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Article ; Online: Do humans have replication-competent endogenous retroviruses?

Tristem Michael / Belshaw Robert

Retrovirology, Vol 6, Iss Suppl 2, p P

2009 Volume 10

Keywords	Medicine (General) ; R5-920 ; Medicine ; R ; DOAJ:Medicine (General) ; DOAJ:Health Sciences ; Immunologic diseases. Allergy ; RC581-607
Language	English
Publishing date	2009-09-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Environmental drivers of SARS-CoV-2 lineage B.1.1.7 transmission in England, October to December 2020

Smith, Thomas P / Dorigatti, Ilaria / Mishra, Swapnil / Volz, Erik / Walker, Patrick G T / Ragonnet-Cronin, Manon / Tristem, Michael / Pearse, William D

medRxiv

Abstract: Previous work has shown that environment affects SARS-CoV-2 transmission, but it is unclear whether emerging strains show similar responses. Here we show that lineage B.1.1.7 spread with greater transmission in colder and more densely populated parts of ... ...

Abstract	Previous work has shown that environment affects SARS-CoV-2 transmission, but it is unclear whether emerging strains show similar responses. Here we show that lineage B.1.1.7 spread with greater transmission in colder and more densely populated parts of England. We also find evidence of B.1.1.79s transmission advantage at warmer temperatures versus other strains, implying that spring conditions may facilitate B.1.1.79s invasion in Europe and across the Northern hemisphere, undermining the effectiveness of public health interventions.
Keywords	covid19
Language	English
Publishing date	2021-03-12
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2021.03.09.21253242
Database	COVID19

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Article ; Online: Temperature and population density influence SARS-CoV-2 transmission in the absence of nonpharmaceutical interventions.

Smith, Thomas P / Flaxman, Seth / Gallinat, Amanda S / Kinosian, Sylvia P / Stemkovski, Michael / Unwin, H Juliette T / Watson, Oliver J / Whittaker, Charles / Cattarino, Lorenzo / Dorigatti, Ilaria / Tristem, Michael / Pearse, William D

Proceedings of the National Academy of Sciences of the United States of America

2021 Volume 118, Issue 25

Abstract: As COVID-19 continues to spread across the world, it is increasingly important to understand the factors that influence its transmission. Seasonal variation driven by responses to changing environment has been shown to affect the transmission intensity ... ...

Abstract	As COVID-19 continues to spread across the world, it is increasingly important to understand the factors that influence its transmission. Seasonal variation driven by responses to changing environment has been shown to affect the transmission intensity of several coronaviruses. However, the impact of the environment on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains largely unknown, and thus seasonal variation remains a source of uncertainty in forecasts of SARS-CoV-2 transmission. Here we address this issue by assessing the association of temperature, humidity, ultraviolet radiation, and population density with estimates of transmission rate (
MeSH term(s)	Basic Reproduction Number ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/transmission ; Cold Temperature ; Communicable Disease Control/legislation & jurisprudence ; Forecasting ; Humans ; Movement ; Population Density ; SARS-CoV-2 ; Seasons ; United States/epidemiology
Language	English
Publishing date	2021-06-11
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.2019284118
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Article ; Online: ICTV Virus Taxonomy Profile:

Coffin, John / Blomberg, Jonas / Fan, Hung / Gifford, Robert / Hatziioannou, Theodora / Lindemann, Dirk / Mayer, Jens / Stoye, Jonathan / Tristem, Michael / Johnson, Welkin / Ictv Report Consortium

The Journal of general virology

2021 Volume 102, Issue 12

Abstract: Viruses in the ... ...

Abstract	Viruses in the family
MeSH term(s)	Animals ; DNA Viruses/classification ; DNA Viruses/genetics ; DNA Viruses/physiology ; DNA Viruses/ultrastructure ; Genome, Viral ; Host Specificity ; Retroviridae/classification ; Retroviridae/genetics ; Retroviridae/physiology ; Retroviridae/ultrastructure ; Vertebrates/virology ; Virion/ultrastructure ; Virus Replication
Language	English
Publishing date	2021-12-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	219316-4
ISSN	1465-2099 ; 0022-1317
ISSN (online)	1465-2099
ISSN	0022-1317
DOI	10.1099/jgv.0.001712
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Article ; Online: Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals.

