4.8 Article

Endogenous Viral Elements in Shrew Genomes Provide Insights into Pestivirus Ancient History

Related references

Note: Only part of the references are listed.
Article Virology

Comparative analysis of genome-encoded viral sequences reveals the evolutionary history of flavivirids (family Flaviviridae)

Connor G. G. Bamford et al.

Summary: Flavivirids, a family of RNA viruses, have been found to be over 100 million years old and have evolved in early animals, co-diverging with major animal phyla. The study also reveals that some classical flaviviruses initially evolved in hematophagous arachnids and later acquired the ability to be transmitted by insects.

VIRUS EVOLUTION (2022)

Article Virology

Insights into the origin and diversification of bovine viral diarrhea virus 1 subtypes

Matheus N. Weber et al.

Summary: Through phylogenetic and temporal analysis, the study revealed the origin and diversification time of BVDV-1 subtypes.

ARCHIVES OF VIROLOGY (2021)

Article Biochemical Research Methods

eMPRess: a systematic cophylogeny reconciliation tool

Santi Santichaivekin et al.

Summary: eMPRess is a software program designed for phylogenetic tree reconciliation under the duplication-transfer-loss model. It addresses the challenges of selecting event costs and representative solutions to enable users to make more robust inferences.

BIOINFORMATICS (2021)

Article Microbiology

Decoding the RNA viromes in rodent lungs provides new insight into the origin and evolutionary patterns of rodent-borne pathogens in Mainland Southeast Asia

Zhiqiang Wu et al.

Summary: This study provides a comprehensive description of the core viromes of rodents and insectivores from Mainland Southeast Asia, highlighting a high diversity of viruses in rodent species in this region. Through meta-transcriptomic analysis, novel viruses from different evolutionary lineages were identified, as well as a characterization of viruses related to known pathogens.

MICROBIOME (2021)

Article Multidisciplinary Sciences

100-My history of bornavirus infections hidden in vertebrate genomes

Junna Kawasaki et al.

Summary: Ancient bornavirus infections have been identified in various vertebrate lineages, especially in primate ancestors. Phylogenetic analyses suggest that primate ancestors were infected with multiple bornaviral lineages during evolution, with some lineages coexisting and repeatedly endogenizing for tens of millions of years. Moreover, a bornaviral lineage coexisted with primate ancestors also endogenized in some ancestral bats, possibly spreading infections as the ancestors migrated.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Article Virology

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

Magda Bletsa et al.

Summary: The study screened small mammal samples from sub-Saharan Africa and confirmed the presence of hepaciviruses in rodents. Eighty samples were found positive for hepaciviruses, increasing the diversity of three different rodent hepacivirus lineages, and evidence of recombination within specific host lineages was also detected.

VIRUS EVOLUTION (2021)

Article Biochemistry & Molecular Biology

A mechanistic evolutionary model explains the time-dependent pattern of substitution rates in viruses

Mahan Ghafari et al.

Summary: This study provides a predictive mechanistic model to explain the rate decay phenomenon of viruses and successfully applies it to re-estimate the date of diversification of hepatitis C virus genotypes, as well as the origin time of the most recent common ancestor of sarbecoviruses. By studying the evolutionary processes of viruses, it offers a new perspective for us to understand the origins of these viruses.

CURRENT BIOLOGY (2021)

Article Biochemistry & Molecular Biology

MEGA11 Molecular Evolutionary Genetics Analysis Version 11

Koichiro Tamura et al.

Summary: MEGA software, a mature tool for computational molecular evolution, has been enhanced with new additions for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. These additions include methods for estimating divergence times, confidence intervals, and new options for tagging sequences with spatiotemporal sampling information. The enhancements aim to improve user experience, result quality, and the pace of biological discovery.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Virology

Molecular detection and genomic characterization of diverse hepaciviruses in African rodents

Magda Bletsa et al.

Summary: This study screened small mammal samples from sub-Saharan Africa, uncovering novel hepacivirus lineages and providing insights into co-infections and recombination in rodent hosts. The findings underscore the importance of rodents as a potential reservoir for hepaciviruses and as models for studying HCV infection dynamics.

