Genome of Lumpy Skin Disease Virus
Abstract
Lumpy skin disease virus (LSDV), a member of the capripoxvirus genus of the Poxviridae, is the etiologic agent of an important disease of cattle in Africa. Here we report the genomic sequence of LSDV. The 151-kbp LSDV genome consists of a central coding region bounded by identical 2.4 kbp-inverted terminal repeats and contains 156 putative genes. Comparison of LSDV with chordopoxviruses of other genera reveals 146 conserved genes which encode proteins involved in transcription and mRNA biogenesis, nucleotide metabolism, DNA replication, protein processing, virion structure and assembly, and viral virulence and host range. In the central genomic region, LSDV genes share a high degree of colinearity and amino acid identity (average of 65%) with genes of other known mammalian poxviruses, particularly suipoxvirus, yatapoxvirus, and leporipoxviruses. In the terminal regions, colinearity is disrupted and poxvirus homologues are either absent or share a lower percentage of amino acid identity (average of 43%). Most of these differences involve genes and gene families with likely functions involving viral virulence and host range. Although LSDV resembles leporipoxviruses in gene content and organization, it also contains homologues of interleukin-10 (IL-10), IL-1 binding proteins, G protein-coupled CC chemokine receptor, and epidermal growth factor-like protein which are found in other poxvirus genera. These data show that although LSDV is closely related to other members of the Chordopoxvirinae, it contains a unique complement of genes responsible for viral host range and virulence.
Capripoxviruses (CaPVs) represent one of eight genera within the chordopoxvirus (ChPV) subfamily of the Poxviridae.
These viruses are responsible for some of the most economically significant diseases of domestic ruminants in Africa and Asia (18). CaPV infections are generally host specific and they have specific geographic distributions (10, 14, 15). CaPVs are, however, serologically indistinguishable from each other, able to induce heterologous cross-protection, and able in some instances to experimentally cross-infect (8, 10, 15, 16). Restriction fragment analysis and limited DNA sequence data support a close relationship between CaPVs (5, 25, 26, 33). The molecular basis of CaPV host range restriction and virulence remains to be elucidated.
LSD is a subacute to acute cattle disease in Africa. It is characterized by extensive cutaneous lesions and signs typical of generalized poxvirus diseases (14, 15). Transmission of LSD between cattle is inefficient, and arthropod-vectored transmission may be significant in epizootic outbreaks and in the spread of LSD into nonenzootic regions (4, 10–12, 15, 36, 54).
Attenuated LSDV strains and ShPV have been successfully used as LSD vaccines in enzootic and outbreak areas; however, vaccine failure and restrictions on the use of live virus vaccines create the need for a safe and effective, live attenuated vaccine (4, 13, 15, 53).
Current molecular data on the LSDV genome consists of restriction endonuclease analysis, cross-hybridization studies, and limited transcriptional and DNA sequence analysis (5, 19, 20, 26, 27, 33). Given the economic significance of LSD, its potential for spread into nonenzootic regions, and the interest in developing more effective LSDV-based vaccines and expression vectors, we have sequenced and analyzed the genome of a pathogenic LSDV. These data provide the first view of a CaPV genome, and they define the gene complement that underlies LSDV virulence and host range.
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LSDV contains 156 ORFs which have been annotated here as putative genes. These genes represent a 95% coding density and encode proteins of 53 to 2,025 amino acids (Fig. 1, Table 1). Similar to other poxviruses, many of the 41 putative early genes are members of gene families and/or putative host range genes, while the 46 genes containing the VV late promoter sequence (TAAATG) at the ATG codon (41) include many of the conserved virion-associated poxviral genes (Table 1).
