A Glimpse on the Evolution of RNA Viruses: Implications and Lessons from SARS-CoV-2

Abstract

RNA viruses are characterised by extremely high genetic variability due to fast replication, large population size, low fidelity, and (usually) a lack of proofreading mechanisms of RNA polymerases leading to high mutation rates. Furthermore, viral recombination and reassortment may act as a significant evolutionary force among viruses contributing to greater genetic diversity than obtainable by mutation alone. The above-mentioned properties allow for the rapid evolution of RNA viruses, which may result in difficulties in viral eradication, changes in virulence and pathogenicity, and lead to events such as cross-species transmissions, which are matters of great interest in the light of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemics. In this review, we aim to explore the molecular mechanisms of the variability of viral RNA genomes, emphasising the evolutionary trajectory of SARS-CoV-2 and its variants. Furthermore, the causes and consequences of coronavirus variation are explored, along with theories on the origin of human coronaviruses and features of emergent RNA viruses in general. Finally, we summarise the current knowledge on the circulating variants of concern and highlight the many unknowns regarding SARS-CoV-2 pathogenesis.

Keywords: RNA virus; SARS-CoV-2; coronavirus; evolution; mutation; quasispecies; recombination.

Figure 1

Baltimore classification of viruses. Seven classes of viruses are depicted based on the genome structure and mRNA synthesis strategy. The polarity of the genome is designated as “+” and “−” strands, or strands of both polarities (“+/−”), reverse transcribing characteristic is abbreviated as “RT”, while “ds” and “ss” indicate double-stranded and single-stranded genomes, respectively. Data are based on the original and updated Baltimore classification [4,22].

Figure 2

Classification of human coronaviruses. Seven currently recognised human coronavirus species are shown in green, their higher taxonomical categories are shown in orange, and other taxonomical categories are shown in blue. *: not all members of the particular taxonomical category are depicted. Data are based on the International Committee on Taxonomy of Viruses: Current Taxonomy Release 2021 and Master Species List 2021 v3 [32,109].

Figure 3

Global genomic epidemiology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) since the start of the coronavirus disease 2019 (COVID-19) pandemic. Visualisation of SARS-CoV-2 evolution and spread since the start of the pandemic was performed using Nextstrain (nextstrain.org), a publicly accessible bioinformatic tool for real-life tracking of pathogen evolution. A depiction of a subsample of 3059 genomes obtained between December 2019 and November 2022 from the GISAID database, with currently recognised SARS-CoV-2 variants indicated by different coloured branches on (a) a time-resolved phylogenetic tree. (b) Frequency visualisation by clade. Isolate Wuhan-Hu-1 (accession number: MN908947.3) was used as a reference. Vector images and live display can be found at: https://nextstrain.org/ncov/gisaid/global/all-time?d=tree,frequencies&p=full&showBranchLabels=all (accessed on 29 November 2022). In addition, a complete list of 3059 sequence authors was downloaded and shown in Table S1 as a tabs-separated value (TSV) file. Vector images are licensed with Attribution 4.0. International (CC BY 4.0) license [180,181].