Causal discovery for the microbiome.

Author(s): Corander J, Hanage WP, Pensar JJournal: Lancet MicrobePMID: 36152674 September 2022
Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases…

Analyzing the impact of a real-life outbreak simulator on pandemic mitigation: An epidemiological modeling study.

Author(s): Specht I, Sani K, Loftness BC, Hoffman C, Gionet G, Bronson A, Marshall J, Decker C, Bailey L, Siyanbade T, Kemball M, Pickett BE, Hanage WP, Brown T, Sabeti PC, Colubri AJournal: Patterns (N Y)PMID: 36033592 August 2022
An app-based educational outbreak simulator, Operation Outbreak (OO), seeks to engage and educate participants to better respond to outbreaks. Here,…

Early introduction and rise of the Omicron SARS-CoV-2 variant in highly vaccinated university populations.

Author(s): Petros BA, Turcinovic J, Welch NL, White LF, Kolaczyk ED, Bauer MR, Cleary M, Dobbins ST, Doucette-Stamm L, Gore M, Nair P, Nguyen TG, Rose S, Taylor BP, Tsang D, Wendlandt E, Hope M, Platt JT, Jacobson KR, Bouton T, Yune S, Auclair JR, Landaverde L, Klapperich CM, Hamer DH, Hanage WP, MacInnis BL, Sabeti PC, Connor JH, Springer MJournal: Clin Infect DisPMID: 35616119 May 2022
The Omicron variant of SARS-CoV-2 is highly transmissible in vaccinated and unvaccinated populations. The dynamics governing its establishment and propensity…

Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota.

Author(s): Petrone ME, Rothman JE, Breban MI, Ott IM, Russell A, Lasek-Nesselquist E, Badr H, 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, St George K, Adams MD, Grubaugh NDJournal: Commun BiolPMID: 35545661 May 2022
SARS-CoV-2 variants shaped the second year of the COVID-19 pandemic and the discourse around effective control measures. Evaluating the threat…

Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints.

Author(s): Senghore M, Chaguza C, Bojang E, Tientcheu PE, Bancroft RE, Lo SW, Gladstone RA, McGee L, Worwui A, Foster-Nyarko E, Ceesay F, Okoi CB, Klugman KP, Breiman RF, Bentley SD, Adegbola R, Antonio M, Hanage WP, Kwambana-Adams BAJournal: Microb GenomPMID: 35119356 February 2022
The transmission dynamics of in sub-Saharan Africa are poorly understood due to a lack of adequate epidemiological and genomic data.…

SARS-CoV-2 epidemic after social and economic reopening in three U.S. 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 EM, Boni MFJournal: Sci AdvPMID: 35080987 January 2022
State-level reopenings in late spring 2020 facilitated the resurgence of severe acute respiratory syndrome coronavirus 2 transmission. Here, we analyze…