Natural variation among human adenoviruses: genome sequence and annotation of human adenovirus serotype 1

Abstract

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.

New Adenovirus Species Found in a Patient Presenting with Gastroenteritis

“…Through sequence analysis, it has been demonstrated that the genomes of all human adenoviruses have similar genetic organization (11,24,26).…”

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

“…Standard PCR methodologies were used to amplify regions to be sequenced, as detailed for HAdV-1 (31). PCR conditions, in brief, called for Pfu Ultra DNA Polymerase (Stratagene, Inc.) at 2.5 units in a total volume of 50 l containing 5 l of 10ϫ polymerase buffer (Stratagene, Inc.), 3.5 l dimethyl sulfoxide (7% final), deoxynucleoside triphosphates (200 M; stock solutions of 1 mM), oligonucleotide primers (0.5 M; stock solutions of 10 M), and template DNA (30 ng; stock solutions of 33.16 ng/l).…”

“…The genome sequence of HAdV-4, determined earlier by the Epidemic Outbreaks Consortium (39), was used to generate a scaffold of minimally tiled and overlapping primers for PCR amplification and DNA sequencing, leading to threefold coverage of each base with complementary reads of the strands. As shown in a study to rapidly resequence the HAdV-1 genome, this strategy allows efficient resequencing of related genomes at minimal cost and effort (31). PCR was performed using Pfu Ultra DNA Polymerase (Stratagene, Inc.) and 30 ng of purified adenoviral DNA as a template.…”

“…This was repeated using windows of 1-kb segments that overlapped by 500 nucleotides. The algorithm is identical to the annotation protocol employed for the HAdV-1 analysis (31). The sequence fragments were queried systematically against the nonredundant NCBI database using the BLASTX program of the BLAST suite sequence alignment software (2).…”

Detection of a putative novel adenovirus by PCR amplification, sequencing and phylogenetic characterisation of two gene fragments from formalin-fixed paraffin-embedded tissues of a cat diagnosed with disseminated adenovirus disease

“…The sequence was identified as originating from HAdV-1 later, when the full genomic sequence of HAdV-1 was published (Lauer et al, 2004). Subsequently, the presence of HAdV-1 was confirmed in cats in Japan (Phan et al, 2006) and Brazil as well (Luiz et al, 2010), but no other reports on sequencelevel identification of AdVs in felid hosts have been published to date.…”