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.

Keywords: Allele-specific RT-qPCR; Delta variant; Public health intervention; Sewage surveillance; Targeted upstream sampling.

Graphical abstract

Fig. 1

An overview of the sewage surveillance for COVID-19 in Hong Kong and the sewershed of the sampling site (TP site 9A) which was tested positive on 21 June 2021.

Fig. 2

The timeline of key events in response to detection of SARS-CoV-2 and the Delta variant in the community sewage during routine sewage surveillance.

Fig. 3

The intensification of sewage surveillance as a response to detection of SARS-CoV-2 in the stationary site and the variant detection. Approximately 24 h were spent in six steps of sequencing, including reverse transcription (~40 mins), multiplex PCR (~6 h, using Artic V3 protocol), PCR product purification (~20 mins), library construction (~4 h, following the protocol of ONT LSK109 kit), sequencing (~12 h), and data analysis (~1 h).

Fig. 4

(a) A timeline for routine daily sewage surveillance in Hong Kong. (b) The source of the positive signal at single building level as determined by the target upstream sampling.

Fig. 5

(a) Hierarchy structure of the first-tier, and its second-tier and third-tier sampling sites. (b) The detection results of these sampling sites.

Fig. 6

Alignments of consensus sequences obtained from the sewage sample and the matched patient's specimen to the reference genome sequence of a SARS-CoV-2 virus isolate strain (GenBank MN908947.3). Genetic disagreements were highlighted in black in the query sequences. Query 1 and 2 refer to the consensus sequences of SARS-CoV-2 in sewage samples obtained using the Nanopore and Illumina sequencing platforms, respectively. Query 3 refers to the consensus sequences of SARS-CoV-2 in the matched patient's specimen using the Illumina sequencing platform.