Whole-genome sequencing of live attenuated bovine adenovirus type 7 vaccine strain TS-GT suggests biomarkers for virulence attenuation

Abstract

Bovine adenovirus type 7 (BAdV-7) is one of the most important respiratory and enteric pathogens in the cattle industry. Although live attenuated vaccines are used to control the virus in Japan, limited information is available on the genomic regions that determine viral pathogenicity. We determined the complete genome sequence of the attenuated BAdV-7 strain TS-GT. The genome is 30,052 bp long and contains 45-bp inverted terminal repeats and 30 predicted genes. A genome sequence comparison showed that 99.9% of the TS-GT genome is identical to the prototypic and pathogenic BAdV-7 strain Fukuroi; however, the TS-GT genome contains a novel mutation and four indels. We describe here potential relationships between these genomic changes and the biological characteristics of BAdV-7.

Combined direct/indirect detection allows identification of DNA termini in diverse sequencing datasets and supports a multiple-initiation-site model for HIV plus-strand synthesis

“…Certain mammalian viruses (e.g., adenoviruses) have linear double-stranded DNA (dsDNA) genomes. [32][33][34][35][36] We used a publicly available dataset of shotgun DNA sequence reads prepared using Illumina TruSeq following infection by an adenovirus (bovine adenovirus type 7) 37 to assess the ability of the different terminus detection approaches to illuminate the end structure in a case where ends are blocked. Adenoviruses replicate through a machinery that utilizes a terminal protein primer, resulting in a protein-modified terminus that is not available for ligation; 38 this mechanism is not unique to adenovirus, but is indeed shared by a number of phage and viruses of eukaryotic cells, including phage phi29, poliovirus, and tectivirus.…”

“…We interpret this as evidence that bovine adenovirus exists in a linear form, consistent with previous experimental observations. [32][33][34] Two significant strand bias peaks are observed: a positive peak at the extreme left of the genome and a negative peak at the far right. In the rest of the genome from 1,000-29,000 base pairs (bp), there are no significant peaks, with only minor peaks, likely occurring from biases in fragmentation.…”

“…38 As such, the case of adenovirus exemplifies the utility of having both direct and indirect methods available. 34 , with display of termini, coverage, and strand bias analysis using PolyBench. Lower plot shows coverage levels for k-mer sequences from read data mapped to the plus-strand (blue) and minus strand (green), with a characteristic shift near the terminus due to the scarcity of outward-facing reads at each end.…”

“…Published sequence datasets described herein for bovine adenovirus, C. reinhardtii, C. elegans, and HIV were obtained from the NCBI short read archive with accession IDs DRR257739 (bovine adenovirus 7 34 ) and SRR879372 (C. reinhardtii), SRR7211661/SRR3536210/SRR7211661 (C. elegans 75,76,79,80 ), and PRJNA559271 (HIV 9 hpi WT, 48 hpi WT, and 9 hpi IN). Additional HIV datasets and sequencing data for full length and cleaved bacteriophage lambda are being provided to NCBI.…”