tetano
Editor, Senior Moderator
Virol J
. 2025 Apr 25;22(1):118.
doi: 10.1186/s12985-025-02711-z. SARS-CoV-2 lineage-dependent temporal phylogenetic distribution and viral load in immunocompromised and immunocompetent individuals
Karen Zafilaza[SUP] 1 [/SUP], Antoine Fauchois[SUP] 2 [/SUP], Valentin Leducq[SUP] 2 [/SUP], Romain Coppée[SUP] 3 4 [/SUP], Romane Guilbaud[SUP] 3 [/SUP], Anna-Maria Franco Yusti[SUP] 3 [/SUP], Eve Todesco[SUP] 2 [/SUP], Antoine Bridier-Nahmias[SUP] 3 [/SUP], Quentin Le Hingrat[SUP] 3 [/SUP], Sylvain Choquet[SUP] 5 [/SUP], Patrice Cacoub[SUP] 6 [/SUP], Zahir Amoura[SUP] 7 [/SUP], Benoit Barrou[SUP] 8 [/SUP], Valérie Pourcher[SUP] 9 [/SUP], Jean-Philippe Spano[SUP] 10 [/SUP], Martine Louet[SUP] 11 [/SUP], Laura Kramer[SUP] 12 [/SUP], Tiphaine Goulenok[SUP] 13 [/SUP], Mathilde Salpin[SUP] 14 [/SUP], Eric Daugas[SUP] 15 [/SUP], Richard Dorent[SUP] 16 [/SUP], Sébastien Ottaviani[SUP] 17 [/SUP], Gérard Zalcman[SUP] 18 [/SUP], Jade Ghosn[SUP] 3 19 [/SUP], Charlotte Charpentier[SUP] 3 [/SUP], Diane Descamps[SUP] 3 [/SUP], Anne-Geneviève Marcelin[SUP] 2 [/SUP], Vincent Calvez[SUP] 2 [/SUP], Valentine Marie Ferre[SUP] 3 [/SUP], Stéphane Marot[SUP] #[/SUP][SUP] 2 [/SUP], Cathia Soulie[SUP] #[/SUP][SUP] 2 [/SUP]
Affiliations
Objectives: Mutational dynamics of SARS-CoV-2 in immunocompromised hosts, although well documented, remain a relatively unexplored mechanism. This study aims to compare the viral replication load and genetic diversity of SARS-CoV-2 in immunocompromised patients and non-immunocompromised individuals (NICs) from two major hospitals in Paris from January 2021 to May 2023.
Methods: Cycle threshold (CT) values were measured by TaqPath COVID-19 RT-PCR (Thermo Fisher Scientific). The SARS-CoV-2 whole-genomes from 683 immunocompromised patients and 296 NICs was sequenced using Oxford Nanopore Technologies and used to determine lineage and mutational profile.
Results: All immunocompromised patients, but not oncology patients, had lower SARS-CoV-2 viral loads than NICs. The genetic distribution of SARS-CoV-2 was homogeneous between immunocompromised individuals and NICs, with more mutations in immunocompromised patients (IRR = 1,013). Indeed, extensive genomic analysis revealed several mutations specifically associated with immunosuppression status, such as S: T95I, S:N764K, M:Q19E and ORF10:L37F. Conversely, the S: R346K and NSP13:T127N mutations were more common in NICs.
Conclusion: Immunocompromised patients have lower viral loads, probably due to their later diagnosis compared to NICs and oncology patients, who have better access to on-site SARS-CoV-2 testing and follow-up. In addition, mutational profiles differ between the two groups, with immunocompromised hosts accumulating more mutations compared to NICs.
Keywords: Immunocompromised host; SARS-CoV-2; Single mutation analysis; Viral load; Whole-Genome sequencing.
. 2025 Apr 25;22(1):118.
doi: 10.1186/s12985-025-02711-z. SARS-CoV-2 lineage-dependent temporal phylogenetic distribution and viral load in immunocompromised and immunocompetent individuals
Karen Zafilaza[SUP] 1 [/SUP], Antoine Fauchois[SUP] 2 [/SUP], Valentin Leducq[SUP] 2 [/SUP], Romain Coppée[SUP] 3 4 [/SUP], Romane Guilbaud[SUP] 3 [/SUP], Anna-Maria Franco Yusti[SUP] 3 [/SUP], Eve Todesco[SUP] 2 [/SUP], Antoine Bridier-Nahmias[SUP] 3 [/SUP], Quentin Le Hingrat[SUP] 3 [/SUP], Sylvain Choquet[SUP] 5 [/SUP], Patrice Cacoub[SUP] 6 [/SUP], Zahir Amoura[SUP] 7 [/SUP], Benoit Barrou[SUP] 8 [/SUP], Valérie Pourcher[SUP] 9 [/SUP], Jean-Philippe Spano[SUP] 10 [/SUP], Martine Louet[SUP] 11 [/SUP], Laura Kramer[SUP] 12 [/SUP], Tiphaine Goulenok[SUP] 13 [/SUP], Mathilde Salpin[SUP] 14 [/SUP], Eric Daugas[SUP] 15 [/SUP], Richard Dorent[SUP] 16 [/SUP], Sébastien Ottaviani[SUP] 17 [/SUP], Gérard Zalcman[SUP] 18 [/SUP], Jade Ghosn[SUP] 3 19 [/SUP], Charlotte Charpentier[SUP] 3 [/SUP], Diane Descamps[SUP] 3 [/SUP], Anne-Geneviève Marcelin[SUP] 2 [/SUP], Vincent Calvez[SUP] 2 [/SUP], Valentine Marie Ferre[SUP] 3 [/SUP], Stéphane Marot[SUP] #[/SUP][SUP] 2 [/SUP], Cathia Soulie[SUP] #[/SUP][SUP] 2 [/SUP]
Affiliations
- PMID: 40281619
- PMCID: PMC12023422
- DOI: 10.1186/s12985-025-02711-z
Objectives: Mutational dynamics of SARS-CoV-2 in immunocompromised hosts, although well documented, remain a relatively unexplored mechanism. This study aims to compare the viral replication load and genetic diversity of SARS-CoV-2 in immunocompromised patients and non-immunocompromised individuals (NICs) from two major hospitals in Paris from January 2021 to May 2023.
Methods: Cycle threshold (CT) values were measured by TaqPath COVID-19 RT-PCR (Thermo Fisher Scientific). The SARS-CoV-2 whole-genomes from 683 immunocompromised patients and 296 NICs was sequenced using Oxford Nanopore Technologies and used to determine lineage and mutational profile.
Results: All immunocompromised patients, but not oncology patients, had lower SARS-CoV-2 viral loads than NICs. The genetic distribution of SARS-CoV-2 was homogeneous between immunocompromised individuals and NICs, with more mutations in immunocompromised patients (IRR = 1,013). Indeed, extensive genomic analysis revealed several mutations specifically associated with immunosuppression status, such as S: T95I, S:N764K, M:Q19E and ORF10:L37F. Conversely, the S: R346K and NSP13:T127N mutations were more common in NICs.
Conclusion: Immunocompromised patients have lower viral loads, probably due to their later diagnosis compared to NICs and oncology patients, who have better access to on-site SARS-CoV-2 testing and follow-up. In addition, mutational profiles differ between the two groups, with immunocompromised hosts accumulating more mutations compared to NICs.
Keywords: Immunocompromised host; SARS-CoV-2; Single mutation analysis; Viral load; Whole-Genome sequencing.