin Glycoproteins, Influenza Virus ; Hemagglutinins ; Host Specificity ; Vaccines ; Influenza, Human ; Influenza Vaccines ; Antibodies, Viral ; Orthomyxoviridae Infections
Chemical Substances	Hemagglutinin Glycoproteins, Influenza Virus ; Hemagglutinins ; Vaccines ; Influenza Vaccines ; Antibodies, Viral
Language	English
Publishing date	2023-12-11
Publishing country	United States
Document type	Journal Article
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.02649-23
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article: Readdressing the genetic diversity and taxonomy of the Mesoniviridae family, as well as its relationships with other nidoviruses and putative mesonivirus-like viral sequences

Morais, Paulo / Trovão, Nídia S. / Abecasis, Ana B. / Parreira, Ricardo

Virus research. 2022 May, v. 313

2022

Abstract	Research on the recently established Mesoniviridae family (Order Nidovirales), RNA genome insect-specific viruses, has been steadily growing in the last decade. However, after the last detailed phylogenetic characterization of mesoniviruses in 2014, numerous new sequences, even in organisms other than mosquitos, have been identified and characterized. In this study, we analyzed nucleotide and protein sequences of mesoniviruses with a wide range of molecular tools including genetic distance, Shannon entropy, selective pressure analysis, polymorphism identification, principal coordinate analysis, likelihood mapping and phylodynamic reconstruction. We also sought to revaluate new mesoniviruses sequence positions within the family, proposing a taxonomic revision. The different sub-lineages of mosquito mesoniviruses sequences presented low sequence diversity and entropy, with incongruences to the existing taxonomy being found after an extensive phylogenetic characterization. High sequence discrepancy and differences in genome organization were found between mosquito mesoniviruses and other mesoniviruses, so their future classification, as other meso-like viruses that are found in other organisms, should be approached with caution. No evidence of frequent recombination was found, and mesonivirus genomes seem to evolve under strong purifying selection. Insufficient data by root-to-tip analysis did not yet allow for an adequate phylogeographic reconstruction.
Keywords	Culicidae ; Nidovirales ; RNA ; entropy ; genetic distance ; genetic variation ; genome ; multidimensional scaling ; phylogeny ; phylogeography ; research ; sequence diversity ; taxonomic revisions ; viruses
Language	English
Dates of publication	2022-05
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2022.198727
Database	NAL-Catalogue (AGRICOLA)

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1965: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article: Insect-specific viruses in the Parvoviridae family: Genetic lineage characterization and spatiotemporal dynamics of the recently established Brevihamaparvovirus genus

Morais, Paulo / Trovão, Nídia S. / Abecasis, Ana B. / Parreira, Ricardo

Virus research. 2022 May, v. 313

2022

Abstract	The analysis of the viruses allocated to the recently established Brevihamaparvovirus genus (Parvoviridae family), which includes all previously known brevidensoviruses, has not yet been carried out on an extensive basis. As a result, no detailed genetic lineage characterization has ever been performed for this group of insect-specific viruses. Using a wide range of molecular tools, we have explored this taxon by calculating Shannon entropy values, intra- and inter-taxon genetic distances, analysed sequence polymorphisms, and evaluated selective pressures acting on the viral genome. While the calculated Brevihamaparvovirus mutation rates were within the range of those of other parvoviruses, their genomes look to be under strong purifying selection, and are also characterized by low diversity and entropy. Furthermore, even though recombination events are quite common among parvoviruses, no evidence of recombination (either intra or intergenic) was found in the Brevihamaparvoviruses sequences analyzed. An extended taxonomic analysis and reevaluation of existing Brevihamaparvoviruses sequences, many still unclassified, was performed using cut-off values defining NS1 identity between viral sequences from the Parvovirus family. Two existing genetic lineages, Dipteran Brevihamaparvovirus 1 and Dipteran Brevihamaparvovirus 2, were rearranged and the creation of a new one, Dipteran Brevihamaparvovirus 3, was suggested. Finally, despite the uncertainties associated with both the time estimates of the most recent common ancestors, which could span from twenty thousand years before the current era to way earlier (in the last century), and the dispersal routes proposed for Brevihamaparvoviruses sequences by phylodynamic reconstruction, the analyses here presented could help define how future studies should be conducted as more isolates continue to be identified in the future, and contribute to eliminating possible analytical biases.
Keywords	Diptera ; Protoparvovirus ; entropy ; mutation ; research ; viral genome ; viruses
Language	English
Dates of publication	2022-05
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2022.198728
Database	NAL-Catalogue (AGRICOLA)

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1965: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article ; Online: Genetic lineage characterization and spatiotemporal dynamics of classical insect-specific flaviviruses: outcomes and limitations.

Morais, Paulo / Trovão, Nídia S / Abecasis, Ana B / Parreira, Ricardo

Virus research

2021 Volume 303, Page(s) 198507

Abstract: The genus Flavivirus incorporates bona fide arboviruses, as well as others viruses with restricted replication in insect cells. Among the latter, a large monophyletic cluster of viruses, known as cISF (classical insect-specific flaviviruses), has been ... ...

Abstract	The genus Flavivirus incorporates bona fide arboviruses, as well as others viruses with restricted replication in insect cells. Among the latter, a large monophyletic cluster of viruses, known as cISF (classical insect-specific flaviviruses), has been sampled in many species of mosquitoes collected over a large geographic range. In this study, we investigated nucleotide and protein sequences with a suite of molecular characterization approaches including genetic distance, Shannon entropy, selective pressure analysis, polymorphism identification, principal coordinate analysis, likelihood mapping, phylodynamic reconstruction, and spatiotemporal dispersal, to further characterize this diverse group of insect-viruses. The different lineages and sub-lineages of viral sequences presented low sequence diversity and entropy (though some displayed lineage-specific polymorphisms), did not show evidence of frequent recombination and evolved under strong purifying selection. Moreover, the reconstruction of the evolutionary history and spatiotemporal dispersal was highly impacted by overall low signals of sequence divergence throughout time but suggested that cISF distribution in space and time is dynamic and may be dependent on human activities, including commercial trading and traveling.
MeSH term(s)	Animals ; Arboviruses/genetics ; Culicidae ; Flavivirus/genetics ; Insecta ; Phylogeny
Language	English
Publishing date	2021-07-13
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2021.198507
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

In stock of ZB MED Cologne/Königswinter

Zs.A 1965: Show issues

Location:
Je nach Verfügbarkeit (siehe Angabe bei Bestand)
bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

Order via subito

Details ▾

Article: The emergence and transmission dynamics of HIV-1 CRF07_BC in Mainland China.

Li, Xingguang / Li, Yanping / Liu, Haizhou / Trovão, Nídia S / Foley, Brian T

Virus evolution

2022 Volume 8, Issue 1, Page(s) veac014

Abstract: A total of 1155 ... ...

Abstract	A total of 1155 partial
Language	English
Publishing date	2022-02-17
Publishing country	England
Document type	Journal Article
ZDB-ID	2818949-8
ISSN	2057-1577
ISSN	2057-1577
DOI	10.1093/ve/veac014
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

To top

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

Full text online

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito