papers

pre-prints

*co-first or co-senior author

Hill V*, Koch RT*, Bialosuknia SM, Ngo KA, Zink SD, Koetzner CA, Maffei JG, Dupuis II A, Backenson PB, Oliver J, Bransfield AB, Misencik MJ, Petruff TA, Shepard JJ, Warren JL, Gill MS, Baele G, Vogels CBF, Gallagher GR, Burns P, Hentoff A, Smole S, Brown C, Osborne M, Kramer L, Armstrong PM*, Ciota AT*, Grubaugh ND*
Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States
medRxiv 23286851 (2023)

Kissler SM, Hay JA, Fauver JR, Mack C, Tai CG, Anderson DJ, Ho DD, Grubaugh ND, Grad Y
Viral kinetics of sequential SARS-CoV-2 infections
medRxiv 23286775 (2023)

Tai CG, Haviland MJ, Kissler SM, Lucia RM, Merson M, Maragakis LL, Ho DD, Anderson DJ, DiFiori J, Grubaugh ND, Grad YH, Mack CD
Low Antibody Titers Demonstrate Significantly Increased Rate of SARS-CoV-2 Infection in a Highly Vaccinated Population from the National Basketball Association
medRxiv 23285780 (2023)

Vogels CBF*, Brackney DE*, Dupuis II AP*, Robich RM*, Fauver JR, Brito AF, Williams SC, Anderson JF, Lubelczyk CB, Lange RE, Prusinski MA, Kramer LD, Gangloff-Kaufmann GL, Goodman LB, Baele G, Smith RP*, Armstrong PM*, Ciota AT*, Dellicour S*, Grubaugh ND*
Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States
bioRxiv 512245 (2022)

Chen NFG, Chaguza C, Gagne L, Doucette M, Smole S, Buzby E, Hall J, Ash S, Harrington R, Cofsky S, Clancy S, Kapsak CJ, Sevinsky J, Libuit K, Park DJ, Hemarajata P, Garrigues JM, Green NM, Sierra-Patev S, Carpenter-Azevedo K, Huard RC, Pearson C, Incekara K, Nishimura C, Huang JP, Gagnon E, Reever E, Razeq J, Muyombwe A, Borges V, Ferreira R, Sobral D, Duarte S, Santos D, Vieira L, Gomes JP, Aquino C, Savino IM, Felton K, Bajwa M, Hayward N, Miller H, Naumann A, Allman R, Greer N, Fall A, Mostafa HH, McHugh MP, Maloney DM, Dewar R, Kenicer J, Parker A, Mathers K, Wild J, Cotton S, Templeton KE, Churchwell G, Lee PH, Pedrosa M, McGruder B, Schmedes S, Plumb MR, Wang X, Barcellos RB, Godinho FMS, Salvato RS, Ceniseros A, Breban MI, Grubaugh ND*, Gallagher GR*, Vogels CBF* 
Multi-site validation of an amplicon-based sequencing approach for human monkeypox virus
medRxiv 22280783 (2022)

Walker J, Grubaugh ND, Gonsalves G, Pitzer V, Rizvi Z
One Million and Counting: Estimates of Deaths in the United States from Ancestral SARS-CoV-2 and Variants
medRxiv 22275835 (2022)

Petrone ME*, Lucas C*, Menasche B*, Breban MI, Yildirim I, Campbell M, Omer SB, Ko AI, Grubaugh ND, Iwasaki A*, Wilen CB*, Vogels CBF*, Fauver JR*
Insights into the limited global spread of the immune evasive SARS-CoV-2 variant Mu
medRxiv 22273077 (2022)

Peña-Hernández MA*, Klein J*, Malik A*, Coppi A*, Kalinich CC*, Vogels CBF, Silva J, Yale SARS-CoV-2 Genomic Surveillance Initiative, Peaper DR, Landry ML, Wilen C, Grubaugh ND, Schulz W, Omer SB, Iwasaki A
Comparison of infectious SARS-CoV-2 from the nasopharynx of vaccinated and unvaccinated individuals
medRxiv 21268460 (2021)

Silva J, Lucas C, Sundaram M, Israelow B, Wong P, Klein J, Tokuyama M, Lu P, Venkataraman A, Liu F, Mao T,  Eun Oh J, Park A, Casanovas-Massana A, Vogels CBF, Muenker MC, Zell J, Fournier JB, Campbell M, Chiorazzi M, Fuentes ER, Yale IMPACT Team, Grubaugh ND, Farhadian S, Dela Cruz CS, Ko AI, Schulz WL, Ring A, Ma S, Omer S, Wyllie AL, Iwasaki A
Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality
medRxiv 21249236 (2021)

Pagano N, Laurent-Rolle M, Hsu JC, Yale IMPACT Research Team, Vogels CBF, Grubaugh ND, Manuelidis L
Detection of long SARS-CoV-2 nucleocapsid sequences in peripheral blood monocytes collected soon after hospital admission
bioRxiv 423113 (2020)

Moore AJ, Nakahata MI, Kalinich CC, Nyhan K, Bromberg DJ, Shi X, Ko AI, Grubaugh ND, Casanovas-Massana A, Wyllie AL
The Sensitivity of Respiratory Tract Specimens for the Detection of SARS-CoV-2: A Protocol for a Living Systematic Review and Meta-Analysis
medRxiv 20144543 (2020)

Black A, Potter B, Dudas G, Feldstein L, Grubaugh ND, Andersen KG, Ellis BR, Ellis EM, Bedford T
Genetic characterization of the Zika virus epidemic in the US Virgin Islands
bioRxiv 113100 (2017)

peer-reviewed publications

2023

Hill V, Githinji G, Vogels CBF, Bento AI, Chaguza C, Carrington CVF, Grubaugh ND
Towards a global virus genomic surveillance network
Cell Host & Microbe In-Press Preview (2023)

Du H, Dong E, Badr HS, Petrone ME, Grubaugh ND, Gardner LM
Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approach
eBioMedicine 89, 104482 (2023)

Filardi BA, Monteiro VS, Schwartzmann PV, Martins VP, Zucca ERO, Baiocchi GC, Hahn AM, Chen NFG, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca RA, Yale SARS-CoV-2 Genomic Surveillance Initiative, Mendez RDR, Silveira DB, Pinto AR, Croda J, Yildirim I, Omer SB, Ko AI, Vermund SH, Grubaugh ND, Iwasaki A, Lucas C
Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose
Science Translational Medicine 15(683), eade6023 (2023)

Oliveira G*, Vogels CBF*, Zolfaghari A, Saraf S, Klitting R, Weger-Lucarelli J, Ontiveros CO, Agarwal R, Leon KP, Tsetsarkin KS, Harris E, Ebel GD, Wohl S, Grubaugh ND*, Andersen KG*
Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages
PLOS Neglected Tropical Diseases 17(2), e0011055 (2023)

Chaguza C*, Hahn AM*, Petrone ME*, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Yale SARS-CoV-2 Genomic Surveillance Initiative, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND
Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection
Cell Reports Medicine In-Press Preview (2023)

Hart C, Hassett E, Vogels CBF, Shapley D, Grubaugh ND, Thangamani S
Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA
Emerging Infectious Diseases 29(2), 415-417 (2023)

Rayack EJ, Askari HM, Zirinsky E, Lapidus S, Sheikha H, Peno C, Kazemi Y, Yolda-Carr D, Liu C, Grubaugh ND, Ko AI, Wyllie AL, Spatz ES, Oliveira CR, Bei AK
Routine saliva testing for SARS-CoV-2 in children: Methods for partnering with community childcare centers
Frontiers in Public Health 11 (2023)

Cheemarla NR*, Hanron A*, Fauver JR*, Bishai J, Watkins TA, Brito AF, Zhao D, Alpert T, Vogels CBF, Ko AI Schulz WL, Landry ML, Grubaugh ND, van Dijk D, Foxman EF
Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study
The Lancet Microbe 4 (2023)

2022

Lange RE, Dupuis II AP, Prusinski AM, Maffei JG, Koetzner CA, Ngo K, Backenson B, Oliver J, Vogels CBF, Grubaugh ND, Kramer LD, Ciota AT
Identification and Characterization of Novel Lineage 1 Powassan Virus Strains in New York State
Emerging Microbes & Infections In-Press Preview (2022)

Paulino-Ramírez R, Pham K, Breban MI, Peguero A, Jabier M, Sánchez N, Eustate I, Ruiz I, Grubaugh ND, Hahn AM
Genome Sequence of a Recombinant SARS-CoV-2 Lineage XAM (BA.1.1/BA.2.9) Strain from a Clinical Sample in Santo Domingo, Dominican Republic
Microbiology Resource Annoncements In-Press Preview (2022)

Garrigues JM, Hemarajata P,  Lucero B, Alarcón J, Ransohoff H, Marutani AN, Kim M, Marlowe EM, Realegeno SE, Kagan RM, Montero CI, Chen NFG, Grubaugh ND, Vogels CBF, Green NM
Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic Assays
Journal of Clinical Microbiology In-Press Preview (2022)

Earnest R, Chen C, Chaguza C, Grubaugh ND, Wilson MS, the Yale COVID-19 Resulting and Isolation Team
Daily Rapid Antigen Testing in a University Setting to Inform COVID-19 Isolation Duration Policy
Emerging Infectious Diseases 28, 12 (2022)

Hay JA*, Kissler SM*, Fauver JR*, Mack C*, Tai CG, Samant RM, Connolly S, Anderson DJ, Khullar G, MacKay M, Patel M, Kelly S, Manhertz A, Eiter I, Salgado D, Baker T, Howard B, Dudley JT, Mason CE, Nair M, Huang Y, DiFiori J, Ho DD, Grubaugh ND*, Grad YH*
Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: a retrospective cohort study
eLife In-Press Preview (2022)

Brito AF*, Semenova E*, Dudas G*, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, View Whittaker C, Danish Covid-19 Genome Consortium, COVID-19 Impact Project, Network for Genomic Surveillance in South Africa (NGS-SA), GISAID core curation team, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende C, Vasconcelos ATR, Spilki FR, Aguiar S, Alexiev I, Ivanov IN, Philipova P, Carrington CVF, Sahadeo NSD, Gurry C, Maurer-Stroh S, Naidoo D, von Eije KJ, Perkins MD, van Kerkhove M, Hill SC, Sabino EC, Pybus OG, Dye C, Bhatt S, Flaxman S, Suchard MA, Grubaugh ND*, Baele G*, Faria NR*
Global disparities in SARS-CoV-2 genomic surveillance
Nature Communications 13, 7003 (2022)

Fang Z, Peng L, Lucas C, Lin Q, Zhou L, Yang L, Feng Y, Ren P, Renauer PA, Monteiro VS, Hahn AM, Park JJ, Zhou X, Yale SARS-CoV-2 Genomic Surveillance Initiative, Grubaugh ND, Wilen CB, Chen S
Heterotypic vaccination responses against SARS-CoV-2 Omicron BA.2
Cell Discovery 8, 69 (2022)

Fang, Z, Monteiro VS, Hahn AM, Grubaugh NG, Lucas C, Chen S
Bivalent mRNA vaccine booster induces robust antibody immunity against Omicron lineages BA.2, BA.2.12.1, BA.2.75 and BA.5
Cell Discovery 8, 108 (2022)

Poterek ML, Vogels CBF, Grubaugh ND, Ebel GD, Perkins TA, Cavany SM
Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence
Royal Society Open Science 9, 220829 (2022)

Baaijens JA*, Zulli A*, Ott IM*, Petrone ME, Alpert T, Fauver JR, Kalinich CC, Vogels CBF, Breban MI, Duvallet C, McElroy K, Ghaeli K, 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 M*
Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques
Genome Biology 23, 236 (2022)

Bart SM, Curtiss CC, Earnest R, Lobe-Costonis R, Peterson H, McWilliams C, Billig K, Hadler JR, Grubaugh ND, Arcelus VJ, Sosa LE
SARS-CoV-2 Outbreak at a College with High COVID-19 Vaccination Coverage—Connecticut, August–September 2021
Clinical Infectious Diseases, ciac422 (2022)

Fang Z, Peng L, Filler R, Suzuki K, McNamara A, Lin Q, Renauer PA, Yang L, Menasche B, Sanchez A, Ren P, Xiong Q, Strine M, Clark P, Lin C, Ko AI, Grubaugh ND, Wilen CB, Chen S
Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2
Nature Communications 13, 3250 (2022)

Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Rolon RM, Westblade L, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann A, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Yale SARS-CoV-2 Genomic Surveillance Initiative, Rhoads DD
Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1
Journal of Clinical Microbiology In-Press Preview (2022)

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, St. George K, Adams MD, Grubaugh ND Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota Communications Biology 5, 429 (2022)

Grubaugh ND*
Translating virus evolution into epidemiology
Cell Host & Microbe 30(4), 444-448 (2022)

