Wastewater surveillance reveals infection dynamics

July 24, 2022 12:00 am | Updated 05:40 am IST

SARS-CoV-2 viral load estimated higher number of cases than the actual number of reported cases 8-14 days in advance

Wastewater or sewage can tell us volumes about the health of a community. The idea here is very simple — most pathogens of interest, e.g., bacteria, virus or protozoa remain viable in the sewage environment for days.

Wastewater-based health surveillance or environmental surveillance is an excellent tool for tracking the presence of different pathogens in the environment. All it needs is a regular and consistent testing of wastewater. It is quite economical and provides real-time data, which makes it very useful for developing countries such as India where not everyone has access to healthcare.

Underestimation of cases

In India,tracking of COVID-19 pandemic relies heavily on testing symptomatic individuals for the presence of SARS-CoV-2 RNA and counting the positive tests over time. With high population density, many infected persons are likely to be asymptomatic or oligosymptomatic (few symptoms). They are generally not tested, leading to underestimation of COVID-19 cases.

Furthermore, infected or asymptomatic individuals start to shed the virus via the faecal route four-seven days in advance of actual testing or symptoms showing up, which means the increase in viral load in sewage water ahead of reported cases works as an early warning system and complements the routine diagnostic surveillance by capturing near real-time virus circulation at the community level.

Using this conceptual background, the Tata Institute for Genetics and Society (TIGS) in collaboration with Biome Environmental Trust and National Centre for Biological Sciences (NCBS), led a longitudinal study (January-June 2022) across 28 Bangalore sewer-shed sites capturing data from more than 11 million people.

Thestudy postedas a preprint in the medRxiv server (preprints are yet to be peer-reviewed) investigated the relationship between SARS-CoV-2 concentrations in wastewater and COVID-19 cases reported on a daily basis. Each sewer-shed site/sewage treatment plant has a specific catchment area i.e., wards served by the treatment plant. Bynormalising the viral load for population size of that catchment, water inflow etc, we could estimate the number of infected individuals in that catchmentareawhich was estimated to be higher than the reported cases in the city.

We were able to detect viral load copies in sewage in areas where there were few or no reported cases. Usingexponentially weighted moving average (EWMA) algorithm (four days and seven days— after adjusting for Omicron and old SARS-CoV-2 lineage incubation period), we observed two major outbreaks in January and June 2022. The viral load estimated a higher number of cases than the number of reported cases 8-14 days in advanceat the city-wide level. This further suggests thatthe viral load pattern mirrored with the clinical data, and COVID-19 positive cases appeared to remain underreported in the city.

This study on Bangalore sewage network has been instrumental in developing an early warning system where real-time genomic surveillance is the backbone in understanding the variants causing the emerging patterns in viral load in wastewater.

Hotspot identification

Wemonitored viral load and simultaneously sequenced samples in real-time to show which variant(s) was causing the increase in cases— not every treatment plant showedhigh viral loads but this helped in identification of hotspots in the city.

Treatment plants with BA.2.10 or mixture of BA.2 sub lineages showed an increase in viral load and this further highlighted that there was no new variant behind the surge, even though BA.4 and BA.5 was seen in minuscule amounts in few plants. Unlike clinical samples, our study used a specialised method designed to capture the abundance and diversity of lineages in mixed community wastewater samples.

Our comparisons with clinical genomic surveillance data from Bangalore (about 13,000 genomes) on GISAID database showed that while the general trend in Variants of Concern (VOC) remained similar, the wastewater genomic surveillance (about 300 samples) recorded a huge diversity in SARS-CoV-2 lineages dominated by theOmicron family.

Specifically, two Omicron sub-lineages—BA.2.10.1 and BA.2.12—were detected two months prior (January 2022) in wastewater to the first detection in clinical samples in March 2022.

The earlyemergence of a variant in the wastewater implies that a significant proportion of individuals in the community are infected with that variant and shedding the virus, whereas a late detection in the clinical sample could happen due to limited or biased testing, sequencing or a large proportion of individuals were asymptomatic or home testing upon COVID-19 symptoms. This further suggests that clinical samples were sequenced from a selected hospital, which is not representative of the Bangalore population.

One of the most important aspect of this study is its open accessdashboard(in partnership with Precision Health Pandemic Response-Bangalore initiative) for reporting viral load, citywide positivity rates and a regular discussion with Bruhat Bengaluru Mahanagara Palike (BBMP) and Bangalore Water Supply and Sewerage Board (BWSSB) so that the information can be used for making policy decisions.

Poliovirus eradication

Wastewater surveillance played a crucial role in eradication of poliovirus in India in 2012. What we need now is to scale-up the environmental surveillance beyond poliovirus and SARS-CoV-2 virus to pan pathogen surveillance and integratewith the main healthcare system.Such surveillancehas the power to predict neglected and emerging diseases.

Our approach and protocols developed lend support to establishingenvironmental surveillancefor monitoring and an early-warning system for detecting multi-pathogens (e.g., dengue, avian influenza, influenza, hepatitis, cholera)— as an evidence-based approach it is very useful for predicting risks to human as well as animal health. Andthat is exactlywhat we need more than ever — a One Health approach — to recognise the connection between the health ofhumans,animalsand the environment.

( Farah Ishtiaq is a Principal Scientist at the Tata Institute for Genetics and Society, Bengaluru. )

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