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1.
Bioinformatics ; 2022 May 31.
Article in English | MEDLINE | ID: covidwho-1873852

ABSTRACT

: Mutation is the key for a variant of concern (VOC) to overcome selective pressures, but this process is still unclear. Understanding the association of the mutational process with VOCs is an unmet need. Here we developed VOC-alarm, a method to predict VOCs and their caused COVID surges, using mutations of about 5.7 million SARS-CoV-2 complete sequences. We found that VOCs rely on lineage-level entropy value of mutation numbers to compete with other variants, suggestive of the importance of population-level mutations in the virus' evolution. Thus, we hypothesized that VOCs are a result of a mutational process across the globe. Analyzing the mutations from January 2020-December 2021, we simulated the mutational process by estimating the pace of evolution, and thus divided the time period, January 2020-March 2022, into eight stages. We predicted Alpha, Delta, Delta Plus (AY.4.2) and Omicron (B.1.1.529) by their mutational entropy values in the stages I, III, V, and VII with accelerated paces, respectively. In late November 2021, VOC-alarm alerted that Omicron strongly competed with Delta and Delta plus to become a highly transmissible variant. Using simulated data, VOC-alarm also predicted that Omicron could lead to another COVID surge from January 2022-March 2022. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

2.
Int J STD AIDS ; 33(5): 462-466, 2022 Apr.
Article in English | MEDLINE | ID: covidwho-1753029

ABSTRACT

OBJECTIVE: This study aimed to compare COVID-19 positivity by HIV status and race/ethnicity using data from the U.S. National COVID Cohort Collaborative (N3C). METHODS: The N3C cohort (≥ 18 years) includes patients with any encounter after 1/1/2020 with SARS-CoV-2 laboratory tests. Detailed electronic medical records are centralized and harmonized across health-care organizations (34 sites). COVID-19 diagnosis was defined by RT-PCR or antibody testing. HIV infection was defined by standard diagnostic codes within 2 years prior to COVID-19 testing. Descriptive statistics and multivariable logistic regression were utilized to compare COVID-19 positivity and HIV status by patient's race/ethnicity. RESULTS: Over 2.1 million patients were captured in the N3C as of 01/29/2021, of whom 372,716 (15%) were positive for COVID-19; 17,820 (0.7%) were PLWH of whom 2428 (13.6%) tested positive for COVID-19. COVID-19 positive PLWH were more likely to be 30+ years of age (90% vs. 70%; χ2p < 0.001), male (67% vs. 46%, χ2p < 0.001), and Black (44% vs. 15%, χ2p < 0.001) compared to HIV-negative patients. Compared to non-Hispanic/Latinx (NH)-White PLWH, NH-Black (aOR: 1.59, 95% CI: 1.37-1.86), Latinx (aOR: 2.17, 95% CI: 1.68-2.83), and NH-Asian (aOR: 2.18, 95% CI: 1.30-3.63) PLWH were more likely to have COVID-19 after adjustment for age, sex, and CharlsonDeyo comorbidity score. CONCLUSION: PLWH and minoritized communities, including NH-Black and Latinx or Hispanic adults, appear to be disproportionately impacted by the COVID-19 pandemic.


Subject(s)
COVID-19 , HIV Infections , Adult , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , HIV Infections/diagnosis , HIV Infections/epidemiology , Humans , Male , Pandemics , SARS-CoV-2 , United States/epidemiology
3.
J Clin Oncol ; 40(13): 1414-1427, 2022 May 01.
Article in English | MEDLINE | ID: covidwho-1741971

