Evidence of transmission from fully vaccinated individuals in a large outbreak of the SARS-CoV-2 Delta variant in Provincetown, Massachusetts.

Author(s): 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 PCJournal: medRxivPMID: 34704102 October 2021
Multiple summer events, including large indoor gatherings, in Provincetown, Massachusetts (MA), in July 2021 contributed to an outbreak of over…

Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.

Author(s): Baaijens JA, Zulli A, Ott IM, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy K, Ghaeli N, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen BB, Yale SARS-CoV-2 Genomic Surveillance Initiative., Hanage WP, Grubaugh ND, Peccia J, Baym MJournal: medRxivPMID: 34494031 September 2021
Effectively monitoring the spread of SARS-CoV-2 variants is essential to efforts to counter the ongoing pandemic. Wastewater monitoring of SARS-CoV-2…

SARS-CoV-2 epidemic after social and economic reopening in three US states reveals shifts in age structure and clinical characteristics.

Author(s): Wikle NB, Tran TN, Gentilesco B, Leighow SM, Albert E, Strong ER, Břinda K, Inam H, Yang F, Hossain S, Chan P, Hanage WP, Messick M, Pritchard JR, Hanks E, Boni MFJournal: medRxivPMID: 34426816 August 2021
In the United States, state-level re-openings in spring 2020 presented an opportunity for the resurgence of SARS-CoV-2 transmission. One important…

Viral loads observed under competing strain dynamics

Author(s): Hay JA, Kennedy-Shaffer L, Mina MJJournal: medRxiv July 2021
A plausible mechanism for the increased transmissibility of SARS-CoV-2 variants of concern (VOCs) results from VOC infections causing higher viral…

Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages.

Author(s): Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Kelly K, Omerza G, Renzette N, Watkins AE, Kalinich CC, Alpert T, Brito AF, Earnest R, Tikhonova IR, Castaldi C, Kelly JP, Shudt M, Plitnick J, Schneider E, Murphy S, Neal C, Laszlo E, Altajar A, Pearson C, Muyombwe A, Downing R, Razeq J, Niccolai L, Wilson MS, Anderson ML, Wang J, Liu C, Hui P, Mane S, Taylor BP, Hanage WP, Landry ML, Peaper DR, Bilguvar K, Fauver JR, Vogels CBF, Gardner LM, Pitzer VE, George KS, Adams MD, Grubaugh NDJournal: medRxivPMID: 34230938 July 2021
Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control…

Deep–sequence phylogenetics to quantify patterns of HIV transmission in the context of a universal testing and treatment trial — BCPP/ Ya Tsie trial

Author(s): Magosi LE, Zhang Y, Golubchick T, Gruttola VD, Tchetgen EJT, Novitsky V, Moore J, Bachanas P, Segolodi T, Lebelonyane R, Holme MP, Moyo S, Makhema J, Lockman S, Fraser C, Essex M, Lipsitch MJournal: medRxiv June 2021
Mathematical models predict that community–wide access to HIV testing–and–treatment can rapidly and substantially reduce new HIV infections. Yet several large…