Skip to main content
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems
  • Log in
  • My alerts
  • My Cart

Main menu

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Minireviews
    • JVI Classic Spotlights
    • Archive
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JVI
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
  • ASM
    • Antimicrobial Agents and Chemotherapy
    • Applied and Environmental Microbiology
    • Clinical Microbiology Reviews
    • Clinical and Vaccine Immunology
    • EcoSal Plus
    • Infection and Immunity
    • Journal of Bacteriology
    • Journal of Clinical Microbiology
    • Journal of Microbiology & Biology Education
    • Journal of Virology
    • mBio
    • Microbiology and Molecular Biology Reviews
    • Microbiology Resource Announcements
    • Microbiology Spectrum
    • Molecular and Cellular Biology
    • mSphere
    • mSystems

User menu

  • Log in
  • My alerts
  • My Cart

Search

  • Advanced search
Journal of Virology
publisher-logosite-logo

Advanced Search

  • Home
  • Articles
    • Current Issue
    • Accepted Manuscripts
    • COVID-19 Special Collection
    • Minireviews
    • JVI Classic Spotlights
    • Archive
  • For Authors
    • Submit a Manuscript
    • Scope
    • Editorial Policy
    • Submission, Review, & Publication Processes
    • Organization and Format
    • Errata, Author Corrections, Retractions
    • Illustrations and Tables
    • Nomenclature
    • Abbreviations and Conventions
    • Publication Fees
    • Ethics Resources and Policies
  • About the Journal
    • About JVI
    • Editor in Chief
    • Editorial Board
    • For Reviewers
    • For the Media
    • For Librarians
    • For Advertisers
    • Alerts
    • RSS
    • FAQ
  • Subscribe
    • Members
    • Institutions
Genetic Diversity and Evolution

Comparative Genome Analysis of Four Elephant Endotheliotropic Herpesviruses, EEHV3, EEHV4, EEHV5, and EEHV6, from Cases of Hemorrhagic Disease or Viremia

Jian-Chao Zong, Erin M. Latimer, Simon Y. Long, Laura K. Richman, Sarah Y. Heaggans, Gary S. Hayward
L. Hutt-Fletcher, Editor
Jian-Chao Zong
aViral Oncology Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Erin M. Latimer
bNational Elephant Herpesvirus Laboratory, Pathology Department, Smithsonian's National Zoo, Washington, DC, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Simon Y. Long
aViral Oncology Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Laura K. Richman
bNational Elephant Herpesvirus Laboratory, Pathology Department, Smithsonian's National Zoo, Washington, DC, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sarah Y. Heaggans
aViral Oncology Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Gary S. Hayward
aViral Oncology Program, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
L. Hutt-Fletcher
Roles: Editor
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
DOI: 10.1128/JVI.01675-14
  • Article
  • Figures & Data
  • Info & Metrics
  • PDF
Loading

Article Figures & Data

Figures

  • Tables
  • Additional Files
  • FIG 1
    • Open in new tab
    • Download powerpoint
    FIG 1

    Schematic map of position coordinates for all sequenced loci in EEHV3, EEHV4, EEHV5A, EEHV5B, and EEHV6 compared to the complete EEHV1A(Kimba) genome. The diagram is drawn to scale with bars representing all of the DNA sequence blocks generated here aligned relative to the complete 177,316-kb genome of EEHV1A(Kimba) (13). The data reported by Ehlers et al. (11) for EEHV1B(Kiba) is also given for comparison in the top line. The locations of the predicted Ori-Lyt dyad symmetry locus (black circle), the large 40-kb inverted (Inv) core domain III-II-I segment (green arrow), the putative immediate early-like ORF-L transactivator protein coding region (blue arrow), and the three major hypervariable domains CD-I, CD-II, and CD-III (yellow boxes) as described by Richman et al. (10) are indicated.

