key publications
A new lineage nomenclature to aid genomic surveillance of dengue virus
medRxiv
Combining genomic data and infection estimates to characterize the complex dynamics of SARS-CoV-2 Omicron variants in the United States
medRxiv
Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean
Nature Communications
DengueSeq: A pan-serotype whole genome amplicon sequencing protocol for dengue virus
BMC Genomics
Dynamics of Eastern equine encephalitis virus during the 2019 outbreak in the Northeast United States
Current Biology
Towards a global virus genomic surveillance network
Cell Host & Microbe
Phylogeographic reconstruction of the emergence and spread of Powassan virus in the northeastern United States
PNAS
Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection
Cell Reports Medicine
Translating virus evolution into epidemiology
Cell Host & Microbe
Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated persons
Med
Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA
Cell Reports Medicine
Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity
Nature
Viral dynamics of SARS-CoV-2 variants in vaccinated and unvaccinated persons
New England Journal of Medicine
Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United States
Cell
Public health actions to control new SARS-CoV-2 variants
Cell
Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil
Nature Communications
SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity
Med
Saliva or nasopharyngeal swab specimens for detection of SARS-CoV-2
New England Journal of Medicine
Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States
Cell
Twenty years of West Nile virus spread and evolution in the Americas visualized by Nextstrain
PLOS Pathogens
Travel surveillance and genomics uncover a hidden Zika outbreak during the waning epidemic
Cell
Tracking virus outbreaks in the twenty-first century
Nature Microbiology
An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVar
Genome Biology
Genomic epidemiology reveals multiple introductions of Zika virus into the United States
Natureresearch topics
Epidemiology
Evolution
& Ecology
Pathogenesis & Immunology
Methods
development
Zika &
dengue virus
West Nile, EEE &
Powassan virus
SARS-CoV-2
Other viruses/
microbes
recent publcations
Below shows our publications from the last couple of years. For a full list of publications by PI Grubaugh, see his Google Scholar profile.
Google Scholar
Hill V*, Cleemput S*, Fonseca V, Tegally H, Brito AF, Gifford R, Tran VT, Kien DTH, Huynh T, Yacoub S, Dieng I, Ndiaye M, Balde D, Diagne MM, Faye O, Salvato R, Wallau GL, Gregianini TS, Godinho FMS, Vogels CBF, Breban MI, Leguia M, Jagtap S, Roy R, Hapuarachchi C, Mwanyika G, Giovanetti M, Alcantara LCJ, Faria NR, Carrington CVF, Hanley KA, Holmes EC, Dumon WC*, de Oliveira T*, Grubaugh ND*
medRxiv 24307504 (2024)
Vogels CBF*, Hill V*, Breban MI, Chaguza C, Paul LM, Sodeinde A, Taylor-Salmon E, Ott IM, Petrone ME, Dijk D, Jonges M, Welkers MRA, Locksmith T, Dong Y, Tarigopula N, Tekin O, Schmedes S, Bunch S, Cano N, Jaber R, Panzera C, Stryker I, Vergara J, Zimler R, Kopp E, Heberlein L, Morrison AM, Michael SF, Grubaugh ND
BMC Genomics 25, 4333 (2024)
Taylor-Salmon E*, Hill V*, Paul LM*, Koch KT*, Breban MI, Chaguza C, Sodeinde A, Warren JL, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán JL, Santiago GA, Adams LE, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman FF, Galán J-C, Huits R, Hamer DH, Vogels CBF*, Morrison A*, Michael SF*, Grubaugh ND*
