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

• Published in: BMC genomics Vol. 25; no. 1; p. 59
• Main Authors: Conway, Michael J, Yang, Hannah, Revord, Lauren A, Novay, Michael P, Lee, Rachel J, Ward, Avery S, Abel, Jackson D, Williams, Maggie R, Uzarski, Rebecca L, Alm, Elizabeth W
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 13.01.2024; BioMed Central; BMC
• Subjects: Analysis; Causes of; Chronic; Chronic infection; Contamination; COVID-19; COVID-19 - epidemiology; Cryptic; Divergence; Environmental aspects; Environmental monitoring; Epidemics; Evolution; Genetic aspects; Genome, Viral; Genomes; Genomics; Health aspects; Health surveillance; Humans; Medical colleges; Medical research; Medicine, Experimental; Methods; Mutation; Public health; Purification; Risk factors; RNA, Viral; Rural areas; Rural communities; SARS-CoV-2; SARS-CoV-2 - genetics; Severe acute respiratory syndrome coronavirus 2; Sewage; Surveillance; Viral diseases; Wastewater; Wastewater treatment; Wastewater treatment plants; Water sampling; Water treatment; Water treatment plants; Michigan; United States > US; Evolution; Chronic; SARS-CoV-2; Surveillance; Wastewater; Cryptic
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-024-09977-7

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. 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. 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.