The Genome Sequence of Yaba-Like Disease Virus, a Yatapoxvirus

Virology 281, 170–192 (2001) doi:10.1006/viro.2000.0761, available online at http://www.idealibrary.com on View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector The Genome Sequence of Yaba-like Disease Virus, a Yatapoxvirus Han-Joo Lee,*,1 Karim Essani,† and Geoffrey L. Smith*,2 *Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, United Kingdom; and †Department of Biological Sciences, Western Michigan University, Michigan 49008 Received July 18, 2000; returned to author for revision August 18, 2000; accepted November 28, 2000 The genome sequence of Yaba-like disease virus (YLDV), an unclassified member of the yatapoxvirus genus, has been determined. Excluding the terminal hairpin loops, the YLDV genome is 144,575 bp in length and contains inverted terminal repeats (ITRs) of 1883 bp. Within 20 nucleotides of the termini, there is a sequence that is conserved in other poxviruses and is required for the resolution of concatemeric replicative DNA intermediates. The nucleotide composition of the genome is 73% AϩT, but the ITRs are only 63% AϩT. The genome contains 151 tightly packed open reading frames (ORFs) that either are Ն180 nucleotides in length or are conserved in other poxviruses. ORFs within 23 kb of each end are transcribed toward the termini, whereas ORFs within the central region of the genome are encoded on either DNA strand. In the central region ORFs have a conserved position, orientation, and sequence compared with vaccinia virus ORFs and encode many enzymes, transcription factors, or structural proteins. In contrast, ORFs near the termini are more divergent and in seven cases are without counterparts in other poxviruses. The YLDV genome encodes several predicted immunomodulators; examples include two proteins with similarity to CC chemokine receptors and predicted secreted proteins with similarity to MHC class I antigen, OX-2, interleukin-10/mda-7, poxvirus growth factor, serpins, and a type I interferon-binding protein. Phylogenic analyses indicated that YLDV is very closely related to yaba monkey tumor virus, but outside the yatapoxvirus genus YLDV is more closely related to swinepox virus and leporipoxviruses than to other chordopoxvirus genera. © 2001 Academic Press Key Words: yatapoxvirus; genome sequence; phylogeny; virus evolution; immune evasion. INTRODUCTION 1994), India-1968 (Shchelkunov et al., 1995), and Garcia- 1966 (Shchelkunov et al., 2000), molluscum contagiosum Poxviruses are large DNA viruses that infect insects virus (MCV) (Senkevich et al., 1997), Melanoplus sangui- (entomopoxviruses) or vertebrates (chordopoxviruses) nipes entomopoxvirus (MSV) (Afonso et al., 1999), Shope (Fenner, 1996). The chordopoxvirus group is divided into fibroma virus (SFV) (Willer et al., 1999), myxoma virus eight genera, orthopox, parapox, capripox, leporipox, sui- (MYX) (Cameron et al., 1999), fowlpox virus (FPV) (Afonso pox, avipox, molluscipox, and yatapox, of which the or- et al., 2000), and camelpox virus (CMPV) (Gubser and thopoxviruses have been the most important for humans and include variola virus (VAR) (the cause of smallpox), Smith, submitted for publication). vaccinia virus (VV) (the vaccine used to eradicate small- The yatapoxvirus genus contains three members: ta- pox), cowpox virus (CPV), and monkeypox virus. All pox- napox virus (TPV), yaba monkey tumor virus (YMTV), and viruses replicate in the cell cytoplasm and encode their yaba-like disease virus (YLDV) (Knight et al., 1989). All own enzymes for transcription and DNA replication these viruses are morphologically similar to orthopoxvi- (Moss, 1996). ruses but are antigenically distinct from members of this The nucleotide sequence of several poxviruses has and other poxvirus genera and hence cannot be neutral- been determined. These include VV strains Copenhagen ized by polyclonal antisera raised against VV, MCV, or orf (CPN) (Goebel et al., 1990), modified virus Ankara virus (OV), a parapoxvirus (Downie et al., 1971). Yatapox- (Antoine et al., 1998), and the majority of Western Re- viruses have a narrow host range and infect monkeys but serve (WR) (Smith et al., 1991, and references therein), can also be transmitted to humans where they may VAR strains Bangladesh-1975 (VAR-BSH) (Massung et al., cause a mild febrile illness lasting a few days with one or two lesions (deHarven and Yohn, 1966; Espanã et al., 1971). The progression of yatapoxvirus-induced pathol- Sequence data from this article have been deposited with the EMBL ogy is considerably slower than that for orthopoxviruses. Data Library under Accession No. AJ293568. TPV was isolated from the skin lesions of patients during 1 Present address: Memorial Slone-Kettering Cancer Center, 1275 outbreaks in the Tana River valley in Kenya in 1957 to York Avenue, RRL 629, Box 362, New York, NY 10021. 