Tracking viral evolution during a disease outbreak: the rapid and complete selective sweep of a circovirus in the endangered Echo parakeet (Q34161860)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22345474%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

title

Tracking viral evolution during a disease outbreak: the rapid and complete selective sweep of a circovirus in the endangered Echo parakeet (English)

1 reference

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23 January 2020

2

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23 January 2020

9

Jim J Groombridge

1 reference

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23 January 2020

author name string

Samit Kundu

1

1 reference

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23 January 2020

Andrew G Greenwood

3

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23 January 2020

Carl G Jones

4

1 reference

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23 January 2020

Pete Kaiser

5

1 reference

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23 January 2020

Owen D Lyne

6

1 reference

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23 January 2020

Simon A Black

7

1 reference

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23 January 2020

Aurelie Chowrimootoo

8

1 reference

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23 January 2020

language of work or name

English

0 references

publication date

15 February 2012

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23 January 2020

1 reference

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23 January 2020

volume

86

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23 January 2020

issue

9

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23 January 2020

page(s)

5221-5229

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A random effects branch-site model for detecting episodic diversifying selection.

23 January 2020

cites work

1 reference

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5 July 2018

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5 July 2018

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TreeGraph 2: Combining and visualizing evidence from different phylogenetic analyses

5 July 2018

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Replication of porcine circoviruses

5 July 2018

1 reference

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MHC standing genetic variation and pathogen resistance in wild Atlantic salmon

5 July 2018

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Adaptive mutations resulting in enhanced polymerase activity contribute to high virulence of influenza A virus in mice

5 July 2018

1 reference

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Reliabilities of identifying positive selection by the branch-site and the site-prediction methods

5 July 2018

1 reference

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Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses

5 July 2018

1 reference

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Circoviruses: immunosuppressive threats to avian species: a review

5 July 2018

1 reference

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Investigating protein-coding sequence evolution with probabilistic codon substitution models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Capturing escape in infectious disease dynamics

5 July 2018

1 reference

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5 July 2018

The Vienna RNA websuite

1 reference

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High rates of molecular evolution in hantaviruses

5 July 2018

1 reference

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jModelTest: phylogenetic model averaging

5 July 2018

1 reference

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Rates of evolutionary change in viruses: patterns and determinants

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Bioinformatic and functional analysis of RNA secondary structure elements among different genera of human and animal caliciviruses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

A point mutation in a herpesvirus polymerase determines neuropathogenicity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

BEAST: Bayesian evolutionary analysis by sampling trees

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Clustal W and Clustal X version 2.0

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

PAML 4: phylogenetic analysis by maximum likelihood

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

The capsid protein of beak and feather disease virus binds to the viral DNA and is responsible for transporting the replication-associated protein into the nucleus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Demonstration of nicking/joining activity at the origin of DNA replication associated with the rep and rep' proteins of porcine circovirus type 1.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Genome of a novel circovirus of starlings, amplified by multiply primed rolling-circle amplification

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Porcine circovirus 2 uses heparan sulfate and chondroitin sulfate B glycosaminoglycans as receptors for its attachment to host cells

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Bayesian coalescent inference of past population dynamics from molecular sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

High rate of viral evolution associated with the emergence of carnivore parvovirus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Two amino acid mutations in the capsid protein of type 2 porcine circovirus (PCV2) enhanced PCV2 replication in vitro and attenuated the virus in vivo

5 July 2018

1 reference

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Evidence of unique genotypes of beak and feather disease virus in southern Africa

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Molecular phylogeny and morphological change in the Psittacula parakeets

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Avian circovirus diseases: lessons for the study of PMWS.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus

5 July 2018

1 reference

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Genetic diversity of beak and feather disease virus detected in psittacine species in Australia.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

A universal polymerase chain reaction for the detection of psittacine beak and feather disease virus

5 July 2018

1 reference

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Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens

5 July 2018

1 reference

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Psittacine beak and feather disease virus nucleotide sequence analysis and its relationship to porcine circovirus, plant circoviruses, and chicken anaemia virus.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Beak and feather disease virus and porcine circovirus genomes: intermediates between the geminiviruses and plant circoviruses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Identification of a protein essential for replication of porcine circovirus

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

A codon-based model of nucleotide substitution for protein-coding DNA sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Pathogen-based models favoring MHC genetic diversity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

The pathology of psittacine beak and feather disease

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

The hitch-hiking effect of a favourable gene

5 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

5 July 2018

https://pubmed.ncbi.nlm.nih.gov/22345474

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Characterization of a new virus from cockatoos with psittacine beak and feather disease

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Ultrastructural, protein composition, and antigenic comparison of psittacine beak and feather disease virus purified from four genera of psittacine birds

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Conserved sequence motifs in the initiator proteins for rolling circle DNA replication encoded by diverse replicons from eubacteria, eucaryotes and archaebacteria

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

The fitness effects of synonymous mutations in DNA and RNA viruses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Evidence for negative frequency-dependent selection during experimental coevolution of a freshwater snail and a sterilizing trematode.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Beak and feather disease virus infection in cockatiels (Nymphicus hollandicus).

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Genetic diversity of the Rep gene of beak and feather disease virus in South Africa

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Automated phylogenetic detection of recombination using a genetic algorithm.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Phylogenetic evidence for the rapid evolution of human B19 erythrovirus

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Positive selection of synonymous mutations in vesicular stomatitis virus

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Accuracy and power of bayes prediction of amino acid sites under positive selection

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3347377

Extracutaneous viral inclusions in psittacine beak and feather disease

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22345474

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Analysis of the beak and feather disease viral genome indicates the existence of several genotypes which have a complex psittacine host specificity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22345474

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1128/JVI.06504-11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22345474%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22345474%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

PubMed publication ID

22345474

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:22345474%20AND%20SRC:MED&resulttype=core&format=json