ABSTRACT

PURPOSE: To provide real-world evidence on risks and outcomes of breakthrough COVID-19 infections in vaccinated patients with cancer using the largest national cohort of COVID-19 cases and controls. METHODS: We used the National COVID Cohort Collaborative (N3C) to identify breakthrough infections between December 1, 2020, and May 31, 2021. We included patients partially or fully vaccinated with mRNA COVID-19 vaccines with no prior SARS-CoV-2 infection record. Risks for breakthrough infection and severe outcomes were analyzed using logistic regression. RESULTS: A total of 6,860 breakthrough cases were identified within the N3C-vaccinated population, among whom 1,460 (21.3%) were patients with cancer. Solid tumors and hematologic malignancies had significantly higher risks for breakthrough infection (odds ratios [ORs] = 1.12, 95% CI, 1.01 to 1.23 and 4.64, 95% CI, 3.98 to 5.38) and severe outcomes (ORs = 1.33, 95% CI, 1.09 to 1.62 and 1.45, 95% CI, 1.08 to 1.95) compared with noncancer patients, adjusting for age, sex, race/ethnicity, smoking status, vaccine type, and vaccination date. Compared with solid tumors, hematologic malignancies were at increased risk for breakthrough infections (adjusted OR ranged from 2.07 for lymphoma to 7.25 for lymphoid leukemia). Breakthrough risk was reduced after the second vaccine dose for all cancers (OR = 0.04; 95% CI, 0.04 to 0.05), and for Moderna's mRNA-1273 compared with Pfizer's BNT162b2 vaccine (OR = 0.66; 95% CI, 0.62 to 0.70), particularly in patients with multiple myeloma (OR = 0.35; 95% CI, 0.15 to 0.72). Medications with major immunosuppressive effects and bone marrow transplantation were strongly associated with breakthrough risk among the vaccinated population. CONCLUSION: Real-world evidence shows that patients with cancer, especially hematologic malignancies, are at higher risk for developing breakthrough infections and severe outcomes. Patients with vaccination were at markedly decreased risk for breakthrough infections. Further work is needed to assess boosters and new SARS-CoV-2 variants.


Subject(s)
COVID-19 , Hematologic Neoplasms , COVID-19/complications , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines/adverse effects , Hematologic Neoplasms/complications , Hematologic Neoplasms/epidemiology , Hematologic Neoplasms/therapy , Humans , SARS-CoV-2
4.
Innovation in aging ; 5(Suppl 1):974-975, 2021.
Article in English | EuropePMC | ID: covidwho-1602494

ABSTRACT

Older age has been consistently associated with adverse COVID-19 outcomes. Frailty, a syndrome characterized by declining function across multiple body systems is common in older adults and may increase vulnerability to adverse outcomes among COVID-19 patients. However, the impacts of frailty on COVID-19 management, severity, or outcomes have not been well characterized in a large, representative US population. Using the National COVID Cohort Collaborative, a multi-institutional US repository for COVID-19 research, we calculated the Hospital Frailty Risk Score (HFRS), a validated EHR-based frailty score, among COVID-19 inpatients age ≥ 65. We examined patient demographics and comorbidities, length of stay (LOS), systemic corticosteroid and remdesivir use, ICU admission, and inpatient mortality across subgroups by HFRS score. Among 58,964 inpatients from 53 institutions (51% male, 65% White, 18% Black, 9% Hispanic, mean age 75, mean Charlson comorbidity count 3.0, and median LOS 7 days), 38,692 (66%), 4,180 (7%), 3,531 (6%), 3,525 (6%) and 7,862 (13%) had HFRS scores of 0-1, 2, 3, 4, and >=5 , respectively. Frailty was only moderately correlated with age and comorbidity (□=0.178 and 0.348, respectively, p<0.001). Overall, 34% received systemic corticosteroid and 19% received remdesivir. We observed 4% ICU admissions and 16% inpatient death. Among non-ICU admissions, after adjusting for demographics and comorbidities, frailty (HFRS ≥ 2) was associated with 79% greater systemic corticosteroid use and 22% greater remdesivir use, whereas a higher HRFS score was marginally associated with higher rates of severe COVID disease, inpatient death, or ICU admission.

