Chronic shedding of a SARS-CoV-2 Alpha variant in wastewater.

BACKGROUND: Central Michigan University (CMU) participated in a state-wide SARS-CoV-2 wastewater monitoring program since 2021. Wastewater samples were collected from on-campus sites and nine off-campus wastewater treatment plants servicing small metropolitan and rural communities. SARS-CoV-2 genome copies were quantified using droplet digital PCR and results were reported to the health department. RESULTS: One rural, off-campus site consistently produced higher concentrations of SARS-CoV-2 genome copies. Samples from this site were sequenced and contained predominately a derivative of Alpha variant lineage B.1.1.7, detected from fall 2021 through summer 2023. Mutational analysis of reconstructed genes revealed divergence from the Alpha variant lineage sequence over time, including numerous mutations  in the Spike RBD and NTD. CONCLUSIONS: We discuss the possibility that a chronic SARS-CoV-2 infection accumulated adaptive mutations that promoted long-term infection. This study reveals that small wastewater treatment plants can enhance resolution of rare events and facilitate reconstruction of viral genomes due to the relative lack of contaminating sequences.

SARS-CoV-2 wastewater monitoring in rural and small metropolitan communities in Central Michigan.

Central Michigan University (CMU) participated in a state-wide SARS-CoV-2 wastewater monitoring program throughout the 2021-2022 academic year. Wastewater samples were collected weekly from ten on-campus sites and nine off-campus wastewater treatment plants servicing small metropolitan and rural communities. SARS-CoV-2 genome copies were quantified using droplet digital PCR. Case data reported by Central Michigan District Health Department and CMU were collected and compared with wastewater data. During the delta wave, wastewater detection and on-campus case reports increased rapidly with the start of the academic semester and peaked quickly, compared with a more gradual and prolonged increase in detection and case reports off-campus. During the omicron wave, transmission dynamics were similar on-campus and off-campus. Normalization of on-campus and off-campus wastewater data with pepper mild mottle virus gene expression suggested lower SARS-CoV-2 shedding per person in on-campus compared to off-campus samples during the delta wave, but no difference in virus shedding during the omicron wave. We discuss the possibility that a higher on-campus vaccination rate may have reduced virus shedding per person during the delta wave, but that this effect was lost with the omicron variant. This study suggests that wastewater monitoring is effective in rural and small metropolitan communities when used in conjunction with case reports to understand regional transmission dynamics and the impact of public health policies at a public university on virus shedding in the community.