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异种移植猪肾治疗终末期肾病
以下内容来源于:NEJM。 Summary Xenotransplantation offers a potential solution to the organ shortage crisis. A 62-year-old hemodialysis-dependent man with long-standing diabetes, advanced vasculopathy, and marked dialysis-access challenges received a gene-edited porcine kidney with 69 genomic edits, including deletion of three glycan antigens, inactivation of porcine endogenous retroviruses, and insertion of seven human transgenes. The xenograft functioned immediately. The patient’s creatinine levels decreased promptly and progressively, and dialysis was no longer needed. After a T-cell–mediated rejection episode on day 8, intensified immunosuppression reversed rejection. Despite sustained kidney function, the patient died from unexpected, sudden cardiac causes on day 52; autopsy revealed severe coronary artery disease and ventricular scarring without evident xenograft rejection. (Funded by Massachusetts General Hospital and eGenesis.) Kidney transplantation has become the ideal standard of care for end-stage kidney disease, but organ shortage remains critical. One promising approach to address this critical shortage is xenotransplantation of porcine organs. Advances in CRISPR–Cas9 gene editing have enabled porcine kidney xenografts to survive for more than 2 years in nonhuman primates. We treated a 62-year-old man with long-standing diabetes and advanced vasculopathy who had lost nearly all viable hemodialysis-access options. His chance of receiving a transplant within 5 years was only 16%, with a 76% likelihood of dying or becoming too ill to receive a transplant, according to the decision-aid calculator for kidney transplantation of the Scientific Registry of Transplant Recipients. With no living donor available, we pursued a gene-edited pig kidney transplant under a single-patient, expanded-access authorization. The patient’s candidacy underwent rigorous evaluation by an independent psychiatrist, the Optimum Care Ethics Committee at Massachusetts General Hospital, and external transplant experts. After iterative protocol review by the Food and Drug Administration and final approval by the institutional review board at Massachusetts General Hospital, we transplanted a gene-edited porcine kidney with deletion of three major glycan xenoantigens (3KO), inactivation of porcine endogenous retroviruses, and insertion of seven human transgenes. Methods Pig Kidney Xenograft A Yucatan miniature pig was engineered to carry 69 genomic edits, eliminating three major glycan antigens, overexpressing seven human transgenes (TNFAIP3, HMOX1, CD47, CD46, CD55, THBD, and EPCR), and inactivating porcine endogenous retroviruses (Fig. S1 in the , available with the full text of this article at NEJM.org). Recipient Evaluation The patient was a 62-year-old man with end-stage kidney disease caused by type 2 diabetes mellitus who had exhausted nearly all viable vascular access for dialysis. His history included myocardial infarction, severe vasculopathy, heart failure, total parathyroidectomy, and receipt of a deceased-donor kidney in 2018. After having graft failure in May 2023 associated with BK virus infection and recurrent diabetic nephropathy, he returned to receiving hemodialysis. Comprehensive evaluation by the multidisciplinary team at Massachusetts General Hospital, along with ethical assessments conducted by an independent psychiatrist and ethics committee, are detailed in the and in Table S1. Transplant Procedure and Immunosuppression Protocol The transplant procedures are detailed in the and the , available at NEJM.org. The immunosuppressive regimen was based on our preclinical studies in nonhuman primates and included antithymocyte globulin (rabbit), rituximab, Fc-modified anti-CD154 monoclonal antibody (tegoprubart), and anti-C5 antibody (ravulizumab) in combination with maintenance immunosuppression with tacrolimus, mycophenolic acid, and prednisone Figure 1 Immunosuppressive Regimen and Post-Transplantation Clinical Course. Disease Surveillance, Histopathological Review, and Transcript Analysis Extensive microbiologic testing of the donor swine herd and the specific porcine donor was conducted before transplantation. Post-transplantation monitoring for both human and porcine pathogens and pathological analyses of biopsy samples are detailed in Tables S2, S3, and S4. Results Early Postoperative Period The transplantation procedure was completed with a cold ischemic time of 4 hours 38 minutes. The xenograft produced urine within 5 minutes after implantation and more than 6 liters in the first 48 hours. Thereafter, urine output stabilized at 1.5 to 2 liters per day (Fig. S2). The patient’s plasma creatinine level dropped from 11.8 to 2.2 mg per deciliter by day 6 The patient recovered from the transplantation procedure. Aside from chills and fever after the first infusion of antithymocyte globulin, he did not have overt problems with the immunosuppressive regimen. Because the patient’s T cells were sufficiently depleted after the initial dose of antithymocyte globulin (Fig. S3), a second dose was not administered. Immunosuppression with anti-CD154 monoclonal antibody resulted in serum trough levels exceeding 1000 μg per milliliter on day 0, after which levels were consistently above 800 μg per milliliter. Tacrolimus trough levels were maintained below 4 ng per milliliter during the first week after transplantation , combined with a lowered dose of 360 mg of mycophenolic acid twice daily owing to concern about overimmunosuppression with lymphocyte depletion, intensive immunosuppression, and his history of BK virus nephropathy. Xenograft Rejection Episode On day 8, the patient’s plasma creatinine level increased from 2.2 (day 7) to 2.9 mg per deciliter, accompanied by fever, allograft tenderness, and decreased urine output. An infectious disease workup was negative. Empirical therapy with glucocorticoid pulse (500 mg of methylprednisolone) and monoclonal antibody against interleukin-6 receptor (tocilizumab at a dose of 8 mg per kilogram of body weight) was initiated for suspected antibody-mediated rejection. A pretreatment, same-day biopsy confirmed acute T-cell–mediated rejection, Banff grade 2A, without evidence of thrombotic microangiopathy or antibody-mediated rejection and Table S5; ; and Fig. S4A, S4B, and S4C). Two glucocorticoid pulses (500 mg each) and antithymocyte globulin (1.5 mg per kilogram) were administered on days 9 and 10, and the doses of tacrolimus and mycophenolic acid were increased. Given the C3 deposition in the biopsy sample (Fig. S5), we administered pegcetacoplan, a targeted C3 and C3b inhibitor. Since the biopsy sample showed no evidence of antibody-mediated rejection, no additional doses of tocilizumab were administered. After these interventions, the patient’s urine output increased, and the plasma creatinine level started to decline. The patient was discharged on day 18 with a plasma creatinine level of 2.5 mg per deciliter. Figure 2 Pathological Analyses of Biopsy Samples Obtained from the Kidney Xenograft. Table 1 Banff Scores on Xenograft Biopsy Samples. On day 34, another xenograft biopsy was performed because of an increase in the creatinine level (to 2.65 from 1.9 mg per deciliter), which showed resolution of the T-cell–mediated rejection but with C3 deposition, focal interstitial fibrosis, and tubular atrophy without evidence of antibody-mediated rejection or thrombotic microangiopathy ; Fig. S4D and S4F; and Fig. S5). The plasma creatinine level decreased to 1.57 mg per deciliter with hydration on day 36. Antiporcine antibody titers remained lower than values in human serum controls (Fig. S6). No new anti-HLA antibodies were detected, and levels of preexisting anti-HLA antibodies were reduced (Fig. S7). Kidney Function, Hemodynamics, and Fluid-Electrolyte Balance Although the plasma creatinine levels occasionally fluctuated with the patient’s volume status, baseline levels ranged from 1.5 to 2.0 mg per deciliter, with an estimated glomerular filtration rate (eGFR) of 40 to 50 ml per minute per 1.73 m2 of body-surface area . The measurement of 24-hour urine creatinine clearance on days 7 and 28 after transplantation was 37 and 59 ml per minute per 1.73 m2, respectively. The mean blood pressure was 131/70 mm Hg (Fig. S8), and a loop diuretic (furosemide) was used to maintain euvolemia. The electrolyte levels remained mostly within normal limits (Figs. S9 and S10). However, the plasma total calcium level was low (Fig. S11) in association with the patient’s previous parathyroidectomy with undetectable levels of parathyroid hormone, which was managed with vitamin D and calcium supplementation. Plasma phosphate levels were elevated throughout the clinical course, necessitating the addition of phosphate binders. There was no hematuria or albuminuria, with a urine albumin-to-creatinine ratio (with both measured in grams) in the range of 0 to 0.2. Although the patient’s hemoglobin levels remained stable, erythropoietin was initiated on day 15 after transplantation because of the low reticulocyte count with appropriate iron stores. Infectious Complications On day 25, a subcutaneous wound infection led to a partial surgical opening of the incision and initiation of antibiotics (linezolid and meropenem). A retroperitoneal fluid collection, positive for Pseudomonas aeruginosa, was drained through percutaneous drain placement. The surgical incision was successfully closed on day 37. After 2 weeks of negative cultures and resolution of the fluid collection confirmed by abdominal computed tomography, the drain was removed on day 51. Cardiac Complication The patient was also evaluated in the outpatient clinic on day 51 after transplantation. He reported low fluid intake, and the plasma creatinine level of 2.7 mg per deciliter was relatively elevated, despite tacrolimus trough levels within target range. He had no symptoms of congestive heart failure or worrisome findings on physical examination, and kidney ultrasonography showed no abnormalities. The overall presentation was similar to a previous episode of an elevated creatinine level on day 34, which had resolved with hydration. Intravenous magnesium (2 g) and a 500-ml bolus of normal saline were administered over a 30-minute period to address hypomagnesemia and presumed volume depletion. The patient’s blood pressure, heart rate, and respiratory rate were all normal. Later that evening, the patient had respiratory distress and rapidly became unresponsive. Despite resuscitative efforts, he died. Autopsy revealed an enlarged heart with severe, diffuse coronary artery disease, diffuse left ventricular fibrosis, and a remote posterior infarct with a subacute ischemic extension, all of which were considered to have been caused by diabetic and ischemic cardiomyopathy (Fig. S12). There was no evidence of acute myocardial infarction, pulmonary embolism, pneumonia, inflammation in other organs, or drug toxicity. We concluded that the patient had probable sudden cardiac death caused by dysrhythmia in the context of severe ischemic cardiomyopathy. The xenograft showed focal fibrosis (attributed to sequelae of the episode of T-cell–mediated rejection) and no histologic evidence of active T-cell– or antibody-mediated rejection or thrombotic microangiopathy ; and Fig. S4G, S4H, and S4I). No porcine pathogens were detected in cultures, on nucleic acid testing, or on metagenomic assays during the clinical course. Retrospective transcriptomic analyses of biopsy samples are shown and discussed in Figure S13 and Table S4. Discussion This report documents the transplantation of a 3KO kidney xenograft with seven human transgenes into a patient with end-stage kidney disease, which built on our preclinical studies. Tegoprubart, an Fc-modified anti-CD154 monoclonal antibody in phase 2 trials for kidney allotransplantation, was part of the immunosuppressive regimen. This agent has shown potent inhibition of antibody production,as well as suppression of innate immune responses by blocking CD11b, another receptor of CD154. The pattern and timing of rejection in this patient suggested that early subtherapeutic levels of tacrolimus and mycophenolic acid may have contributed to the development of T-cell–mediated rejection, which was successfully treated with standard antirejection therapy. On biopsy, there was no evidence of antibody-mediated rejection, a common complication observed in the preclinical and decedent models of kidney xenotransplantation. Thrombotic microangiopathy has been a frequent cause of xenograft loss in previous studies in nonhuman primates. This condition can arise from incompatibilities between porcine endothelial cells and the human complement system. Therefore, we