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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

Selection of hypervariable nucleotide changes for phylogenetic analysis.In a hypervariable region of the glycoprotein B gene spanning across approximately 250 nt, are clustered 22 of the 33 unambiguous nucleotide changes differentiating the A and B genogroups within TeHV3. This region was selected for a high-resolution phylogenetic analysis of TeHV3 strains. The light blue block highlights the selected region of the gene. (* = not available nucleotide for the putative group C TeHV strain).
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pone.0134897.g006: Selection of hypervariable nucleotide changes for phylogenetic analysis.In a hypervariable region of the glycoprotein B gene spanning across approximately 250 nt, are clustered 22 of the 33 unambiguous nucleotide changes differentiating the A and B genogroups within TeHV3. This region was selected for a high-resolution phylogenetic analysis of TeHV3 strains. The light blue block highlights the selected region of the gene. (* = not available nucleotide for the putative group C TeHV strain).

Mentions: Either complete or partial amplification of the gB gene was successfully obtained for all tortoises in the study (N = 15). In particular, the full amplification of the gB gene was obtained for strains US1976/98, IT191/12 and CH1458/12, and CH6883/03 (Table 1). The sequences obtained showed the highest variability in the 3’half of the gene. The 3’ half partial sequence of the gB gene was then selected for phylogenetic analysis. The amplified portion of the gB gene was 1084 nt long (1069–1084 nt readable according to the amplicons, including the primers) and was obtained from all the remaining tortoises in the study (Table 1). The alignment of the complete and partial sequences of the gB genes of the different TeHVs strains revealed the existence of a total of 66 single nt polymorphisms (SNP) between two groups (genogroups) of strains (n = 11 and n = 3) named A and B, respectively. Two SNPs were located within the first 102 nt of the gB sequence, while the remaining 64 clustered in the 3’half of the gene. Furthermore, the strain CH3429/01 showed intermediate features between genogroup A and B and was identified as an additional putative group C. Of the 66 SNPs 33 were uniquely differentiating genogroup A from B (Fig 4). Five of the SNPs were missense, resulting in aa changes (Fig 5). All the missense SNPs clustered in the 3’ half of the gene. Within a 250 nt-long region of the highly variable portion of the gB gene were clustered most of the SNPs (22 SNPs; 1,521–1,779 nt) differentiating genogroup A and B; similarly for the additional putative recombinant strain (genogroup C) (Fig 6). This region of the gB gene was then selected as target region for TeHV3 genotyping.


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)

Selection of hypervariable nucleotide changes for phylogenetic analysis.In a hypervariable region of the glycoprotein B gene spanning across approximately 250 nt, are clustered 22 of the 33 unambiguous nucleotide changes differentiating the A and B genogroups within TeHV3. This region was selected for a high-resolution phylogenetic analysis of TeHV3 strains. The light blue block highlights the selected region of the gene. (* = not available nucleotide for the putative group C TeHV strain).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0134897.g006: Selection of hypervariable nucleotide changes for phylogenetic analysis.In a hypervariable region of the glycoprotein B gene spanning across approximately 250 nt, are clustered 22 of the 33 unambiguous nucleotide changes differentiating the A and B genogroups within TeHV3. This region was selected for a high-resolution phylogenetic analysis of TeHV3 strains. The light blue block highlights the selected region of the gene. (* = not available nucleotide for the putative group C TeHV strain).
Mentions: Either complete or partial amplification of the gB gene was successfully obtained for all tortoises in the study (N = 15). In particular, the full amplification of the gB gene was obtained for strains US1976/98, IT191/12 and CH1458/12, and CH6883/03 (Table 1). The sequences obtained showed the highest variability in the 3’half of the gene. The 3’ half partial sequence of the gB gene was then selected for phylogenetic analysis. The amplified portion of the gB gene was 1084 nt long (1069–1084 nt readable according to the amplicons, including the primers) and was obtained from all the remaining tortoises in the study (Table 1). The alignment of the complete and partial sequences of the gB genes of the different TeHVs strains revealed the existence of a total of 66 single nt polymorphisms (SNP) between two groups (genogroups) of strains (n = 11 and n = 3) named A and B, respectively. Two SNPs were located within the first 102 nt of the gB sequence, while the remaining 64 clustered in the 3’half of the gene. Furthermore, the strain CH3429/01 showed intermediate features between genogroup A and B and was identified as an additional putative group C. Of the 66 SNPs 33 were uniquely differentiating genogroup A from B (Fig 4). Five of the SNPs were missense, resulting in aa changes (Fig 5). All the missense SNPs clustered in the 3’ half of the gene. Within a 250 nt-long region of the highly variable portion of the gB gene were clustered most of the SNPs (22 SNPs; 1,521–1,779 nt) differentiating genogroup A and B; similarly for the additional putative recombinant strain (genogroup C) (Fig 6). This region of the gB gene was then selected as target region for TeHV3 genotyping.

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