Revealing patterns of SARS-CoV-2 variant emergence and evolution using RBD amplicon sequencing of wastewater.

OBJECTIVES: Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study aimed to monitor the SARS-CoV-2 variant community dynamics and evolution using receptor-binding domain (RBD) amplicon sequencing of wastewater samples. METHODS: We sequenced wastewater from El Paso, Texas, over 17 months, compared the sequencing data with clinical genome data, and performed biodiversity analysis to reveal SARS-CoV-2 variant dynamics and evolution. RESULTS: We identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Comparison with clinical genome sequencing data revealed earlier detection of variants and identification of unreported outbreaks. Our results also showed strong consistency with clinical data for dominant variants at the local, state, and national levels. Alpha diversity analyses revealed significant seasonal variations, with the highest diversity observed in winter. By segmenting the outbreak into lag, growth, stationary, and decline phases, we found higher variant diversity during the lag phase, likely due to lower inter-variant competition preceding outbreak growth. CONCLUSIONS: Our findings underscore the importance of low transmission periods in facilitating rapid mutation and variant evolution. Our approach, integrating RBD amplicon sequencing with wastewater surveillance, demonstrates effectiveness in tracking viral evolution and understanding variant emergence, thus enhancing public health preparedness.

COVID-19 Risk Assessment among Vulnerable Small Business Owners in El Paso County, Texas.

BACKGROUND: Our objective was to deliver actionable, worksite-specific COVID-19 risk assessments and mitigation strategies tailored to vulnerable workers in one of the highest-risk areas in the US. METHODS: Four trained, bilingual (English/Spanish) Community Health Workers (CHWs) recruited small businesses (i.e., ≤20 employees) across various industries and executed novel on-site infectious disease risk assessment surveys of at least one employer and one employee. RESULTS: Of 102 participating businesses (95% Hispanic-owned), 96% were characterized as "high risk" or "very high risk" for disease transmission. All businesses reported implementing at least one practice to reduce disease transmission; however, almost half of businesses lacked at least 13 of the 17 controls identified to mitigate risk. CONCLUSIONS: Tailored, culturally sensitive outreach led by CHWs identified and educated businesses on critical hazards, and these methods may be transferable to similar communities.

RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.

Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study utilized receptor-binding domain (RBD) amplicon sequencing of wastewater samples to monitor the SARS-CoV-2 community dynamics and evolution in El Paso, TX. Over 17 months, we identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Our findings demonstrated early detection of variants and identification of unreported outbreaks, while showing strong consistency with clinical genome sequencing data at the local, state, and national levels. Alpha diversity analyses revealed significant periodical variations, with the highest diversity observed in winter and the outbreak lag phases, likely due to lower competition among variants before the outbreak growth phase. The data underscores the importance of low transmission periods for rapid mutation and variant evolution. This study highlights the effectiveness of integrating RBD amplicon sequencing with wastewater surveillance in tracking viral evolution, understanding variant emergence, and enhancing public health preparedness.

Health Care Workers' Comfort Ratings for Elastomeric Half-Mask Respirators Versus N95® Filtering Facepiece Respirators During the COVID-19 Pandemic.

BACKGROUND: Reusable elastomeric half-mask respirators (EHMR) are an alternative to address shortages of disposable respirators. While respirator discomfort has been noted as a barrier to adherence to wearing an N95 filtering facepiece respirator (FFR) among health care personnel (HCP), few have examined EHMR comfort while providing patient care, which was the purpose of this study. METHOD: Among a cohort of 183 HCP, we prospectively examined how HCP rated EHMR tolerability using the Respirator Comfort, Wearing Experience, and Function Instrument (R-COMFI) questionnaire at Study Week 2 and Week 10. At the completion of the study (Week-12), HCP compared EHMR comfort with their prior N95 FFR use. Overall R-COMFI scores and three subscales (comfort, wear experience, and function) were examined as well as individual item scores. FINDINGS: The HCP reported an improved overall R-COMFI score (lower score more favorable, 30.0 vs. 28.7/47, respectively) from Week 2 to Week 10. Many individual item scores improved or remained low over this period, except difficulty communicating with patients and coworkers. The overall R-COMFI scores for the EHMR were more favorable than for the N95 FFR (33.7 vs. 37.4, respectively), with a large proportion of workers indicating their perception that EHMR fit better, provided better protection, and they preferred to wear it in pandemic conditions compared with the N95 FFR. CONCLUSION/APPLICATION TO PRACTICE: Findings suggest that the EHMR is a feasible respiratory protection device with respect to tolerance. EHMRs can be considered as a possible alternative to the N95 FFR in the health care setting. Future work is needed in the EHMR design to improve communication.

