Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance
- High-Performance Computing Center, Oklahoma State University, United States
- Department of Physiological Sciences, Oklahoma State University, United States
- University College London School of Pharmacy, Pharmaceutical and Biological Chemistry, United Kingdom
- University College London Centre for Advanced Research Computing, United Kingdom
Figures
Figure 1 with 6 supplements
Mutations in SARS-CoV-2 proteins increase before COVID19 surges.
Non-synonymous mutations over the course of the COVID19 outbreak were identified by analysis of 6.4 million sequences. Gray dots indicate individual mutations, while black lines show weighted means …
Figure 1—figure supplement 1
Unnormalized results for the mutations in SARS-CoV-2 proteins.
See Figure 1 in the main manuscript for more details. Here, the raw results for the four proteins are plotted for the non-synonymous mutations. Note that the same y-axis scale is used for comparison …
Figure 1—figure supplement 2
Ratio of non-synonymous mutations/synonymous mutations in SARS-CoV-2 proteins.
This commonly used indicator did not provide a reliable signal for surge prediction for most proteins. The ratio for only the membrane protein shows increase before the surges associated with some …
Figure 1—figure supplement 3
Daily rate of non-synonymous mutations in SARS-CoV-2 proteins.
The rate is calculated as a numerical derivative of data shown in Figure 1—figure supplement 1. The rate shows most noticeable increase before the Omicron surge, other periods are inconclusive. Note …
Figure 1—figure supplement 4
Side-by-side comparison of various metrics considered in this study.
The quantities shown here are same as depicted in Figure 1 (main manuscript) and Figure 1—figure supplements 2 and 3. See the legends of other figures for details.
Figure 1—figure supplement 5
Performance of the surge watch and warning issued on June 29, 2022, and July 14, 2022, respectively.
The number of infection cases showed a sustained increase after the issue of our watch on June 29. This watch was elevated to a warning on July 14 (note, warning is considered more severe than a …
Figure 1—figure supplement 6
Performance of the surge watch issued on September 7, 2022.
The number of infection cases showed a sustained increase in Europe and several individual countries, after we issued our watch. The data did not warrant a further elevation and this watch was …
Tables
Table 1
Number of unique records for the 26 proteins/open reading frames (ORFs).
Total number of quality-controlled SARS-CoV-2 sequences analyzed: 3,126,129 (as of November 21, 2022). Only three proteins showing the most relevant results and one other protein (marked by *) for …
| Name | Unique records |
|---|---|
| Envelope protein | 1314 |
| Membrane protein | 11,338 |
| Nucleocapsid protein | 70,579 |
| Spike protein | 188,166 |
| Non-structural protein 1 (NSP1), leader protein | 11,656 |
| NSP2 | 67,837 |
| NSP3 | 245,627 |
| NSP4 | 31,257 |
| NSP5, 3C-like proteinase | 11,879 |
| NSP6 | 16,479 |
| NSP7 | 1304 |
| NSP8 | 4490 |
| NSP9 | 2848 |
| NSP10 | 2429 |
| NSP11 | 88 |
| NSP12, RNA-dependent RNA polymerase (RDRP)* | 60,575 |
| NSP13, helicase | 35,421 |
| NSP14, 3'-to-5' exonuclease | 28,501 |
| NSP15, endoRNAse | 12,901 |
| NSP16, 2'-O-ribose methyltransferase | 7636 |
| ORF3a | 41,694 |
| ORF6 | 2117 |
| ORF7a | 9312 |
| ORF7b | 1368 |
| ORF8 | 7036 |
| ORF10 | 710 |
