{"id":"https://openalex.org/W7143332848","doi":"https://doi.org/10.1371/journal.pcbi.1014124","title":"WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology","display_name":"WEPP: Phylogenetic placement achieves near-haplotype resolution in wastewater-based epidemiology","publication_year":2026,"publication_date":"2026-03-30","ids":{"openalex":"https://openalex.org/W7143332848","doi":"https://doi.org/10.1371/journal.pcbi.1014124","pmid":"https://pubmed.ncbi.nlm.nih.gov/41911220"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1014124","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1014124","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1014124","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5118329136","display_name":"Pranav Gangwar","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pranav Gangwar","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of California, San Diego, California, United States of America"],"raw_orcid":"https://orcid.org/0009-0002-9738-900X","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California, San Diego, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5118278143","display_name":"Pratik Katte","orcid":"https://orcid.org/0000-0001-9976-1675"},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pratik Katte","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California, Santa Cruz, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California, Santa Cruz, California, United States of America","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5130916263","display_name":"Manu Bhat","orcid":null},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manu Bhat","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of California, San Diego, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California, San Diego, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080797757","display_name":"Yatish Turakhia","orcid":"https://orcid.org/0000-0001-5600-2900"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yatish Turakhia","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of California, San Diego, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-5600-2900","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California, San Diego, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5118329136"],"corresponding_institution_ids":["https://openalex.org/I36258959"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.75446491,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"3","first_page":"e1014124","last_page":"e1014124"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11754","display_name":"SARS-CoV-2 detection and testing","score":0.7394999861717224,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11754","display_name":"SARS-CoV-2 detection and testing","score":0.7394999861717224,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11331","display_name":"Fecal contamination and water quality","score":0.03610000014305115,"subfield":{"id":"https://openalex.org/subfields/2312","display_name":"Water Science and Technology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.01899999938905239,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/haplotype","display_name":"Haplotype","score":0.7120000123977661},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6462000012397766},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.48190000653266907},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.47909998893737793},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.43149998784065247},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.4083000123500824},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.3693000078201294},{"id":"https://openalex.org/keywords/pedigree-chart","display_name":"Pedigree chart","score":0.3479999899864197}],"concepts":[{"id":"https://openalex.org/C197754878","wikidata":"https://www.wikidata.org/wiki/Q80711","display_name":"Haplotype","level":4,"score":0.7120000123977661},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6462000012397766},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49470001459121704},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.48190000653266907},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.47909998893737793},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.43149998784065247},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.4083000123500824},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38519999384880066},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.3693000078201294},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3677000105381012},{"id":"https://openalex.org/C22593422","wikidata":"https://www.wikidata.org/wiki/Q3242583","display_name":"Pedigree