Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.

Author(s): Baaijens JA, Zulli A, Ott IM, Nika I, van der Lugt MJ, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy KA, Ghaeli N, Imakaev M, Mckenzie-Bennett MF, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer ML, Simen BB, Yale SARS-CoV-2 Genomic Surveillance Initiative., Hanage WP, Grubaugh ND, Peccia J, Baym MJournal: Genome BiolPMID: 36348471 November 2022
Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from…

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…

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…

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…

Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies.

Author(s): Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich CC, Jednak S, Ott IM, Vogels CBF, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho DD, Grubaugh ND, Grad YHJournal: PLoS BiolPMID: 34252080 July 2021
SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding.…

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…

Viral dynamics of acute SARS-CoV-2 infection

Author(s): Kissler SM, Fauver JR, Mack C, Olesen SW, Tai C, Shiue KY, Kalinich C, Jednak S, Ott I, Vogels C, Wohlgemuth J, Weisberger J, DiFiori J, Anderson DJ, Mancell J, Ho D, Grubaugh ND, Grad YHJournal: medRxiv June 2021
SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level viral RNA shedding. The…