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A Genomic Approach to Unravel Host-Pathogen Interaction in Chelonians: The Example of Testudinid Herpesvirus 3.

Origgi FC, Tecilla M, Pilo P, Aloisio F, Otten P, Aguilar-Bultet L, Sattler U, Roccabianca P, Romero CH, Bloom DC, Jacobson ER - PLoS ONE (2015)

Bottom Line: Consistently, the phylogenetic analysis positions TeHV3 among the Alphaherpesvirinae, closely associated with Chelonid herpesvirus 5, a Scutavirus.To exemplify the potential benefits of the novel genomic information provided by this first whole genome analysis, we selected the glycoprotein B (gB) gene, for detailed comparison among different TeHV3 isolates.Viral isolation, TeHV identification, phylogenetic analysis and pathological characterization of the associated lesions, were performed.

View Article: PubMed Central - PubMed

Affiliation: Centre for Fish and Wildlife Health (FIWI), Vetsuisse Faculty, University of Bern, Bern, Switzerland.

ABSTRACT
We report the first de novo sequence assembly and analysis of the genome of Testudinid herpesvirus 3 (TeHV3), one of the most pathogenic chelonian herpesviruses. The genome of TeHV3 is at least 150,080 nucleotides long, is arranged in a type D configuration and comprises at least 102 open reading frames extensively co-linear with those of Human herpesvirus 1. Consistently, the phylogenetic analysis positions TeHV3 among the Alphaherpesvirinae, closely associated with Chelonid herpesvirus 5, a Scutavirus. To date, there has been limited genetic characterization of TeHVs and a resolution beyond the genotype was not feasible because of the lack of informative DNA sequences. To exemplify the potential benefits of the novel genomic information provided by this first whole genome analysis, we selected the glycoprotein B (gB) gene, for detailed comparison among different TeHV3 isolates. The rationale for selecting gB is that it encodes for a well-conserved protein among herpesviruses but is coupled with a relevant antigenicity and is consequently prone to accumulate single nucleotide polymorphisms. These features were considered critical for an ideal phylogenetic marker to investigate the potential existence of distinct TeHV3 genogroups and their associated pathology. Fifteen captive tortoises presumptively diagnosed to be infected with TeHVs or carrying compatible lesions on the basis of either the presence of intranuclear inclusions (presumptively infected) and/or diphtheronecrotic stomatitis-glossitis or pneumonia (compatible lesions) were selected for the study. Viral isolation, TeHV identification, phylogenetic analysis and pathological characterization of the associated lesions, were performed. Our results revealed 1) the existence of at least two distinct TeHV3 genogroups apparently associated with different pathologies in tortoises and 2) the first evidence for a putative homologous recombination event having occurred in a chelonian herpesvirus. This novel information is not only fundamental for the genetic characterization of this virus but is also critical to lay the groundwork for an improved understanding of host-pathogen interactions in chelonians and contribute to tortoise conservation.

No MeSH data available.


Related in: MedlinePlus

TeHV3 genome map.The TeHV3 genome is composed of a unique long region (UL) (blue bar) and a unique short region (US) (green bar) flanked by two inverted repeats (red bars). The progressive numbers and the homologous herpesvirus genes of the identified sense (orange) and antisense (green) open reading frames (ORFs) are shown in the map (SnapGene Viewer-V2.7; www.snapgene.com).
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pone.0134897.g001: TeHV3 genome map.The TeHV3 genome is composed of a unique long region (UL) (blue bar) and a unique short region (US) (green bar) flanked by two inverted repeats (red bars). The progressive numbers and the homologous herpesvirus genes of the identified sense (orange) and antisense (green) open reading frames (ORFs) are shown in the map (SnapGene Viewer-V2.7; www.snapgene.com).

Mentions: Next generation sequencing (NGS): A total yield of 1.598 mega bases (Mb) was obtained with 31,959,585 clusters. 95.8% of the bases had a Q-score (measure of base-calling accuracy) larger than 30. The de novo assembly of the reads led to a total of 24 contigs spanning from 107 to 64,501 nt long and accounting for 140,195 nt (N50 of 23,603 nt). The average base coverage (depth) was 8,984. Bridging of the contigs was carried out by PCR and with the aid of the sequencing information derived from the HindIII and EcoRI subgenomic libraries as previously mentioned. The final sequence of the genome comprised 150,080 nt (Fig 1). The TeHV3 genome is composed of a unique long (UL) and a unique short (US) region, with the US flanked by inverted repeats consistent with a type D arrangement similar to that of Human herpesvirus 3 (HHV3-VZV) and the recently described genome of ChHV5 [22]. The GC content was 45.8%.


