Confusions in orbivirus protein classification

  • Meik Dilcher1Email author and

    Affiliated with

    • Manfred Weidmann1

      Affiliated with

      Virology Journal20129:166

      DOI: 10.1186/1743-422X-9-166

      Received: 1 February 2012

      Accepted: 24 July 2012

      Published: 21 August 2012

      Abstract

      An extensive comparative analysis of orbivirus genomes revealed four cases of unclear numeration and protein designation, due to confused reference to protein size or segment size by which they are encoded. A concise nomenclature based on type species, sequence homology and functional characteristics independent of segment or protein size is suggested.

      Keywords

      Reoviridae Orbivirus Protein classification

      Background

      The genus Orbivirus is one of 15 in the family of Reoviridae containing 22 serogroups (species) and at least 160 different serotypes (strains) [1]. Orbiviruses are transmitted by insects (midges, flies, mosquitoes) or by ticks. Their double-stranded RNA (dsRNA) genomes consist of 10 segments coding for seven structural and at least three non-structural proteins. Orbiviruses have no envelope but a double-shelled icosahedral capsid [2] and include pathogenic agents of wild animals (Epizootic hemorrhagic disease virus (EHDV)), domestic animals (Bluetongue virus (BTV) and African horse sickness virus (AHSV)), and of man (Kemerovo virus (KEMV)) [3]. Type species of the genus is the Culicoides midge transmitted BTV. Insect-borne orbiviruses are much better characterized than tick-transmitted orbiviruses for which few sequences have been described: Broadhaven virus (BRDV, partial) [4], Sandy Bay virus (SBaV, partial (formerly Nugget virus)) [58], St Croix River virus (SCRV, complete genome) [9], Great Island virus (GIV, complete genome) [7].

      Recently we determined the complete genomes of Tribeč virus (TRBV) and KEMV in a pyrosequencing approach [10] complementing available partial information on segments 1, 2 and 6 of these viruses and of Lipovnik virus (LIPV) [7].

      During our extensive comparative analysis of orbivirus genomes we noticed four cases of unclear numeration and protein designation (see Tables 1 and 2). Some laboratories classify orbivirus proteins according to the size of the proteins whereas others use the size of genome segments from which they are encoded.

      (i) The inner shell protein T2 for example can be encoded by segment 2 (tick- and mosquito-borne orbiviruses) or segment 3 (Culicoides-borne orbiviruses). This leads to some laboratories labeling this protein VP2(T2) (e.g. GIV), while others designate it VP3(T2) as in the type species BTV. For Peruvian horse sickness virus (PHSV) however, the segment 2 encoded protein is designated VP3(T2) although it is larger (925 amino acids) than the segment 3 encoded VP2 protein (881 amino acids) [11]. To avoid confusion with the outer shell protein VP2 we suggest to exclusively use VP3(T2) for all T2 proteins.

      (ii) VP2 and VP2 homologous proteins can be encoded by segments 2, 3, 4 and 5 and are designated VP2, VP3 (YUOV, SCRV) or VP4 (BRDV segment 4 ( [12, 13], sequence entry to GenBank missing)), GIV segment 5). Because of the location on the outer capsid and the described sequence similarity with other VP2 proteins, we suggest that the VP4 proteins (BRDV, GIV) as well as the VP3 proteins (YUOV, SCRV) should be uniformly termed VP2, even though tick-borne VP2 proteins have only half the size of insect-borne VP2 proteins [13].

      (iii) The capping enzyme VP4(CaP) can be encoded by segment 4 (BTV, YUOV, SCRV etc.) or segment 3 (TRBV, KEMV). In GIV this protein is designated VP3(CaP) [7] and should be renamed VP4(CaP) to avoid confusions with VP3(T2).

      (iv) In most cases VP5 is encoded by segment 6 and comprises a component of the outer shell that might be involved in membrane fusion and penetration [14]. TRBV and KEMV also encode VP5 on segment 6. The highest similarity of TRBV VP5 is to LIPV VP5 (95.6%), again encoded by segment 6 [7]. However, VP5 of BRDV is described as encoded by segment 5 [15]. Since in the classification of the viral genome segments bigger segments have smaller segment numbers, and the size of BRDV segment 6 (1714 bp) encoding the NS1(TuP) [16] is larger than the size of BRDV segment 5 (1658 bp) encoding VP5, a reassignment of BRDV segment 5 and 6 (a vice versa switch) seems necessary.