included an anti-C5 monoclonal antibody, ravulizumab, in the patient’s regimen, and no thrombotic microangiopathy was observed in the xenograft. Upon encountering T-cell–mediated rejection with C3 deposition and inflammation on biopsy, we also added pegcetacoplan to inhibit the proximal complement pathway. Our intention was to cautiously taper the use of anticomplement agents while closely monitoring for the development of thrombotic microangiopathy through protocol biopsies, as the clinical necessity for these agents remains to be fully established. Comprehensive monitoring for zoonotic pathogens was performed with the use of targeted nucleic acid testing and metagenomic sequencing. No porcine-derived pathogens were detected throughout the clinical course. Certain physiological differences between porcine and human kidney function remain to be elucidated. In studies involving nonhuman primates, porcine renin did not efficiently cleave angiotensin I from angiotensinogen, resulting in a dysfunctional renin–angiotensin–aldosterone system (RAAS). Given the incompatibility of primate antidiuretic hormone in nonhuman primates that have received xenografts, dehydration accompanied by elevated creatinine levels often develops. In our patient, blood pressure was well maintained at an average of 131/70 mm Hg, with stable plasma sodium levels and the use of diuretics to maintain euvolemia. Although reversible kidney dysfunction was observed on day 34 and improved with hydration, additional studies are needed to clarify potential differences in the hemodynamic regulation of glomerular filtration by porcine kidneys transplanted to humans. Whether this diuretic requirement in our patient stemmed from the propensity for sodium reabsorption of the porcine kidney or the patient’s preexisting heart disease (cardiorenal syndrome) is unclear and warrants further investigation in future xenotransplant recipients. In contrast with the hypercalcemia and hypophosphatemia that are observed in nonhuman primate recipients, our patient had hypocalcemia and hyperphosphatemia, findings that potentially could be attributed to the patient’s previous parathyroidectomy. Finally, although the 155-g kidney xenograft obtained from a 75-kg pig donor was relatively small for the 100-kg patient, the average creatinine level was 1.85 mg per deciliter after recovery from the rejection episode — a level that was reasonable for kidney function, given the size difference. The patient died from unanticipated, sudden cardiac causes, despite a functioning kidney xenograft. An autopsy revealed severe coronary artery disease with diffuse ventricular scarring but no evidence of acute thrombi, and we surmise that the cause of death was probably due to ventricular dysrhythmia. With such severe ischemic heart disease, the risk of sudden death from dysrhythmia remains substantial in any patient, 14 especially after a major surgical procedure. However, we cannot exclude the possibility that frequent fluctuations in intravascular volume, possibly caused by a dysfunctional RAAS in the pig kidney, may have increased the risk of cardiac dysrhythmia in a patient with severe ischemic heart disease. Despite the short observation period, this case demonstrated that a genetically modified kidney xenograft with human transgenes provided life-supporting kidney function in a living human patient. This outcome supports the feasibility of using genetically modified pig kidney xenografts to expand transplant access for patients with end-stage kidney disease. Although the identification of suitable candidates for kidney xenotransplantation is complex and debated, a small, pilot clinical trial for well-informed dialysis patients who face a high risk of dying while awaiting a human transplant may be a logical next step. Despite stable kidney function, our study patient who had undergone kidney xenotransplantation died from apparent sudden cardiac causes on day 52. The autopsy revealed severe coronary artery disease and ventricular scarring but no evidence of xenograft rejection.
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哺乳动物不同类型运动纤毛中轴突结构的多样性
以下内容来源于: Nature Portfolio 。 Abstract Reproduction, development and homeostasis depend on motile cilia, whose rhythmic beating is powered by a microtubule-based molecular machine called the axoneme. Although an atomic model of the axoneme is available for the alga Chlamydomonas reinhardtii 1, structures of mammalian axonemes are incomplete 1,2,3,4,5. Furthermore, we do not fully understand how molecular structures of axonemes vary across motile-ciliated cell types in the body. Here we use cryoelectron microscopy, cryoelectron tomography and proteomics to resolve the 96-nm modular repeat of axonemal doublet microtubules (DMTs) from both sperm flagella and epithelial cilia of the oviduct, brain ventricles and respiratory tract. We find that sperm DMTs are the most specialized, with epithelial cilia having only minor differences across tissues. We build a model of the mammalian sperm DMT, defining the positions and interactions of 181 proteins including 34 newly identified proteins. We elucidate the composition of radial spoke 3 and uncover binding sites of kinases associated with regeneration of ATP and regulation of ciliary motility. We discover a sperm-specific, axoneme-tethered T-complex protein ring complex (TRiC) chaperone that may contribute to construction or maintenance of the long flagella of mammalian sperm. We resolve axonemal dyneins in their prestroke states, illuminating conformational changes that occur during ciliary movement. Our results illustrate how elements of chemical and mechanical regulation are embedded within the axoneme, providing valuable resources for understanding the aetiology of ciliopathy and infertility, and exemplifying the discovery power of modern structural biology. Similar content being viewed by others In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes Article Open access 02 January 2023 In-cell structural insight into the stability of sperm microtubule doublet Article Open access 21 November 2023 Native doublet microtubules from Tetrahymena thermophila reveal the importance of outer junction proteins Article Open access 15 April 2023 Main Motile cilia are used by unicellular and multicellular organisms either to propel themselves through fluid or to move