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High-dimensional characterization of post-acute sequelae of COVID-19
Open accessPublished version of a preprint
Abstract
The acute clinical manifestations of COVID-19 have been well characterized 1,2, but the post-acute sequelae of this disease have not been comprehensively described. Here we use the national healthcare databases of the US Department of Veterans Affairs to systematically and comprehensively identify 6-month incident sequelae-including diagnoses, medication use and laboratory abnormalities-in patients with COVID-19 who survived for at least 30 days after diagnosis. We show that beyond the first 30 days of illness, people with COVID-19 exhibit a higher risk of death and use of health resources. Our high-dimensional approach identifies incident sequelae in the respiratory system, as well as several other sequelae that include nervous system and neurocognitive disorders, mental health disorders, metabolic disorders, cardiovascular disorders, gastrointestinal disorders, malaise, fatigue, musculoskeletal pain and anaemia. We show increased incident use of several therapeutic agents-including pain medications (opioids and non-opioids) as well as antidepressant, anxiolytic, antihypertensive and oral hypoglycaemic agents-as well as evidence of laboratory abnormalities in several organ systems. Our analysis of an array of prespecified outcomes reveals a risk gradient that increases according to the severity of the acute COVID-19 infection (that is, whether patients were not hospitalized, hospitalized or admitted to intensive care). Our findings show that a substantial burden of health loss that spans pulmonary and several extrapulmonary organ systems is experienced by patients who survive after the acute phase of COVID-19. These results will help to inform health system planning and the development of multidisciplinary care strategies to reduce chronic health loss among individuals with COVID-19.
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BackgroundData-driven identification of post-acute SARS-CoV-2 infection subphenotypes
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“Several studies have found that PASC could include a diverse set of symptoms and signs involving many organ systems 10–12 .”
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Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes
Reese, J., Blau, H., Casiraghi, E., Bergquist, T., Loomba, J. J., Callahan, T. J., Laraway, B. J., Antonescu, C., Coleman, B., Gargano, M. A., et al. (2022) · EBioMedicine · doi:10.1016/j.ebiom.2022.104413 · Cited by 190
“54 We suggest that analogous algorithms could be used to evaluate data gathered from prospective studies of long COVID patients to extend and deepen our characterization of phenotypic clusters by including data that are currently dif fi cult to ascertain reliably from EHR data, including symptoms…”
Reduction in life expectancy in Brazil after COVID-19
Castro, M. C., Gurzenda, S., Turra, C. M., Kim, S., Andrasfay, T., & Goldman, N. (2021) · Nature Medicine · doi:10.1038/s41591-021-01437-z · Cited by 164
Kikkenborg Berg, S., Dam Nielsen, S., Nygaard, U., Bundgaard, H., Palm, P., Rotvig, C., & Vinggaard Christensen, A. (2022) · The Lancet Child & Adolescent Health · doi:10.1016/s2352-4642(22)00004-9 · Cited by 168
Proposed subtypes of post‐COVID‐19 syndrome (or long‐COVID) and their respective potential therapies
Yong, S. J., & Liu, S. (2021) · Reviews in Medical Virology · doi:10.1002/rmv.2315 · Cited by 173
“), among 73,435 COVID‐19 survivors (non‐hospitalised) compared to matched controls and influenza patients at 4‐month.(57) Another controlled cohort study involving 236,379 COVID‐19 patients also found that the risks of neurological and psychiatric diseases were higher than matched controls with other respiratory tract…”
ResultMagnúsdóttir, I., Lovik, A., Unnarsdóttir, A. B., McCartney, D. L., Ask, H., Kõiv, K., Christoffersen, L. A. N., Johnson, S. U., Hauksdóttir, A., Fawns‐Ritchie, C., et al. (2022) · The Lancet Public Health · doi:10.1016/s2468-2667(22)00042-1 · Cited by 164
Acute and chronic neurological disorders in COVID-19: potential mechanisms of disease
Balcom, E. F., Nath, A., & Power, C. (2021) · Brain · doi:10.1093/brain/awab302 · Cited by 163
“Many survivors of the acute infection experience persistent and incapacitating neurological symptoms, which can have socioeconomic and personal consequences.(1) It is thus imperative that there is a thorough understanding of the evolving clinical syndromes and the underlying pathophysiological mechanisms, enabling rat…”
BackgroundS1-Leitlinie Post-COVID/Long-COVID
Koczulla, A. R., Ankermann, T., Behrends, U., Berlit, P., Böing, S., Brinkmann, F., Franke, C., Glöckl, R., Gogoll, C., Hummel, T. R., et al. (2021) · Pneumologie · doi:10.1055/a-1551-9734 · Cited by 164
Zhou, Y., Xu, J., Hou, Y., Leverenz, J. B., Kallianpur, A. R., Mehra, R., Liu, Y., Yu, H., Pieper, A. A., Jehi, L. E., et al. (2021) · Alzheimer s Research & Therapy · doi:10.1186/s13195-021-00850-3 · Cited by 165
“Another study using 73,000 non-hospitalized COVID-19 survivors shows various incident sequalae, such as mental health disorders and neurocognitive disorders [15].”
