PMID- 25312450
OWN - NLM
STAT- MEDLINE
DCOM- 20150717
LR  - 20211021
IS  - 1872-7492 (Electronic)
IS  - 0168-1702 (Print)
IS  - 0168-1702 (Linking)
VI  - 194
DP  - 2014 Dec 19
TI  - Beyond the whole genome consensus: unravelling of PRRSV phylogenomics using next 
      generation sequencing technologies.
PG  - 167-74
LID - S0168-1702(14)00408-0 [pii]
LID - 10.1016/j.virusres.2014.10.004 [doi]
AB  - The highly heterogeneous porcine reproductive and respiratory syndrome virus 
      (PRRSV) is the causative agent responsible for an economically important pig 
      disease with the characteristic symptoms of reproductive losses in breeding sows 
      and respiratory illnesses in young piglets. The virus can be broadly divided into 
      the European and North American-like genotype 1 and 2 respectively. In addition 
      to this intra-strains variability, the impact of coexisting viral quasispecies on 
      disease development has recently gained much attention; owing very much to the 
      advent of the next-generation sequencing (NGS) technologies. Genomic data 
      produced from the massive sequencing capacities of NGS have enabled the study of 
      PRRSV at an unprecedented rate and details. Unlike conventional sequencing 
      methods which require knowledge of conserved regions, NGS allows de novo assembly 
      of the full viral genomes. Evolutionary variations gained from different 
      genotypic strains provide valuable insights into functionally important regions 
      of the virus. Together with the advancement of sophisticated bioinformatics 
      tools, ultra-deep NGS technologies make the detection of low frequency 
      co-evolving quasispecies possible. This short review gives an overview, including 
      a proposed workflow, on the use of NGS to explore the genetic diversity of PRRSV 
      at both macro- and micro-evolutionary levels.
CI  - Copyright (c) 2014 The Authors. Published by Elsevier B.V. All rights reserved.
FAU - Lu, Zen H
AU  - Lu ZH
AD  - The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of 
      Edinburgh, Easter Bush, EH25 9RG Midlothian, United Kingdom. Electronic address: 
      zen.lu@roslin.ed.ac.uk.
FAU - Archibald, Alan L
AU  - Archibald AL
AD  - The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of 
      Edinburgh, Easter Bush, EH25 9RG Midlothian, United Kingdom.
FAU - Ait-Ali, Tahar
AU  - Ait-Ali T
AD  - The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of 
      Edinburgh, Easter Bush, EH25 9RG Midlothian, United Kingdom. Electronic address: 
      tahar.aitali@roslin.ed.ac.uk.
LA  - eng
GR  - Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PT  - Review
DEP - 20141012
PL  - Netherlands
TA  - Virus Res
JT  - Virus research
JID - 8410979
SB  - IM
MH  - Animals
MH  - Evolution, Molecular
MH  - *Genetic Variation
MH  - *Genome, Viral
MH  - *High-Throughput Nucleotide Sequencing
MH  - *Phylogeny
MH  - Porcine Reproductive and Respiratory Syndrome/virology
MH  - Porcine respiratory and reproductive syndrome 
      virus/*classification/*genetics/isolation & purification
MH  - Swine
PMC - PMC4275598
OTO - NOTNLM
OT  - PRRSV
OT  - Phylogenomics
OT  - Quasispecies
OT  - Ultra-deep next generation sequencing
EDAT- 2014/10/15 06:00
MHDA- 2015/07/18 06:00
PMCR- 2014/12/19
CRDT- 2014/10/15 06:00
PHST- 2014/08/25 00:00 [received]
PHST- 2014/10/01 00:00 [revised]
PHST- 2014/10/01 00:00 [accepted]
PHST- 2014/10/15 06:00 [entrez]
PHST- 2014/10/15 06:00 [pubmed]
PHST- 2015/07/18 06:00 [medline]
PHST- 2014/12/19 00:00 [pmc-release]
AID - S0168-1702(14)00408-0 [pii]
AID - 10.1016/j.virusres.2014.10.004 [doi]
PST - ppublish
SO  - Virus Res. 2014 Dec 19;194:167-74. doi: 10.1016/j.virusres.2014.10.004. Epub 2014 
      Oct 12.