chart","level":3,"score":0.3479999899864197},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34369999170303345},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.33739998936653137},{"id":"https://openalex.org/C3020199158","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"High resolution","level":2,"score":0.33219999074935913},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.3221000134944916},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3197999894618988},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.31700000166893005},{"id":"https://openalex.org/C112789634","wikidata":"https://www.wikidata.org/wiki/Q18207010","display_name":"False positives and false negatives","level":3,"score":0.31349998712539673},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3005000054836273},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.29510000348091125},{"id":"https://openalex.org/C77434933","wikidata":"https://www.wikidata.org/wiki/Q4043440","display_name":"Multilocus sequence typing","level":4,"score":0.2913999855518341},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.29030001163482666},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2802000045776367},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.2728999853134155},{"id":"https://openalex.org/C97669555","wikidata":"https://www.wikidata.org/wiki/Q4118435","display_name":"Molecular epidemiology","level":4,"score":0.26030001044273376},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26019999384880066},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.25609999895095825},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.2540000081062317}],"mesh":[{"descriptor_ui":"D000079686","descriptor_name":"Wastewater-Based Epidemiological Monitoring","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000079686","descriptor_name":"Wastewater-Based Epidemiological Monitoring","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006239","descriptor_name":"Haplotypes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D062065","descriptor_name":"Wastewater","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D062065","descriptor_name":"Wastewater","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1371/journal.pcbi.1014124","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1014124","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41911220","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41911220","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1014124","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1014124","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Clean water and sanitation","score":0.7159306406974792,"id":"https://metadata.un.org/sdg/6"}],"awards":[{"id":"https://openalex.org/G3074089942","display_name":null,"funder_award_id":"Fall 2022 CFP","funder_id":"https://openalex.org/F2471752397","funder_display_name":"Amazon Research Awards"},{"id":"https://openalex.org/G7401018214","display_name":null,"funder_award_id":"75D30123C17463","funder_id":"https://openalex.org/F4320319715","funder_display_name":"Centers for Disease Control and Prevention Foundation"}],"funders":[{"id":"https://openalex.org/F2471752397","display_name":"Amazon Research Awards","ror":null},{"id":"https://openalex.org/F4320311968","display_name":"Hellman Foundation","ror":"https://ror.org/02g98ya79"},{"id":"https://openalex.org/F4320319715","display_name":"Centers for Disease Control and Prevention Foundation","ror":"https://ror.org/050103r16"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":80,"referenced_works":["https://openalex.org/W2157539385","https://openalex.org/W2336957559","https://openalex.org/W2789843538","https://openalex.org/W2952045272","https://openalex.org/W2952946229","https://openalex.org/W3025983200","https://openalex.org/W3029878358","https://openalex.org/W3034071161","https://openalex.org/W3043124965","https://openalex.org/W3093782372","https://openalex.org/W3124772303","https://openalex.org/W3127798546","https://openalex.org/W3130152469","https://openalex.org/W3139094717","https://openalex.org/W3160568774","https://openalex.org/W3173130814","https://openalex.org/W3177716023","https://openalex.org/W3188100398","https://openalex.org/W3194120601","https://openalex.org/W3196426464","https://openalex.org/W3198177518","https://openalex.org/W3201073213","https://openalex.org/W3210167380","https://openalex.org/W4210266936","https://openalex.org/W4210512509","https://openalex.org/W4213210289","https://openalex.org/W4221092123","https://openalex.org/W4225517141","https://openalex.org/W4225851399","https://openalex.org/W4247111930","https://openalex.org/W4281383093","https://openalex.org/W4281641403","https://openalex.org/W4283010087","https://openalex.org/W4283021534","https://openalex.org/W4284696817","https://openalex.org/W4285730114","https://openalex.org/W4285730961","https://openalex.org/W4297248853","https://openalex.org/W4306248136","https://openalex.org/W4308542029","https://openalex.org/W4308963287","https://openalex.org/W4309338001","https://openalex.org/W4312065016","https://openalex.org/W4313252333","https://openalex.org/W4313278733","https://openalex.org/W4315778613","https://openalex.org/W4317698849","https://openalex.org/W4317780078","https://openalex.org/W4320718706","https://openalex.org/W4353049630","https://openalex.org/W4376959751","https://openalex.org/W4380872791","https://openalex.org/W4386322157","https://openalex.org/W4388033386","https://openalex.org/W4389193853","https://openalex.org/W4390332165","https://openalex.org/W4390345660","https://openalex.org/W4390631105","https://openalex.org/W4391539704","https://openalex.org/W4392637100","https://openalex.org/W4392765068","https://openalex.org/W4394933742","https://openalex.org/W4399069773","https://openalex.org/W4400292185","https://openalex.org/W4400359605","https://openalex.org/W4400370651","https://openalex.org/W4400378303","https://openalex.org/W4402037851","https://openalex.org/W4402207564","https://openalex.org/W4402990601","https://openalex.org/W4406929306","https://openalex.org/W4407416130","https://openalex.org/W4408148219","https://openalex.org/W4408205014","https://openalex.org/W4409249448","https://openalex.org/W4409788635","https://openalex.org/W4409948511","https://openalex.org/W4410088111","https://openalex.org/W4410119884","https://openalex.org/W4411142262"],"related_works":[],"abstract_inverted_index":{"Wastewater-based":[0],"epidemiology":[1,229],"(WBE)":[2],"is":[3],"a":[4,50,90,97,130,152,196,231],"cost-effective,":[5],"unbiased,":[6],"and":[7,35,58,82,87,107,109,143,148,163,174,214,237],"time-efficient":[8],"tool":[9,234],"for":[10,134,235],"public":[11],"health":[12],"surveillance.":[13,221],"Although":[14],"widely":[15],"adopted":[16],"since":[17],"the":[18,56,102,116],"COVID-19":[19],"pandemic,":[20],"WBE":[21,61,177],"remains":[22],"underutilized":[23],"in":[24,96,115,195],"genomic":[25],"epidemiology,":[26],"as":[27,185],"most":[28],"tools":[29,173],"are":[30],"limited":[31],"to":[32,140,157,181,203],"lineage-level":[33],"resolution":[34,57],"focus":[36],"only":[37],"on":[38],"estimating":[39],"lineage":[40,144],"abundances":[41],"from":[42,160,211],"wastewater":[43,158],"sequencing":[44,68],"reads.":[45],"Here,":[46],"we":[47],"present":[48,95],"WEPP,":[49],"pathogen-agnostic":[51],"pipeline":[52],"that":[53],"improves":[54],"both":[55],"capabilities":[59],"of":[60,67,76,92,104],"analysis.":[62],"WEPP":[63,128,165,225],"uses":[64],"phylogenetic":[65,154],"placement":[66],"reads":[69],"onto":[70],"mutation-annotated":[71],"trees":[72],"(MATs)-daily":[73],"updated":[74],"phylogenies":[75],"all":[77],"globally":[78],"available":[79],"clinical":[80,182,207,220],"sequences":[81],"their":[83],"inferred":[84],"ancestors-to":[85],"sensitively":[86],"precisely":[88],"identify":[89],"subset":[91],"haplotypes":[93],"likely":[94],"sample.":[98],"It":[99],"also":[100],"reports":[101],"abundance":[103],"each":[105],"haplotype":[106,142,189,200],"lineage,":[108],"flags":[110],"\"unaccounted":[111],"alleles\"-":[112],"those":[113],"found":[114],"sample":[117],"but":[118],"not":[119],"explained":[120],"by":[121,171,219],"selected":[122],"haplotypes-that":[123],"may":[124],"indicate":[125],"novel":[126,212],"variants.":[127],"includes":[129],"powerful":[131,233],"interactive":[132],"dashboard":[133],"high-resolution":[135],"visual":[136],"analysis,":[137],"allowing":[138],"users":[139],"explore":[141],"abundances,":[145],"read-to-haplotype":[146],"mappings,":[147],"unaccounted":[149],"alleles":[150],"within":[151],"global":[153],"context.":[155],"Applied":[156],"samples":[159],"multiple":[161,192],"cities":[162],"pathogens,":[164],"uncovered":[166],"biological":[167],"insights":[168],"sometimes":[169],"missed":[170,218],"other":[172],"enabled":[175],"new":[176],"applications":[178],"previously":[179],"confined":[180],"sequencing,":[183],"such":[184],"identifying":[186],"(i)":[187],"intra-lineage":[188],"clusters,":[190],"(ii)":[191],"cluster":[193],"introductions":[194],"city,":[197],"(iii)":[198],"early":[199],"detection":[201],"up":[202],"five":[204],"weeks":[205],"before":[206],"confirmation,":[208],"(iv)":[209],"mutations":[210],"variants,":[213],"(v)":[215],"circulating":[216],"lineages":[217],"With":[222],"these":[223],"capabilities,":[224],"can":[226],"transform":[227],"wastewater-based":[228],"into":[230],"more":[232],"monitoring":[236],"managing":[238],"infectious":[239],"disease":[240],"outbreaks.":[241]},"counts_by_year":[],"updated_date":"2026-04-02T13:48:15.688549","created_date":"2026-03-31T00:00:00"}