MONITORING OF OUTBREAKS –

WHAT CAN WASTEWATER

REVEAL?

● Jay Bhagwan

● Preparing for epidemics in South Africa – human and animal

● NSTF Discussion Forum - 25-26 February 2021

This Photo by Unknown Author is licensed under CC BY-NC-ND

Reservoir of health information and knowlegde

Wastewater based epidemiology – what can wastewater reveal?

• Illicit drugs use

• Pharmaceuticals and

other substances use

• Diet choices

• Genetic markers

• Biomarkers

Use of environmental disease surveillance dataObjective Results interpretation

Qualitative analysis of environmental samples - For determining general pathogen circulation within populations

Establishing trends and/or changes in the

number of disease incidences

- Characterising trends and/or changes in number of infections in

communities.

Tracking the number of infections (disease

burden) and mapping of hot spot areas in

communities

- Useful for determining the risk levels in communities and for

supporting decision making on the lifting and imposing of mitigation

interventions

Metagenomics in infectious disease - Provides a full spectrum of genetic diversity of pathogenic strains,

epigenetic changes, altered gene expressions, and gene fusions—

both known and novel

- Molecular method, does not provide info on viability

Assessing occupational human health risks - Based on the detection of live and infectious pathogenic strains –

can inform on the risk of infections and appropriate PPE

Disease surveillance

Water quality and health

WEF nexus

Climate change/Extreme

weather

Water, ICT and data

Sustainable water

behaviors

Sanitation and health

Linkages with WRC RDI themes

• Water quality and health – impact of

pollutants of concern to human and

environmental health

• Linkage between irrigation microbial water

quality and food safety

• ICTs in the WASH sector – data management

and decision making

• Climate change & water related diseases

• Sanitation and health – safe sanitation &

surveillance of diseases

WATER QUALITY SANITATION AND HEALTH PROGRAMME

CL

US

TE

R

3:

TIE

R 2

TIER 2 RESEARCH▪ Transmission and preparedness

CL

US

TE

R

2:

TIE

R 1

CL

US

TE

R

1:

WB

E

TIER 1 RESEARCH ▪ presence and persistence of SARS-CoV-2 in

water and sanitation environments.

NATIONAL WASTEWATER SURVEILLANCE▪ tracking and monitoring the presence of the SARS-CoV-2 virus

in sewage to provide information on prevalence and burden of COVID-19 in the communities and health delivery.

