WEPP

WEPP enhances wastewater-based epidemiology by incorporating phylogenetic placement of sequencing reads into mutation-annotated trees to identify haplotypes present in wastewater samples.

Key Features:

• Phylogenetic Placement: WEPP places wastewater sequencing reads onto comprehensive mutation-annotated trees (MATs) that include all globally available clinical sequences and their inferred ancestral nodes.
• Haplotype Identification: WEPP identifies a subset of haplotypes most likely present in the sample and reports the abundance of each haplotype and its corresponding lineage.
• Parsimonious Read Mapping: WEPP provides parsimonious mappings of individual reads to haplotypes.
• Unaccounted Allele Detection: WEPP flags unaccounted alleles observed in the sample but unexplained by selected haplotypes, which may signal novel circulating variants.
• Near-Haplotype Resolution: WEPP achieves near-haplotype-level resolution, typically selecting haplotypes within an average distance of one single-nucleotide mutation from the true haplotype.
• Pathogen Agnosticism: WEPP is a pathogen-agnostic pipeline demonstrated on SARS-CoV-2 and two additional pathogens.

Scientific Applications:

• Intra-Lineage Haplotype Tracking: WEPP enables tracking of intra-lineage haplotype clusters that were previously confined to clinical sequencing.
• Geographical Origin Identification: WEPP supports identifying the geographical origins of newly introduced clusters.
• Emerging Variant Detection: WEPP detects emerging variants by analyzing unaccounted alleles and haplotype patterns.
• Public Health Surveillance: WEPP provides cost-effective and unbiased detection of emerging variants days to weeks ahead of clinical reporting.

Methodology:

WEPP uses phylogenetic placement of wastewater sequencing reads onto mutation-annotated trees (MATs) that include all globally available clinical sequences and their inferred ancestral nodes to identify haplotypes most likely present in the sample.