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1.
Microbiol Spectr ; 11(3): e0039123, 2023 Jun 15.
Article in English | MEDLINE | ID: covidwho-2315092

ABSTRACT

Wastewater-based epidemiology has emerged as a powerful public health tool to trace new outbreaks, detect trends in infection, and provide an early warning of COVID-19 community spread. Here, we investigated the spread of SARS-CoV-2 infections across Utah by characterizing lineages and mutations detected in wastewater samples. We sequenced over 1,200 samples from 32 sewersheds collected between November 2021 and March 2022. Wastewater sequencing confirmed the presence of Omicron (B.1.1.529) in Utah in samples collected on November 19, 2021, up to 10 days before its corresponding detection via clinical sequencing. Analysis of diversity of SARS-CoV-2 lineages revealed Delta as the most frequently detected lineage during November 2021 (67.71%), but it started declining in December 2021 with the onset of Omicron (B.1.1529) and its sublineage BA.1 (6.79%). The proportion of Omicron increased to ~58% by January 4, 2022, and completely displaced Delta by February 7, 2022. Wastewater genomic surveillance revealed the presence of Omicron sublineage BA.3, a lineage that was not identified from Utah's clinical surveillance. Interestingly, several Omicron-defining mutations began to appear in early November 2021 and increased in prevalence across sewersheds from December to January, aligning with the surge in clinical cases. Our study highlights the importance of tracking epidemiologically relevant mutations in detecting emerging lineages in the early stages of an outbreak. Wastewater genomic epidemiology provides an unbiased representation of community-wide infection dynamics and is an excellent complementary tool to SARS-CoV-2 clinical surveillance, with the potential of guiding public health action and policy decisions. IMPORTANCE SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has had a significant impact on public health. Global emergence of novel SARS-CoV-2 variants, shift to at-home tests, and reduction in clinical tests demonstrate the need for a reliable and effective surveillance strategy to contain COVID-19 spread. Monitoring of SARS-CoV-2 viruses in wastewater is an effective way to trace new outbreaks, establish baseline levels of infection, and complement clinical surveillance efforts. Wastewater genomic surveillance, in particular, can provide valuable insights into the evolution and spread of SARS-CoV-2 variants. We characterized the diversity of SARS-CoV-2 mutations and lineages using whole-genome sequencing to trace the introduction of lineage B.1.1.519 (Omicron) in Utah. Our data showed that Omicron appeared in Utah on November 19, 2021, up to 10 days prior to its detection in patient samples, indicating that wastewater surveillance provides an early warning signal. Our findings are important from a public health perspective as timely identification of communities with high COVID-19 transmission could help guide public health interventions.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Wastewater , Wastewater-Based Epidemiological Monitoring , Utah/epidemiology , Pandemics , COVID-19/diagnosis , COVID-19/epidemiology , Genomics
2.
Emerg Infect Dis ; 29(2): 422-425, 2023 02.
Article in English | MEDLINE | ID: covidwho-2278819

ABSTRACT

Candida auris transmission is steadily increasing across the United States. We report culture-based detection of C. auris in wastewater and the epidemiologic link between isolated strains and southern Nevada, USA, hospitals within the sampled sewershed. Our results illustrate the potential of wastewater surveillance for containing C. auris.


Subject(s)
Candida , Candidiasis , Humans , United States/epidemiology , Candidiasis/drug therapy , Candida auris , Wastewater , Nevada/epidemiology , Wastewater-Based Epidemiological Monitoring , Disease Outbreaks , Antifungal Agents/therapeutic use
3.
MMWR Morb Mortal Wkly Rep ; 70(36): 1242-1244, 2021 Sep 10.
Article in English | MEDLINE | ID: covidwho-1441395

ABSTRACT

Wastewater surveillance, the measurement of pathogen levels in wastewater, is used to evaluate community-level infection trends, augment traditional surveillance that leverages clinical tests and services (e.g., case reporting), and monitor public health interventions (1). Approximately 40% of persons infected with SARS-CoV-2, the virus that causes COVID-19, shed virus RNA in their stool (2); therefore, community-level trends in SARS-CoV-2 infections, both symptomatic and asymptomatic (2) can be tracked through wastewater testing (3-6). CDC launched the National Wastewater Surveillance System (NWSS) in September 2020 to coordinate wastewater surveillance programs implemented by state, tribal, local, and territorial health departments to support the COVID-19 pandemic response. In the United States, wastewater surveillance was not previously implemented at the national level. As of August 2021, NWSS includes 37 states, four cities, and two territories. This report summarizes NWSS activities and describes innovative applications of wastewater surveillance data by two states, which have included generating alerts to local jurisdictions, allocating mobile testing resources, evaluating irregularities in traditional surveillance, refining health messaging, and forecasting clinical resource needs. NWSS complements traditional surveillance and enables health departments to intervene earlier with focused support in communities experiencing increasing concentrations of SARS-CoV-2 in wastewater. The ability to conduct wastewater surveillance is not affected by access to health care or the clinical testing capacity in the community. Robust, sustainable implementation of wastewater surveillance requires public health capacity for wastewater testing, analysis, and interpretation. Partnerships between wastewater utilities and public health departments are needed to leverage wastewater surveillance data for the COVID-19 response for rapid assessment of emerging threats and preparedness for future pandemics.


