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Page 1
Geospatial and demographic patterns of SARS-CoV-2 spread in Massachusetts from over 130,000 genomes.
Moreno GK, Brock-Fisher T, Krasilnikova LA, Schaffner SF, Burns M, Casiello CE, Messer KS, Petros B, Specht I, DeRuff KC, Siddle KJ, Loreth C, Fitzgerald NA, Rooke HM, Gabriel SB, Smole S, Wohl S, Park DJ, Madoff LC, Brown CM, MacInnis BL, Sabeti PC. Moreno GK, et al. Among authors: loreth c. medRxiv [Preprint]. 2025 Apr 6:2025.04.04.25324273. doi: 10.1101/2025.04.04.25324273. medRxiv. 2025. PMID: 40236398 Free PMC article. Preprint.
Accelerating bioinformatics implementation in public health.
Libuit KG, Doughty EL, Otieno JR, Ambrosio F, Kapsak CJ, Smith EA, Wright SM, Scribner MR, Petit Iii RA, Mendes CI, Huergo M, Legacki G, Loreth C, Park DJ, Sevinsky JR. Libuit KG, et al. Among authors: loreth c. Microb Genom. 2023 Jul;9(7):mgen001051. doi: 10.1099/mgen.0.001051. Microb Genom. 2023. PMID: 37428142 Free PMC article.
Viral Lineages in the 2022 RSV Surge in the United States.
Adams G, Moreno GK, Petros BA, Uddin R, Levine Z, Kotzen B, Messer KS, Dobbins ST, DeRuff KC, Loreth CM, Brock-Fisher T, Schaffner SF, Chaluvadi S, Kanjilal S, Luban J, Ozonoff A, Park DJ, Turbett SE, Siddle KJ, MacInnis BL, Sabeti PC, Lemieux JE. Adams G, et al. Among authors: loreth cm. N Engl J Med. 2023 Apr 6;388(14):1335-1337. doi: 10.1056/NEJMc2216153. Epub 2023 Feb 22. N Engl J Med. 2023. PMID: 36812457 Free PMC article. No abstract available.
The 2022 RSV surge was driven by multiple viral lineages.
Adams G, Moreno GK, Petros BA, Uddin R, Levine Z, Kotzen B, Messer K, Dobbins ST, DeRuff KC, Loreth C, Brock-Fisher T, Schaffner SF, Chaluvadi S, Kanjilal S, Luban J, Ozonoff A, Park D, Turbett S, Siddle KJ, MacInnis BL, Sabeti P, Lemieux J. Adams G, et al. Among authors: loreth c. medRxiv [Preprint]. 2023 Jan 5:2023.01.04.23284195. doi: 10.1101/2023.01.04.23284195. medRxiv. 2023. Update in: N Engl J Med. 2023 Apr 6;388(14):1335-1337. doi: 10.1056/NEJMc2216153. PMID: 36656774 Free PMC article. Updated. Preprint.
Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework.
Petros BA, Paull JS, Tomkins-Tinch CH, Loftness BC, DeRuff KC, Nair P, Gionet GL, Benz A, Brock-Fisher T, Hughes M, Yurkovetskiy L, Mulaudzi S, Leenerman E, Nyalile T, Moreno GK, Specht I, Sani K, Adams G, Babet SV, Baron E, Blank JT, Boehm C, Botti-Lodovico Y, Brown J, Buisker AR, Burcham T, Chylek L, Cronan P, Dauphin A, Desreumaux V, Doss M, Flynn B, Gladden-Young A, Glennon O, Harmon HD, Hook TV, Kary A, King C, Loreth C, Marrs L, McQuade KJ, Milton TT, Mulford JM, Oba K, Pearlman L, Schifferli M, Schmidt MJ, Tandus GM, Tyler A, Vodzak ME, Krohn Bevill K, Colubri A, MacInnis BL, Ozsoy AZ, Parrie E, Sholtes K, Siddle KJ, Fry B, Luban J, Park DJ, Marshall J, Bronson A, Schaffner SF, Sabeti PC. Petros BA, et al. Among authors: loreth c. Med. 2022 Dec 9;3(12):883-900.e13. doi: 10.1016/j.medj.2022.09.003. Epub 2022 Sep 19. Med. 2022. PMID: 36198312 Free PMC article.
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.
Earnest R, Uddin R, Matluk N, Renzette N, Turbett SE, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HB, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Novitsky V, Howison M, Darpolor J, Manne A, Kantor R, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Pitzer VE, Sabeti PC, Gabriel S, MacInnis BL; New England Variant Investigation Team; Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Earnest R, et al. Among authors: loreth c. Cell Rep Med. 2022 Mar 11;3(4):100583. doi: 10.1016/j.xcrm.2022.100583. eCollection 2022 Apr 19. Cell Rep Med. 2022. PMID: 35480627 Free PMC article.
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak.
