SARS-CoV-2 lineage-dependent temporal phylogenetic distribution and viral load in immunocompromised and immunocompetent individuals

Zafilaza, Karen; Fauchois, Antoine; Leducq, Valentin; Coppée, Romain; Guilbaud, Romane; Yusti, Anna-Maria Franco; Todesco, Eve; Bridier-Nahmias, Antoine; Hingrat, Quentin Le; Choquet, Sylvain; Cacoub, Patrice; Amoura, Zahir; Barrou, Benoit; Pourcher, Valérie; Spano, Jean-Philippe; Louet, Martine; kramer, Laura; Goulenok, Tiphaine; Salpin, Mathilde; Daugas, Eric; Dorent, Richard; ottaviani, Sébastien; Zalcman, Gérard; Ghosn, Jade; Charpentier, Charlotte; Descamps, Diane; Marcelin, Anne-Geneviève; Calvez, Vincent; Ferre, Valentine Marie; Marot, Stéphane; Soulie, Cathia

doi:10.1186/s12985-025-02711-z

Virology Journal

Table 3 Pairwise comparisons of mutations count between patient groups stratified by type of immunosuppression using Dunn’s post-hoc test

From: SARS-CoV-2 lineage-dependent temporal phylogenetic distribution and viral load in immunocompromised and immunocompetent individuals

Comparison	z	W_i	W_j	r_rb	p	p_holm
Autoimmune or inflammatory diseases– Hemato-oncology	1.709	576.206	511.489	0.149	0.088	0.963
Autoimmune or inflammatory diseases - HIV infection	3.690	576.206	407.882	0.345	< 0.001	0.005
Autoimmune or inflammatory diseases - Intensive care	-3.397	576.206	807.368	0.470	< 0.001	0.016
Autoimmune or inflammatory diseases - Control	5.747	576.206	410.553	0.336	< 0.001	< 0.001
Autoimmune or inflammatory diseases - Oncology	0.869	576.206	545.847	0.051	0.385	1.000
Autoimmune or inflammatory diseases - Respiratory disease	0.068	576.206	571.444	0.039	0.946	1.000
Autoimmune or inflammatory diseases - Anti-CD20 treatment including Rituximab	5.702	576.206	314.200	0.509	< 0.001	< 0.001
Autoimmune or inflammatory diseases - Solid organ transplantation	2.619	576.206	494.389	0.190	0.009	0.159
Hemato-oncology - HIV infection	2.123	511.489	407.882	0.230	0.034	0.445
Hemato-oncology - Intensive care	-4.214	511.489	807.368	0.658	< 0.001	< 0.001
Hemato-oncology - Control	3.002	511.489	410.553	0.211	0.003	0.054
Hemato-oncology - Oncology	-0.881	511.489	545.847	0.080	0.378	1.000
Hemato-oncology - Respiratory disease	-0.835	511.489	571.444	0.135	0.404	1.000
Hemato-oncology - Anti-CD20 treatment including Rituximab	4.018	511.489	314.200	0.438	< 0.001	0.002
Hemato-oncology - Solid organ transplantation	0.479	511.489	494.389	0.042	0.632	1.000
HIV infection - Intensive care	-5.350	407.882	807.368	0.838	< 0.001	< 0.001
HIV infection - Control	-0.063	407.882	410.553	0.021	0.949	1.000
HIV infection - Oncology	-2.963	407.882	545.847	0.304	0.003	0.058
HIV infection - Respiratory disease	-2.147	407.882	571.444	0.364	0.032	0.445
HIV infection - Anti-CD20 treatment including Rituximab	1.694	407.882	314.200	0.190	0.090	0.963
HIV infection - Solid organ transplantation	-1.973	407.882	494.389	0.201	0.048	0.582
Intensive care - Control	6.033	807.368	410.553	0.793	< 0.001	< 0.001
Intensive care - Oncology	3.808	807.368	545.847	0.508	< 0.001	0.004
Intensive care - Respiratory disease	2.582	807.368	571.444	0.579	0.010	0.167
Intensive care - Anti-CD20 treatment including Rituximab	6.587	807.368	314.200	0.952	< 0.001	< 0.001
Intensive care - Solid organ transplantation	4.681	807.368	494.389	0.715	< 0.001	< 0.001
Control - Oncology	-4.466	410.553	545.847	0.278	< 0.001	< 0.001
Control - Respiratory disease	-2.385	410.553	571.444	0.327	0.017	0.273
Control - Anti-CD20 treatment including Rituximab	2.267	410.553	314.200	0.208	0.023	0.351
Control - Solid organ transplantation	-3.234	410.553	494.389	0.180	0.001	0.026
Oncology - Respiratory disease	-0.364	545.847	571.444	0.056	0.716	1.000
Oncology - Anti-CD20 treatment including Rituximab	4.941	545.847	314.200	0.440	< 0.001	< 0.001
Oncology - Solid organ transplantation	1.579	545.847	494.389	0.102	0.114	1.000
Respiratory disease - Anti-CD20 treatment including Rituximab	3.369	571.444	314.200	0.530	< 0.001	0.017
Respiratory disease - Solid organ transplantation	1.124	571.444	494.389	0.189	0.261	1.000
Anti-CD20 treatment including Rituximab - Solid organ transplantation	-4.078	314.200	494.389	0.408	< 0.001	0.001

The table summarizes the results of Dunn’s post-hoc tests following the Kruskal-Wallis analysis. For each comparison, the z-value, Wilcoxon rank-sum statistics (Wi and Wj), p-value (p) and Bonferroni and holm Bonferroni adjustment (p_bonf and p_holm) are reported. Significant p-values (p < 0.05) are highlighted in bold, indicating statistically significant differences in mutation counts between the compared groups. The results emphasize key differences, such as a higher mutation burden in patients admitted to intensive care compared to most other groups. A negative z-value refers to a lower mutation count for a group compare to the other and a positive z-value refers to an higher mutations count for a group to the other

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ISSN: 1743-422X

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