Modeling the spread of COVID-19 in New York City.
Ontology highlight
ABSTRACT:
SUBMITTER: Olmo J
PROVIDER: S-EPMC8242800 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:As the COVID-19 pandemic continues, formulating targeted policy interventions that are informed by differential severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission dynamics will be of vital importance to national and regional governments. We develop an individual-level model for SARS-CoV-2 transmission that accounts for location-dependent distributions of age, household structure, and comorbidities. We use these distributions together with age-stratified contact matrices to instantiate specific models for Hubei, China; Lombardy, Italy; and New York City, United States. Using data on reported deaths to obtain a posterior distribution over unknown parameters, we infer differences in the progression of the epidemic in the three locations. We also examine the role of transmission due to particular age groups on total infections and deaths. The effect of limiting contacts by a particular age group varies by location, indicating that strategies to reduce transmission should be tailored based on population-specific demography and social structure. These findings highlight the role of between-population variation in formulating policy interventions. Across the three populations, though, we find that targeted "salutary sheltering" by 50% of a single age group may substantially curtail transmission when combined with the adoption of physical distancing measures by the rest of the population.
| S-EPMC7568285 | biostudies-literature
Project description:BackgroundFollowing the start of COVID-19 vaccination in New York City (NYC), cases have declined over 10-fold from the outbreak peak in January 2020, despite the emergence of highly transmissible variants. We evaluated the impact of NYC's vaccination campaign on saving lives as well as averting hospitalizations and cases.MethodsWe used an age-stratified agent-based model of COVID-19 to include transmission dynamics of Alpha, Gamma, Delta and Iota variants as identified in NYC. The model was calibrated and fitted to reported incidence in NYC, accounting for the relative transmissibility of each variant and vaccination rollout data. We simulated COVID-19 outbreak in NYC under the counterfactual scenario of no vaccination and compared the resulting disease burden with the number of cases, hospitalizations and deaths reported under the actual pace of vaccination.FindingsWe found that without vaccination, there would have been a spring-wave of COVID-19 in NYC due to the spread of Alpha and Delta variants. The COVID-19 vaccination campaign in NYC prevented such a wave, and averted 290,467 (95% CrI: 232,551 - 342,664) cases, 48,076 (95% CrI: 42,264 - 53,301) hospitalizations, and 8,508 (95% CrI: 7,374 - 9,543) deaths from December 14, 2020 to July 15, 2021.InterpretationOur study demonstrates that the vaccination program in NYC was instrumental to substantially reducing the COVID-19 burden and suppressing a surge of cases attributable to more transmissible variants. As the Delta variant sweeps predominantly among unvaccinated individuals, our findings underscore the urgent need to accelerate vaccine uptake and close the vaccination coverage gaps.FundingThis study was supported by The Commonwealth Fund.
| S-EPMC8556548 | biostudies-literature
Project description:BackgroundCOVID-19 has affected millions of people, and several chronic medical conditions appear to increase the risk of severe COVID-19. However, our understanding of COVID-19 outcomes in patients with CKD remains limited.MethodsThis was a retrospective cohort study of patients with and without CKD consecutively admitted with COVID-19 to three affiliated hospitals in New York City. Pre-COVID-19 CKD diagnoses were identified by billing codes and verified by manual chart review. In-hospital mortality was compared between patients with and without underlying CKD. Logistic regression was used to adjust this analysis for confounders and to identify patient characteristics associated with mortality.ResultsWe identified 280 patients with CKD, and 4098 patients without CKD hospitalized with COVID-19. The median age of the CKD group was 75 (65-84) years, and age of the non-CKD group 62 (48-75) years. Baseline (pre-COVID-19) serum creatinine in patients with CKD was 1.5 (1.2-2.2) mg/dl. In-hospital mortality was 30% in patients with CKD versus 20% in patients without CKD (P<0.001). The risk of in-hospital death in patients with CKD remained higher than in patients without CKD after adjustment for comorbidities (hypertension, diabetes mellitus, asthma, and chronic obstructive pulmonary disease), adjusted OR 1.4 (95% CI,1.1 to 1.9), P=0.01. When stratified by age, elderly patients with CKD (age >70 years) had higher mortality than their age-matched control patients without CKD. In patients with CKD, factors associated with in-hospital mortality were age (adjusted OR, 1.09 [95% CI, 1.06 to 1.12]), P<0.001, baseline and admission serum phosphorus (adjusted OR, 1.5 [95% CI, 1.03 to 2.1], P=0.03 and 1.4 [95% CI, 1.1 to 1.7], P=0.001), serum creatinine on admission >0.3 mg/dl above the baseline (adjusted OR 2.6 [95% CI, 1.2 to 5.4]P=0.01), and diagnosis of acute on chronic kidney injury during hospitalization (adjusted OR 4.6 [95% CI, 2.3 to 8.9], P<0.001).ConclusionsCKD is an independent risk factor for COVID-19-associated in-hospital mortality in elderly patients. Acute-on-chronic kidney injury increases the odds of in-hospital mortality in patients with CKD hospitalized with COVID-19.
