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Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.
Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou J, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RT, Freitas L, Maurer-Stroh S; GISAID core and curation team; Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Gangavarapu K, et al. Among authors: levy ji. Res Sq [Preprint]. 2022 Jun 28:rs.3.rs-1723829. doi: 10.21203/rs.3.rs-1723829/v1. Res Sq. 2022. PMID: 35794893 Free PMC article. Updated. Preprint.
Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission.
Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McD… See abstract for full author list ➔ Karthikeyan S, et al. Among authors: levy ji. medRxiv [Preprint]. 2022 Apr 4:2021.12.21.21268143. doi: 10.1101/2021.12.21.21268143. medRxiv. 2022. PMID: 35411350 Free PMC article. Updated. Preprint.
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.
Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S; GISAID Core and Curation Team; Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD. Gangavarapu K, et al. Among authors: levy ji. Nat Methods. 2023 Apr;20(4):512-522. doi: 10.1038/s41592-023-01769-3. Epub 2023 Feb 23. Nat Methods. 2023. PMID: 36823332 Free PMC article.
Utilizing river and wastewater as a SARS-CoV-2 surveillance tool to predict trends and identify variants of concern in settings with limited formal sewage systems.
Barnes K, Levy J, Andersen K, Gauld J, Rigby J, Kanjerwa O, Uzzell C, Chilupsya C, Anscombe C, Tomkins-Tinch C, Mbeti O, Cairns E, Thole H, McSweeney S, Chibwana M, Ashton P, Jere K, Meschke J, Diggle P, Cornick J, Jambo K, Kawalazira G, Paterson S, Nyirenda T, Feasey N, Chilima B. Barnes K, et al. Res Sq [Preprint]. 2023 Apr 14:rs.3.rs-2801767. doi: 10.21203/rs.3.rs-2801767/v1. Res Sq. 2023. PMID: 37090541 Free PMC article. Updated. Preprint.
Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.
Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F. Crits-Christoph A, et al. Among authors: levy ji. bioRxiv [Preprint]. 2023 Sep 14:2023.09.13.557637. doi: 10.1101/2023.09.13.557637. bioRxiv. 2023. PMID: 37745602 Free PMC article. Preprint.
Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data.
Sutcliffe SG, Kraemer SA, Ellmen I, Knapp JJ, Overton AK, Nash D, Nissimov JI, Charles TC, Dreifuss D, Topolsky I, Baykal PI, Fuhrmann L, Jablonski KP, Beerenwinkel N, Levy JI, Olabode AS, Becker DG, Gugan G, Brintnell E, Poon AFY, Valieris R, Drummond RD, Defelicibus A, Dias-Neto E, Rosales RA, Tojal da Silva I, Orfanou A, Psomopoulos F, Pechlivanis N, Pipes L, Chen Z, Baaijens JA, Baym M, Shapiro BJ. Sutcliffe SG, et al. Among authors: levy ji. Microb Genom. 2024 May;10(5). doi: 10.1099/mgen.0.001249. Microb Genom. 2024. PMID: 38785221 Free article.
212 results