Lee, Adam / Nolan, Alison / Watson, Jason / Tristem, Michael

Philosophical transactions of the Royal Society of London. Series B, Biological sciences

2013 Volume 368, Issue 1626, Page(s) 20120503

Abstract: The evolutionary arms race between mammals and retroviruses has long been recognized as one of the oldest host-parasite interactions. Rapid evolution rates in exogenous retroviruses have often made accurate viral age estimations highly problematic. ... ...

Abstract	The evolutionary arms race between mammals and retroviruses has long been recognized as one of the oldest host-parasite interactions. Rapid evolution rates in exogenous retroviruses have often made accurate viral age estimations highly problematic. Endogenous retroviruses (ERVs), however, integrate into the germline of their hosts, and are subjected to their evolutionary rates. This study describes, for the first time, a retroviral orthologue predating the divergence of placental mammals, giving it a minimum age of 104-110 Myr. Simultaneously, other orthologous selfish genetic elements (SGEs), inserted into the ERV sequence, provide evidence for the oldest individual mammalian-wide interspersed repeat and medium-reiteration frequency interspersed repeat mammalian repeats, with the same minimum age. The combined use of shared SGEs and reconstruction of viral orthologies defines new limits and increases maximum 'lookback' times, with subsequent implications for the field of paleovirology.
MeSH term(s)	Animals ; Base Sequence ; Endogenous Retroviruses/genetics ; Genome ; Host-Pathogen Interactions/genetics ; Mammals/genetics ; Mammals/virology ; Molecular Sequence Data ; Phylogeny ; Sequence Alignment
Language	English
Publishing date	2013-08-12
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	208382-6
ISSN	1471-2970 ; 0080-4622 ; 0264-3839 ; 0962-8436
ISSN (online)	1471-2970
ISSN	0080-4622 ; 0264-3839 ; 0962-8436
DOI	10.1098/rstb.2012.0503
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Article ; Online: Nomenclature for endogenous retrovirus (ERV) loci.

Gifford, Robert J / Blomberg, Jonas / Coffin, John M / Fan, Hung / Heidmann, Thierry / Mayer, Jens / Stoye, Jonathan / Tristem, Michael / Johnson, Welkin E

Retrovirology

2018 Volume 15, Issue 1, Page(s) 59

Abstract: Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. ... ...

Abstract	Retroviral integration into germline DNA can result in the formation of a vertically inherited proviral sequence called an endogenous retrovirus (ERV). Over the course of their evolution, vertebrate genomes have accumulated many thousands of ERV loci. These sequences provide useful retrospective information about ancient retroviruses, and have also played an important role in shaping the evolution of vertebrate genomes. There is an immediate need for a unified system of nomenclature for ERV loci, not only to assist genome annotation, but also to facilitate research on ERVs and their impact on genome biology and evolution. In this review, we examine how ERV nomenclatures have developed, and consider the possibilities for the implementation of a systematic approach for naming ERV loci. We propose that such a nomenclature should not only provide unique identifiers for individual loci, but also denote orthologous relationships between ERVs in different species. In addition, we propose that-where possible-mnemonic links to previous, well-established names for ERV loci and groups should be retained. We show how this approach can be applied and integrated into existing taxonomic and nomenclature schemes for retroviruses, ERVs and transposable elements.
MeSH term(s)	Animals ; Endogenous Retroviruses/classification ; Endogenous Retroviruses/genetics ; Evolution, Molecular ; Genetic Loci ; Genetic Variation ; Genomics ; Humans ; Terminology as Topic ; Vertebrates/genetics ; Vertebrates/virology
Language	English
Publishing date	2018-08-28
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2142602-8
ISSN	1742-4690 ; 1742-4690
ISSN (online)	1742-4690
ISSN	1742-4690
DOI	10.1186/s12977-018-0442-1
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Article ; Online: Novel Denisovan and Neanderthal retroviruses.

