Breakthrough SARS-CoV-2 infections, morbidity, and seroreactivity following initial COVID-19 vaccination series and additional dose in patients with SLE in New York City.
Ontology highlight
ABSTRACT:
SUBMITTER: Saxena A
PROVIDER: S-EPMC9275793 | biostudies-literature | 2022 Sep
REPOSITORIES: biostudies-literature
Publications
Breakthrough SARS-CoV-2 infections, morbidity, and seroreactivity following initial COVID-19 vaccination series and additional dose in patients with SLE in New York City.
Saxena Amit A Engel Alexis J AJ Banbury Brittany B Hasan Ghadeer G Fraser Nicola N Zaminski Devyn D Masson Mala M Haberman Rebecca H RH Scher Jose U JU Ho Gary G Law Jammie J Rackoff Paula P Tseng Chung-E CE Belmont H Michael HM Clancy Robert M RM Buyon Jill P JP Izmirly Peter M PM
The Lancet. Rheumatology 20220712 9
Similar Datasets
Project description:Bacteriophages are abundant members of all microbiomes studied to date, influencing microbial communities through interactions with their bacterial hosts. Despite their functional importance and ubiquity, phages have been underexplored in urban environments compared to their bacterial counterparts. We profiled the viral communities in New York City (NYC) wastewater using metagenomic data collected in November 2014 from 14 wastewater treatment plants. We show that phages accounted for the largest viral component of the sewage samples and that specific virus communities were associated with local environmental conditions within boroughs. The vast majority of the virus sequences had no homology matches in public databases, forming an average of 1,700 unique virus clusters (putative genera). These new clusters contribute to elucidating the overwhelming proportion of data that frequently goes unidentified in viral metagenomic studies. We assigned potential hosts to these phages, which appear to infect a wide range of bacterial genera, often outside their presumed host. We determined that infection networks form a modular-nested pattern, indicating that phages include a range of host specificities, from generalists to specialists, with most interactions organized into distinct groups. We identified genes in viral contigs involved in carbon and sulfur cycling, suggesting functional importance of viruses in circulating pathways and gene functions in the wastewater environment. In addition, we identified virophage genes as well as a nearly complete novel virophage genome. These findings provide an understanding of phage abundance and diversity in NYC wastewater, previously uncharacterized, and further examine geographic patterns of phage-host association in urban environments.IMPORTANCE Wastewater is a rich source of microbial life and contains bacteria, viruses, and other microbes found in human waste as well as environmental runoff sources. As part of an effort to characterize the New York City wastewater metagenome, we profiled the viral community of sewage samples across all five boroughs of NYC and found that local sampling sites have unique sets of viruses. We focused on bacteriophages, or viruses of bacteria, to understand how they may influence the microbial ecology of this system. We identified several new clusters of phages and successfully associated them with bacterial hosts, providing insight into virus-host interactions in urban wastewater. This study provides a first look into the viral communities present across the wastewater system in NYC and points to their functional importance in this environment.
| S-EPMC7300365 | biostudies-literature
Project description:Study on SARS-CoV-2 breaktrough infections at University Hospital Essen
| PRJEB59607 | ENA
Project description:ObjectiveTo investigate differences in severe maternal morbidity between Hispanic mothers and three major Hispanic subgroups compared with non-Hispanic white mothers and the extent to which differences in delivery hospitals may contribute to excess morbidity among Hispanic mothers.MethodsWe conducted a population-based cross-sectional study using linked 2011-2013 New York City discharge and birth certificate data sets (n=353,773). Rates of severe maternal morbidity were calculated using a published algorithm based on diagnosis and procedure codes. Mixed-effects logistic regression with a random hospital-specific intercept was used to generate risk-standardized severe maternal morbidity rates for each hospital taking into consideration patient sociodemographic characteristics and comorbidities. Differences in the distribution of Hispanic and non-Hispanic white deliveries were assessed among these hospitals in relation to their risk-adjusted morbidity. Sensitivity analyses were conducted after excluding isolated blood transfusion from the morbidity composite.ResultsSevere maternal morbidity occurred in 4,541 deliveries and was higher among Hispanic than non-Hispanic white women (2.7% compared with 1.5%, P<.001); this rate was 2.9% among those who were Puerto Rican, 2.7% among those who were foreign-born Dominican, and 3.3% among those who were foreign-born Mexican. After adjustment for patient characteristics, the risk remained elevated for Hispanic women (odds ratio [OR] 1.42, 95% confidence interval [CI] 1.22-1.66) and for all three subgroups compared with non-Hispanic white women (P<.001). Risk for Hispanic women was attenuated in sensitivity analyses (OR 1.17, 95% CI 1.02-1.33). Risk-standardized morbidity across hospitals varied sixfold. We estimate that Hispanic-non-Hispanic white differences in delivery location may contribute up to 37% of the ethnic disparity in severe maternal morbidity rates in New York City hospitals.ConclusionHispanic compared with non-Hispanic white mothers are more likely to deliver at hospitals with higher risk-adjusted severe maternal morbidity rates and these differences in site of delivery may contribute to excess morbidity among Hispanic mothers. Our results suggest improving quality at the lowest performing hospitals could benefit both non-Hispanic white and Hispanic women and reduce ethnic disparities in severe maternal morbidity rates.