      Table 1

      Comparison of the genome segments and encoded proteins of BTV, YUOV, TRBV, KEMV and GIV

      BTV (insect-transmitted)

      YUOV (insect-transmitted)

      TRBV (tick-transmitted)

      KEMV (tick-transmitted)

      GIV (tick-transmitted)

      Segment 1

      VP1 (Pol)

      150 kDa

      RNA-dep.-RNA- Polymerase

      Segment 1

      VP1 (Pol)

      151 kDa

      RNA-dep.-RNA- Polymerase

      Segment 1

      VP1 (Pol)

      146 kDa

      RNA-dep.-RNA- Polymerase

      Segment 1

      VP1 (Pol)

      146 kDa

      RNA-dep.-RNA- Polymerase

      Segment 1

      VP1 (Pol)

      147 kDa

      RNA-dep.-RNA- Polymerase

      3944 bp

      ACR58458

      1302 AA

       

      3393 bp

      YP_443925

      1315 AA

       

      3892 bp

      HQ266581

      1284 AA

       

      3896 bp

      HQ266591

      1285 AA

       

      3897 bp

      ADM88592

      1285 AA

       

      Segment 2

      VP2

      111 kDa

      Outer shell

      Segment 2

      VP2 (T2)

      107 kDa

      Inner shell

      Segment 2

      VP3 (T2)

      102 kDa

      Inner shell

      Segment 2

      VP3 (T2)

      103 kDa

      Inner shell

      Segment 2

      VP2 (T2)

      103 kDa

      Inner shell

      2953 bp

      ACR58459

      956 AA

       

      2900 bp

      YP_443926

      940 AA

       

      2793 bp

      HQ266582

      908 AA

       

      2792 bp

      HQ266592

      908 AA

       

      2794 bp

      ADM88593

      908 AA

       

      Segment 3

      VP3 (T2)

      103 kDa

      Inner shell

      Segment 3

      VP3

      100 kDa

      Outer shell

      Segment 3

      VP4 (CaP)

      72 kDa

      Capping Enzyme

      Segment 3

      VP4 (CaP)

      72 kDa

      Capping Enzyme

      Segment 3

      VP3 (CaP)

      73 kDa

      Capping Enzyme

      2772 bp

      ACR58460

      901 AA

      2688 bp

      YP_443927

      873 AA

      1935 bp

      HQ266583

      628 AA

      1934 bp

      HQ266593

      632 AA

      1936 bp

      ADM88594

      635 AA

      Segment 4

      VP4 (CaP)

      75 kDa

      Capping Enzyme

      Segment 4

      VP4 (CaP)

      74 kDa

      Capping Enzyme

      Segment 4

      NS1 (TuP)

      62 kDa

      Formes Tubules

      Segment 4

      VP2

      63 kDa

      Outer shell

      Segment 4

      NS1 (TuP)

      60 kDa

      Formes Tubules

      1980 bp

      ACR58461

      644 AA

      1993 bp

      YP_443928

      645 AA

      1734 bp

      HQ266584

      529 AA

      1730 bp

      HQ266594

      554 AA

      1731 bp

      ADM88595

      531 AA

      Segment 5

      NS1 (TuP)

      64 kDa

      Forms Tubules

      Segment 5

      NS1 (TuP)

      67 kDa

      Forms Tubules

      Segment 5

      VP2

      62 kDa

      Outer shell

      Segment 5

      NS1 (TuP)

      60 kDa

      Formes Tubules

      Segment 5

      VP4

      62 kDa

      Outer shell

      1769 bp

      ACR58463

      552 AA

      1957 bp

      YP_443929

      574 AA

      1730 bp

      HQ266585

      554 AA

      1719 bp

      HQ266595

      529 AA

      1722 bp

      ADM88596

      551 AA

      Segment 6

      VP5

      59 kDa

      Outer shell

      Segment 6

      VP5

      59 kDa

      Outer shell

      Segment 6

      VP5

      59 kDa

      Outer shell

      Segment 6

      VP5

      59 kDa

      Outer shell

      Segment 6

      VP5

      60 kDa

      Outer shell

      1638 bp

      ACR58462

      526 AA

       

      1683 bp

      YP_443930

      535 AA

       

      1668 bp

      HQ266586

      537 AA

       

      1668 bp

      HQ266596

      537 AA

       

