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  1. Article ; Online: Clockor2: Inferring global and local strict molecular clocks using root-to-tip regression.

    Featherstone, Leo A / Rambaut, Andrew / Duchene, Sebastian / Wirth, Wytamma

    Systematic biology

    2024  

    Abstract: Molecular sequence data from rapidly evolving organisms are often sampled at different points in time. Sampling times can then be used for molecular clock calibration. The root-to-tip (RTT) regression is an essential tool to assess the degree to which ... ...

    Abstract Molecular sequence data from rapidly evolving organisms are often sampled at different points in time. Sampling times can then be used for molecular clock calibration. The root-to-tip (RTT) regression is an essential tool to assess the degree to which the data behave in a clock-like fashion. Here, we introduce Clockor2, a client-side web application for conducting RTT regression. Clockor2 allows users to quickly fit local and global molecular clocks, thus handling the increasing complexity of genomic datasets that sample beyond the assumption of homogeneous host populations. Clockor2 is efficient, handling trees of up to the order of 104 tips, with significant speed increases compared to other RTT regression applications. Although clockor2 is written as a web application, all data processing happens on the client-side, meaning that data never leaves the user's computer. Clockor2 is freely available at https : //clockor2.github.io/.
    Language English
    Publishing date 2024-02-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 1482572-7
    ISSN 1076-836X ; 1063-5157
    ISSN (online) 1076-836X
    ISSN 1063-5157
    DOI 10.1093/sysbio/syae003
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: SCORPIO: a utility for defining and classifying mutation constellations of virus genomes.

    Colquhoun, Rachel / Jackson, Ben / O'Toole, Áine / Rambaut, Andrew

    Bioinformatics (Oxford, England)

    2023  Volume 39, Issue 10

    Abstract: Summary: Scorpio provides a set of command line utilities for classifying, haplotyping, and defining constellations of mutations for an aligned set of genome sequences. It was developed to enable exploration and classification of variants of concern ... ...

    Abstract Summary: Scorpio provides a set of command line utilities for classifying, haplotyping, and defining constellations of mutations for an aligned set of genome sequences. It was developed to enable exploration and classification of variants of concern within the SARS-CoV-2 pandemic, but can be applied more generally to other species.
    Availability and implementation: Scorpio is an open-source project distributed under the GNU GPL version 3 license. Source code and binaries are available at https://github.com/cov-lineages/scorpio, and binaries are also available from Bioconda. SARS-CoV-2 specific definitions can be installed as a separate dependency from https://github.com/cov-lineages/constellations.
    MeSH term(s) Software ; Genome, Viral ; SARS-CoV-2/genetics ; Mutation ; Drugs, Chinese Herbal
    Chemical Substances scorpio ; Drugs, Chinese Herbal
    Language English
    Publishing date 2023-09-15
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 1422668-6
    ISSN 1367-4811 ; 1367-4803
    ISSN (online) 1367-4811
    ISSN 1367-4803
    DOI 10.1093/bioinformatics/btad575
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 2374: Show issues Location:
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  3. Article: Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation.

    Parino, Francesco / Gustani-Buss, Emanuele / Bedford, Trevor / Suchard, Marc A / Trovão, Nídia Sequeira / Rambaut, Andrew / Colizza, Vittoria / Poletto, Chiara / Lemey, Philippe

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: Global seasonal influenza circulation involves a complex interplay between local (seasonality, demography, host immunity) and global factors (international mobility) shaping recurrent epidemic patterns. No studies so far have reconciled the two spatial ... ...

    Abstract Global seasonal influenza circulation involves a complex interplay between local (seasonality, demography, host immunity) and global factors (international mobility) shaping recurrent epidemic patterns. No studies so far have reconciled the two spatial levels, evaluating the coupling between national epidemics, considering heterogeneous coverage of epidemiological and virological data, integrating different data sources. We propose a novel combined approach based on a dynamical model of global influenza spread (GLEAM), integrating high-resolution demographic and mobility data, and a generalized linear model of phylogeographic diffusion that accounts for time-varying migration rates. Seasonal migration fluxes across global macro-regions simulated with GLEAM are tested as phylogeographic predictors to provide model validation and calibration based on genetic data. Seasonal fluxes obtained with a specific transmissibility peak time and recurrent travel outperformed the raw air-transportation predictor, previously considered as optimal indicator of global influenza migration. Influenza A subtypes supported autumn-winter reproductive number as high as 2.25 and an average immunity duration of 2 years. Similar dynamics were preferred by influenza B lineages, with a lower autumn-winter reproductive number. Comparing simulated epidemic profiles against FluNet data offered comparatively limited resolution power. The multiscale approach enables model selection yielding a novel computational framework for describing global influenza dynamics at different scales - local transmission and national epidemics vs. international coupling through mobility and imported cases. Our findings have important implications to improve preparedness against seasonal influenza epidemics. The approach can be generalized to other epidemic contexts, such as emerging disease outbreaks to improve the flexibility and predictive power of modeling.
    Language English
    Publishing date 2024-03-15
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.14.24303719
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  4. Article ; Online: Publisher Correction: Monitoring key epidemiological parameters of SARS-CoV-2 transmission.