A Genomic Approach to Unravel Host-Pathogen Interaction in Chelonians: The Example of Testudinid Herpesvirus 3.

Origgi FC, Tecilla M, Pilo P, Aloisio F, Otten P, Aguilar-Bultet L, Sattler U, Roccabianca P, Romero CH, Bloom DC, Jacobson ER - PLoS ONE (2015)

TeHV3 genome map.The TeHV3 genome is composed of a unique long region (UL) (blue bar) and a unique short region (US) (green bar) flanked by two inverted repeats (red bars). The progressive numbers and the homologous herpesvirus genes of the identified sense (orange) and antisense (green) open reading frames (ORFs) are shown in the map (SnapGene Viewer-V2.7; www.snapgene.com).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4526542&req=5

pone.0134897.g001: TeHV3 genome map.The TeHV3 genome is composed of a unique long region (UL) (blue bar) and a unique short region (US) (green bar) flanked by two inverted repeats (red bars). The progressive numbers and the homologous herpesvirus genes of the identified sense (orange) and antisense (green) open reading frames (ORFs) are shown in the map (SnapGene Viewer-V2.7; www.snapgene.com).
Mentions: Next generation sequencing (NGS): A total yield of 1.598 mega bases (Mb) was obtained with 31,959,585 clusters. 95.8% of the bases had a Q-score (measure of base-calling accuracy) larger than 30. The de novo assembly of the reads led to a total of 24 contigs spanning from 107 to 64,501 nt long and accounting for 140,195 nt (N50 of 23,603 nt). The average base coverage (depth) was 8,984. Bridging of the contigs was carried out by PCR and with the aid of the sequencing information derived from the HindIII and EcoRI subgenomic libraries as previously mentioned. The final sequence of the genome comprised 150,080 nt (Fig 1). The TeHV3 genome is composed of a unique long (UL) and a unique short (US) region, with the US flanked by inverted repeats consistent with a type D arrangement similar to that of Human herpesvirus 3 (HHV3-VZV) and the recently described genome of ChHV5 [22]. The GC content was 45.8%.

Bottom Line: Consistently, the phylogenetic analysis positions TeHV3 among the Alphaherpesvirinae, closely associated with Chelonid herpesvirus 5, a Scutavirus.To exemplify the potential benefits of the novel genomic information provided by this first whole genome analysis, we selected the glycoprotein B (gB) gene, for detailed comparison among different TeHV3 isolates.Viral isolation, TeHV identification, phylogenetic analysis and pathological characterization of the associated lesions, were performed.

View Article: PubMed Central - PubMed

Affiliation: Centre for Fish and Wildlife Health (FIWI), Vetsuisse Faculty, University of Bern, Bern, Switzerland.

ABSTRACT
We report the first de novo sequence assembly and analysis of the genome of Testudinid herpesvirus 3 (TeHV3), one of the most pathogenic chelonian herpesviruses. The genome of TeHV3 is at least 150,080 nucleotides long, is arranged in a type D configuration and comprises at least 102 open reading frames extensively co-linear with those of Human herpesvirus 1. Consistently, the phylogenetic analysis positions TeHV3 among the Alphaherpesvirinae, closely associated with Chelonid herpesvirus 5, a Scutavirus. To date, there has been limited genetic characterization of TeHVs and a resolution beyond the genotype was not feasible because of the lack of informative DNA sequences. To exemplify the potential benefits of the novel genomic information provided by this first whole genome analysis, we selected the glycoprotein B (gB) gene, for detailed comparison among different TeHV3 isolates. The rationale for selecting gB is that it encodes for a well-conserved protein among herpesviruses but is coupled with a relevant antigenicity and is consequently prone to accumulate single nucleotide polymorphisms. These features were considered critical for an ideal phylogenetic marker to investigate the potential existence of distinct TeHV3 genogroups and their associated pathology. Fifteen captive tortoises presumptively diagnosed to be infected with TeHVs or carrying compatible lesions on the basis of either the presence of intranuclear inclusions (presumptively infected) and/or diphtheronecrotic stomatitis-glossitis or pneumonia (compatible lesions) were selected for the study. Viral isolation, TeHV identification, phylogenetic analysis and pathological characterization of the associated lesions, were performed. Our results revealed 1) the existence of at least two distinct TeHV3 genogroups apparently associated with different pathologies in tortoises and 2) the first evidence for a putative homologous recombination event having occurred in a chelonian herpesvirus. This novel information is not only fundamental for the genetic characterization of this virus but is also critical to lay the groundwork for an improved understanding of host-pathogen interactions in chelonians and contribute to tortoise conservation.

No MeSH data available.


Related in: MedlinePlus