PMID- 24698958
OWN - NLM
STAT- MEDLINE
DCOM- 20150127
LR  - 20211021
IS  - 1932-6203 (Electronic)
IS  - 1932-6203 (Linking)
VI  - 9
IP  - 4
DP  - 2014
TI  - Genomic evolution of porcine reproductive and respiratory syndrome virus (PRRSV) 
      isolates revealed by deep sequencing.
PG  - e88807
LID - 10.1371/journal.pone.0088807 [doi]
LID - e88807
AB  - Most studies on PRRSV evolution have been limited to a particular region of the 
      viral genome. A thorough genome-wide understanding of the impact of different 
      mechanisms on shaping PRRSV genetic diversity is still lacking. To this end, deep 
      sequencing was used to obtain genomic sequences of a diverse set of 16 isolates 
      from a region of Hong Kong with a complex PRRSV epidemiological record. Genome 
      assemblies and phylogenetic typing indicated the co-circulation of strains of 
      both genotypes (type 1 and type 2) with varying Nsp2 deletion patterns and 
      distinct evolutionary lineages ("High Fever"-like and local endemic type). 
      Recombination analyses revealed genomic breakpoints in structural and 
      non-structural regions of genomes of both genotypes with evidence of many 
      recombination events originating from common ancestors. Additionally, the high 
      fold of coverage per nucleotide allowed the characterization of minor variants 
      arising from the quasispecies of each strain. Overall, 0.56-2.83% of sites were 
      found to be polymorphic with respect to cognate consensus genomes. The 
      distribution of minor variants across each genome was not uniform indicating the 
      influence of selective forces. Proportion of variants capable of causing an amino 
      acid change in their respective codons ranged between 25-67% with many predicted 
      to be non-deleterious. Low frequency deletion variants were also detected 
      providing one possible mechanism for their sudden emergence as cited in previous 
      reports.
FAU - Brar, Manreetpal Singh
AU  - Brar MS
AD  - School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
FAU - Shi, Mang
AU  - Shi M
AD  - Sydney Emerging Infections & Biosecurity Institute, School of Biological Sciences 
      and Sydney Medical School, The University of Sydney, Darlington, Australia.
FAU - Hui, Raymond Kin-Hi
AU  - Hui RK
AD  - School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
FAU - Leung, Frederick Chi-Ching
AU  - Leung FC
AD  - School of Biological Sciences, The University of Hong Kong, Hong Kong, China.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140403
PL  - United States
TA  - PLoS One
JT  - PloS one
JID - 101285081
RN  - 0 (RNA, Messenger)
SB  - IM
MH  - Animals
MH  - *Biological Evolution
MH  - *Genome, Viral
MH  - *Genomics
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - Phylogeny
MH  - Porcine Reproductive and Respiratory Syndrome/*genetics/*virology
MH  - Porcine respiratory and reproductive syndrome 
      virus/classification/genetics/*isolation & purification
MH  - RNA, Messenger/genetics
MH  - Real-Time Polymerase Chain Reaction
MH  - Reverse Transcriptase Polymerase Chain Reaction
MH  - Swine
PMC - PMC3974674
COIS- Competing Interests: One of the co-authors, Prof. Frederick C.C. Leung, is a PLOS 
      ONE Academic Editor. This does not alter the authors' adherence to all the PLOS 
      ONE policies on sharing data and materials.
EDAT- 2014/04/05 06:00
MHDA- 2015/01/28 06:00
PMCR- 2014/04/03
CRDT- 2014/04/05 06:00
PHST- 2013/09/11 00:00 [received]
PHST- 2014/01/15 00:00 [accepted]
PHST- 2014/04/05 06:00 [entrez]
PHST- 2014/04/05 06:00 [pubmed]
PHST- 2015/01/28 06:00 [medline]
PHST- 2014/04/03 00:00 [pmc-release]
AID - PONE-D-13-37498 [pii]
AID - 10.1371/journal.pone.0088807 [doi]
PST - epublish
SO  - PLoS One. 2014 Apr 3;9(4):e88807. doi: 10.1371/journal.pone.0088807. eCollection 
      2014.