Chaguza C*, Coppi A*, Earnest R*, Ferguson D, Kerantzas N, Warner F, Young HP, Breban MI, Billig K, Koch RT, Pham K, Kalinich CC, Ott IM, Fauver JR, Hahn AM, Tikhonova IR, Castaldi C, De Kumar B, Pettker CM, Warren JM, Weinberger DM, Landry ML, Peaper DR, Schulz W*, Vogels CBF*, Grubaugh ND*
Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons
Med In-press Preview (2022)

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 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*
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Cell Reports Medince  3, 100583 (2022)

Alpert T, Vogels CBF, Breban MI, Petrone ME, Yale IMPACT Research Team, Wyllie AL, Grubaugh ND, Fauver JR
Sequencing SARS-CoV-2 genomes from saliva
Virus Evolution veab098 (2022)

Allicock OM*, Petrone ME*, Yolda-Carr D*, Breban MI, Walsh H, Watkins AE, Rothman JE, Farhadian SF, Grubaugh ND, Wyllie AL
Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics
BMC Infectious Diseases 22(284) (2022)

George S, Chattopadhyay Pal A, Gagnon J, Timalsina S, Singh P, Vydyam P, Munshi M, Chiu JE, Renard I, Harden CA, Ott IM, Watkins AE, Vogels CBF, Lu P, Tokuyama M, Venkataraman A, Casanovas-Massana A, Wyllie AL, Rao C, Campbell M, Farhadian SF, Grubaugh ND, Dela Cruz CS, Ko AI, Yale IMPACT Research Team, Berna Perez A, Akaho E, Moledina DG, Testani J, John AR, Ledizet M, Ben Mamoun C
Evidence for SARS-CoV-2 Spike Protein in the Urine of COVID-19 patients
Kidney360 2(6), 924-936 (2022)

Oliveira CR, Niccolai LM, Sheikha H, Elmansy L, Kalinich CC, Grubaugh ND, Shapiro ED, Yale SARS-CoV-2 Genomic Surveillance Initiative
Assessment of Clinical Effectiveness of BNT162b2 COVID-19 Vaccine in US Adolescents
JAMA Network Open 5(3), e220935 (2022)

Perez-Then E, Lucas C, Silva Monteiro V, Miric M, Brache V, Cochon L, Vogels CBF, De la Cruz E, Jorge A, De los Santos M, Leon P, Breban MI, Billig K, Yildirim I, Pearson C, Downing R, Gagnon E, Muyombwe A, Razeq J, Campbell M, Ko AI, Omer SB, Grubaugh ND, Vermund SH, Iwasaki A
Neutralizing antibodies against the SARS-CoV-2 Delta and Omicron variants following heterologous CoronaVac plus BNT162b2 booster vaccination
Nature Medicine In-press Preview (2022)

Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Brickman Raredon MS, Hoehn K, Wang G, Wang Z, Deiuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Minasyan M, Yale IMPACT Research Team, Niklason LE, Ko AI, Montgomery RR, Farhadian SF, Iwasaki A, Shaw AC, van Dijk D, Zhao H, Kleinstein SH, Hafler DA, Kaminski N, Dela Cruz CS
Single-Cell Omics Reveals Dyssynchrony of the Innate and Adaptive Immune System in Progressive COVID-19
Nature Communications 13(440), (2022) 

Radcliffe C, Azar MM, Cohen E, Tucker M, Grubaugh ND, Malinis M
Clinical effectiveness of additional primary SARS-CoV-2 vaccine doses for solid organ transplant recipients
Clinical Transplantation In-press Preview (2022)

Klein J*, Brito AF*, Trubin P*, Lu P*, Wong P, Alpert T, Peña-Hernández MA, Haynes W, Kamath K, Liu F, Vogels CBF, Fauver JR, Lucas C, Oh J, Mao T, Silva J, Wyllie AL, Muenker MC, Casanovas-Massana A, Moore AJ, Petrone ME, Kalinich CC, Yale IMPACT Research Team, Dela Cruz C, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B*, Iwasaki A*, Azar MM*
Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient
Journal of Infectious Diseases  225(3), 374-384 (2022)

2021

Grubaugh ND, Cobey S
Of variants and vaccines
Cell 184(26), 6222-6223 (2021)

Lee M*, Sallah YH*, Petrone ME*, Ringer M, Cosentino D, Vogels CBF, Fauver JR, Alpert T, Grubaugh ND, Gupta S
COVID-19 Outcomes and Genomic characterization of SARS-CoV-2 isolated from Veterans in New England States
JMIRx Med 2(4), e31503 (2021)

Roberts SC, Palacios CF, Grubaugh ND, Alpert T, Ott IM, Breban MI, Yale SARS-CoV-2 Genomic Surveillance Initiative, Martinello RA, Smith C, Davis MW, Mcmanus D, Tirmizi S, Topal JE, Azar MA, Malinis M
An outbreak of SARS-CoV-2 on a transplant unit in the early vaccination era
Transplant Infectious Disease In-Press Preview (2021)

Kissler SM*, Fauver JR*, Mack C*, Tai CG, Breban MI, Watkins AE, Samant RM, Anderson DJ, Ho DD, Metti J, Khullar G, Baits R, MacKay M, Salgado D, Baker T, Dudley JT, Mason CE, Grubaugh ND*, Grad YH*
Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated persons
New England Journal of Medicine 385, 2489-2491 (2021)

Mao T, Israelow B, Lucas C, Vogels CBF, Gomez-Calvo ML, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Yale SARS-CoV-2 Genomic Surveillance Initiative, Wilen CB, Landry ML, Grubaugh ND, Pyle AM, Iwasaki A
A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice
Journal of Experimental Medicine 219(1):e20211818 (2021)

Santiago GA*, Kalinich CC*, Cruz-López F, González GL, Flores B, Hentoff A, Charriez KN, Fauver JR, Adams LE, Sharp TM, Black A, Bedford T, Ellis E, Ellis B, Waterman SH, Paz-Bailey G, Grubaugh ND*, Muñoz-Jordán JL*
Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016–2017
Emerging Infectious Diseases 27(11), (2021)

Lucas C*, Vogels CBF*, Yildirim I*, Rothman J, Lu P, Monteiro V, Gelhausen JR, Campbell M, Silva J, Tabachikova A, Munker MC, Breban MI, Fauver JR, Mohanty S, Huang J, Yale SARS-CoV-2 Genomic Surveillance Initiative, Shaw AC, Ko AI, Omer SA*, Grubaugh ND*, Iwasaki A*
Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity
Nature 600, 523–529 (2021)

Bart SM, Flaherty E, Alpert T, Carlson S, Fasulo L, Earnest R, White EB, Dickens N, Brito AF, Grubaugh ND, Hadler JL, Sosa LE
Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020
Emerging Infectious Diseases 27(10) (2021)

