Attenuation and Degeneration of SARS-CoV-2 Despite Adaptive Evolution

Abstract

The evolution of severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) has followed similar trends as other RNA viruses, such as human immunodeficiency virus type 1 and the influenza A virus. Rapid initial diversification was followed by strong competition and a rapid succession of dominant variants. Host-initiated RNA editing has been the primary mechanism for introducing mutations. A significant number of mutations detrimental to viral replication have been quickly purged. Fixed mutations are mostly diversifying mutations selected for host adaptation and immune evasion, with the latter accounting for the majority of the mutations. However, immune evasion often comes at the cost of functionality, and thus, optimal functionality is still far from being accomplished. Instead, selection for antibody-escaping variants and accumulation of near-neutral mutations have led to suboptimal codon usage and reduced replicative capacity, as demonstrated in non-respiratory cell lines. Beneficial adaptation of the virus includes reduced infectivity in lung tissues and increased tropism for the upper airway, resulting in shorter incubation periods, milder diseases, and more efficient transmission between people.

Keywords: attenuation; codon usage; covid-19; degeneration; evolution; genome degradation; immune evasion; mutation; natural selection; pneumonia.

Figure 1. Decline of intra-clade mutation rate from early to later clades.

Figure 2. Degenerative mutations of SARS-CoV-2, the role of selection by immune evasion, and the change in tissue tropism.

Dark arrows indicate viral evolution, while gray arrows indicate tissue tropism. The thickness of the gray arrows represents the relative intensity of tropism. Phenotypic consequences of mutations are represented by the colors of the viral particles. Neutralizing antibodies are drawn around unchanged viruses. The figure is the author’s own creation with the assistance of scientific illustrator Peng Wang.