{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T10:30:40Z","timestamp":1787567440893,"version":"build-2736575974"},"reference-count":227,"publisher":"eLife Sciences Publications, Ltd","license":[{"start":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T00:00:00Z","timestamp":1763337600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"},{"start":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T00:00:00Z","timestamp":1763337600000},"content-version":"am","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"},{"start":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T00:00:00Z","timestamp":1763337600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"content-domain":{"domain":["elifesciences.org"],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,10,14]]},"abstract":"<jats:p>A major health challenge resulting from the COVID-19 pandemic is the manifestation of post-acute sequelae of SARS-CoV-2 (PASC). PASC (or long COVID) is a collective term used for clinical symptoms, various pathologies, and life-quality-changing functional impairment that persist for months to years after the initial SARS-CoV-2 infection. The mechanisms underlying PASC are not understood, although advances have been made in identifying factors that may contribute to long-term pathology. Recent data have emerged, showing an association between SARS-CoV-2 viral persistence and non-SARS-CoV-2 infections (pre-existing, viral reactivation, or new infections) in facilitating or mediating PASC. However, the heterogeneous nature and timing of co-infections have made it challenging to understand, interpret, and contextualize their contribution to PASC. Here, we summarize the impact of potential viral, bacterial, and fungal infections on SARS-CoV-2 pathogenesis, with a focus on their possible roles in the development of PASC. We also provide a framework to understand the mechanisms of PASC and inform basic, translational, and clinical research initiatives, including RECOVER, a large and ongoing research initiative to understand, treat, and prevent long COVID.<\/jats:p>","DOI":"10.7554\/elife.106308","type":"journal-article","created":{"date-parts":[[2025,11,17]],"date-time":"2025-11-17T16:35:44Z","timestamp":1763397344000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.106308","source":"Crossref","is-referenced-by-count":2,"title":["The role of co-infection in the pathogenesis of acute SARS-CoV-2 infection and development of post-acute sequelae: A perspective"],"prefix":"10.7554","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6684-0622","authenticated-orcid":true,"given":"Timothy J","family":"Henrich","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043mz5j54","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Experimental Medicine, University of California, San Francisco","place":["San Francisco, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Christopher P","family":"Montgomery","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/003rfsp33","id-type":"ROR","asserted-by":"publisher"}],"name":"Center for Microbial Pathogenesis, Abigail Wexner Research Institute; Division of Critical Care Medicine, Nationwide Children\u2019s Hospital","place":["Columbus, United States"]},{"id":[{"id":"https:\/\/ror.org\/00rs6vg23","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pediatrics, The Ohio State University College of Medicine","place":["Columbus, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Joerg","family":"Graf","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01wspgy28","id-type":"ROR","asserted-by":"publisher"}],"name":"Pacific Biosciences Research Center, University of Hawai\u02bbi at M\u0101noa","place":["Honolulu, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Nahed","family":"Ismail","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02mpq6x41","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Pathology, University of Illinois at Chicago","place":["Chicago, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8397-6249","authenticated-orcid":true,"given":"Sindhu","family":"Mohandas","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03taz7m60","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Infectious Diseases, Children\u2019s Hospital Los Angeles, Keck School of Medicine, University of Southern California","place":["Los Angeles, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Mehul S","family":"Suthar","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/03czfpz43","id-type":"ROR","asserted-by":"publisher"}],"name":"Emory Vaccine Center, Department of Pediatrics, Emory University School of Medicine","place":["Atlanta, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Hassan","family":"Brim","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05gt1vc06","id-type":"ROR","asserted-by":"publisher"}],"name":"Howard University Pathology Department","place":["Washington DC, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"John M","family":"Coffin","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05wvpxv85","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Molecular Biology and Microbiology, Tufts University","place":["Boston, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-9972-9608","authenticated-orcid":true,"given":"Aayush","family":"Pagaria","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043mz5j54","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Experimental Medicine, University of California, San Francisco","place":["San Francisco, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8799-6629","authenticated-orcid":true,"given":"Jeisac","family":"Guzm\u00e1n Rivera","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/014ye1258","id-type":"ROR","asserted-by":"publisher"}],"name":"PHRI, Rutgers New Jersey Medical School","place":["Newark, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Urmila","family":"Vudali","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/043mz5j54","id-type":"ROR","asserted-by":"publisher"}],"name":"Division of Experimental Medicine, University of California, San Francisco","place":["San Francisco, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"visualization","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Paul","family":"Keim","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0272j5188","id-type":"ROR","asserted-by":"publisher"}],"name":"Pathogen and Microbiome Institute, Northern Arizona University","place":["Flagstaff, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"}]},{"given":"Guangming","family":"Zhong","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/01kd65564","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology, Immunology and Molecular Genetics, University Texas Health","place":["San Antonio, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"}]},{"given":"Rebecca","family":"McGrath","sequence":"additional","affiliation":[{"name":"NIH RECOVER Research Initiative: Patient representative","place":["Attleboro, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"}]},{"given":"Belinda","family":"Edwards","sequence":"additional","affiliation":[{"name":"NIH RECOVER Research Initiative: Patient representative","place":["Odenton, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6551-1827","authenticated-orcid":true,"given":"Adolfo","family":"Garc\u00eda-Sastre","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/0317dzj93","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Microbiology, Global Health and Emerging Pathogens Institute, Department of Medicine, The Tisch Cancer Institute, The Icahn Genomics Institute, and Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai","place":["New York, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4801-3567","authenticated-orcid":true,"given":"Maria Laura","family":"Gennaro","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/014ye1258","id-type":"ROR","asserted-by":"publisher"}],"name":"PHRI, Rutgers New Jersey Medical School","place":["Newark, United States"]},{"id":[{"id":"https:\/\/ror.org\/014ye1258","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Medicine, Rutgers New Jersey Medical School","place":["Newark, United States"]}],"role":[{"role":"author","vocabulary":"crossref"},{"role":"corresponding-author","vocabulary":"crossref"},{"role":"conceptualization","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"4374","published-online":{"date-parts":[[2025,11,17]]},"reference":[{"key":"bib1","doi-asserted-by":"publisher","first-page":"2155","DOI":"10.1093\/infdis\/jiac017","type":"journal-article","article-title":"Persistent autoimmune activation and proinflammatory state in post-coronavirus disease 2019 syndrome","volume":"225","author":"Acosta-Ampudia","year":"2022","journal-title":"The Journal of Infectious Diseases"},{"key":"bib2","doi-asserted-by":"publisher","DOI":"10.1172\/JCI148517","type":"journal-article","article-title":"Nasal ciliated cells are primary targets for SARS-CoV-2 replication in the early stage of COVID-19","volume":"131","author":"Ahn","year":"2021","journal-title":"The Journal of Clinical Investigation"},{"key":"bib3","doi-asserted-by":"publisher","first-page":"1461","DOI":"10.1038\/s41591-022-01840-0","type":"journal-article","article-title":"Long COVID after breakthrough SARS-CoV-2 infection","volume":"28","author":"Al-Aly","year":"2022","journal-title":"Nature Medicine"},{"key":"bib4","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1093\/infdis\/jiac020","type":"journal-article","article-title":"Cytomegalovirus latent infection is associated with an increased risk of COVID-19-related hospitalization","volume":"226","author":"Alanio","year":"2022","journal-title":"The Journal of Infectious Diseases"},{"key":"bib5","doi-asserted-by":"publisher","first-page":"820","DOI":"10.5588\/ijtld.20.0067","type":"journal-article","article-title":"Post-tuberculosis lung health: perspectives from the first international symposium","volume":"24","author":"Allwood","year":"2020","journal-title":"The International Journal of Tuberculosis and Lung Disease"},{"key":"bib6","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1016\/S1474-4422(22)00086-2","type":"journal-article","article-title":"Epstein-Barr virus and multiple sclerosis: supporting