Genome sequencing of a novel variant of fowl adenovirus B reveals mosaicism in the pattern of homologous recombination events

Abstract

We determined the genomic sequence of a Ukrainian strain of fowl adenovirus B (FAdV-B). The isolate (D2453/1) shared 97.2% to 98.4% nucleotide sequence identity with other viruses belonging to the species Fowl aviadenovirus B . Marked genetic divergence was seen in the hexon, fiber, and ORF19 genes, and phylogenetic analysis suggested that recombination events had occurred in these regions. Our analysis revealed mosaicism in the recombination patterns, a finding that has also been described in the genomes of strains of FAdV-D and FAdV-E. The shared recombination breakpoints, affecting the same genomic regions in viruses belonging to different species, suggest that similar selection mechanisms are acting on the key neutralization antigens and epitopes in viruses of different FAdV species. Supplementary Information The online version contains supplementary material available at 10.1007/s00705-021-04972-9.

Genomic Epidemiology and Evolution of Fowl Adenovirus 1

“…Both homologous and heterologous recombination have been published previously in aviadenoviruses [ 5 , 20 , 21 ]; however, the few available genome sequences seem to have prevented the recognition of such events occurring in FAdV-1 strains. In this study, we presented evidence for multiple recombination events that have occurred in the past and identified the major recombination breakpoints where genomic information exchange is most likely to occur between parental strains.…”

Rapid genotyping of viral samples using Illumina short-read sequencing data

“…We checked the identity of samples by submitting the consensus genome sequences to the RABV-GLUE identification tool (http://rabv-glue.cvr.gla.ac.uk/), then compared the most probable lineage uncovered by this tool with the identity of the originally reported lineage. Furthermore, we re-analyzed the feline coronavirus (FCoV) sequence data of de Barros et al (2019) [21] and the avian adenovirus sequencing reads of Homonnay et al (2021) [22], latter of which was the only single-end read sequencing dataset included in the benchmarking. For the FCoV dataset, we reduced the minimum read depth required for variant calling to three, as this sample showed the lowest vertical coverage after aligning the reads to the reference genome of feline coronavirus (isolate UG-FH8) (KX722529) also used by de Barros et al ( 2019) [21].…”

Rapid genotyping of targeted viral samples using Illumina short-read sequencing data

“…We checked the identity of samples by submitting the consensus genome sequences to the RABV-GLUE identification tool (http://rabv-glue.cvr.gla.ac.uk/), then compared the most probable lineage uncovered by this tool with the identity of the originally reported lineage. Furthermore, we re-analyzed the feline coronavirus (FCoV) sequence data of de Barros et al (2019) [45], and the avian adenovirus sequencing reads of Homonnay et al (2021) [46], the latter of which was the only single-end read sequencing dataset included in the benchmarking. For the FCoV dataset, we reduced the minimum read depth required for variant calling to three, as this sample showed the lowest mean read depth after aligning the reads to the reference genome of feline coronavirus (isolate UG-FH8) (KX722529) also used by de Barros et al ( 2019) [45].…”

“…� Raw Illumina reads were kindly made available for us byHomonnay et al (2021) [46] upon request. https://doi.org/10.1371/journal.pone.0274414.t001…”