The Revolution in Viral Genomics as Exemplified by the Bioinformatic Analysis of Human Adenoviruses
Abstract
:1. Introduction
2. The Labor of Human Adenovirus Genomics
First Example of Comparative Genomics in Human Adenoviruses
3. The Birth of Human Adenovirus Genomics
3.1. HAdV-C2: The First HAdV Sequenced
3.2. HAdV-C5
3.3. Illegitimate Recombination Offered as a Possible Mechanism for Molecular Evolution
3.4. HAdV-B11
HAdV | Year sequenced | Reference |
---|---|---|
HAdV-C2 | 1984 | [5] |
HAdV-C5 | 1992 | [7] |
HAdV-F40 | 1993 | [9] |
HAdV-A12 | 1994 | [10] |
HAdV-D17 | 1999 | NP |
HAdV-B11 | 2003 | [18] |
HAdV-B35 | [19] | |
[28] | ||
[29] | ||
HAdV-C1 | 2004 | [27] |
HAdV-D9 | NP | |
HAdV-B16 | NP | |
HAdV-B21 | NP | |
HAdV-B34 | NP | |
HAdV-B50 | NP | |
HAdV-E4 | 2005 | [26] |
HAdV-B7 | [26] | |
HAdV-F41 | NP | |
HAdV-B3 | 2006 | [30] |
HAdV-D26 | [31] | |
HAdV-D46 | NP | |
HAdV-D48 | NP | |
HAdV-D49 | NP | |
NP | ||
HAdV-G52 | 2007 | [32] |
HAdV-D37 | 2008 | [8] |
HAdV-D19 | [33] | |
HAdV-B14 | 2009 | [34] |
HAdV-D8 | NP | |
HAdV-D22 | [16] | |
HAdV-D28 | NP | |
HAdV-A31 | [35] | |
HAdV-D53 | [6] | |
HAdV-D54 | [36] | |
HAdV-A18 | 2010 | [12] |
HAdV-D36 | [37] | |
HAdV-B55 | [17] |
4. Major Advances in the Bioinformatic Revolution of Human Adenoviruses
4.1. HAdV-G52
4.2. Simplot Analysis of Novel Adenovirus in Species HAdV-C
4.3. HAdV-D53
4.4. Recombination is Common in the Penton Gene of Species HAdV-D
4.5. Hypothetical Recognition Sites for Recombination in the Hexon Gene
4.6. HAdV-B55
5. The Future
6. Conclusions
HAdV | ATCC number |
---|---|
HAdV-D10 | VR-1087 |
HAdV-D13 | VR-14 |
HAdV-D15 | VR-16 |
HAdV-D20 | VR-255 |
HAdV-D23 | VR-258 |
HAdV-D24 | VR-259 |
HAdV-D25 | VR-223 |
HAdV-D27 | VR-1105 |
HAdV-D28 | VR-226 |
HAdV-D29 | VR-272 |
HAdV-D30 | VR-273 |
HAdV-D32 | VR-625 |
HAdV-D33 | VR-626 |
HAdV-D38 | VR-988 |
HAdV-D39 | VR-932 |
HAdV-D42 | VR-1304 |
HAdV-D44 | VR-1306 |
HAdV-D45 | VR-1307 |
HAdV-D47 | VR-1309 |
HAdV-D51 | VR-1603 |
Acknowledgments
References
- Mautner, V.; Williams, J.; Sambrook, J.; Sharp, P.A.; Grodzicker, T. The location of the genes coding for hexon and fiber proteins in adenovirus DNA. Cell 1975, 5, 93–99. [Google Scholar] [CrossRef] [PubMed]
- Maxam, A.M.; Gilbert, W. A new method for sequencing DNA. Proc. Natl. Acad. Sci. U. S. A. 1977, 74, 560–564. [Google Scholar] [CrossRef] [PubMed]
- Akusjarvaiand, G.; Pettersson, U. Nucleotide sequence at the junction between the coding region of the adenovirus 2 hexon messenger RNA and its leader sequence. Proc. Natl. Acad. Sci. U. S. A. 1978, 75, 5822–5826. [Google Scholar] [CrossRef] [PubMed]
- Kinloch, R.; Mackay, N.; Mautner, V. Adenovirus hexon sequence comparison of subgroup C serotypes 2 and 5. J. Biol. Chem. 1984, 259, 6431–6436. [Google Scholar] [PubMed]
- Roberts, R.J.; O’Neill, K.E.; Yen, C.T. DNA Sequences from the Adenovirus 2 Genome. J. Biol. Chem. 1984, 259, 13968–13975. [Google Scholar] [PubMed]
- Walsh, M.P.; Chintakuntlawar, A.; Robinson, C.M.; Madisch, I.; Harrach, B.; Hudson, N.R.; Schnurr, D.; Heim, A.; Chodosh, J.; Seto, D.; Jones, M.S. Evidence of molecular evolution driven by recombination events influencing tropism in a novel human adenovirus that causes epidemic keratoconjunctivitis . PLoS One 2009, 4, e5635. [Google Scholar] [CrossRef] [PubMed]
