Early detection and quicker response: Highlights and lessons learned from COVID-19 wastewater surveillance of congregate settings in New Mexico

In December 2020, the New Mexico Environment Department (NMED) launched an innovative wastewater surveillance program to monitor SARS-CoV-2 (the virus that causes COVID-19) at correctional facilities, shelters, youth homes, and other congregate settings across the state. NMED is supported by Eastern Research Group, Inc. (ERG) to provide field teams, data analysis, and epidemiology expertise and LuminUltra Technologies for laboratory analysis support. For this program, wastewater samples are collected twice weekly at one or more locations, intentionally selected to represent distinct populations, at each facility. Results from these samples have successfully triggered additional individual testing for SARS-CoV-2, leading to earlier detection of viral spread than otherwise would have occurred under limited individual testing. As one such example, ERG identified and notified NMED of a spike in SARS-CoV-2 from wastewater (i.e., concentration >10^-6 copies/L) collected at one of the sampling locations at the Luna County Detention Center in January 2021 (Figure 1). NMED staff immediately notified facility staff, who then promptly initiated individual testing of more than 300 individuals - inmates and staff - for COVID-19. The individual test results revealed 27 inmates and 10 staff with COVID-19, all of whom immediately isolated to control the virus' spread and prevent a much larger outbreak. Through examples like this, NMED has found wastewater surveillance to be a cost-effective, early warning indicator of SARS-CoV-2 spread in congregate settings that can complement other data and further inform public health action. While this program provides valuable information to decision-makers and helps reduce the spread of COVID-19, it was not developed or implemented without challenges. These challenges included access to sampling equipment in the face of increased demand during a global pandemic; limited in-state laboratory capabilities and capacity; and interpreting and communicating results to facility staff and the public taking into consideration the various scientific unknowns. Through collaboration with multiple entities and as more scientific information became available on wastewater epidemiology for disease surveillance, the NMED project team was able to address and overcome these challenges. The team has also explored the utility of alternative passive sampling methods as a way to further improve data interpretation and reduce costs. Whenever possible, ERG's field teams collect 24-hour composite samples using automatic samplers (Figure 2). These samplers are, however, costly to rent; time consuming to set up and take down; and sometimes impractical due to physical constraints, low flow, or security concerns. When unable to use an automatic composite sampler, ERG's field teams collect grab samples. However, data from grab samples represent only the wastewater flowing through the sewer at the moment that the sample is collected and have the potential to miss SARS-CoV-2 shed from COVID-19 positive individuals in a facility. Given the limitations of composite and grab samples, there is a need for a more practical and cost-effective composite sampling method. One such approach is the 'Moore swab' method, which involves suspending gauze in the wastewater stream to collect microorganisms/pathogens for a time period comparable to a composite sample (e.g., 24-hours). This method was first used in the 1940s to track Salmonella Paratyphi B and has since been used to detect several other fecal borne pathogens such as Vibrio cholerae, poliovirus, and Escherichia coli (Sikorski and Levine, 2020). Recent literature suggests that this type of passive sampling approach can also be used to monitor SARS-CoV-2 in wastewater. In some cases, research and field teams have explored the use of gauze swabs, while others have assessed the utility of tampons as a modified passive sampler (e.g., Liu et al., 2021, Rafiee et al., 2021, Bivens et al., 2021). The tampon, in particular, has potential to serve as an inexpensive and simple passive sampling tool that could be easily implemented by staff with no prior sampling experience and little training. To explore the utility of this method, our field teams collected grab samples, 24-hour composite samples, and 24-hour passive samples using rayon-based super/maximum absorbent tampons concurrently at six facility locations and one community location twice weekly for three consecutive weeks. The goal of this effort was to determine whether 24-hour passive samples provide equivalent or better detection for the presence of SARS-CoV-2 in comparison to grab samples, and if the data from passive samples correlate to 24-hour composites. For passive samples, field staff tied tampons to fishing line with weights and then secured the line to a manhole cover (Figure 3). They set up the composite and passive samples at the same time and then collected a grab sample at the start of the 24-hour sample period. The grab samples were shipped the day of collection to LuminUltra Technologies for analysis. The passive and composite samples were collected after 24-hours and also shipped to LuminUltra Technologies for analysis. LuminUltra squeezed the water from the passive samples, rinsed with a lysate buffer to extract additional RNA, and then filtered and processed the extracted wastewater using the same method as for the composite and grab samples. All samples were analyzed via reverse transcription-polymerase chain reaction (RT-qPCR) for two SARS-CoV-2 associated genetic markers (N1 and N2) and one fecal indicator (pepper mild mottle virus [PMMoV)]). ERG scientists compared the presence and absence of the virus and evaluated trends and correlations across the three sample types. Preliminary results indicate that the 24-hour passive samples provide equivalent or better detection of SARS-CoV-2 than both 24-hour composite and grab samples. Of the six rounds of samples collected at each of the seven locations (n=42 samples), the passive samples detected SARS-CoV-2 when the virus was detected in the corresponding grab and/or 24-hour composite samples with only two exceptions. These exceptions were at low concentrations (<10,000 copies/L) and likely due to varying limits of detection between the passive, composite, and grab samples. The passive samples also detected SARS-CoV-2 in six instances when the virus was not detected in analogous 24-hour composite or grab samples. Furthermore, the overall trends observed across sample types were generally consistent, especially between 24-hour composite and 24-hour passive samples, and results from composite and passive samples were moderately to highly correlated (see example from one sampling location in Figure 4). These results suggest that passive sampling approaches may be useful for monitoring SARS-CoV-2 in wastewater at the facility level and that additional study is warranted.