  • FIG 2
    • Open in new tab
    • Download powerpoint
    FIG 2

    Radial phylogenetic tree showing evolutionary relationships between EEHV1, EEHV2, EEHV3, EEHV4, EEHV5, and EEHV6 in the highly conserved U38(POL) DNA gene. The diagram shows a distance-based Bayesian nearest-neighbor evolutionary tree dendrogram produced in MEGA5 illustrating the branching patterns of the GC-rich (EEHV3 plus EEHV4) compared to the AT-rich EEHV groups and of the two distinct subgroups (EEHV1 plus EEHV6 compared to EEHV2 and EEHV5) within the AT-rich branch. After several small gaps and nonaligned nucleotides were omitted, the final data set for the segment of U38(POL) gene DNA used that is common to all eight EEHV types was 1,077 bp. The number of nucleotide substitutions per site is shown by the bar.

  • FIG 3
    • Open in new tab
    • Download powerpoint
    FIG 3

    Evaluation of EEHV1A-1B chimeric domain CD-I patterns and boundaries relative to EEHV6. The diagrams show SimPlot comparisons of the nucleotide identity patterns between EEHV6, EEHV1A, EEHV1B, and EEHV2 across the 3.0-kb EEHV1B chimeric domain CD-I. (a) CD-I. The 5,000-bp U39(gB)-U38(POL) segment from EEHV1A(Kala, NAP18) map coordinates 73,959 to 79,043 compared to EEHV6(NAP35) (blue) and to EEHV2(Kijana, NAP12) (gray) is shown. (b) CD-I. The 4,800-bp U39(gB)-U38(POL) segment from EEHV1A(Kala, NAP18) map coordinates 73,987 to 78,860 compared to EEHV1B(Kiba, NAP14) (red) and to EEHV6(NAP35) (blue) is shown. (c) CD-I. The 5,000-bp U39(gB)-U38(POL) segment from EEHV1A(Kala, NAP18) map coordinates 73,959 to 79,043 compared to EEHV1B(Haji, NAP19) (green) and to EEHV6(NAP35) (blue) is shown. Arrows mark the positions of the chimeric domain boundary transitions, and the relevant DNA accession numbers are included in Table S1 in the supplemental material.

  • FIG 4
    • Open in new tab
    • Download powerpoint
    FIG 4

    Evaluation of EEHV1A-1B chimeric domain CD-II and CD-III patterns and boundaries relative to EEHV6. The diagrams show SimPlot comparisons of the nucleotide similarity patterns between EEHV6, EEHV1A, and EEHV1B across both the left-hand side (LHS) and right-hand side (RHS) boundaries of the 3.7-kb CD-II region and across the LHS boundary only of the 8.3-kb CD-III region of EEHV1B. (a) CD-II LHS. The left-hand side of the 2.6-kb U27(PPF)-U47(gO) segment across map coordinates 101,128 to 103,703 for EEHV1A(Kala, NAP18) compared to EEHV1B(Kiba, NAP14) (red) and to EEHV6(NAP35) (blue). (b) CD-II RHS. The right-hand side of the 2.7-kb U48(gH)-U50(PAC2) segment across map coordinates 105,364 to 108,084 for EEHV1A(Kala, NAP18) compared to EEHV1B(Kiba, NAP14) (red) and to EEHV6(NAP35) (blue) is shown. (c) CD-III LHS. The left-hand side of the 4.3-kb U77-U82.5(ORF-O) segment across map coordinates 143,644 to 147,936 for EEHV1A(Kala, NAP18) compared to EEHV1B(Kiba, NAP14) (red) and to EEHV6(NAP35) (blue) is shown. (Data for the right-hand segment of CD-III are not yet available for EEHV6.) Arrows mark the positions of the chimeric domain boundary transitions, and the relevant DNA accession numbers are included in Table S1 in the supplemental material.

