Use of sewage surveillance for COVID-19 to guide public health response: A case study in Hong Kong

Abstract

Sewage surveillance could help develop proactive response to the Coronavirus Disease 2019 (COVID-19) pandemic, but currently there are limited reports about examples in practical exercises. Here, we report a use case of intensified sewage surveillance to initiate public health action to thwart a looming Delta variant outbreak in Hong Kong. On 21 June 2021, albeit under basically contained COVID-19 situation in Hong Kong, routine sewage surveillance identified a high viral load of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a sewage sample from one site covering over 33,000 population, suggesting infected cases living in the respective sewershed. The use of a newly developed method based on allele-specific real-time quantitative polymerase chain reaction (AS RT-qPCR) served to alert the first documentation of the Delta variant in local community sewage three days before the case was confirmed to be a Delta variant carrier. Intensified sewage surveillance was triggered. Targeted upstream sampling at sub-sewershed areas pinpointed the source of positive viral signal across spatial scales from sewershed to building level, and assisted in determining the specific area for issuing a compulsory testing order for individuals on 23 June 2021. A person who lived in a building with the positive result of sewage testing was confirmed to be infected with COVID-19 on 24 June 2021. Viral genome sequences determined from the sewage sample were compared to those from the clinic specimens of the matched patient, and confirmed that the person was the source of the positive SARS-CoV-2 signal in the sewage sample. This study could help build confidences for public health agencies in using the sewage surveillance in their own communities.