Here we present complete genome sequences, including a comparative analysis, of 103 isolates of foot-andmouth disease virus (FMDV) representing all seven serotypes and including the first complete sequences of the SAT1 and SAT3 genomes. The data reveal novel highly conserved genomic regions, indicating functional constraints for variability as well as novel viral genomic motifs with likely biological relevance. Previously undescribed invariant motifs were identified in the 5 and 3 untranslated regions (UTR), as was tolerance for insertions/deletions in the 5 UTR. Fifty-eight percent of the amino acids encoded by FMDV isolates are invariant, suggesting that these residues are critical for virus biology. Novel, conserved sequence motifs with likely functional significance were identified within proteins L pro , 1B, 1D, and 3C. An analysis of the complete FMDV genomes indicated phylogenetic incongruities between different genomic regions which were suggestive of interserotypic recombination. Additionally, a novel SAT virus lineage containing nonstructural proteinencoding regions distinct from other SAT and Euroasiatic lineages was identified. Insights into viral RNA sequence conservation and variability and genetic diversity in nature will likely impact our understanding of FMDV infections, host range, and transmission.

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Although North American and European serotypes of porcine reproductive and respiratory syndrome virus (PRRSV) are recognized, only the genome of the European Lelystad strain (LV) has been sequenced completely. Here, the genome of the pathogenic North American PRRSV isolate 16244B has been sequenced and compared with LV. The genomic organization of 16244B was the same as LV but with only 63n4 % nucleotide identity. The 189 nucleotide 5h non-coding region (NCR) of 16244B was distinct from the LV NCR, with good conservation (83 %) only over a 43 base region immediately upstream of open reading frame (ORF) 1a. Major differences were found in the region encoding the non-structural part of the ORF1a polyprotein, which shared only 47 % amino acid identity over 2503 residues of the six non-structural proteins (Nsps) encoded. Nsp2, thought to have a species-specific function, showed the greatest divergence, sharing only 32 % amino acid identity with LV and containing 120 additional amino acids in the central region. Nsps encoded by the 5h-proximal and central regions of ORF1b had from 66 to 75 % amino acid identity ; however, the carboxy-terminal protein CP4 was distinct (42 % identity). The ORF1a-1b frameshift region of 16244B had 98 % nucleotide identity with LV. Consistent with previous reports for North American isolates, the six structural proteins encoded were 58 to 79 % identical to LV proteins. The 3h NCR (150 nucleotides) was 76 % identical between isolates. These genomic differences confirm the presence of distinct North American and European PRRSV genotypes.

Bovine papular stomatitis virus (BPSV) and orf virus (ORFV), members of the genus

Sheeppox virus (SPPV) and goatpox virus (GTPV), members of the Capripoxvirus genus of the Poxviridae, are etiologic agents of important diseases of sheep and goats in northern and central Africa, southwest and central Asia, and the Indian subcontinent. Here we report the genomic sequence and comparative analysis of five SPPV and GTPV isolates, including three pathogenic field isolates and two attenuated vaccine viruses. SPPV and GTPV genomes are approximately 150 kbp and are strikingly similar to each other, exhibiting 96% nucleotide identity over their entire length. Wild-type genomes share at least 147 putative genes, including conserved poxvirus replicative and structural genes and genes likely involved in virulence and host range. SPPV and GTPV genomes are very similar to that of lumpy skin disease virus (LSDV), sharing 97% nucleotide identity. All SPPV and GTPV genes are present in LSDV. Notably in both SPPV and GTPV genomes, nine LSDV genes with likely virulence and host range functions are disrupted, including a gene unique to LSDV (LSDV132) and genes similar to those coding for interleukin-1 receptor, myxoma virus M003.2 and M004.1 genes (two copies each), and vaccinia virus F11L, N2L, and K7L genes. The absence of these genes in SPPV and GTPV suggests a significant role for them in the bovine host range. SPPV and GTPV genomes contain specific nucleotide differences, suggesting they are phylogenetically distinct. Relatively few genomic changes in SPPV and GTPV vaccine viruses account for viral attenuation, because they contain 71 and 7 genomic changes compared to their respective field strains. Notable genetic changes include mutation or disruption of genes with predicted functions involving virulence and host range, including two ankyrin repeat proteins in SPPV and three kelch-like proteins in GTPV. These comparative genomic data indicate the close genetic relationship among capripoxviruses, and they suggest that SPPV and GTPV are distinct and likely derived from an LSDV-like ancestor.

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.

