Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1 Kim P. Lauer, 1 Isabel Llorente, 1 Eric Blair, 1 Jason Seto, 1 Vladimir Krasnov, 1 Anjan Purkayastha, 1,4,5 Susan E. Ditty, 2,5 Ted L. Hadfield, 2,5 Charles Buck, 3 Clark Tibbetts 4,5 and Donald Seto 1,4,5 Correspondence Donald Seto dseto@gmu.edu 1 Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA 2 Division of Microbiology, Department of Infectious and Parasitic Diseases Pathology, Armed Forces Institute of Pathology, 5300 Georgia Avenue NW, Washington, DC 20306, USA 3 Department of Virology, American Type Culture Collection (ATCC), Manassas, VA 20108, USA 4,5 HQ USAF Surgeon General Office, Directorate of Modernization (SGR) 4 and Epidemic Outbreak Surveillance (EOS) Consortium 5 , 5201 Leesburg Pike, Suite 1401, Falls Church, VA 22041, USA Received 18 March 2004 Accepted 10 May 2004 The 36 001 base pair DNA sequence of human adenovirus serotype 1 (HAdV-1) has been determined, using a ‘leveraged primer sequencing strategy’ to generate high quality sequences economically. This annotated genome (GenBank AF534906) confirms anticipated similarity to closely related species C (formerly subgroup), human adenoviruses HAdV-2 and -5, and near identity with earlier reports of sequences representing parts of the HAdV-1 genome. A first round of HAdV-1 sequence data acquisition used PCR amplification and sequencing primers from sequences common to the genomes of HAdV-2 and -5. The subsequent rounds of sequencing used primers derived from the newly generated data. Corroborative re-sequencing with primers selected from this HAdV-1 dataset generated sparsely tiled arrays of high quality sequencing ladders spanning both complementary strands of the HAdV-1 genome. These strategies allow for rapid and accurate low-pass sequencing of genomes. Such rapid genome determinations facilitate the development of specific probes for differentiation of family, serotype, subtype and strain (e.g. pathogen genome signatures). These will be used to monitor epidemic outbreaks of acute respiratory disease in a defined test bed by the Epidemic Outbreak Surveillance (EOS) project. INTRODUCTION Through five decades, since the first detailed characteriza- tions of human adenoviruses (HAdVs) (Rowe et al., 1953; Hillemann & Werner, 1954; Buescher, 1967; Benko et al., 2000), this host–pathogen system has repeatedly served to catalyse insights into molecular biology and genetics, as well as complex epidemiology and pathogenesis (Wadell, 1984). Recognized diversity among the HAdV serotypes became understood in relation to six clades or species (formerly subgroups). Among these, members of the HAdV-C (sero- types 1, 2, 5 and 6) cause typically benign respiratory and gastrointestinal infections in endemic pattern among most human hosts in early childhood. The serotypes of this species can establish lifelong persistent shedding infections of lymphoid tissues accounting for their early identification as outgrowths of human cell culture exposed to tissue extracts from even apparently healthy individuals. A strikingly different pattern of epidemiology and patho- genesis is shared by species B1 and E serotypes HAdV-3, -4, -7 and -21. In contrast, these adenoviruses (AdV) have been associated with otherwise healthy young adults, causing epidemic outbreaks of acute respiratory disease (ARD) among basic military trainees (Dudding et al., 1972). These costly outbreaks were controlled by the introduction of effective live virus vaccines since about 1970. However, the manufacture of HAdV vaccines ceased in 1996, which has led to the recurrence of frequent HAdV-based ARD epide- mics at military basic training venues (Gray et al., 2000). Such outbreaks are characterized by extensive morbidity and occasional mortality, adding a human toll to high economic costs, and reviving earlier broad interest in HAdV 0008-0118 G 2004 SGM Printed in Great Britain 2615 Journal of General Virology (2004), 85, 2615–2625 DOI 10.1099/vir.0.80118-0