{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T06:33:58Z","timestamp":1777358038560,"version":"3.51.4"},"reference-count":60,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T00:00:00Z","timestamp":1777334400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH","award":["GM103408"],"award-info":[{"award-number":["GM103408"]}]},{"name":"NIH","award":["P20"],"award-info":[{"award-number":["P20"]}]},{"name":"NIH","award":["GM109007"],"award-info":[{"award-number":["GM109007"]}]},{"name":"NIH","award":["P20"],"award-info":[{"award-number":["P20"]}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Public Health"],"abstract":"<jats:sec>\n                    <jats:title>Purpose<\/jats:title>\n                    <jats:p>To investigate associations between cardiopulmonary, neuropsychiatric, and multisystem long COVID phenotypes, and sequence-defined SARS-CoV-2 viral variant and sociodemographic predictors in a population from a rural state.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>SARS-CoV-2 clinical samples were collected from 1,120 veterans treated at the Veterans Affairs (VA) Medical Center in Boise, Idaho from April 2, 2020 to December 20, 2022. Viral variants were identified through sequencing and annotated with clinical data from the VA Corporate Data Warehouse, as well as CDC rurality and social vulnerability. Cardiopulmonary, neuropsychiatric, and multisystem long COVID phenotypes were determined by the addition of one or more ICD-10 codes 90\u2013270\u202fdays post-infection. Multinomial logistic regression was used to estimate phenotype prevalence in a base model with predictors viral variant, age, sex, rurality, and social vulnerability, as well as in models that adjusted for patient health (comorbidity, healthcare utilization, and smoking status), and treatments (vaccination and Paxlovid).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Findings<\/jats:title>\n                    <jats:p>Female patients experienced more neuropsychiatric long COVID and less recovery, whereas the neuropsychiatric phenotype was less prevalent among older patients. Omicron variants had less recovery and more multisystem long COVID relative to pre-Delta\u2014a finding that may indicate an association between infection with Omicron and post-acute gastrointestinal symptoms.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>This study is perhaps the largest to investigate viral variant effects on long COVID using sequence rather than date-based variant definitions, and is also unique in its focus on a population living in one of the most rural states in the United States. Our results are consistent with other studies finding contributions from both biological and social predictors to long COVID outcomes.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fpubh.2026.1625363","type":"journal-article","created":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T05:36:20Z","timestamp":1777354580000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["A retrospective cohort study of viral and sociodemographic determinants of long COVID among Idaho veterans"],"prefix":"10.3389","volume":"14","author":[{"given":"Ian","family":"Taylor","sequence":"first","affiliation":[{"name":"Boise Veterans Affairs Medical Center","place":["Boise, ID, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeremy K.","family":"Boyd","sequence":"additional","affiliation":[{"name":"Boise Veterans Affairs Medical Center","place":["Boise, ID, United States"]},{"name":"Idaho Veterans Research and Education Foundation","place":["Boise, ID, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"McIndoo","sequence":"additional","affiliation":[{"name":"Boise Veterans Affairs Medical Center","place":["Boise, ID, United States"]},{"name":"Idaho Veterans Research and Education Foundation","place":["Boise, ID, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mary Cloud B.","family":"Ammons","sequence":"additional","affiliation":[{"name":"Boise Veterans Affairs Medical Center","place":["Boise, ID, United States"]},{"name":"Idaho Veterans Research and Education Foundation","place":["Boise, ID, United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2026,4,28]]},"reference":[{"key":"ref1","year":"2024"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"135","DOI":"10.15585\/mmwr.mm7306a4","article-title":"Notes from the field: Long COVID prevalence among adults\u2014United States, 2022","volume":"73","author":"Ford","year":"2024","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"100137","DOI":"10.1016\/j.ahr.2023.100137","article-title":"A descriptive exploration of younger and older adults\u2019 experiences of integrative medical group visits for long COVID","volume":"3","author":"Mata","year":"2023","journal-title":"Aging Health Res"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"830","DOI":"10.1126\/science.adl0867","article-title":"Solving the puzzle of Long