Provider experiences with daily use of elastomeric half-mask respirators in health care.

BACKGROUND: During public health emergencies, demand for N95 filtering facepiece respirators (N95 FFRs) can outpace supply. Elastomeric half-mask respirators (EHMRs) are a potential alternative that are reusable and provide the same or higher levels of protection. This study sought to examine the practical aspects of EHMR use among health care personnel (HCP). METHODS: Between September and December 2021, 183 HCPs at 2 tertiary referral centers participated in this 3-month EHMR deployment, wearing the EHMR whenever respiratory protection was required according to hospital protocols (ie, when an N95 FFR would typically be worn) and responding to surveys about their experience. RESULTS: Participants wore EHMRs typically 1 to 3 hours per shift, reported disinfecting the respirator after 85% of the removals, and reported high confidence in using the EHMR following the study. EHMRs caused minimal interference with patient care tasks, though they did inhibit communication. DISCUSSION: HCP who had not previously worn an EHMR were able to wear it as an alternative to an N95 FFR without much-reported interference with their job tasks and with high disinfection compliance. CONCLUSIONS: This study highlights the feasibility of the deployment of EHMRs during a public health emergency when an alternative respirator option is necessary.

Wastewater analysis of Mpox virus in a city with low prevalence of Mpox disease: an environmental surveillance study.

Background: Tracking infectious diseases at the community level is challenging due to asymptomatic infections and the logistical complexities of mass surveillance. Wastewater surveillance has emerged as a valuable tool for monitoring infectious disease agents including SARS-CoV-2 and Mpox virus. However, detecting the Mpox virus in wastewater is particularly challenging due to its relatively low prevalence in the community. In this study, we aim to characterize three molecular assays for detecting and tracking the Mpox virus in wastewater from El Paso, Texas, during February and March 2023. Methods: In this study, a combined approach utilizing three real-time PCR assays targeting the C22L, F3L, and F8L genes and sequencing was employed to detect and track the Mpox virus in wastewater samples. The samples were collected from four sewersheds in the City of El Paso, Texas, during February and March 2023. Wastewater data was compared with reported clinical case data in the city. Findings: Mpox virus DNA was detected in wastewater from all the four sewersheds, whereas only one Mpox case was reported during the sampling period. Positive signals were still observed in multiple sewersheds after the Mpox case was identified. Higher viral concentrations were found in the pellet than in the supernatant of wastewater. Notably, an increasing trend in viral concentration was observed approximately 1-2 weeks before the reporting of the Mpox case. Further sequencing and epidemiological analysis provided supporting evidence for unreported Mpox infections in the city. Interpretation: Our analysis suggests that the Mpox cases in the community is underestimated. The findings emphasize the value of wastewater surveillance as a public health tool for monitoring infectious diseases even in low-prevalence areas, and the need for heightened vigilance to mitigate the spread of Mpox disease for safeguarding global health. Funding: Center of Infectious Diseases at UTHealth, the University of Texas System, and the Texas Epidemic Public Health Institute. The content of this paper is solely the responsibility of the authors and does not necessarily represent the official views of these funding organizations.

Wastewater sequencing reveals community and variant dynamics of the collective human virome.

Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks of poliovirus decades ago, but so-called wastewater-based epidemiology was reinvigorated to monitor SARS-CoV-2 levels while bypassing the difficulties and pit falls of individual testing. Current approaches overlook the activity of most human viruses and preclude a deeper understanding of human virome community dynamics. Here, we conduct a comprehensive sequencing-based analysis of 363 longitudinal wastewater samples from ten distinct sites in two major cities. Critical to detection is the use of a viral probe capture set targeting thousands of viral species or variants. Over 450 distinct pathogenic viruses from 28 viral families are observed, most of which have never been detected in such samples. Sequencing reads of established pathogens and emerging viruses correlate to clinical data sets of SARS-CoV-2, influenza virus, and monkeypox viruses, outlining the public health utility of this approach. Viral communities are tightly organized by space and time. Finally, the most abundant human viruses yield sequence variant information consistent with regional spread and evolution. We reveal the viral landscape of human wastewater and its potential to improve our understanding of outbreaks, transmission, and its effects on overall population health.

Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program.

Molecular analysis of public wastewater has great potential as a harbinger for community health and health threats. Long-used to monitor the presence of enteric viruses, in particular polio, recent successes of wastewater as a reliable lead indicator for trends in SARS-CoV-2 levels and hospital admissions has generated optimism and emerging evidence that similar science can be applied to other pathogens of pandemic potential (PPPs), especially respiratory viruses and their variants of concern (VOC). However, there are substantial challenges associated with implementation of this ideal, namely that multiple and distinct fields of inquiry must be bridged and coordinated. These include engineering, molecular sciences, temporal-geospatial analytics, epidemiology and medical, and governmental and public health messaging, all of which present their own caveats. Here, we outline a framework for an integrated, state-wide, end-to-end human pathogen monitoring program using wastewater to track viral PPPs.