P1

P2

P3

P1

P2

P3

P1

P2

P3

❖ Early warning system for re-emergence of COVID-19

❖ Measure of the prevalence of the outbreak

❖ Provide decision support and extent of impact

❖ Tracking effectiveness of the interventions

❖ Provide decision support and anticipation of impact

OU

TCO

MES

&

IMP

AC

TS

❖ small, portable device for detecting SARS-CoV-2 in wastewater

❖ Scientific evidence on SARS-CoV-2 survival, risks and its attenuation

FUN

DIN

G

SOU

RC

ES

❖WRC to provide bulk of funding supported by relevant partners

❖WRC to provide seed funds❖WRC to provide bulk of funding

P4

SAMPLING AND ANALYSIS

Establishment of national sampling

protocols, sample

collection and analysis

DATA ANALYSIS

National data analysis & integration into national

COVID-19 data

GIS MAPPING Overlay of

sewer networks map with areas of

reported high or low cases

COMMUNICATI

ONDev. of strategies

for communicating

implications of ES results with PH

community, elected officials,

wastewater professionals &

the public

ADVANCED CHARACTERIZATION

TECHNIQUES

Development of novel methods for detecting of SARS-CoV-2 in different

water and sanitation

environments

FATE, BEHAVIOUR AND HUMAN RISKS

ASSESSMENT

Persistence of SARS-CoV-2 in

water and sludge, and human health risks assessments

and mitigation

ONE-HEALTH APPROACH

Determination of the role of water in the transport and transmission of

diseases (including COVID-19) between

humans, the environment, and food production

❖ Preparedness and readiness for novel pathogens

❖ Improved sanitation and hygiene in the food value chain

❖ Risk reduction from novel pathogens

ECOSYSTEM RESPONSEEcosystem

Responses to The Large

Scale Use of SARS-CoV-2

Disinfectants

TRANSMISSION THROUGH WATER AND

FOOD

Presence of SAR-CoV-2 in food products

and water

PREPAREDNESS AND READINESS

Nexus planning transformative approaches and

the Epidemic Preparedness

Index for South Africa

INDEPENDENT ADVISORY PANEL

LABORATORY

SERVICES

Presence of SARS –COV2 virus• Enveloped virus, surrounded by weak lipid membrane

• •Relatively fragile in the environment and will become inactivated much faster than non-enveloped human enteric viruses (e.g. norovirus, rotavirus, hepatitis A virus)

• •Three studies have detected infectious COVID-19 virus in feces, however other studies have not found infectious COVID-19 virus in feces. Shed virus is rapidly inactivated during transit through the colon.

• •Several studies have found COVID-19 RNA fragments in faecal matter during illness and after recovery.

• •Detection of COVID-19 RNA fragments indicate that the virus is not infectious

• •Risk of transmission of COVID-19 virus from the faeces of an infected person appears to be low.

The WRC approach

PILOT SCALE MONITORING

-partnership-wide monitoring of provincial hotspots (Gauteng,

KZN & Western Cape) using established sampling protocols

and design – Focus of EOI

NATIONAL WASTEWATER SURVEILLANCE

-Full scale national sewershed surveillance, including data

analysis, integration, communication & research

▪ Established monitoring partnerships covering provincial hot spots

▪ Preliminary pilot surveillance monitoring data

▪ Rolled out national surveillance▪ National data analysis and integration ▪ GIS mapping – heat maps▪ National communication

PHASE ONE PHASE TWO PHASE THREE

▪ Established sampling program & protocol▪ Preliminary sample analysis▪ Established sewershed sampling profile

PROOF OF CONCEPT- Sample design, testing & fine-

tuning sampling protocol, preliminary sampling and characterization based on

current Water Lab approved proposal

❖ 100 % WRC-Funded

3 months 6 months 12 months +

❖ 100 % WRC-Funded ❖ WRC-Funding Supported by Partners

COVID-19 National Surveillance Programme (3 phases)

Programme Outputs and Outcomes

OutputsInterlab Proficiency

Data integration and Trends

Established Networks

OutcomesHeatmaps

Established institutional Partnerships

Established strategic partnerships

ImpactEarly warning System Pilot

Development

Model for National WQ Surveillance

Sewer vs Non-Sewer

This Photo by Unknown Author is licensed under CC BY-SA-NC

Planning for national surveillance

Excreted virus (or remnants) in

• Wastewater (hospital, municipal, household)

• Surface water

• Faecal and/or urine samples

Sampling and testing

• Quantification of SARS-Cov-2 biomarkers

• Viral sequencing

Estimate number of infections

• Independent from patient testing

Risk mapping

Overlay of sewer networks map with areas of reported high or low

cases – Heat Map

Data communication

Compare with health data

Communication to stakeholders

Integration into national reporting

Establishment of a national advisory panel

Implementation by WRC and partners – Gov departments, research & diagnostic laboratories

Outcomes and impacts(i) Early warning system for re-emergence of COVID-19; (ii) Measure of the prevalence of the outbreak; (iii) Provide

decision support and extent of impact; and (iv) Tracking effectiveness of the interventions

The WRC approach

❑ Ct values were used as a measure of the

presence or absence of SARS-CoV-2 RNA in the

sample, where:

Ct values below 40 considered positive

Ct values above 40 considered negative

NB: a result where there was no amplification of

target genes was regarded negative

Results interpretation and visualisation

SARS-CoV-2 detection in municipal WWTW samples - Gauteng and KZN

• Results show proof of concept in terms of

both virus recovery methods and positive

gene amplification of SARS-CoV-2 at all

WWTWs sampled over the 4-week period.