Here we present the first complete genomic sequence, with analysis, of a very virulent strain of Marek's disease virus serotype 1 (MDV1), Md5. The genome is 177,874 bp and is predicted to encode 103 proteins. MDV1 is colinear with the prototypic alphaherpesvirus herpes simplex virus type 1 (HSV-1) within the unique long (UL) region, and it is most similar at the amino acid level to MDV2, herpesvirus of turkeys (HVT), and nonavian herpesviruses equine herpesviruses 1 and 4. MDV1 encodes 55 HSV-1 UL homologues together with 6 additional UL proteins that are absent in nonavian herpesviruses. The unique short (US) region is colinear with and has greater than 99% nucleotide identity to that of MDV1 strain GA; however, an extra nucleotide sequence at the Md5 US/short terminal repeat boundary results in a shorter US region and the presence of a second gene (encoding MDV097) similar to the SORF2 gene. MD5, like HVT, encodes an ICP4 homologue that contains a 900-amino-acid amino-terminal extension not found in other herpesviruses. Putative virulence and host range gene products include the oncoprotein MEQ, oncogenicity-associated phosphoproteins pp38 and pp24, a lipase homologue, a CxC chemokine, and unique proteins of unknown function MDV087 and MDV097 (SORF2 homologues) and MDV093 (SORF4). Consistent with its virulent phenotype, Md5 contains only two copies of the 132-bp repeat which has previously been associated with viral attenuation and loss of oncogenicity.Marek's disease (MD) is a lymphoproliferative disease of chickens caused by the highly infectious cell-associated alphaherpesvirus MD virus serotype 1 (MDV1) (18). Yearly economic losses from MD total $1 billion worldwide (18). MDV1 infection results in a rapid onset of malignant T-cell lymphomas within several weeks of infection. Tumor infiltration results in a neural form of disease, which causes progressive paralysis, or a visceral form of disease, which is usually very acute and accompanied by high mortality. Productive virus replication in the skin and feather follicle epithelia with subsequent virus shedding is responsible for disease transmission (18).MD is controlled by vaccination and good management practices (18). Naturally occurring nonpathogenic strains of MDV1, MDV2, and herpesvirus of turkey (HVT or MDV3) have been used individually or together in bivalent vaccines (18,40). Recent increases in MD-related mortality and condemnations among vaccinated poultry have occurred in the United States. These increases in disease have occurred approximately 6 years after the introduction of new vaccines (99). In the late 1970s, following the introduction of HVT vaccines, and since 1992, after the introduction of bivalent MDV2-HVTbased vaccines, new MDV1 strains of greater virulence (very virulent [vv] and very virulent plus [vv ϩ ] MDV1) were isolated. These viruses are characterized by higher cytolytic activity, unusual tissue tropism, increased atrophy of lymphoid organs, immunosuppression, enhanced capacity to transform T cells, and earlier host death (7...

Here we present the genomic sequence, with analysis, of a canarypox virus (CNPV). The 365-kbp CNPV genome contains 328 potential genes in a central region and in 6.5-kbp inverted terminal repeats. Comparison with the previously characterized fowlpox virus (FWPV) genome revealed avipoxvirus-specific genomic features, including large genomic rearrangements relative to other chordopoxviruses and novel cellular homologues and gene families. CNPV also contains many genomic differences with FWPV, including over 75 kbp of additional sequence, 39 genes lacking FWPV homologues, and an average of 47% amino acid divergence between homologues. Differences occur primarily in terminal and, notably, localized internal genomic regions and suggest significant genomic diversity among avipoxviruses. Divergent regions contain gene families, which overall comprise over 49% of the CNPV genome and include genes encoding 51 proteins containing ankyrin repeats, 26 N1R/p28-like proteins, and potential immunomodulatory proteins, including those similar to transforming growth factor ␤ and ␤-nerve growth factor. CNPV genes lacking homologues in FWPV encode proteins similar to ubiquitin, interleukin-10-like proteins, tumor necrosis factor receptor, PIR1 RNA phosphatase, thioredoxin binding protein, MyD116 domain proteins, circovirus Rep proteins, and the nucleotide metabolism proteins thymidylate kinase and ribonucleotide reductase small subunit. These data reveal genomic differences likely affecting differences in avipoxvirus virulence and host range, and they will likely be useful for the design of improved vaccine vectors.Within the Chordopoxvirinae subfamily (poxviruses of vertebrates) of the Poxviridae, Avipoxvirus is the only characterized genus to infect nonmammalian hosts (57, 60), including more than 60 species of wild birds representing 20 families (60, 97). Variable restriction enzyme profiles suggest significant genomic differences among avipoxviruses (32,97,98). Crossinfection studies also suggest genetic differences among avipoxviruses, as specific virus-host combinations may not be cross-protective and result in a wide range of pathogenic effects, from absence of clinical disease to generalized infection and death (8,97).Canarypox virus (CNPV) is an avipoxvirus and etiologic agent of canarypox, a disease of birds both in the wild and in commercial aviaries, where significant losses result (15,16,33,45). Canarypox has been described broadly as the poxviral disease of passeriform (song) birds, efficiently causing disease in passerine hosts compared to galliform (domestic fowl) and columbiform (pigeon) hosts (8,15,22,33). However, passerine host preferences exist, and current International Committee on Taxonomy of Viruses classification differentiates between CNPV and several other passerine isolates (60, 97). CNPV produces clinical signs similar to generalized poxviral infections of other birds, including both cutaneous and diptheretic disease forms caused by the prototypical galliform avipoxvirus, fowlpox virus (FWPV), and incl...