Nature Communications

Latent transition analysis for longitudinal studies of post-acute infection syndromes

R Roy Gusinow A Anna Górska L Lorenzo Maria Canziani I Iris Lopes-Rafegas C Carolina Alvarez Garavito A Adriana Tami E Elisa Gentilotti E Elisa Sicuri C Cedric Laouenan (Assistance Publique–Hôpitaux de Paris.Nord, Hopital Bichat-Claude Bernard, Service des Maladies Infectieuses, Paris F75018, France and Universite Paris Cite, INSERM UMR 1137 IAME) J Jade Ghosn (Assistance Publique–Hôpitaux de Paris.Nord, Hopital Bichat-Claude Bernard, Service des Maladies Infectieuses, Paris F75018, France and Universite Paris Cite, INSERM UMR 1137 IAME) A Aline-Marie Florence N Nadhem Lahfej F Fulvia Mazzaferri L Lidia Del Piccolo M Maddalena Giannella A Alice Toschi M Michela Di Chiara M Maria Giulia Caponcello Z Zaira R. Palacios-Baena K Karin I. Wold E Elisa Rossi E Evelina Tacconelli J Jan Hasenauer E Elena Addis M Maddalena Armellini A Anna Maria Azzini B Benedetta Barana L Lucia Bonato E Elena Carrara A Alessandro Castelli F Filippo Cioli Puviani M Michela Conti R Raffaella Cordioli C Carmine Cutone R Ruth Joanna Davis P Pasquale De Nardo M Miriam Emiliani A Alessio Esposito D Daniele Fasan G Giada Fasani G Giorgia Franchina J Jacopo Garlasco E Enrico Gibbin S Salvatore Hermes Dall’O’ C Chiara Konishi De Toffoli L Lorenza Lambertenghi F Federico Lattanzi A Andrea Leonardi F Francesco Luca G Gaia Maccarrone M Massimo Mirandola M Matteo Morra A Alessandra Nazeri M Matilde Rocchi G Giulia Rosini C Chiara Perlini M Maria Diletta Pezzani L Laura Rovigo A Anna Giulia Salvadori A Andrea Sartori (Experimental Division, European Synchrotron Radiation Facility, 71 Av. des Martyrs, 38000, Grenoble, France) A Alessia Savoldi R Rebecca Scardellato M Marcella Sibani E Erica Sodano S Simona Sorbello L Lorenzo Tavernaro G Giorgia Tomassini A Alessandro Visentin S Stefania Vitali A Andrea Volpe C Chiara Zanchi G Gloria Mazzali G Giovanni Stabile G Gianluca Vantini R Riccardo Cecchetto D Davide Gibellini N Nicolò Cardobi D Debora Calì M Maria Paola Cecchini M Maddalena Marcanti A Anna Mason S Salvatore Monaco M Marco Pattaro Zonta C Cinzia Perlini G Gianluigi Zanusso E Elda Righi M Mariana Nunes Pinho Guedes M Maria Mongardi C Concetta Sciammarella C Claudio Micheletto P Paolo Gisondi N Natascia Caroccia C Cecilia Bonazzetti B Beatrice Tazza Z Zeno Igor Adrien Pasquini D Domenico Marzolla G Giacomo Fornaro F Fabio Trapani L Lorenzo Marconi L Luciano Attard S Sara Tedeschi S Silvia Vituliano L Liliana Gabrielli T Tiziana Lazzarotto J Jesús Rodrguez-Baño M Mara Isabel Garcia Sánchez A Ana Belén Hidalgo Céspedes A Aurora Aleman Rodriguez L Lola Cubero Aranda P Paula Olivares Navarro S Sandra De la Rosa Riestra J José M. Bravo-Ferrero G Gerolf de Boer B Bernardina T. F. van der Gun M Mara F. Vincenti-González A Alida C. M. Veloo D Daniele Pantano M Margriet van der Meer L Lilli Gard E Erley F. Lizarazo M Marjolein Knoester A Alex W. Friedrich H Hubert G. M. Niesters S Salvatore Cataudella C Chiara Dellacasa M Manuel Huth C Clemens Peiter

Abstract

Abstract Post-Acute Infectious Syndromes (PAIS) refer to the symptoms persisting months after initial infection. Clinical research studies on this topic often collect rich, multi-modal datasets. Yet, the complexity of the datasets and the lack of a precise clinical case definition pose difficulties in creating comprehensive analyses. Here, we present a generalisable framework for analysing data from longitudinal studies of PAIS using Latent Transition Analysis (LTA). It enables the identification of disease phenotypes and the patient-level analysis of transitions between them, without relying on predefined clinical categorisations. Furthermore, we introduce a method for incorporating covariate information, which enables exploration of how patient characteristics influence disease trajectories. We apply this methodology to the ORCHESTRA dataset, composed of individuals affected by SARS-CoV-2 infection from multiple European centres, for investigation into Post-COVID-19 condition (PCC). 5094 patient assessments were collected at SARS-CoV-2 infection, and at 6, 12, 18, and 24 months of follow-up. Our model identifies distinct PCC phenotypes with patient trajectories impacted by age and sex. Our results highlight how LTA can enhance the interpretability of complex, time-resolved clinical data, support personalized patient monitoring and management, and accelerate therapeutic development for other PAISs, too.

