Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design

Jacob Kames; David Dillon Holcomb; Ofer Kimchi; Michael DiCuccio; Nobuko Hamasaki-Katagiri; Tony Wang; Anton A Komar; Aikaterini Alexaki; Chava Kimchi-Sarfaty

The recent emergence of the 2019 novel coronavirus (SARS-CoV-2) has gained worldwide attention and sparked an international effort to develop treatments and a vaccine. To date, there have been 693,224 confirmed cases and 33,106 deaths from COVID-19 worldwide, with 136 countries implementing additional health measures [1] . Given the urgency to combat this emerging disease, multiple efforts to develop an effective vaccine are underway. A relatively recent approach for vaccine development, first proposed by Coleman et al. in 2008 for the attenuation of poliovirus [2] , has been used for the attenuation of dozens of viruses, and more recently for bacteria [3] . This approach accomplishes viral attenuation through codon pair deoptimization and appears to be promising for vaccine development, particularly against emerging viruses, as it does not require extensive virusspecific knowledge. It does, however, require knowledge of the viral genome sequence and extensive characterization of its codon and codon pair usage characteristics.