fluid across their surfaces. Ciliary motility is driven by a microtubule-based supramolecular assembly known as the axoneme, which consists of nine doublet microtubules (DMTs) surrounding a central apparatus of two singlet microtubules. DMTs are patterned into repeating 96-nm units by two rows of dynein arms (outer dynein arms (ODAs) and inner dynein arms (IDAs)), up to three T-shaped mechanoregulatory complexes called radial spokes (RSs), the nexin–dynein regulatory complex (N-DRC) that links neighbouring DMTs and a network of coiled coils that regulates the docking and periodicity of the aforementioned complexes. In addition, the DMT lumen is extensively decorated with microtubule inner proteins (MIPs) that bind in varying multiples of the 8-nm tubulin repeat, but with an overall periodicity of 48 nm that is in coherent register with the external 96-nm repeat. Over the past 20 years, cryoelectron tomography (cryo-ET) and cryoelectron microscopy (cryo-EM) have brought our understanding of the axoneme to the molecular level, culminating in a recent atomic model of the 96-nm modular repeat from the green alga C hlamydomonas reinhardtii 1,6. However, corresponding models of mammalian axonemes are incomplete 1,2,3,4,5. For instance, the model of a human DMT from respiratory cilia 1 lacks RS3, a prominent complex present in most ciliated organisms but absent from Chlamydomonas, and does not account for many enzymes or regulatory kinases thought to be anchored to the axoneme 7. Cryo-EM and cryo-ET have also shown marked variation in axonemal subcomplexes across species and cell types 1,2,3,8,9,10,11,12. This variation reflects the diversity of ciliary form and function in nature, and even within an organism; for instance, ependymal cilia in brain ventricles drive the flow of watery cerebrospinal fluid, whereas respiratory cilia in the trachea propel viscous mucus along the airway surface. Epithelial cilia and sperm flagella have distinct waveforms 13 and vary greatly in length, ranging from a few microns in the respiratory tract to tens or even hundreds of microns in sperm. They also respond differently to mutations in proteins that they are proposed to share. However, the lack of high-resolution structures of axonemes from different mammalian cell types prevents a full understanding of how differences in individual proteins or protein complexes contribute to ciliary diversity in normal function and in disease. Comparison of epithelial and sperm DMTs To shed light on the structural diversity of axonemes across different mammalian motile-ciliated cell types, we used single-particle analysis (SPA) cryo-EM to reconstruct the native 96-nm repeat of DMTs from disintegrated axonemes of sperm flagella (Bos taurus) and epithelial cilia isolated from either the oviduct (B. taurus and Homo sapiens) or brain ventricles (Sus scrofa) (Fig. 1, Extended Data Fig. 1a–d, Supplementary Figs. 1–7, Supplementary Tables 1, 2 and Methods). Separately, we reconstructed the 96-nm repeat from intact porcine (S. scrofa) oviduct cilia using cryo-ET and subtomogram averaging, showing consistency with our SPA structures, especially near the microtubule surfaces (Extended Data Fig. 1e–g and Methods). By comparison of these reconstructions with published maps of human respiratory cilia 1, we define how the structure of the axoneme varies across motile-ciliated cell types of the mammalian body. Fig. 1: Cryo-EM reconstructions of the 96-nm axonemal repeat of motile cilia from different mammalian cell types. Each panel shows a longitudinal and cross-sectional view of a composite cryo-EM map of a 96-nm repeat unit of a doublet microtubule from bovine sperm flagella (a), bovine oviductal cilia (b), porcine brain ventricle cilia (c) and human respiratory cilia (d). The reconstruction in d is EMD-35888 (ref. 1). Each major axonemal complex is given a unique colour with the doublet microtubule in grey. IJ, inner junction; MAP, microtubule-associated protein; OJ, outer junction. Full size image Our work demonstrates that the DMTs of multiciliated epithelial cells are almost structurally indistinguishable, with differences restricted to the intraluminal tektin bundle and associated proteins RIBC1/2 (Extended Data Fig. 2). The overall similarity of epithelial DMTs reflects the similarity of epithelial cilia in general—they are all approximately 5–10 µm long, consist of an axoneme sheathed by a ciliary membrane and have similar waveform dynamics. Nevertheless, the absence of obvious structural specializations in DMTs from epithelial cilia is somewhat unexpected considering their roles in propelling liquids of very different viscosity, and the different sensitivities of tissues to ciliopathic mutations. For example, genetic ablation of the β-tubulin isotype TUBB4B causes severe loss of tracheal and oviductal cilia in mice, but has no apparent effect on the number, length or beat frequency of brain ependymal cilia 14. Our structural and proteomic data confirm that TUBB4B is the main β-tubulin isotype of pig ependymal DMTs—as it is in all motile cilia examined (Supplementary Tables 3 and 4)—suggesting that differential sensitivity to TUBB4B depletion cannot be explained solely by gross differences in DMT structure. In contrast to the relatively homogeneous structures of epithelial DMTs, direct comparison of bovine DMTs from three different tissues shows that sperm DMTs have an additional layer of complexity (Fig. 1) that extends to the MIPs that decorate the lumen of axonemal DMTs 2,3 (Extended Data Fig. 2). Our structures further show that ciliary microtubule-associated proteins (CIMAPs) bound close to the external surface of the DMT 2,15 are ubiquitous features of mammalian axonemes but have cilium-specific distribution (Extended Data Fig. 3a,b). For example, CIMAP3 is present in all mammalian axonemes hitherto studied, yet CIMAP2, which binds the same protofilament cleft, is found only in sperm (Extended Data Fig. 3b). These structural observations are supported by both proteomics (Supplementary Table 4) and expression data 16.
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一项队列研究:COVID-19与季节性流感住院患者的长期预后对比
