L18F substrain of SARS-CoV-2 VOC-202012/01 is rapidly spreading in England
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Abstract
The Variant of Concern (VOC)-202012/01 (also known as B.1.1.7) is a rapidly growing lineage of SARS-CoV-2. In January 2021, VOC-202012/01 constituted about 80% of SARS-CoV-2 genomes sequenced in England and was present in 27 out of 29 countries that reported at least 50 viral genomes. As this strain will likely spread globally towards fixation, it is important to monitor its molecular evolution. Based on GISAID data we systematically estimated growth rates of mutations acquired by the VOC lineage to find that L18F substitution in viral spike protein has initiated a substrain characterized by replicative advantage of 1.70 [95% CI: 1.56–1.96] in relation to the remaining VOC-202012/01 substrains. The L18F mutation is of significance because when recently analyzed in the context of the South African strain 501Y.V2 it has been found to compromise binding of neutralizing antibodies. We additionally indicate three mutations that were acquired by VOC-202012/01 in the receptor binding motif of spike, specifically E484K, F490S, and S494P, that may also give rise to escape mutants. Such mutants may hinder efficiency of existing vaccines and expand in response to the increasing after-infection or vaccine-induced seroprevalence.
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SciScore for 10.1101/2021.02.07.21251262: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources Estimation of confidence interval for the growth rate of the ratio of strains: To estimate the confidence interval for k subsequent weeks a priori we assume that genomes of two compared strands in each week of the considered period follow a respective binomial distribution having success probability pi = nstrain1/(nstrain1 + nstrain2), where nstrain1 and nstrain2 are the numbers of compared two strain genomes, VOC and non-VOC (in Figure 1) and L18F VOC and L18 VOC (in Figure 2). nstrain1 + nstrain2suggested: NoneResults from OddPub: We did not detect open data. We also did …
SciScore for 10.1101/2021.02.07.21251262: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Experimental Models: Organisms/Strains Sentences Resources Estimation of confidence interval for the growth rate of the ratio of strains: To estimate the confidence interval for k subsequent weeks a priori we assume that genomes of two compared strands in each week of the considered period follow a respective binomial distribution having success probability pi = nstrain1/(nstrain1 + nstrain2), where nstrain1 and nstrain2 are the numbers of compared two strain genomes, VOC and non-VOC (in Figure 1) and L18F VOC and L18 VOC (in Figure 2). nstrain1 + nstrain2suggested: NoneResults 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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