• Initially, better virus recovery was found in

composite wastewater samples when

compared to grab samples taken during peak

flow times. However, by weeks 2 and 3

comparable results were found for the grab

and composite samples. This is possibly due

to an increase in the viral load over time.

SARS-CoV-2 detection in municipal WWTW samples – Western Cape

• Positive gene amplification of

SARS-CoV-2 was observed in

most WWTWs sampled over the

4-week period.

Trends in Ct values

SARS-CoV-2 detection in wastewater

Industrial and prison facility WWTW

samples

• Industrial and Prison WWTWs

samples – positive amplification was

observed for the WW sample

SARS-CoV-2 detection in wastewater

Power station and mine WWTW

samples

• Positive amplification was

observed for the power

station (Mpumalanga &

Western Cape) and mine

(FS) WWTW samples

Non- seweredSurface Water

• L volumes to enable gene detection.

• SARS-CoV-2 was detected in all surface water samples tested, but not all targets amplified

• It is interesting to note that recovery from the surface waters was sufficient even in the 200 mL volumes to enable gene detection.

• the recovery efficiency from the surface samples which were expected to be more dilute than the wastewater treatment plant influent samples

Science Brief for Phase 1: Proof of Concept

• Detected SARS-CoV2 RNA in 98% of wastewater samples from upstream and downstream WWTW of prisons, hospitals, industries and mines

• Positive gene amplification observed in environmental (NSS) samples – ie river water samples

• WBE proven to be a useful complementary surveillance tool for management of COVID-19

• Wastewater surveillance – cost effective, less invasive continuous screening approach

• Correlation between increase in viral load and increase in case numbers with time

• Method efficiencies – Skimmed milk flocculation and Al(OH)3

adsorption-flocculation cost effective and faster than PEG/NaCl precipitation;

• Built a robust collaborative platform of scientists, laboratories and WSIs

Pilot phase – WBE COVID-19 surveillance

• In partnership with NICD and SACCESSnetwork

• Scale up in the number of WWTWs sampling sites in hotpot areas

• Increased collection of non sewered samples

• Network of laboratories involved - inter-lab comparison scheme

• Development of training materials / guides

• Surveillance results have been presented to the National Incident Management Team for COVID-19 in November 2020

Takeaways• Science and techniques keep on improving• Cost of testing and surveillance becoming

lower• Interlab testing validating methods and results• Operational uncertainties such as influent

variability, temperature etc are all focus of ongoing detail research

• Many of the countries and institutions have demonstrated effectiveness• Being adopted by national governments• Big industries and universities to manage their

populations

• Seen as an important contributor to complementing current activities.

Other examples - Waterborne disease surveillance

• Assess the prevalence of pathogenic bacteria (diarrhoeagenic strains of E. coli; Vibrio cholerae; Salmonella spp; Shigella sppetc.)

• Determine the presence of enteric viruses [adenovirus, reovirus, norovirus (GI, GII), enterovirus, astrovirus, sapovirus, rotavirus and hepatitis A virus]

• Determine the presence of protozoan parasites

• Make recommendations to the relevant policymakers to improve water quality in rural and peri-urban communities in South Africa.

Surveillance of antibiotic resistant agents

WRC Report No. 2585/1/19 - http://wrcwebsite.azurewebsites.net/wp-content/uploads/mdocs/2585_final.pdf

Monitoring substance abuse

Long term substance abuse can result in the development of one or more health

issues e.g. lung or heart disease, stroke, cancer, or mental health conditions.

Thank you

WRC knowledge hub - http://search.wrc.org.za/

WRC COVID-19 programme - http://www.wrc.org.za/corona-virus/

covid19@wrc.org.za