Samples with detected SARS-CoV-2 results are genetically sequenced to identify the multiple variants or lineages of SARS-CoV-2 and to estimate the relative proportions of these lineages.

Unlike patient samples, wastewater samples contain multiple lineages of SARS-CoV-2. Because of this complexity, the sequence data is analyzed by a lineage decomposition mixture model to assess the different lineages that make up the sample and the relative proportions of these lineages.

These samples are distributed to the NYS SARS-CoV-2 Genetic Sequencing Laboratory Consortium, which consists of the NYSDOH Wadsworth Center and four contracted academic laboratories: New York Medical Center, SUNY Upstate, University at Buffalo SUNY, and the University of Rochester.

Following sequencing, whole-genome sequence data files are sent to Syracuse University for data interpretation and dissemination.