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Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the Americas.

Abstract Venezuelan equine encephalitis (VEE) complex alphaviruses are important re-emerging arboviruses that cause life-threatening disease in equids during epizootics as well as spillover human infections. We conducted a comprehensive analysis of VEE complex alphaviruses by sequencing the genomes of 94 strains and performing phylogenetic analyses of 130 isolates using complete open reading frames for the nonstructural and structural polyproteins. Our analyses confirmed purifying selection as a major mechanism influencing the evolution of these viruses as well as a confounding factor in molecular clock dating of ancestors. Times to most recent common ancestors (tMRCAs) could be robustly estimated only for the more recently diverged subtypes; the tMRCA of the ID/IAB/IC/II and IE clades of VEE virus (VEEV) were estimated at ca. 149-973 years ago. Evolution of the IE subtype has been characterized by a significant evolutionary shift from the rest of the VEEV complex, with an increase in structural protein substitutions that are unique to this group, possibly reflecting adaptation to its unique enzootic mosquito vector Culex (Melanoconion) taeniopus. Our inferred tree topologies suggest that VEEV is maintained primarily in situ, with only occasional spread to neighboring countries, probably reflecting the limited mobility of rodent hosts and mosquito vectors.
PMID
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Authors

Mayor MeshTerms

Evolution, Molecular

Keywords
Journal Title plos neglected tropical diseases
Publication Year Start




PMID- 28771475
OWN - NLM
STAT- MEDLINE
DA  - 20170803
DCOM- 20170823
LR  - 20170827
IS  - 1935-2735 (Electronic)
IS  - 1935-2727 (Linking)
VI  - 11
IP  - 8
DP  - 2017 Aug
TI  - Evolution and spread of Venezuelan equine encephalitis complex alphavirus in the 
      Americas.
PG  - e0005693
LID - 10.1371/journal.pntd.0005693 [doi]
AB  - Venezuelan equine encephalitis (VEE) complex alphaviruses are important
      re-emerging arboviruses that cause life-threatening disease in equids during
      epizootics as well as spillover human infections. We conducted a comprehensive
      analysis of VEE complex alphaviruses by sequencing the genomes of 94 strains and 
      performing phylogenetic analyses of 130 isolates using complete open reading
      frames for the nonstructural and structural polyproteins. Our analyses confirmed 
      purifying selection as a major mechanism influencing the evolution of these
      viruses as well as a confounding factor in molecular clock dating of ancestors.
      Times to most recent common ancestors (tMRCAs) could be robustly estimated only
      for the more recently diverged subtypes; the tMRCA of the ID/IAB/IC/II and IE
      clades of VEE virus (VEEV) were estimated at ca. 149-973 years ago. Evolution of 
      the IE subtype has been characterized by a significant evolutionary shift from
      the rest of the VEEV complex, with an increase in structural protein
      substitutions that are unique to this group, possibly reflecting adaptation to
      its unique enzootic mosquito vector Culex (Melanoconion) taeniopus. Our inferred 
      tree topologies suggest that VEEV is maintained primarily in situ, with only
      occasional spread to neighboring countries, probably reflecting the limited
      mobility of rodent hosts and mosquito vectors.
FAU - Forrester, Naomi L
AU  - Forrester NL
AUID- ORCID: http://orcid.org/0000-0001-8892-5216
AD  - Institute for Human Infections and Immunity, Department of Pathology and
      Department of Microbiology and Immunology, University of Texas Medical Branch,
      Galveston, Texas, United States of America.
FAU - Wertheim, Joel O
AU  - Wertheim JO
AD  - Department of Medicine, University of California, San Diego, La Jolla,
      California, United States of America.
FAU - Dugan, Vivian G
AU  - Dugan VG
AD  - Virology Group J. Craig Venter Institute, Rockville, Maryland, United States of
      America.