Subject(s)
COVID-19/prevention & control , Pandemics/prevention & control , Public Health Surveillance/methods , SARS-CoV-2/isolation & purification , Wastewater/virology , COVID-19/epidemiology , Centers for Disease Control and Prevention, U.S. , Humans , United States/epidemiology
4.
Emerg Infect Dis ; 27(9): 1-8, 2021 09.
Article in English | MEDLINE | ID: covidwho-1369632

ABSTRACT

Wastewater surveillance for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has garnered extensive public attention during the coronavirus disease pandemic as a proposed complement to existing disease surveillance systems. Over the past year, methods for detection and quantification of SARS-CoV-2 viral RNA in untreated sewage have advanced, and concentrations in wastewater have been shown to correlate with trends in reported cases. Despite the promise of wastewater surveillance, for these measurements to translate into useful public health tools, bridging the communication and knowledge gaps between researchers and public health responders is needed. We describe the key uses, barriers, and applicability of SARS-CoV-2 wastewater surveillance for supporting public health decisions and actions, including establishing ethics consideration for monitoring. Although wastewater surveillance to assess community infections is not a new idea, the coronavirus disease pandemic might be the initiating event to make this emerging public health tool a sustainable nationwide surveillance system, provided that these barriers are addressed.


Subject(s)
COVID-19 , Public Health , Humans , Pandemics , SARS-CoV-2 , Wastewater
5.
MMWR Morb Mortal Wkly Rep ; 70(15): 557-559, 2021 Apr 16.
Article in English | MEDLINE | ID: covidwho-1187180

ABSTRACT

During December 3, 2020-January 31, 2021, CDC, in collaboration with the University of Utah Health and Economic Recovery Outreach Project,* Utah Department of Health (UDOH), Salt Lake County Health Department, and one Salt Lake county school district, offered free, in-school, real-time reverse transcription-polymerase chain reaction (RT-PCR) saliva testing as part of a transmission investigation of SARS-CoV-2, the virus that causes COVID-19, in elementary school settings. School contacts† of persons with laboratory-confirmed SARS-CoV-2 infection, including close contacts, were eligible to participate (1). Investigators approached parents or guardians of student contacts by telephone, and during January, using school phone lines to offer in-school specimen collection; the testing procedures were explained in the preferred language of the parent or guardian. Consent for participants was obtained via an electronic form sent by e-mail. Analyses examined participation (i.e., completing in-school specimen collection for SARS-CoV-2 testing) in relation to factors§ that were programmatically important or could influence likelihood of SARS-CoV-2 testing, including race, ethnicity, and SARS-CoV-2 incidence in the community (2). Crude prevalence ratios (PRs) were calculated using univariate log-binomial regression.¶ This activity was reviewed by CDC and was conducted consistent with federal law and CDC policy.*.


Subject(s)
COVID-19 Nucleic Acid Testing/statistics & numerical data , COVID-19/prevention & control , School Health Services/statistics & numerical data , COVID-19/epidemiology , COVID-19/transmission , Child , Contact Tracing , Humans , Schools/statistics & numerical data , Socioeconomic Factors , Utah/epidemiology
6.
Sci Total Environ ; 775: 145790, 2021 Jun 25.
Article in English | MEDLINE | ID: covidwho-1093220

ABSTRACT

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the coronavirus disease (COVID-19), is shed in feces and the viral ribonucleic acid (RNA) is detectable in wastewater. A nine-week wastewater epidemiology study of ten wastewater facilities, serving 39% of the state of Utah or 1.26 M individuals was conducted in April and May of 2020. COVID-19 cases were tabulated from within each sewershed boundary. RNA from SARS-CoV-2 was detectable in 61% of 126 wastewater samples. Urban sewersheds serving >100,000 individuals and tourist communities had higher detection frequencies. An outbreak of COVID-19 across two communities positively correlated with an increase in wastewater SARS-CoV-2 RNA, while a decline in COVID-19 cases preceded a decline in RNA. SARS-CoV-2 RNA followed a first order decay rate in wastewater, while 90% of the RNA was present in the liquid phase of the influent. Infiltration and inflow, virus decay and sewershed characteristics should be considered during correlation analysis of SAR-CoV-2 with COVID-19 cases. These results provide evidence of the utility of wastewater epidemiology to assist in public health responses to COVID-19.