| S-EPMC7901833 | biostudies-literature
Project description:INTRODUCTION:Existing socioeconomic and racial disparities in healthcare access in New York City have likely impacted the public health response to COVID-19. An ecological study was performed to determine the spatial distribution of COVID-19 testing by ZIP code Tabulation Area and investigate if testing was associated with race or SES. METHODS:Data were obtained from the New York City coronavirus data repository and 2018 American Community Survey 5-year estimates. A combined index of SES was created using principal component analysis and incorporated household income, gross rent, poverty, education, working class status, unemployment, and occupants per room. Multivariable Poisson regressions were performed to predict the number of total tests and the ratio of positive tests to total tests performed, using the SES index, racial composition, and Hispanic composition as predictors. RESULTS:The number of total tests significantly increased with the increasing proportion of white residents (?=0.004, SE=0.001, p=0.0032) but not with increasing Hispanic composition or SES index score. The ratio of positive tests to total tests significantly decreased with the increasing proportion of white residents in the ZIP code Tabulation Area (?= -0.003, SE=0.000 6, p<0.001) and with increasing SES index score (?= -0.001 6, SE=0.0007, p=0.0159). CONCLUSIONS:In New York City, COVID-19 testing has not been proportional to need; existing socioeconomic and racial disparities in healthcare access have likely impacted public health response. There is urgent need for widespread testing and public health outreach for the most vulnerable communities in New York City.
| S-EPMC7316038 | biostudies-literature
Project description: Not available
| S-EPMC8025442 | biostudies-literature
Project description:A surveillance system that uses census tract resolution and the SaTScan prospective space-time scan statistic detected clusters of increasing severe acute respiratory syndrome coronavirus 2 test percent positivity in New York City, NY, USA. Clusters included one in which patients attended the same social gathering and another that led to targeted testing and outreach.
| S-EPMC8084513 | biostudies-literature
Project description:PurposeNew York City (NYC) was the global epicenter of the COVID-19 pandemic in spring 2020. A "shelter in place" mandate was issued in March 2020. The effect on vulnerable populations of adolescent and young adult females has not been well documented.MethodsWe administered a monthly online survey between May and November 2020 to adolescent and young adult females participating in a longitudinal study at Mount Sinai Adolescent Health Center. Surveys asked about death of loved ones, financial impacts, social interactions, exposure to dangerous situations, and mental health impacts. Differences in responses by age, race/ethnicity, and living situation were assessed, and compared to data obtained on the same cohort prior to the pandemic.ResultsFour hundred seventeen females aged 15-28 years completed at least one survey, 94% of whom were youth of color. A third of responders (33%) had lost relatives or other people they were close to (loved ones). Most (68%) reported one or more financial losses, and 21% reported food insecurity, with those not living with parents or a guardian experiencing significantly higher rates. One in 10 reported experiencing sexual abuse or interpersonal partner violence during the "shelter in place" period. Over a third (37%) reported symptoms of clinical depression, which represented a significant increase compared to before the pandemic (p = .01). The negative financial impacts and higher proportion of patients with depressive symptomatology remained elevated for adolescents without support at home.ConclusionsThe COVID-19 pandemic had unprecedented negative short-term financial and psychosocial health impacts on inner-city female youth with potential long-term negative impacts.