Lee, Adam / Huntley, Derek / Aiewsakun, Pakorn / Kanda, Ravinder K / Lynn, Claire / Tristem, Michael

Journal of virology

2014 Volume 88, Issue 21, Page(s) 12907–12909

Abstract: Following the recent availability of high-coverage genomes for Denisovan and Neanderthal hominids, we conducted a screen for endogenized retroviruses, identifying six novel, previously unreported HERV-K(HML2) elements (HERV-K is human endogenous ... ...

Abstract	Following the recent availability of high-coverage genomes for Denisovan and Neanderthal hominids, we conducted a screen for endogenized retroviruses, identifying six novel, previously unreported HERV-K(HML2) elements (HERV-K is human endogenous retrovirus K). These elements are absent from the human genome (hg38) and appear to be unique to archaic hominids. These findings provide further evidence supporting the recent activity of the HERV-K(HML2) group, which has been implicated in human disease. They will also provide insights into the evolution of archaic hominids.
MeSH term(s)	Animals ; Endogenous Retroviruses/classification ; Endogenous Retroviruses/genetics ; Endogenous Retroviruses/isolation & purification ; Female ; Fossils/virology ; Genome ; Hominidae/virology
Language	English
Publishing date	2014-08-20
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	80174-4
ISSN	1098-5514 ; 0022-538X
ISSN (online)	1098-5514
ISSN	0022-538X
DOI	10.1128/JVI.01825-14
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Article ; Online: Evolution of endogenous retroviruses in the Suidae

Charleston Michael / Gongora Jaime / Nascimento Fabrícia F / Tristem Michael / Lowden Stewart / Moran Chris

BMC Evolutionary Biology, Vol 11, Iss 1, p

evidence for different viral subpopulations in African and Eurasian host species

2011 Volume 139

Abstract: Abstract Background Porcine endogenous retroviruses (PERVs) represent remnants of an exogenous form that have become integrated in the domestic pig ( Sus scrofa ) genome. Although they are usually inactive, the capacity of γ1 ERVs to infect human cells ... ...

Abstract	Abstract Background Porcine endogenous retroviruses (PERVs) represent remnants of an exogenous form that have become integrated in the domestic pig ( Sus scrofa ) genome. Although they are usually inactive, the capacity of γ1 ERVs to infect human cells in vitro has raised concerns about xenotransplantation because the viruses could cross the species barrier to humans. Here we have analyzed the evolution of γ1 ERVs in ten species of Suidae (suids, pigs and hogs) from Eurasia and Africa using DNA sequences for their coding domains ( gag , pro / pol and env genes). For comparison with γ1 PERVs, we have also analysed γ2 ERVs which in domestic pigs are known to be inactive and do not pose a risk to xenotransplantation. Results Phylogenetic analysis using Bayesian inference showed that γ1 and γ2 ERVs have distinctive evolutionary histories. Firstly, two different viral lineages of γ1 ERVs were found and a coevolutionary analysis demonstrated that they correspond broadly to their host phylogeny, one of Eurasian and another of African species, and show no evidence of horizontal transmission. γ2 ERVs, however, show a bush-like evolution, suggesting a rapid viral radiation from a single common ancestor with no correspondence between host and viral evolutionary trees. Furthermore, though γ1 ERV env genes do not possess frequent stop codons, γ2 env genes do. To understand whether γ1 suid ERVs may be still replicating, we have also evaluated their likely mechanism of proliferation by statistically testing internal to terminal branches using nonsynonymous versus synonymous substitution ratios. Our results suggest that γ1 ERVs are increasing in copy number by reinfection, which requires the translocation of the virus from one cell to another. Conclusions Evidence of at least two viral subpopulations was observed in γ1 ERVs from Eurasian and African host species. These results should be taken into account in xenotransplantation since γ1 ERVs appear to be codiverging with their host and maintaining ongoing capacity to infect somatic and germ cells.
Keywords	Biology (General) ; QH301-705.5 ; Science ; Q ; DOAJ:Biology ; DOAJ:Biology and Life Sciences ; Evolution ; QH359-425
Subject code	572
Language	English
Publishing date	2011-05-01T00:00:00Z
Publisher	BioMed Central
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: The evolution, distribution and diversity of endogenous retroviruses.

