Coronavirus variants in wastewater

Wastewater monitoring can be used to determine variations in the proportions of different coronavirus variants in Finland.

Why is it necessary to examine the prevalence of different virus variants in wastewater?

Wastewater monitoring is a way to determine the infection situation of communities that is independent of the testing activity of health care services. Coronavirus is excreted into the nasal secretions, faeces and urine of infected persons and through that into the sewer. The information collected on wastewater supports the epidemic’s situational picture of the prevalence of virus variants in different localities.

In coronavirus infections, the incubation time and severity of the disease and the amount and duration of virus particle excretion may vary between different virus strains. Wastewater variant data is therefore relevant for the interpretation of wastewater results ¹. A virus variant that is excreted in large quantities and over a long period of time produces a higher signal from each infected person to the wastewater in the area than another virus variant that is excreted in smaller quantities and for a shorter period of time from infected persons.

That is, a change in virus strains changes the relationship between the wastewater finding and the number of infections in the population. For example, according to preliminary data, the quantity of the Delta variant, which was the predominant virus strain in Finland until the end of 2021, in human secretions has been higher and its virus excretion after infection has lasted longer compared to the Omicron variant, which has become more common at the beginning of 2022 ².

Method for the identification of virus variants in wastewater

Identification of coronavirus variants in wastewater is possible, albeit challenging and requiring specialist analytics. Coronavirus’s genetic material, viral RNA, is diluted in wastewater and may be damaged by environmental factors. Advanced sequencing techniques can be used with the genetic material in wastewater to indicate which coronavirus variants are present in the area at the time of sampling. Identifying the different variants is based on observing mutations specific to each variant. The mutations to be monitored can vary with the fluctuation of the dominant virus variants and as genome information accumulates.

In March 2021, the European Commission’s recommendation launched the development and deployment of methodology for reporting the prevalence of coronavirus variants in wastewater in almost all EU member states³. Funded by the European Commission, THL launched the ESI-WBE development project in Finland at the beginning of 2022 to support this work to develop the reporting of coronavirus variants. Before the prevalence of virus variants in wastewater can be examined, it is necessary to define characteristic mutations, or specific changes in the genome, for each variant. Wastewater monitoring for coronavirus mutations has already been developed in several countries, such as Switzerland and the Netherlands ^4,7.

The genome composition in wastewater is analysed with advanced next-generation sequencing techniques to detect coronavirus mutations. The success of the sequencing of each wastewater sample is assessed by examining the coverage and uniformity of the sequences throughout the genome. The prevalence of a single mutation in a wastewater sample can be verified if the area of that mutation has been sufficiently sequenced ^5,6. THL will continue to develop methods for identifying virus variants in wastewater.

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Updated: Tue Dec 05 18:03:56 EET 2023