Covid","volume":"383","author":"Al-Aly","year":"2024","journal-title":"Science"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"ofaf533","DOI":"10.1093\/ofid\/ofaf533","article-title":"Global prevalence of long COVID, its subtypes, and risk factors: an updated systematic review and meta-analysis","volume":"12","author":"Hou","year":"2025","journal-title":"Open Forum Infect Dis"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"515","DOI":"10.1056\/NEJMoa2403211","article-title":"Postacute sequelae of SARS-CoV-2 infection in the pre-delta, delta, and omicron eras","volume":"391","author":"Xie","year":"2024","journal-title":"N Engl J Med"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1001\/jamainternmed.2023.0750","article-title":"Risk factors associated with post\u2212COVID-19 condition: a systematic review and meta-analysis","volume":"183","author":"Tsampasian","year":"2023","journal-title":"JAMA Intern Med"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"e2238804","DOI":"10.1001\/jamanetworkopen.2022.38804","article-title":"Prevalence and correlates of long COVID symptoms among US adults","volume":"5","author":"Perlis","year":"2022","journal-title":"JAMA Netw Open"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1111\/jrh.12807","article-title":"Cross-sectional population-based estimates of a rural-urban disparity in prevalence of long COVID among Michigan adults with polymerase chain reaction-confirmed COVID-19, 2020-2022","volume":"40","author":"MacCallum-Bridges","year":"2024","journal-title":"J Rural Health"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1758","DOI":"10.1186\/s12889-025-22987-8","article-title":"Prevalence of and factors associated with long COVID among US adults: a nationwide survey","volume":"25","author":"Shi","year":"2025","journal-title":"BMC Public Health"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"2019378118","DOI":"10.1073\/pnas.2019378118","article-title":"Impacts of the COVID-19 pandemic on rural America","volume":"118","author":"Mueller","year":"2021","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1186\/s13690-025-01553-z","article-title":"Minority health social vulnerability index and long COVID illness among a statewide, population-based study of adults with polymerase chain reaction-confirmed SARS-CoV-2","volume":"83","author":"Ryu","year":"2025","journal-title":"Arch Public Health"},{"key":"ref13","doi-asserted-by":"publisher","first-page":"e038073","DOI":"10.1161\/JAHA.124.038073","article-title":"Social vulnerability and long-term cardiovascular outcomes after COVID-19 hospitalization: an analysis of the American Heart Association COVID-19 registry linked with Medicare claims data","volume":"14","author":"Fakhraei","year":"2025","journal-title":"J Am Heart Assoc"},{"key":"ref14","year":"2021"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1016\/j.jagp.2020.08.006","article-title":"Successful aging in older US veterans: results from the 2019\u20132020 National Health and resilience in veterans study","volume":"29","author":"Pietrzak","year":"2021","journal-title":"Am J Geriatr Psychiatry"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"604","DOI":"10.3390\/healthcare9050604","article-title":"Exploring health outcomes for U.S. veterans compared to non-veterans from 2003 to 2019","volume":"9","author":"Betancourt","year":"2021","journal-title":"Healthcare"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"ofac641","DOI":"10.1093\/ofid\/ofac641","article-title":"<article-title update=\"added\">the US department of veterans affairs science and health initiative to combat infectious and emerging life-threatening diseases (VA SHIELD): a biorepository addressing national health threats","volume":"9","author":"Harley","year":"2022","journal-title":"Open Forum Infect Dis"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"S44","DOI":"10.12788\/fp.0417","article-title":"Nationwide genomic surveillance and response to COVID-19: the VA SeqFORCE and SeqCURE consortiums","volume":"40","author":"Krishnan","year":"2023","journal-title":"Fed Pract"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"S48","DOI":"10.12788\/fp.0424","article-title":"VA SHIELD: a biorepository for veterans and the nation","volume":"40","author":"Epstein","year":"2023","journal-title":"Fed Pract"},{"key":"ref20","year":"2023"},{"key":"ref21","year":"2013"},{"key":"ref22","year":"2022"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"3773","DOI":"10.21105\/joss.03773","article-title":"Nextclade: clade assignment, mutation calling and quality control for viral genomes","volume":"6","author":"Aksamentov","year":"2021","journal-title":"J Open Source Softw"},{"key":"ref24","doi-asserted-by":"publisher","first-page":"5","DOI":"10.15386\/mpr-2340","article-title":"Digestive involvement in the Long-COVID syndrome","volume":"95","author":"Bogariu","year":"2022","journal-title":"Med Pharm Rep"},{"key":"ref25","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1113\/EP090802","article-title":"Long