Gifford, Robert / Tristem, Michael

Virus genes

2003 Volume 26, Issue 3, Page(s) 291–315

Abstract: The retroviral capacity for integration into the host genome can give rise to endogenous retroviruses (ERVs): retroviral sequences that are transmitted vertically as part of the host germ line, within which they may continue to replicate and evolve. ERVs ...

Abstract	The retroviral capacity for integration into the host genome can give rise to endogenous retroviruses (ERVs): retroviral sequences that are transmitted vertically as part of the host germ line, within which they may continue to replicate and evolve. ERVs represent both a unique archive of ancient viral sequence information and a dynamic component of host genomes. As such they hold great potential as informative markers for studies of both virus evolution and host genome evolution. Numerous novel ERVs have been described in recent years, particularly as genome sequencing projects have advanced. This review discusses the evolution of ERV lineages, considering the processes by which ERV distribution and diversity is generated. The diversity of ERVs isolated so far is summarised in terms of both their distribution across host taxa, and their relationships to recognised retroviral genera. Finally the relevance of ERVs to studies of genome evolution, host disease and viral ecology is considered, and recent findings discussed.
MeSH term(s)	Animals ; Endogenous Retroviruses/classification ; Endogenous Retroviruses/genetics ; Endogenous Retroviruses/isolation & purification ; Evolution, Molecular ; Genetic Variation ; Humans ; Vertebrates/virology
Language	English
Publishing date	2003-07-08
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	639496-6
ISSN	1572-994X ; 0920-8569
ISSN (online)	1572-994X
ISSN	0920-8569
DOI	10.1023/a:1024455415443
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Article: A co-opted gypsy-type LTR-retrotransposon is conserved in the genomes of humans, sheep, mice, and rats.

Lynch, Clare / Tristem, Michael

Current biology : CB

2003 Volume 13, Issue 17, Page(s) 1518–1523

Abstract: One subset of sequences present within mammalian genomes is the retroelements, which include endogenous retroviruses and retrotransposons. While there are typically thousands of copies of endogenous retroviruses within mammalian hosts, almost no LTR- ... ...

Abstract	One subset of sequences present within mammalian genomes is the retroelements, which include endogenous retroviruses and retrotransposons. While there are typically thousands of copies of endogenous retroviruses within mammalian hosts, almost no LTR-retrotransposon-like sequences have been identified. Here, we report the presence of a remarkably intact and conserved gypsy-type LTR-retrotransposon sequence within the genomes of several mammals, including humans and mice. Each host probably contains a single orthologous element, indicating that the original, ancestral gypsy LTR-retrotransposon first integrated into mammals over 70 million years ago. It is thus the first described example of a near-intact orthologous retroelement within humans and mice and is one of the most ancient retroelement sequences described to date. Despite their extreme age, the orthologs within each species examined contain a large ORF, between 4.0 and 5.2 kb in length, encoding proteins with sequence similarity to LTR-retrotransposon-derived Capsid (CA), Protease (PR), Reverse Transcriptase (RT), RibonucleaseH (RNaseH), and Integrase (IN). Calculation of nonsynonymous and synonymous nucleotide substitution frequencies indicated that the encoded proteins are under purifying selection, suggesting that these elements have, in fact, been co-opted by their hosts. A possible function for these elements, involving gypsy LTR-retrotransposon restriction in mammals, is discussed.
MeSH term(s)	Amino Acid Sequence ; Animals ; Chromosome Mapping ; Evolution, Molecular ; Genome ; Humans ; Mammals/genetics ; Mice/genetics ; Molecular Sequence Data ; Phylogeny ; Rats/genetics ; Retroelements/genetics ; Selection, Genetic ; Sequence Alignment ; Sequence Homology ; Terminal Repeat Sequences/genetics
Chemical Substances	Retroelements
Language	English
Publishing date	2003-09-02
Publishing country	England
Document type	Comparative Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1071731-6
ISSN	1879-0445 ; 0960-9822
ISSN (online)	1879-0445
ISSN	0960-9822
DOI	10.1016/s0960-9822(03)00618-3
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