  • FIG 5
    • Open in new tab
    • Download powerpoint
    FIG 5

    Evaluation of the EEHV5A-5B chimeric domain patterns and boundaries relative to EEHV2. The diagrams show SimPlot comparisons between EEHV5A, EEHV5B, and EEHV2 across all three EEHV5B chimeric domain regions, including all of CD-I (2.4 kb) and CD-II (1.1 kb) and the left-hand side boundary of CD-III (>2.7 kb). (a) CD-I. The 4,800-bp U39(gB)-U38(POL) segment from across map coordinates 74,002 to 78,861 for EEHV5A(NAP50) compared to EEHV5B(NAP58) (blue) and to EEHV2(NAP12) (red) is shown. (b) CD-II. The 2.8-kb U48(gH)–U48.5(TK)–U49–U50 segment from across map coordinates 105,396 to 108,178 for EEHV5A(NAP50) compared to EEHV5B(NAP58) (blue) and to EEHV2(NAP12) (red) is shown. (c) CD-III. The left-hand side only of the 4,300-bp segment across map coordinates 143,644 to 147,958 for EEHV5A(NAP50) encompassing U77(HEL C terminus), U77.5(ORF-M), U80.5(ORF-N), U81(UDG), U82(gL), and U82.5(ORF-Oex3) compared to EEHV5B(NAP58) (blue) and EEHV2(NAP12) (red) is shown.

  • FIG 6
    • Open in new tab
    • Download powerpoint
    FIG 6

    Linear DNA level phylogenetic trees comparing four gene loci from EEHV3, EEHV4, EEHV5A, EEHV5B, and EEHV6 with their orthologues in EEHV1, EEHV2, and other key herpesviruses. The diagrams present linear Bayesian maximum likelihood phylogenetic dendrograms at the nucleotide level for a set of representative EEHV gene loci from the five EEHV3, EEHV4, EEHV5A, EEHV5B, and EEHV6 (proposed Deltaherpesvirinae [δ]) genomes determined here, together with orthologues from EEHV1A, EEHV1B, and EEHV2 (10). These are compared with matching segments of selected orthologous gene loci among representative herpesviruses from all three other mammalian subfamilies, Alphaherpesvirinae (α), Gammaherpesvirinae (γ), and Betaherpesvirinae (β). Alternative virus names and GenBank accession numbers for both the non-EEHV and EEHV genome file sources used are listed in supplemental material or in Table S1 in the supplemental material. Bootstrap values are shown as percentages at the nodes. The final DNA segment sizes were as follows for panels a to d: (a) U38(POL) locus, DNA polymerase, 927 bp; (b) U73(OBP) locus, origin binding protein, 576 bp; (c) U76(POR)-U77(HEL) locus, portal protein plus helicase subunit; (d) U71-U72(gM) locus, myristylated tegument protein plus glycoprotein M, 353 bp. All four panels use Marek's disease alphaherpesvirus (MDV) as an outgroup.

  • FIG 7
    • Open in new tab
    • Download powerpoint
    FIG 7

    Linear protein level phylogenetic trees comparing five protein segments from EEHV5 and EEHV6 with their orthologues in EEHV1, EEHV2, and other key herpesviruses. The diagrams present linear Bayesian maximum likelihood phylogenetic dendrograms at the amino acid level for a set of representative proteins from the prototype EEHV5A, EEHV5B, and EEHV6 genomes, as well as up to five other orthologues from EEHV1A, EEHV1B, and EEHV2 (proposed Deltaherpesvirinae [δ]). These are compared to matching segments of orthologous gene loci from selected herpesviruses representative of the Alphaherpesvirinae (α), Gammaherpesvirinae (γ), or Betaherpesvirinae (β) subfamilies. Bootstrap values are shown as percentages. The final protein segment sizes used were as follows for panels a to e: (a) U48.5(TK), thymidine kinase, 244 aa, with turtle herpesvirus (TurtleHV) used as the outgroup; (b) U27(PPF), polymerase processivity factor, 110 aa, with MDV used as the outgroup; (c) U39(gB), glycoprotein B, 727 aa, including only the Betaherpesvirinae as references with EBV used as the outgroup; (d) U82(gL), glycoprotein L, 85 aa, with only Betaherpesvirinae included as references and EBV used as the outgroup; (e) U81(UDG), uracil DNA glycosylase, 252 aa, with only Roseolovirus species used for reference and HHV7 used as the outgroup.