    Kraemer, Moritz U G / Pybus, Oliver G / Fraser, Christophe / Cauchemez, Simon / Rambaut, Andrew / Cowling, Benjamin J

    Nature medicine

    2022  Volume 28, Issue 1, Page(s) 213

    Language English
    Publishing date 2022-01-12
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-021-01670-6
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    Zs.A 4212: Show issues Location:
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  5. Article ; Online: Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences.

    O'Toole, Áine / Pybus, Oliver G / Abram, Michael E / Kelly, Elizabeth J / Rambaut, Andrew

    BMC genomics

    2022  Volume 23, Issue 1, Page(s) 121

    Abstract: Background: More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. ... ...

    Abstract Background: More than 2 million SARS-CoV-2 genome sequences have been generated and shared since the start of the COVID-19 pandemic and constitute a vital information source that informs outbreak control, disease surveillance, and public health policy. The Pango dynamic nomenclature is a popular system for classifying and naming genetically-distinct lineages of SARS-CoV-2, including variants of concern, and is based on the analysis of complete or near-complete virus genomes. However, for several reasons, nucleotide sequences may be generated that cover only the spike gene of SARS-CoV-2. It is therefore important to understand how much information about Pango lineage status is contained in spike-only nucleotide sequences. Here we explore how Pango lineages might be reliably designated and assigned to spike-only nucleotide sequences. We survey the genetic diversity of such sequences, and investigate the information they contain about Pango lineage status.
    Results: Although many lineages, including the main variants of concern, can be identified clearly using spike-only sequences, some spike-only sequences are shared among tens or hundreds of Pango lineages. To facilitate the classification of SARS-CoV-2 lineages using subgenomic sequences we introduce the notion of designating such sequences to a "lineage set", which represents the range of Pango lineages that are consistent with the observed mutations in a given spike sequence.
    Conclusions: We find that many lineages, including the main variants-of-concern, can be reliably identified by spike alone and we define lineage-sets to represent the lineage precision that can be achieved using spike-only nucleotide sequences. These data provide a foundation for the development of software tools that can assign newly-generated spike nucleotide sequences to Pango lineage sets.
    MeSH term(s) Base Sequence ; COVID-19 ; Humans ; Mutation ; Pandemics ; Phylogeny ; SARS-CoV-2 ; Spike Glycoprotein, Coronavirus/genetics
    Chemical Substances Spike Glycoprotein, Coronavirus
    Language English
    Publishing date 2022-02-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 2041499-7
    ISSN 1471-2164 ; 1471-2164
    ISSN (online) 1471-2164
    ISSN 1471-2164
    DOI 10.1186/s12864-022-08358-2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: A framework for automated scalable designation of viral pathogen lineages from genomic data.

    McBroome, Jakob / de Bernardi Schneider, Adriano / Roemer, Cornelius / Wolfinger, Michael T / Hinrichs, Angie S / O'Toole, Aine Niamh / Ruis, Christopher / Turakhia, Yatish / Rambaut, Andrew / Corbett-Detig, Russell

    Nature microbiology

    2024  Volume 9, Issue 2, Page(s) 550–560

    Abstract: Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by ... ...

    Abstract Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays as well as regional and personal bias. Here we developed a simple heuristic approach for dividing phylogenetic trees into lineages, including the prioritization of key mutations or genes. Our implementation is efficient on extremely large phylogenetic trees consisting of millions of sequences and produces similar results to existing manually curated lineage designations when applied to SARS-CoV-2 and other viruses including chikungunya virus, Venezuelan equine encephalitis virus complex and Zika virus. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever-increasing genomic datasets.
    MeSH term(s) Animals ; Horses/genetics ; Phylogeny ; Encephalitis Virus, Venezuelan Equine/genetics ; Genomics ; Base Sequence ; Genome, Viral ; SARS-CoV-2/genetics ; Zika Virus/genetics ; Zika Virus Infection
    Language English
    Publishing date 2024-02-05
    Publishing country England
    Document type Journal Article
    ISSN 2058-5276
    ISSN (online) 2058-5276
    DOI 10.1038/s41564-023-01587-5
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Monitoring key epidemiological parameters of SARS-CoV-2 transmission.

    Kraemer, Moritz U G / Pybus, Oliver G / Fraser, Christophe / Cauchemez, Simon / Rambaut, Andrew / Cowling, Benjamin J

    Nature medicine

    2021  Volume 27, Issue 11, Page(s) 1854–1855

    MeSH term(s) COVID-19/epidemiology ; COVID-19/transmission ; Contact Tracing/methods ; Databases as Topic ; Humans ; Infection Control/methods ; Pandemics/prevention & control ; Population Surveillance/methods ; Risk Factors ; SARS-CoV-2/pathogenicity ; SARS-CoV-2/physiology ; Time Factors ; Virulence ; Virus Replication
    Language English
    Publishing date 2021-11-02
    Publishing country United States
    Document type Letter
    ZDB-ID 1220066-9
    ISSN 1546-170X ; 1078-8956
    ISSN (online) 1546-170X
    ISSN 1078-8956
    DOI 10.1038/s41591-021-01545-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 4212: Show issues Location:
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    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 39: Show issues

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  8. Article: MERS-CoV recombination: implications about the reservoir and potential for adaptation.