FAU - Auguste, Albert J
AU  - Auguste AJ
AD  - Institute for Human Infections and Immunity, Department of Pathology and
      Department of Microbiology and Immunology, University of Texas Medical Branch,
      Galveston, Texas, United States of America.
FAU - Lin, David
AU  - Lin D
AD  - cBio, Fremont, California, United States of America.
FAU - Adams, A Paige
AU  - Adams AP
AD  - Institute for Human Infections and Immunity, Department of Pathology and
      Department of Microbiology and Immunology, University of Texas Medical Branch,
      Galveston, Texas, United States of America.
FAU - Chen, Rubing
AU  - Chen R
AD  - Institute for Human Infections and Immunity, Department of Pathology and
      Department of Microbiology and Immunology, University of Texas Medical Branch,
      Galveston, Texas, United States of America.
FAU - Gorchakov, Rodion
AU  - Gorchakov R
AD  - Institute for Human Infections and Immunity, Department of Pathology and
      Department of Microbiology and Immunology, University of Texas Medical Branch,
      Galveston, Texas, United States of America.
FAU - Leal, Grace
AU  - Leal G
AD  - Institute for Human Infections and Immunity, Department of Pathology and
      Department of Microbiology and Immunology, University of Texas Medical Branch,
      Galveston, Texas, United States of America.
FAU - Estrada-Franco, Jose G
AU  - Estrada-Franco JG
AD  - Institute for Human Infections and Immunity, Department of Pathology and
      Department of Microbiology and Immunology, University of Texas Medical Branch,
      Galveston, Texas, United States of America.
FAU - Pandya, Jyotsna
AU  - Pandya J
AD  - Institute for Human Infections and Immunity, Department of Pathology and
      Department of Microbiology and Immunology, University of Texas Medical Branch,
      Galveston, Texas, United States of America.
FAU - Halpin, Rebecca A
AU  - Halpin RA
AD  - Virology Group J. Craig Venter Institute, Rockville, Maryland, United States of
      America.
FAU - Hari, Kumar
AU  - Hari K
AD  - cBio, Fremont, California, United States of America.
FAU - Jain, Ravi
AU  - Jain R
AD  - cBio, Fremont, California, United States of America.
FAU - Stockwell, Timothy B
AU  - Stockwell TB
AD  - Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States 
      of America.
FAU - Das, Suman R
AU  - Das SR
AD  - Informatics Group, J. Craig Venter Institute, Rockville, Maryland, United States 
      of America.
FAU - Wentworth, David E
AU  - Wentworth DE
AD  - Virology Group J. Craig Venter Institute, Rockville, Maryland, United States of
      America.
FAU - Smith, Martin D
AU  - Smith MD
AD  - Bioinformatics and Systems Biology Graduate Program, University of California,
      San Diego, La Jolla, California, United States of America.
FAU - Kosakovsky Pond, Sergei L
AU  - Kosakovsky Pond SL
AD  - Department of Medicine, University of California, San Diego, La Jolla,
      California, United States of America.
FAU - Weaver, Scott C
AU  - Weaver SC
AD  - Institute for Human Infections and Immunity, Department of Pathology and
      Department of Microbiology and Immunology, University of Texas Medical Branch,
      Galveston, Texas, United States of America.
LA  - eng
PT  - Journal Article
DEP - 20170803
PL  - United States
TA  - PLoS Negl Trop Dis
JT  - PLoS neglected tropical diseases
JID - 101291488
SB  - IM
MH  - Americas
MH  - Amino Acid Sequence
MH  - Animals
MH  - Culex/virology
MH  - Encephalitis Virus, Venezuelan Equine/*genetics/isolation & purification
MH  - Encephalomyelitis, Venezuelan Equine/*epidemiology/virology
MH  - *Evolution, Molecular
MH  - Horse Diseases/epidemiology/*virology
MH  - Horses/virology
MH  - Humans
MH  - Insect Vectors/virology
MH  - Phylogeny
PMC - PMC5557581
EDAT- 2017/08/05 06:00
MHDA- 2017/08/24 06:00
CRDT- 2017/08/04 06:00
PHST- 2016/11/15 [received]
PHST- 2017/06/08 [accepted]
PHST- 2017/08/15 [revised]
AID - 10.1371/journal.pntd.0005693 [doi]
AID - PNTD-D-16-01990 [pii]
PST - epublish
SO  - PLoS Negl Trop Dis. 2017 Aug 3;11(8):e0005693. doi: 10.1371/journal.pntd.0005693.
      eCollection 2017 Aug.