  • FIG 8
    • Open in new tab
    • Download powerpoint
    FIG 8

    Comparison of EEHV POL protein divergence levels with great ape plus New World and Old World primate versions within the alpha-, beta-, and gammaherpesvirus subfamilies. The diagram shows a linear distance-based Bayesian phylogenetic tree dendrogram at the amino acid level for each of the eight prototype EEHV genomes (proposed Deltaherpesvirinae [δ]) across the largest segment of U38(POL) in common (1,080 bp, Kimba equivalent coordinates 77,783 to 78,863). To allow direct comparisons of estimated ages of divergence (see the text), these are compared with matching segments of orthologous gene loci from selected primate herpesviruses representative of just the Simplexvirus (Alphaherpesvirinae [α]), Lymphocryptovirus genus (Gammaherpesvirinae [γ]), and Cytomegalovirus (Betaherpesvirinae [β]) genera. Human VZV (Varicellovirus genus) was used as the outgroup. The evolutionary history was inferred by using the maximum likelihood method based on the Kimura two-parameter model with initial trees for the heuristic model obtained by applying the neighbor-joining method. The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. Evolutionary analyses were conducted in MEGA5. Bootstrap values are shown as percentages.

  • FIG 9
    • Open in new tab
    • Download powerpoint
    FIG 9

    Clustal alignment illustrating variability patterns among the intact glycoprotein L (gL) and uracil DNA glycosylase (UDG) proteins from distinct types of EEHV genomes. Clustal-W presentations comparing the predicted primary amino acid sequence alignments of the prototypes of all six available types and subtypes of AT-rich branch Proboscivirus genomes compared to their closest orthologues in either all Betaherpesvirinae or in just the Roseolovirus genus. GenBank accession numbers for the EEHV proteins and betaherpesvirus reference species used are given in the supplemental material. (a) U82(gL), glycoprotein L, intact proteins; (b) U81(UDG), uracil DNA glycosylase, intact proteins. Positions with 100% similarity are boxed. Gaps introduced to maximize alignment are indicated by hyphens.

  • FIG 10
    • Open in new tab
    • Download powerpoint
    FIG 10

    Clustal alignments illustrating variability patterns among the intact ORF-J, glycoprotein N (gN), and ORF-N(vCXCL1) proteins of AT-rich branch EEHV genomes. Clustal-W presentations comparing the primary amino acid sequence alignments for all available predicted Proboscivirus versions of three small unique or poorly conserved proteins that do not have orthologues in other herpesviruses for comparison are shown. (a) U45.7(ORF-J), intact novel proteins. (Data are not yet available for ORF-J of EEHV5A or EEHV5B.) (b) U46(gN), glycoprotein N, intact proteins. (Data are not yet available for gN of EEHV5A or EEHV5B.) (c) U80.5(vCXCL1, ORF-N), possible inhibitory alpha-chemokine ligand. [The vCXCL1(ORF-N) gene is absent from EEHV1B.] Positions with 100% similarity are boxed.