Cevik M, Grubaugh ND, Iwasaki A, Openshaw P
COVID-19 vaccines: Keeping pace with SARS-CoV-2 variants
Cell 184(20), 5077-5081 (2021)

Mack CD, Tai C, Sikka R, Grad YH, Maragakis LL, Grubaugh ND, Anderson DJ, Ho D, Merson M, Samant RM, Fauver JR, Barrett J, Sims L, DiFiori J
SARS-CoV-2 Reinfection: A Case Series from a 12-Month Longitudinal Occupational Cohort
Clinical Infectious Diseases ciab738 (2021)

Beddingfield BJ, Hartnett JN, Wilson RB, Kulakosky PC, Andersen KG, Robles-Sikisaka R, Grubaugh ND, Aybar A, Nunez M-Z, Fermin CD,  Garry RF
Zika Virus Non-Structural Protein 1 Antigen-Capture Immunoassay
Viruses 13(9), 1771 (2021)

Mytle N, Leyrer S, Inglefield JR, Harris AM, Hickey TE, Minang J, Lu H, Ma Z, Andersen H, Grubaugh ND, Guina T, Skiadopoulos MH, Lacy MJ
Influenza Antigens NP and M2 Confer Cross Protection to BALB/c Mice against Lethal Challenge with H1N1, Pandemic H1N1 or H5N1 Influenza A Viruses
Viruses 13(9), 1708 (2021)

Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Snyder DJ, Dudas G, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos Jr G, Bell-Kareem AR, Hughes LD, Alkuzweny M, Snarski P, Garcia-Diaz J, Scott RS, Melnik LI, Klitting R, McGraw M, Belda-Ferre P, DeHoff P, Sathe S, Marotz C, Grubaugh ND, Nolan DJ, Drouin AC, Genemaras KJ, Chao K, Topol S, Spencer E, Nicholson L, Aigner S, Yeo GW, Farnaes L, Hobbs CA, Laurent LC, Knight R, Hodcroft EB, Khan K, Fusco DN, Cooper VS, Lemey P, Gardner L, Lamers SL, Kamil JP, Garry RF, Suchard MA, Andersen KG
Emergence of an early SARS-CoV-2 epidemic in the United States
Cell 184(19) P4939-4952.E15 (2021)

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 D, Grubaugh ND*, Grad YH* 
Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies 
PLOS Biology 19(7): e3001333 (2021)

Wang EY*, Mao T*, Klein J*, Dai Y*, Huck JD, Liu F, Zheng NS, Zhou T, Israelow B, Wong P, Lucas C, Silva J, Eun Oh J, Song E, Perotti ES, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Yale IMPACT Team, Dela Cruz CS, Farhadian SF, Schulz WL, Grubaugh ND, Ko AI, Iwasaki A*, Ring AM* 
Diverse Functional Autoantibodies in Patients with COVID-19
Nature 595, 283–288 (2021)

Novelli G, Biancolella M, Mehrian-Shai R, Colona VL, Brito AF, Grubaugh ND, Vasiliou V, Luzzatto L, Reichardt JKV
COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policy
Human Genomics 15, 27 (2021) 

Brito AF*, Machado LC*, Oidtman RJ*, Siconelli MJL*, Tran QM, Fauver JR, Carvalho RDO, Dezordi FZ, Pereira MR, Castro-Jorge LA, Minto ECM, Passos LMR, Kalinich CC, Petrone ME, Allen E, Espana GC, Huang AT, Cummings DAT, Baele G, Franca RFO, Fonseca BAL*, Perkins TA*, Wallau GL*, Grubaugh ND* 
Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil
Nature Communications 12:2619, (2021)

Vogels CBF*, Breban MI*, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, de Jesus JG, Claro IM, Ferreira GM, Crispim MAE, Brazil-UK CADDE Genomic Network, Singh L, Tegally H, Anyaneji UJ, Network for Genomic Surveillance in South Africa, Hodcroft EB, Mason CE, Khullar G, Metti J, Dudley JT, MacKay MJ, Nash M, Wang J, Liu C, Hui P, Murphy S, Neal C, Laszlo E, Landry ML, Muyombwe A, Downing R, Razeq J, de Oliveira T, Faria NR, Sabino EC, Neher RA, Fauver JF*, Grubaugh ND*
Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2
PLOS Biology 19(5): e3001236, (2021)

Lucas C*, Klein J*, Sundaram M, Liu F, Wong P, Silva J, Mao T, Oh JE, Mohanty S, Huang J, Tokuyama M, Lu P, Venkataraman A, Park A, Israelow B,  Vogels CBF, Muenker MC, Chang C-H, Casanovas-Massana A, Moore AJ, Zell J, Fournier JB, Yale IMPACT Research Team, Wyllie AL, Campbell M, Lee A, Chun HJ, Grubaugh ND, Schulz WL, Farhadian S, Dela Cruz C, Ring AI, Shaw A, Wisnewski AV, Yildirim I, Ko AI, Omer S, Iwasaki A 
Delayed production of neutralizing antibodies correlates with fatal COVID-19
Nature Medicine 27, 1178–1186 (2021)

Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano CM, Tang Z, Pope SD,  Song E, Vogels CBF,  Lu-Culligan WJ, Campbell KH, Casanovas-Massana A, Bermejo S, Toothaker JM, Lee HJ, Liu F, Schulz W, Fournier J, Muenker MC, Moore AJ, Yale IMPACT Team, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF
Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interface
Med 2(5) P591-610.E10 (2021)

Song E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman N, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander J, Gallego JS, Lencz T, Walsh H, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, DeRisi JL, Iwasaki A, Pleasure SJ, Wilson MR, Farhadian SF
Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptoms
Cell Reports Medicine 2(5) 100288 (2021)



Alpert T*, Brito AF*, Lasek-Nesselquist E*, Rothman J*, Valesano AL*, MacKay MJ*, Petrone ME, Breban MI, Watkins AE, Vogels CBF, Kalinich CC, Dellicour S, Russell A, Kelly JP, Shudt M, Plitnick J, Schneider E, Fitzsimmons WJ, Khullar G, Metti J, Dudley JT, Nash M, Beaubier N, Wang J, Liu C, Hui P, Muyombwe A, Downing R, Razeq J, Bart SM, Grills A, Morrison SM, Murphy S, Neal C, Laszlo E, Rennert H, Cushing M, Westblade L, Velu P, Craney A, Cong L, Peaper DR, Landry ML, Cook PW, Fauver JR*, Mason CE*, Lauring AS*, St. George K*, MacCannell DR*, Grubaugh ND*  
Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States
Cell 184(10), P2595-2604.E13 (2021)

