Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission

Abstract As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases 1–3 . SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing 4,5 . Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence…

• NS
  National Science Foundation

  Awards: 2029069, U19AI135995
• CD
  California Department of Public Health
• NI
  National Institutes of Health

  Awards: 3U19AI135995, UL1TR002550, U01AI151812, S10OD026929, U19AI135995, 1DP1AT010885
• CF
  Centers for Disease Control and Prevention

  Award: 75D30120C09795
• UO
  University of California, San Diego
• NI
  National Institute of Allergy and Infectious Diseases

  Awards: UL1TR002550, U01AI151812, U19AI135995
• NC
  National Center for Advancing Translational Sciences

  Award: UL1TR002550
• CF
  Center for Aerosol Impacts on Chemistry of the Environment, University of California, San Diego