以下内容来源于:The Lancet 。 Summary Background Previous comparative analyses of people admitted to hospital for COVID-19 versus influenza evaluated the risk of death, hospital readmission, and a narrow set of health outcomes up to 6 months following infection. We aimed to do a comparative evaluation of both acute and long-term risks and burdens of a comprehensive set of health outcomes following hospital admission for COVID-19 or seasonal influenza. Methods For this cohort study we used the health-care databases of the US Department of Veterans Affairs to analyse data from 81280 participants admitted to hospital for COVID-19 between March 1, 2020, and June 30, 2022, and 10 985 participants admitted to hospital for seasonal influenza between Oct 1, 2015, and Feb 28, 2019. Participants were followed up for up to 18 months to comparatively evaluate risks and burdens of death, a prespecified set of 94 individual health outcomes, ten organ systems, overall burden across all organ systems, readmission, and admission to intensive care. Inverse probability weighting was used to balance the baseline characteristics. Cox and Poisson models were used to generate estimates of risk on both the relative scale and absolute scale as the event rate and disability-adjusted life-years (DALYs) per 100 persons. Findings Over 18 months of follow-up, compared to seasonal influenza, the COVID-19 group had an increased risk of death (hazard ratio [HR] 1·51 [95% CI 1·45–1·58]), corresponding to an excess death rate of 8·62 (95% CI 7·55–9·44) per 100 persons in the COVID-19 group versus the influenza group. Comparative analyses of 94 prespecified health outcomes showed that COVID-19 had an increased risk of 68·1% (64 of 94) pre-specified health outcomes; seasonal influenza was associated with an increased risk of 6·4% (six of 94) pre-specified health outcomes, including three out of four pre-specified pulmonary outcomes. Analyses of organ systems showed that COVID-19 had a higher risk across all organ systems except for the pulmonary system, the risk of which was higher in seasonal influenza. The cumulative rates of adverse health outcomes across all organ systems were 615·18 (95% CI 605·17–624·88) per 100 persons in COVID-19 and 536·90 (527·38–544·90) per 100 persons in seasonal influenza, corresponding to an excess rate of 78·72 (95% CI 66·15–91·24) per 100 persons in COVID-19. The total number of DALYs across all organ systems were 287·43 (95% CI 281·10–293·59) per 100 persons in the COVID-19 group and 242·66 (236·75, 247·67) per 100 persons in the seasonal influenza group, corresponding to 45·03 (95% CI 37·15–52·90) higher DALYs per 100 persons in COVID-19. Decomposition analyses showed that in both COVID-19 and seasonal influenza, there was a higher burden of health loss in the post-acute than the acute phase; and comparatively, except for the pulmonary system, COVID-19 had a higher burden of health loss across all other organ systems than seasonal influenza in both the acute and post-acute phase. Compared to seasonal influenza, COVID-19 also had an increased risk of hospital readmission (excess rate 20·50 [95% CI 16·10–24·86] per 100 persons) and admission to intensive care (excess rate 9·23 [6·68–11·82] per 100 persons). The findings were consistent in analyses comparatively evaluating risks in seasonal influenza versus COVID-19 by individuals’ respective vaccination status and in those admitted to hospital during the pre-delta, delta, and omicron eras. Interpretation Although rates of death and adverse health outcomes following hospital admission for either seasonal influenza or COVID-19 are high, this comparative analysis shows that hospital admission for COVID-19 was associated with higher long-term risks of death and adverse health outcomes in nearly every organ system (except for the pulmonary system) and significant cumulative excess DALYs than hospital admission for seasonal influenza. The substantial cumulative burden of health loss in both groups calls for greater prevention of hospital admission for these two viruses and for greater attention to the care needs of people with long-term health effects due to either seasonal influenza or SARS-CoV-2 infection. Research in context Evidence before this study We searched PubMed for studies published between Dec 12, 2019, and Sept 10, 2023, using the search terms “COVID-19” and “SARS-CoV-2” in combination with the search terms “seasonal influenza”, “flu”, OR “influenza”, with no language restrictions. Comparative studies of people admitted to hospital for COVID-19 versus influenza evaluated the risk of death, hospital readmission, and a narrow set of health outcomes up to 6 months following SARS-CoV-2 infection. These studies showed that, despite some decline during the course of the pandemic, COVID-19 was still associated with a higher risk of death and hospital readmission at 6 months than seasonal influenza. However, a comparative evaluation of both acute and long-term risks and burdens of death, a comprehensive set of health outcomes, and health-care utilisation (eg, hospital readmission) following hospital admission for COVID-19 or seasonal influenza has not been done. Added value of this study The findings of this cohort study show that the cumulative rates of death, adverse health outcomes, and health-care utilisation were high in both those admitted to hospital for COVID-19 and those admitted to hospital for seasonal influenza, but the risks and burdens were comparatively higher in people admitted to hospital for COVID-19. Risks were higher in COVID-19 for all organ systems except for the pulmonary system, the risk of which was higher in seasonal influenza in both the acute and post-acute phase of the infection, suggesting the possibility that seasonal influenza might have a higher affinity to affect the pulmonary system than SARS-CoV-2 infection and that SARS-CoV-2 infection manifests more systemically than seasonal influenza. Although COVID-19 had a comparatively higher burden of health loss than seasonal influenza in both the acute and post-acute phase, both COVID-19 and seasonal influenza had a higher burden of health loss in the post-acute phase of infection compared to their respective acute phases, suggesting that hospital admission for either COVID-19 or seasonal influenza has a greater long-term impact on health than the immediately manifested health effects during the acute phase. Implications of all the available evidence The findings illustrate the high toll of death and health loss following hospital admission for either seasonal influenza or COVID-19. The risks