5.
JAMA Intern Med ; 182(2): 153-162, 2022 02 01.
Article in English | MEDLINE | ID: covidwho-1598451

ABSTRACT

Importance: Persons with immune dysfunction have a higher risk for severe COVID-19 outcomes. However, these patients were largely excluded from SARS-CoV-2 vaccine clinical trials, creating a large evidence gap. Objective: To identify the incidence rate and incidence rate ratio (IRR) for COVID-19 breakthrough infection after SARS-CoV-2 vaccination among persons with or without immune dysfunction. Design, Setting, and Participants: This retrospective cohort study analyzed data from the National COVID Cohort Collaborative (N3C), a partnership that developed a secure, centralized electronic medical record-based repository of COVID-19 clinical data from academic medical centers across the US. Persons who received at least 1 dose of a SARS-CoV-2 vaccine between December 10, 2020, and September 16, 2021, were included in the sample. Main Outcomes and Measures: Vaccination, COVID-19 diagnosis, immune dysfunction diagnoses (ie, HIV infection, multiple sclerosis, rheumatoid arthritis, solid organ transplant, and bone marrow transplantation), other comorbid conditions, and demographic data were accessed through the N3C Data Enclave. Breakthrough infection was defined as a COVID-19 infection that was contracted on or after the 14th day of vaccination, and the risk after full or partial vaccination was assessed for patients with or without immune dysfunction using Poisson regression with robust SEs. Poisson regression models were controlled for a study period (before or after [pre- or post-Delta variant] June 20, 2021), full vaccination status, COVID-19 infection before vaccination, demographic characteristics, geographic location, and comorbidity burden. Results: A total of 664 722 patients in the N3C sample were included. These patients had a median (IQR) age of 51 (34-66) years and were predominantly women (n = 378 307 [56.9%]). Overall, the incidence rate for COVID-19 breakthrough infection was 5.0 per 1000 person-months among fully vaccinated persons but was higher after the Delta variant became the dominant SARS-CoV-2 strain (incidence rate before vs after June 20, 2021, 2.2 [95% CI, 2.2-2.2] vs 7.3 [95% CI, 7.3-7.4] per 1000 person-months). Compared with partial vaccination, full vaccination was associated with a 28% reduced risk for breakthrough infection (adjusted IRR [AIRR], 0.72; 95% CI, 0.68-0.76). People with a breakthrough infection after full vaccination were more likely to be older and women. People with HIV infection (AIRR, 1.33; 95% CI, 1.18-1.49), rheumatoid arthritis (AIRR, 1.20; 95% CI, 1.09-1.32), and solid organ transplant (AIRR, 2.16; 95% CI, 1.96-2.38) had a higher rate of breakthrough infection. Conclusions and Relevance: This cohort study found that full vaccination was associated with reduced risk of COVID-19 breakthrough infection, regardless of the immune status of patients. Despite full vaccination, persons with immune dysfunction had substantially higher risk for COVID-19 breakthrough infection than those without such a condition. For persons with immune dysfunction, continued use of nonpharmaceutical interventions (eg, mask wearing) and alternative vaccine strategies (eg, additional doses or immunogenicity testing) are recommended even after full vaccination.


Subject(s)
COVID-19 Testing/statistics & numerical data , COVID-19/diagnosis , COVID-19/epidemiology , Health Status , Vaccination/statistics & numerical data , Adult , Aged , COVID-19 Vaccines , Cohort Studies , Female , Humans , Incidence , Male , Middle Aged , Retrospective Studies , Risk Factors , SARS-CoV-2/isolation & purification , Sex Distribution
6.
J Clin Oncol ; 39(35): 3997-3998, 2021 12 10.
Article in English | MEDLINE | ID: covidwho-1581947
7.
EBioMedicine ; 74: 103722, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1536517

ABSTRACT

BACKGROUND: Numerous publications describe the clinical manifestations of post-acute sequelae of SARS-CoV-2 (PASC or "long COVID"), but they are difficult to integrate because of heterogeneous methods and the lack of a standard for denoting the many phenotypic manifestations. Patient-led studies are of particular importance for understanding the natural history of COVID-19, but integration is hampered because they often use different terms to describe the same symptom or condition. This significant disparity in patient versus clinical characterization motivated the proposed ontological approach to specifying manifestations, which will improve capture and integration of future long COVID studies. METHODS: The Human Phenotype Ontology (HPO) is a widely used standard for exchange and analysis of phenotypic abnormalities in human disease but has not yet been applied to the analysis of COVID-19. FUNDING: We identified 303 articles published before April 29, 2021, curated 59 relevant manuscripts that described clinical manifestations in 81 cohorts three weeks or more following acute COVID-19, and mapped 287 unique clinical findings to HPO terms. We present layperson synonyms and definitions that can be used to link patient self-report questionnaires to standard medical terminology. Long COVID clinical manifestations are not assessed consistently across studies, and most manifestations have been reported with a wide range of synonyms by different authors. Across at least 10 cohorts, authors reported 31 unique clinical features corresponding to HPO terms; the most commonly reported feature was Fatigue (median 45.1%) and the least commonly reported was Nausea (median 3.9%), but the reported percentages varied widely between studies. INTERPRETATION: Translating long COVID manifestations into computable HPO terms will improve analysis, data capture, and classification of long COVID patients. If researchers, clinicians, and patients share a common language, then studies can be compared/pooled more effectively. Furthermore, mapping lay terminology to HPO will help patients assist clinicians and researchers in creating phenotypic characterizations that are computationally accessible, thereby improving the stratification, diagnosis, and treatment of long COVID. FUNDING: U24TR002306; UL1TR001439; P30AG024832; GBMF4552; R01HG010067; UL1TR002535; K23HL128909; UL1TR002389; K99GM145411.


