Near real-time surveillance of the SARS-CoV-2 epidemic with incomplete data.

Author(s): De Salazar PM, Lu F, Hay JA, Gomez-Barroso D, Fernandez-Navarro P, Martinez EV, Astray-Mochales J, Amillategui R, Garcia-Fulgueiras A, Chirlaque MD, Sanchez-Migallon A, Larrauri A, Sierra MJ, Lipsitch M, Simon F, Santillana M, Hernán MAJournal: PLoS Comput BiolPMID: 35358171 March 2022
When responding to infectious disease outbreaks, rapid and accurate estimation of the epidemic trajectory is critical. However, two common data…

Viral dynamics and duration of PCR positivity of the SARS-CoV-2 Omicron variant

Author(s): Hay JA, Kissler SM, Fauver JR, Mack C, Tai CG, Samant RM, Connelly S, Anderson DJ, Khullar G, MacKay M, Patel M, Kelly S, Manhertz A, Eiter I, Salgado D, Baker T, Dudley JT, Mason CE, Ho DD, Grubaugh ND, Grad YHJournal: DASH January 2022
The Omicron SARS-CoV-2 variant is responsible for a major wave of COVID-19, with record case counts reflecting high transmissibility and…

Correction: Practical considerations for measuring the effective reproductive number, Rt.

Author(s): Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey SJournal: PLoS Comput BiolPMID: 34879070 December 2021
[This corrects the article DOI: 10.1371/journal.pcbi.1008409.].

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…

Practical considerations for measuring the effective reproductive number, Rt.

Author(s): Gostic KM, McGough L, Baskerville EB, Abbott S, Joshi K, Tedijanto C, Kahn R, Niehus R, Hay JA, De Salazar PM, Hellewell J, Meakin S, Munday JD, Bosse NI, Sherrat K, Thompson RN, White LF, Huisman JS, Scire J, Bonhoeffer S, Stadler T, Wallinga J, Funk S, Lipsitch M, Cobey SJournal: PLoS Comput BiolPMID: 33301457 December 2020
Estimation of the effective reproductive number Rt is important for detecting changes in disease transmission over time. During the Coronavirus…