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Article Details

Volume / Issue Vol. 17, Issue 1
Published February 10, 2026
ISSN 2041-1723
Publisher Nature Portfolio

Journal Info

Nature Communications

Nature Portfolio
ISSN: 2041-1723 Open Access Life Sciences

Authors (127)

R

Roy Gusinow

A

Anna Górska

L

Lorenzo Maria Canziani

I

Iris Lopes-Rafegas

C

Carolina Alvarez Garavito

A

Adriana Tami

E

Elisa Gentilotti

E

Elisa Sicuri

C

Cedric Laouenan

Assistance Publique–Hôpitaux de Paris.Nord, Hopital Bichat-Claude Bernard, Service des Maladies Infectieuses, Paris F75018, France and Universite Paris Cite, INSERM UMR 1137 IAME

J

Jade Ghosn

Assistance Publique–Hôpitaux de Paris.Nord, Hopital Bichat-Claude Bernard, Service des Maladies Infectieuses, Paris F75018, France and Universite Paris Cite, INSERM UMR 1137 IAME

A

Aline-Marie Florence

N

Nadhem Lahfej

F

Fulvia Mazzaferri

L

Lidia Del Piccolo

M

Maddalena Giannella

A

Alice Toschi

M

Michela Di Chiara

M

Maria Giulia Caponcello

Z

Zaira R. Palacios-Baena

K

Karin I. Wold

E

Elisa Rossi

E

Evelina Tacconelli

J

Jan Hasenauer

E

Elena Addis

M

Maddalena Armellini

A

Anna Maria Azzini

B

Benedetta Barana

L

Lucia Bonato

E

Elena Carrara

A

Alessandro Castelli

F

Filippo Cioli Puviani

M

Michela Conti

R

Raffaella Cordioli

C

Carmine Cutone

R

Ruth Joanna Davis

P

Pasquale De Nardo

M

Miriam Emiliani

A

Alessio Esposito

D

Daniele Fasan

G

Giada Fasani

G

Giorgia Franchina

J

Jacopo Garlasco

E

Enrico Gibbin

S

Salvatore Hermes Dall’O’

C

Chiara Konishi De Toffoli

L

Lorenza Lambertenghi

F

Federico Lattanzi

A

Andrea Leonardi

F

Francesco Luca

G

Gaia Maccarrone

M

Massimo Mirandola

M

Matteo Morra

A

Alessandra Nazeri

M

Matilde Rocchi

G

Giulia Rosini

C

Chiara Perlini

M

Maria Diletta Pezzani

L

Laura Rovigo

A

Anna Giulia Salvadori

A

Andrea Sartori

Experimental Division, European Synchrotron Radiation Facility, 71 Av. des Martyrs, 38000, Grenoble, France

A

Alessia Savoldi

R

Rebecca Scardellato

M

Marcella Sibani

E

Erica Sodano

S

Simona Sorbello

L

Lorenzo Tavernaro

G

Giorgia Tomassini

A

Alessandro Visentin

S

Stefania Vitali

A

Andrea Volpe

C

Chiara Zanchi

G

Gloria Mazzali

G

Giovanni Stabile

G

Gianluca Vantini

R

Riccardo Cecchetto

D

Davide Gibellini

N

Nicolò Cardobi

D

Debora Calì

M

Maria Paola Cecchini

M

Maddalena Marcanti

A

Anna Mason

S

Salvatore Monaco

M

Marco Pattaro Zonta

C

Cinzia Perlini

G

Gianluigi Zanusso

E

Elda Righi

M

Mariana Nunes Pinho Guedes

M

Maria Mongardi

C

Concetta Sciammarella

C

Claudio Micheletto

P

Paolo Gisondi

N

Natascia Caroccia

C

Cecilia Bonazzetti

B

Beatrice Tazza

Z

Zeno Igor Adrien Pasquini

D

Domenico Marzolla

G

Giacomo Fornaro

F

Fabio Trapani

L

Lorenzo Marconi

L

Luciano Attard

S

Sara Tedeschi

S

Silvia Vituliano

L

Liliana Gabrielli

T

Tiziana Lazzarotto

J

Jesús Rodrguez-Baño

M

Mara Isabel Garcia Sánchez

A

Ana Belén Hidalgo Céspedes

A

Aurora Aleman Rodriguez

L

Lola Cubero Aranda

P

Paula Olivares Navarro

S

Sandra De la Rosa Riestra

J

José M. Bravo-Ferrero

G

Gerolf de Boer

B

Bernardina T. F. van der Gun

M

Mara F. Vincenti-González

A

Alida C. M. Veloo

D

Daniele Pantano

M

Margriet van der Meer

L

Lilli Gard

E

Erley F. Lizarazo

M

Marjolein Knoester

A

Alex W. Friedrich

H

Hubert G. M. Niesters

S

Salvatore Cataudella

C

Chiara Dellacasa

M

Manuel Huth

C

Clemens Peiter

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