Implications of altered replication fidelity on the evolution and pathogenesis of coronaviruses

Abstract

RNA virus evolution results from viral replication fidelity and mutational robustness in combination with selection. Recent studies have confirmed the impact of increased fidelity on RNA virus replication and pathogenesis; however, the impact of decreased fidelity is less defined. Coronaviruses have the largest RNA genomes, and encode an exoribonuclease activity that is required for high-fidelity replication. Genetically stable exoribonuclease mutants will allow direct testing of viral mutational tolerance to RNA mutagens and other selective pressures. Recent studies support the hypothesis that coronavirus replication fidelity may result from a multi-protein complex, suggesting multiple pathways to disrupt or alter virus fidelity and diversity, and attenuate pathogenesis.

Figure 1

Coronavirus genome organization and identified viral nsp interactions. (a) Coronaviruses express 16 nonstructural proteins (nsps1–16) from open reading frames ORF1a and ORF1b, along with several structural and accessory proteins. Several nsps have been shown to have roles in RNA synthesis or modification: nsp12 (RdRp, green), nsp13 [helicase (Hel)], nsp14 [3′-to-5′ exoribonuclease (ExoN) and N7-methyltransferase (N7-MT); blue], nsp15 [endoribonuclease (NEndoU)], and nsp16 [2′-O-methyltransferase (2′-O-MT), red]. (b) ExoN shares conserved motifs (I, II and III) with other identified 3′-to-5′ exonucleases, and requires the amino acids D-E-D-D (white boxes) for activity. Nsp14 also contains a zinc finger (Zn²⁺ F, grey box) and a functional N7-methyltransferase domain. (c) Multiple nsps have been demonstrated to form higher-order complexes, and/or functionally regulate one another in vitro and in recombinant viruses.

Figure 2

Relationship between ssRNA virus genome size and the presence or absence of ExoN. The sizes of full viral genomes identified using the NCBI Viral Genome Resource [48] (with the exception of Yellow head virus strain YHV1999, GenBank ID: FJ848675.1) are plotted, and the average genome size per virus family or subfamily is shown as a horizontal black bar. Members of the order Nidovirales are denoted with an N, while the proposed new Nidovirales candidate family, Mesoniviridae [31], is denoted with an asterisk.