Decoding SARS-CoV-2 transmission, evolution and ramification on COVID-19 diagnosis, vaccine, and medicine

TL;DR

This paper analyzes the genetic mutations of SARS-CoV-2, revealing significant variations that impact the development of diagnostics, vaccines, and medicines for COVID-19, with implications for ongoing and future efforts.

Contribution

It introduces mutation ratio and mutation h-index metrics to characterize SARS-CoV-2 protein conservation and reports extensive mutations affecting key viral proteins.

Findings

SARS-CoV-2 has 4459 mutations clustered into five subtypes.

Envelope, main protease, and endoribonuclease are relatively conserved.

Nucleocapsid protein has undergone significant gene changes recently.

Abstract

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 6156 genome samples collected up to April 24, 2020, we report that SARS-CoV-2 has had 4459 alarmingly mutations which can be clustered into five 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 non-conservative. In particular, the nucleocapsid protein has more than half its genes changed in the past few months, signaling devastating impacts on the ongoing development of COVID-19 diagnosis, vaccines, and drugs.