DOI: 10.5061/dryad.x0k6djhrk
title: Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments

description: 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.
description: # Phylogenetic and Recombination Analysis of Adenovirus Isolates Reveals
 Discordance between Serotype and Phylogeny: Multiple Sequence Alignments
 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](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: 1. Mastadenovirus Genome Alignment.txt 2. HAdV-B Genome Alignment.txt 3. HAdV-B Sub-sample Genome Alignment.txt Three are protein sequence based: 1. HAdV-B Fiber Protein Alignment.txt 2. HAdV-B Hexon Protein Alignment.txt 3. 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)](https://doi.org/10.1167%2Fiovs.65.2.12). ## Code/Software Not applicable