1962 (Downie et al., 1971). YMTV was isolated from a 2 To whom correspondence and reprint requests should be ad- dressed at present address: Wright-Fleming Institute, Imperial College colony of rhesus monkeys near Lagos, West Africa in School of Medicine, St. Mary’s Campus, Norfolk Place, London W2 1958 (Bearcroft and Jamieson, 1958) and can produce 1PG, United Kingdom. Fax: 0207-592-3973. E-mail: [email protected]. tumor-like lesions with masses of mesodermal tissue 0042-6822/01 $35.00 Copyright © 2001 by Academic Press 170 All rights of reproduction in any form reserved. GENOME SEQUENCE OF YLDV 171 (Niven et al., 1961). YLDV was isolated in 1965–1966 from monkeys and animal handlers in primate centers in the United States (Casey et al., 1967; Hall and McNulty, 1967; Nicholas and McNulty, 1968; Espanã, 1971). The YLDV- induced lesions in monkeys and clinical signs in humans are similar to TPV and these viruses are biologically indistinguishable (McNulty et al., 1968; Downie and Es- panã, 1972). Serological cross-reactivity between yatapoxviruses has been reported (Nicholas and McNulty, 1968; Kupper et al., 1970). Yatapoxviruses have a 145-kb, linear, double-stranded (ds) DNA genome with covalently closed hairpin ends and variations have been noted in the restriction patterns of the different viruses (Knight et al., 1989). Cross-hybrid- ization experiments indicated some sequence conserva- tion between YMTV and monkeypox virus (Rouhandeh et al., 1982), but until recently very little sequence data were available for the yatapoxviruses. Part of the YMTV genome was deposited in a public database (Amano et al., 1995, 2000a, b; Amano and Miyamura, 2000) and small fragments of the TPV genome have been sequenced (Neering and Essani, 1999). To gain an increased understanding of the yatapoxviruses and their evolutionary relationships with other poxviruses, we have determined the sequence of YLDV with FIG. 1. Schematic representation of the YLDV ITRs. Each ITR is the exception of the terminal hairpins. The genome is shown together with the positions of the terminal ORFs, the concate- 144,575 bp and contains 151 open reading frames mer resolution sequence, and the presumed terminal hairpin. Shown (ORFs). The ORFs within the central 100 kb of the ge- beneath the right ITR is the concatemeric resolution sequence from VV, nome show considerable similarity to corresponding MCV, FPV, SFV, and YLDV. Nucleotides conserved in at least four of five sequences are boxed. ORFs in VV in their deduced amino acid sequence, position, and direction of transcription. Several potential immunomodulators are identified and the evolutionary of the virus genome is unknown. However, several lines relationship of YLDV with other poxviruses is discussed. of evidence indicate that the sequence obtained came very close to the terminal hairpins. First, the length ob- RESULTS AND DISCUSSION tained (144,575 bp) was very similar to the total length of the YLDV genome (146.5 bp) estimated from restriction Genome structure of YLDV enzyme digestion and gel electrophoresis (Knight et al., A total of 1,098,770 nucleotides of YLDV DNA were 1989). Second, the size of the terminal PstI restriction assembled into a contiguous sequence of 144,575 bp. fragments described by others (Knight et al., 1989) and Ninety-seven point nine percent of these data were ob- observed experimentally by us was indistinguishable tained from sequencing random clones and the remain- from the length predicted by computer from the se- ing 2.1% were obtained from direct sequencing of either quence generated here. Third, and most compelling, a genomic DNA or 10-kb clones using specific oligonucle- sequence motif was identified within 20 nucleotides of otide primers. The average character density was 7.6 per each terminus that is conserved perfectly with se- nucleotide and 99.0% of the sequence was obtained from quences found very close to the terminal hairpins of both DNA strands. Every position was sequenced at other poxviruses and known to be required for the res- least twice. The genome was composed of 73% AϩT, olution of concatemeric DNA replicative intermediates making YLDV the most AϩT-rich chordopoxvirus to have (Merchlinsky and Moss, 1989) (Fig. 1). In VV strains WR been sequenced. Only the genome of the entomopoxvi- (Baroudy et al., 1982) and CPN (Goebel et al., 1990) and rus MSV has a higher AϩT content (81%) (Afonso et al., VAR-BSH (Massung et al., 1994) this conserved se- 1999). quence is located within 60 bp of the terminal hairpins. The sequence obtained did not include the terminal The motif is also present in FPV (Afonso et al., 2000), SFV hairpins because, as expected, these were not cloned and MYX (Cameron et al., 1999; Willer et al., 1999), and into either library and attempts to sequence these di- MCV (Senkevich et al., 1996). This observation extended rectly using virus DNA as template and specific oligonu- the number of chordopoxvirus genera known to contain cleotides were unsuccessful. Therefore, the exact length this sequence and suggested that the mechanism of 172 LEE, ESSANI, AND SMITH FIG. 2. YLDV genetic map.

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