| S-EPMC5380443 | biostudies-literature
Project description:The efficacy of COVID-19 mRNA vaccines is high, but breakthrough infections still occur. We compared the SARS-CoV-2 genomes of 76 breakthrough cases after full vaccination with BNT162b2 (Pfizer/BioNTech), mRNA-1273 (Moderna), or JNJ-78436735 (Janssen) to unvaccinated controls (February-April 2021) in metropolitan New York, including their phylogenetic relationship, distribution of variants, and full spike mutation profiles. The median age of patients in the study was 48 years; 7 required hospitalization and 1 died. Most breakthrough infections (57/76) occurred with B.1.1.7 (Alpha) or B.1.526 (Iota). Among the 7 hospitalized cases, 4 were infected with B.1.1.7, including 1 death. Both unmatched and matched statistical analyses considering age, sex, vaccine type, and study month as covariates supported the null hypothesis of equal variant distributions between vaccinated and unvaccinated in χ2 and McNemar tests (P > 0.1), highlighting a high vaccine efficacy against B.1.1.7 and B.1.526. There was no clear association among breakthroughs between type of vaccine received and variant. In the vaccinated group, spike mutations in the N-terminal domain and receptor-binding domain that have been associated with immune evasion were overrepresented. The evolving dynamic of SARS-CoV-2 variants requires broad genomic analyses of breakthrough infections to provide real-life information on immune escape mediated by circulating variants and their spike mutations.
| S-EPMC8439605 | biostudies-literature
Project description:ImportanceNew York City, an early epicenter of the pandemic, invested heavily in its COVID-19 vaccination campaign to mitigate the burden of disease outbreaks. Understanding the return on investment (ROI) of this campaign would provide insights into vaccination programs to curb future COVID-19 outbreaks.ObjectiveTo estimate the ROI of the New York City COVID-19 vaccination campaign by estimating the tangible direct and indirect costs from a societal perspective.Design, setting, and participantsThis decision analytical model of disease transmission was calibrated to confirmed and probable cases of COVID-19 in New York City between December 14, 2020, and January 31, 2022. This simulation model was validated with observed patterns of reported hospitalizations and deaths during the same period.ExposuresAn agent-based counterfactual scenario without vaccination was simulated using the calibrated model.Main outcomes and measuresCosts of health care and deaths were estimated in the actual pandemic trajectory with vaccination and in the counterfactual scenario without vaccination. The savings achieved by vaccination, which were associated with fewer outpatient visits, emergency department visits, emergency medical services, hospitalizations, and intensive care unit admissions, were also estimated. The value of a statistical life (VSL) lost due to COVID-19 death and the productivity loss from illness were accounted for in calculating the ROI.ResultsDuring the study period, the vaccination campaign averted an estimated $27.96 (95% credible interval [CrI], $26.19-$29.84) billion in health care expenditures and 315 724 (95% CrI, 292 143-340 420) potential years of life lost, averting VSL loss of $26.27 (95% CrI, $24.39-$28.21) billion. The estimated net savings attributable to vaccination were $51.77 (95% CrI, $48.50-$55.85) billion. Every $1 invested in vaccination yielded estimated savings of $10.19 (95% CrI, $9.39-$10.87) in direct and indirect costs of health outcomes that would have been incurred without vaccination.Conclusions and relevanceResults of this modeling study showed an association of the New York City COVID-19 vaccination campaign with reduction in severe outcomes and avoidance of substantial economic losses. This significant ROI supports continued investment in improving vaccine uptake during the ongoing pandemic.
| S-EPMC9679875 | biostudies-literature
Project description:BackgroundAlthough relatively rare, rifampin mono-resistant tuberculosis (RMR TB) poses important challenges to effective TB treatment and control. Information on the burden of RMR TB and treatment outcomes is needed to inform diagnosis and management.MethodsStandardized variables were collected from the New York City (NYC) tuberculosis surveillance system for patients treated for RMR TB in NYC during 2010-2021.ResultsOf 7097 TB cases reported in 2010-2021, 31 (<1%) were treated clinically as RMR TB. Five (16%) of these patients had HIV. Seventeen patients (55%) had TB that was rifampin-resistant by both molecular and phenotypic drug susceptibility testing; 2 (6%) had rifampin resistance by phenotypic tests, and molecular tests were not done; and 12 (39%) were identified based only on molecular tests. Among these 12, 7 were rifampin-sensitive by phenotypic tests, and phenotypic testing could not be done for the other 5. Ten of the 31 (32%) were diagnosed in 2010-2015; the other 21 (including 10/12 diagnosed by molecular tests alone) were diagnosed in 2016-2021. Of the 31 patients, 21 (68%) completed treatment (median treatment duration of 18 months). Although the interval between tuberculosis treatment initiation and change to a non-rifamycin-containing regimen decreased significantly during the study period, the overall duration of treatment did not decrease significantly between 2010 and 2021.ConclusionsMolecular drug susceptibility tests identified cases of RMR TB that were not detected by phenotypic testing and helped enable timely adjustment of tuberculosis treatment regimens. Short-course regimens are needed to reduce duration of treatment for RMR TB.
| S-EPMC10662657 | biostudies-literature
Project description:Shotgun metagenomic sequencing of NYC raw sewage samples
| PRJEB28033 | ENA
Project description:18S rRNA gene V4 region amplicon sequencing of protists in NYC environmental samples
| PRJEB23950 | ENA
Project description:18S rRNA gene V9 region amplicon sequencing of protists in NYC environmental samples
| PRJEB26690 | ENA
Project description: Not available
| S-EPMC7879030 | biostudies-literature