COVID-19 Wastewater Variant Data

One way COVID-19 variants are tracked is through analyzing data from patients who test positive for COVID-19 in clinical settings. We can estimate the levels of different SARS-CoV-2 variants from our wastewater testing data, providing insight into the prevalence of variants among all infected individuals, including those who do not undergo clinical testing. Selected wastewater samples with positive SARS-CoV-2 results are genetically sequenced to identify specific variants, which are aggregated into broader lineages for population-level analysis. This approach allows us to assess the relative proportions of these lineages across various locations, such as counties, regions, and sewersheds. The results of this variant and lineage analysis are presented below. These dashboards will be updated Monday through Friday with the most recent available data from each facility.

 

While the terms are sometimes used interchangeably, understanding the distinction between variant and lineage is crucial for accurately tracking and interpreting changes in SARS-CoV-2 evolution. A variant is a specific mutation or group of mutations that arise within a lineage, often leading to differences in traits such as transmissibility or resistance. In contrast, a lineage refers to a distinct genetic descent or branch within a larger phylogenetic tree, representing the evolutionary history of a virus or pathogen.

 

For a more detailed explanation of variants, please see the COVID-19 Variant Data page. View the Wastewater Surveillance Methodological Notes for more information about how these data are reported. Learn more here about wastewater surveillance in New York State.

Genetic sequencing lineage data note: Samples are only sequenced if SARS-CoV-2 is detected- samples without a detection will show up as “No SARS-CoV-2 detected in sample” on the lineage map. The date range for sequencing data is different than for quantification data because sequencing of viral genomes from wastewater happens at separate laboratories. The most recent data for sequencing are shown for each site.

 

What is the difference between the detailed and the simplified lineage data? The simplified lineage data chart is aligned with lineages included on the CDC Nowcast, while the detailed data is aligned with the Global Initiative on Sharing Avian Influenza Data (GISAID) categorizations on the clinical variant data page. Nowcast data is grouped into broader categories in order to better understand more general lineage trends.