Brito AF, Baele G, Nahata KD, Grubaugh ND, Pinney JW
Intrahost speciations and host switches played an important role in the evolution of herpesviruses
Virus Evolution veab025 (2021)

Ott IM*, Strine MS*, Watkins AE, Boot M, Kalinich CC, Harden CA, Vogels CBF, Casanovas-Massana A, Moore AJ, Muenker MC, Nakahata M, Tokuyama M, Nelson A, Fournier J, Bermejo S, Campbell M, Datta R, Yale IMPACT Research Team, Dela Cruz CS, Farhadian SF, Ko AI, Iwasaki A, Grubaugh ND*, Wilen CB*, Wyllie AL*
Stability of SARS-CoV-2 RNA in Nonsupplemented Saliva
Emerging Infectious Diseases 27 (2021)

Watkins AE, Fenichel EI, Weinberger DM, Vogels CBF, Brackney DE, Casanovas-Massana A, Campbell M, Fournier J, Bermejo S, Datta R, Yale IMPACT Research Team, Dela Cruz CS, Farhadian SF, Iwasaki A, Ko AI, Grubaugh ND*, Wyllie AL*
Increasing SARS-CoV-2 Testing Capacity with Pooled Saliva Samples 
Emerging Infectious Diseases 27 (2021)

Peters J, Alhasana S, Vogels, CBF, Grubaugh ND, Farhadian S, Longbrakea EE
MOG-associated encephalitis following SARS-COV-2 infection
Multiple Sclerosis and Related Disorders 50 (2021)

Weiss JJ, Attuquayefio TN, White EB, Li F, Herz RS, White TL, Campbell M, Geng B, Datta R, Wyllie AL, Grubaugh ND, Casanovas-Massana A, Muenker MC, Handoko R, Iwasaki A, Yale IMPACT Research Team, Martinello RA, Ko AI, Small DM, Farhadian SF
Tracking Smell Loss to Identify Healthcare Workers with SARS-CoV-2 Infection
PLoS ONE e0248025 (2021)

Grubaugh ND, Hodcroft EB, Fauver JR, Phelan AL, Cevik M
Public health actions to control new SARS-CoV-2 variants
Cell 184(5), 1127-1132 (2021)

Petrone ME*, Earnest R*, Lourenço J, Kraemer MUG, Paulino-Ramirez R, Grubaugh ND*, Tapia L*  
Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic
Nature Communications 12:151, (2021)

Vogels CBF*, Watkins AE*, Harden CA*, Brackney DE*, Shafer J, Wang J, Caraballo C, Kalinich CC, Ott IM, Fauver JR, Kudo E, Lu P, Venkataraman A, Tokuyama M, Moore AJ, Muenker MC, Casanovas-Massana A, Fournier J, Bermejo S, Campbell M, Datta R, Nelson A, Yale IMPACT Research Team, Dela Cruz CS, Ko AI, Iwasaki A, Krumholz HM, Matheus JD, Hui P, Liu C, Farhadian S, Sikka R, Wyllie AL*, Grubaugh ND*
SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity
Med 2 (3), 263-280 (2021)

2020

Petrone M 
Virus genomics as a clinical and epidemiological tool 
EBioMedicine 62, 103141 (2020)

Dellicour S, Lequime S, Vrancken B, Gill MS, Bastide P, Gangavarapu K, Matteson NL, Tan Y, du Plessis L, Fisher AA, Nelson MI, Gilbert M, Suchard MA, Andersen KG, Grubaugh ND, Pybus OG, Lemey P 
Epidemiological hypothesis testing using a phylogeographic and phylodynamic framework 
Nature Communications 11:5620, (2020)

Kalinich CC*, Jensen CG*, Neugebauer P, Petrone ME, Peña-Hernández M, Ott IM, Wyllie AL, Alpert T, Vogels CBF,  Fauver JR, Grubaugh ND*, Brito AF*
Real-time public health communication of local SARS-CoV-2 genomic epidemiology
PLOS Biology 3000869 (2020)  

Lemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Sanchez-San Martin C, Li T, Martyn C, Oliveira GM, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY,  Van Rompay KA, Coffey LL
Two sides of a coin: a Zika virus mutation selected in pregnant rhesus macaques promotes fetal infection in mice but at a cost of reduced fitness in nonpregnant macaques and diminished transmissibility by vectors
Journal of Virology 94(24), e01605-20 (2020)

Grubaugh ND, Hanage WP, Rasmussen AL 
Making sense of mutation: what D614G means for the COVID-19 pandemic remains unclear
Cell  182(4), 794-795 (2020)

Lucas C, Wong P, Klein J, Castro T, Silva J, Sundaram M, Ellingson M, Mao T, Oh J, Israelow B, Tokuyama M, Lu P, Venkataraman A, Park A, Mohanty S, Wang H, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott I, Moore M, Muenker C, Fournier J, Campbell M, Odio C,  Casanovas-Massana A, Yale IMPACT Research Team, Herbst R, Shaw A, Medzhitov R, Schulz WL, Grubaugh NG, Dela Cruz C, Farhadian S, Ko AI, Omer S, Iwasaki A
Longitudinal immunological analyses reveal inflammatory misfiring in severe COVID-19 patients
Nature 584, 463–469 (2020)

Kudo E, Israelow B, Vogels CBF, Lu P, Wyllie AL, Tokuyama M, Venkataraman A, Brackney DE, Ott IM, Petrone ME, Earnest R, Lapidus S, Muenker MC, Moore AJ, Casanovas-Massana A, Yale IMPACT Research Team, Omer SB, Dela Cruz CS, Farhadian SF, Ko AI, Grubaugh ND*, Iwasaki A*
Detection of SARS-CoV-2 RNA by multiplex RT-qPCR
PLOS Biology 18(10), e3000867 (2020)

Takahashi T*, Ellingson M*, Wong P*, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh J, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang E, Casanovas A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore A, Yale IMPACT Research Team, Shaw A, Fournier J, Odio C, Farhadian S, Dela Cruz C, Grubaugh ND, Schultz W, Ko AI, Ring A, Omer S, Iwasaki A
Sex differences in immune responses to SARS-CoV-2 that underlie disease outcomes
Nature 588, 315–320 (2020)

Peccia J*, Zulli A*, Brackney DE*, Grubaugh ND, Kaplan EH, Casanovas-Massana A, AKo AI, Malik AA, Wang D, Wang M, Weinberger DM, Arnold W, Omer SB
Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics 
Nature Biotechnology 38, 1164–1167 (2020)



