Detecting SARS-CoV-2 cryptic lineages using publicly available whole genome wastewater sequencing data

Area of Science:

• Virology
• Genomics
• Epidemiology

Background:

• Unique SARS-CoV-2 lineages, termed "cryptic lineages", were sporadically detected in wastewater starting in early 2021.
• These lineages were identified using a sequencing strategy targeting the rapidly evolving receptor binding domain (RBD) of SARS-CoV-2.
• Over 20 cryptic lineages had been identified previously via this targeted sequencing approach.

Purpose of the Study:

• To identify and characterize additional cryptic lineages of SARS-CoV-2 within wastewater sequence data.
• To analyze mutations within these lineages for evolutionary insights.
• To investigate potential origins or evolutionary pathways of SARS-CoV-2.

Main Methods:

• Screened SARS-CoV-2 wastewater sequence data from NCBI's Sequence Read Archives (SRA).
• Identified sequence reads with mutation combinations characteristic of cryptic lineages but not contemporary strains.
• Generated partial consensus sequences for newly identified cryptic lineages by mapping relevant sequence reads.

Main Results:

• Identified 18 additional cryptic lineages present in multiple samples from the same sewershed.
• Twelve of these 18 lineages were previously unreported.
• Seven mutations in these cryptic lineages were reversions to sequences conserved in SARS-CoV-2-related enteric bat Sarbecoviruses.

Conclusions:

• Wastewater surveillance effectively identified novel and divergent SARS-CoV-2 lineages.
• The observed reversion to bat Sarbecovirus sequences supports the hypothesis that SARS-CoV-2 adaptation for efficient respiratory replication predates the COVID-19 pandemic.
• Continued genomic surveillance of wastewater is crucial for understanding viral evolution and emergence.