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1.
J Acquir Immune Defic Syndr ; 90(3): 249-255, 2022 07 01.
Article in English | MEDLINE | ID: covidwho-1702599

ABSTRACT

BACKGROUND: It is not definitively known if persons with HIV (PWH) are more likely to be SARS-CoV-2 tested or test positive than persons without HIV (PWoH). We describe SARS-CoV-2 testing and positivity in 6 large geographically and demographically diverse cohorts of PWH and PWoH in the United States. SETTING: The Corona Infectious Virus Epidemiology Team comprises 5 clinical cohorts within a health system (Kaiser Permanente Northern California, Oakland, CA; Kaiser Permanente Mid-Atlantic States, Rockville, MD; University of North Carolina Health, Chapel Hill, NC; Vanderbilt University Medical Center, Nashville, TN; and Veterans Aging Cohort Study) and 1 interval cohort (Multicenter AIDS Cohort Study/Women's Interagency HIV Study Combined Cohort Study). METHODS: We calculated the proportion of patients SARS-CoV-2 tested and the test positivity proportion by HIV status from March 1 to December 31, 2020. RESULTS: The cohorts ranged in size from 1675 to 31,304 PWH and 1430 to 3,742,604 PWoH. The proportion of PWH who were tested for SARS-CoV-2 (19.6%-40.5% across sites) was significantly higher than PWoH (14.8%-29.4%) in the clinical cohorts. However, among those tested, the proportion of patients with positive SARS-CoV-2 tests was comparable by HIV status; the difference in proportion of SARS-CoV-2 positivity ranged from 4.7% lower to 1.4% higher. CONCLUSIONS: Although PWH had higher testing proportions compared with PWoH, we did not find evidence of increased positivity in 6 large, diverse populations across the United States. Ongoing monitoring of testing, positivity, and COVID-19-related outcomes in PWH are needed, given availability, response, and durability of COVID-19 vaccines; emergence of SARS-CoV-2 variants; and latest therapeutic options.


Subject(s)
COVID-19 , HIV Infections , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19 Testing , COVID-19 Vaccines , Cohort Studies , Female , HIV Infections/complications , HIV Infections/diagnosis , HIV Infections/epidemiology , Humans , SARS-CoV-2 , United States/epidemiology
3.
JAMA Netw Open ; 4(7): e2117175, 2021 07 01.
Article in English | MEDLINE | ID: covidwho-1306629
4.
J Biomed Inform ; 117: 103777, 2021 05.
Article in English | MEDLINE | ID: covidwho-1171479

ABSTRACT

From the start of the coronavirus disease 2019 (COVID-19) pandemic, researchers have looked to electronic health record (EHR) data as a way to study possible risk factors and outcomes. To ensure the validity and accuracy of research using these data, investigators need to be confident that the phenotypes they construct are reliable and accurate, reflecting the healthcare settings from which they are ascertained. We developed a COVID-19 registry at a single academic medical center and used data from March 1 to June 5, 2020 to assess differences in population-level characteristics in pandemic and non-pandemic years respectively. Median EHR length, previously shown to impact phenotype performance in type 2 diabetes, was significantly shorter in the SARS-CoV-2 positive group relative to a 2019 influenza tested group (median 3.1 years vs 8.7; Wilcoxon rank sum P = 1.3e-52). Using three phenotyping methods of increasing complexity (billing codes alone and domain-specific algorithms provided by an EHR vendor and clinical experts), common medical comorbidities were abstracted from COVID-19 EHRs, defined by the presence of a positive laboratory test (positive predictive value 100%, recall 93%). After combining performance data across phenotyping methods, we observed significantly lower false negative rates for those records billed for a comprehensive care visit (p = 4e-11) and those with complete demographics data recorded (p = 7e-5). In an early COVID-19 cohort, we found that phenotyping performance of nine common comorbidities was influenced by median EHR length, consistent with previous studies, as well as by data density, which can be measured using portable metrics including CPT codes. Here we present those challenges and potential solutions to creating deeply phenotyped, acute COVID-19 cohorts.