Nature Communications 15, 3508 (2024)
Huits R, Grubaugh ND, Libman M, Hamer DH
Annals of Internal Medicine In-Press Preview (2024)
Tai CG, Haviland MJ, Kissler SM, Lucia RM, Merson M, Maragakis LL, Ho DD, Anderson DJ, DiFiori J, Grubaugh ND, Grad YH, Mack CD
Journal of Medical Virology 96(3), e29505 (2024)
Miguel I, Feliz E, Agramonte R, Martinez PV, Vergara C, Imbert Y, de la cruz L, de Castro N, Cedano O, De la Paz Y, Fonseca V, Santiago GA, Munoz-Jordan JL, Peguero A, Paulino-Ramirez R, Grubaugh ND, Bispo de Filippis AM, Alcantara LCJ, Rico JM, Lourenco J, Franco L, Giovanetti M
medRxiv 24302795 (2024)
Crandell J, Silva Monteiro V, Pischel L, Fang Z, Zhong Y, Lawres L, Conde L, Meira de Asis G, Maciel G, Zaleski A, Lira GS, Higa LM, Breban MI, Vogels CBF, Grubaugh ND, Aoun-Barakat L, Grifoni A, Sette A, Castineiras TM, Chen S, Yildirim I, View ORCID Vale AM, Omer SB, Lucas C
medRxiv 24302065 (2024)
Erazo D, Grant L, Ghisbain G, Marini G, Colón-González FJ, Wint W, Rizzoli A, Van Bortel W, Vogels CBF, Grubaugh ND, Mengel M, Frieler K, Thiery W, Dellicour S
Nature Communications 15, 1196 (2024)
Machkovech HM, Hahn AM, Wang JG, Grubaugh ND, Halfmann PJ, Johnson MC, Lemieux JE, O’Connor DH, Piantadosi A, Wei W, Friedrich TC
The Lancet Infectious Diseases In-Press Preview (2024)
Smith TC, Bart SM, Loh SM, Rothman JE, Grubaugh ND, Gardner L, Morfino RC, Rome BH, Rothstein AP, Li SL, Ernst E, Olesen SW, Taylor Walker A, Friedman CR, Guagliardo SAJ
SSRN 4720735 (2024)
Jones FK*,1 Morrison AM*, Santiago GA, Rysava K, Zimler RA, Heberlein LA, Kopp E, Florida Department of Health Bureau of Public Health Laboratory Team, Saunders KE, Baudin S, Rico E, Mejía-Echeverri A, Taylor-Salmon E, Hill V, Breban MI, Vogels CBF, Grubaugh ND, Paul LM, Michael SF, Johansson MA, Adams LE, Munoz-Jordan J, Paz-Bailey G, Stanek DR
Emerging Infecious Diseases 30, 2 (2024)
Koch RT, Erazo D, Folly AJ, Johnson N, Dellicour S, Grubaugh ND, Vogels CBF
One Health 100664 (2023)
Earnest R*, Hahn AM*, Feriancek NM, Brandt M, Filler RB, Zhao Z, Breban MI, Vogels CBF, Chen NFG, Koch RT, Porzucek AJ, Sodeinde A, Garbiel A, Keanna C, Litwak H, Stuber HR, Cantoni JL, Pitzer VE, Olarte Castillo XA, Goodman LB, Wilen CB, Linske MA, Williams SC*, Grubaugh ND*
npj Viruses 1(1), 20 (2023)
Kissler SM, Hay JA, Fauver JR, Mack C, Tai CG, Anderson DJ, Ho DD, Grubaugh ND, Grad Y
Nature Communications 14 (1), 6206 (2023)
Walker J, Chaguza C, Grubaugh ND, Carey M, Baker S, Khan K, Bogoch II, Pitzer VE
Nature Communications 14 (1), 6502 (2023)
Hollingsworth BD, Grubaugh ND, Lazzaro BP, Murdock CC
PLOS Pathogens 19 (8), e1011588 (2023)
Diray-Arce J, Fourati S, Jayavelu ND, Patel R, Maguire C, Chang AC, Dandekar R, Qi J, Lee BH, van Zalm P, Schroeder A, Chen E, Konstorum A, Brito A, Gygi JP, Kho A, Chen J, Pawar S, Gonzalez-Reiche AS, Hoch A, Milliren CE, Overton JA, Westendorf K, IMPACC Network, Cairns CB, Rouphael N, Bosinger SE, Kim-Schulze S, Krammer F, Rosen L, Grubaugh ND, van Bakel H, Wilson M, Rajan J, Steen H, Eckalbar W, Cotsapas C, Langelier CR, Levy O, Altman MC, Maecker H, Montgomery RR, Haddad EK, Sekaly RP, Esserman D, Ozonoff A, Becker PM, Augustine AD, Guan L, Peters B, Kleinstein SH
Cell Reports Medicine 4(6), 101079 (2023)
