Translation of a genetic codon without a cognate tRNA gene is affected by both the cognate tRNA availability and the interaction with non-cognate isoacceptor tRNAs. Moreover, two consecutive slow codons (slow di-codons) lead to a much slower translation rate. Calculating the composition of host specific slow codons and slow di-codons in the viral protein coding sequences can predict the order of viral protein synthesis rates between different virus strains. Comparison of human-specific slow codon and slow di-codon compositions in the genomes of 590 coronaviruses infect humans revealed that the protein synthetic rates of 2019 novel coronavirus (2019-nCoV) and severe acute respiratory syndrome-related coronavirus (SARS-CoV) may be much faster than other coronaviruses infect humans. Analysis of host-specific slow codon and di-codon compositions provides links between viral genomic sequences and capability of virus replication in host cells that may be useful for surveillance of the transmission potential of novel viruses.

Introduction

No organism has a full set of tRNA species for all 61 amino acid-encoded codons.1 Codons without cognate tRNA gene can be referred to as slow codons of the organism. These codons are organism specific codons because different organisms have different tRNA gene compositions. For example, 13 amino acid-encoding codons have no cognate tRNA genes in the human genome. Studies have revealed by ribosomal profiling experiments that translation of codons by rare tRNAs and non-cognate isoacceptor tRNAs (by wobble base pairing of codons and tRNAs) reduces translation efficiency2,3, . 4 Moreover, it has been reported that the efficiency of translating a particular codon is affected by the nature of the immediately adjacent codons.5,6 Two consecutive slow codons (slow di-codons) lead to a much slower translation rate. Conversely, coding sequences (CDSs) with low composition of slow codons and slow dicodons may possess fast translation rates. Translation of viral proteins is completely dependent on the translation machinery of host cells. Therefore, the proportions of host-specific slow codons and slow di-codons in the viral CDSs can be used to predict the order of viral protein synthesis rates between different viruses of different genera, serotypes, and strains.