Subject(s)
COVID-19/diagnosis , Electronic Health Records , Phenotype , Comorbidity , Diabetes Mellitus, Type 2 , Global Health , Humans , Influenza, Human , Likelihood Functions , Pandemics
5.
J Am Med Inform Assoc ; 28(2): 393-401, 2021 02 15.
Article in English | MEDLINE | ID: covidwho-1054313

ABSTRACT

Our goal is to summarize the collective experience of 15 organizations in dealing with uncoordinated efforts that result in unnecessary delays in understanding, predicting, preparing for, containing, and mitigating the COVID-19 pandemic in the US. Response efforts involve the collection and analysis of data corresponding to healthcare organizations, public health departments, socioeconomic indicators, as well as additional signals collected directly from individuals and communities. We focused on electronic health record (EHR) data, since EHRs can be leveraged and scaled to improve clinical care, research, and to inform public health decision-making. We outline the current challenges in the data ecosystem and the technology infrastructure that are relevant to COVID-19, as witnessed in our 15 institutions. The infrastructure includes registries and clinical data networks to support population-level analyses. We propose a specific set of strategic next steps to increase interoperability, overall organization, and efficiencies.


Subject(s)
COVID-19 , Electronic Health Records , Information Dissemination , Information Systems/organization & administration , Public Health Practice , Academic Medical Centers , Humans , Registries , United States
7.
Am J Hum Genet ; 108(1): 194-201, 2021 01 07.
Article in English | MEDLINE | ID: covidwho-971875

ABSTRACT

Given the coronavirus disease 2019 (COVID-19) pandemic, investigations into host susceptibility to infectious diseases and downstream sequelae have never been more relevant. Pneumonia is a lung disease that can cause respiratory failure and hypoxia and is a common complication of infectious diseases, including COVID-19. Few genome-wide association studies (GWASs) of host susceptibility and severity of pneumonia have been conducted. We performed GWASs of pneumonia susceptibility and severity in the Vanderbilt University biobank (BioVU) with linked electronic health records (EHRs), including Illumina Expanded Multi-Ethnic Global Array (MEGAEX)-genotyped European ancestry (EA, n= 69,819) and African ancestry (AA, n = 15,603) individuals. Two regions of large effect were identified: the CFTR locus in EA (rs113827944; OR = 1.84, p value = 1.2 × 10-36) and HBB in AA (rs334 [p.Glu7Val]; OR = 1.63, p value = 3.5 × 10-13). Mutations in these genes cause cystic fibrosis (CF) and sickle cell disease (SCD), respectively. After removing individuals diagnosed with CF and SCD, we assessed heterozygosity effects at our lead variants. Further GWASs after removing individuals with CF uncovered an additional association in R3HCC1L (rs10786398; OR = 1.22, p value = 3.5 × 10-8), which was replicated in two independent datasets: UK Biobank (n = 459,741) and 7,985 non-overlapping BioVU subjects, who are genotyped on arrays other than MEGAEX. This variant was also validated in GWASs of COVID-19 hospitalization and lung function. Our results highlight the importance of the host genome in infectious disease susceptibility and severity and offer crucial insight into genetic effects that could potentially influence severity of COVID-19 sequelae.


Subject(s)
COVID-19/complications , COVID-19/genetics , Host-Pathogen Interactions/genetics , Pneumonia, Viral/complications , Pneumonia, Viral/genetics , Bronchitis/genetics , COVID-19/pathology , COVID-19/physiopathology , Cystic Fibrosis Transmembrane Conductance Regulator/genetics , Databases, Genetic , Electronic Health Records , Female , Genome-Wide Association Study , Genotype , Hemoglobins/genetics , Humans , Inpatients , Linkage Disequilibrium , Male , Outpatients , Pneumonia, Viral/pathology , Pneumonia, Viral/physiopathology , Polymorphism, Single Nucleotide/genetics , Principal Component Analysis , Pulmonary Disease, Chronic Obstructive/genetics , Reproducibility of Results , United Kingdom
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