BackgroundCOVID-19 therapeutics: Challenges and directions for the future
Robinson, P. C., Liew, D. F. L., Tanner, H. L., Grainger, J. R., Dwek, R. A., Reisler, R. B., Steinman, L., Feldmann, M., Ho, L., Hussell, T., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2119893119 · Cited by 158
“Encouragingly, studies are shedding light on the pathogenesis of the most common complaints in long-COVID, namely pulmonary and neurologic symptoms (14, 16).”
BackgroundKompaniyets, L., Bull–Otterson, L., Boehmer, T. K., Baca, S., Alvarez, P., Hong, K., Hsu, J., Harris, A. M., Gundlapalli, A. V., & Saydah, S. (2022) · MMWR Morbidity and Mortality Weekly Report · doi:10.15585/mmwr.mm7131a3 · Cited by 161
Risk for newly diagnosed diabetes after COVID-19: a systematic review and meta-analysis
Zhang, T., Mei, Q., Zhang, Z., Walline, J. H., Liu, Y., Zhu, H., & Zhang, S. (2022) · BMC Medicine · doi:10.1186/s12916-022-02656-y · Cited by 173
Xie, Y., Choi, T., & Al‐Aly, Z. (2023) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(23)00684-9 · Cited by 154
Nalbandian, A., Desai, A. D., & Wan, E. Y. (2022) · Annual Review of Medicine · doi:10.1146/annurev-med-043021-030635 · Cited by 163
A Longitudinal Study of COVID-19 Sequelae and Immunity: Baseline Findings
Sneller, M. C., Liang, C., Marques, A. R., Chung, J. Y., Shanbhag, S. M., Fontana, J. R., Raza, H., Okeke, O., Dewar, R. L., Higgins, B. P., et al. (2022) · Annals of Internal Medicine · doi:10.7326/m21-4905 · Cited by 160
“001 Chest pain/discomfort 0 (0) 16 (8) 1 (2.”
Pathogenesis of Respiratory Viral and Fungal Coinfections
Salazar, F., Bignell, E., Brown, G. D., Cook, P. C., & Warris, A. (2021) · Clinical Microbiology Reviews · doi:10.1128/cmr.00094-21 · Cited by 164
Rao, S., Lee, G. M., Razzaghi, H., Lorman, V., Mejías, A., Pajor, N. M., Thacker, D., Webb, R. D., Dickinson, K., Bailey, L. C., et al. (2022) · Archives of Pediatrics and Adolescent Medicine · doi:10.1001/jamapediatrics.2022.2800 · Cited by 152
Long-term cardiac pathology in individuals with mild initial COVID-19 illness
Püntmann, V. O., Martin, S. S., Shchendrygina, A., Hoffmann, J., Ka, M. M., Giokoglu, E., Vanchin, B., Holm, N., Karyou, A., Laux, G. S., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-02000-0 · Cited by 161
Evolving phenotypes of non-hospitalized patients that indicate long COVID
Estiri, H., Strasser, Z. H., Brat, G. A., Semenov, Y. R., Aaron, J. R., Agapito, G., Albayrak, A., ALESSIANI, M., Amendola, D. F., Anthony, L. L. L. J., et al. (2021) · BMC Medicine · doi:10.1186/s12916-021-02115-0 · Cited by 155
“Al-Aly specifically documents increased memory problems and strokes [40].”