and burdens of death, health loss, and health-care utilisation are substantially higher for COVID-19 than for seasonal influenza. Our evaluation of health loss by organ systems showed some differentiating features, in that seasonal influenza had a higher risk of pulmonary system involvement, whereas COVID-19 was a multisystemic disease showing higher risks in all other organ systems. Hospital admission for both COVID-19 and seasonal influenza generated a higher burden of health loss in the post-acute phase, suggesting that conceptualisation of these infections solely as acute illnesses will overlook their larger post-acute health effects and underestimate their cumulative burden on human health. The substantial cumulative burden of health loss in both groups highlights the need for greater prevention of hospital admission for these two viruses and for greater attention towards the care needs of people with long-term health effects due to either seasonal influenza or SARS-CoV-2 infection. Comparative analyses of COVID-19 and influenza are useful because they juxtapose the relatively new COVID-19 and a respiratory viral illness that has been known for at least a century—allowing a better understanding of the similarities and differences between the acute and post-acute health trajectories of people infected with these two viruses. We aimed to examine acute and long-term risks and burdens of death, health-care utilisation, and a comprehensive array of 94 health outcomes over an 18-month period in people admitted to hospital with COVID-9 and those admitted to hospital with seasonal influenza. Methods Study design and setting This cohort study was conducted with the health-care databases of the US Department of Veterans Affairs (VA). The VA operates the largest integrated health-care system in the USA and provides health-care services to veterans of the US Armed Forces. The services included preventative and health maintenance, outpatient care, inpatient hospital care, prescriptions, mental health care, home health care, primary care, specialty care, geriatric and extended care, medical equipment, and prosthetics. The VA operates 1323 VA health-care facilities, which include 173 VA medical centres and 1137 outpatient sites. Data sources We used the health-care databases of the VA, which include information collected during patients' routine health-care encounters. Data were obtained from VA Corporate Data Warehouse (CDW), which collected and managed electronic health records from all VA health-care facilities. Data domains included outpatient, inpatient, pharmacy, laboratory, health factors, VA COVID-19 Shared Data Resource, and vital status. The Area Deprivation Index (ADI)—a composite measure of income, education, employment, and housing—was obtained from the Neighborhood Atlas and used as a summary measure of contextual disadvantage at participants' residential locations. 5 All data were accessed through the VA Informatics and Computing Infrastructure. Cohort The cohort flow of the study is presented in appendix 1 (p 2). 573 612 participants who had a positive SARS-CoV-2 test result between March 1, 2020, and June 30, 2022, were included in the COVID-19 group. We then selected those admitted to hospital with an admission diagnosis for COVID-19 within 5 days before or within 30 days after the positive test results (n=82 188). Because hospital admission for seasonal influenza was rare in the USA during the COVID-19 group enrolment period, we enrolled a historical seasonal influenza group; 50 509 participants who had a positive influenza test result between Oct 1, 2015, and Feb 28, 2019, were included in the seasonal influenza group. We then selected those admitted to hospital with an admission diagnosis for seasonal influenza within 5 days before or within 30 days after the positive test results (n=11 893). After removing 908 participants who were included in both the COVID-19 and seasonal influenza groups, the final cohort comprised 81 280 participants in the COVID-19 group and 10 985 participants in the seasonal influenza group. Within the seasonal influenza group, 8360 (76·1%) of 10 985 participants had influenza type A and 2625 (23·9%) had other types of influenza. The date of hospital admission was defined as T0. The last date of follow-up for the COVID-19 group was set to be the first occurrence of 540 days after T0 or July 20, 2023. The last date of follow-up for the seasonal influenza group was set to be the first occurrence of 540 days after T0 or Feb 29, 2020. For additional comparisons between different eras of the pandemic and seasonal influenza, the COVID-19 groups were further separated into three groups (pre-delta, delta, and omicron) based on the predominant SARS-CoV-2 variant at the date of infection according to the US Centers for Disease Control and Prevention (CDC). 6 There were 40 481 participants in the COVID-19 group who had a positive SARS-CoV-2 test before June 19, 2021, and were thus defined as the pre-delta group; 18 106 participants had a positive test between June 20, 2021, and Dec 18, 2021, and were thus defined as the delta group; and 22 693 participants had a positive test between Dec 19, 2021, and June 30, 2022, and were thus defined as the omicron group. To facilitate comparisons based on similar follow-up time across groups, we randomly assigned potential follow-up times to participants not in the omicron group based on values drawn from the follow-up distribution in the omicron group (the group with shortest potential follow-up time). Administrative censoring of the seasonal influenza, pre-delta, and delta groups based on the follow-up distribution of the omicron group resulted in a similar follow-up distribution across groups. After the application of administrative censoring, 100% of participants had at least 360 days of potential follow-up; 4620 (42·06%) of 10 985 participants in the seasonal influenza group, 17 027 (42·06%) of 40 481 in the pre-delta group, 7616 (42·06%) of 18 106 in the delta group, and 9545 (42·06%) of 22 693 in the omicron group had 540 days of follow-up. Outcomes A list of 94 pre-specified health outcomes that could be associated with COVID-19 or seasonal influenza were defined on the basis of the International Classification of Diseases 10th Revision (ICD-10) diagnosis codes, laboratory values, and prescription records. 