Hosier H*, Farhadian S*, Morotti R, Deshmukh U, Lu-Culligans A, Campbell K, Yasumoto Y, Vogels CBF, Casanovas-Massana A, Vijayakumar P, Geng B, Odio C, Fournier J, Brito AF, Fauver JR, Liu F, Alpert T, Tal R, Szigeti-Buck K, Perincheri S, Larsen C, Gariepy A, Aguilar G, Fardelmann K, Harigopal M, Taylor H, Pettker C, Wyllie AL, Dela Cruz C, Ring A, Grubaugh ND, Ko AI, Horvath T, Iwasaki A, Reddy U, Lipkind H
SARS-CoV-2 Infection of the Placenta 
Journal of Clinical Investigation 130(9), 4947-4953 (2020)

Farhadian S, Glick LR, Vogels CBF, Thomas J, Chiarella J, Casanovas-Massana A, Zhou J, Odio C, Vijayakumar P, Geng B, Fournier J, Bermejo S, Fauver JR, Alpert T, Wyllie AL, Turcotte C, Steinle M, Paczkowski P, Dela Cruz C, Wilen C, Ko AI, MacKay S, Grubaugh ND, Spudich S, Aoun Barakat L
Acute encephalopathy with elevated CSF inflammatory markers as the initial presentation of COVID-19
BMC Neurology 248(20), (2020)

Mavian C, Pond SK, Marini S, Magalis BF, Vandamme A-F, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NV, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Tsan-Yuk Lam T, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T,  Bento AI, Schmidt HA, Martin D, Hadfield J, Faria NR, Grubaugh ND, Neher RA, Baele G, Lemey P, Stadler T, Albert J, Crandall KA, Leitner T, Stamatakis A, Prosperi M, Salemi M
Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliable
PNAS 117(23), 12522-12523 (2020)

Wyllie AL, Fournier J, Casanovas-Massana A, Campbell M, Tokuyama M, Vijayakumar P, Geng B, Muenker MC, Moore AJ, Vogels CBF, Petrone ME, Ott IM, Lu P, Lu-Culligan A, Klein J, Venkataraman A, Earnest R, Simonov M, Datta R, Handoko R, Naushad N, Sewanan LR, Valdez J, White EB, Lapidus S, Kalinich CC, Jiang X, Kim DJ, Kudo E, Linehan M, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takahashi T, Taura M, Weizman O-E, Wong P, Yang Y, Bermejo S, Odio C, Omer SB, Dela Cruz CS, Farhadian S, Martinello RA, Iwasaki A, Grubaugh ND*, Ko AI*
Saliva or nasopharyngeal swab specimens for detection of SARS-CoV-2
New England Journal of Medicine 383, 1283-1286 (2020)

Iwasaki A, Grubaugh ND
Why does Japan have so few cases of COVID19? 
EMBO Molecular Medicine 12, e12481 (2020)

Vogels CBF, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC, Petrone ME, Casanovas-Massana A, Muenker AC, Moore AJ, Klein J, Lu P, Lu-Culligan A, Jiang X, Kim DJ, Kudo E, Mao T, Moriyama M, Oh JE, Park A, Silva J, Song E, Takehashi T, Taura M, Tokuyama M, Venkataraman A, Weizman O, Wong P, Yang Y, Cheemarla NR, White E, Lapidus S, Earnest R, Geng B, Vijayakumar P, Odio C, Fournier J, Bermejo S, Farhadian S, Dela Cruz C, Iwasaki A, Ko AI, Landry ML, Foxman EF, Grubaugh ND
Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR primer-probe sets 
Nature Microbiology 5, 1299–1305 (2020)

Fauver JR*, Petrone ME*, Hodcroft EB*, Shioda K, Ehrlich HY, Watts AG, Vogels CBF, Brito AF, Alpert T, Muyombwe A, Razeq J,  Downing R, Cheemarla NR, Wyllie AL, Kalinich CC, Ott IM, Quick J, Loman NL, Neugebauer KM, Greninger AL, Jerome KR, Roychoundhury P, Xie H, Shrestha L, Huang M-L, Pitzer VE, Iwasaki A, Omer SB, Khan K,  Bogoch II, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND  
Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States
Cell  181(5), 990-996 (2020)

Grubaugh ND, Petrone ME, Holmes EC
We shouldn’t worry when a virus mutates during disease outbreaks
Nature Microbiology 5, 529–530 (2020)

Pollett S, Faver JR, Berry IM, Melendrez M, Morrison A, Gillis LD, Johansson MA, Jarman RG, Grubaugh ND 
Genomic epidemiology as a public health tool to combat mosquito-borne virus outbreaks
Journal of Infectious Diseases Supp 3, S308–S318 (2020)

2019

Hadfield J*, Brito AF*, Swetnam DM, Vogels CBF, Tokarz RE, Andersen KG, Smith RC, Bedford T, Grubaugh ND
Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain 
PLOS Pathogens 15(10): e1008042 (2019)



Grubaugh ND*, Saraf S*, Gangavarapu K*, Watts A, Tan AL, Oidtman RJ, Ladner JT, Oliveira G, Matteson NL, Kraemer MUG, Vogels CBF, Hentoff A, Bhatia D, Stanek D, Scott B, Landis V, Stryker I, Cone MR, Kopp EW, Cannons AC, Heberlein-Larson L, White S, Gillis LD, Ricciardi MJ, Kwal J, Lichtenberger PK, Magnani DM, Watkins DI, Palacios G, Hamer DH for the GeoSentinel Surveillance Network, Gardner LM, Perkins AT, Baele G, Khan K, Morrison A, Isern S, Michael SM, Andersen KG
Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic 
Cell 178(5), 1057-1071 (2019)

Scroggs SL, Grubaugh ND, Sena JA, Sundararajan A, Schilkey FD, Smith DR,Ebel GD, Hanley KA
Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird Hosts
mSphere 4(3), e00291-19 (2019)

Rückert C, Prasad AN, Garcia-Luna SM, Robinson A, Grubaugh ND, Weger-Lucarelli J, Ebel GD
Small RNA responses of Culex mosquitoes and cell lines during acute and persistent virus infection
Insect Biochemistry and Molecular Biology 109, 13-23 (2019)

Grubaugh ND, Ishtiaq F, Setoh YX, Ko AI
Misperceived Risks of Zika-related Microcephaly in India
Trends in Microbiology 27(5), 381-383 (2019)

