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Comparative Genetic Analysis of Genomic DNA Sequences of Two Human Isolates of Tanapox Virus

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Comparative Genetic Analysis of Genomic DNA Sequences of Two Human Isolates of Tanapox Virus View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by UNL | Libraries University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Public Health Resources Public Health Resources 2007 Comparative Genetic Analysis of Genomic DNA Sequences of Two Human Isolates of Tanapox virus Steven H. Nazarian Biotherapeutics Research Group, Robarts Research Institute, and Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6G 2V4, Canada John W. Barrett Biotherapeutics Research Group, Robarts Research Institute, and Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6G 2V4, Canada A. Michael Frace Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Preparedness, Detection, and Control of Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA Melissa Olsen-Rasmussen Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Preparedness, Detection, and Control of Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA Marina Khristova FBiotechnologyollow this and Cor additionale Facility works Branch, at: Divisionhttps://digitalcommons.unl.edu/publichealthr of Scientific Resources, National Centeresour forces Prepar edness, Detection, and Control of Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, Par tUSA of the Public Health Commons See next page for additional authors Nazarian, Steven H.; Barrett, John W.; Frace, A. Michael; Olsen-Rasmussen, Melissa; Khristova, Marina; Shaban, Mae; Neering, Sarah; Li, Yu; Damon, Inger K.; Esposito, Joseph J.; Essani, Karim; and McFadden, Grant, "Comparative Genetic Analysis of Genomic DNA Sequences of Two Human Isolates of Tanapox virus" (2007). Public Health Resources. 61. https://digitalcommons.unl.edu/publichealthresources/61 This Article is brought to you for free and open access by the Public Health Resources at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Public Health Resources by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Authors Steven H. Nazarian, John W. Barrett, A. Michael Frace, Melissa Olsen-Rasmussen, Marina Khristova, Mae Shaban, Sarah Neering, Yu Li, Inger K. Damon, Joseph J. Esposito, Karim Essani, and Grant McFadden This article is available at DigitalCommons@University of Nebraska - Lincoln: https://digitalcommons.unl.edu/ publichealthresources/61 Virus Research 129 (2007) 11–25 Comparative genetic analysis of genomic DNA sequences of two human isolates of Tanapox virusଝ Steven H. Nazarian a, John W. Barrett a, A. Michael Frace b, Melissa Olsen-Rasmussen b, Marina Khristova b, Mae Shaban a, Sarah Neering d,YuLic, Inger K. Damon c, Joseph J. Esposito b, Karim Essani d, Grant McFadden a,∗ a Biotherapeutics Research Group, Robarts Research Institute, and Department of Microbiology and Immunology, University of Western Ontario, London, Ontario N6G 2V4, Canada b Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Preparedness, Detection, and Control of Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA c Poxvirus and Rabiesvirus Branch, Division of Viral and Rickettsial Diseases, National Center for Zoonotic, Vector-Borne, and Enteric Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA d Laboratory of Virology, Department of Biological Science, Western Michigan University, Kalamazoo, MI 49008, USA Received 10 March 2007; received in revised form 1 May 2007; accepted 1 May 2007 Available online 14 June 2007 Abstract Members of the genus Yatapoxvirus, which include Tanapox virus (TPV) and Yaba monkey tumor virus, infect primates including humans. Two strains of TPV isolated 50 years apart from patients infected from the equatorial region of Africa have been sequenced. The original isolate from a human case in the Tana River Valley, Kenya, in 1957 (TPV-Kenya) and an isolate from an infected traveler in the Republic of Congo in 2004 (TPV-RoC). Although isolated 50 years apart the genomes were highly conserved. The genomes differed at only 35 of 144,565 nucleotide positions (99.98% identical). We predict that TPV-RoC encodes 155 ORFs, however a single transversion (at nucleotide 10241) in TPV-Kenya resulted in the coding capacity for two predicted ORFs (11.1L and 11.2L) in comparison to a single ORF (11L) in TPV-RoC. The genomes of TPV are A + T rich (73%) and 96% of the sequence encodes predicted ORFs. Comparative genomic analysis identified several features shared with other chordopoxviruses. A conserved sequence within the terminal inverted repeat region that is also present in the other members of the Yatapoxviruses