causality","volume":"21","author":"Aloisi","year":"2022","journal-title":"The Lancet. Neurology"},{"key":"bib7","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1038\/s41577-023-00904-7","type":"journal-article","article-title":"The immunology of long COVID","volume":"23","author":"Altmann","year":"2023","journal-title":"Nature Reviews. Immunology"},{"key":"bib8","doi-asserted-by":"publisher","first-page":"2263","DOI":"10.1016\/S0140-6736(22)00941-2","type":"journal-article","article-title":"Risk of long COVID associated with delta versus omicron variants of SARS-CoV-2","volume":"399","author":"Antonelli","year":"2022","journal-title":"The Lancet"},{"key":"bib9","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1002\/acn3.51498","type":"journal-article","article-title":"Risk factors and abnormal cerebrospinal fluid associate with cognitive symptoms after mild COVID-19","volume":"9","author":"Apple","year":"2022","journal-title":"Annals of Clinical and Translational Neurology"},{"key":"bib10","doi-asserted-by":"publisher","DOI":"10.3390\/jof6040211","type":"journal-article","article-title":"COVID-19-Associated Candidiasis (CAC): an underestimated complication in the absence of immunological predispositions?","volume":"6","author":"Arastehfar","year":"2020","journal-title":"Journal of Fungi"},{"key":"bib11","doi-asserted-by":"publisher","DOI":"10.3390\/jof6020091","type":"journal-article","article-title":"COVID-19 Associated Pulmonary Aspergillosis (CAPA)\u2014from immunology to treatment","volume":"6","author":"Arastehfar","year":"2020","journal-title":"Journal of Fungi"},{"key":"bib12","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1007\/s11904-023-00647-z","type":"journal-article","article-title":"Immunologic interplay between HIV\/AIDS and COVID-19: adding fuel to the flames?","volume":"20","author":"Augello","year":"2023","journal-title":"Current HIV\/AIDS Reports"},{"key":"bib13","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-23977-1","type":"journal-article","article-title":"Immunological imprinting of the antibody response in COVID-19 patients","volume":"12","author":"Aydillo","year":"2021","journal-title":"Nature Communications"},{"key":"bib14","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1002\/cdt3.74","type":"journal-article","article-title":"Posttreatment Lyme disease syndrome and myalgic encephalomyelitis\/chronic fatigue syndrome: A systematic review and comparison of pathogenesis","volume":"9","author":"Bai","year":"2023","journal-title":"Chronic Diseases and Translational Medicine"},{"key":"bib15","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1038\/nrmicro2236","type":"journal-article","article-title":"The spectrum of latent tuberculosis: rethinking the biology and intervention strategies","volume":"7","author":"Barry","year":"2009","journal-title":"Nature Reviews. Microbiology"},{"key":"bib16","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1038\/nature05762","type":"journal-article","article-title":"Herpesvirus latency confers symbiotic protection from bacterial infection","volume":"447","author":"Barton","year":"2007","journal-title":"Nature"},{"key":"bib17","doi-asserted-by":"publisher","DOI":"10.1177\/20499361231207178","type":"journal-article","article-title":"Bacterial bloodstream infection in critically ill patients with COVID-19: a retrospective cohort study","volume":"10","author":"Bartoszewicz","year":"2023","journal-title":"Therapeutic Advances in Infectious Disease"},{"key":"bib18","doi-asserted-by":"publisher","first-page":"38","DOI":"10.1002\/ppul.25719","type":"journal-article","article-title":"Influenza and respiratory syncytial virus during the COVID-19 pandemic: Time for a new paradigm?","volume":"57","author":"Binns","year":"2022","journal-title":"Pediatric Pulmonology"},{"key":"bib19","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1016\/j.it.2009.07.009","type":"journal-article","article-title":"Endotoxin tolerance: new mechanisms, molecules and clinical significance","volume":"30","author":"Biswas","year":"2009","journal-title":"Trends in Immunology"},{"key":"bib20","doi-asserted-by":"publisher","DOI":"10.1016\/j.jneuroim.2023.578180","type":"journal-article","article-title":"Microglia mediated neuroinflammation in neurodegenerative diseases: A review on the cell signaling pathways involved in microglial activation","volume":"383","author":"Biswas","year":"2023","journal-title":"Journal of Neuroimmunology"},{"key":"bib21","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1126\/science.abj8222","type":"journal-article","article-title":"Longitudinal analysis reveals high prevalence of Epstein-Barr virus associated with multiple sclerosis","volume":"375","author":"Bjornevik","year":"2022","journal-title":"Science"},{"key":"bib22","doi-asserted-by":"publisher","first-page":"622","DOI":"10.1021\/acs.estlett.3c00385","type":"journal-article","article-title":"More than a Tripledemic: Influenza A virus, respiratory syncytial virus, SARS-CoV-2, and human metapneumovirus in wastewater during winter 2022-2023","volume":"10","author":"Boehm","year":"2023","journal-title":"Environmental Science & Technology Letters"},{"key":"bib23","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-26239-2","type":"journal-article","article-title":"Preclinical characterization of an intravenous coronavirus 3CL protease inhibitor for the potential treatment of COVID19","volume":"12","author":"Boras","year":"2021","journal-title":"Nature Communications"},{"key":"bib24","doi-asserted-by":"publisher","first-page":"1433","DOI":"10.1097\/QAD.0b013e32835f6b0c","type":"journal-article","article-title":"Predicting risk of cancer during HIV infection: the role of inflammatory and coagulation biomarkers","volume":"27","author":"Borges","year":"2013","journal-title":"AIDS"},{"key":"bib25","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1017\/ice.2020.1360","type":"journal-article","article-title":"Change in hospital antibiotic use and acquisition of multidrug-resistant gram-negative organisms after the onset of coronavirus disease 2019","volume":"42","author":"Bork","year":"2021","journal-title":"Infection Control and Hospital Epidemiology"},{"key":"bib26","doi-asserted-by":"publisher","first-page":"e2005","DOI":"10.1093\/cid\/ciaa1198","type":"journal-article","article-title":"Risk Factors for Coronavirus Disease 2019 (COVID-19) death in a population cohort study from the western cape province, South Africa","volume":"73","author":"Boulle","year":"2021","journal-title":"Clinical Infectious Diseases"},{"key":"bib27","doi-asserted-by":"publisher","first-page":"44","DOI":"10.1016\/j.ijregi.2022.02.008","type":"journal-article","article-title":"Secondary infections modify the overall course of hospitalized patients with COVID-19: a retrospective study from a network of hospitals across North India","volume":"3","author":"Budhiraja","year":"2022","journal-title":"IJID Regions"},{"key":"bib28","doi-asserted-by":"publisher","DOI":"10.1016\/j.xcrm.2021.100229","type":"journal-article","article-title":"Bacterial pulmonary superinfections are associated with longer duration of ventilation in critically ill COVID-19 patients","volume":"2","author":"Buehler","year":"2021","journal-title":"Cell Reports. Medicine"},{"key":"bib29","doi-asserted-by":"publisher","first-page":"1824","DOI":"10.1111\/liv.14804","type":"journal-article","article-title":"Mortality is not increased in SARS-CoV-2 infected persons with hepatitis C virus infection","volume":"41","author":"Butt","year":"2021","journal-title":"Liver International"},{"key":"bib30","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1016\/j.cmi.2020.08.012","type":"journal-article","article-title":"Co-infection with other respiratory pathogens in COVID-19 patients","volume":"27","author":"Calcagno","year":"2021","journal-title":"Clinical Microbiology and Infection"},{"key":"bib31","doi-asserted-by":"publisher","DOI":"10.1016\/j.socscimed.2020.113426","type":"journal-article","article-title":"How and why patients made long covid","volume":"268","author":"Callard","year":"2021","journal-title":"Social Science & Medicine"},{"key":"bib32","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1146\/annurev-immunol-083122-043054","type":"journal-article","article-title":"SARS-CoV-2: The interplay between evolution and host immunity","volume":"43","author":"Case","year":"2025","journal-title":"Annual Review of Immunology"},{"key":"bib33","doi-asserted-by":"publisher","first-page":"1473","DOI":"10.1080\/07853890.2022.2076901","type":"journal-article","article-title":"Pathophysiology and mechanism of long COVID: a comprehensive review","volume":"54","author":"Castanares-Zapatero","year":"2022","journal-title":"Annals of Medicine"},{"key":"bib34","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-022-07743-2","type":"journal-article","article-title":"Secondary respiratory early and late infections in mechanically ventilated patients with COVID-19","volume":"22","author":"Ceballos","year":"2022","journal-title":"BMC Infectious Diseases"},{"key":"bib35","doi-asserted-by":"publisher","first-page":"6463","DOI":"10.2147\/IDR.S424061","type":"journal-article","article-title":"Secondary infection surveillance with metagenomic next-generation sequencing in COVID-19 patients: a cross-sectional study","volume":"16","author":"Chen","year":"2023","journal-title":"Infection and Drug Resistance"},{"key":"bib36","doi-asserted-by":"publisher","DOI":"10.1172\/JCI174439","type":"journal-article","article-title":"Evolution of nasal and olfactory infection characteristics of SARS-CoV-2 variants","volume":"134","author":"Chen","year":"2024","journal-title":"The Journal of Clinical Investigation"},{"key":"bib37","doi-asserted-by":"publisher","DOI":"10.1177\/2049936120978095","type":"journal-article","article-title":"Bacterial co-infections and antibiotic prescribing practice in adults with COVID-19: experience from a single hospital cluster","volume":"7","author":"Cheng","year":"2020","journal-title":"Therapeutic Advances in Infectious Disease"},{"key":"bib38","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1136\/gutjnl-2021-324280","type":"journal-article","article-title":"Residual SARS-CoV-2 viral antigens detected in GI and hepatic tissues