1,4,7–11 Outcomes were also composited into ten organ systems: cardiovascular, coagulation and haematological, fatigue, gastrointestinal, kidney, mental health, metabolic, musculoskeletal, neurological, and pulmonary. Incident outcomes were defined as the first occurrence of outcomes during follow-up that was not present before T0. A composite of adverse health outcomes across all organ systems was further defined as the number of incident organ systems affected. Outcomes were ascertained from T0 until end of follow-up. To evaluate outcomes during the post-acute phase of infection, we separately ascertained outcomes from 30 days after T0 until the end of follow-up. For the composite outcomes and to account for both the occurrence of individual outcomes and the influence of each outcome on overall health, we used the Global Burden of Disease Study (GBD) methodologies to estimate disability-adjusted life-years (DALYs) for the composite outcomes (in each organ system and across all organ systems). 7,12–14 For each composite outcome, DALYs were computed as the summation of the DALYs of all individual outcomes under the composite outcome (the product of the occurrence of the outcome and its associated health burden coefficient). 7,12–14 We also examined death (all-cause mortality) since hospital admission and health-care resource utilisation, including number of hospital readmissions and ICU admission after the index hospitalisation. Covariates Covariates were defined on the basis of previous knowledge and following directed acyclic graph (appendix 1 p 3). 1,8–11,15–17 Baseline covariates were collected from 1 year before T0 until T0. Demographic variables including age, race (White, Black, and other), self-reported sex, area deprivation index based on residential address, smoking status (current, former, and never) and use of long-term care were used. We also selected laboratory and vital measurements including estimated glomerular filtration rate (eGFR), systolic and diastolic blood pressure and BMI; and diseases including cancer, cardiovascular disease, chronic lung disease, coronary artery disease, dementia, diabetes, hyperlipidaemia, HIV, immune dysfunction, liver diseases, and peripheral artery diseases. We selected the number of outpatient visits and hospital admissions, number of blood panel tests, number of medications received, and number of Medicare outpatient visits and hospital admissions to represent potential differences in health-care resource utilisation between the COVID-19 and the seasonal influenza groups. We also standardised vaccination rates in the COVID-19 group to the rate during the delta and omicron eras in the cohort. In this study, 4·32% of data on eGFR, 4·01% of data on BMI, and 0·06% of data on blood pressure were missing and imputed with multivariate imputation by chained equations and the predictive mean matching method conditional on all covariates. Continuous variables were transformed into restricted cubic spline functions to account for potential non-linear relationships, where four knots were placed at 5th, 35th, 65th, and 95th precentiles. 18 Statistical analysis We performed power analyses using 1000 simulations based on the parameters from the study cohort and power was defined by the proportion of simulations with a 95% CI of the hazard ratio that did not include 1. We varied the event rate from 1% to 20% and the strength of confounding based on C-statistics from 0·5 to 0·8. Given the study sample size, and under the setting of strong confounding, we observed a power of 99% to detect a hazard ratio (HR) of 0·70, a power of 91% to detect a HR of 0·80, and a power of 72% to detect a HR of 0·90, in a scenario where the event rate was 1%; and a power of 99% to detect a HR of 0·70, a power of 99% to detect a HR of 0·80, and a power of 99% to detect a HR of 0·90 in a scenario where the event rate was 20%. Baseline characteristics of the COVID-19 and seasonal influenza groups were reported. Distributions of continuous variables were reported as means and SDs and categorical variables were described as frequencies and percentages. Differences of baseline characteristics between groups were measured with absolute standardised differences, where a value of less than 0·1 was considered evidence of good balance. Inverse probability weighting based on propensity score was used to balance baseline differences between the COVID-19 and seasonal influenza groups. Logistic regression was applied to estimate the probability of being assigned to the seasonal influenza group (the propensity score), given all covariates previously described. In order to provide a comparative risk assessment based on the same underlying risk, the common reference group of seasonal influenza was selected as the target population. The inverse probability weight was computed as the propensity score divided by (1–propensity score) for the COVID-19 group and was defined as 1 for the seasonal influenza group. HRs of the occurrence of incident outcomes were estimated on the basis of the weighted Cox survival model, where death was considered as competing risk and cause-specific hazards were estimated for non-death outcomes. The estimated rate in each group and the difference between groups were generated on the basis of estimated survival probability. The relative and absolute risk of overall disease, DALYs, and health-care utilisation were estimated on the basis of weighted Poisson regression where the sums of the events during follow-up were set to be the dependent variables and follow-up times were set to be the offsets in the model. The cumulative difference between COVID-19 and seasonal influenza from T0 until 30, 180, 360, and 540 days was estimated. To examine the distributional contribution of acute and post-acute disease to the overall burden of disease after infection, we first examined the risk and risk difference between COVID-19 and seasonal influenza during the post-acute phase based on outcomes ascertained 30 days after T0. We then evaluated the proportion of risk from the acute phase (0–30 days) and post-acute phase within the COVID-19 and seasonal influenza groups, as well as the difference between the two groups across each organ system and across all organ systems. We then evaluated the comparative risks and burdens of death, organ system involvement, and health-care utilisation between