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A patient-centric modeling framework captures recovery from SARS-CoV-2 infection.

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Hanson, Aimee L 
Lodge, Samantha 
Whiley, Luke 


The biology driving individual patient responses to severe acute respiratory syndrome coronavirus 2 infection remains ill understood. Here, we developed a patient-centric framework leveraging detailed longitudinal phenotyping data and covering a year after disease onset, from 215 infected individuals with differing disease severities. Our analyses revealed distinct 'systemic recovery' profiles, with specific progression and resolution of the inflammatory, immune cell, metabolic and clinical responses. In particular, we found a strong inter-patient and intra-patient temporal covariation of innate immune cell numbers, kynurenine metabolites and lipid metabolites, which highlighted candidate immunologic and metabolic pathways influencing the restoration of homeostasis, the risk of death and that of long COVID. Based on these data, we identified a composite signature predictive of systemic recovery, using a joint model on cellular and molecular parameters measured soon after disease onset. New predictions can be generated using the online tool , designed to test our findings prospectively.


Funder: Lopez-Loreta Foundation

Funder: Australian Federal Government’s Medical Research Future Fund (MRFF-ARAPC ARG76435); Western Australian Department of Health; Spinnaker Health Research Foundation; McCusker Charitable Foundation

Funder: Medical Research Council Programme Grant (MR/L019027)

Funder: Botnar Research Centre for Child Health (BRCCH)

Funder: COVID-19 Rapid Response DCF (RG93172/HESS/40558); Botnar Research Centre for Child Health (BRCCH)


Resource, /692/699/255, /631/250/255, resource

Journal Title

Nat Immunol

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Springer Science and Business Media LLC
Medical Research Council (MR/L019027/1)
Wellcome Trust (200871/Z/16/Z)
Wellcome Trust (219506/Z/19/Z)