Importance: The origin of highly divergent "cryptic" SARS-CoV-2 Spike sequences, which appear in wastewater but not clinical samples, is unknown. These wastewater sequences have harbored many of the same variants that later emerged in Omicron. If these enigmatic sequences are human-derived and transmissible, they could both be a source of future variants and a valuable tool for forecasting sequences that should be incorporated into vaccines and therapeutics. Objective: To determine whether enigmatic SARS-CoV-2 lineages detected in wastewater have a human or non-human (i.e., animal) source. Design: On January 11, 2022, an unusual Spike sequence was detected in municipal wastewater from a metropolitan area. Over the next four months, more focused wastewater sampling resolved the source of this variant. Setting: This study was performed in Wisconsin, United States, which has a comprehensive program for detecting SARS-CoV-2 in wastewater. Participants: Composite wastewater samples were used for this study; therefore, no individuals participated. Main Outcome(s) and Measure(s): The primary outcome was to determine the host(s) responsible for shedding this variant in wastewater. Both human and non-human hosts were plausible candidates at the study's outset. Results: The presence of the cryptic virus was narrowed from a municipal wastewater sample (catchment area >100,000 people) to an indoor wastewater sample from a single facility (catchment area ~30 people), indicating the human origin of this virus. Extraordinarily high concentrations of viral RNA (~520,000,000 genome copies / L and ~1,600,000,000 genome copies / L in June and August 2022, respectively) were detected in the indoor wastewater sample. The virus sequence harbored a combination of fixed nucleotide substitutions previously observed only in Pango lineage B.1.234, a variant that circulated at low levels in Wisconsin from October 2020 to February 2021. Conclusions and Relevance: High levels of persistent SARS-CoV-2 shedding from the gastrointestinal tract of an infected individual likely explain the presence of evolutionarily advanced, "cryptic variants" observed in some wastewater samples.

### Competing Interest Statement

The authors have declared no competing interest.

### Funding Statement

This study was made possible by the generous support of the Rockefeller Foundation's Regional Accelerators for Genomics Surveillance (DHO/TCF), Wisconsin Department of Health Services Epidemiology and Laboratory Capacity funds (www.dhs.wisconsin.gov, 144 AAJ8216) to DHO, CDC contract 75D30121C11060 (DHO/TCF), Wisconsin Department of Health Services ELC Wastewater Surveillance funds (www.dhs.wisconsin.gov, 130:AAI8627) to the UW-Madison Wisconsin State Laboratory of Hygiene (WSLH), and NIDA contract 1U01DA053893-01 (MJ).

### Author Declarations

I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.

Yes

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Yes

I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).

Yes

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Yes

Sequencing data is available in NCBI SRA and Genbank. Additional data is available from https://go.wisc.edu/4134pl.

<https://go.wisc.edu/4134pl>