High throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics

medRxiv preprint 11/15/2020

High throughput wastewater SARS-CoV-2 detection enables forecasting of community infection dynamics in San Diego county

Large-scale wastewater surveillance has the ability to greatly augment the tracking of infection dynamics especially in communities where the prevalence rates far exceed the testing capacity. However, current methods for viral detection in wastewater are severely lacking in terms of scaling up for high throughput. In the present study, we employed an automated magnetic-bead based concentration approach for viral detection in sewage that can effectively be scaled up for processing 24 samples in a single 40-minute run. The method compared favorably to conventionally used methods for viral wastewater concentrations with a limit of detection of 8.809 viral gene copies/ml from input sample volumes as low as 10ml and can enable the processing of over 100 wastewater samples in a day. Using the high throughput pipeline, samples from the influent stream of the primary wastewater treatment plant of San Diego county (serving 2.3 million residents) were processed for a period of 13 weeks. Wastewater estimates of SARS-CoV-2 viral genome copies in raw untreated wastewater correlated strongly with clinically reported cases by the county, and enabled prediction of cases up to 3 weeks in advance. Taken together, the results show that the high-throughput surveillance could greatly ameliorate comprehensive community prevalence assessments by providing robust, rapid estimates.

Wastewater monitoring has a lot of potential for revealing COVID-19 outbreaks before they happen because the virus is found in the wastewater before people have clinical symptoms. However, application of wastewater based surveillance has been limited by long processing times specifically at the concentration step. Here we introduce a much faster method of processing the samples, and show that its robustness by demonstrating direct comparisons with existing methods and showing that we can predict cases in San Diego by a week with excellent accuracy, and three weeks with fair accuracy, using city sewage. The automated viral concentration method will greatly alleviate the major bottleneck in wastewater processing by reducing the turnaround time during epidemics.

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