- Chroboczek, J.; Bieber, F.; Jacrot, B. The sequence of the genome of adenovirus type 5 and its comparison with the genome of adenovirus type 2. Virology 1992, 186, 280–285. [Google Scholar] [CrossRef] [PubMed]
- Robinson, C.M.; Shariati, F.; Gillaspy, A.F.; Dyer, D.W.; Chodosh, J. Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism. BMC Genomics 2008, 9, 213. [Google Scholar] [CrossRef]
- Davison, A.J.; Benkö, M.; Harrach, B. Genetic content and evolution of adenoviruses . J. Gen. Virol. 2003, 84, 2895–2908. [Google Scholar] [CrossRef] [PubMed]
- Sprengel, J.; Schmitz, B.; Heuss-Neitzel, D.; Zock, C.; Doerfler, W. Nucleotide sequence of human adenovirus type 12 DNA: comparative functional analysis. J. Virol. 1994, 68, 379–389. [Google Scholar] [PubMed]
- Hofmayer, S.; Madisch, I.; Darr, S.; Rehren, F.; Heim, A. Unique sequence features of the Human Adenovirus 31 complete genomic sequence are conserved in clinical isolates. BMC Genomics 2009, 10, 557. [Google Scholar] [CrossRef] [PubMed]
- Walsh, M.P.; Seto, J; Tirado, D.; Chodosh, J.; Schnurr, D.; Seto, D.; Jones, M.S. Genomic analysis of human adenovirus prototype 18 . Virology In press.
- Crawford-Miksza, L.; Schnurr, D.P. Analysis of 15 adenovirus hexon proteins reveals the location and structure of seven hypervariable regions containing serotype-specific residues. J. Virol. 1996, 70, 1836–1844. [Google Scholar] [PubMed]
- Rux, J.J.; Burnett, R.M. Type-specific epitope locations revealed by X-ray crystallographic study of adenovirus type 5 hexon. Mol. Ther. 2000, 1, 18–30. [Google Scholar] [CrossRef] [PubMed]
- Lukashev, A.N.; Ivanova, O.E.; Eremeeva, T.P.; Iggo, R.D. Evidence of frequent recombination among human adenoviruses. J. Gen. Virol. 2008, 89, 380–388. [Google Scholar] [CrossRef] [PubMed]
- Robinson, C.M.; Rajaiya, J.; Walsh, M.P.; Seto, D.; Dyer, D.W.; Jones, M.S.; Chodosh, J. Computational analysis of human adenovirus type 22 provides evidence for recombination between human adenoviruses species D in the penton base gene. J. Virol. 2009, 83, 8980–8985. [Google Scholar] [CrossRef] [PubMed]
- Walsh, M.P.; Seto, J.; Jones, M.S.; Chodosh, J.; Xu, W.; Seto, D. Computational analysis identifies human adenovirus type 55 as a re-emergent acute respiratory disease pathogen. J. Clin. Microbiol. 2010, 48, 991–993. [Google Scholar] [CrossRef] [PubMed]
- Stone, D.; Furthmann, A.; Sandig, V.; Lieber, A. The complete nucleotide sequence, genome organization, and origin of human adenovirus type 11. Virology 2003, 309, 152–165. [Google Scholar] [CrossRef] [PubMed]
- Mei, Y.F.; Skog, J.; Lindman, K.; Wadell, G. Comparative analysis of the genome organization of human adenovirus 11, a member of the human adenovirus species B, and the commonly used human adenovirus 5 vector, a member of species C. J. Gen. Virol. 2003, 84, 2061–2071. [Google Scholar] [CrossRef] [PubMed]
- Hilleman, M.R.; Werner, J.H. Recovery of new agent from patients with acute respiratory illness. Proc. Soc. Exp. Biol. Med. 1954, 851, 183–188. [Google Scholar]
- Hilleman, M.R.; Anderson, S.A.; Levinson, D.J.; Luecking, M.L. Occurrence and significance of adenovirus antibody in sera of recruit and cadre military personnel. Am. J. Hyg. 1958, 67, 179–186. [Google Scholar] [PubMed]
