Quantitative Reverse Transcription PCR Surveillance of SARS-CoV-2 Variants of Concern in Wastewater of Two Counties in Texas, United States
Ontology highlight
ABSTRACT:
SUBMITTER: Langan L
PROVIDER: S-EPMC9291321 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:IntroductionPrevious studies have shown that delayed detection of several cancers is related to socioeconomic deprivation as measured by the Wellbeing Index (WI) in Texas, the United States of America (USA). The current study investigates whether delayed cancer detection is related to lack of health insurance, physician shortage and higher percentages of Hispanics rather than WI per se since these factors are directly related to delayed cancer detection and may confound WI.MethodsCancer data and potential determinants of delayed cancer detection are derived from Texas Cancer Registry, Texas State Data Center, and Texas Department of State Health Services and U.S. Census Bureau. Texas cancer data from 1997 to 2003 are aggregated to calculate age-adjusted late- and early-stage cancer detection rates. The WI for each county is computed using data from the USA Census 2000. A weighted Tobit regression model is used to account for population size and censoring. The percentage of late-stage cancer cases is the dependent variable while independent variables include WI and the aforementioned potential confounders.ResultsDelayed detection of breast, lung, colorectal and female genital cancers is associated with higher percentage of uninsured residents (p < 0.05). Delayed detection is also associated with physician shortage and lower percentages of Hispanics for certain cancers ceteris paribus ( p < 0.05). The percentage of late-stage cases is positively correlated with WI for lung, and prostate cancers after adjusting for confounders ( p < 0.05).ConclusionsThe percentages of uninsured and Hispanic residents as well as physician supply are determinants of delayed detection for several cancers independently of WI, and vice versa. Identification of these determinants provides the evidence-base critical for decision makers to address specific issues for promoting early detection in effective cancer control.
| S-EPMC3517382 | biostudies-literature
Project description:Rabies virus found worldwide and prevalent throughout the United States continues to be a public health concern. Direct-fluorescent antibody (DFA) detection remains the gold standard for rabies virus diagnostics. Assessing the utility of a high-throughput molecular platform such as the QIAsymphony SP/AS, in conjunction with quantitative reverse transcription-PCR (qRT-PCR), to augment or potentially replace the DFA test, was the focus of this project. Here we describe a triplex qRT-PCR assay, including assembly and evaluation for sensitivity, specificity, and ability to detect variants. Additionally, we compared the qRT-PCR assay to the gold standard direct fluorescent-antibody test. More than 1,000 specimens submitted for routine rabies diagnosis were tested to directly compare the two methods. All results were in agreement between the two methods, with one additional specimen detected by qRT-PCR below the limits of the DFA sensitivity. With the proper continued validation for variant detection, molecular methods have a place in routine rabies diagnostics within the United States.
| S-EPMC4540915 | biostudies-literature
Project description:BackgroundThe gap between the highest and lowest life expectancies for race-county combinations in the United States is over 35 y. We divided the race-county combinations of the US population into eight distinct groups, referred to as the "eight Americas," to explore the causes of the disparities that can inform specific public health intervention policies and programs.Methods and findingsThe eight Americas were defined based on race, location of the county of residence, population density, race-specific county-level per capita income, and cumulative homicide rate. Data sources for population and mortality figures were the Bureau of the Census and the National Center for Health Statistics. We estimated life expectancy, the risk of mortality from specific diseases, health insurance, and health-care utilization for the eight Americas. The life expectancy gap between the 3.4 million high-risk urban black males and the 5.6 million Asian females was 20.7 y in 2001. Within the sexes, the life expectancy gap between the best-off and the worst-off groups was 15.4 y for males (Asians versus high-risk urban blacks) and 12.8 y for females (Asians versus low-income southern rural blacks). Mortality disparities among the eight Americas were largest for young (15-44 y) and middle-aged (45-59 y) adults, especially for men. The disparities were caused primarily by a number of chronic diseases and injuries with well-established risk factors. Between 1982 and 2001, the ordering of life expectancy among the eight Americas and the absolute difference between the advantaged and disadvantaged groups remained largely unchanged. Self-reported health plan coverage was lowest for western Native Americans and low-income southern rural blacks. Crude self-reported health-care utilization, however, was slightly higher for the more disadvantaged populations.ConclusionsDisparities in mortality across the eight Americas, each consisting of millions or tens of millions of Americans, are enormous by all international standards. The observed disparities in life expectancy cannot be explained by race, income, or basic health-care access and utilization alone. Because policies aimed at reducing fundamental socioeconomic inequalities are currently practically absent in the US, health disparities will have to be at least partly addressed through public health strategies that reduce risk factors for chronic diseases and injuries.