Ladner JT, Grubaugh ND, Pybus OG, Andersen KG
Precision epidemiology for infectious disease control
Nature Medicine 25, 206-211 (2019)

Vogels CBF*, Rückert C*, Cavany SM*, Perkins TA, Ebel GD, Grubaugh ND
Arbovirus coinfection and co-transmission: A neglected public health concern?
PLOS Biology 17(1), e3000130 (2019)

Grubaugh ND*, Gangavarapu K*, Quick J, Matteson NL, De Jesus JG, Main BJ, Tan AL, Paul LM, Brackney DE, Grewal S, Gurfield N, Van Rompay KKA, Isern S, Michael SF, Coffey LL, Loman NJ, Andersen KG
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Genome Biology 20:8 (2019)

Grubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG
Tracking virus outbreaks in the twenty-first century
Nature Microbiology 4, 10–19 (2019)

2018

Weger-Lucarelli J, Rückert C, Grubaugh ND, Misencik MJ, Armstrong PM, Stenglein PM, Ebel GD, Brackney D
Adventitious viruses persistently infect three commonly used mosquito cell lines
Virology 521, 175-180 (2018)

Magnani DM, Roger TF, Maness NJ, Grubaugh ND, Beutler N, Bailey VK, Gonzalez-Nieto L, Gutman ML, Pedreno-Lopez N, Kwal JM, Ricciardi MJ, Myers TA, Julander JG, Bohm RP, Gilbert MH, Schiro F, Aye PP, Blair RV, Martins MA, Falkenstein KP, Kaur A, Curry CL, Kallas EG, Desrosiers RC, Goldshmidt-Clermont PJ, Whitehead SS, Andersen KG, Bonaldo MC, Lackner AA, Panganiban AT, Burton DR, Watkins DI
Fetal demise and failed antibody therapy during Zika virus infection of pregnant macaques
Nature Communications 9(1624), (2018)

Ma S, Cahalan S, LaMonte G, Grubaugh ND, Zeng W, Murthy SE, Paytas E, Gamini R, Lukacs V, Whitwam T, Loud M, Lohia R, Berry L, Khan SM, Janse CJ, Bandell M, Schmedt C, Wengelnik K, Su AI, Honore E, Winzeler EA, Andersen KG, Patapoutian A
Common PIEZO1 allele in African populations causes RBC dehydration and attenuates Plasmodium infection
Cell 173(2), 1-13 (2018)

Grubaugh ND, Faria NR, Andersen KG, Pybus OG
Genomic insights into Zika virus emergence and spread
Cell 172(6), 1160-1162 (2018)

Gardner LM, Bóta A, Gangavarapu K, Kraemer MUG, Grubaugh ND
Inferring the risk factors behind the geographical spread and transmission of Zika in the Americas
PLOS Neglected Tropical Diseases 12(1), e0006194 (2018)

2017

Ricciardi MJ, Magnani DM, Grifoni A, Kwon Y-C, Gutman MJ, Grubaugh ND, Gangavarapu K, Sharkey M, Silveira CGT, Bailey VK, Pedreno-Lopez N, Gonzalez-Nieto L, Maxwell HS, Domingues A, Martins MA, Pham J, Weiskopf D, Altman J, Kallas EG, Andersen KG, Stevenson M, Lichtenberger P, Choe H, Whitehead SS, Sette A, Watkins DI
Ontogeny of the B- and T-cell response in a primary Zika virus infection of a dengue-naïve individual during the 2016 outbreak in Miami, FL
PLOS Neglected Tropical Diseases 11(12), e0006000 (2017)

Magnani DM, Rogers TF, Beutler N, Ricciardi MJ, Bailey VK, Gonzalez-Nieto L, Briney B, Sok D, Le K, Strubel A, Gutman MJ, Pedreño-Lopez N, Grubaugh ND, Silveira CGT, Maxwell HS, Domingues A, Martins MA, Lee DE, Okwuazi EE, Jean S, Strobert EA, Chahroudi A, Silvestri G, Vanderford TH, Kallas EG, Desrosiers RC, Bonaldo MC, Whitehead SS, Burton DR, Watkins DI
Neutralizing human monoclonal antibodies prevent Zika virus infection in macaques
Science Translational Medicine 9(410), eaan8184 (2017)

Fauver JR, Gendernalik A, Weger-Lucarelli, Grubaugh ND, Brackney DE, Foy BD, Ebel GD
The use of xenosurveillance to detect human bacteria, parasites, and viruses in mosquito bloodmeals
The American Journal of Tropical Medicine Hygiene 97(2), 324-329 (2017)

Grubaugh ND*, Ladner JT*, Kraemer MUG*, Dudas G*, Tan AL*, Gangavarapu K*, Wiley MR*, White S*, Theze J, Magnani DM, Prieto K, Reyes D, Bingham A, Paul LM, Robles-Sikisaka R, Oliveira G, Pronty D, Barcellona CM, Metsky HC, Baniecki ML, Barnes KG, Chak B, Freije CA, Gladden-Young A, Gnirke A, Lou C, MacInnis B, Matranga CB, Park DJ, Qu J, Schaffner SF, Tomkins-Tinch C, West KL, Winnicki SM, Wohl S, Yozwiak NL, Quick J, Fauver JR, Khan K, Brent SE, Reiner RC, Lichtenberger PN, Ricciardi M, Bailey VK, Watkins DI, Cone MR, Kopp EW, Hogan KN, Cannons AC, Jean R, Monaghan AJ, Garry RF, Loman NJ, Faria NR, Porcelli MC, Vasquez C, Nagle ER, Cummings DAT, Stanek D, Rambaut A, Sanchez-Lockhart M, Sabeti PC, Gillis LD, Michael SF, Bedford T, Pybus OG, Isern S, Palacios G, Andersen KG
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Nature 545(7656), 401-405 (2017)

Faria NR, Quick J, Morales I, Theze J, Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu CH, Ragwhani J, Cauchemez S, du Plessis L, Verotti MP, de Oliveira WK, Carmo EH, Coelho GE, Santelli ACFS, Vinhal LC, Henriques CM, Simpson JT, Loose M, Andersen KG, Grubaugh ND, Somasekar S, Chis CY, Lewis-Ximenez LL, Baylis SA, Chieppe AO, Aguiar SF, Fernandes CA, Lemos PS, Nascimento BLS, Monteiro HAO, Siqueira IC, de Queiroz MG, de Souza TR, Bezerra JF, Lemos MR, Pereira GF, Loudal D, Moura LC, Dhalia R, Franca RF, Magalhaes T, Marques ET, Jaenish T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Moura Neto JP, Levin AS, Tozetto-Mendoza TR, Fonseca SN, Mendes-Correa MC, Milagres FP, Segurado A, Holmes EC, Rambaut A, Bedford T, Nunes MRT, Sabino EC, Alcantara LCJ, Loman N, Pybus OG
Establishment and cryptic transmission of Zika virus in Brazil and the Americas
Nature 545(7656), 406-410 (2017)

Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Park DJ, Lou CY, Barnes KG, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Gelvez Ramirez RM, Miranda Montoya, MC, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar Centeno LA, Mattar S, Lorenzana I, Cerbino-Neto J, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael S, Bozza F, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC
Zika virus evolution and spread in the Americas
Nature 545(7656), 411-415 (2017)

Quick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lexis-Ximenez LL, Jesus JG, Giovanetti M, Hill S, Black A, Bedford T, Carrol MW, Nunes M, Alcantara LC, Sabino EC, Baylis SA, Faria N, Loose M, Simpson JT, Pybus OG, Andersen KG, Loman NJ
Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples
Nature Protocols 12(6), 1261-1276 (2017)

Grubaugh ND, Andersen KG
Experimental evolution to study virus emergence
Cell 169(1), 1-3 (2017)

Grubaugh ND, Fauver JR, Rückert C, Weger-Lucarelli J, Garcia-Luna S, Murrieta RA, Gendernalik A, Smith DR, Brackney DE, Ebel GD
Mosquitoes transmit unique West Nile virus populations during each feeding episode
Cell Reports 19(4), 709-718 (2017)



2016

Grubaugh ND*, Rückert C*, Armstrong PM, Bransfield A, Anderson JF, Ebel GD, Brackney DE
Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolution
Virus Evolution 2(2), vew033 (2016)

Fauver JR, Grubaugh ND, Krajacich BJ, Weger-Lucarelli J, Lakin SM, Fakoli LS, Bolay FK, Diclaro JW, Dabire KR, Foy BD, Brackney DE, Ebel GE, Stenglein MD
West African Anopheles gambiae mosquitoes harbor a taxonomically diverse virome including new insect-specific flaviviruses, mononegavirueses, and totiviruses
Virology 498, 288-299 (2016)

Diehl WE*, Lin AE*, Grubaugh ND*, Carvalho LM*, Kim K, Kyawe PP, McCauley SM, Donnard E, Kucukural A, McDonel P, Schaffner SF, Garber M, Rambaut A, Andersen KG, Sabeti PC, Luban J
Ebola virus glycoprotein with increased infectivity dominated the 2013–2016 epidemic
Cell 167(4), 1088-1098, e6 (2016)

Grubaugh ND, Andersen KG
Navigating the Zika panic
F1000 5:1914 (2016)

Grubaugh ND, Ebel GD
Dynamics of West Nile virus evolution in mosquito vectors
Current Opinion in Virology 21, 132-138 (2016)

Grubaugh ND, Weger-Lucarelli J, Murrieta RA, Fauver JR, Garcia-Luna SM, Prasad AN, Black WC, Ebel GD
Genetic drift during systemic arbovirus infection of mosquito vectors leads to decreased relative fitness during host switching
Cell Host & Microbe 19(4), 481-492 (2016)

Misencik MJ, Grubaugh ND, Andreadis TG, Ebel GD, Armstrong PM
Isolation of a novel insect-specific Flavivirus from Culiseta melanura in the Northeastern United States
Vector-Borne and Zoonotic Diseases 16(3), 181-190 (2016)

Grubaugh ND, Massey A, Shives KD, Stenglein MD, Ebel GD, Beckham JD
West Nile virus population structure, injury, and interferon-stimulated gene expression in the brain from a fatal case of encephalitis
Open Forum Infectious Diseases 3(1), ofv182 (2016)



2015

Fauver JR, Pecher L, Schurich JA, Bolling BG, Calhoon M, Grubaugh ND, Burkhalter KL, Eisen L, Andre BG, Nasci RS, LeBailly A, Ebel GD, Moore CG
Temporal and spatial variability of entomological risk indices for West Nile virus infection in Northern Colorado: 2006-2013
Journal of Medical Entomology tjv234 (2015)

Grubaugh ND*, Smith DR*, Brackney DE, Bosco-Lauth, AM, Fauver JR, Campbell CL, Felix TA, Romo H, Duggal NK, Dietrich EA, Eike T, Beane JE, Bowen RA, Black WC, Brault AC, Ebel GD
Experimental evolution of an RNA virus in wild birds: evidence for host-dependent impacts on population structure and competitive fitness
PLOS Pathogens 11(5), e100487 (2015)

Grubaugh ND, Sharma S, Krajacich BJ, Fakoli III LS, Bolay FK, Diclaro II JW, Johnson WE, Ebel GD, Foy BD, Brackney DE
Xenosurveillance: a novel mosquito-based approach for examining the human-pathogen landscape
PLOS Neglected Tropical Diseases 9(3), e0003628 (2015)

Krajacich BJ, Slade JR, Mulligan RF, LaBrecque B, Alout H, Grubaugh ND, Meyers JI, Fakoli III LS, Bolay FK, Brackney DE, Burton TA, Seaman JA, Diclaro II JW, Dabire RK, Foy BD
Sampling host-seeking anthropophilic mosquito vectors in West Africa: comparisons of an active human-baited tent-trap against gold standard methods
The American Journal of Tropical Medicine Hygiene 92(2), 415-421 (2015)



2014

Alout H, Krajacich BJ, Meyers JI, Grubaugh ND, Brackney DE, Kobylinski KC, Diclaro II JW, Bolay FK, Fakoli III LS, Diabate A, Dabire RK, Bougma RW, Foy BD
Evaluation of ivermectin mass drug administration for malaria transmission control across different West African environments
Malaria 13(1), 417 (2014)



2013

Grubaugh ND, McMenamy SS, Turell MJ, Lee JS
Multi-gene detection and identification of mosquito-borne RNA viruses using an oligonucleotide microarray
PLOS Neglected Tropical Diseases 7(8), e2349 (2013)

Grubaugh ND, Petz LN, Melanson VR, McMenamy SS, Turell MJ, Long LS, Pisarcik SE, Kengluecha A, Jaichapor B, O’Guinn ML, Lee JS
Evaluation of a field-portable DNA microarray platform and nucleic acid amplification strategies for the detection of arboviruses, arthropods, and bloodmeals
The American Journal of Tropical Medicine Hygiene 88(2), 245-253 (2013)

Lee JS, Grubaugh ND, Kondig JP, Turell MJ, Kim HC, Klein TA, O’Guinn ML
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