Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant
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Abstract
The D614G mutation in the Spike protein of the SARS-CoV-2 has effectively replaced the early pandemic-causing variant. Using pseudotyped lentivectors, we confirmed that the aspartate replacement by glycine in position 614 is markedly more infectious. Molecular modelling suggests that the G614 mutation facilitates transition towards an open state of the Spike protein. To explain the epidemiological success of D614G, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, the exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase, is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2. However, we did not observe a significant correlation between reported COVID-19 mortality in different countries and the prevalence of the Wuhan versus G/L variant. Nevertheless, when comparing the speed of emergence and the ultimate predominance in individual countries, it is clear that the G/L variant displays major epidemiological supremacy over the original variant.
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SciScore for 10.1101/2020.08.23.20180281: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Human cell lines used in the study were HEK 293T/17 (human kidney, ATC C#CRL-11268), A549 cells and HeLa cells Luciferase reporter assay: Cells were transduced with SARS-CoV-2 S-protein lentiviral vectors encoding GFP and Gaussia luciferase (Gluc). HEK 293T/17suggested: ATCC Cat# CRL-11268G-1, RRID:CVCL_UE07)HeLasuggested: CLS Cat# 300194/p772_HeLa, RRID:CVCL_0030)Generation of cell lines expressing ACE2 and TMPRSS2: HeLa and A549 … SciScore for 10.1101/2020.08.23.20180281: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Experimental Models: Cell Lines Sentences Resources Human cell lines used in the study were HEK 293T/17 (human kidney, ATC C#CRL-11268), A549 cells and HeLa cells Luciferase reporter assay: Cells were transduced with SARS-CoV-2 S-protein lentiviral vectors encoding GFP and Gaussia luciferase (Gluc). HEK 293T/17suggested: ATCC Cat# CRL-11268G-1, RRID:CVCL_UE07)HeLasuggested: CLS Cat# 300194/p772_HeLa, RRID:CVCL_0030)Generation of cell lines expressing ACE2 and TMPRSS2: HeLa and A549 cells were plated at a density of 2E05 cells per well in a 12 well plate. A549suggested: NoneLentivirus production: For recombinant-lentivirus production, plasmids were transfected in 293T cells using the calcium phosphate method. 293Tsuggested: NCBI_Iran Cat# C498, RRID:CVCL_0063)Software and Algorithms Sentences Resources Data were analysed using FlowJo 11 (FlowJo, LLC, Ashland, OR) Real-time quantitative RT-PCR: Total RNA was extracted from A549 and HeLa cell lines using RNeasy Micro Kit (Qiagen) FlowJosuggested: (FlowJo, RRID:SCR_008520)All plots were done using ggplot2 in R. ggplot2suggested: (ggplot2, RRID:SCR_014601)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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