| S-EPMC8547169 | biostudies-literature
Project description:BACKGROUND:Little is known about the effect of the Coronavirus disease 2019 pandemic on stroke care and the impact of the epidemic on acute stroke hospitalizations has not been described. METHODS:We analyze the stroke admission rate in three hospitals in New York City from January 1, 2020 through April 17, 2020, identifying all cases of acute ischemic stroke, intraparenchymal hemorrhage and subarachnoid hemorrhage. RESULTS:We confirmed 518 cases of out-of-hospital stroke. During the baseline period up to February 25, 2020, the daily stroke admission rate was stable, with the slope of the regression describing the number of admissions over time equal to -0.33 (se?=?1.21), not significantly different from 0 (p?=?0.79), with daily admissions averaging 41. During the pandemic period, the slope was -4.4 (se?=?1.00); i.e., the number of stroke admissions decreased an average of 4.4 per week, (p?=?0.005), with weekly admissions averaging 23, a reduction of 44% versus baseline. This general result was not different by patient age, sex, or race/ethnicity. CONCLUSIONS:The weekly stroke admission rate started declining two weeks prior to the local surge of coronavirus admissions. The consequences of lack of diagnosis and treatment of a large proportion of acute stroke patients are likely severe and lasting.
| S-EPMC7355321 | biostudies-literature
Project description:Black and Hispanic communities in the U.S. have endured a disproportionate burden of COVID-19-related morbidity and mortality. Racial and ethnic health disparities such as these are frequently aggravated by inequitable access to healthcare resources in disadvantaged communities. Yet, no known studies have investigated disadvantaged communities' access to COVID-19-related healthcare resources. The current study accordingly examined racial and ethnic differences in (1) April 2020 COVID-19 total and positive viral test rates across 177 New York City (NYC) ZIP Code Tabulation Areas (ZCTA); and (2) November 2019-April 2020 licensed and intensive care unit (ICU) hospital bed access across 194 NYC ZCTAs. Pairwise analyses indicated higher COVID-19 total and positive test rates per 1000 persons in majority Black and Hispanic vs. majority White ZCTAs (CI [0.117, 4.55]; CI [2.53, 5.14]). Multiple linear regression analyses indicated that higher percentage of Black and Hispanic residents predicted more total COVID-19 tests per 1000 persons (p < 0.05). In contrast, majority Black and Hispanic ZCTAs had fewer licensed and ICU beds (CI [6.50, 124.25]; CI [0.69, 7.16]), with social disadvantage predicting lower licensed and ICU bed access per 1000 persons (p < 0.01). While news reports of inequitable access to COVID-19-related healthcare resources in ethnocultural minority communities have emerged, this is the first study to reveal that social disadvantage may be a major driver of hospital resource inequities in Black and Hispanic communities. Thus, it will be imperative to enact policies that ensure equitable allocation of healthcare resources to socially disadvantaged communities to address current and future public health crises.
| S-EPMC7536513 | biostudies-literature
Project description:In December 2019, a new, severe coronavirus (COVID-19) appeared in Wuhan, China. Shortly after, the first COVID-19 case was confirmed in the United States. The emergence of this virus led many United States governors to enact executive orders in an effort to limit the person-to-person spread of the virus. One state that utilized such measures was New York, which contains New York City (NYC), the most populous city in the United States. Many reports have shown that due to the government-backed shutdowns, the air quality in major global cities improved. However, there has been only limited work on whether this same trend is seen throughout the United States, specifically within the densely populated NYC area. Thus, the focus of this study was to examine whether changes in air quality were observed in NYC resulting from New York State's COVID-19-associated shutdown measures. To do this, daily concentrations of fine particulate matter (PM2.5) and nitrogen dioxide (NO2) were obtained from 15 central monitoring stations throughout the five NYC boroughs for the first 17 weeks (January through May) of 2015-2020. Decreases in PM2.5 (36%) and NO2 (51%) concentrations were observed shortly after the shutdown took place; however, using a linear time lag model, when changes in these pollutant concentrations were compared to those measured during the same span of time in 2015-2019, no significant difference between the years was found. Therefore, we highlight the importance of considering temporal variability and long-term trends of pollutant concentrations when analyzing for short-term differences in air pollutant concentrations related to the COVID-19 shutdowns.
| S-EPMC7314691 | biostudies-literature