Evidence map›Paper›PMID 40281619›Full record

ArticleVirology journal2025

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

Karen Zafilaza, Antoine Fauchois, Valentin Leducq, Romain Coppée, Romane Guilbaud, Anna-Maria Franco Yusti, Eve Todesco, Antoine Bridier-Nahmias, Quentin Le Hingrat, Sylvain Choquet and 21 more

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Article in Virology journal, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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0citing papers in PubMed
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1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

31 authors.

Karen ZafilazaService de Virologie, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Paris, France. karen.zafilaza@aphp.fr.
Antoine FauchoisService de Virologie, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Valentin LeducqService de Virologie, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Romain CoppéeService de Virologie, Université Paris Cité, INSERM, UMR1137, IAME, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
Romane GuilbaudService de Virologie, Université Paris Cité, INSERM, UMR1137, IAME, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
Anna-Maria Franco YustiService de Virologie, Université Paris Cité, INSERM, UMR1137, IAME, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
Eve TodescoService de Virologie, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Antoine Bridier-NahmiasService de Virologie, Université Paris Cité, INSERM, UMR1137, IAME, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
Quentin Le HingratService de Virologie, Université Paris Cité, INSERM, UMR1137, IAME, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
Sylvain ChoquetService d'Hématologie Clinique, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Patrice CacoubService de Médecine Interne et Immunologie Clinique, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Zahir AmouraService de Médecine Interne 2, Centre National de Référence des Histiocytoses, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Benoit BarrouService d'Urologie et de Transplantation Rénale, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Valérie PourcherService de Maladies infectieuses et Tropicales, AP-HP, Hôpitaux Universitaires Pitié- Salpêtrière, Paris, France.
Jean-Philippe SpanoService d'Oncologie Médicale, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Martine LouetService de Santé au Travail, AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Laura KramerService de Pharmacie, AP-HP, Hôpital Bichat- Claude-Bernard, Paris, France.
Tiphaine GoulenokService de Médecine Interne, AP-HP, Hôpital Bichat- Claude-Bernard, Paris, France.
Mathilde SalpinService de Pneumologie, AP-HP, Hôpital Bichat- Claude-Bernard, Paris, France.
Eric DaugasService de Néphrologie, Université Paris Cité, INSERM U1149, AP-HP, Hôpital Bichat- Claude-Bernard, Paris, France.
Richard DorentService de Cardiologie, AP-HP, Hôpital Bichat- Claude-Bernard, Paris, France.
Sébastien OttavianiService de Rhumatologie, AP-HP, Hôpital Bichat- Claude-Bernard, Paris, France.
Gérard ZalcmanService d'Oncologie Thoracique, AP-HP, Hôpital Bichat- Claude-Bernard, Paris, France.
Jade GhosnService de Virologie, Université Paris Cité, INSERM, UMR1137, IAME, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
Charlotte CharpentierService de Virologie, Université Paris Cité, INSERM, UMR1137, IAME, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
Diane DescampsService de Virologie, Université Paris Cité, INSERM, UMR1137, IAME, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
Anne-Geneviève MarcelinService de Virologie, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Vincent CalvezService de Virologie, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Valentine Marie FerreService de Virologie, Université Paris Cité, INSERM, UMR1137, IAME, Hôpital Bichat-Claude Bernard, AP-HP, Paris, France.
Stéphane Marot *Service de Virologie, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.
Cathia Soulie *Service de Virologie, Sorbonne Université, INSERM, Institut Pierre Louis d'Epidémiologie et de Santé Publique (iPLESP), AP-HP, Hôpital Pitié-Salpêtrière, Paris, France.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

objectivesMutational 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.

methodsCycle 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.

resultsAll 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.

conclusionImmunocompromised 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.

Indexed as

COVID-19Immunocompromised HostSARS-CoV-2Viral LoadAdultAgedFemaleGenetic VariationGenome, ViralHumansImmunocompetenceMaleMiddle AgedMutationPhylogenyImmunocompromised hostSARS-CoV-2Single mutation analysisViral loadWhole-Genome sequencing

Identifiers

PMID40281619
PMCPMC12023422

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