- Rosenbaum, M.J.; Edwards, E.A.; Hoeffler, D.C. Recent experiences with live adenovirus vaccines in Navy recruits. Mil. Med. 1975, 140, 251–257. [Google Scholar] [PubMed]
- Top Jr., F.H.; Grossman, R.A.; Bartelloni, P.J.; Segal, H.; Dudding, B.; Russell, P.; Buescher, E. Immunization with live types 7 and 4 adenovirus vaccines. I. Safety, infectivity, antigenicity, and potency of adenovirus type 7 vaccine in humans . J. Infect. Dis. 1971, 124, 148–154. [Google Scholar] [PubMed]
- Hendrix, R.M.; Lindner, J.L.; Benton, F.R.; Monteith, S.C.; Tuchscherer, M.A.; Gray, G.C.; Gaydos, J.C. Large, Persistent Epidemic of Adenovirus Type 4-Associated Acute Respiratory Disease in U. S. Army Trainees. Emer. Inf. Dis. 1999, 5, 798–801. [Google Scholar] [CrossRef]
- Purkayastha, A.; Su, J.; McGraw, J.; Ditty, S.E.; Hadfield, T.L.; Seto, J.; Russell, K.L.; Tibbetts, C.; Seto, D. Genomic and bioinformatics analyses of HAdV-4vac and HAdV-7vac, two human adenovirus (HAdV) strains that constituted original prophylaxis against HAdV-related acute respiratory disease, a reemerging epidemic disease. J. Clin. Microbiol. 2005, 43, 3083–3094. [Google Scholar] [CrossRef] [PubMed]
- Purkayastha, A.; Ditty, S.E.; Su, J.; McGraw, J.; Hadfield, T.L.; Tibbetts, C.; Seto, D. Genomic and bioinformatics analysis of HAdV-4, a human adenovirus causing acute respiratory disease: implications for gene therapy and vaccine vector development. J. Virol. 2005, 79, 2559–2572. [Google Scholar] [CrossRef] [PubMed]
- Lauer, K.P.; Llorente, I.; Blair, E.; Seto, J.; Krasnov, V.; Purkayastha, A.; Ditty, S.E.; Hadfield, T.L.; Buck, C.; Tibbetts, C.; Seto, D. Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1. J. Gen. Virol. 2004, 85, 2615–2625. [Google Scholar] [CrossRef] [PubMed]
- Gao, W.; Robbins, P.D.; Gambotto, A. Human adenovirus type 35: nucleotide sequence and vector development. Gene Therapy 2003, 10, 1941–1949. [Google Scholar] [CrossRef] [PubMed]
- Vogels, R.; Zuijdgeest, D.; van Rijnsoever, R.; Hartkoorn, E.; Damen, I.; de Béthune, M.P.; Kostense, S;; Helmus, N.; Koudstaal, W.; et al. Replication-deficient human adenovirus type 35 vectors for gene transfer and vaccination: efficient human cell infection and bypass of preexisting adenovirus immunity . J. Virol. 2002, 77, 8263–8271. [Google Scholar] [CrossRef]
- Zhang, Q.; Su, X.; Gong, S.; Zeng, Q.; Zhu, B.; Wu, Z.; Peng, T.; Zhang, C.; Zhou, R. Comparative genomic analysis of two strains of human adenovirus type 3 isolated from children with acute respiratory infection in southern China. J. Gen. Virol. 2006, 87, 1531–1541. [Google Scholar] [CrossRef] [PubMed]
- Mahadevan, P.; Seto, J.; Tibbetts, C.; Seto, D. Natural variants of human adenovirus type 3 provide evidence for relative genome stability across time and geographic space . Virology 2010, 397, 113–118. [Google Scholar] [CrossRef] [PubMed]
- Jones, M.S.; Harrach, B.; Ganac, R.D.; Gozum, M.M.; Dela Cruz, W.P.; Riedel, B.; Pan, C.; Delwart, E.L.; Schnurr, D.P. New adenovirus species found in a patient presenting with gastroenteritis. J. Virol. 2007, 81, 5978–5984. [Google Scholar] [CrossRef] [PubMed]