      1666 bp

      ADM88597

      537 AA

       

      Segment 7

      VP7 (T13)

      39 kDa

      Inner shell

      Segment 7

      NS2 (ViP)

      48 kDa

      Viral inclusion body matrix protein

      Segment 7

      NS2 (ViP)

      41 kDa

      Viral inclusion body matrix protein

      Segment 7

      NS2 (ViP)

      41 kDa

      Viral inclusion body matrix protein

      Segment 7

      VP7 (T13)

      40 kDa

      Inner shell

      1156 bp

      ACR58464

      349 AA

      1504 bp

      YP_443931

      435 AA

      1196 bp

      HQ266587

      368 AA

      1197 bp

      HQ266597

      368 AA

      1181 bp

      ADM88598

      357 AA

      Segment 8

      NS2 (ViP)

      41 kDa

      Viral inclusion body matrix protein

      Segment 8

      VP7 (T13)

      40 kDa

      Inner shell

      Segment 8

      VP7 (T13)

      40 kDa

      Inner shell

      Segment 8

      VP7 (T13)

      40 kDa

      Inner shell

      Segment 8

      NS2 (ViP)

      39 kDa

      Viral inclusion body matrix protein

      1125 bp

      ACR58465

      354 AA

      1191 bp

      YP_443932

      355 AA

      1184 bp

      HQ266588

      357 AA

      1183 bp

      HQ266598

      357 AA

      1172 bp

      ADM88599

      359 AA

      Segment 9

      VP6 (Hel)

      36 kDa

      ssRNA and dsRNA binding helicase

      Segment 9

      VP6 (Hel)

      37 kDa

      ssRNA and dsRNA binding helicase

      Segment 9

      VP6 (Hel)

      33 kDa

      ssRNA and dsRNA binding helicase

      Segment 9

      VP6 (Hel)

      34 kDa

      ssRNA and dsRNA binding helicase

      Segment 9

      VP6 (Hel)

      34 kDa

      ssRNA and dsRNA binding helicase

      1049 bp

      ACR58466

      329 AA

      1082 bp

      YP_443933

      338 AA

      1034 bp

      HQ266589

      312 AA

      1049 bp

      HQ266599

      317 AA

      1056 bp

      AMD88600

      321 AA

      Segment 10

      NS3

      26 kDa

      Glycoprotein

      Segment 10

      NS3

      28 kDa

      Glycoprotein

      Segment 10

      NS3

      23 kDa

      Glycoprotein

      Segment 10

      NS3

      23 kDA

      Glycoprotein

      Segment 10

      NS3

      19 kDa

      Glycoprotein

      822 bp

      ACR58467

      229 AA

       

      825 bp

      YP_443934

      253 AA

       

      705 bp

      HQ266590

      214 AA

       

      707 bp

      HQ266600

      214AA

       

      703 bp

      ADM88602

      171 AA

       

      Outer and inner shell proteins are labeled in bold. GenBank and SwissProt accession numbers are indicated.

      Table 2

      Comparison of the genome segments and encoded proteins of SCRV, PHSV, BRDV and LIPV

      SCRV (tick-transmitted)

      PHSV (isolates only known from horses)

      BRDV (tick-transmitted)

      LIPV (tick-transmitted)

      Segment 1

      VP1 (Pol)

      151 kDa

      RNA-dep.-RNA-Polymerase

      Segment 1

      VP1 (Pol)

      151 kDa

      RNA-dep.-RNA-Polymerase

      Segment 1

         

      Segment 1

      VP1 (Pol)

      146 kDa

      RNA-dep.-RNA-Polymerase

      4089 bp

      YP_052942

      1345 AA

      3987 bp

      YP_460038

      1311 AA

      3892 bp

      ADM88603

      1284 AA

      Segment 2

      VP2 (T2)

      98 kDa

      Inner shell

      Segment 2

      VP3 (T2)

      105 kDa

      Inner shell

      Segment 2

      VP2 (T2)

      103 kDa

      Inner shell

      Segment 2

      VP2 (T2)

      103 kDa

      Inner shell

      2747 bp

      YP_052943

      890 AA

       

      2856 bp

      YP_460039

      925 AA

        

      P35934

      908 AA

       

      2793 bp

      ADM88604

      908 AA

       

      Segment 3

      VP3

      74 kDa

      Outer shell

      Segment 3

      VP2

      104 kDa

      Outer shell

      Segment 3

         

