Phylogenetic and recombination analysis of adenovirus isolates reveals discordance between serotype and phylogeny: Multiple sequence alignments

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 t..., , , # 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, adenovi...