- Robinson, C.M.; Shariati, F.; Zaitshik, J.; Gillaspy, A.F.; Dyer, D.W.; Chodosh, J. Human adenovirus type 19: Genomic and bioinformatics analysis of a keratoconjunctivitis isolate. Virus Res. 2009, 139, 122–126. [Google Scholar] [CrossRef] [PubMed]
- Seto, J.; Walsh, M.P.; Mahadevan, P.; Purkayastha, A.; Clark, J.M.; Tibbetts, C.; Seto, D. Genomic and bioinformatics analyses of HAdV-14p, reference strain of are-emerging respiratory pathogen and analysis of B1/B2. Virus Res. 2009, 143, 94–105. [Google Scholar] [CrossRef] [PubMed]
- Darr, S.; Madisch, I.; Hofmayer, S.; Rehren, F.; Heim, A. Phylogeny and primary structure analysis of fiber shafts of all human adenovirus types for rational design of adenoviral gene-therapy vectors. J. Gen.Virol. 2009, 90, 2849–2854. [Google Scholar] [CrossRef] [PubMed]
- Kaneko, H.; Iida, T.; Ishiko, H.; Ohguchi, T.; Ariga, T.; Tagawa, Y.; Aoki, K.; Ohno, S.; Suzutani, T. Analysis of the complete genome sequence of epidemic keratoconjunctivitis-related human adenovirus type 8, 19, 37 and a novel serotype. J. Gen. Virol. 2009, 90, 1471–1476. [Google Scholar] [CrossRef] [PubMed]
- Arnold, J.; Jánoska, M.; Kajon, A.E.; Metzgar, D.; Hudson, N.R.; Torres, S.; Harrach, B.; Seto, D.; Chodosh, J.; Jones, M.S. Genomic characterization of human adenovirus 36, a putative obesity agent. Virus Res. 2010, 149, 152–161. [Google Scholar] [CrossRef] [PubMed]
- de Jong, J.C.; Osterhaus, A.D.; Jones, M.S.; Harrach, B. Human adenovirus type 52: a type 41 in disguise? J. Virol. 2008, 82, 3809–3810. [Google Scholar] [CrossRef] [PubMed]
- Schnurr, D.; Dondero, M. Two new candidate adenovirus serotypes. Intervirology 1993, 36, 79–83. [Google Scholar] [PubMed]
- Engelmann, I.; Madisch, I.; Pommer, H.; Heim, A. An outbreak of epidemic keratoconjunctivitis caused by a new intermediate adenovirus 22/H8 identified by molecular typing . Clin. Infect. Dis. 2006, 43, e64–e66. [Google Scholar] [CrossRef] [PubMed]
- Ishiko, H.; Aoki, K. Spread of epidemic keratoconjunctivitis due to a novel serotype of human adenovirus in Japan. J. Clin. Microbiol. 2009, 47, 2678–2679. [Google Scholar] [CrossRef] [PubMed]
- Yang, Z.; Zhu, Z.; Tang, L.; Wang, L; Tan, X.; Yu, P.; Zhang, Y.; Tian, X.; Wang, J.; Zhang, Y.; Li, D.; Xu, W. Genomic analyses of recombinant adenovirus type 11a in China . J. Clin. Microbiol. 2009, 47, 3082–3090. [Google Scholar] [CrossRef] [PubMed]
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Torres, S.; Chodosh, J.; Seto, D.; Jones, M.S. The Revolution in Viral Genomics as Exemplified by the Bioinformatic Analysis of Human Adenoviruses. Viruses 2010, 2, 1367-1381. https://doi.org/10.3390/v2071367
Torres S, Chodosh J, Seto D, Jones MS. The Revolution in Viral Genomics as Exemplified by the Bioinformatic Analysis of Human Adenoviruses. Viruses. 2010; 2(7):1367-1381. https://doi.org/10.3390/v2071367
Chicago/Turabian StyleTorres, Sarah, James Chodosh, Donald Seto, and Morris S. Jones. 2010. "The Revolution in Viral Genomics as Exemplified by the Bioinformatic Analysis of Human Adenoviruses" Viruses 2, no. 7: 1367-1381. https://doi.org/10.3390/v2071367
APA StyleTorres, S., Chodosh, J., Seto, D., & Jones, M. S. (2010). The Revolution in Viral Genomics as Exemplified by the Bioinformatic Analysis of Human Adenoviruses. Viruses, 2(7), 1367-1381. https://doi.org/10.3390/v2071367