Background and objective:
Surveillance of SARS-CoV-2 during the pandemic has shifted from individual PCR testing to population-based surveillance using wastewater (WW). Our ongoing WW surveillance of SARS-CoV-2 load/types has been effective in Ontario, Canada and Otago, New Zealand, a catchment of ~13 million people. With minimal sewage processing in low-income, densely populated regions (slums), WW collection should involve sampling open sewage streams for optimal pathogen surveillance and for future targeted public health initiatives.

Methods:
During June-August of 2021 and 2022, over 1000 samples were collected from streams in slum areas of Medellin–Columbia, Caracas–Venezuela, Kampala–Uganda, and Suva–Fiji. Extracted RNA, converted to cDNA was subject to qRT-PCR and Artic v4 Illumina sequencing to measure SARS-CoV-2 load and type. Chemical composition of WW, sample clarity, rainfall, and GPS coordinates for all collection sites were recorded.

Results:
Over 40% of stream samples were positive by qRT-PCR for SARS-CoV-2 with the Delta variant dominating in summer 2021. Rainfall diluted viral levels even when standardizing with Pepper mild mottle virus, a “human” excrement standard. Populations in these slums were estimated based on roof density from satellite imagery using GISArcPro. Expected SARS-CoV-2 case loads from WW virus levels were modeled from WW and case load monitoring for SARS-CoV-2 cases in Ontario, Canada during the Delta wave. Based on these models, case loads predicted from WW in the slums of Caracas and Kampala were at least 100x higher than the total cases reported for the entire country of Venezuela and Uganda during the Delta wave.

Conclusions:
During the pandemic, SARS-CoV-2 case loads have been under reported in low-income settings. Improve pathogen surveillance directly impacting public health response is feasible through WW but for low income countries, proper sampling and procedures are critical.