Exploring Diversity of COVID‑19 Based on Substitution Distance

Figures & data

Figure 1 Key residues in the spike protein that make contact to the ACE2 receptor are marked with blue boxes in SARS-CoV-2 and related viruses. More details are referred to Andersen, et al (2020).⁸

Table 1 The Means and Standard Deviations for China, Europe, and the USA

Models	Mean (Standard Deviation)			p-value** (ANOVA)
	China	Europe	USA
raw	0.0001048666 (7.896388e-05)	0.0002572972 (1.860513e-04)	0.0003481381 (2.058586e-04)	<0.00001
N	3.119048(2.348623)	5.634551(4.074337)	6.955102 (4.112643)	<0.00001
TS	2.420068 (1.904639)	3.813953 (2.869819)	5.372245 (3.655761)	<0.00001
TV*	0.6989796 (0.9026857)	1.8205980 (1.7671983)	1.5828571 (1.4279653)	<0.00001
JC69	0.0001048781 (7.897694e-05)	0.0002573644 (1.861160e-04)	0.0003482471 (2.059534e-04)	<0.00001
K80	0.0001048810 (7.897975e-05)	0.0002573747 (1.861239e-04)	0.0003482756 (2.059788e-04)	<0.00001
F81	0.0001048783 (7.897721e-05)	0.0002573658 (1.861173e-04)	0.0003482493 (2.059553e-04)	<0.00001
K81	0.0001048812 (7.898006e-05)	0.0002573751 (1.861241e-04)	0.0003482766 (2.059792e-04)	<0.00001
F84	0.0001048816 (7.898048e-05)	0.0002573779 (1.861267e-04)	0.0003482824 (2.059848e-04)	<0.00001
BH87	0.0001079938 (8.461228e-05)	0.0002608000 (1.950313e-04)	0.0003598358 (2.233953e-04)	<0.00001
T92	0.0001048816 (7.898047e-05)	0.0002573778 (1.861266e-04)	0.0003482823 (2.059847e-04)	<0.00001
TN93	0.0001048886 (7.898629e-05)	0.0002573992 (1.861434e-04)	0.0003483246 (2.060194e-04)	<0.00001
GG95	7.778456e-05 (0.0001004559)	2.573644e-04 (0.0002498545)	3.663608e-04 (0.0003305383)	<0.00001
Logdet*	0.03027763 (8.818082e-05)	0.03196718 (1.899310e-04)	0.02781502 (2.252642e-04)	<0.00001
paralin	0.0001102436 (8.301758e-05)	0.0002670095 (1.924433e-04)	0.0003671794 (2.187228e-04)	<0.00001
indel	59.52721 (40.39569)	73.61240 (65.53877)	117.59265 (97.64568)	<0.00001
Indelblock*	2.709184 (0.8447791)	1.843854 (1.2770286)	3.005714 (0.6435705)	<0.00001

Notes: *The three models with different results are marked with gray color. **The ANOVA p-values are all less than 2.2e-16. We denote them as “<0.00001”.

Figure 2 (A) The boxplot of “JC69” model, (B) the boxplot of “ TV” model, (C) the boxplot of “logdet” model, (D) the boxplot of “ indelblock” model.

Andersen KG, et al. The proximal origin of SARS-CoV-2. Nat Med. 2020;26(4):p. 450–452.

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