from five recovered patients with COVID-19","volume":"71","author":"Cheung","year":"2022","journal-title":"Gut"},{"key":"bib39","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/s41579-022-00807-9","type":"journal-article","article-title":"The effects of the COVID-19 pandemic on community respiratory virus activity","volume":"21","author":"Chow","year":"2023","journal-title":"Nature Reviews. Microbiology"},{"key":"bib40","doi-asserted-by":"publisher","DOI":"10.1242\/dmm.052086","type":"journal-article","article-title":"Translating animal models of SARS-CoV-2 infection to vascular, neurological and gastrointestinal manifestations of COVID-19","volume":"18","author":"Chung","year":"2025","journal-title":"Disease Models & Mechanisms"},{"key":"bib41","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.00655-2019","type":"journal-article","article-title":"The global prevalence of latent tuberculosis: a systematic review and meta-analysis","volume":"54","author":"Cohen","year":"2019","journal-title":"The European Respiratory Journal"},{"key":"bib42","doi-asserted-by":"publisher","DOI":"10.3390\/antibiotics11080991","type":"journal-article","article-title":"Antibiotic use and bacterial infection in COVID-19 patients in the second phase of the SARS-CoV-2 Pandemic: A scoping review","volume":"11","author":"Cong","year":"2022","journal-title":"Antibiotics"},{"key":"bib43","doi-asserted-by":"publisher","first-page":"567","DOI":"10.1038\/s41586-020-2622-0","type":"journal-article","article-title":"SARS-CoV-2 mRNA vaccine design enabled by prototype pathogen preparedness","volume":"586","author":"Corbett","year":"2020","journal-title":"Nature"},{"key":"bib44","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1016\/S1470-2045(23)00056-6","type":"journal-article","article-title":"SARS-CoV-2 omicron (B.1.1.529)-related COVID-19 sequelae in vaccinated and unvaccinated patients with cancer: results from the OnCovid registry","volume":"24","author":"Cortellini","year":"2023","journal-title":"The Lancet. Oncology"},{"key":"bib45","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1038\/s41579-018-0118-9","type":"journal-article","article-title":"Origin and evolution of pathogenic coronaviruses","volume":"17","author":"Cui","year":"2019","journal-title":"Nature Reviews. Microbiology"},{"key":"bib46","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2025.1521029","type":"journal-article","article-title":"Animal models of post-acute COVID-19 syndrome: a call for longitudinal animal studies","volume":"16","author":"Dai","year":"2025","journal-title":"Frontiers in Immunology"},{"key":"bib47","doi-asserted-by":"publisher","first-page":"3652","DOI":"10.1016\/j.cell.2022.08.026","type":"journal-article","article-title":"Epstein-Barr virus: Biology and clinical disease","volume":"185","author":"Damania","year":"2022","journal-title":"Cell"},{"key":"bib48","doi-asserted-by":"publisher","first-page":"133","DOI":"10.1038\/s41579-022-00846-2","type":"journal-article","article-title":"Long COVID: major findings, mechanisms and recommendations","volume":"21","author":"Davis","year":"2023","journal-title":"Nature Reviews. Microbiology"},{"key":"bib49","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.60361","type":"journal-article","article-title":"Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage","volume":"10","author":"Deinhardt-Emmer","year":"2021","journal-title":"eLife"},{"key":"bib50","doi-asserted-by":"publisher","DOI":"10.1186\/s13045-022-01329-w","type":"journal-article","article-title":"Evidence of SARS-CoV-2 spike protein on retrieved thrombi from COVID-19 patients","volume":"15","author":"De Michele","year":"2022","journal-title":"Journal of Hematology & Oncology"},{"key":"bib51","doi-asserted-by":"publisher","first-page":"4","DOI":"10.1016\/j.jiph.2022.11.024","type":"journal-article","article-title":"Global emerging Omicron variant of SARS-CoV-2: Impacts, challenges and strategies","volume":"16","author":"Dhama","year":"2023","journal-title":"Journal of Infection and Public Health"},{"key":"bib52","doi-asserted-by":"publisher","first-page":"603","DOI":"10.1016\/S2213-2600(22)00092-3","type":"journal-article","article-title":"The intersecting pandemics of tuberculosis and COVID-19: population-level and patient-level impact, clinical presentation, and corrective interventions","volume":"10","author":"Dheda","year":"2022","journal-title":"The Lancet. Respiratory Medicine"},{"key":"bib53","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.abo5070","type":"journal-article","article-title":"SARS-CoV-2 infection produces chronic pulmonary epithelial and immune cell dysfunction with fibrosis in mice","volume":"14","author":"Dinnon","year":"2022","journal-title":"Science Translational Medicine"},{"key":"bib54","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01150-22","type":"journal-article","article-title":"HCV infection increases the expression of ACE2 receptor, leading to enhanced entry of both HCV and SARS-CoV-2 into Hepatocytes and a coinfection state","volume":"10","author":"Domovitz","year":"2022","journal-title":"Microbiology Spectrum"},{"key":"bib55","doi-asserted-by":"publisher","first-page":"3042","DOI":"10.1016\/j.mayocp.2021.09.004","type":"journal-article","article-title":"Decline of influenza and respiratory viruses with COVID-19 public health measures: Alberta, Canada","volume":"96","author":"Doroshenko","year":"2021","journal-title":"Mayo Clinic Proceedings"},{"key":"bib56","doi-asserted-by":"publisher","first-page":"1850","DOI":"10.1002\/jmv.26549","type":"journal-article","article-title":"Human herpesvirus-6, -7, and Epstein-Barr virus reactivation in pityriasis rosea during COVID-19","volume":"93","author":"Drago","year":"2021","journal-title":"Journal of Medical Virology"},{"key":"bib57","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1016\/j.pulmoe.2021.02.002","type":"journal-article","article-title":"Different disease, same challenges: Social determinants of tuberculosis and COVID-19","volume":"27","author":"Duarte","year":"2021","journal-title":"Pulmonology"},{"key":"bib58","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1016\/j.jcv.2018.03.001","type":"journal-article","article-title":"Primary Epstein-Barr virus infection","volume":"102","author":"Dunmire","year":"2018","journal-title":"Journal of Clinical Virology"},{"key":"bib59","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.157053","type":"journal-article","article-title":"Role of antibodies, inflammatory markers, and echocardiographic findings in postacute cardiopulmonary symptoms after SARS-CoV-2 infection","volume":"7","author":"Durstenfeld","year":"2022","journal-title":"JCI Insight"},{"key":"bib60","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.q1348","type":"journal-article","article-title":"Analysis reveals global post-covid surge in infectious diseases","volume":"385","author":"Feinmann","year":"2024","journal-title":"BMJ"},{"key":"bib61","doi-asserted-by":"publisher","DOI":"10.1186\/s41479-021-00083-w","type":"journal-article","article-title":"The role of co-infections and secondary infections in patients with COVID-19","volume":"13","author":"Feldman","year":"2021","journal-title":"Pneumonia"},{"key":"bib62","doi-asserted-by":"publisher","first-page":"S788","DOI":"10.1093\/ofid\/ofab466.1601","type":"journal-article","article-title":"1409. Pulmonary Non-tuberculous Mycobacterium Infection (PNTMI) and COVID-19: Characterization of the National COVID Collaborative Cohort (N3C)","volume":"8","author":"Figueroa Castro","year":"2021","journal-title":"Open Forum Infectious Diseases"},{"key":"bib63","doi-asserted-by":"publisher","first-page":"4682","DOI":"10.1016\/j.cell.2022.10.025","type":"journal-article","article-title":"Immune cell interactions in tuberculosis","volume":"185","author":"Flynn","year":"2022","journal-title":"Cell"},{"key":"bib64","doi-asserted-by":"publisher","first-page":"e825","DOI":"10.1016\/S2542-5196(22)00174-7","type":"journal-article","article-title":"Interactions between climate and COVID-19","volume":"6","author":"Ford","year":"2022","journal-title":"The Lancet. Planetary Health"},{"key":"bib65","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1016\/j.molmed.2023.01.003","type":"journal-article","article-title":"Upper respiratory tract mucosal immunity for SARS-CoV-2 vaccines","volume":"29","author":"Fraser","year":"2023","journal-title":"Trends in Molecular Medicine"},{"key":"bib66","doi-asserted-by":"publisher","DOI":"10.1136\/bcr-2021-247562","type":"journal-article","article-title":"Reactivation of latent tuberculosis in a COVID-19 patient on corticosteroid treatment","volume":"15","author":"Friedman","year":"2022","journal-title":"BMJ Case Reports"},{"key":"bib67","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aaa2293","type":"journal-article","article-title":"Cytomegalovirus infection enhances the immune response to influenza","volume":"7","author":"Furman","year":"2015","journal-title":"Science Translational Medicine"},{"key":"bib68","doi-asserted-by":"publisher","DOI":"10.1002\/iid3.1343","type":"journal-article","article-title":"Post-COVID pulmonary injury in K18-hACE2 mice shows persistent neutrophils and neutrophil extracellular trap formation","volume":"12","author":"Giannakopoulos","year":"2024","journal-title":"Immunity, Inflammation and Disease"},{"key":"bib69","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.160989","type":"journal-article","article-title":"Markers of fungal translocation are elevated during post-acute sequelae of SARS-CoV-2 and induce NF-\u03baB signaling","volume":"7","author":"Giron","year":"2022","journal-title":"JCI Insight"},{"key":"bib70","doi-asserted-by":"publisher","DOI":"10.3390\/pathogens10060763","type":"journal-article","article-title":"Investigation of long COVID prevalence and its relationship to Epstein-Barr virus reactivation","volume":"10","author":"Gold","year":"2021","journal-title":"Pathogens"},{"key":"bib71","doi-asserted-by":"publisher","DOI":"10.1186\/s13054-021-03672-9","type":"journal-article","article-title":"Secondary infections in critically ill patients with COVID-19","volume":"25","author":"Grasselli","year":"2021","journal-title":"Critical