BackgroundKhullar, D., Zhang, Y., Zang, C., Xu, Z., Wang, F., Weiner, M. G., Carton, T. W., Rothman, R. L., Block, J. P., & Kaushal, R. (2023) · Journal of General Internal Medicine · doi:10.1007/s11606-022-07997-1 · Cited by 149
Systematic Review of the Prevalence of Long COVID
Woodrow, M., Carey, C., Ziauddeen, N., Thomas, R., Akrami, A., Lutje, V., Greenwood, D. C., & Alwan, N. A. (2023) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofad233 · Cited by 162
“Studies such as Al-Aly et al [16] that investigated medical diagnoses in the period after COVID-19, report cardiovascular, neurological, and other system-specific clinical sequelae, providing a substantial excess burden in those who survived the acute phase of COVID-19 [13].”
Solving the puzzle of Long Covid
Al‐Aly, Z., & Topol, E. J. (2024) · Science · doi:10.1126/science.adl0867 · Cited by 142
Incident autoimmune diseases in association with SARS-CoV-2 infection: a matched cohort study
Tesch, F., Ehm, F., Vivirito, A., Wende, D., Batram, M., Loser, F., Menzer, S., Jacob, J., Roessler, M., Seifert, M., et al. (2023) · Clinical Rheumatology · doi:10.1007/s10067-023-06670-0 · Cited by 142
Long COVID: aiming for a consensus
Munblit, D., O’Hara, M. E., Akrami, A., Perego, E., Olliaro, P., & Needham, D. M. (2022) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(22)00135-7 · Cited by 138
Long-term gastrointestinal outcomes of COVID-19
Xu, E., Xie, Y., & Al‐Aly, Z. (2023) · Nature Communications · doi:10.1038/s41467-023-36223-7 · Cited by 141
“(1) we modified our covariate selection by increasing covariate inclusion to 300 high dimensional variables (instead of the 100 high dimensional variables used in the main analysis)when constructing the inverse probabilityweight; (2) we restricted covariate selection only to pre-defined variables when constructing the…”
MethodBajema, K. L., Berry, K., Streja, E., Rajeevan, N., Li, Y., Mutalik, P., Yan, L., Cunningham, F. E., Hynes, D. M., Rowneki, M., et al. (2023) · Annals of Internal Medicine · doi:10.7326/m22-3565 · Cited by 134
“We also assessed the incidence of 34 potential post-COVID conditions described in the literature (17-20) (Supplemental Table 8) from day 31-180 following the index date.”
MethodLi, J., Zhou, Y., Ma, J., Zhang, Q., Shao, J., Liang, S., Yu, Y., Li, W., & Wang, C. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01640-z · Cited by 150
Cardiometabolic outcomes up to 12 months after COVID-19 infection. A matched cohort study in the UK
Rezel‐Potts, E., Douiri, A., Sun, X., Chowienczyk, P., Shah, A. M., & Gulliford, M. C. (2022) · PLoS Medicine · doi:10.1371/journal.pmed.1004052 · Cited by 136
“New-onset hyperglycaemia has been reported in COVID-19 patients, sometimes representing “stress hyperglycaemia,” and is associated with worse prognosis [5,11].”