VIRUS EVOLUTION (2021)

Article Biochemistry & Molecular Biology

Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

Li-Gen Wang et al.

MOLECULAR BIOLOGY AND EVOLUTION (2020)

Article Parasitology

Yellow fever epizootics in non-human primates, Southeast and Northeast Brazil (2017 and 2018)

Maria Angelica Monteiro de Mello Mares-Guia et al.

PARASITES & VECTORS (2020)

Article Virology

The Potential Role of Endogenous Viral Elements in the Evolution of Bats as Reservoirs for Zoonotic Viruses

Emilia C. Skirmuntt et al.

ANNUAL REVIEW OF VIROLOGY, VOL 7, 2020 (2020)

Article Biochemistry & Molecular Biology

Non-retroviral Endogenous Viral Element Limits Cognate Virus Replication in Aedes aegypti Ovaries

Yasutsugu Suzuki et al.

CURRENT BIOLOGY (2020)

Article Biochemistry & Molecular Biology

Endogenous viral elements integrated into the genome of the soybean aphid, Aphis glycines

Sijun Liu et al.

INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY (2020)

Article Biochemical Research Methods

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

Emmanuel Paradis et al.

BIOINFORMATICS (2019)

Article Virology

An endogenous adeno-associated virus element in elephants

Yuki Kobayashi et al.

VIRUS RESEARCH (2019)

Letter Biology

Novel hepacivirus in Asian house shrew, China

Hua Guo et al.

SCIENCE CHINA-LIFE SCIENCES (2019)

Article Biochemistry & Molecular Biology

Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates

Jade Vincent Membrebe et al.

MOLECULAR BIOLOGY AND EVOLUTION (2019)

Article Microbiology

Assessing the Diversity of Endogenous Viruses Throughout Ant Genomes

Peter J. Flynn et al.

FRONTIERS IN MICROBIOLOGY (2019)

Article Biochemistry & Molecular Biology

The EMBL-EBI search and sequence analysis tools APIs in 2019

Fabio Madeira et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Multidisciplinary Sciences

Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago

Stephen Sameroff et al.

SCIENTIFIC REPORTS (2019)

Review Immunology

piRNA-Guided CRISPR-like Immunity in Eukaryotes

Youdiil Ophinni et al.

TRENDS IN IMMUNOLOGY (2019)

Article Multidisciplinary Sciences

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

L. E. Kafetzopoulou et al.

SCIENCE (2019)

Article Biodiversity Conservation

Shrews (Soricidae) of the lowland forests around Kisangani (DR Congo)

Frederik Van de Perre et al.

BIODIVERSITY DATA JOURNAL (2019)

Review Biochemistry & Molecular Biology

The Widespread Occurrence and Potential Biological Roles of Endogenous Viral Elements in Insect Genomes

Carol D. Blair et al.

CURRENT ISSUES IN MOLECULAR BIOLOGY (2019)

Article Biochemical Research Methods

Minimap2: pairwise alignment for nucleotide sequences

Heng Li

BIOINFORMATICS (2018)

Article Evolutionary Biology

Breeding consequences of flavivirus infection in the collared flycatcher

Tanja M. Strand et al.

BMC EVOLUTIONARY BIOLOGY (2018)

Article Multidisciplinary Sciences

Reconciling biodiversity and carbon stock conservation in an Afrotropical forest landscape

Frederik Van de Perre et al.

SCIENCE ADVANCES (2018)

Correction Multidisciplinary Sciences

The evolutionary history of vertebrate RNA viruses (vol 556, pg 197, 2018)

Mang Shi et al.

NATURE (2018)

Article Virology

Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10

Marc A. Suchard et al.

VIRUS EVOLUTION (2018)

Article Virology

Time-Dependent Rate Phenomenon in Viruses

Pakorn Aiewsakun et al.

JOURNAL OF VIROLOGY (2016)

Review Virology

The Strange, Expanding World of Animal Hepaciviruses

Alex S. Hartlage et al.

ANNUAL REVIEW OF VIROLOGY, VOL 3 (2016)

Review Genetics & Heredity

Dating Tips for Divergence-Time Estimation

Joseph E. O'Reilly et al.