Care"},{"key":"bib72","doi-asserted-by":"publisher","first-page":"454","DOI":"10.1016\/j.chest.2021.04.002","type":"journal-article","article-title":"Hospital-acquired infections in critically Ill patients with COVID-19","volume":"160","author":"Grasselli","year":"2021","journal-title":"Chest"},{"key":"bib73","doi-asserted-by":"publisher","DOI":"10.1042\/BSR20210611","type":"journal-article","article-title":"SARS-CoV-2 spike protein S1 induces fibrin(ogen) resistant to fibrinolysis: implications for microclot formation in COVID-19","volume":"41","author":"Grobbelaar","year":"2021","journal-title":"Bioscience Reports"},{"key":"bib74","doi-asserted-by":"publisher","DOI":"10.1183\/13993003.02538-2021","type":"journal-article","article-title":"Tuberculosis and COVID-19 co-infection: description of the global cohort","volume":"59","author":"Group","year":"2022","journal-title":"European Respiratory Journal"},{"key":"bib75","doi-asserted-by":"publisher","first-page":"7892","DOI":"10.1016\/j.vaccine.2020.10.064","type":"journal-article","article-title":"NVX-CoV2373 vaccine protects cynomolgus macaque upper and lower airways against SARS-CoV-2 challenge","volume":"38","author":"Guebre-Xabier","year":"2020","journal-title":"Vaccine"},{"key":"bib76","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.oraloncology.2019.04.024","type":"journal-article","article-title":"Intermittent abortive reactivation of Epstein-Barr virus during the progression of nasopharyngeal cancer as indicated by elevated antibody levels","volume":"93","author":"Guo","year":"2019","journal-title":"Oral Oncology"},{"key":"bib77","doi-asserted-by":"publisher","first-page":"3904","DOI":"10.1016\/j.csbj.2023.08.002","type":"journal-article","article-title":"The microbiome in post-acute infection syndrome (PAIS)","volume":"21","author":"Guo","year":"2023","journal-title":"Computational and Structural Biotechnology Journal"},{"key":"bib78","doi-asserted-by":"publisher","first-page":"783","DOI":"10.1038\/nri1706","type":"journal-article","article-title":"Perils at mucosal front lines for HIV and SIV and their hosts","volume":"5","author":"Haase","year":"2005","journal-title":"Nature Reviews. Immunology"},{"key":"bib79","doi-asserted-by":"publisher","first-page":"631","DOI":"10.1002\/path.1570","type":"journal-article","article-title":"Tissue distribution of ACE2 protein, the functional receptor for SARS coronavirus: a first step in understanding SARS pathogenesis","volume":"203","author":"Hamming","year":"2004","journal-title":"The Journal of Pathology"},{"key":"bib80","doi-asserted-by":"publisher","first-page":"1010","DOI":"10.1126\/science.abd0827","type":"journal-article","article-title":"Studies in humanized mice and convalescent humans yield a SARS-CoV-2 antibody cocktail","volume":"369","author":"Hansen","year":"2020","journal-title":"Science"},{"key":"bib81","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1038\/s41588-018-0102-3","type":"journal-article","article-title":"Transcription factors operate across disease loci, with EBNA2 implicated in autoimmunity","volume":"50","author":"Harley","year":"2018","journal-title":"Nature Genetics"},{"key":"bib82","doi-asserted-by":"publisher","first-page":"245","DOI":"10.3934\/microbiol.2023015","type":"journal-article","article-title":"SARS-CoV-2 infection and immune responses","volume":"9","author":"Harne","year":"2023","journal-title":"AIMS Microbiology"},{"key":"bib83","doi-asserted-by":"publisher","first-page":"3467","DOI":"10.1016\/j.cell.2021.05.040","type":"journal-article","article-title":"Low-dose Ad26.COV2.S protection against SARS-CoV-2 challenge in rhesus macaques","volume":"184","author":"He","year":"2021","journal-title":"Cell"},{"key":"bib84","doi-asserted-by":"publisher","first-page":"825","DOI":"10.1097\/CCM.0000000000005462","type":"journal-article","article-title":"Ventilator-associated lower respiratory tract bacterial infections in COVID-19 compared with non-COVID-19 patients","volume":"50","author":"Hedberg","year":"2022","journal-title":"Critical Care Medicine"},{"key":"bib85","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.adf6598","type":"journal-article","article-title":"Humoral immunity to an endemic coronavirus is associated with postacute sequelae of COVID-19 in individuals with rheumatic diseases","volume":"15","author":"Herman","year":"2023","journal-title":"Science Translational Medicine"},{"key":"bib86","doi-asserted-by":"publisher","first-page":"555","DOI":"10.1038\/s41586-023-05948-2","type":"journal-article","article-title":"Adeno-associated virus 2 infection in children with non-A-E hepatitis","volume":"617","author":"Ho","year":"2023","journal-title":"Nature"},{"key":"bib87","doi-asserted-by":"publisher","first-page":"e543","DOI":"10.1016\/S2666-5247(21)00237-8","type":"journal-article","article-title":"The emergence of COVID-19 associated mucormycosis: a review of cases from 18 countries","volume":"3","author":"Hoenigl","year":"2022","journal-title":"The Lancet. Microbe"},{"key":"bib88","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1016\/j.cell.2020.02.052","type":"journal-article","article-title":"SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor","volume":"181","author":"Hoffmann","year":"2020","journal-title":"Cell"},{"key":"bib89","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1016\/j.cell.2020.05.042","type":"journal-article","article-title":"SARS-CoV-2 reverse genetics reveals a variable infection gradient in the respiratory tract","volume":"182","author":"Hou","year":"2020","journal-title":"Cell"},{"key":"bib90","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2020.587078","type":"journal-article","article-title":"Epstein-Barr virus and systemic autoimmune diseases","volume":"11","author":"Houen","year":"2020","journal-title":"Frontiers in Immunology"},{"key":"bib91","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1038\/s41590-023-01661-4","type":"journal-article","article-title":"SARS-CoV-2 viral persistence in lung alveolar macrophages is controlled by IFN-\u03b3 and NK cells","volume":"24","author":"Huot","year":"2023","journal-title":"Nature Immunology"},{"key":"bib92","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1038\/s41580-021-00418-x","type":"journal-article","article-title":"Mechanisms of SARS-CoV-2 entry into cells","volume":"23","author":"Jackson","year":"2022","journal-title":"Nature Reviews. Molecular Cell Biology"},{"key":"bib93","doi-asserted-by":"publisher","first-page":"10","DOI":"10.3390\/life12030357","type":"journal-article","article-title":"Pulmonary complications following COVID-19 infection","volume":"28","author":"Jakubec","year":"2022","journal-title":"Klinicka Mikrobiologie a Infekcni Lekarstvi"},{"key":"bib94","doi-asserted-by":"publisher","first-page":"2892","DOI":"10.3201\/eid2711.211174","type":"journal-article","article-title":"Multinational observational cohort study of COVID-19\u2013Associated Pulmonary Aspergillosis1","volume":"27","author":"Janssen","year":"2021","journal-title":"Emerging Infectious Diseases"},{"key":"bib95","doi-asserted-by":"publisher","DOI":"10.1016\/j.envres.2020.109819","type":"journal-article","article-title":"Transmission of COVID-19 virus by droplets and aerosols: A critical review on the unresolved dichotomy","volume":"188","author":"Jayaweera","year":"2020","journal-title":"Environmental Research"},{"key":"bib96","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00029-17","type":"journal-article","article-title":"Candida auris: a review of the literature","volume":"31","author":"Jeffery-Smith","year":"2018","journal-title":"Clinical Microbiology Reviews"},{"key":"bib97","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1038\/s41579-020-0331-1","type":"journal-article","article-title":"Non-tuberculous mycobacteria and the rise of Mycobacterium abscessus","volume":"18","author":"Johansen","year":"2020","journal-title":"Nature Reviews. Microbiology"},{"key":"bib98","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adp2636","type":"journal-article","article-title":"CD4(+) and CD8(+) T cells are required to prevent SARS-CoV-2 persistence in the nasal compartment","volume":"10","author":"Kar","year":"2024","journal-title":"Science Advances"},{"key":"bib99","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofaa578","type":"journal-article","article-title":"Prevalence of co-infection at the time of hospital admission in COVID-19 patients, a multicenter study","volume":"8","author":"Karaba","year":"2021","journal-title":"Open Forum Infectious Diseases"},{"key":"bib100","doi-asserted-by":"publisher","first-page":"102","DOI":"10.1080\/23744235.2020.1839672","type":"journal-article","article-title":"Few bacterial co-infections but frequent empiric antibiotic use in the early phase of hospitalized patients with COVID-19: results from a multicentre retrospective cohort study in The Netherlands","volume":"53","author":"Karami","year":"2021","journal-title":"Infectious Diseases"},{"key":"bib101","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1010738","type":"journal-article","article-title":"Evolution of functional antibodies following acute Epstein-Barr virus infection","volume":"18","author":"Karsten","year":"2022","journal-title":"PLOS Pathogens"},{"key":"bib102","doi-asserted-by":"publisher","first-page":"3055","DOI":"10.1080\/21645515.2020.1796425","type":"journal-article","article-title":"Role of antibody-dependent enhancement (ADE) in the virulence of SARS-CoV-2 and its mitigation strategies for the development of vaccines and immunotherapies to counter COVID-19","volume":"16","author":"Karthik","year":"2020","journal-title":"Human Vaccines & Immunotherapeutics"},{"key":"bib103","doi-asserted-by":"publisher","first-page":"929","DOI":"10.1126\/science.aan6836","type":"journal-article","article-title":"Antibody-dependent enhancement of severe dengue disease in humans","volume":"358","author":"Katzelnick","year":"2017","journal-title":"Science"},{"key":"bib104","doi-asserted-by":"publisher","first-page":"5932","DOI":"10.1016\/j.cell.2021.10.027","type":"journal-article","article-title":"Visualizing in deceased COVID-19 patients how SARS-CoV-2 attacks the respiratory and olfactory mucosae but spares the olfactory