Loss of nsp14-exonuclease activity impairs the replication, proofreading, fitness, and pathogenesis of SARS-CoV-2.

UNLABELLED: Coronaviruses (CoVs) replicate their RNA genomes with a higher degree of fidelity than other RNA viruses, a mechanism mediated by the proofreading and recombination activities of the exoribonuclease domain of replicase nonstructural protein 14 (nsp14-ExoN). Both murine hepatitis virus (MHV) and SARS-CoV tolerate nsp14-ExoN loss-of-function mutations (ExoN-) (D90A and E92A), but have impaired replication fidelity and pathogenesis; yet identical substitutions in MERS-CoV and SARS-CoV-2 have been reported to be lethal. Here, we report a saturation mutagenesis approach facilitating the recovery and analysis of several constellations of SARS-CoV-2 nsp14 ExoN-inactivating, loss-of-function substitutions, including the canonical D90A and E92A. Biochemical assays with purified WT or ExoN-nsp10-14 fusion proteins confirmed that active site substitutions abolished ExoN activity (ExoN-). SARS-CoV-2 ExoN- viruses exhibited impaired replication, RNA synthesis, and recombination, as well as decreased replication fidelity and loss of fitness in vitro. ExoN- viruses were significantly attenuated for replication in human primary airway epithelial cells and were attenuated for replication and pathogenesis in WT mice, as well as the highly susceptible K18 transgenic mice. In the absence of interferon signaling in vivo, SARS-CoV and SARS-CoV-2 ExoN- viral replication could be partially restored. These results demonstrate that SARS-CoV-2 ExoN- viruses are viable but highly impaired for replication, fitness, and fidelity in vitro, as well as innate immune antagonism and pathogenesis in vivo. Collectively, our results solidify the multiple critical roles of nsp14-ExoN across CoV genera and establish new approaches for rescuing and analyzing loss-of-function substitutions in studies of CoV replication, pathogenesis, and evolution. IMPORTANCE: Coronaviruses (CoV) are important human pathogens causing hundreds of millions of infections and millions of deaths over the past 20 years. The study of how these viruses multiply and cause disease identifies points of attack for therapeutics. Using a high-throughput genetic approach, we systematically inactivated an essential enzyme CoV needs for replication called ExoN. We show that without ExoN, CoV replication fidelity and fitness are reduced in cell culture. Replication without ExoN in mice was diminished but could be partially restored in mice that lack key components of the immune response. Altogether, we reveal new insights into the complexities of CoV replication and virus and host interactions, which could be leveraged for the development of novel multifaceted therapeutics that attack the ever-expanding functions of the CoV replication complex in replication and pathogenesis.

Duke Scholars

Author Nicholas Scott Heaton Molecular Genetics and Microbiology