The Tijuana River is an international river, shared by the United States and Mexico, that flows into the Pacific Ocean near the City of Imperial Beach, California. For decades, severe pollution of the Tijuana River and its frequent transport of raw sewage to the Pacific Ocean, which impacts surrounding coastal areas, has been a contentious and complex transboundary water issue. The goals of this study were to determine if SARS-CoV-2 could be detected in this waterway and, if so, track concentrations of SARS-CoV-2 in the Tijuana River during 2020 and 2021 and compare those results to community infection rates in the city of Tijuana.

Our team, led by graduate student Alma Rocha, collected grab samples from two sites on the Tijuana River: Boca Rio at the mouth of the Tijuana River and Radio Club further upstream near the border (Figure 2 and Figure 3). Samples were collected 1) after storm events, 2) during dry weather conditions, 3) when COVID-19 infection rates were high in Tijuana, and 4) following an increase in vaccination rates and a decrease in COVID-19 cases in Tijuana. For comparison, samples of raw sewage and biosolids (the sludge that settles out in basins during wastewater treatment) were also collected from the Point Loma Wastewater Treatment Plant and the San Elijo Water Reclamation Facility in San Diego County. Samples were analyzed for chemical water quality and microbial constituents, including total coliforms, Escherichia coli, enterococci, and pepper mild mottle virus (PMMoV), a human-associated viral indicator derived from pepper plants and found in human fecal material.

​An important initial step in the project was the development of methods for detecting and measuring SARS-CoV-2 in wastewater and natural waters. We had to address filter clogging issues, optimize the sample preparation workflow, and decrease the long sample preparation time. We did a significant amount of laboratory experimentation to develop refined methods that allowed us to detect and measure the concentration of SARS-CoV-2 in wastewater influent, sludge, and surface waters. ​​​​ ​​​

Figure 3. Map showing Boca Rio and Radio Club sampling sites on the Tijuana River north of the 

US-Mexico border. Photo credit: K. Sant

​​​​Using our newly developed methods, SARS-CoV-2 was detected and measured in raw sewage, sludge, and at the more upstream Radio Club site on the Tijuana River on six out of eight occasions. The SARS-CoV-2 concentrations at the upstream Radio Club site were as high or higher than those detected in untreated wastewater collected in the spring and summer of 2020 (Figure 4). Other indicators of human fecal contamination (PMMoV and E. coli) at Radio Club were also as high as in raw sewage samples. The virus was not, however, detected at the downstream Boca Rio estuarine sampling location, despite the consistent detection of high concentrations of PMMoV at that location, which indicates human fecal contamination. This lack of SARS-CoV-2 detection at Boca Rio may be due to a combination of factors: 1) its occurrence just below detection limits, 2) removal or degradation of the virus during transport along the Tijuana River, and 3) mixing of river water with uncontaminated ocean water in the coastal zone around the Boca Rio site.

Covid-19 infection rates tracked changes in SARS-CoV-2 concentrations at Radio Club: high riverine concentrations occurred just before high infection rates were observed among citizens of Tijuana. Our study did not seek to evaluate the viability or infectivity of the virus in raw sewage or surface water, and there is currently no evidence that the virus maintains viability in sewage or surface waters. However, due to the persistence of the genetic material of SARS-CoV-2 in the Tijuana River, surveillance of the virus in this waterway may be useful for tracking prevalence and future outbreaks.