Genetic Variation and Evolution of the 2019 Novel Coronavirus

Abstract

Introduction: SARS-CoV-2 is a new type of coronavirus causing a pandemic severe acute respiratory syndrome (SARS-2). Coronaviruses are very diverting genetically and mutate so often periodically. The natural selection of viral mutations may cause host infection selectivity and infectivity.

Methods: This study was aimed to indicate the diversity between human and animal coronaviruses through finding the rate of mutation in each of the spike, nucleocapsid, envelope, and membrane proteins.

Results: The mutation rate is abundant in all 4 structural proteins. The most number of statistically significant amino acid mutations were found in spike receptor-binding domain (RBD) which may be because it is responsible for a corresponding receptor binding in a broad range of hosts and host selectivity to infect. Among 17 previously known amino acids which are important for binding of spike to angiotensin-converting enzyme 2 (ACE2) receptor, all of them are conservative among human coronaviruses, but only 3 of them significantly are mutated in animal coronaviruses. A single amino acid aspartate-454, that causes dissociation of the RBD of the spike and ACE2, and F486 which gives the strength of binding with ACE2 remain intact in all coronaviruses.

Discussion/conclusion: Observations of this study provided evidence of the genetic diversity and rapid evolution of SARS-CoV-2 as well as other human and animal coronaviruses.

Keywords: Biodiversity; Clinical genetics; Ecology; Mutation rate; Pandemics; Prevalence.

Fig. 1

Frequencies of SARS viruses' amino acid changes in envelope protein. Frequencies of envelope signatures in animal viral isolates (dark gray) and human viral isolates (light gray). The analysis was performed in sequences derived from 106 subjects; 51 reported animal viral strains, and 55 reported human viral strains. Statistically significant differences were assessed by χ² tests of independence. All p values were calculated from 2-sided tests using 0.001 as the significance level (p ≤ 0.001).

Fig. 2

a, b Frequencies of SARS viruses' amino acid changes in neutralizing antibody (m396 and 80R) epitope (336–516 amino acid domain) spike protein. b The SARS-CoV-2 RBD/ACE2 interface corresponds to 387–516 amino acid domain. Frequencies of spike signatures in animal viral isolates (dark gray) and human viral isolates (light gray). The analysis was performed in sequences derived from 103 subjects; 51 reported animal viral strains, and 52 reported human viral strains. Statistically significant differences were assessed by χ² tests of independence. All p values were calculated from 2-sided tests using 0.001 as the significance level (p ≤ 0.001).

Fig. 3

Frequencies of SARS viruses' amino acid changes in membrane protein. Frequencies of membrane signatures in animal viral isolates (dark gray) and human viral isolates (light gray). The analysis was performed in sequences derived from 106 subjects; 51 reported animal viral strains, and 55 reported human viral strains. Statistically significant differences were assessed by χ² tests of independence. All p values were calculated from 2-sided tests using 0.001 as the significance level (p ≤ 0.001).

Fig. 4

Frequencies of SARS viruses' amino acid changes in nucleocapsid protein. Frequencies of nucleocapsid signatures in animal viral isolates (dark gray) and human viral isolates (light gray). The analysis was performed in sequences derived from 105 subjects; 51 reported animal viral strains, and 54 reported human viral strains. Statistically significant differences were assessed by χ² tests of independence. All p values were calculated from 2-sided tests using 0.001 as the significance level (p ≤ 0.001).