Evaluating the Effect of SARS-CoV-2 Spike Mutations by Causal Inference (preprint)

Driven by various mutations on the viral Spike protein, diverse variants of SARS-CoV-2 have emerged and prevailed repeatedly, which necessitates the identification of key Spike mutations for fitness enhancement. To address the need, this manuscript formulates a principled framework of causal inference for evaluating Spike mutations. In the context of large-scale genomes of SARS-CoV-2, it estimates the contribution of mutations to viral fitness across lineages and validates mutational effects on the Spike stability, receptor-binding affinity, and potential for immune escape. Key fitness-enhancing mutations and protein regions are recognized and studied. The transmission capacity of any new variant possessing these mutations can be predicted based on our model, solely based on the viral sequence. This research produces an innovative and systematic insight into SARS-CoV-2 and promotes functional studies of its key mutations.

Global Mutational Sweep of SARS-CoV-2: from Chaos to Order (preprint)

Analysis of large-scale genome sequences demonstrates the mutation of SARS-CoV-2 has been undergoing significant sweeps. Driven by emerging variants, global sweeps are accelerated and purified over time. This may prolong the pandemic with repeating epidemics, presenting challenges to the control and prevention of SARS-CoV-2.

In vivo structure and dynamics of the RNA genome of SARS-Cov-2 (preprint)

The SARS-CoV-2 coronavirus, which causes the COVID-19 pandemic, is one of the largest positive strand RNA viruses. Here we developed a simplified SPLASH assay and comprehensively mapped the in vivo RNA-RNA interactome of SARS-CoV-2 RNA during the viral life cycle. We observed canonical and alternative structures including 3-UTR and 5-UTR, frameshifting element (FSE) pseudoknot and genome cyclization in cells and in virions. We provide direct evidence of interactions between Transcription Regulating Sequences (TRS-L and TRS-Bs), which facilitate discontinuous transcription. In addition, we reveal alternative short and long distance arches around FSE, forming a "high-order pseudoknot" embedding FSE, which might help ribosome stalling at frameshift sites. More importantly, we found that within virions, while SARS-CoV-2 genome RNA undergoes intensive compaction, genome cyclization is weakened and genome domains remain stable. Our data provides a structural basis for the regulation of replication, discontinuous transcription and translational frameshifting, describes dynamics of RNA structures during life cycle of SARS-CoV-2, and will help to develop antiviral strategies.