{'fraction_non_alphanumeric': 0.015907447577729574, 'fraction_numerical': 0.0, 'mean_word_length': 5.635491606714628, 'pattern_counts': {'":': 0, '<': 0, '<?xml version=': 0, '>': 0, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
Identification of “Missing Link” Families of Small DNA Tumor Viruses

Adenoviruses, papillomaviruses, parvoviruses and polyomaviruses are collectively known as small DNA tumor viruses. Although it has long been recognized that small DNA tumor virus oncoproteins and capsid proteins show a variety of structural and functional similarities, it is unclear whether these similarities reflect descent from a common ancestor, convergent evolution, horizontal gene transfer among virus lineages, or repeated acquisition of genes from host cells. We report the discovery of a dozen new members of an emerging fourth family of small DNA tumor viruses, the Adomaviridae. Cell culture-based expression of adomavirus open reading frames showed that the virion structural proteins of adomaviruses are homologous to those of adenoviruses. The search for adomaviruses unexpectedly revealed the existence of a previously unrecognized family of animal DNA viruses that are distantly similar to virophages and other polinton-like viruses of unicellular eukaryotes. Members of the emerging “adintovirus” family encode retrovirus-like integrase proteins and adenovirus-like DNA polymerase and virion structural proteins. Adintovirus sequences were found in genomics datasets for all major groups of animals, including terrestrial vertebrates. Analysis of the gene content of adintoviruses supports a model in which small DNA tumor viruses descended from more complex adintovirus-like ancestors through gene-loss and horizontal gene transfer events occurring hundreds of millions of years ago. Author Summary In contrast to cellular organisms, viruses do not encode any universally conserved genes. Even within a given family of viruses, the primary amino acid sequences of homologous genes can rapidly diverge to the point of unrecognizability. Although modern metagenomic surveys have begun to expose the wide sequence diversity within known virus families, it is unclear how much of the unidentifiable sequence “dark matter” typically observed in these surveys represents unknown virus groups. Our searches of sequence databases revealed more than a dozen highly divergent new members of an emerging virus family, the Adomaviridae. Using structure-guided methods for detection of distant homologs, we also discovered the existence of an apparently older lineage of viruses that we name “adintoviruses.” Adintovirus sequences can be found as integrated into host animal germline DNA and as apparently linear DNA molecules in genome sequencing datasets for all major animal phyla. The results suggest a framework that ties small DNA tumor viruses into a shared evolutionary history in which key family-level divergence events occurred in early animals and their unicellular precursors.