Analysis of the evolution of SARS-CoV-2 RNA polymerase in humans

Recent works posted by researchers bioRxiv* The preprint server investigated the evolutionary aspects of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2).

study: Covariant fitness clusters reveal structural evolution of SARS-CoV-2 polymerase throughout the human population.. Image Credits: Naeblys / Shutterstock

Worldwide, more than 300 million cases of coronavirus disease (COVID-19) in 2019 and more than 5.48 million related deaths have been officially reported so far. The SARS-CoV-2 genome is a positive-strand single-stranded (ss) RNA, approximately 30 kb in length, with an estimated variability of 1.12 x 10.^-3 Mutations per site / year.

To date, over 3.7 million SARS-CoV-2 genomes have been sequenced, which has identified over 150,000 unique gene mutations. In order to understand the functional and structural effects of these mutations and to clarify the mechanism of adaptation of SARS-CoV-2 in the human environment, it is important to identify their correlation with their spread in humans. is.

the study

In this study, researchers investigated the effect of mutations in SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) on structural thermodynamic stability (structural stability) through free energy calculations. The author adopted variable space profiling (VSP), a Gaussian process regression (GPR) -based machine learning approach.

Using GPR to generate spatial covariance (SCV) relationships, the authors constructed a fitness landscape and 1) determined the molecular mechanisms driving SARS-CoV-2RdRp fitness in early Phase I of the COVID-19 pandemic. Did. Variant of concern (VOC), 2) Pandemic Phase II characterized by the emergence of alpha variants, and 3) Pandemics when delta variants lead to a large proliferation of COVID-19 cases worldwide. Phase III.

result

The authors analyzed more than 87,468 SARS-CoV-2 genomes registered in the GISAID database between December 24, 2019 and September 8, 2020 (Pandemic Phase I), and nsp12 throughout the pandemic. Understood the evolution (of RdRp). Approximately 1,569 missense mutations were detected in nsp12, more than half of which were detected in one virus sample, and the remaining 699 mutations were at least two that reflect human-to-human transmission of at least one of these mutations. It was present in the virus sample. The team found that the majority of mutations (57%) had a neutral to slight effect on the structural stability of RdRp, while the remaining mutations were destabilized (19%), highly destabilized (19%), and stable. It was observed that it showed the effect of mutation (4%). ..

Substituted P323L was the most frequent mutation observed (80% sample of Phase I), followed by A97V observed in approximately 2% of the SARS-CoV-2 genomic sample. Although P323L has been shown to have a neutral effect on structural stability, it has been shown to stabilize the binding energy between nsp12 and nsp8-1 due to significant RdRp activity. A97V mapped to the NiRAN (N-terminal nidoviral RdRp-related nucleotidyltransferase) domain provided an overall destabilizing effect on the structural stability of RdRp.

In addition, a GPR-based fitness landscape based on the structural stability of RdRp was constructed using 63 mutations with significant stabilization (4) or destabilization (59) effects.The team noted that residues with relatively high GPR compatibility scores were concentrated in one of the Zns.⁺² Mutations adjacent to binding motifs, especially C487-G642-C645-C646 Zn (C563F, M629I, L636I, L638F, S647I, and A690D)⁺² It was shown that the binding site and SCV relationship connect Zn.⁺² An RNA substrate that forms the binding motif of nsp8-1 to the nsp12 binding site and covariant fitness cluster I, which has a significant effect on structural stability.

The most frequent P323L mutations in Phase I of the pandemic were also observed in almost all sequences of the SARS-CoV-2 alpha mutant. Fitness cluster I around the zinc binding motif mentioned above has been shown to recur in the fitness landscape and structure of the alpha variant. This shows the features related to C487-G642-C645-C646Zn.⁺² The binding motif is the key to the repeated evolution of SARS-CoV-2 to adapt to the human environment. The second fitness cluster (Cluster II) is observed within the NiRAN domain, has a significant impact on structure, and has a high GPR fitness score.

Similar to previous observations, the P323L mutation was found in the> 99.9% delta mutation sequence, and the G671S substitution was observed in the> 98% sequence, making it the second basal mutation. It was revealed that fitness clusters I and II recurred in DeltaVOC and a new cluster (cluster III) was also found around the second basis mutation G671S.

Conclusion

Current research results have shown that a GPR-based approach helps to understand important evolutionary aspects of the viral genome. Fitness scores based on GPR identified structural covariant fitness clusters that were not previously detected. These clusters were defined by changes in thermodynamic stability and residue binding during a pandemic viral infection and included structural adjustment of Zn._­⁺² Binding and multi-residue interactions in the NiRAN domain.

In conclusion, the GPR approach applied in this study calculates and experiments the relationship between multiple SCV-based structures and functions of RdRp to monitor and predict key events driving the evolution of SARS-CoV-2. Essentially emphasized the need for targeted monitoring.

*Important Notices

bioRxiv publishes unpeer-reviewed preliminary scientific reports and should not be considered definitive, guide clinical / health-related behaviors, or be treated as established information.