bulb","volume":"184","author":"Khan","year":"2021","journal-title":"Cell"},{"key":"bib105","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1093\/jimmun\/vkaf006","type":"journal-article","article-title":"A genetically modulated Toll-like receptor-tolerant phenotype in peripheral blood cells of children with multisystem inflammatory syndrome","volume":"214","author":"Khan","year":"2025","journal-title":"Journal of Immunology"},{"key":"bib106","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofab339","type":"journal-article","article-title":"Hospital-Acquired bloodstream infections in patients hospitalized with severe acute respiratory syndrome coronavirus 2 infection (Coronavirus Disease 2019): Association with immunosuppressive therapies","volume":"8","author":"Khatri","year":"2021","journal-title":"Open Forum Infectious Diseases"},{"key":"bib107","doi-asserted-by":"publisher","DOI":"10.1016\/j.rmcr.2021.101344","type":"journal-article","article-title":"COVID-19 promoting the development of active tuberculosis in a patient with latent tuberculosis infection: A case report","volume":"32","author":"Khayat","year":"2021","journal-title":"Respiratory Medicine Case Reports"},{"key":"bib108","doi-asserted-by":"publisher","DOI":"10.3346\/jkms.2022.37.e250","type":"journal-article","article-title":"The higher incidence of COVID-19 in patients with non-tuberculous mycobacterial pulmonary disease: a single center experience in Korea","volume":"37","author":"Kim","year":"2022","journal-title":"Journal of Korean Medical Science"},{"key":"bib109","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1038\/s41586-023-06651-y","type":"journal-article","article-title":"Distinguishing features of long COVID identified through immune profiling","volume":"623","author":"Klein","year":"2023","journal-title":"Nature"},{"key":"bib110","doi-asserted-by":"publisher","first-page":"528","DOI":"10.1111\/myc.13096","type":"journal-article","article-title":"COVID-19 associated pulmonary aspergillosis","volume":"63","author":"Koehler","year":"2020","journal-title":"Mycoses"},{"key":"bib111","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofaa484","type":"journal-article","article-title":"Assessment of respiratory bacterial coinfections among severe acute respiratory syndrome Coronavirus 2-Positive patients hospitalized in intensive care units using conventional culture and bioFire, filmarray pneumonia panel plus assay","volume":"7","author":"Kolenda","year":"2020","journal-title":"Open Forum Infectious Diseases"},{"key":"bib112","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2023.1270414","type":"journal-article","article-title":"A phosphodiesterase-4 inhibitor reduces lung inflammation and fibrosis in a hamster model of SARS-CoV-2 infection","volume":"14","author":"Kolloli","year":"2023","journal-title":"Frontiers in Immunology"},{"key":"bib113","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1136\/thoraxjnl-2014-206291","type":"journal-article","article-title":"The clinical spectrum of pulmonary aspergillosis","volume":"70","author":"Kosmidis","year":"2015","journal-title":"Thorax"},{"key":"bib114","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pmed.0050203","type":"journal-article","article-title":"Inflammatory and coagulation biomarkers and mortality in patients with HIV infection","volume":"5","author":"Kuller","year":"2008","journal-title":"PLOS Medicine"},{"key":"bib115","doi-asserted-by":"publisher","first-page":"270","DOI":"10.1038\/s41579-022-00713-0","type":"journal-article","article-title":"SARS-CoV-2 pathogenesis","volume":"20","author":"Lamers","year":"2022","journal-title":"Nature Reviews. Microbiology"},{"key":"bib116","doi-asserted-by":"publisher","first-page":"1622","DOI":"10.1016\/j.cmi.2020.07.016","type":"journal-article","article-title":"Bacterial co-infection and secondary infection in patients with COVID-19: a living rapid review and meta-analysis","volume":"26","author":"Langford","year":"2020","journal-title":"Clinical Microbiology and Infection"},{"key":"bib117","doi-asserted-by":"publisher","first-page":"1374","DOI":"10.1093\/cid\/civ584","type":"journal-article","article-title":"Poor positive predictive value of lyme disease serologic testing in an area of low disease incidence","volume":"61","author":"Lantos","year":"2015","journal-title":"Clinical Infectious Diseases"},{"key":"bib118","doi-asserted-by":"publisher","first-page":"446","DOI":"10.3390\/idr14030048","type":"journal-article","article-title":"A rare case of latent tuberculosis reactivation secondary to a COVID-19 infection","volume":"14","author":"Leonso","year":"2022","journal-title":"Infectious Disease Reports"},{"key":"bib119","doi-asserted-by":"crossref","DOI":"10.1128\/9781555817947.ch19","type":"book-chapter","article-title":"Virus-induced immunosuppression","volume-title":"Polymicrobial Diseases","author":"Libbey","year":"2002"},{"key":"bib120","doi-asserted-by":"publisher","DOI":"10.1128\/jvi.00905-24","type":"journal-article","article-title":"Efficacy of late-onset antiviral treatment in immunocompromised hosts with persistent SARS-CoV-2 infection","volume":"98","author":"Lieber","year":"2024","journal-title":"Journal of Virology"},{"key":"bib121","type":"book-chapter","article-title":"Chronic fatigue syndrome","volume-title":"Endotext","author":"Lim","year":"2000"},{"key":"bib122","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1001\/jama.2017.10569","type":"journal-article","article-title":"Effect of Ganciclovir on IL-6 levels among cytomegalovirus-seropositive adults with critical illness: a randomized clinical trial","volume":"318","author":"Limaye","year":"2017","journal-title":"JAMA"},{"key":"bib123","doi-asserted-by":"publisher","first-page":"2957","DOI":"10.2147\/IJGM.S343940","type":"journal-article","article-title":"Decreased incidence of influenza during the COVID-19 Pandemic","volume":"15","author":"Lu","year":"2022","journal-title":"International Journal of General Medicine"},{"key":"bib124","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1192832","type":"journal-article","article-title":"Viable SARS-CoV-2 Omicron sub-variants isolated from autopsy tissues","volume":"14","author":"Maffia-Bizzozero","year":"2023","journal-title":"Frontiers in Microbiology"},{"key":"bib125","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgph.0003043","type":"journal-article","article-title":"The global impact of COVID-19 on tuberculosis: a thematic scoping review, 2020-2023","volume":"4","author":"Marco","year":"2024","journal-title":"PLOS Global Public Health"},{"key":"bib126","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1038\/s41575-021-00426-4","type":"journal-article","article-title":"COVID-19 and liver disease: mechanistic and clinical perspectives","volume":"18","author":"Marjot","year":"2021","journal-title":"Nature Reviews. Gastroenterology & Hepatology"},{"key":"bib127","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1016\/j.idc.2022.04.004","type":"journal-article","article-title":"Persistent symptoms after treatment of lyme disease","volume":"36","author":"Marques","year":"2022","journal-title":"Infectious Disease Clinics of North America"},{"key":"bib128","doi-asserted-by":"publisher","DOI":"10.1016\/j.jctube.2021.100257","type":"journal-article","article-title":"Reactivation of Mycobacterium simiae after the recovery of COVID-19 infection","volume":"24","author":"Masoumi","year":"2021","journal-title":"Journal of Clinical Tuberculosis and Other Mycobacterial Diseases"},{"key":"bib129","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1126\/science.abd3871","type":"journal-article","article-title":"Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans","volume":"370","author":"Mateus","year":"2020","journal-title":"Science"},{"key":"bib130","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1080\/13550280801995445","type":"journal-article","article-title":"The relationship between encephalitis lethargica and influenza: a critical analysis","volume":"14","author":"McCall","year":"2008","journal-title":"Journal of Neurovirology"},{"key":"bib131","doi-asserted-by":"publisher","first-page":"194","DOI":"10.1038\/s41590-021-01104-y","type":"journal-article","article-title":"Pathological sequelae of long-haul COVID","volume":"23","author":"Mehandru","year":"2022","journal-title":"Nature Immunology"},{"key":"bib132","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1007\/978-3-319-22834-1_10","type":"journal-article","article-title":"Epstein-Barr virus-specific humoral immune responses in health and disease","volume":"391","author":"Middeldorp","year":"2015","journal-title":"Current Topics in Microbiology and Immunology"},{"key":"bib133","doi-asserted-by":"publisher","first-page":"599","DOI":"10.1126\/science.aay6485","type":"journal-article","article-title":"Measles virus infection diminishes preexisting antibodies that offer protection from other pathogens","volume":"366","author":"Mina","year":"2019","journal-title":"Science"},{"key":"bib134","doi-asserted-by":"publisher","first-page":"684","DOI":"10.1016\/j.neubiorev.2014.10.024","type":"journal-article","article-title":"A systematic review of fatigue in patients with traumatic brain injury: the course, predictors and consequences","volume":"47","author":"Mollayeva","year":"2014","journal-title":"Neuroscience and Biobehavioral Reviews"},{"key":"bib135","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1016\/j.ijid.2022.03.003","type":"journal-article","article-title":"Bacterial co-infection at hospital admission in patients with COVID-19","volume":"118","author":"Moreno-Garc\u00eda","year":"2022","journal-title":"International Journal of Infectious Diseases"},{"key":"bib136","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.1007\/s10238-022-00959-1","type":"journal-article","article-title":"The impact of the secondary infections in ICU patients affected by COVID-19 during three different phases of the SARS-CoV-2 pandemic","volume":"23","author":"Murgia","year":"2023","journal-title":"Clinical and Experimental Medicine"},{"key":"bib137","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0251170","type":"journal-article","article-title":"Prevalence and outcomes of co-infection and superinfection with SARS-CoV-2 and other pathogens: A systematic