COVID: mechanisms, risk factors and recovery","volume":"108","author":"Astin","year":"2023","journal-title":"Exp Physiol"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"2195","DOI":"10.1016\/j.cgh.2022.05.044","article-title":"The COVID-19 pandemic and post-infection irritable bowel syndrome: what lies ahead for gastroenterologists","volume":"20","author":"Chan","year":"2022","journal-title":"Clin Gastroenterol Hepatol"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"363","DOI":"10.3892\/etm.2022.11290","article-title":"Long COVID and neuropsychiatric manifestations (review)","volume":"23","author":"Efstathiou","year":"2022","journal-title":"Exp Ther Med"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/ofid\/ofad277","article-title":"Long COVID clinical phenotypes up to 6 months after infection identified by latent class analysis of self-reported symptoms","volume":"10","author":"Gottlieb","year":"2023","journal-title":"Open Forum Infect Dis"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"93","DOI":"10.2147\/POR.S316186","article-title":"Risk predictors and symptom features of Long COVID within a broad primary care patient population including both tested and untested patients","volume":"12","author":"Jones","year":"2021","journal-title":"Pragmat Obs Res"},{"key":"ref30","doi-asserted-by":"publisher","DOI":"10.1097\/CRD.0000000000000552","article-title":"Cardiovascular manifestations of the long COVID syndrome","author":"Lorente-Ros","year":"2023","journal-title":"Cardiol Rev"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1097\/SGA.0000000000000676","article-title":"Gastrointestinal bleeding in COVID-19 patients: a rapid review","volume":"45","author":"Negro","year":"2022","journal-title":"Gastroenterol Nurs"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12916-023-02737-6","article-title":"Coding long COVID: characterizing a new disease through an ICD-10 lens","volume":"21","author":"Pfaff","year":"2023","journal-title":"BMC Med"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"589","DOI":"10.48550\/arXiv.2303.12813","article-title":"Computable phenotypes for post-acute sequelae of SARS-CoV-2: a national COVID cohort collaborative analysis","volume":"2023","author":"Pungitore","year":"2024","journal-title":"AMIA Annu Symp Proc"},{"key":"ref34","doi-asserted-by":"publisher","first-page":"323","DOI":"10.5662\/wjm.v13.i4.323","article-title":"Potential long-term neurological and gastrointestinal effects of COVID-19: a review of adult cohorts","volume":"13","author":"Sherif","year":"2023","journal-title":"World J Methodol"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"1706","DOI":"10.1038\/s41591-022-01909-w","article-title":"Symptoms and risk factors for long COVID in non-hospitalized adults","volume":"28","author":"Subramanian","year":"2022","journal-title":"Nat Med"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1934","DOI":"10.1001\/jama.2023.8823","article-title":"Development of a definition of postacute sequelae of SARS-CoV-2 infection","volume":"329","author":"Thaweethai","year":"2023","journal-title":"JAMA"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1016\/j.tem.2023.03.002","article-title":"Long COVID: pathophysiological factors and abnormalities of coagulation","volume":"34","author":"Turner","year":"2023","journal-title":"Trends Endocrinol Metab"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"103951","DOI":"10.1016\/j.jbi.2021.103951","article-title":"PASCLex: a comprehensive post-acute sequelae of COVID-19 (PASC) symptom lexicon derived from electronic health record clinical notes","volume":"125","author":"Wang","year":"2022","journal-title":"J Biomed Inform"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"583","DOI":"10.1038\/s41591-022-01689-3","article-title":"Long-term cardiovascular outcomes of COVID-19","volume":"28","author":"Xie","year":"2022","journal-title":"Nat Med"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"422","DOI":"10.1186\/s12879-023-08401-x","article-title":"Post-infection functional gastrointestinal disorders following coronavirus disease-19: a prospective follow-up cohort study","volume":"23","author":"Zhang","year":"2023","journal-title":"BMC Infect Dis"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1177\/00033197231153204","article-title":"Vascular \u201clong COVID\u201d: a new vessel disease?","volume":"75","author":"Zanini","year":"2024","journal-title":"Angiology"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1016\/0021-9681(87)90171-8","article-title":"A new method of classifying prognostic comorbidity in longitudinal studies: development and validation","volume":"40","author":"Charlson","year":"1987","journal-title":"J Chronic Dis"},{"key":"ref43","doi-asserted-by":"crossref","DOI":"10.1007\/978-0-387-21706-2","volume-title":"Modern Applied Statistics with S","author":"Venables","year":"2002"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1393","DOI":"10.1016\/0270-0255(86)90088-6","article-title":"A