Genetic variability of SARS-CoV-2 in wastewater and associations with community transmission

Sequencing genetic material from community wastewater facilitates the study of virus diversity. Diversity can be estimated using the variation in nucleotides and number of variants identified, increasing the information obtained from one wastewater sample. Using 12,290 wastewater sequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we found that virus diversity is a strong indicator of disease transmission, with a significant correlation between average weekly diversity and average weekly new COVID-19 infections. Although the concentration of viruses is the common measure of disease transmission from wastewater, we found that diversity is a better indicator, as it is unhampered by the noise inherent in the wastewater. We show that multiple measures of diversity yield similar results, which suggests that genetic diversity could be useful for increasing the utility of wastewater data.