review and meta-analysis","volume":"16","author":"Musuuza","year":"2021","journal-title":"PLOS ONE"},{"key":"bib138","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1038\/s41586-024-07926-8","type":"journal-article","article-title":"An aberrant immune-epithelial progenitor niche drives viral lung sequelae","volume":"634","author":"Narasimhan","year":"2024","journal-title":"Nature"},{"key":"bib139","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1590\/1806-9282.66.8.1027","type":"journal-article","article-title":"Coinfection of SARS-CoV-2 and Measles morbillivirus in a front-line health worker in Rio de Janeiro, Brasil","volume":"66","author":"Nascimento","year":"2020","journal-title":"Revista Da Associacao Medica Brasileira"},{"key":"bib140","doi-asserted-by":"publisher","DOI":"10.3390\/vaccines11020412","type":"journal-article","article-title":"Trends in hospitalization and mortality for influenza and other respiratory viruses during the COVID-19 Pandemic in the United States","volume":"11","author":"Nasrullah","year":"2023","journal-title":"Vaccines"},{"key":"bib141","doi-asserted-by":"publisher","first-page":"371","DOI":"10.1016\/j.medj.2022.04.001","type":"journal-article","article-title":"Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection","volume":"3","author":"Natarajan","year":"2022","journal-title":"Med"},{"key":"bib142","doi-asserted-by":"publisher","first-page":"1","DOI":"10.17226\/27756","type":"book-chapter","article-title":"Board on health care services; committee on the long-term health effects stemming from COVID-19 and implications for the social security administration. 2024","volume-title":"Long-Term Health Effects of COVID-19: Disability and Function Following SARS-CoV-2 Infection","author":"National Academies of Sciences E, and Medicine","year":"2024"},{"key":"bib143","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1089\/vim.2022.0204","type":"journal-article","article-title":"Immunity debt, a gap in learning, or immune dysfunction?","volume":"36","author":"Needle","year":"2023","journal-title":"Viral Immunology"},{"key":"bib144","doi-asserted-by":"publisher","first-page":"890","DOI":"10.1016\/j.chom.2023.05.004","type":"journal-article","article-title":"The role of trained immunity in COVID-19: Lessons for the next pandemic","volume":"31","author":"Netea","year":"2023","journal-title":"Cell Host & Microbe"},{"key":"bib145","doi-asserted-by":"publisher","first-page":"S100","DOI":"10.1093\/infdis\/jiu147","type":"journal-article","article-title":"Biological differences between the sexes and susceptibility to tuberculosis","volume":"209 Suppl 3","author":"Nhamoyebonde","year":"2014","journal-title":"The Journal of Infectious Diseases"},{"key":"bib146","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2022.103852","type":"journal-article","article-title":"Primary immune responses are negatively impacted by persistent herpesvirus infections in older people: results from an observational study on healthy subjects and a vaccination trial on subjects aged more than 70 years old","volume":"76","author":"Nicoli","year":"2022","journal-title":"EBioMedicine"},{"key":"bib147","doi-asserted-by":"publisher","DOI":"10.1161\/JAHA.114.000844","type":"journal-article","article-title":"Severity of cardiovascular disease outcomes among patients with HIV is related to markers of inflammation and coagulation","volume":"3","author":"Nordell","year":"2014","journal-title":"Journal of the American Heart Association"},{"key":"bib148","doi-asserted-by":"publisher","first-page":"667","DOI":"10.1002\/jgh3.12811","type":"journal-article","article-title":"Symptomatology and microbiology of the gastrointestinal tract in post-COVID conditions","volume":"6","author":"Norouzi Masir","year":"2022","journal-title":"JGH Open"},{"key":"bib149","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2020.102976","type":"journal-article","article-title":"Heterogeneous expression of the SARS-Coronavirus-2 receptor ACE2 in the human respiratory tract","volume":"60","author":"Ortiz","year":"2020","journal-title":"EBioMedicine"},{"key":"bib150","doi-asserted-by":"publisher","DOI":"10.1186\/s13054-023-04312-0","type":"journal-article","article-title":"COVID-19 bacteremic co-infection is a major risk factor for mortality, ICU admission, and mechanical ventilation","volume":"27","author":"Patton","year":"2023","journal-title":"Critical Care"},{"key":"bib151","doi-asserted-by":"publisher","first-page":"e2845","DOI":"10.1093\/cid\/ciaa1754","type":"journal-article","article-title":"A high percentage of people with Human Immunodeficiency Virus (HIV) on antiretroviral therapy experience detectable low-level plasma HIV-1 RNA following Coronavirus Disease 2019 (COVID-19)","volume":"73","author":"Peluso","year":"2021","journal-title":"Clinical Infectious Diseases"},{"key":"bib152","doi-asserted-by":"publisher","first-page":"1839","DOI":"10.1093\/infdis\/jiab490","type":"journal-article","article-title":"Markers of immune activation and inflammation in individuals with postacute sequelae of severe acute respiratory syndrome coronavirus 2 infection","volume":"224","author":"Peluso","year":"2021","journal-title":"The Journal of Infectious Diseases"},{"key":"bib153","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1016\/j.it.2022.02.008","type":"journal-article","article-title":"Early clues regarding the pathogenesis of long-COVID","volume":"43","author":"Peluso","year":"2022","journal-title":"Trends in Immunology"},{"key":"bib154","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1002\/ana.26350","type":"journal-article","article-title":"SARS-CoV-2 and Mitochondrial proteins in neural-derived exosomes of COVID-19","volume":"91","author":"Peluso","year":"2022","journal-title":"Annals of Neurology"},{"key":"bib155","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofab640","type":"journal-article","article-title":"Persistence, magnitude, and patterns of postacute symptoms and quality of life following onset of sars-cov-2 infection: cohort description and approaches for measurement","volume":"9","author":"Peluso","year":"2022","journal-title":"Open Forum Infectious Diseases"},{"key":"bib156","doi-asserted-by":"publisher","DOI":"10.1212\/NXI.0000000000200003","type":"journal-article","article-title":"Plasma markers of neurologic injury and inflammation in people with self-reported neurologic postacute sequelae of SARS-CoV-2 infection","volume":"9","author":"Peluso","year":"2022","journal-title":"Neurology Neuroimmunology & Neuroinflammation"},{"key":"bib157","doi-asserted-by":"publisher","first-page":"F7","DOI":"10.1097\/QAD.0000000000003338","type":"journal-article","article-title":"Postacute sequelae and adaptive immune responses in people with HIV recovering from SARS-COV-2 infection","volume":"36","author":"Peluso","year":"2022","journal-title":"AIDS"},{"key":"bib158","doi-asserted-by":"publisher","DOI":"10.1172\/JCI163669","type":"journal-article","article-title":"Chronic viral coinfections differentially affect the likelihood of developing long COVID","volume":"133","author":"Peluso","year":"2023","journal-title":"The Journal of Clinical Investigation"},{"key":"bib159","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-023-38382-5","type":"journal-article","article-title":"SARS-CoV-2 spike protein induces lung endothelial cell dysfunction and thrombo-inflammation depending on the C3a\/C3a receptor signalling","volume":"13","author":"Perico","year":"2023","journal-title":"Scientific Reports"},{"key":"bib160","doi-asserted-by":"publisher","first-page":"83","DOI":"10.1093\/cid\/ciab223","type":"journal-article","article-title":"Coronavirus disease 2019-associated pulmonary aspergillosis in mechanically ventilated patients","volume":"74","author":"Permpalung","year":"2022","journal-title":"Clinical Infectious Diseases"},{"key":"bib161","doi-asserted-by":"publisher","first-page":"1015","DOI":"10.1007\/s11357-022-00700-6","type":"journal-article","article-title":"Liver alterations and detection of SARS-CoV-2 RNA and proteins in COVID-19 autopsies","volume":"45","author":"Pesti","year":"2023","journal-title":"GeroScience"},{"key":"bib162","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aay6125","type":"journal-article","article-title":"Incomplete genetic reconstitution of B cell pools contributes to prolonged immunosuppression after measles","volume":"4","author":"Petrova","year":"2019","journal-title":"Science Immunology"},{"key":"bib163","doi-asserted-by":"publisher","first-page":"1184","DOI":"10.1017\/ice.2021.341","type":"journal-article","article-title":"Risk factors and outcomes associated with community-onset and hospital-acquired coinfection in patients hospitalized for coronavirus disease 2019 (COVID-19): A multihospital cohort study","volume":"43","author":"Petty","year":"2022","journal-title":"Infection Control & Hospital Epidemiology"},{"key":"bib164","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1038\/s41590-021-01113-x","type":"journal-article","article-title":"Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection","volume":"23","author":"Phetsouphanh","year":"2022","journal-title":"Nature Immunology"},{"key":"bib165","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1016\/j.cmi.2021.08.014","type":"journal-article","article-title":"Risk factors and outcome of pulmonary aspergillosis in critically ill coronavirus disease 2019 patients-a multinational observational study by the European Confederation of Medical Mycology","volume":"28","author":"Prattes","year":"2022","journal-title":"Clinical Microbiology and Infection"},{"key":"bib166","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2020.107940","type":"journal-article","article-title":"Remdesivir inhibits SARS-CoV-2 in human lung cells and chimeric SARS-CoV expressing the SARS-CoV-2 RNA polymerase in mice","volume":"32","author":"Pruijssers","year":"2020","journal-title":"Cell Reports"},{"key":"bib167","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1002\/glia.20467","type":"journal-article","article-title":"Systemic LPS causes chronic neuroinflammation and progressive neurodegeneration","volume":"55","author":"Qin","year":"2007","journal-title":"Glia"},{"key":"bib168","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2024.1384939","type":"journal-article","article-title":"COVID-19 