Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study

Gurjit S. Randhawa; Maximillian P.M. Soltysiak; Hadi El Roz; Camila P.E. de Souza; Kathleen A. Hill; Lila Kari

Dinucleotide composition and biases are pervasive across the genome and make up a 409 part of the organism's genomic signature [83] . These host genomes have evolutionary 410 pressures that shape the host genomic signature, such as the pressure to eliminate CG 411 dinucleotides within protein coding genes in humans [82] . Viral genomes have been 412 shown to mimic the same patterns of the hosts, including single-stranded positive-sense 413 RNA viruses, which suggests that many RNA viruses can evolve to mimic the same 414 features of their host's genes and genomic signature [81] [82] [83] [84] [85] . As genomic composition, 415 specifically in mRNA, can be used as a way of discriminating self vs non-self RNA, the 416 viral genomes are likely shaped by the same pressures that influence the host 417 genome [82] . One such pressure on DNA and RNA is the APOBEC family of enzymes, 418 members of which are known to cause G to A mutations [85] [86] [87] . While these enzymes 419 primarily work on DNA, it has been demonstrated that these enzymes can also target 420 RNA viral genomes [86] . The APOBEC enzymes therefore have RNA editing capability 421 and may help contribute to the innate defence system against various RNA viruses [85] . 422 This could therefore have a direct impact on the genomic signature of RNA viruses.