as well as members of the Capripoxviruses, Swinepox virus and an unclassified Deerpox virus suggests the existence of a conserved near-terminal sequence secondary structure. Two previously unidentified gene families were annotated that are represented by ORF TPV28L, which matched homologues in certain other chordopoxviruses, and TPV42.5L, which is highly conserved among currently reported chordopoxvirus sequences. © 2007 Elsevier B.V. All rights reserved. Keywords: Tanapox; Yatapoxvirus; Poxvirus; Comparative genomics 1. Introduction tebrate and insect hosts, respectively (Buller et al., 2005). Characteristic features of poxviruses include a cytoplasmic Poxviruses constitute two sub-families, Chordopoxvirinae life cycle, a large virion size and large genome compared and Entomopoxvirinae, which infect a wide range of ver- to other viruses (Moss, 2007). Poxviruses contain a linear, double-stranded DNA genome with palindromic, covalently- closed ends. Sequenced poxvirus genomes vary from ∼134 to ଝ ∼ Disclaimer: The findings and conclusions in this report are those of the 360 kbp in length and 130 to 328 open reading frames (ORFs) authors and do not necessarily represent the views of the funding agencies. Use can be predicted from the sequences. At the ends of poxvirus of trade names or commercial sources is for identification only and does not DNA genomes are mirror image terminal inverted repeat (TIR) imply endorsement by the funding agencies. ∗ regions, however, among different strains the lengths of the Corresponding author. Present address: University of Florida, 1600 SW TIR regions vary from a few hundred nucleotides, such as in Archer Road, ARB Room R4-295, P.O. Box 100332, Gainesville, FL 32610, USA. Tel.: +1 352 273 6852; fax: +1 352 273 6849. Variola virus (VARV), to approximately 12 kbp, such as in E-mail address: grantmcf@ufl.edu (G. McFadden). Shope fibroma virus (SHFV). In general, the chordopoxvirus 0168-1702/$ – see front matter © 2007 Elsevier B.V. All rights reserved. doi:10.1016/j.virusres.2007.05.001 12 S.H. Nazarian et al. / Virus Research 129 (2007) 11–25 genome is organized so that the essential housekeeping genes, by the development of few nodular skin lesions (Downie including those required for transcription, replication and mor- and Espana, 1972; Damon, 2007; Knight et al., 1989). In phogenesis, are located within the central region of the genome. contrast, YMTV produces a very distinct disease, primarily Genes nearer to the DNA ends are generally more variable in non-human primates, which is characterized by epidermal and encode for a wide variety of functions, including genes histiocytomas of the head and limbs (Downie and Espana, dedicated to ensure virus replication within the host by mod- 1972; Knight et al., 1989). The observed biological differences ulating the host innate and adaptive immune response (Seet et between YMTV and YLDV are likely explained by the 82% al., 2003). nucleotide identity and an approximately 10 kbp deletion from The genomic DNA sequences of over 100 different poxvirus YMTV compared to YLDV (Brunetti et al., 2003; Downie and strains have been determined. The particular poxvirus sequences Espana, 1972; Espana et al., 1971; Knight et al., 1989; Lee et al., used in the present study are listed in Table 1. All of the 2001). sequences used are available through GenBank and two curated A previous study, in which the genome of YMTV was poxvirus sites—www.poxvirus.org/ and www.biovirus.org/. sequenced, examined the conservation of certain gene fami- There are two species in the genus Yatapoxvirus: Yaba lies that were found to be below the usual 50 codon cutoff monkey tumor virus (YMTV) and Tanapox virus (TPV). Both (Brunetti et al., 2003). To further this research, two isolates of species have caused human infection. A previously sequenced TPV were sequenced; one is the first isolate from a 1957 human poxvirus, Yaba-like disease virus (YLDV) (Lee et al., 2001), outbreak of TPV in the Tana River valley in Kenya (TPV-Kenya) is a TPV from an infected non-human primate (Brunetti et and the other was isolated from an infected college student al., 2003; Espana et al., 1971; Esposito and Fenner, 2001; traveling in the Congo Basin in the Republic of Congo (TPV- McNulty et al., 1968). TPV and YLDV are suspected to be RoC) (Dhar et al., 2004). The current study is a comparative transmitted by arthropod vectors and both produce a similar genomic analysis of these two isolates of TPV that are from dis- rash illness, fever with prodromal symptoms that is followed crete geographic regions of Africa and isolated 50 years apart. Table 1 Summary information of poxvirus sequences
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