influenced gut dysbiosis, post-acute sequelae, immune regulation, and therapeutic regimens","volume":"14","author":"Raj","year":"2024","journal-title":"Frontiers in Cellular and Infection Microbiology"},{"key":"bib169","doi-asserted-by":"publisher","DOI":"10.1016\/j.jpeds.2023.113491","type":"journal-article","article-title":"Respiratory syncytial virus, influenza, and coronavirus disease 2019 hospitalizations in children in colorado during the 2021-2022 respiratory virus season","volume":"260","author":"Rao","year":"2023","journal-title":"The Journal of Pediatrics"},{"key":"bib170","doi-asserted-by":"publisher","DOI":"10.1016\/S2213-2600(21)00265-4","type":"journal-article","article-title":"Rising incidence of mucormycosis in patients with COVID-19: another challenge for India amidst the second wave?","volume":"9","author":"Raut","year":"2021","journal-title":"The Lancet. Respiratory Medicine"},{"key":"bib171","doi-asserted-by":"publisher","first-page":"1563","DOI":"10.4103\/ijo.IJO_310_21","type":"journal-article","article-title":"Rise of the phoenix: Mucormycosis in COVID-19 times","volume":"69","author":"Ravani","year":"2021","journal-title":"Indian Journal of Ophthalmology"},{"key":"bib172","doi-asserted-by":"publisher","DOI":"10.1183\/16000617.0077-2017","type":"journal-article","article-title":"Tuberculosis and lung damage: from epidemiology to pathophysiology","volume":"27","author":"Ravimohan","year":"2018","journal-title":"European Respiratory Review"},{"key":"bib173","doi-asserted-by":"publisher","DOI":"10.1172\/JCI149125","type":"journal-article","article-title":"Relationship of SARS-CoV-2-specific CD4 response to COVID-19 severity and impact of HIV-1 and tuberculosis coinfection","volume":"131","author":"Riou","year":"2021","journal-title":"The Journal of Clinical Investigation"},{"key":"bib174","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1016\/j.cmi.2020.10.021","type":"journal-article","article-title":"Secondary infections in patients hospitalized with COVID-19: incidence and predictive factors","volume":"27","author":"Ripa","year":"2021","journal-title":"Clinical Microbiology and Infection"},{"key":"bib175","doi-asserted-by":"publisher","DOI":"10.1093\/ofid\/ofac454","type":"journal-article","article-title":"High risk of secondary infections following thrombotic complications in patients with COVID-19","volume":"9","author":"Ripa","year":"2022","journal-title":"Open Forum Infectious Diseases"},{"key":"bib176","doi-asserted-by":"publisher","DOI":"10.1155\/2021\/8840536","type":"journal-article","article-title":"COVID-19 coinfection with Mycobacterium abscessus in a Patient with Multiple Myeloma","volume":"2021","author":"Rodriguez","year":"2021","journal-title":"Case Reports in Infectious Diseases"},{"key":"bib177","doi-asserted-by":"publisher","first-page":"2112","DOI":"10.1016\/j.chom.2024.11.007","type":"journal-article","article-title":"Persistence of spike protein at the skull-meninges-brain axis may contribute to the neurological sequelae of COVID-19","volume":"32","author":"Rong","year":"2024","journal-title":"Cell Host & Microbe"},{"key":"bib178","doi-asserted-by":"publisher","DOI":"10.4081\/mrm.2021.793","type":"journal-article","article-title":"Dexamethasone therapy and rates of secondary pulmonary and bloodstream infections in critically ill COVID-19 patients","volume":"16","author":"Rothe","year":"2021","journal-title":"Multidisciplinary Respiratory Medicine"},{"key":"bib179","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2023.26608","type":"journal-article","article-title":"From \u201cImmunity Debt\u201d to \u201cImmunity Theft\u201d\u2014How COVID-19 might be tied to recent respiratory disease surges","volume":"331","author":"Rubin","year":"2024","journal-title":"JAMA"},{"key":"bib180","doi-asserted-by":"publisher","first-page":"e354","DOI":"10.1016\/S2666-5247(21)00090-2","type":"journal-article","article-title":"Co-infections, secondary infections, and antimicrobial use in patients hospitalised with COVID-19 during the first pandemic wave from the ISARIC WHO CCP-UK study: a multicentre, prospective cohort study","volume":"2","author":"Russell","year":"2021","journal-title":"The Lancet. Microbe"},{"key":"bib181","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.3201\/eid2704.204895","type":"journal-article","article-title":"COVID-19-associated pulmonary aspergillosis, March-August 2020","volume":"27","author":"Salmanton-Garc\u00eda","year":"2021","journal-title":"Emerging Infectious Diseases"},{"key":"bib182","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1004543","type":"journal-article","article-title":"Initiation of ART during early acute HIV infection preserves mucosal Th17 function and reverses HIV-related immune activation","volume":"10","author":"Schuetz","year":"2014","journal-title":"PLOS Pathogens"},{"key":"bib183","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1093\/cid\/ciab562","type":"journal-article","article-title":"The landscape of candidemia during the coronavirus disease 2019 (COVID-19) Pandemic","volume":"74","author":"Seagle","year":"2022","journal-title":"Clinical Infectious Diseases"},{"key":"bib184","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1093\/cid\/ciab611","type":"journal-article","article-title":"Persistent symptoms in adult patients 1 year after coronavirus disease 2019 (COVID-19): a prospective cohort study","volume":"74","author":"See\u00dfle","year":"2022","journal-title":"Clinical Infectious Diseases"},{"key":"bib185","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00875-20","type":"journal-article","article-title":"Bacteremia and blood culture utilization during COVID-19 Surge in New York City","volume":"58","author":"Sepulveda","year":"2020","journal-title":"Journal of Clinical Microbiology"},{"key":"bib186","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1093\/cid\/ciw683","type":"journal-article","article-title":"Persistent, Albeit Reduced, chronic inflammation in persons starting antiretroviral therapy in acute HIV infection","volume":"64","author":"Sereti","year":"2017","journal-title":"Clinical Infectious Diseases"},{"key":"bib187","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1038\/s41586-023-05949-1","type":"journal-article","article-title":"Adeno-associated virus type 2 in US children with acute severe hepatitis","volume":"617","author":"Servellita","year":"2023","journal-title":"Nature"},{"key":"bib188","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-020-05374-z","type":"journal-article","article-title":"Evaluation of bacterial co-infections of the respiratory tract in COVID-19 patients admitted to ICU","volume":"20","author":"Sharifipour","year":"2020","journal-title":"BMC Infectious Diseases"},{"key":"bib189","doi-asserted-by":"publisher","DOI":"10.1183\/16000617.0264-2021","type":"journal-article","article-title":"COVID-19 and tuberculosis: the double whammy of respiratory pathogens","volume":"31","author":"Shariq","year":"2022","journal-title":"European Respiratory Review"},{"key":"bib190","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1038\/mi.2008.23","type":"journal-article","article-title":"Immune reconstitution in the sigmoid colon after long-term HIV therapy","volume":"1","author":"Sheth","year":"2008","journal-title":"Mucosal Immunology"},{"key":"bib191","doi-asserted-by":"publisher","first-page":"171","DOI":"10.1038\/s41423-023-01104-y","type":"journal-article","article-title":"SARS-CoV-2 and innate immunity: the good, the bad, and the \"goldilocks","volume":"21","author":"Sievers","year":"2024","journal-title":"Cellular & Molecular Immunology"},{"key":"bib192","doi-asserted-by":"publisher","first-page":"4292","DOI":"10.1093\/brain\/awad155","type":"journal-article","article-title":"Neurologic sequelae of COVID-19 are determined by immunologic imprinting from previous coronaviruses","volume":"146","author":"Spatola","year":"2023","journal-title":"Brain"},{"key":"bib193","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.00163-21","type":"journal-article","article-title":"Coinfections with other respiratory pathogens among patients with COVID-19","volume":"9","author":"Sreenath","year":"2021","journal-title":"Microbiology Spectrum"},{"key":"bib194","doi-asserted-by":"publisher","first-page":"758","DOI":"10.1038\/s41586-022-05542-y","type":"journal-article","article-title":"SARS-CoV-2 infection and persistence in the human body and brain at autopsy","volume":"612","author":"Stein","year":"2022","journal-title":"Nature"},{"key":"bib195","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1016\/j.cell.2022.01.014","type":"journal-article","article-title":"Multiple early factors anticipate post-acute COVID-19 sequelae","volume":"185","author":"Su","year":"2022","journal-title":"Cell"},{"key":"bib196","doi-asserted-by":"publisher","first-page":"e487","DOI":"10.1093\/cid\/ciac722","type":"journal-article","article-title":"Persistent circulating severe acute respiratory syndrome coronavirus 2 spike is associated with post-acute coronavirus disease 2019 sequelae","volume":"76","author":"Swank","year":"2023","journal-title":"Clinical Infectious Diseases"},{"key":"bib197","doi-asserted-by":"publisher","first-page":"1599","DOI":"10.1016\/j.cmi.2024.09.001","type":"journal-article","article-title":"Measurement of circulating viral antigens post-SARS-CoV-2 infection in a multicohort study","volume":"30","author":"Swank","year":"2024","journal-title":"Clinical Microbiology and Infection"},{"key":"bib198","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-20202-x","type":"journal-article","article-title":"Correlation between COVID-19 severity and previous exposure of patients to Borrelia spp","volume":"12","author":"Szewczyk-D\u0105browska","year":"2022","journal-title":"Scientific Reports"},{"key":"bib199","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-38682-4","type":"journal-article","article-title":"Persistent serum protein signatures define an inflammatory subcategory of long COVID","volume":"14","author":"Talla","year":"2023","journal-title":"Nature Communications"},{"key":"bib200","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-020-05450-4","type":"journal-article","article-title":"Implications