BackgroundMethodWarren, C. M., Snow, T. T., Lee, A., Shah, M. M., Heider, A., Blomkalns, A. L., Betts, B. A., Buzzanco, A. S., González, J. C., Chinthrajah, R. S., et al. (2021) · JAMA Network Open · doi:10.1001/jamanetworkopen.2021.25524 · Cited by 135
“millions ill—some for manymonths, with a subset whomay continue to experience long-term adverse health effects.(31,32)Moreover, allergic reactions are highly treatable, and even severe anaphylaxis usually can be promptly mitigated with appropriate preparation andmedication, as all patients in the present case series e…”
BackgroundPeluso, M. J., Kelly, J. D., Lu, S., Goldberg, S. A., Davidson, M. C., Mathur, S., Durstenfeld, M. S., Spinelli, M. A., Hoh, R., Tai, V., et al. (2021) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofab640 · Cited by 128
Angiotensin-converting enzyme 2—at the heart of the COVID-19 pandemic
Oudit, G. Y., Wang, K., Viveiros, A., Kellner, M. J., & Penninger, J. M. (2023) · Cell · doi:10.1016/j.cell.2023.01.039 · Cited by 136
Gut Microbiome Alterations in COVID-19
Zuo, T., Wu, X., Wen, W., & Lan, P. (2021) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2021.09.004 · Cited by 134
Post-Acute Sequelae of COVID-19 and Cardiovascular Autonomic Dysfunction: What Do We Know?
Bisaccia, G., Ricci, F., Recce, V., Serio, A., Iannetti, G., Chahal, A. A., Ståhlberg, M., Khanji, M. Y., Fedorowski, A., & Gallina, S. (2021) · Journal of Cardiovascular Development and Disease · doi:10.3390/jcdd8110156 · Cited by 129
“disorders, and a spectrum of symptoms related to poor general wellbeing, even after the resolution of the acute illness [2].”
BackgroundPost-Acute COVID-19 Syndrome and the cardiovascular system: What is known?
Dixit, N. M., Churchill, A., Nsair, A., & Hsu, J. J. (2021) · American Heart Journal Plus Cardiology Research and Practice · doi:10.1016/j.ahjo.2021.100025 · Cited by 129
“7 times higher incidence of arrhythmia at 6-months post-COVID-19 in non-hospitalized patients compared to matched controls; however, whether this was due to truly higher arrhythmia burden or higher rate of detection in the COVID-19 cohort is unknown [47].”
Risks and burdens of incident dyslipidaemia in long COVID: a cohort study
Xu, E., Xie, Y., & Al‐Aly, Z. (2023) · The Lancet Diabetes & Endocrinology · doi:10.1016/s2213-8587(22)00355-2 · Cited by 130
Hou, Y., Gu, T., Ni, Z., Shi, X., Ranney, M. L., & Mukherjee, B. (2025) · Open Forum Infectious Diseases · doi:10.1093/ofid/ofaf533 · Cited by 165
“Different studies considered different comorbidities, listed in Supplementary Results 3.”
Influential
Metadata
- Authors
- Al-Aly, Z., Xie, Y., & Bowe, B.
- Affiliations
- VA St. Louis Health Care System (US)
- Venue
- Nature
- Published
- 2021-04-22
- Volume
- 594
- Issue
- 7862
- Pages
- 259-264
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- OpenAlex
- W3153493739
- Cited by
- 1,518
- References
- 46
- Citations by year
- 2026: 95 · 2025: 170 · 2024: 268 · 2023: 365 · 2022: 391 · 2021: 228
- FWCI
- 149.17
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Nature (publishedVersion)
- Research Square (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- U.S. Department of Veterans Affairs
- American Society of Nephrology
- McDonnell Center for Systems Neuroscience
- Topics
- Health Sciences › Medicine › Clinical Neurology › Long-Term Effects of COVID-19
- Health Sciences › Medicine › Infectious Diseases › COVID-19 Clinical Research Studies
- Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
- Keywords
- post-COVID-19 sequelae, long COVID, COVID-19 mortality, health resource utilization, pulmonary sequelae, neurocognitive disorders, mental illness, metabolic disorders, cardiovascular disease, gastrointestinal diseases, fatigue, musculoskeletal pain, anemia, medication use, laboratory abnormalities, disease severity, intensive care unit admission, veterans
- MeSH terms
- COVID-19, SARS-CoV-2, COVID-19 Drug Treatment, Post-Acute COVID-19 Syndrome, Female, Hospitalization, Humans, Influenza, Human, Male, Outpatients, Risk, Time Factors, United States, United States Department of Veterans Affairs, Cohort Studies, Databases, Factual, Electronic Health Records, Datasets as Topic
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