| S-EPMC1564165 | biostudies-literature
Project description:In this study, we reported the first long-term monitoring of SARS-CoV-2 in wastewater in Mainland China from November 2021 to October 2023. The city of Shijiazhuang was employed for this case study. We developed a triple reverse transcription droplet digital PCR (RT-ddPCR) method using triple primer-probes for simultaneous detection of the N1 gene, E gene, and Pepper mild mottle virus (PMMoV) to achieve accurate quantification of SARS-CoV-2 RNA in wastewater. Both the RT-ddPCR method and the commercial multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) method were implemented for the detection of SARS-CoV-2 in wastewater in Shijiazhuang City over a 24-month period. Results showed that SARS-CoV-2 was detected for the first time in the wastewater of Shijiazhuang City on 10 November 2022. The peak of COVID-19 cases occurred in the middle of December 2022, when the concentration of SARS-CoV-2 in the wastewater was highest. The trend of virus concentration increases and decreases forming a "long-tailed" shape in the COVID-19 outbreak and recession cycle. The results indicated that both multiplex RT-ddPCR and RT-qPCR are effective in detecting SARS-CoV-2 in wastewater, but RT-ddPCR is capable of detecting low concentrations of SARS-CoV-2 in wastewater which is more efficient. The SARS-CoV-2 abundance in wastewater is correlated to clinical data, outlining the public health utility of this work.HighlightsFirst long-term monitoring of SARS-CoV-2 in wastewater in Mainland ChinaCOVID-19 outbreak was tracked in Shijiazhuang City from outbreak to containmentWastewater was monitored simultaneously using RT-ddPCR and RT-qPCR methodsTriple primer-probe RT-ddPCR detects N1 and E genes of SARS-CoV-2 and PMMoV.
| S-EPMC10930138 | biostudies-literature
Project description:(1) Background: Stroke incidence and outcomes are influenced by socioeconomic status. There is a paucity of reported population-level studies regarding these determinants. The goal of this ecological analysis was to determine the county-level associations of social determinants of stroke hospitalization and death rates in the United States. (2) Methods: Publicly available data as of 9 April 2021, for the socioeconomic factors and outcomes, was extracted from the Centers for Disease Control and Prevention. The outcomes of interest were "all stroke hospitalization rates per 1000 Medicare beneficiaries" (SHR) and "all stroke death rates per 100,000 population" (SDR). We used a multivariate binomial generalized linear mixed model after converting the outcomes to binary based on their median values. (3) Results: A total of 3226 counties/county-equivalents of the states and territories in the US were analyzed. Heart disease prevalence (odds ratio, OR = 2.03, p < 0.001), blood pressure medication nonadherence (OR = 2.02, p < 0.001), age-adjusted obesity (OR = 1.24, p = 0.006), presence of hospitals with neurological services (OR = 1.9, p < 0.001), and female head of household (OR = 1.32, p = 0.021) were associated with high SHR while cost of care per capita for Medicare patients with heart disease (OR = 0.5, p < 0.01) and presence of hospitals (OR = 0.69, p < 0.025) were associated with low SHR. Median household income (OR = 0.6, p < 0.001) and park access (OR = 0.84, p = 0.016) were associated with low SDR while no college degree (OR = 1.21, p = 0.049) was associated with high SDR. (4) Conclusions: Several socioeconomic factors (e.g., education, income, female head of household) were found to be associated with stroke outcomes. Additional research is needed to investigate intermediate and potentially modifiable factors that can serve as targeted interventions.
| S-EPMC9320068 | biostudies-literature
Project description:This report updates surveillance results for COPD in the United States. For 1999 to 2011, data from national data systems for adults aged?25 years were analyzed. In 2011, 6.5% of adults (approximately 13.7 million) reported having been diagnosed with COPD. From 1999 to 2011, the overall age-adjusted prevalence of having been diagnosed with COPD declined (P=.019). In 2010, there were 10.3 million (494.8 per 10,000) physician office visits, 1.5 million (72.0 per 10,000) ED visits, and 699,000 (32.2 per 10,000) hospital discharges for COPD. From 1999 to 2010, no significant overall trends were noted for physician office visits and ED visits; however, the age-adjusted hospital discharge rate for COPD declined significantly (P=.001). In 2010 there were 312,654 (11.2 per 1,000) Medicare hospital discharge claims submitted for COPD. Medicare claims (1999-2010) declined overall (P=.045), among men (P=.022) and among enrollees aged 65 to 74 years (P=.033). There were 133,575 deaths (63.1 per 100,000) from COPD in 2010. The overall age-adjusted death rate for COPD did not change during 1999 to 2010 (P=.163). Death rates (1999-2010) increased among adults aged 45 to 54 years (P<.001) and among American Indian/Alaska Natives (P=.008) but declined among those aged 55 to 64 years (P=.002) and 65 to 74 years (P<.001), Hispanics (P=.038), Asian/Pacific Islanders (P<.001), and men (P=.001). Geographic clustering of prevalence, Medicare hospitalizations, and deaths were observed. Declines in the age-adjusted prevalence, death rate in men, and hospitalizations for COPD since 1999 suggest progress in the prevention of COPD in the United States.