of COVID-19 in high burden countries for HIV\/TB: A systematic review of evidence","volume":"20","author":"Tamuzi","year":"2020","journal-title":"BMC Infectious Diseases"},{"key":"bib201","doi-asserted-by":"publisher","first-page":"1248","DOI":"10.1093\/infdis\/jiu254","type":"journal-article","article-title":"Soluble markers of inflammation and coagulation but not T-cell activation predict non-AIDS-defining morbid events during suppressive antiretroviral treatment","volume":"210","author":"Tenorio","year":"2014","journal-title":"The Journal of Infectious Diseases"},{"key":"bib202","doi-asserted-by":"publisher","first-page":"5547","DOI":"10.1002\/jmv.27986","type":"journal-article","article-title":"Rhinovirus persistence during the COVID-19 pandemic-Impact on pediatric acute wheezing presentations","volume":"94","author":"Teo","year":"2022","journal-title":"Journal of Medical Virology"},{"key":"bib203","doi-asserted-by":"publisher","DOI":"10.7759\/cureus.28309","type":"journal-article","article-title":"A systematic review of neurological manifestations of COVID-19","volume":"14","author":"Thapa Magar","year":"2022","journal-title":"Cureus"},{"key":"bib204","doi-asserted-by":"publisher","first-page":"1934","DOI":"10.1001\/jama.2023.8823","type":"journal-article","article-title":"Development of a definition of postacute sequelae of SARS-CoV-2 infection","volume":"329","author":"Thaweethai","year":"2023","journal-title":"JAMA"},{"key":"bib205","doi-asserted-by":"publisher","DOI":"10.1186\/s12879-021-05902-5","type":"journal-article","article-title":"Community-acquired bacteraemia in COVID-19 in comparison to influenza A and influenza B: a retrospective cohort study","volume":"21","author":"Thelen","year":"2021","journal-title":"BMC Infectious Diseases"},{"key":"bib206","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20653-8","type":"journal-article","article-title":"SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice","volume":"12","author":"Tian","year":"2021","journal-title":"Nature Communications"},{"key":"bib207","doi-asserted-by":"publisher","first-page":"2759","DOI":"10.1152\/physrev.00012.2023","type":"journal-article","article-title":"Mechanisms of SARS-CoV-2-associated anosmia","volume":"103","author":"Tsukahara","year":"2023","journal-title":"Physiological Reviews"},{"key":"bib208","doi-asserted-by":"publisher","DOI":"10.3390\/v17010098","type":"journal-article","article-title":"Animal models of non-respiratory, post-acute sequelae of COVID-19","volume":"17","author":"Vanderheiden","year":"2025","journal-title":"Viruses"},{"key":"bib209","doi-asserted-by":"publisher","first-page":"578","DOI":"10.1038\/s41586-020-2608-y","type":"journal-article","article-title":"ChAdOx1 nCoV-19 vaccine prevents SARS-CoV-2 pneumonia in rhesus macaques","volume":"586","author":"van Doremalen","year":"2020","journal-title":"Nature"},{"key":"bib210","doi-asserted-by":"publisher","first-page":"2137","DOI":"10.1007\/s10096-017-3037-1","type":"journal-article","article-title":"Disagreement between the results from three commercial tests for the detection of Borrelia-specific serum antibodies in the Netherlands associated with antibiotic treatment for Lyme borreliosis: a retrospective study","volume":"36","author":"van Gorkom","year":"2017","journal-title":"European Journal of Clinical Microbiology & Infectious Diseases"},{"key":"bib211","doi-asserted-by":"publisher","first-page":"e533","DOI":"10.1093\/cid\/ciaa1239","type":"journal-article","article-title":"Empiric antibacterial therapy and community-onset bacterial coinfection in patients hospitalized with coronavirus disease 2019 (COVID-19): a multi-hospital cohort study","volume":"72","author":"Vaughn","year":"2021","journal-title":"Clinical Infectious Diseases"},{"key":"bib212","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.160277","type":"journal-article","article-title":"SARS-CoV-2 infection of sustentacular cells disrupts olfactory signaling pathways","volume":"7","author":"Verma","year":"2022","journal-title":"JCI Insight"},{"key":"bib213","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1177\/1352458513490545","type":"journal-article","article-title":"Oligoclonal bands in multiple sclerosis reactive against two herpesviruses and association with magnetic resonance imaging findings","volume":"20","author":"Virtanen","year":"2014","journal-title":"Multiple Sclerosis"},{"key":"bib214","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1038\/s41586-021-03275-y","type":"journal-article","article-title":"BNT162b vaccines protect rhesus macaques from SARS-CoV-2","volume":"592","author":"Vogel","year":"2021","journal-title":"Nature"},{"key":"bib215","doi-asserted-by":"publisher","DOI":"10.1172\/jci.insight.146757","type":"journal-article","article-title":"Increased long noncoding RNA LINK-A contributes to rheumatoid synovial inflammation and aggression","volume":"6","author":"Wang","year":"2021","journal-title":"JCI Insight"},{"key":"bib216","doi-asserted-by":"publisher","first-page":"1233","DOI":"10.1016\/j.cmi.2019.02.020","type":"journal-article","article-title":"Lyme disease overdiagnosis in a large healthcare system: a population-based, retrospective study","volume":"25","author":"Webber","year":"2019","journal-title":"Clinical Microbiology and Infection"},{"key":"bib217","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0268530","type":"journal-article","article-title":"CMV seropositivity is a potential novel risk factor for severe COVID-19 in non-geriatric patients","volume":"17","author":"Weber","year":"2022","journal-title":"PLOS ONE"},{"key":"bib218","doi-asserted-by":"publisher","first-page":"6243","DOI":"10.1016\/j.cell.2021.11.033","type":"journal-article","article-title":"SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis","volume":"184","author":"Wendisch","year":"2021","journal-title":"Cell"},{"key":"bib219","doi-asserted-by":"publisher","DOI":"10.1038\/s41392-022-01230-5","type":"journal-article","article-title":"CD147 contributes to SARS-CoV-2-induced pulmonary fibrosis","volume":"7","author":"Wu","year":"2022","journal-title":"Signal Transduction and Targeted Therapy"},{"key":"bib220","doi-asserted-by":"publisher","DOI":"10.1084\/jem.20232192","type":"journal-article","article-title":"Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung","volume":"221","author":"Wu","year":"2024","journal-title":"The Journal of Experimental Medicine"},{"key":"bib221","doi-asserted-by":"publisher","first-page":"1145","DOI":"10.1111\/bjd.19484","type":"journal-article","article-title":"Co-reactivation of the human herpesvirus alpha subfamily (herpes simplex virus-1 and varicella zoster virus) in a critically ill patient with COVID-19","volume":"183","author":"Xu","year":"2020","journal-title":"The British Journal of Dermatology"},{"key":"bib222","doi-asserted-by":"publisher","DOI":"10.3389\/fimmu.2022.1061686","type":"journal-article","article-title":"Omicron variants of SARS-CoV-2 and long COVID","volume":"13","author":"Yang","year":"2022","journal-title":"Frontiers in Immunology"},{"key":"bib223","doi-asserted-by":"publisher","first-page":"e55","DOI":"10.1016\/j.jinf.2020.06.056","type":"journal-article","article-title":"Improving antibiotic stewardship in COVID-19: Bacterial co-infection is less common than with influenza","volume":"81","author":"Youngs","year":"2020","journal-title":"The Journal of Infection"},{"key":"bib224","doi-asserted-by":"publisher","DOI":"10.1080\/22221751.2024.2353302","type":"journal-article","article-title":"The lethal K18-hACE2 knock-in mouse model mimicking the severe pneumonia of COVID-19 is practicable for antiviral development","volume":"13","author":"Zhang","year":"2024","journal-title":"Emerging Microbes & Infections"},{"key":"bib225","doi-asserted-by":"publisher","first-page":"1054","DOI":"10.1016\/S0140-6736(20)30566-3","type":"journal-article","article-title":"Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study","volume":"395","author":"Zhou","year":"2020","journal-title":"Lancet"},{"key":"bib226","doi-asserted-by":"publisher","DOI":"10.1002\/rmv.2034","type":"journal-article","article-title":"Estimation of the worldwide seroprevalence of cytomegalovirus: A systematic review and meta-analysis","volume":"29","author":"Zuhair","year":"2019","journal-title":"Reviews in Medical Virology"},{"key":"bib227","doi-asserted-by":"publisher","first-page":"944","DOI":"10.1053\/j.gastro.2020.05.048","type":"journal-article","article-title":"Alterations in gut microbiota of patients with COVID-19 during time of hospitalization","volume":"159","author":"Zuo","year":"2020","journal-title":"Gastroenterology"}],"container-title":["eLife"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/cdn.elifesciences.org\/articles\/106308\/elife-106308-v2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/cdn.elifesciences.org\/articles\/106308\/elife-106308-v2.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/elifesciences.org\/articles\/106308","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T09:14:34Z","timestamp":1787562874000},"score":1,"resource":{"primary":{"URL":"https:\/\/elifesciences.org\/articles\/106308"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,17]]},"references-count":227,"alternative-id":["10.7554\/eLife.106308"],"URL":"https:\/\/doi.org\/10.7554\/elife.106308","archive":["CLOCKSS"],"relation":{},"ISSN":["2050-084X"],"issn-type":[{"value":"2050-084X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,17]]},"assertion":[{"value":"single anonymised","name":"peer_review_transparency","label":"Peer review transparency","group":{"name":"peer_review_taxonomy"}},{"value":"other reviewer(s), editor","name":"peer_review_interaction","label":"Peer review interaction","group":{"name":"peer_review_taxonomy"}},{"value":"review summaries, review reports, author\/editor communication, reviewer identities reviewer opt in, editor identities","name":"peer_review_published","label":"Peer review published","group":{"name":"peer_review_taxonomy"}},{"value":"open (sign in with ORCID iD required)","name":"post_publication_commenting","label":"Post publication commenting","group":{"name":"post_publication_commenting"}}],"article-number":"e106308"}}