Subject(s)
COVID-19/complications , COVID-19/pathology , COVID-19/diagnosis , Humans , SARS-CoV-2
8.
J Clin Oncol ; 39(20): 2232-2246, 2021 07 10.
Article in English | MEDLINE | ID: covidwho-1484813

ABSTRACT

PURPOSE: Variation in risk of adverse clinical outcomes in patients with cancer and COVID-19 has been reported from relatively small cohorts. The NCATS' National COVID Cohort Collaborative (N3C) is a centralized data resource representing the largest multicenter cohort of COVID-19 cases and controls nationwide. We aimed to construct and characterize the cancer cohort within N3C and identify risk factors for all-cause mortality from COVID-19. METHODS: We used 4,382,085 patients from 50 US medical centers to construct a cohort of patients with cancer. We restricted analyses to adults ≥ 18 years old with a COVID-19-positive or COVID-19-negative diagnosis between January 1, 2020, and March 25, 2021. We followed N3C selection of an index encounter per patient for analyses. All analyses were performed in the N3C Data Enclave Palantir platform. RESULTS: A total of 398,579 adult patients with cancer were identified from the N3C cohort; 63,413 (15.9%) were COVID-19-positive. Most common represented cancers were skin (13.8%), breast (13.7%), prostate (10.6%), hematologic (10.5%), and GI cancers (10%). COVID-19 positivity was significantly associated with increased risk of all-cause mortality (hazard ratio, 1.20; 95% CI, 1.15 to 1.24). Among COVID-19-positive patients, age ≥ 65 years, male gender, Southern or Western US residence, an adjusted Charlson Comorbidity Index score ≥ 4, hematologic malignancy, multitumor sites, and recent cytotoxic therapy were associated with increased risk of all-cause mortality. Patients who received recent immunotherapies or targeted therapies did not have higher risk of overall mortality. CONCLUSION: Using N3C, we assembled the largest nationally representative cohort of patients with cancer and COVID-19 to date. We identified demographic and clinical factors associated with increased all-cause mortality in patients with cancer. Full characterization of the cohort will provide further insights into the effects of COVID-19 on cancer outcomes and the ability to continue specific cancer treatments.


Subject(s)
COVID-19/therapy , Neoplasms/mortality , Adolescent , Adult , Aged , COVID-19/diagnosis , COVID-19/mortality , Case-Control Studies , Cause of Death , Electronic Health Records , Female , Humans , Male , Middle Aged , Neoplasms/diagnosis , Neoplasms/therapy , Prognosis , Registries , Risk Assessment , Risk Factors , Time Factors , United States , Young Adult
9.
Ann Intern Med ; 174(10): 1395-1403, 2021 10.
Article in English | MEDLINE | ID: covidwho-1481181

ABSTRACT

BACKGROUND: Relatively little is known about the use patterns of potential pharmacologic treatments of COVID-19 in the United States. OBJECTIVE: To use the National COVID Cohort Collaborative (N3C), a large, multicenter, longitudinal cohort, to characterize the use of hydroxychloroquine, remdesivir, and dexamethasone, overall as well as across individuals, health systems, and time. DESIGN: Retrospective cohort study. SETTING: 43 health systems in the United States. PARTICIPANTS: 137 870 adults hospitalized with COVID-19 between 1 February 2020 and 28 February 2021. MEASUREMENTS: Inpatient use of hydroxychloroquine, remdesivir, or dexamethasone. RESULTS: Among 137 870 persons hospitalized with confirmed or suspected COVID-19, 8754 (6.3%) received hydroxychloroquine, 29 272 (21.2%) remdesivir, and 53 909 (39.1%) dexamethasone during the study period. Since the release of results from the RECOVERY (Randomised Evaluation of COVID-19 Therapy) trial in mid-June, approximately 78% to 84% of people who have had invasive mechanical ventilation have received dexamethasone or other glucocorticoids. The use of hydroxychloroquine increased during March 2020, peaking at 42%, and started declining by April 2020. By contrast, remdesivir and dexamethasone use gradually increased over the study period. Dexamethasone and remdesivir use varied substantially across health centers (intraclass correlation coefficient, 14.2% for dexamethasone and 84.6% for remdesivir). LIMITATION: Because most N3C data contributors are academic medical centers, findings may not reflect the experience of community hospitals. CONCLUSION: Dexamethasone, an evidence-based treatment of COVID-19, may be underused among persons who are mechanically ventilated. The use of remdesivir and dexamethasone varied across health systems, suggesting variation in patient case mix, drug access, treatment protocols, and quality of care. PRIMARY FUNDING SOURCE: National Center for Advancing Translational Sciences; National Heart, Lung, and Blood Institute; and National Institute on Aging.