| S-EPMC3707177 | biostudies-literature
Project description:Pulmonary hypertension (PH) is an uncommon but progressive condition, and much of what we know about it comes from specialized disease registries. With expanding research into the diagnosis and treatment of PH, it is important to provide updated surveillance on the impact of this disease on hospitalizations and mortality. This study, which builds on previous PH surveillance of mortality and hospitalization, analyzed mortality data from the National Vital Statistics System and data from the National Hospital Discharge Survey between 2001 and 2010. PH deaths were identified using International Classification of Diseases, Tenth Revision codes I27.0, I27.2, I27.8, or I27.9 as any contributing cause of death on the death certificate. Hospital discharges associated with PH were identified using International Classification of Diseases, Ninth Revision, Clinical Modification codes 416.0, 416.8, or 416.9 as one of up to seven listed medical diagnoses. The decline in death rates associated with PH among men from 1980 to 2005 has reversed and now shows a significant increasing trend. Similarly, the death rates for women with PH have continued to increase significantly during the past decade. PH-associated mortality rates for those aged 85 years and older have accelerated compared with rates for younger age groups. There have been significant declines in PH-associated mortality rates for those with pulmonary embolism and emphysema. Rates of hospitalization for PH have increased significantly for both men and women during the past decade; for those aged 85 years and older, hospitalization rates have nearly doubled. Continued surveillance helps us understand and address the evolving trends in hospitalization and mortality associated with PH and PH-associated conditions, especially regarding sex, age, and race/ethnicity disparities.
| S-EPMC4122278 | biostudies-other
Project description:Since the start of the COVID-19 pandemic in 2020, wastewater surveillance programs were established, or upscaled, in many countries around the world and have proven to be a cost-effective way of monitoring infectious disease pathogens. Many of these programs use RT-qPCR, and quantify the viral concentrations in samples based on standard curves, by including preparations of a reference material with known nucleic acid or virus concentrations in the RT-qPCR analyses. In high-throughput monitoring programs it is possible to combine data from multiple previous runs, circumventing the need for duplication and resulting in decreased costs and prolonged periods during which the reference material is obtained from the same batch. However, over time, systematic shifts in standard curves are likely to occur. This would affect the reliability and usefulness of wastewater surveillance as a whole. We aim to find an optimal combination of standard curve data to compensate for run-to-run measurement variance while ensuring enough flexibility to capture systematic longitudinal shifts. Based on more than 4000 observations obtained with the CDC N1 and N2 assays, taken as a part of the National Sewage Surveillance program at the Dutch National Institute for Public Health and the Environment, we show that seasonal and long-term shifts in RT-qPCR efficiency and sensitivity occur. We find that in our setting, using five days of standard-curve data to quantify, results in the least error prone curve or best approximation. This results in differences up to 100% in quantified viral loads when averaged out over a nationwide program of >300 treatment plants. Results show that combining standard curves from a limited set of runs can be a valid approach to quantification without obscuring the trends in the viral load of interest.
| S-EPMC10652756 | biostudies-literature
Project description: Not available
| S-EPMC8007286 | biostudies-literature
Project description:Monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) is critical for public health management of coronavirus disease. Sequencing is resource-intensive and incompletely representative, and not all isolates can be sequenced. Because wastewater SARS-CoV-2 RNA concentrations correlate with coronavirus disease incidence in sewersheds, tracking VOCs through wastewater is appealing. We developed digital reverse transcription PCRs to monitor abundance of select mutations in Alpha and Delta VOCs in wastewater settled solids, applied these to July 2020-August 2021 samples from 2 large US metropolitan sewersheds, and compared results to estimates of VOC abundance from case isolate sequencing. Wastewater measurements tracked closely with case isolate estimates (Alpha, rp 0.82-0.88; Delta, rp 0.97). Mutations were detected in wastewater even at levels <5% of total SARS-CoV-2 RNA and in samples available 1-3 weeks before case isolate results. Wastewater variant monitoring should be strategically deployed to complement case isolate sequencing.
| S-EPMC9045426 | biostudies-literature