TRENDS IN GENETICS (2015)

Review Virology

Endogenous viruses: Connecting recent and ancient viral evolution

Pakorn Aiewsakun et al.

VIROLOGY (2015)

Article Multidisciplinary Sciences

Hepatitis C-like viruses are produced in cells from rabbit and hare DNA

Eliane Silva et al.

SCIENTIFIC REPORTS (2015)

Article Biochemistry & Molecular Biology

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

Lam-Tung Nguyen et al.

MOLECULAR BIOLOGY AND EVOLUTION (2015)

Article Biochemistry & Molecular Biology

CDD: NCBI's conserved domain database

Aron Marchler-Bauer et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biotechnology & Applied Microbiology

Dating the origin of the genus Flavivirus in the light of Beringian biogeography

John H. -O Pettersson et al.

JOURNAL OF GENERAL VIROLOGY (2014)

Review Biology

Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes

Masayuki Horie et al.

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2013)

Article Biochemical Research Methods

Fast gapped-read alignment with Bowtie 2

Ben Langmead et al.

NATURE METHODS (2012)

Review Genetics & Heredity

Endogenous viruses: insights into viral evolution and impact on host biology

Cedric Feschotte et al.

NATURE REVIEWS GENETICS (2012)

Review Microbiology

The Evolution of Endogenous Viral Elements

Edward C. Holmes

CELL HOST & MICROBE (2011)

Article Biochemistry & Molecular Biology

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

Fabian Sievers et al.

MOLECULAR SYSTEMS BIOLOGY (2011)

Article Biochemistry & Molecular Biology

The Sequence Read Archive

Rasko Leinonen et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Evolutionary Biology

Filoviruses are ancient and integrated into mammalian genomes

Derek J. Taylor et al.

BMC EVOLUTIONARY BIOLOGY (2010)

Article Multidisciplinary Sciences

Endogenous non-retroviral RNA virus elements in mammalian genomes

Masayuki Horie et al.

NATURE (2010)

Review Biochemistry & Molecular Biology

T2 Family ribonucleases: ancient enzymes with diverse roles

Natalie Luhtala et al.

TRENDS IN BIOCHEMICAL SCIENCES (2010)

Article Biochemistry & Molecular Biology

Genomic Fossils Calibrate the Long-Term Evolution of Hepadnaviruses

Clement Gilbert et al.

PLOS BIOLOGY (2010)

Article Genetics & Heredity

Endogenous Viral Elements in Animal Genomes

Aris Katzourakis et al.

PLOS GENETICS (2010)

Article Biochemical Research Methods

The Sequence Alignment/Map format and SAMtools

Heng Li et al.

BIOINFORMATICS (2009)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Evolutionary Biology

Secondary contact zones and hybridizations: the case of the lesser white-toothed shrew (Crocidura suaveolens group, Soricidae)

Sylvain Dubey et al.

BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2008)

Review Genetics & Heredity

Rates of evolutionary change in viruses: patterns and determinants

Siobain Duffy et al.

NATURE REVIEWS GENETICS (2008)

Article Biochemistry & Molecular Biology

Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations

Sylvain Dubey et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2007)

Article Biochemistry & Molecular Biology

Pliocene and Pleistocene diversification and multiple refugia in a Eurasian shrew (Crocidura suaveolens group)

S Dubey et al.

MOLECULAR PHYLOGENETICS AND EVOLUTION (2006)

Article Biochemistry & Molecular Biology

Not so different after all: A comparison of methods for detecting amino acid sites under selection

SLK Pond et al.

MOLECULAR BIOLOGY AND EVOLUTION (2005)

Article Biochemical Research Methods

HyPhy: hypothesis testing using phylogenies

SLK Pond et al.

BIOINFORMATICS (2005)

Article Biotechnology & Applied Microbiology

Sequences of flavivirus-related RNA viruses persist in DNA form integrated in the genome of Aedes spp. mosquitoes

S Crochu et al.

JOURNAL OF GENERAL VIROLOGY (2004)

Review Virology

Molecular clocks and the puzzle of RNA virus origins

EC Holmes

JOURNAL OF VIROLOGY (2003)

Article Biochemistry & Molecular Biology

MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform

K Katoh et al.

NUCLEIC ACIDS RESEARCH (2002)