Open Access

Confusions in orbivirus protein classification

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.
  1. (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.

     
  2. (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].

     
  3. (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).

     
  4. (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.

Author’s contributions

MD and MW wrote the paper. Both authors read and approved the final manuscript.

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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