those admitted to hospital for seasonal influenza and those admitted to hospital for COVID-19 during the pre-delta, delta, and omicron periods according to the CDC. 6 Propensity scores and inverse probability weights for each group were computed and applied. To examine the influence of previous vaccination on the comparative risk between COVID-19 and seasonal influenza, we further separated COVID-19 groups on the basis of their COVID-19 vaccination status and the seasonal influenza group on the basis of their seasonal influenza vaccination status. Comparisons were conducted for unvaccinated individuals with COVID-19 compared to unvaccinated, and separately, vaccinated individuals with seasonal influenza, and for vaccinated individuals with COVID-19 compared to unvaccinated and vaccinated individuals with seasonal influenza. Propensity scores and inverse probability weights for each group were computed and applied. Multiple sensitivity analyses were conducted to test the robustness of the findings. First, because differences in screening practices for these infections during admission might have resulted in misspecification of exposure, we varied our definition of exposure by including those admitted to hospital within 5 days before or after SARS-CoV-2 or seasonal influenza infection, and separately, included those admitted to hospital within 5 days after the infection, compared to the main approach where we included those admitted to hospital within 5 days before or 30 days after the infection. Second, we adjusted for ICU admission during the first hospital admission, compared to the main approach where no adjustments were made for variables after T0. Third, we adjusted for the seasonal influenza vaccine in both groups, compared to the main approach in which it was not a covariate in the model. Fourth, we applied a doubly robust method that conducted adjustment in both the exposure model and outcome model to adjust for differences between groups, 19 compared to the main approach where only inverse probability weight was used in the outcome model. Fifth, we used the overlap weighting approach to balance baseline characteristics and estimated the average treatment effect for the overlap population, compared to the main approach that used the inverse probability of treatment weighting. 20 Sixth, we estimated risk based on weighed Kaplan-Meier estimator, compared to the main approach that was based on the Cox model. Seventh, we censored participants at their date of reinfection and applied the inverse probability of censoring weight to account for informative censoring, compared to the main approach that continued following them up after reinfection. Finally, we compared COVID-19 with seasonal influenza A and, separately, with all other (non-A) seasonal influenza viruses, compared to the main approach that evaluated COVID-19 versus all seasonal influenza. For all analyses, 95% CIs were estimated on the basis of the 2·5th and 97·5th percentile of 1000 times parametric bootstrapping. A risk on the relative scale with a 95% CI that does not cross 1 and a rate difference with a 95% CI that does not cross 0 were considered statistically significant. Analyses were done with SAS Enterprise Guide (version 8.3) and data visualisations were done in R (version 4.3.0). The study was approved, and a waiver of informed consent was granted, by the Institutional Review Board of St Louis Health Care System, US Department of Veteran Affairs. Role of the funding source The sponsor of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. Results There were 81 280 people in the COVID-19 cohort and 10 985 people in the seasonal influenza cohort. The COVID-19 cohort had a median follow-up of 1·46 (IQR 1·26–1·51) years and the seasonal influenza cohort had a median follow-up of 1·46 (1·18–1·53) years, altogether corresponding to 127 640 person-years of follow up. The demographic and health characteristics of the two groups before weighting are presented in appendix 2 (supplementary table 1) and those after weighting are summarised in the table. The distribution of the propensity score before and after weighting is presented in appendix 1 (p 4). After inverse probability weighting, all baseline characteristics had an SMD less than 0·1, suggested good balance was achieved. Table Demographic and health characteristics of the overall, COVID-19, and seasonal influenza groups after weighting Data are n (%), mean (SD), or median (IQR). eGFR=estimated glomerular filtration rate. SMD=absolute standardised mean difference. An SMD of less than 0·1 was considered evidence of good balance. * Area Deprivation Index is a measure of socioeconomic disadvantage, with a range from low to high disadvantage of 0 to 100. We examined the COVID-19 and seasonal influenza cohorts to comparatively evaluate the risks and burdens of death, 94 individual health outcomes, ten organ systems aggregated from individual health outcomes, a composite of adverse health outcomes across all ten organ systems, and readmission and admission to intensive care. Risks were estimated on both the relative scale as HRs or relative risks, and on the absolute scale as rates and DALYs per 100 persons in several time periods, including 0–30 days, 0–180 days, 0–360 days, and 0–540 days, where time zero was designated as the date of hospital admission. The absolute death rate was higher in the COVID-19 group than in the influenza group in each time period (0–30 days, 0–180 days, 0–360 days, and 0–540 days); the cumulative death rates at 540 days were 28·46 (95% CI 28·14–28·78) per 100 persons for COVID-19 and 19·84 (19·07–20·59) per 100 persons for seasonal influenza; the excess death rate in the COVID-19 versus influenza group was 8·62 (95% CI 7·55–9·44) per 100 persons. Compared to the seasonal influenza group, the COVID-19 group had an increased risk of death in all time periods: 0–30 days (HR 2·51; 95% CI 2·28–2·78), 0–180 days (1·86; 1·75–1·98), 0–360 days (1·61; 1·54–1·69), and 0–540 days (1·51; 1·45–1·58; figure 1; appendix 2 supplementary table 2). We also examined the risk of death within non-overlapping time periods during follow-up (0–30 days, 31–180 days, 181–360 days, and 361–540 days); COVID-19 was associated with a higher risk of death within all these time periods (appendix 2 supplementary table 3).
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