A Means of Codifying Safety Cross-Training Knowledge Expectations for Biosafety Professionals.

Introduction: The health and safety issues encountered by biosafety professionals in the daily conduct of their work is rarely limited solely to potentially infectious pathogens. A basic understanding of the other types of hazards inherent to laboratories is necessary. As such, management of the health and safety program at an academic health institution sought to ensure crosscutting competency for its technical staff, including staff members within the biosafety program. Methods: Using a focus group approach, a team of safety professionals from a variety of specialties developed a list of 50 basic health and safety items that any safety specialist should know, inclusive of basic but important information about biosafety that was considered imperative for staff members to understand. This list was used as the basis for a formal cross-training effort. Results: Staff responded positively to the approach and the associated cross-training, and overall compliance with an array of health and safety expectations was experienced across the institution. Subsequently, the list of questions has been shared broadly with other organizations for their own consideration and use. Discussion/Conclusion: The codification of the basic knowledge expectations for technical staff within a health and safety program at an academic health institution, which includes the biosafety program technical staff, was warmly received and helped establish what information was expected to be known and what issues warranted input from other specialty areas. The cross-training expectations served to expand the health and safety services provided despite resource limitations and organizational growth.

Assessing the Established Competency Categories of the Biosafety, Infection Prevention, and Public Health Professions: A Guide for Addressing Needed Professional Development Training for the Current and Next Pandemic.

A recent series of widespread infectious disease outbreaks has highlighted commonalities and differences between three key professions that operate on the front lines of response in support of research and/or direct healthcare providers: biosafety, infection prevention, and public health. This assessment, which builds upon previous study by the authors, examines the stated professional competency categories for these three areas, highlighting similarities and differences. This assessment is important as these professions are being drawn together in an operational environment driven by the current pandemic and inevitably future disease outbreaks. Cross-training opportunities for the various professions are proposed.

Pivoting the Biosafety Program in Response to COVID-19: Recommendations of Key Services and Tasks to Consider for the Next Pandemic.

Introduction: With the onset of the COVID-19 pandemic, a rapid adjustment of work tasks was necessary for many biosafety programs (and other safety programs) to address drastic shifts in workload demands amid pandemic-related shutdowns and subsequent needs for supporting COVID-19-related safe work protocols, diagnostic testing, research, vaccine development, and so forth. From a program management standpoint, evaluating and understanding these tasks were critically important to ensure that appropriate support and resources were in place, especially during such unprecedented times of rapid change and significant impact to normal life and routine. Methods: Described here are examples of how the biosafety program at The University of Texas Health Science Center at Houston (UTHealth Houston) addressed these challenges. Results: As part of this required pivot, key services and tasks emerged into three distinct categories: (1) those that were temporarily diminished, (2) those that had to continue despite COVID-19 and the associated shutdowns for safety or compliance purposes, and (3) those that dramatically increased in volume, frequency, and novelty. Conclusion: Although the adjustments described were made in situ as the pandemic evolved, the cataloging of these tasks throughout the experience can serve as a template for biosafety programs to plan and prepare for the next pandemic, which will inevitably occur.

Characterization of Work Settings in Which Biosafety Professionals Conduct Operations: Results from the First Survey of the Biosafety Analytics Initiative Survey Series.

Introduction: With the endorsement and support of the ABSA International Council and the Prevention, Preparedness and Response (P2R) Academy of The University of Texas Health Science Center at Houston (UTHealth) School of Public Health, a survey to characterize the work settings in which biosafety professionals operate was conducted. The survey was the first of a planned series of 10 solicitations in support of an overarching "Biosafety Analytics Initiative," the goal of which is to identify commonalities, trends, possible benchmarking opportunities, and professional training needs. Methods: The survey was developed, tested, and then distributed electronically for a 3-week period between May 29 and June 19, 2019. Results: A total of 228 ABSA International members completed responses (15.6% of total membership). The results of the survey indicate that 59.7% of the total membership respondents conduct operations in the public or private academic setting, but when separated by domestic vs international respondents, 38% of the international respondents operate in government (nonacademic) settings. The bulk of biosafety activities were reported as providing support to BSL-1 and BSL-2 laboratories, with more than 90% of respondents indicating that they support work with risk group 1 and 2 organisms. Approximately 60% of the biosafety programs responding reported being organizationally aligned within institutional Environmental Health & Safety programs. Conclusion: The results of this survey serve as a foundation for current and future ABSA International priorities regarding professional development, recruitment, and training opportunities.

