Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity

Abstract

Global dispersal and increasing frequency of the SARS-CoV-2 spike protein variant D614G are suggestive of a selective advantage but may also be due to a random founder effect. We investigate the hypothesis for positive selection of spike D614G in the United Kingdom using more than 25,000 whole genome SARS-CoV-2 sequences. Despite the availability of a large dataset, well represented by both spike 614 variants, not all approaches showed a conclusive signal of positive selection. Population genetic analysis indicates that 614G increases in frequency relative to 614D in a manner consistent with a selective advantage. We do not find any indication that patients infected with the spike 614G variant have higher COVID-19 mortality or clinical severity, but 614G is associated with higher viral load and younger age of patients. Significant differences in growth and size of 614G phylogenetic clusters indicate a need for continued study of this variant.

Keywords: COVID-19; SARS-CoV-2; epidemiology; evolution; founder effect; spike.

Graphical abstract

Figure 1

Maximum Likelihood Phylogeny Estimated from a Representative Set of 900 SARS-CoV-2 Genome Sequences, Showing global Lineage Assignments and the Origins of the Spike Protein D614G Mutation, which Seeded Many Introductions in the United Kingdom Putative reversions to 614D and independently arising D614G mutations are shown as large circles. The D614N genomes shown as red circles indicated two independent clusters in the United Kingdom.

Figure S1

Expanded Phylogenetic Tree, Related to Figure 1 This shows the early stages of emergence of D614G into Europe from China. Acknowledgments and details for highlighted genome sequences are given in Table S3.

Figure 2

Geographic and Temporal Distribution of UK Phylogenetic Clusters, Classified as 614D or 614G According to the Residue They Carry at Spike Protein Position 614D (A) Shaded regions show the predominant residue in each region on the 15th of each month for March, April, May, and June 2020, with orange indicating that 614G was more frequently sampled and green indicating that 614D was more (or equally) frequent. Light gray indicates that no sequences had been sampled by that point in time. Dark gray indicates the Republic of Ireland. (B) The date when each cluster was first detected in the United Kingdom for variants 614D and 614G. Each cluster contains two or more sampled genomes. Solid lines show the total number of sequences collected by day of each 614 variant. (C) The log odds of sampling a 614G variant over time. (D) The size of cluster versus time of first sample collected within a cluster.

Figure 3

Relative Frequency of Spike 614D and G over Time, Phylodynamic Growth Rates and Comparison of Clinical Severity Metrics Relative frequency of spike 614D and G over time (A and B), phylodynamic growth rates (C and D), and comparison of clinical severity metrics (E–G). (A) Frequency of sampling spike 614G over time for clusters sampled during exponential growth phase. The size of points represents the number of samples collected on each day. The line and shaded region showed the maximum likelihood estimate (MLE) and confidence interval fit of the logistic growth model. (B) As in (A) but including samples during a period after April 15 during a period of epidemic decline. (C) Distribution of exponential growth rate for spike 614G (brown) and 614D (gray) in units of 1/year. Solid areas span the 95% credible interval. Points indicate the rates estimated for specific clusters and are sized by the number of sequences in that cluster. (D) Log odds of sampling spike 614G in London comparing empirical values (black line) and estimates based on the phylodynamic susceptible-exposed-infectious-recovered (SEIR) model (shaded regions). The green shaded region shows estimates making use of both genetic data and sample frequency data. (E) The probability over time of fatal outcome within 28 days of diagnosis among UK patients with sequence data that can be matched to clinical records. Shaded regions show 95% confidence region of a 7-day moving average. Points with fewer than 20 observations are omitted. (F) Moving average of age among samples included in (E). (G) Viral load (real-time qPCR mean genome copies) estimated using SARS-CoV-2 RNA strands from 31 614D (614D) and 290 614G samples.

Figure S2

Frequency of Sampling Spike 614G over Time, Related to Figure 3 This shows frequency and numbers of Spike 614G and Spike 614D samples over time. The size of points represents the number of samples collected on each day. The line and shaded region showed the MLE and confidence interval fit of the logistic growth model.

Figure S3

Frequency of Sampling Spike 614G after April 15, Related to Figure 3 This shows frequency and numbers of Spike 614G and Spike 614D samples over time using 37 DT clusters detected before March 31, 2020. The size of points represents the number of samples collected on each day. The line and shaded region showed the MLE and confidence interval fit of the logistic growth model.

Figure S4

The Estimated TMRCA for Each of 50 UK Clusters (Shaded Density) and Time of Each Sequence Sampled (Points), Related to Figure 3 Brown and gray respectively indicate Spike 614G and 614D clusters.

Figure S5

Distribution of Exponential Growth Rates (Left) and Rates of Decline (Right) for Spike 614G (Brown) and 614D (Gray) in Units of 1/Year, Related to Figure 3 Solid areas span the 95% credible interval. Points indicate the rates estimated for specific clusters, and are sized by the number of sequences in that cluster.

Figure S6

Non-parametric Phylodynamic Estimates for Representative Clusters, Related to Figure 3 Estimated growth rates (A and C) and effective population size (B and D) for the two largest clusters with genotypes Spike 614D/G. The growth rate at the beginning of the time axis (Feb 1, 2020) is shown in panel E and provides a data point for the statistical comparisons between clusters. The size of points corresponds to the number of samples in each cluster.

Figure 4

Clinical Severity in Patients in Association with the D614G Polymorphism and Age Clinical severity was measured on a four-point ordinal scale based on requirement for respiratory support. Upper panel: proportion of outcomes by age; lower panel: absolute counts. I&V, intubation and ventilation; NIV, non-invasive ventilation; HFNC, high-flow nasal cannulae; Oxygen, supplemental oxygen delivered by face mask or low-flow nasal cannulae.

Figure S7

Probability of Observing Spike 614G Virus in Patients Grouped by Age and Sex, Related to Figure 4 Panels on the lower diagonal show collected pairwise plots based on a UK-wide (England, Wales, Scotland, and Northern Ireland) multivariate dataset for the sample collection date, and the age and sex of the patient. Kernel Density Estimation (KDE) and count plots are on the diagonal. The upper right panel shows the estimated frequency of PCR cycle threshold (Ct) for D/G variants overlaid with kernel density estimates. Samples where the amino acid at position 614 was not recorded and samples with a Ct value of less than 14 or greater than 40 were excluded.