Subject(s)
Adenosine Monophosphate/analogs & derivatives , Alanine/analogs & derivatives , Antiviral Agents/therapeutic use , COVID-19/drug therapy , Dexamethasone/therapeutic use , Hydroxychloroquine/therapeutic use , Practice Patterns, Physicians' , Adenosine Monophosphate/therapeutic use , Adolescent , Adult , Aged , Alanine/therapeutic use , Anti-Inflammatory Agents/therapeutic use , COVID-19/therapy , Female , Humans , Male , Middle Aged , Pandemics , Respiration, Artificial , Retrospective Studies , SARS-CoV-2 , United States , Young Adult
10.
Transplant Direct ; 7(11): e775, 2021 Nov.
Article in English | MEDLINE | ID: covidwho-1467456

ABSTRACT

Coronavirus disease 2019 (COVID-19) has resulted in significant morbidity and mortality in solid organ transplant (SOT) recipients. The National COVID Cohort Collaborative was developed to facilitate analysis of patient-level data for those tested for COVID-19 across the United States. METHODS: In this study, we identified a cohort of SOT recipients testing positive or negative for COVID-19 (COVID+ and COVID-, respectively) between January 1, 2020, and November 20, 2020. Univariable and multivariable logistic regression were used to determine predictors of a positive result among those tested. Outcomes following COVID-19 diagnosis were also explored. RESULTS: Of 18 121 SOT patients tested, 1925 were positive (10.6%). COVID+ SOT patients were more likely to have a kidney transplant and be non-White race. Comorbidities were common in all SOT patients but significantly more common in those who were COVID+. Of COVID+ SOT, 42.9% required hospital admission. COVID+ status was the strongest predictor of acute kidney injury (AKI), rejection, and graft failure in the 90 d after testing. A total of 40.9% of COVID+ SOT experienced a major adverse renal or cardiac event, 16.3% experienced a major adverse cardiac event, 35.3% experienced AKI, and 1.5% experienced graft loss. CONCLUSIONS: In the largest US cohort of COVID+ SOT recipients to date, we identified patient factors associated with the diagnosis of COVID-19 and outcomes following infection, including a high incidence of major adverse renal or cardiac event and AKI.

11.
Am J Transplant ; 22(1): 245-259, 2022 01.
Article in English | MEDLINE | ID: covidwho-1462722

ABSTRACT

While older males are at the highest risk for poor coronavirus disease 2019 (COVID-19) outcomes, it is not known if this applies to the immunosuppressed recipient of a solid organ transplant (SOT), nor how the type of allograft transplanted may impact outcomes. In a cohort study of adult (>18 years) patients testing positive for COVID-19 (January 1, 2020-June 21, 2021) from 56 sites across the United States identified using the National COVID Cohort Collaborative (N3C) Enclave, we used multivariable Cox proportional hazards models to assess time to MARCE after COVID-19 diagnosis in those with and without SOT. We examined the exposure of age-stratified recipient sex overall and separately in kidney, liver, lung, and heart transplant recipients. 3996 (36.4%) SOT and 91 646 (4.8%) non-SOT patients developed MARCE. Risk of post-COVID outcomes differed by transplant allograft type with heart and kidney recipients at highest risk. Males with SOT were at increased risk of MARCE, but to a lesser degree than the non-SOT cohort (HR 0.89, 95% CI 0.81-0.98 for SOT and HR 0.61, 95% CI 0.60-0.62 for non-SOT [females vs. males]). This represents the largest COVID-19 SOT cohort to date and the first-time sex-age-stratified and allograft-specific COVID-19 outcomes have been explored in those with SOT.


Subject(s)
COVID-19 , Organ Transplantation , Adult , COVID-19 Testing , Cohort Studies , Female , Humans , Kidney , Male , Organ Transplantation/adverse effects , SARS-CoV-2 , Transplant Recipients , United States
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