Dataset Open Access

Data from: Footprint of the host restriction factors APOBEC3 on the genome of human viruses

Gillet, Nicolas; Poulain, Florian

APOBEC3 enzymes are innate immune effectors that introduce mutations into viral genomes. These enzymes are cytidine deaminases which transform cytosine into uracil. They preferentially mutate cytidine preceded by thymidine making the 5'TC motif their favored target. Viruses have evolved different strategies to evade APOBEC3 restriction. Certain viruses actively encode viral proteins antagonizing the APOBEC3s, others passively face the APOBEC3 selection pressure thanks to a depleted genome for APOBEC3-targeted motifs. Hence, the APOBEC3s left on the genome of certain viruses an evolutionary footprint.

The aim of our study is the identification of these viruses having a genome shaped by the APOBEC3s. We analyzed the genome of 33,400 human viruses for the depletion of APOBEC3-favored motifs. We demonstrate that the APOBEC3 selection pressure impacts at least 22% of all currently annotated human viral species. The papillomaviridae and polyomaviridae are the most intensively footprinted families; evidencing a selection pressure acting genome-wide and on both strands. Members of the parvoviridae family are differentially targeted in term of both magnitude and localization of the footprint. Interestingly, a massive APOBEC3 footprint is present on both strands of the B19 erythroparvovirus; making this viral genome one of the most cleaned sequences for APOBEC3-favored motifs. We also identified the endemic coronaviridae as significantly footprinted. Interestingly, no such footprint has been detected on the zoonotic MERS-CoV, SARS-CoV-1 and SARS-CoV-2 coronaviruses. In addition to viruses that are footprinted genome-wide, certain viruses are footprinted only on very short sections of their genome. That is the case for the gamma-herpesviridae and adenoviridae where the footprint is localized on the lytic origins of replication. A mild footprint can also be detected on the negative strand of the reverse transcribing HIV-1, HIV-2, HTLV-1 and HBV viruses.

Together, our data illustrate the extent of the APOBEC3 selection pressure on the human viruses and identify new putatively APOBEC3-targeted viruses.

S1 Table: Genomic K-mer ratios for human viruses.

Observed/expected K-mer ratios for each genomic human viral sequence.

 

S2 Table: Genic K-mer ratios for human viruses.

Observed/expected K-mer ratios for each genic human viral sequence.

 

S3 Table: Genomic K-mer ratios for non-human viruses.

Observed/expected K-mer ratios for each genomic and genic non-human viral sequence.

Funding provided by: Fonds De La Recherche Scientifique - FNRS
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002661
Award Number: 31270116

Funding provided by: Fonds De La Recherche Scientifique - FNRS
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002661
Award Number: 34972507

Funding provided by: Fonds De La Recherche Scientifique - FNRS
Crossref Funder Registry ID: http://dx.doi.org/10.13039/501100002661
Award Number: 31454280

Files (152.3 MB)
Name Size
S1_Table_Genomic_K-mer_ratios_A3_footprint_Poulain.txt
md5:d1ead27a11ec6be1cfd046e00e7b1256
22.3 MB Download
S2_Table_Genic_K-mer_ratios_A3_footprint_Poulain.txt
md5:de0bb6e212670c8fa01894da409f60cb
123.1 MB Download
S3_Table_Animals_Genomic_K-mer_ratios_A3_footprint_Poulain.txt
md5:cdc0d206360f92e60c51c5545c3a1e55
6.9 MB Download
35
13
views
downloads
Views 35
Downloads 13
Data volume 515.1 MB
Unique views 31
Unique downloads 8

Share

Cite as