Tables

  • Figures
  • Additional Files
  • TABLE 1

    Summary of six EEHV-positive elephant cases evaluated in these studies

    CaseVirus typeStrainElephant nameaHost species, sex, and agebLocationYrPathologyc (reference)DNA sourcedSequenced DNA (bp)
    1EEHV3NAP27HansaEM, F, 7ySeattle, WA2007Fatality (3)Necropsy tissue sample4,117
    2EEHV4NAP22NAEM, F, 5yOklahoma2004Fatality (3)Necropsy tissue sample5,743
    3EEHV5ANAP28NAEM, F, 69yWashington, DC2007Routine (4)WB sample14,615
    4EEHV5ANAP50Methai2EM, F, 40yTexas2011Letharg. (17)WB sample26,090
    5EEHV5BNAP58Tucker3EM, M, 8yTexas2011Asympt. (17)WB, TW samples29,347
    6EEHV6eNAP35NALA, F, 15mArkansas2009Sympt. (4)WB sample31,828
    Total111,749
    • ↵a NA, not available.

    • ↵b The host animal species (Elephas maximus [EM] or Loxodonta africana [LA]), sex (female [F] or male [M]), and age (in months [m] or years [y]) is shown.

    • ↵c Letharg., lethargic; Asympt, asymptomatic; Sympt, symptomatic.

    • ↵d WB, whole blood; TW, trunk wash fluid.

    • ↵e Survived after FCV treatment.

  • TABLE 2

    Summary of PCR-sequenced EEHV3, EEHV4, EEHV5A, EEHV5B, and EEHV6 gene coding regions

    Gene/ORF no./IDaHCMV ORFHSV ORFOrientationbProtein nameStatuscPresence/absence of the indicated ORFd
    EEHV3 NAP27EEHV4 NAP22EEHV5A NAP28EEHV5A NAP50EEHV5B NAP58EEHV6 NAP35
    U39UL55UL29FgBCore+++++
    U38UL54UL30FPOLCore++++++
    U33UL49NilFCys-richβ/γ++++
    U28UL45UL39FRRACore++++
    U27.5/ORF-HNilUL40FRRBα/β2++++
    U27/ORF-IUL44UL42FPPFCore+++
    U45.7/ORF-JNilNilFNovel+
    U46UL73UL49AFgNCore+
    U47/ORF-DUL74NilRgOβ+
    U48UL75UL22RgHCore++++
    U48.5/ORF-ENilUL23RTKα/γ++++
    U49UL76UL24FCore++++
    U50UL77UL25FPAC2Core+++
    U51UL78NilFvGPCR1β++++
    U57UL86UL19RMCPCore++++
    U60ex3UL89UL15ex2RTERex3Core+++++
    U62UL91NilFβ/γ+++
    U63UL92NilFβ/γ+
    U66ex2NilNilRTERex2Core+
    U66ex1UL89ex1UL15ex1RTERex1Core+
    U70UL98UL12FEXOCore++++++
    U71UL99UL11FmyrTeg.Core++++++
    U72UL100UL10RgMCore++++++
    U73/ORF-GNilUL09FOBPα/β++++++
    U76UL104UL06RPORCore++++++
    U77UL105UL05FHELCore++++++
    U77.5/ORF-MNilNilFNuclearNovel+++
    U80.5/ORF-NNilNilRvCXCL1Novel+++
    U81UL114UL02RUDGCore+++
    U82UL115UL01RgLCore+++
    U82.5/ORF-Oex3NilNilRS/TGlyPNovel+++
    U82.5/ORF-Oex2NilNilRS/TGlyPNovel+++
    U82.5/ORF-Oex1NilNilRS/TGlyPNovel+++
    U83.5/ORF-Pex2NilNilRS/TGlyPNovel+
    U83.5/ORF-Pex1NilNilRS/TGlyPNovel+
    U84.5/ORF-QNilNilRS/TGlyPNovelA
    U85.5/ORF-Kex3NilNilRSplGlyPNovel+++
    U85.5/ORF-Kex2NilNilRSplGlyPNovel+++
    U85.5/ORF-Kex1NilNilRSplGlyPNovel+++
    U86.5/ORF-LNilNilRIE-likeNovel+++
    • ↵a ID, identification.

    • ↵b F, forward; R, reverse.

