Continued selection on cryptic SARS-CoV-2 observed in Missouri wastewater

Area of Science:

• Environmental microbiology
• Virology
• Public health surveillance

Background:

• Wastewater-based epidemiology (WBE) is crucial for monitoring SARS-CoV-2 circulation.
• Cryptic SARS-CoV-2 lineages, undetected in clinical samples, can persist in communities.
• Previous WBE studies have identified unique lineages from specific geographic locations.

Purpose of the Study:

• To track the continued presence and evolution of a specific cryptic SARS-CoV-2 lineage detected in wastewater.
• To understand the evolutionary dynamics of cryptic lineages in response to selective pressures.
• To assess the utility of WBE in identifying and monitoring novel or uncharacterized viral strains.

Main Methods:

• Deep sequencing of wastewater samples from a specific site.
• Phylogenetic analysis to track lineage evolution.
• Comparison of evolutionary patterns with known SARS-CoV-2 variants.

Main Results:

• A previously identified cryptic SARS-CoV-2 lineage was repeatedly detected at a Missouri wastewater site.
• This cryptic lineage exhibited ongoing evolution.
• The observed evolutionary trajectory showed similarities to those of known Omicron lineages.

Conclusions:

• Cryptic SARS-CoV-2 lineages can persist and evolve within communities.
• Wastewater surveillance is effective in detecting and monitoring such lineages.
• The evolution of this cryptic lineage suggests it is under similar selective pressures as globally dominant variants.