Subject(s)
COVID-19 , Coronavirus , Cost of Illness , Humans , RNA, Viral , SARS-CoV-2 , Utah , Wastewater
7.
MMWR Morb Mortal Wkly Rep ; 69(38): 1369-1373, 2020 Sep 25.
Article in English | MEDLINE | ID: covidwho-792654

ABSTRACT

Coronavirus disease 2019 (COVID-19) has had a substantial impact on racial and ethnic minority populations and essential workers in the United States, but the role of geographic social and economic inequities (i.e., deprivation) in these disparities has not been examined (1,2). As of July 9, 2020, Utah had reported 27,356 confirmed COVID-19 cases. To better understand how area-level deprivation might reinforce ethnic, racial, and workplace-based COVID-19 inequities (3), the Utah Department of Health (UDOH) analyzed confirmed cases of infection with SARS-CoV-2 (the virus that causes COVID-19), COVID-19 hospitalizations, and SARS-CoV-2 testing rates in relation to deprivation as measured by Utah's Health Improvement Index (HII) (4). Age-weighted odds ratios (weighted ORs) were calculated by weighting rates for four age groups (≤24, 25-44, 45-64, and ≥65 years) to a 2000 U.S. Census age-standardized population. Odds of infection increased with level of deprivation and were two times greater in high-deprivation areas (weighted OR = 2.08; 95% confidence interval [CI] = 1.99-2.17) and three times greater (weighted OR = 3.11; 95% CI = 2.98-3.24) in very high-deprivation areas, compared with those in very low-deprivation areas. Odds of hospitalization and testing also increased with deprivation, but to a lesser extent. Local jurisdictions should use measures of deprivation and other social determinants of health to enhance transmission reduction strategies (e.g., increasing availability and accessibility of SARS-CoV-2 testing and distributing prevention guidance) to areas with greatest need. These strategies might include increasing availability and accessibility of SARS-CoV-2 testing, contact tracing, isolation options, preventive care, disease management, and prevention guidance to facilities (e.g., clinics, community centers, and businesses) in areas with high levels of deprivation.


Subject(s)
Clinical Laboratory Techniques/statistics & numerical data , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Health Status Disparities , Healthcare Disparities/statistics & numerical data , Hospitalization/statistics & numerical data , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , Poverty Areas , Adult , Aged , COVID-19 , COVID-19 Testing , Coronavirus Infections/diagnosis , Humans , Incidence , Middle Aged , Risk Factors , Utah/epidemiology , Young Adult
8.
MMWR Morb Mortal Wkly Rep ; 69(33): 1133-1138, 2020 Aug 21.
Article in English | MEDLINE | ID: covidwho-724119

ABSTRACT

Improved understanding of the overall distribution of workplace coronavirus disease 2019 (COVID-19) outbreaks by industry sector could help direct targeted public health action; however, this has not been described. The Utah Department of Health (UDOH) analyzed COVID-19 surveillance data to describe workplace outbreaks by industry sectors. In this report, workplaces refer to non-health care, noncongregate-living, and noneducational settings. As of June 5, 2020, UDOH reported 277 COVID-19 outbreaks, 210 (76%) of which occurred in workplaces. Approximately 12% (1,389 of 11,448) of confirmed COVID-19 cases in Utah were associated with workplace outbreaks. The 210 workplace outbreaks occurred in 15 of 20 industry sectors;* nearly one half of all workplace outbreaks occurred in three sectors: Manufacturing (43; 20%), Construction (32; 15%) and Wholesale Trade (29; 14%); 58% (806 of 1,389) of workplace outbreak-associated cases occurred in these three sectors. Although 24% of Utah's workforce in all 15 affected sectors identified as Hispanic or Latino (Hispanic) or a race other than non-Hispanic white (nonwhite†) (1), 73% (970 of 1,335) of workplace outbreak-associated COVID-19 cases were in persons who identified as Hispanic or nonwhite. Systemic social inequities have resulted in the overrepresentation of Hispanic and nonwhite workers in frontline occupations where exposure to SARS-CoV-2, the virus that causes COVID-19, might be higher (2); extra vigilance in these sectors is needed to ensure prevention and mitigation strategies are applied equitably and effectively to workers of racial and ethnic groups disproportionately affected by COVID-19. Health departments can adapt workplace guidance to each industry sector affected by COVID-19 to account for different production processes and working conditions.


Subject(s)
Coronavirus Infections/ethnology , Disease Outbreaks , Ethnicity/statistics & numerical data , Health Status Disparities , Industry/statistics & numerical data , Occupational Diseases/ethnology , Pneumonia, Viral/ethnology , Racial Groups/statistics & numerical data , Adolescent , Adult , Aged , COVID-19 , Female , Humans , Male , Middle Aged , Pandemics , Utah/epidemiology , Workplace , Young Adult
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