    • ↵c Novel, not found in any other herpesviruses; β, betaherpesvirus subfamily only; Core, common to all herpesvirus subfamilies; β/γ, betaherpesvirus and gammaherpesvirus subfamilies only; α/β, alphaherpesvirus and betaherpesvirus subfamilies only; α/β2, alphaherpesvirus subfamily and roseoloviruses only.

    • ↵d +, partial or intact ORF present (see Table S1 in supplemental material for detailed coordinates, percent divergence, and GenBank accession numbers); A, gene absent.

  • TABLE 3

    DNA and protein divergence in ORFs across EEHV3, EEHV4, and EEHV1A

    Gene locusEEHV1A coordinatesaProtein size (no. of aa)bNucleotide level divergence (%)cAmino acid level divergence (%)cOverall % G+C contentdWobble % G+C contentd
    3/43/1A4/1A3/43/1A4/1A341A341A
    U38(POL)(77782–78912)(412)7.034347.52625676842898943
    U60(TERex3)(123721–124037)(105)3.82223155575642918641
    U71(MyrTeg)132954–13324196265049296366615846766141
    U72(gM)(133320–133608)(95)1445135255408042
    U72(gM)(133316–134404)372343555408949
    U73(OBP)(134645–135283)(237)1748223963419146
    U73(OBP)(134404–135284)(438)545464448849
    U76(POR)(140967–141295)(104)3.3343012121646342989947
    U77(HEL)(141246–141878)(189)3.530302.52322676741969750
    • ↵a The EEHV1A coordinates are based on Ling et al. (13). Entries shown in parentheses indicate that an incomplete ORF or smaller region was used.

    • ↵b aa, amino acids.

    • ↵c Divergence of EEHV3, EEHV4, and EEHV1A is indicated as follows: EEHV3 and EEHV4 (3/4), EEHV3 and EEHV1A (3/1A), and EEHV4 andEEHV1A (4/1A).

    • ↵d The total guanine-plus-cytosine nucleotide percentages of EEHV3, EEHV4, and EEHV1A (indicated by 3, 4, and 1A in the table) compared to those at just the third nucleotide position in all codons from the predicted proteins.

  • TABLE 4

    DNA and protein divergence in ORFs across the EEHV1A, EEHV1B, and EEHV6 genomesa

    Gene locusEEHV1A(Kimba) coordinatesbProtein sizebNucleotide level divergence (%)cAmino acid level divergence (%)cChimeric domain
    1A-1B1A-61B-61A-1B1A-61B-6
    U39(gB)73959–76511836211620141113CD-I
    U38/(POL)(76544–79043)(832)5171641212CD-I
    U33(83628–84428)(266)1.322210.31918
    U28(RRA)99358–997608011.11415088
    U27.5(RRB)99804–1007093021.414140.31717
    U27(PPF)100960–1021864081.816160.566
    U45.7(ORF-J)102168–102775168261625321433CD-II
    U46(gN)102759–10371396291628206.218CD-II
    U47(gO)103075–103713212351635381137CD-II
    U48(gH)(105363–105903)(179)311728332137CD-II
    U48.5(TK)105835–106908356131618162120CD-II
    U49106910–1076082323.615150.41213
    U50(PAC2)(107427–108083)(220)4.023233.12021
    U51(vGPCR1)(109398–110239)(286)4.222233.31417
    U57(MCP)(115577–117866)(748)2.717171.277
    U60(TERex3)123601–124175(194)2.912130d0d0d
    U62124231–124477880.81313099
    U71(MyrTeg)132954–133241968252592326
    U72(gM)(133320–133614)(97)4.413143.39.27.2
    U73(OBP)(134615–135415)(277)3.014141.96.06.7
    U76(POR)(139998–141295)(433)1.9131304.24.2
    U77(HEL)(141294–141864)(190)2.812130.57.07.5
    U77.5(ORF-M)143988–145502503161619131316CD-III
    U80.5(ORF-N)145642–145959106Del31DelDel29DelCD-III
    U81(UDG)146027–146980317291930291930CD-III
    U82(gL)146946–147860304311830332241CD-III
    U82.5(ORF-O)(147700–147910)(78)331631341837CD-III
    U85.5(ORF-K)(152200–153350)(380)1.726260.82525
    U86.5(ORF-L)(155324–158615)(1084)2.411110.61818
    • ↵a The rows in the table shown in bold type indicate ORFs that are highly variable between EEHV1A and EEHV1B.