Otan vain yhden proteiinin rrakenteen, siin on KELCH-proteiinin rakenne selvittettynä, propellitLOCUS VC13_SWPVK 500 aa linear VRL 05-FEB-2025 DEFINITION RecName: Full=Protein C13. ACCESSION P32206 VERSION P32206.1 DBSOURCE UniProtKB: locus VC13_SWPVK, accession P32206; class: standard. created: Oct 1, 1993. sequence updated: Oct 1, 1993. annotation updated: Feb 5, 2025. xrefs: L22013.1, AAC37858.1 xrefs (non-sequence databases): SMR:P32206, Gene3D:1.25.40.420, Gene3D:2.120.10.80, Gene3D:3.30.710.10, InterPro:IPR011705, InterPro:IPR000210, InterPro:IPR015915, InterPro:IPR006652, InterPro:IPR011333, PANTHER:PTHR24412, PANTHER:PTHR24412:SF489, Pfam:PF07707, Pfam:PF00651, Pfam:PF01344, SMART:SM00875, SMART:SM00225, SMART:SM00612, SUPFAM:SSF117281, SUPFAM:SSF54695, PROSITE:PS50097 KEYWORDS Kelch repeat; Repeat. SOURCE Swinepox virus (STRAIN KASZA) ORGANISM Swinepox virus (STRAIN KASZA) Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota; Pokkesviricetes; Chitovirales; Poxviridae; Chordopoxvirinae; Suipoxvirus; Suipoxvirus swinepox. REFERENCE 1 (residues 1 to 500) AUTHORS Massung,R.F., Jayarama,V. and Moyer,R.W. TITLE DNA sequence analysis of conserved and unique regions of swinepox virus: identification of genetic elements supporting phenotypic observations including a novel G protein-coupled receptor homologue JOURNAL Virology 197 (2), 511-528 (1993) PUBMED 8249275 REMARK NUCLEOTIDE SEQUENCE. COMMENT [SIMILARITY] Belongs to the poxviruses Kelch family. {ECO:0000305}. FEATURES Location/Qualifiers source 1..500 /organism="Swinepox virus (STRAIN KASZA)" /host="Sus scrofa (Pig)" /db_xref="taxon:10277" gene 1..500 /locus_tag="C13L" Protein 1..500 /product="Protein C13" /UniProtKB_evidence="Inferred from homology" Region 1..500 /region_name="Mature chain" /note="Protein C13. /id=PRO_0000119169." Region 17..500 /region_name="PHA03098" /note="kelch-like protein; Provisional" /db_xref="CDD:222983" Region 27..89 /region_name="Domain" /note="BTB. /evidence=ECO:0000255|PROSITE-ProRule:PRU00037." Region 301..348 /region_name="Repetitive region" /note="Kelch 1." Region 338..381 /region_name="KELCH repeat" /note="KELCH repeat [structural motif]" /db_xref="CDD:276965" Region 349..395 /region_name="Repetitive region" /note="Kelch 2." Region 385..427 /region_name="KELCH repeat" /note="KELCH repeat [structural motif]" /db_xref="CDD:276965" Region 397..440 /region_name="Repetitive region" /note="Kelch 3." Region 430..477 /region_name="KELCH repeat" /note="KELCH repeat [structural motif]" /db_xref="CDD:276965" Region 441..490 /region_name="Repetitive region" /note="Kelch 4." ORIGIN 1 mskqetyidy nyierlnavn lnrsydeeiv fimtvggvvk vkkellvsvs nyfklitknq 61 sneitvsfqy esfldiikyi etgivtidld nvenifsisc skaidflkns cidfmskhit 121 dstcvkiyki gfsngcfavy ndaiayirkr ftkietdill slslfdlrii lksgeldvss 181 eddvllfiik wsrhkksnrr ksftlvtevl rynylsiygk ykltkwlarf gknnnvelne 241 nelprisyqh rftnrrytmv tpssfsinml gnvsvknels iinsiaenhn pycgsvlmnd 301 ilyliggink sldpvsdits vdtrsfielh tppllhprkc pgvaifknri yvvggigydg 361 plktveswsp geqqwreevp llqprfnpci igtdndlyvv ggiseddkti eiysyeentw 421 signamnysh fggciayhhg yiymigglsf idnihvftmv ekynphsnkw tvekslpfpr 481 fnsslciied siaiigwiyy //
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