Genetic diversity and evolutionary convergence of cryptic SARS- CoV-2 lineages detected via wastewater sequencing

• DOI: 10.1371/journal.ppat.1010636
• Publication Date: 2022-10-14T18:32:34Z
• Authors: Devon A. Gregory; Monica Trujillo; Clayton Rushford; Anna Flury; Sherin Kannoly; Kaung Myat San; Dustin T. Lyfoung; Roger W. Wiseman; Karen Bromert; Ming-Yi Zhou; Ellen Kesler; Nathan J. Bivens; Jay Hoskins; Chung-Ho Lin; David H. O’Connor; Chris Wieberg; Jeff Wenzel; Rose S. Kantor; John J. Dennehy; Marc C. Johnson
• Keywords: Lineage (genetic); Species complex; Viral quasispecies

Wastewater-based epidemiology (WBE) is an effective way of tracking the appearance and spread SARS-COV-2 lineages through communities. Beginning in early 2021, we implemented a targeted approach to amplify sequence receptor binding domain (RBD) characterize viral present sewersheds. Over course reproducibly detected multiple RBD that have never been observed patient samples 9 sewersheds located 3 states USA. These cryptic contained between 4 24 amino acid substitutions were intermittently which they found for as long 14 months. Many these occurred at residues also mutated Omicron variant concern (VOC), often with same substitutions. One lineage appeared be derived from Alpha VOC, but majority pre-VOC lineages. Specifically, several New York City common ancestor most likely diverged 2020. While source has not resolved, it seems increasingly long-term infections or animal reservoirs. Our findings demonstrate genetic diversity greater than what commonly routine SARS-CoV-2 surveillance. Wastewater sampling may more fully capture could reveal new VOCs before emerge wider human population.