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Cold Spring Harb Mol Case Stud ; 2022 Jul 13.
Article in English | MEDLINE | ID: covidwho-1932006


The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of 104 SARS-CoV-2 genomes across the Bronx from March October 2020. Although the local structure of SARS-CoV-2 lineages mirrored those of New York City and New York State, temporal sampling revealed a dynamic and changing landscape of SARS-CoV-2 genomic diversity. Mapping the trajectories of mutations, we found that while some became 'endemic' to the Bronx, other, novel mutations rose in prevalence in the late summer/early fall. Geographically resolved genomes enabled us to distinguish between cases of reinfection and persistent infection in two pediatric patients. We propose that limited, targeted, temporal genomic surveillance has clinical and epidemiological utility in managing the ongoing COVID pandemic.

PLoS Med ; 18(12): e1003872, 2021 12.
Article in English | MEDLINE | ID: covidwho-1581903


BACKGROUND: The United States (US) Expanded Access Program (EAP) to coronavirus disease 2019 (COVID-19) convalescent plasma was initiated in response to the rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19. While randomized clinical trials were in various stages of development and enrollment, there was an urgent need for widespread access to potential therapeutic agents. The objective of this study is to report on the demographic, geographical, and chronological characteristics of patients in the EAP, and key safety metrics following transfusion of COVID-19 convalescent plasma. METHODS AND FINDINGS: Mayo Clinic served as the central institutional review board for all participating facilities, and any US physician could participate as a local physician-principal investigator. Eligible patients were hospitalized, were aged 18 years or older, and had-or were at risk of progression to-severe or life-threatening COVID-19; eligible patients were enrolled through the EAP central website. Blood collection facilities rapidly implemented programs to collect convalescent plasma for hospitalized patients with COVID-19. Demographic and clinical characteristics of all enrolled patients in the EAP were summarized. Temporal patterns in access to COVID-19 convalescent plasma were investigated by comparing daily and weekly changes in EAP enrollment in response to changes in infection rate at the state level. Geographical analyses on access to convalescent plasma included assessing EAP enrollment in all national hospital referral regions, as well as assessing enrollment in metropolitan areas and less populated areas that did not have access to COVID-19 clinical trials. From April 3 to August 23, 2020, 105,717 hospitalized patients with severe or life-threatening COVID-19 were enrolled in the EAP. The majority of patients were 60 years of age or older (57.8%), were male (58.4%), and had overweight or obesity (83.8%). There was substantial inclusion of minorities and underserved populations: 46.4% of patients were of a race other than white, and 37.2% of patients were of Hispanic ethnicity. Chronologically and geographically, increases in the number of both enrollments and transfusions in the EAP closely followed confirmed infections across all 50 states. Nearly all national hospital referral regions enrolled and transfused patients in the EAP, including both in metropolitan and in less populated areas. The incidence of serious adverse events was objectively low (<1%), and the overall crude 30-day mortality rate was 25.2% (95% CI, 25.0% to 25.5%). This registry study was limited by the observational and pragmatic study design that did not include a control or comparator group; thus, the data should not be used to infer definitive treatment effects. CONCLUSIONS: These results suggest that the EAP provided widespread access to COVID-19 convalescent plasma in all 50 states, including for underserved racial and ethnic minority populations. The study design of the EAP may serve as a model for future efforts when broad access to a treatment is needed in response to an emerging infectious disease. TRIAL REGISTRATION: NCT#: NCT04338360.

COVID-19/therapy , Compassionate Use Trials/methods , Health Services Needs and Demand/statistics & numerical data , Hospital Distribution Systems/organization & administration , Registries , Transfusion Reaction/complications , Transfusion Reaction/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/epidemiology , Ethnic and Racial Minorities , Female , Humans , Immunization, Passive/adverse effects , Immunization, Passive/methods , Inpatients , Male , Medically Underserved Area , Middle Aged , Pandemics , Patient Safety , SARS-CoV-2 , Treatment Outcome , United States
mSystems ; 5(4)2020 Jul 14.
Article in English | MEDLINE | ID: covidwho-646159


The coronavirus disease 2019 (COVID-19) pandemic currently in process differs from other infectious disease calamities that have previously plagued humanity in the vast amount of information that is produced each day, which includes daily estimates of the disease incidence and mortality data. Apart from providing actionable information to public health authorities on the trend of the pandemic, the daily incidence reflects the process of disease in a susceptible population and thus reflects the pathogenesis of COVID-19, the public health response, and diagnosis and reporting. Both new daily cases and daily mortality data in the United States exhibit periodic oscillatory patterns. By analyzing New York City (NYC) and Los Angeles (LA) testing data, we demonstrate that this oscillation in the number of cases can be strongly explained by the daily variation in testing. This seems to rule out alternative hypotheses, such as increased infections on certain days of the week, as driving this oscillation. Similarly, we show that the apparent oscillation in mortality in the U.S. data are mostly an artifact of reporting, which disappears in data sets that record death by episode date, such as the NYC and LA data sets. Periodic oscillations in COVID-19 incidence and mortality data reflect testing and reporting practices and contingencies. Thus, these contingencies should be considered first prior to suggesting biological mechanisms.IMPORTANCE The incidence and mortality data for the COVID-19 data in the United States show periodic oscillations, giving the curve a distinctive serrated pattern. In this study, we show that these periodic highs and lows in incidence and mortality data are due to daily differences in testing for the virus and death reporting, respectively. These findings are important because they provide an explanation based on public health practices and shortcomings rather than biological explanations, such as infection dynamics. In other words, when oscillations occur in epidemiological data, a search for causes should begin with how the public health system produces and reports the information before considering other causes, such as infection cycles and higher incidences of events on certain days. Our results suggest that when oscillations occur in epidemiological data, this may be a signal that there are shortcomings in the public health system generating that information.