Improving Hurricane Harvey Disaster Research Response Through Academic-Practice Partnerships.

After Hurricane Harvey, researchers, media, and public health agencies collected data in Houston, Texas, to assess potential health effects and inform the public. To limit redundancy and ensure sampling coverage of impacted areas, research and practice partners used disaster research response (DR2) resources and relied on partnerships formed during a 2015 DR2 workshop in Houston. Improved coordination after the disaster can improve the effectiveness and efficiency of DR2 and enable the use of data to improve recovery and preparedness for future disasters.

Building Back Better: Local Health Department Engagement and Integration of Health Promotion into Hurricane Harvey Recovery Planning and Implementation.

Disaster recovery provides an opportunity to build healthier and more resilient communities. However, opportunities and challenges encountered by local health departments (LHDs) when integrating health considerations into recovery have yet to be explored. Following Hurricane Harvey, 17 local health and emergency management officials from 10 agencies in impacted Texas, USA jurisdictions were interviewed to describe the types and level of LHD engagement in disaster recovery planning and implementation and the extent to which communities leveraged recovery to build healthier, more resilient communities. Interviews were conducted between December 2017 and January 2018 and focused on if and how their communities were incorporating public health considerations into the visioning, planning, implementation, and assessment phases of disaster recovery. Using a combined inductive and deductive approach, we thematically analyzed interview notes and/or transcripts. LHDs reported varied levels of engagement and participation in activities to support their community's recovery. However, we found that LHDs rarely articulated or informed decision makers about the health impacts of recovery activities undertaken by other sectors. LHDs would benefit from additional resources, support, and technical assistance designed to facilitate working across sectors and building resilience during recovery.

U.S. Medical Examiner/Coroner capability to handle highly infectious decedents.

In the United States of America, Medical Examiners and Coroners (ME/Cs) investigate approximately 20% of all deaths. Unexpected deaths, such as those occurring due to a deceased person under investigation for a highly infectious disease, are likely to fall under ME/C jurisdiction, thereby placing the ME/C and other morgue personnel at increased risk of contracting an occupationally acquired infection. This survey of U.S. ME/Cs' capabilities to address highly infectious decedents aimed to determine opportunities for improvement at ME/C facilities serving a state or metropolitan area. Data for this study was gathered via an electronic survey. Of the 177 electronic surveys that were distributed, the overall response rate was N = 108 (61%), with 99 of those 108 respondents completing all the questions within the survey. At least one ME/C responded from 47 of 50 states, and the District of Columbia. Select results were: less than half of respondents (44%) stated that their office had been involved in handling a suspected or confirmed highly infectious remains case and responses indicated medical examiners. Additionally, ME/C altered their personal protective equipment based on suspected versus confirmed highly infectious remains rather than taking an all-hazards approach. Standard operating procedures or guidelines should be updated to take an all-hazards approach, best-practices on handling highly infectious remains could be integrated into a standardized education, and evidence-based information on appropriate personal protective equipment selection could be incorporated into a widely disseminated learning module for addressing suspected or confirmed highly infectious remains, as those areas were revealed to be currently lacking.

Preliminary Assessment of Hurricane Harvey Exposures and Mental Health Impact.

Hurricane Harvey made landfall in Houston, Texas on 25 August 2017, the psychological and physical effects of which are still unknown. We assessed hurricane exposure and the immediate mental health needs of the population to define public health priorities for a larger epidemiological study. Convenience sampling was used to recruit participants (n = 41) from the greater Houston area aged ≥18 years. Participants completed a questionnaire about demographics, hurricane exposures, and physical/mental health. Post-Traumatic Stress Disorder (PTSD) was measured with the Post-Traumatic Stress Disorder Checklist-S (PCL-S; a score ≥30 indicated probable PTSD symptoms). The Patient Health Questionnaire-4 (PHQ-4) was used to assess symptoms of depression and generalized anxiety disorder. The average PTSD score was 32.9 (SD = 17.1); a total of 46% of participants met the threshold for probable PTSD. Increased overall hurricane exposure (adjusted odds ratio (ORadj) 1.42; 95% confidence interval (CI): 1.06⁻2.05) and property-related exposure (ORadj 1.53; 95% CI: 1.07⁻2.18) were both statistically significantly associated with increased odds of probable PTSD symptoms. A perception of chemical/toxin exposure due to Hurricane Harvey was reported by 44% of participants. A higher number of personal or property exposures were associated with greater mental health symptoms three weeks post-hurricane. This work has implications for the ongoing response to Hurricane Harvey and for assessing the immediate needs of the population.