Siddle KJ, Krasilnikova LA, Moreno GK, Schaffner SF, Vostok J, Fitzgerald NA, Lemieux JE, Barkas N, Loreth C, Specht I, Tomkins-Tinch CH, Paull JS, Schaeffer B, Taylor BP, Loftness B, Johnson H, Schubert PL, Shephard HM, Doucette M, Fink T, Lang AS, Baez S, Beauchamp J, Hennigan S, Buzby E, Ash S, Brown J, Clancy S, Cofsky S, Gagne L, Hall J, Harrington R, Gionet GL, DeRuff KC, Vodzak ME, Adams GC, Dobbins ST, Slack SD, Reilly SK, Anderson LM, Cipicchio MC, DeFelice MT, Grimsby JL, Anderson SE, Blumenstiel BS, Meldrim JC, Rooke HM, Vicente G, Smith NL, Messer KS, Reagan FL, Mandese ZM, Lee MD, Ray MC, Fisher ME, Ulcena MA, Nolet CM, English SE, Larkin KL, Vernest K, Chaluvadi S, Arvidson D, Melchiono M, Covell T, Harik V, Brock-Fisher T, Dunn M, Kearns A, Hanage WP, Bernard C, Philippakis A, Lennon NJ, Gabriel SB, Gallagher GR, Smole S, Madoff LC, Brown CM, Park DJ, MacInnis BL, Sabeti PC. Siddle KJ, et al. Among authors: loreth c. Cell. 2022 Feb 3;185(3):485-492.e10. doi: 10.1016/j.cell.2021.12.027. Epub 2021 Dec 23. Cell. 2022. PMID: 35051367 Free PMC article.
Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows.
Lagerborg KA, Normandin E, Bauer MR, Adams G, Figueroa K, Loreth C, Gladden-Young A, Shaw BM, Pearlman LR, Berenzy D, Dewey HB, Kales S, Dobbins ST, Shenoy ES, Hooper D, Pierce VM, Zachary KC, Park DJ, MacInnis BL, Tewhey R, Lemieux JE, Sabeti PC, Reilly SK, Siddle KJ. Lagerborg KA, et al. Among authors: loreth c. Nat Microbiol. 2022 Jan;7(1):108-119. doi: 10.1038/s41564-021-01019-2. Epub 2021 Dec 14. Nat Microbiol. 2022. PMID: 34907347 Free PMC article.
Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts.
Siddle KJ, Krasilnikova LA, Moreno GK, Schaffner SF, Vostok J, Fitzgerald NA, Lemieux JE, Barkas N, Loreth C, Specht I, Tomkins-Tinch CH, Silbert J, Schaeffer B, Taylor BP, Loftness B, Johnson H, Schubert PL, Shephard HM, Doucette M, Fink T, Lang AS, Baez S, Beauchamp J, Hennigan S, Buzby E, Ash S, Brown J, Clancy S, Cofsky S, Gagne L, Hall J, Harrington R, Gionet GL, DeRuff KC, Vodzak ME, Adams GC, Dobbins ST, Slack SD, Reilly SK, Anderson LM, Cipicchio MC, DeFelice MT, Grimsby JL, Anderson SE, Blumenstiel BS, Meldrim JC, Rooke HM, Vicente G, Smith NL, Messer KS, Reagan FL, Mandese ZM, Lee MD, Ray MC, Fisher ME, Ulcena MA, Nolet CM, English SE, Larkin KL, Vernest K, Chaluvadi S, Arvidson D, Melchiono M, Covell T, Harik V, Brock-Fisher T, Dunn M, Kearns A, Hanage WP, Bernard C, Philippakis A, Lennon NJ, Gabriel SB, Gallagher GR, Smole S, Madoff LC, Brown CM, Park DJ, MacInnis BL, Sabeti PC. Siddle KJ, et al. Among authors: loreth c. medRxiv [Preprint]. 2021 Oct 20:2021.10.20.21265137. doi: 10.1101/2021.10.20.21265137. medRxiv. 2021. Update in: Cell. 2022 Feb 3;185(3):485-492.e10. doi: 10.1016/j.cell.2021.12.027. PMID: 34704102 Free PMC article. Updated. Preprint.
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.
Earnest R, Uddin R, Matluk N, Renzette N, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Turbett S, Bilguvar K, De Kumar B, Landry ML, Peaper DR, Kelly K, Omerza G, Grieser H, Meak S, Martha J, Dewey HH, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Sabeti PC, Gabriel S, MacInnis BL; New England Variant Investigation Team; Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Earnest R, et al. Among authors: loreth c. medRxiv [Preprint]. 2021 Oct 7:2021.10.06.21264641. doi: 10.1101/2021.10.06.21264641. medRxiv. 2021. Update in: Cell Rep Med. 2022 Mar 11;3(4):100583. doi: 10.1016/j.xcrm.2022.100583. PMID: 34642698 Free PMC article. Updated. Preprint.
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