new approach to causal inference in mortality studies with a sustained exposure period\u2014application to control of the healthy worker survivor effect","volume":"7","author":"Robins","year":"1986","journal-title":"Math Model"},{"key":"ref45","volume-title":"Causal Inference: What If?","author":"Hern\u00e1n","year":"2024"},{"key":"ref46","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v111.i09","article-title":"How to interpret statistical models using marginal effects in R and Python","volume":"111","author":"Arel-Bundock","year":"2024","journal-title":"J Stat Softw"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"e2224359","DOI":"10.1001\/jamanetworkopen.2022.24359","article-title":"Rates and factors associated with documentation of diagnostic codes for Long COVID in the national veterans affairs health care system","volume":"5","author":"Ioannou","year":"2022","journal-title":"JAMA Netw Open"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"292","DOI":"10.1111\/jrh.12796","article-title":"SARS-CoV-2 infection and long COVID among California farmworkers","volume":"40","author":"Mora","year":"2024","journal-title":"J Rural Health"},{"key":"ref49","year":"2022"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"426","DOI":"10.1159\/000540919","article-title":"Gender disparities in neurological symptoms of long COVID: a systematic review and meta-analysis","volume":"59","author":"Gorenshtein","year":"2025","journal-title":"Neuroepidemiology"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"369","DOI":"10.1002\/ana.27128","article-title":"Neurologic manifestations of long COVID disproportionately affect young and middle-age adults","volume":"97","author":"Choudhury","year":"2025","journal-title":"Ann Neurol"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"3123","DOI":"10.1111\/jgs.70043","article-title":"Age-related changes in the clinical picture of long COVID","volume":"73","author":"Fain","year":"2025","journal-title":"J Am Geriatr Soc"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"2253","DOI":"10.1001\/jama.2020.21753","article-title":"Older adults and the mental health effects of COVID-19","volume":"324","author":"Vahia","year":"2020","journal-title":"JAMA"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"e17898","DOI":"10.7717\/peerj.17898","article-title":"Biological factors associated with long COVID and comparative analysis of SARS-CoV-2 spike protein variants: a retrospective study in Thailand","volume":"12","author":"Kiatratdasakul","year":"2024","journal-title":"PeerJ"},{"key":"ref55","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2024.109536","article-title":"Long COVID across SARS-CoV-2 variants, lineages, and sublineages","volume":"27","author":"Padilla","year":"2024","journal-title":"iScience"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"2263","DOI":"10.1016\/S0140-6736(22)00941-2","article-title":"Risk of long COVID associated with delta versus omicron variants of SARS-CoV-2","volume":"399","author":"Antonelli","year":"2022","journal-title":"Lancet"},{"key":"ref57","doi-asserted-by":"publisher","first-page":"2629","DOI":"10.3390\/v14122629","article-title":"Long-COVID symptoms in individuals infected with different SARS-CoV-2 variants of concern: a systematic review of the literature","volume":"14","author":"Fern\u00e1ndez-de-las-Pe\u00f1as","year":"2022","journal-title":"Viruses"},{"key":"ref58","doi-asserted-by":"publisher","first-page":"657","DOI":"10.1007\/s15010-024-02438-z","article-title":"Post-COVID recovery is faster after an infection with the SARS-CoV-2 omicron variant: a population-based cohort study","volume":"53","author":"Pfrommer","year":"2025","journal-title":"Infection"},{"key":"ref59","doi-asserted-by":"publisher","first-page":"2398","DOI":"10.1038\/s41591-022-02051-3","article-title":"Acute and postacute sequelae associated with SARS-CoV-2 reinfection","volume":"28","author":"Bowe","year":"2022","journal-title":"Nat Med"},{"key":"ref60","doi-asserted-by":"publisher","first-page":"e00427","DOI":"10.1128\/spectrum.00427-25","article-title":"Direct comparison of Nanopore and Illumina sequencing of SARS-CoV-2","volume":"13","author":"Hottel","year":"2025","journal-title":"Microbiol Spectrum"}],"container-title":["Frontiers in Public Health"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpubh.2026.1625363\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,28]],"date-time":"2026-04-28T05:36:22Z","timestamp":1777354582000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpubh.2026.1625363\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,28]]},"references-count":60,"alternative-id":["10.3389\/fpubh.2026.1625363"],"URL":"https:\/\/doi.org\/10.3389\/fpubh.2026.1625363","relation":{},"ISSN":["2296-2565"],"issn-type":[{"value":"2296-2565","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,28]]},"article-number":"1625363"}}