Matches in SemOpenAlex for { <https://semopenalex.org/work/W4297248853> ?p ?o ?g. }
- W4297248853 endingPage "100313" @default.
- W4297248853 startingPage "100313" @default.
- W4297248853 abstract "Wastewater surveillance has become essential for monitoring the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The quantification of SARS-CoV-2 RNA in wastewater correlates with the coronavirus disease 2019 (COVID-19) caseload in a community. However, estimating the proportions of different SARS-CoV-2 haplotypes has remained technically difficult. We present a phylogenetic imputation method for improving the SARS-CoV-2 reference database and a method for estimating the relative proportions of SARS-CoV-2 haplotypes from wastewater samples. The phylogenetic imputation method uses the global SARS-CoV-2 phylogeny and imputes based on the maximum of the posterior probability of each nucleotide. We show that the imputation method has error rates comparable to, or lower than, typical sequencing error rates, which substantially improves the reference database and allows for accurate inferences of haplotype composition. Our method for estimating relative proportions of haplotypes uses an initial step to remove unlikely haplotypes and an expectation maximization (EM) algorithm for obtaining maximum likelihood estimates of the proportions of different haplotypes in a sample. Using simulations with a reference database of >3 million SARS-CoV-2 genomes, we show that the estimated proportions reflect the true proportions given sufficiently high sequencing depth." @default.
- W4297248853 created "2022-09-28" @default.
- W4297248853 creator A5048736318 @default.
- W4297248853 creator A5067569888 @default.
- W4297248853 creator A5071836973 @default.
- W4297248853 creator A5088476239 @default.
- W4297248853 date "2022-10-01" @default.
- W4297248853 modified "2023-10-13" @default.
- W4297248853 title "Estimating the relative proportions of SARS-CoV-2 haplotypes from wastewater samples" @default.
- W4297248853 cites W1525734744 @default.
- W4297248853 cites W2008049885 @default.
- W4297248853 cites W2087036932 @default.
- W4297248853 cites W2141052558 @default.
- W4297248853 cites W2151409320 @default.
- W4297248853 cites W2170551349 @default.
- W4297248853 cites W2558624268 @default.
- W4297248853 cites W3017092394 @default.
- W4297248853 cites W3028152077 @default.
- W4297248853 cites W3034926680 @default.
- W4297248853 cites W3039901154 @default.
- W4297248853 cites W3042091277 @default.
- W4297248853 cites W3044459694 @default.
- W4297248853 cites W3046192791 @default.
- W4297248853 cites W3065795114 @default.
- W4297248853 cites W3098182612 @default.
- W4297248853 cites W3101667854 @default.
- W4297248853 cites W3124259713 @default.
- W4297248853 cites W3180301457 @default.
- W4297248853 cites W4210735121 @default.
- W4297248853 cites W4283515938 @default.
- W4297248853 doi "https://doi.org/10.1016/j.crmeth.2022.100313" @default.
- W4297248853 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36159190" @default.
- W4297248853 hasPublicationYear "2022" @default.
- W4297248853 type Work @default.
- W4297248853 citedByCount "3" @default.
- W4297248853 countsByYear W42972488532022 @default.
- W4297248853 countsByYear W42972488532023 @default.
- W4297248853 crossrefType "journal-article" @default.
- W4297248853 hasAuthorship W4297248853A5048736318 @default.
- W4297248853 hasAuthorship W4297248853A5067569888 @default.
- W4297248853 hasAuthorship W4297248853A5071836973 @default.
- W4297248853 hasAuthorship W4297248853A5088476239 @default.
- W4297248853 hasBestOaLocation W42972488531 @default.
- W4297248853 hasConcept C104317684 @default.
- W4297248853 hasConcept C105795698 @default.
- W4297248853 hasConcept C135763542 @default.
- W4297248853 hasConcept C142724271 @default.
- W4297248853 hasConcept C153209595 @default.
- W4297248853 hasConcept C182081679 @default.
- W4297248853 hasConcept C193252679 @default.
- W4297248853 hasConcept C197754878 @default.
- W4297248853 hasConcept C2779134260 @default.
- W4297248853 hasConcept C3007834351 @default.
- W4297248853 hasConcept C3008058167 @default.
- W4297248853 hasConcept C33923547 @default.
- W4297248853 hasConcept C49781872 @default.
- W4297248853 hasConcept C524204448 @default.
- W4297248853 hasConcept C54355233 @default.
- W4297248853 hasConcept C58041806 @default.
- W4297248853 hasConcept C71924100 @default.
- W4297248853 hasConcept C86803240 @default.
- W4297248853 hasConcept C9357733 @default.
- W4297248853 hasConcept C97425143 @default.
- W4297248853 hasConceptScore W4297248853C104317684 @default.
- W4297248853 hasConceptScore W4297248853C105795698 @default.
- W4297248853 hasConceptScore W4297248853C135763542 @default.
- W4297248853 hasConceptScore W4297248853C142724271 @default.
- W4297248853 hasConceptScore W4297248853C153209595 @default.
- W4297248853 hasConceptScore W4297248853C182081679 @default.
- W4297248853 hasConceptScore W4297248853C193252679 @default.
- W4297248853 hasConceptScore W4297248853C197754878 @default.
- W4297248853 hasConceptScore W4297248853C2779134260 @default.
- W4297248853 hasConceptScore W4297248853C3007834351 @default.
- W4297248853 hasConceptScore W4297248853C3008058167 @default.
- W4297248853 hasConceptScore W4297248853C33923547 @default.
- W4297248853 hasConceptScore W4297248853C49781872 @default.
- W4297248853 hasConceptScore W4297248853C524204448 @default.
- W4297248853 hasConceptScore W4297248853C54355233 @default.
- W4297248853 hasConceptScore W4297248853C58041806 @default.
- W4297248853 hasConceptScore W4297248853C71924100 @default.
- W4297248853 hasConceptScore W4297248853C86803240 @default.
- W4297248853 hasConceptScore W4297248853C9357733 @default.
- W4297248853 hasConceptScore W4297248853C97425143 @default.
- W4297248853 hasFunder F4320332161 @default.
- W4297248853 hasIssue "10" @default.
- W4297248853 hasLocation W42972488531 @default.
- W4297248853 hasLocation W42972488532 @default.
- W4297248853 hasLocation W42972488533 @default.
- W4297248853 hasOpenAccess W4297248853 @default.
- W4297248853 hasPrimaryLocation W42972488531 @default.
- W4297248853 hasRelatedWork W1968654496 @default.
- W4297248853 hasRelatedWork W1978153144 @default.
- W4297248853 hasRelatedWork W2122946544 @default.
- W4297248853 hasRelatedWork W2126214064 @default.
- W4297248853 hasRelatedWork W2178628622 @default.
- W4297248853 hasRelatedWork W2216458865 @default.
- W4297248853 hasRelatedWork W4286002085 @default.
- W4297248853 hasRelatedWork W4317801964 @default.