      Segment 3

         

      2024 bp

      YP_052944

      654 AA

       

      2747 bp

      YP_460040

      881 AA

               

      Segment 4

      VP4 (CaP)

      74 kDa

      Capping Enzyme

      Segment 4

      VP4 (CaP)

      74 kDa

      Capping Enzyme

      Segment 4

      VP4

      63 kDa †

      Outer shell

      Segment 4

         

      2017 bp

      YP_052945

      643 AA

      1996 bp

      YP_460041

      646 AA

      Segment 5

      VP5

      57 kDa

      Outer shell

      Segment 5

      NS1 (TuP)

      64 kDa

      Forms Tubules

      Segment 5

      VP5

      53 kDa

      Outer shell

      Segment 5

         

      1664 bp

      YP_052946

      517 AA

       

      1784 bp

      YP_460045

      554 AA

       

      1658 bp

      P21230

      480 AA

           

      Segment 6

      NS1 (TuP)

      58 kDa

      Forms Tubules

      Segment 6

      VP5

      59 kDa

      Outer shell

      Segment 6

      NS1 (TuP)

      60 kDa

      Formes Tubules

      Segment 6

      VP5

      502 AA ††

      Outer shell

      1657 bp

      YP_052947

      517 AA

       

      1695 bp

      YP_460042

      529 AA

       

      1714 bp

      2115436A

      537 AA

       

      1509 bp ††

      ADM88605

        

      Segment 7

      NS2 (ViP)

      51 kDa

      Viral inclusion body matrix protein

      Segment 7

      NS2 (ViP)

      48 kDa

      Viral inclusion body matrix protein

      Segment 7

      VP7 (T13)

      40 kDa

      Inner shell

      Segment 7

         

      1463 bp

      YP_052948

      462 AA

      1613 bp

      YP_460046

      435 AA

       

      P35935

      356 AA

      Segment 8

      VP7 (T13)

      41 kDa

      Inner shell

      Segment 8

      VP7 (T13)

      40 kDa

      Inner shell

      Segment 8

         

      Segment 8

         

      1256 bp

      YP_052949

      379 AA

       

      1180 bp

      YP_460044

      353 AA

               

      Segment 9

      VP6 (Hel)

      26 kDa

      ssRNA and dsRNA binding helicase

      Segment 9

      VP6 (Hel)

      37 kDa

      ssRNA and dsRNA binding helicase

      Segment 9

         

      Segment 9

         

      764 bp

      YP_052950

      232 AA

        

      1071 bp

      YP_460043

      334 AA

              

      Segment 10

      NS3

      24 kDa

      Glycoprotein

      Segment 10

      NS3

      28 kDa

      Glycoprotein

      Segment 10

      NS3

      22 kDa

      Glycoprotein

      Segment 10

         

      764 bp

      YP_052951

      224 AA

       

      819 bp

      YP_460047

      255 AA

        

      P32555

      205 AA

           

      Outer and inner shell proteins are labeled in bold. GenBank and SwissProt accession numbers are indicated.

      †: [12, 13], GenBank entry missing.

      ††: partial sequence.

      To summarize, it would be much more helpful if the nomenclature of the viral proteins in orbiviruses would reflect the sequence homology and functional relationship rather than protein size or encoding segment size, since the sizes of the orbivirus genome segments sometimes only differ slightly, which leads to even closely related viruses such as TRBV and KEMV encoding VP2 and NS1(TuP) on different genome segments. We therefore suggest the following concise nomenclature based on the type species BTV and on sequence homology and functional characteristics independent of segment or protein size: VP1(Pol), VP2, VP3(T2), VP4(CaP), VP5, VP6(Hel), VP7(T13), NS1(TuP), NS2(ViP), NS3.

      Declarations

      Acknowledgments

      This work was supported by the Federal Ministry of Education and Research (BMBF), grant number 01KI0710, “Research on Zoonotic Infectious Diseases” program, “Emerging arthropode-borne viral infections in Germany: Pathogenesis, diagnostics and surveillance” and the BMBF funded research program “Potential release-oriented biothreat emergency diagnostics (P.R.O.B.E)” for civil security of the German Federal Government as part of the high-tech strategy for Germany.

      Authors’ Affiliations

      (1)
      Department of Virology, University Medical Center Göttingen

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      Copyright

      © Dilcher and Weidmann; licensee BioMed Central Ltd. 2012

      This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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