Limits...
Genomic evolution of porcine reproductive and respiratory syndrome virus (PRRSV) isolates revealed by deep sequencing.

Brar MS, Shi M, Hui RK, Leung FC - PLoS ONE (2014)

Bottom Line: Overall, 0.56-2.83% of sites were found to be polymorphic with respect to cognate consensus genomes.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.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, The University of Hong Kong, Hong Kong, China.

ABSTRACT
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.

Show MeSH

Related in: MedlinePlus

Phylogenomic and recombination characterization of HK PRRSV strains.(A) Genotype-specific (type 1 left; type 2 right) phylogenies of HK and globally sequenced PRRSV genomes. Type 1 strains form a monophyletic clade separate from isolates of any other country or region. Type 2 strains classified with either previously known local as known as “endemic” diversity or the “High-Fever”-like variants isolated during virulent outbreaks of PRRS in China. (B) Mapped recombination breakpoints and potential minor parental-like strains of mosaic HK PRRSV strains. Unknown designation (for a missing parental-like strain) was assigned when a recombination event was characterized from an alignment involving only one parental-like strain and the recombinant.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3974674&req=5

pone-0088807-g002: Phylogenomic and recombination characterization of HK PRRSV strains.(A) Genotype-specific (type 1 left; type 2 right) phylogenies of HK and globally sequenced PRRSV genomes. Type 1 strains form a monophyletic clade separate from isolates of any other country or region. Type 2 strains classified with either previously known local as known as “endemic” diversity or the “High-Fever”-like variants isolated during virulent outbreaks of PRRS in China. (B) Mapped recombination breakpoints and potential minor parental-like strains of mosaic HK PRRSV strains. Unknown designation (for a missing parental-like strain) was assigned when a recombination event was characterized from an alignment involving only one parental-like strain and the recombinant.

Mentions: Phylogenetic and recombination analyses in context of our previously established genotyping system [18] was performed to elucidate the significant genetic diversity seen amongst local isolates. From an evolutionary standpoint, all of the HK type 1 strains were closely-related forming a monophyletic group whereas type 2 strains were classified to either “endemic” diversity or the “High-Fever”-like group of isolates that widely circulated on the mainland (China) during virulent outbreaks of PRRS (Figure 2A). Strains belonging to the latter group represented introduced PRRSV incidents to Hong Kong explaining the genetic disparity with “local or endemic” isolates. Moreover, majority of the sequenced isolates registered recombination breakpoints as well with type 1 strains being much more mosaic in nature compared to the type 2 strains (Figure 2B). A complete description of the location of breakpoints, parental-like strains, and support from the different detection methods is given in Table S2 in File S1 and Figure S1File S1 for all recombination events. The topology of the phylogeny, potential minor parental-like strains, and breakpoint locations in the genome suggested most of the recombination events were not independent but took place in a common ancestor followed by successful circulation of descendant recombinants in the field. There was also evidence of recombination in local isolates, in the cases of strains #3, #6, and #10, with other strains of their same genotype but no indication of genomic exchange between endemic and High Fever-like strains.


Genomic evolution of porcine reproductive and respiratory syndrome virus (PRRSV) isolates revealed by deep sequencing.

Brar MS, Shi M, Hui RK, Leung FC - PLoS ONE (2014)

Phylogenomic and recombination characterization of HK PRRSV strains.(A) Genotype-specific (type 1 left; type 2 right) phylogenies of HK and globally sequenced PRRSV genomes. Type 1 strains form a monophyletic clade separate from isolates of any other country or region. Type 2 strains classified with either previously known local as known as “endemic” diversity or the “High-Fever”-like variants isolated during virulent outbreaks of PRRS in China. (B) Mapped recombination breakpoints and potential minor parental-like strains of mosaic HK PRRSV strains. Unknown designation (for a missing parental-like strain) was assigned when a recombination event was characterized from an alignment involving only one parental-like strain and the recombinant.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3974674&req=5

pone-0088807-g002: Phylogenomic and recombination characterization of HK PRRSV strains.(A) Genotype-specific (type 1 left; type 2 right) phylogenies of HK and globally sequenced PRRSV genomes. Type 1 strains form a monophyletic clade separate from isolates of any other country or region. Type 2 strains classified with either previously known local as known as “endemic” diversity or the “High-Fever”-like variants isolated during virulent outbreaks of PRRS in China. (B) Mapped recombination breakpoints and potential minor parental-like strains of mosaic HK PRRSV strains. Unknown designation (for a missing parental-like strain) was assigned when a recombination event was characterized from an alignment involving only one parental-like strain and the recombinant.
Mentions: Phylogenetic and recombination analyses in context of our previously established genotyping system [18] was performed to elucidate the significant genetic diversity seen amongst local isolates. From an evolutionary standpoint, all of the HK type 1 strains were closely-related forming a monophyletic group whereas type 2 strains were classified to either “endemic” diversity or the “High-Fever”-like group of isolates that widely circulated on the mainland (China) during virulent outbreaks of PRRS (Figure 2A). Strains belonging to the latter group represented introduced PRRSV incidents to Hong Kong explaining the genetic disparity with “local or endemic” isolates. Moreover, majority of the sequenced isolates registered recombination breakpoints as well with type 1 strains being much more mosaic in nature compared to the type 2 strains (Figure 2B). A complete description of the location of breakpoints, parental-like strains, and support from the different detection methods is given in Table S2 in File S1 and Figure S1File S1 for all recombination events. The topology of the phylogeny, potential minor parental-like strains, and breakpoint locations in the genome suggested most of the recombination events were not independent but took place in a common ancestor followed by successful circulation of descendant recombinants in the field. There was also evidence of recombination in local isolates, in the cases of strains #3, #6, and #10, with other strains of their same genotype but no indication of genomic exchange between endemic and High Fever-like strains.

Bottom Line: Overall, 0.56-2.83% of sites were found to be polymorphic with respect to cognate consensus genomes.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.

View Article: PubMed Central - PubMed

Affiliation: School of Biological Sciences, The University of Hong Kong, Hong Kong, China.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus