Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

Bahir, Iris; Fromer, Menachem; Prat, Yosef; Linial, Michal

The collection of proteins from ViralZone, a manually reviewed virus-host web portal that provides information on all known virus genera, overcomes some of these biases. ViralZone lists B300 genera of viruses belonging to 80 major families. Associated with each genus is information on the host range and tissue tropism. All viruses are classified by their taxonomical order as well as by the accepted index that divides them into seven classes (Baltimore index I-VII), based on their genetic material and mode of replication. One hundred twentyone human-infecting viruses that belong to 50 genera are currently known (Supplementary Table S1 ). The uneven partition for human-infecting viruses among the seven classes is shown ( Figure 1B ). Class I (dsDNA) and class V (ssRNA(À)) account for 70% of the proteins, but all other classes are also represented among human viruses. By considering all proteins that are known from UniProtKB (a unification of SwissProt and TrEMBL), only 25% of the relevant proteomes are included in classes I and V, whereas the dominating class in terms of the quantity of protein sequences is class VI (ssRNA (RT), including HIV). Proteins belonging to class IV account for B50% of the proteins of human-infecting viruses (total B568 000). We used the manually compiled set from SwisProt for analyzing the human viruses throughout this study. Thus, in summary, we chose to focus only on complete proteomes of the representative species to ensure an unbiased and unabridged data set for subsequent analysis, as an uneven Partition of all proteins of 121 human-infecting viruses (from 50 virus genera) by viral classification into the 7 Baltimore classes and by the number of proteins in each class. Note the significant change in the fraction of proteins in each class when the manually reviewed data resource (SwissProt) or all data (UniProtKB) are considered. Source data and additional clinical information can be found in Supplementary Table S1 .