    Dudas, Gytis / Rambaut, Andrew

    Virus evolution

    2016  Volume 2, Issue 1, Page(s) vev023

    Abstract: Recombination is a process that unlinks neighboring loci allowing for independent evolutionary trajectories within genomes of many organisms. If not properly accounted for, recombination can compromise many evolutionary analyses. In addition, when ... ...

    Abstract Recombination is a process that unlinks neighboring loci allowing for independent evolutionary trajectories within genomes of many organisms. If not properly accounted for, recombination can compromise many evolutionary analyses. In addition, when dealing with organisms that are not obligately sexually reproducing, recombination gives insight into the rate at which distinct genetic lineages come into contact. Since June 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has caused 1,106 laboratory-confirmed infections, with 421 MERS-CoV-associated deaths as of 16 April 2015. Although bats are considered as the likely ultimate source of zoonotic betacoronaviruses, dromedary camels have been consistently implicated as the source of current human infections in the Middle East. In this article, we use phylogenetic methods and simulations to show that MERS-CoV genome has likely undergone numerous recombinations recently. Recombination in MERS-CoV implies frequent co-infection with distinct lineages of MERS-CoV, probably in camels given the current understanding of MERS-CoV epidemiology.
    Keywords covid19
    Language English
    Publishing date 2016-01-20
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/vev023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article: Increasing intra- and inter-subtype HIV diversity despite declining HIV incidence in Uganda.

    Kim, Seungwon / Kigozi, Godfrey / Martin, Michael A / Galiwango, Ronald M / Quinn, Thomas C / Redd, Andrew D / Ssekubugu, Robert / Bonsall, David / Ssemwanga, Deogratius / Rambaut, Andrew / Herbeck, Joshua T / Reynolds, Steven J / Foley, Brian / Abeler-Dörner, Lucie / Fraser, Christophe / Ratmann, Oliver / Kagaayi, Joseph / Laeyendecker, Oliver / Grabowski, M Kate

    medRxiv : the preprint server for health sciences

    2024  

    Abstract: HIV incidence has been declining in Africa with scale-up of HIV interventions. However, there is limited data on HIV evolutionary trends in African populations with waning epidemics. We evaluated changes in HIV viral diversity and genetic divergence in ... ...

    Abstract HIV incidence has been declining in Africa with scale-up of HIV interventions. However, there is limited data on HIV evolutionary trends in African populations with waning epidemics. We evaluated changes in HIV viral diversity and genetic divergence in southern Uganda over a twenty-five-year period spanning the introduction and scale-up of HIV prevention and treatment programs using HIV sequence and survey data from the Rakai Community Cohort Study, an open longitudinal population-based HIV surveillance cohort.
    Language English
    Publishing date 2024-03-15
    Publishing country United States
    Document type Preprint
    DOI 10.1101/2024.03.14.24303990
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: SPREAD 4: online visualisation of pathogen phylogeographic reconstructions.

    Nahata, Kanika D / Bielejec, Filip / Monetta, Juan / Dellicour, Simon / Rambaut, Andrew / Suchard, Marc A / Baele, Guy / Lemey, Philippe

    Virus evolution

    2022  Volume 8, Issue 2, Page(s) veac088

    Abstract: Phylogeographic analyses aim to extract information about pathogen spread from genomic data, and visualising spatio-temporal reconstructions is a key aspect of this process. Here we present SPREAD 4, a feature-rich web-based application that visualises ... ...

    Abstract Phylogeographic analyses aim to extract information about pathogen spread from genomic data, and visualising spatio-temporal reconstructions is a key aspect of this process. Here we present SPREAD 4, a feature-rich web-based application that visualises estimates of pathogen dispersal resulting from Bayesian phylogeographic inference using BEAST on a geographic map, offering zoom-and-filter functionality and smooth animation over time. SPREAD 4 takes as input phylogenies with both discrete and continuous location annotation and offers customised visualisation as well as generation of publication-ready figures. SPREAD 4 now features account-based storage and easy sharing of visualisations by means of unique web addresses. SPREAD 4 is intuitive to use and is available online at https://spreadviz.org, with an accompanying web page containing answers to frequently asked questions at https://beast.community/spread4.
    Language English
    Publishing date 2022-09-26
    Publishing country England
    Document type Journal Article
    ZDB-ID 2818949-8
    ISSN 2057-1577
    ISSN 2057-1577
    DOI 10.1093/ve/veac088
    Database MEDical Literature Analysis and Retrieval System OnLINE

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