Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments
Data files
Jun 07, 2024 version files 57.74 MB
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HAdV-B_Fiber_Protein_Alignment.txt
156.32 KB
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HAdV-B_Genome_Alignment.txt
12.75 MB
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HAdV-B_Hexon_Protein_Alignment.txt
324.36 KB
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HAdV-B_Penton_Protein_Alignment.txt
197.33 KB
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HAdV-B_Subsample_Genome_Alignment.txt
1.65 MB
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Mastadenovirus_Genome_Alignment.txt
42.66 MB
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README.md
2.10 KB
Abstract
Background
Human adenovirus (HAdV) infections are caused by seven mastadenovirus species (A-G) and are the source for a variety of pathologies including gastrointestinal, respiratory, neurological, and ocular disease. While HAdV-D is the most common cause of adenovirus ocular infections, human adenoviruses B and E have also been isolated from the eye.
Results
In the course of classifying three new atypical ocular adenovirus samples, taken from the vitreous humor, we found that all three isolates were HAdV-B species, with isolate BP-AdV1 sorting with the B1 clade, and isolates BP-AdV2 and BP-AdV3 grouping into the B2 clade. The three Bascom Palmer HAdV-B genomes were then combined with over 300 HAdV-B genome sequences, including 9 ocular HAdV-B genome sequences. The whole genome phylogenetic analysis showed that 9 of the 11 ocular sequences grouped into the B1 clade, forming two clusters within B1. Attempts to categorize the penton, hexon and fiber serotypes using phylogeny of the three Bascom Palmer samples were inconclusive due to incongruence between serotype and phylogeny in the dataset. Recombination analysis using a subset of HAdV-B strains to generate a hybridization network detected recombination between non-human primate and human derived strains, recombination between one HAdV-B strain and the HAdV-E outgroup and limited recombination between the B1 and B2 clades.
Conclusions
The discordance between serotype and phylogeny detected in this study suggests that the current penton/hexon/fiber-based classification mechanism does not accurately describe the natural history and phylogenetic relationships amongst adenoviruses. A new adenovirus strain classification strategy may be beneficial to the field.
This dataset contains a total of 6 multiple sequences alignments.
Dataset Summary: Prior to phylogenetic and recombination analysis, the genomes of 722 adenovirus strains were downloaded from GenBank (Supplementary Table 1 of the manuscript). The genomes of the 722 isolates were combined with the three Bascom Palmer adenovirus isolates, and a genome based multiple sequence alignment (MSA) was generated using MAFFT v. 7.45 (https://doi.org/10.1093/molbev/mst010). MAFFT was used to generate an additional full genome alignment of 318 human adenovirus B (HAdV-B) strains. Protein sequence based multiple sequence alignments of human adenovirus B fiber, penton and hexon proteins. Last a genomic alignment containing a subsampled selection of 42 adenovirus strains was produced. For all of the MSAs, adenovirus E isolate 4482 (accession MT771648) was used as an outgroup. The results show discordance between adenoviral serotype and phylogeny.
Description of the data and file structure
There are a total of 6 multiple sequence alignments, all of which are in FASTA format.
Three are nucleotide based alignments:
- Mastadenovirus Genome Alignment.txt
- HAdV-B Genome Alignment.txt
- HAdV-B Sub-sample Genome Alignment.txt
Three are protein sequence based:
- HAdV-B Fiber Protein Alignment.txt
- HAdV-B Hexon Protein Alignment.txt
- HAdV-B Penton Protein Alignment.txt
The name of each sequence in the alignments is the viral strain designation.
Abbreviations:
HAdV-B: Human Adenovirus B
A user may use these alignments to examine phylogeny and/or recombination in Mastadenoviruses or HAdV-B specifically.
Sharing/Access information
The GenBank accession numbers for the adenovirus strains found in the overall dataset are found in Supplementary Table 1 of the manuscript (doi: 10.1167/iovs.65.2.12).
Code/Software
Not applicable