Rich SN, Richards V, Mavian C, Magalis BR, Rich SN, Richards V, Mavian C, Magalis BR, Grubaugh ND, Rasmussen SA, Dellicour S, Vrancken B, Carrington C, Fisk-Hoffman R, Danso-Odei D, Chacreton D, Shapiro J, Seraphin MN, Hepp C, Black A, Dennis A, Trovão NS, Vandamme A, Rasmussen A, Lauzardo M, Dean N, Salemi M, Prosperi M
JMIR Formative Research 7(1), e39409 (2023)
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*
PLOS Biology 21(6), e3002151 (2023)
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*
Current Biology 33(12), 2515-2527 (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*
PNAS 120(16), e2218012120 (2023)
Petrone ME*, Lucas C, Menasche B, Breban MI, Yildirim I, Campbell M, Omer SB, Holmes EC, Ko AI, Grubaugh ND, Iwasaki A, Wilen CB, Vogels CBF*, Fauver JR*
Genome Biology and Evolution evad052 (2023)
Hill V, Githinji G, Vogels CBF, Bento AI, Chaguza C, Carrington CVF, Grubaugh ND
Cell Host & Microbe 31(6), 861-873 (2023)
Du H, Dong E, Badr HS, Petrone ME, Grubaugh ND, Gardner LM
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
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*
PLOS Neglected Tropical Diseases 17(2), e0011055 (2023)
Hart C, Hassett E, Vogels CBF, Shapley D, Grubaugh ND, Thangamani S
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
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
The Lancet Microbe 4 (1), e38-e46 (2023)
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
Emerging Microbes & Infections 12, e2155585 (2022)
Paulino-Ramírez R, Pham K, Breban MI, Peguero A, Jabier M, Sánchez N, Eustate I, Ruiz I, Grubaugh ND, Hahn AM
Microbiology Resource Annoncements 12 (1), e01113-22 (2022)
Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic Assays
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
Journal of Clinical Microbiology 60 (12), e01655-22 (2022)
Earnest R, Chen C, Chaguza C, Grubaugh ND, Wilson MS, the Yale COVID-19 Resulting and Isolation Team
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*
eLife 11, e81849 (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*
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
Cell Discovery 8, 69 (2022)
Fang, Z, Monteiro VS, Hahn AM, Grubaugh NG, Lucas C, Chen S
Cell Discovery 8, 108 (2022)
Poterek ML, Vogels CBF, Grubaugh ND, Ebel GD, Perkins TA, Cavany SM
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*
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
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
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
Journal of Clinical Microbiology 60 (6), e00600-22 (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
Communications Biology 5, 429 (2022)
Grubaugh ND
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*
Med 3, 1-10 (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*
Cell Reports Medince 3, 100583 (2022)
Alpert T, Vogels CBF, Breban MI, Petrone ME, Yale IMPACT Research Team, Wyllie AL, Grubaugh ND, Fauver JR
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
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
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
JAMA Network Open 5(3), e220935 (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
Nature Communications 13(440), (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
Nature Medicine 28 (3), 481-485 (2022)
Radcliffe C, Azar MM, Cohen E, Tucker M, Grubaugh ND, Malinis M
Clinical Transplantation 36 (3), e14601 (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*
Journal of Infectious Diseases 225(3), 374-384 (2022)