Decoding SARS-CoV‑2 Transmission and Evolution and Ramifications for COVID-19 Diagnosis, Vaccine, and Medicine

Tremendous effort has been given
to the development of diagnostic
tests, preventive vaccines, and therapeutic medicines for coronavirus
disease 2019 (COVID-19) caused by severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2). Much of this development has been based
on the reference genome collected on January 5, 2020. Based on the
genotyping of 15 140 genome samples collected up to June 1,
2020, we report that SARS-CoV-2 has undergone 8309 single mutations
which can be clustered into six subtypes. We introduce mutation ratio
and mutation h-index to characterize the protein
conservativeness and unveil that SARS-CoV-2 envelope protein, main
protease, and endoribonuclease protein are relatively conservative,
while SARS-CoV-2 nucleocapsid protein, spike protein, and papain-like
protease are relatively nonconservative. In particular, we have identified
mutations on 40% of nucleotides in the nucleocapsid gene in the population
level, signaling potential impacts on the ongoing development of COVID-19
diagnosis, vaccines, and antibody and small-molecular drugs.