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Viral surveillance


Viral surveillance allows researchers to track the spread of viral infectious diseases over time and determine the intensity of outbreaks at a community level.


What is viral surveillance?

Viral surveillance allows researchers to monitor the spread of viral infectious diseases over time and geographic space and determine the intensity of outbreaks at a community level. Viral infectious diseases can spread through a population when individuals are exposed to contaminated food, water, animals or to people who are infected with a virus. Examples of viral infectious diseases include but are not limited to influenza, human immunodeficiency virus (HIV), Ebola, Zika, Middle East Respiratory syndrome (MERS), COVID-19, and monkeypox.

Types of viral surveillance methods

Case surveillance

One way of monitoring the spread of viral infectious diseases is called case surveillance. This is a global effort which has medical professionals report cases of viral infectious diseases of interest (e.g., MERS) as they are identified, usually through rapid approaches such as antibody-based immunological assays, qPCR, PCR, and next generation sequencing (NGS). Case surveillance can be a very effective method for tracking viral outbreaks, however it does imply that individuals need to be symptomatic in order to be tested positive for infectious viral diseases. Therefore, while this method does effectively monitor viral spread, it can fail to give early warnings about new outbreaks to public health officials.

Wastewater surveillance

Viral surveillance using wastewater-based epidemiology (WBE), or wastewater surveillance has proven to be instrumental in understanding and responding to the spread of COVID-19, as well as monitoring emerging variants [1]. This approach to viral surveillance observes community infection rates at a large scale because individuals infected with SARS-CoV-2 shed viral particles in their feces even if they are asymptomatic. The result of this method is that researchers can capture outbreak events earlier and observe, at the community level, people that are not yet symptomatic [1].

qPCR and amplicon sequencing have both been used to track SARS-CoV-2 in wastewater samples. qPCR can provide information concerning the viral loads present in samples [2], while amplicon sequencing has been used to gather data about SARS-CoV-2 variants circulating in a population [1-3]. Amplicon sequencing is a type of targeted NGS that allows researchers to enrich for and sequence genetic information from only organisms of interest. When researchers use amplicon sequencing panels, they can target multiple regions of DNA and amplify or enrich those regions in their samples.

Future potential benefits of wastewater surveillance also include approaches to track multiple infectious diseases at the same time. This could be done either through deep-sequencing, untargeted NGS methods [2] or through expanding targeted NGS technologies that allow researchers to simultaneously monitor multiple diseases.

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  1. Karthikeyan S, Levy JI, De Hoff P, et al. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature. 2022.
  2. Spurbeck RR, Minard-Smith A, Catlin L. Feasibility of neighborhood and building scale wastewater-based genomic epidemiology for pathogen surveillance. Sci Total Environ. 2021;789:147829.
  3. Fontenele RS, Kraberger S, Hadfield J, et al. High-throughput sequencing of SARS-CoV-2 in wastewater provides insights into circulating variants. Water Res. 2021;205:117710.