    • ↵b The EEHV1A coordinates are based on Ling et al. (13). The values shown in parentheses indicate that an incomplete ORF or shorter region was used.

    • ↵c The divergence between EEHV1A and EEHV1B (1A-1B), EEHV1A and EEHV6 (1A-6), and EEHV1B and EEHV6 (1B-6) is shown. Del, ORF-N is absent (deleted) in all EEHV1B strains.

    • ↵d All three TER proteins are identical or only 1 aa different over this 194-aa segment.

  • TABLE 5

    DNA and protein divergence in ORFs across EEHV5A, EEHV5B, EEHV2, and EEHV1Aa

    Gene locusEEHV1A coordinatesbProtein sizebNucleotide level divergence (%)cAmino acid level divergence (%)cChimeric domain
    5A-5B5A-25B-25A-15A-5B5A-25B-25A-1
    U39(gB)(74091–76511)(837)101615274.27.66.321CD-I
    U38(POL)(76583–79038)(818)1.31817241.4111121CD-1
    U33(83648–84183)(176)0.82828370252543
    U28(RRA)(98637–99760)(374)0.417172308.68.616
    U27.5(RRB)99804–100709(301)0.91616240.76.36.315
    U27(PPF)(100960–101609)(216)0.81919310.9141425
    U48(gH)(105396–105911)(172)01818380161634
    U48.5(TK)105835–1069083441418203013191927CD-II
    U49106910–1076282336.01110242.16.94.724CD-II
    U50(PAC2)(107428–108178)(261)0.21818320191934
    U51(vGPCR1)(109225–110065)(292)4.62223322.7171725
    U57(MCP)(116671–117809)(380)0.21919270.39.29.219
    U60(TERex3)(123674–124180)(169)1.213132101.31.33.0
    U62(124231–124434)(75)0.51616290101019
    U71(MyrTeg)132954–133241988.724234414273056
    U72(gM)133316–133613(101)0.31617210101012
    U73(OBP)(134605–134430)(269)012122104.44.410
    U76(POR)(139815–141295)(493)0.21313220.44.14.17.8
    U77(HEL)(141294–141793)(181)0.41414240.76.06.014
    U77.5(ORF-M)143988–1455114841.11617290101017CD-III
    U80.5(ORF-N)145642–1459591062823273832243347CD-III
    U81(UDG)146027–1469803242723283323212029CD-III
    U82(gL)146946–1477763122717273426162644CD-III
    U82.5(ORF-Oex3)147694–147958(88)2321253221202025CD-III
    U82.5(ORF-O)147700–1489854873654d3453d
    U83.5(ORF-P)146932–1506385263348d3352d
    U85.5(ORF-K)152042–154436(678)1.32322410.4292748
    U86.5(ORF-L)155053–155356(97)1.41012301.07.08.420
    • ↵a The prototype genomes used were EEHV5A(NAP50), EEHV5B(NAP58), EEHV2(NAP12), and EEHV1A(NAP18). The rows in the table shown in bold type indicate ORFs with high-level variability (hypervariable genes) between EEHV5A and EEHV5B.

    • ↵b The values in parentheses indicate that incomplete ORFs were used.

    • ↵c The divergence between EEHV5A and EEHV5B (5A-5B), EEHV5A and EEHV2 (5A-2), EEHV5B and EEHV2 (5B-2), and EEHV5A and EEHV1 (5A-1) is shown.

