SARS-CoV-2 detected in Santiago, Chile wastewater with very little loss of viral RNA

By Dr. Liji Thomas, MDJul 7 2020

From the last days of December 2019, when the occurrence of several cases of unfamiliar pneumonia were reported in Wuhan, China, to the present day where more than 11.5 million cases and well over 500,000 deaths have resulted from infection with the causative agent, SARS-CoV-2, it has been a matter of concern to find effective ways of surveillance and management of this illness, now termed COVID-19.

Novel Coronavirus SARS-CoV-2 Colorized scanning electron micrograph of an apoptotic cell (tan) heavily infected with SARS-CoV-2 virus particles (orange), isolated from a patient sample. Image captured at the NIAID Integrated Research Facility (IRF) in Fort Detrick, Maryland. Credit: NIAID

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Sewage May Predict Outbreak

A preliminary report from Chile describes the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in sewage as a sensitive method to assess the circulation of viruses within a community.

The study, published on the preprint server medRxiv* in July 2020, shows that this could become an important surveillance tool to warn of an impending epidemic or a rise in cases.

The first case in Chile was detected on March 3, 2020. From then onwards, the number of cases has surged, with nearly 300,000 cases as of July 7, 2020. This comes to a rate of over 1,500 per 100,000 inhabitants.

The peak appears to be in the metropolitan area of Santiago, where there are more than 220,000 cases and the cumulative incidence rate of over 2,700 per 100,000 residents. To gauge the intensity of viral circulation, the researchers used an established method of epidemiological surveillance – detection of the virus in wastewater.

Fecal Shedding of SARS-CoV-2

This method has been used to assess the circulation of various viral agents, including hepatitis A, hepatitis E, wild and vaccine-derived strains, norovirus, and human polyomavirus 2. Infected individuals shed viruses in their feces, secondary to infection of the intestinal epithelium with the virus.

Fecal shedding is often heavy and typically prolonged. The viral load may go up to more than 1 x 10⁶ copies of the viral RNA. However, many infected individuals are asymptomatic, and therefore never diagnosed or detected, even though they can shed the virus through their respiratory and gastrointestinal secretions and excretion.

In essence, the level of circulating virus is known only from the appearance of moderate to severe symptoms that may require hospitalization, or unless mass screening is carried out in order to allow early detection of the infection. This is the context in which the current study on detecting viral loads in sewage. The potential role that could be played by this tool in the surveillance of the pandemic is borne out by some earlier studies.

The Study: Detecting the Virus in Sewage

The current study used composite raw sewage samples collected over 24 hours from two wastewater treatment plants (WWTPs). These plants collect and treat approximately 85% of the wastewater from the city of Santiago, a place that is home to about 8 million inhabitants. These two plants were sampled monthly from March to June 2020, using the inflow as well as the outflow from each.

The samples were collected in sterile polypropylene bottles, and care was taken to examine each the same day of collection. The investigators found that the virus was absent in all samples collected in March and April, probably because the number of cases was low. Below the critical level, the virus is undetectable.

Rising Viral Load Corresponds to Rising Cases

The samples from May and June were positive for the virus, with the copy number being within ranges that are comparable to those reported in earlier studies. The mean cycle threshold values were from about 28 to about 38. The number of genome copies rose steadily from May to June, in both WWTPs. This trend corresponded to the rise in the number of confirmed cases in Santiago.

All the samples were also examined for human polyomavirus 2, and were positive for it. The range of genomic copies/ml recovered for this virus was similar to the prior descriptions. This confirms the correctness of the procedure followed.

Conclusion and Application

The researchers conclude, “In both WWTP’s, the SARS-CoV-2 genome copy numbers progressively increased from May to June, which correlated with the increase in the number of estimated virus shedders in the community.”

The spread of the virus through feces, or the risk of acquiring infection via sewage exposure, is a theoretical possibility. However, it is not determined whether the virus remains stable in the environment for long.

“Our results demonstrated that the search for SARS-CoV-2 in sewage can be used as a predictive marker of the circulation of the virus in the population, including symptomatic and asymptomatic shedders, and therefore can be used as an early warning system as demonstrated years ago for the detection and control of poliovirus worldwide,” the researchers conclude.

*Important notice: medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.