    • ↵d These values show divergence between EEHV5B and EEHV1A.

Additional Files

  • Figures
  • Tables
  • Supplemental material

    Files in this Data Supplement:

    • Supplemental file 1 -

      Section S1 (Detailed ORF coordinate data for individual EEHV PCR loci.)

      Table S1 (Details of sequenced EEHV3, EEHV4, EEHV5A, EEHV5B, and EEHV6 gene coding regions.)

      Section S2 (Examples of primers used to amplify specific gene loci.)

      Section S3 (Full or alternative virus names and non-EEHV GenBank accession numbers.)

      Section S4 (EEHV GenBank accession numbers for EEHV DNA or protein files used in the phylogenetic dendrograms or Clustal comparisons.)

      PDF, 206K

PreviousNext
Back to top
Download PDF
Citation Tools
Comparative Genome Analysis of Four Elephant Endotheliotropic Herpesviruses, EEHV3, EEHV4, EEHV5, and EEHV6, from Cases of Hemorrhagic Disease or Viremia
Jian-Chao Zong, Erin M. Latimer, Simon Y. Long, Laura K. Richman, Sarah Y. Heaggans, Gary S. Hayward
Journal of Virology Oct 2014, 88 (23) 13547-13569; DOI: 10.1128/JVI.01675-14

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
Print

Alerts
Sign In to Email Alerts with your Email Address
Email

Thank you for sharing this Journal of Virology article.

NOTE: We request your email address only to inform the recipient that it was you who recommended this article, and that it is not junk mail. We do not retain these email addresses.

Enter multiple addresses on separate lines or separate them with commas.
Comparative Genome Analysis of Four Elephant Endotheliotropic Herpesviruses, EEHV3, EEHV4, EEHV5, and EEHV6, from Cases of Hemorrhagic Disease or Viremia
(Your Name) has forwarded a page to you from Journal of Virology
(Your Name) thought you would be interested in this article in Journal of Virology.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Comparative Genome Analysis of Four Elephant Endotheliotropic Herpesviruses, EEHV3, EEHV4, EEHV5, and EEHV6, from Cases of Hemorrhagic Disease or Viremia
Jian-Chao Zong, Erin M. Latimer, Simon Y. Long, Laura K. Richman, Sarah Y. Heaggans, Gary S. Hayward
Journal of Virology Oct 2014, 88 (23) 13547-13569; DOI: 10.1128/JVI.01675-14
del.icio.us logo Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
  • Top
  • Article
    • ABSTRACT
    • INTRODUCTION
    • MATERIALS AND METHODS
    • RESULTS
    • DISCUSSION
    • ACKNOWLEDGMENTS
    • FOOTNOTES
    • REFERENCES
  • Figures & Data
  • Info & Metrics
  • PDF

Related Articles

Cited By...

About

  • About JVI
  • Editor in Chief
  • Editorial Board
  • Policies
  • For Reviewers
  • For the Media
  • For Librarians
  • For Advertisers
  • Alerts
  • RSS
  • FAQ
  • Permissions
  • Journal Announcements

Authors

  • ASM Author Center
  • Submit a Manuscript
  • Article Types
  • Ethics
  • Contact Us

Follow #Jvirology

@ASMicrobiology

       

 

JVI in collaboration with

American Society for Virology

ASM Journals

ASM journals are the most prominent publications in the field, delivering up-to-date and authoritative coverage of both basic and clinical microbiology.

About ASM | Contact Us | Press Room

 

ASM is a member of

Scientific Society Publisher Alliance

 

American Society for Microbiology
1752 N St. NW
Washington, DC 20036
Phone: (202) 737-3600

Copyright © 2021 American Society for Microbiology | Privacy Policy | Website feedback

Print ISSN: 0022-538X; Online ISSN: 1098-5514