Nathan Grubaugh, PhD

• Adam V Wisnewski
• Akiko Iwasaki
• Albert C Shaw
• Albert Ko
• Amy Bei
• Anasuya Pal
• Andreas Coppi
• Anne Wyllie
• Arun Chavan
• Benjamin Goldman-Israelow
• Bertie Geng
• Bony De Kumar
• Carlos R Oliveira
• Carolina Lucas
• Chantal Vogels
• Chikondi Peno
• Chrispin Chaguza
• Craig B. Wilen
• Dana Small
• Daniel Weinberger
• David A. Hafler
• David van Dijk
• Dejian Zhao
• Dennis G Moledina
• Ellen F Foxman
• Erin Longbrake
• Fangyong Li
• Guilin Wang
• Harlan Krumholz
• Harvey Kliman
• Hassan Sheikha
• Huiping Dong
• Inci Yildirim
• Jeffrey Testani
• Jennifer Chiarella
• Joshua Warren
• Katherine Harper Campbell
• Kenneth Hoehn
• Kien Pham
• Kristen L. Fardelmann
• Lindsay McAlpine
• Liza Konnikova
• Lydia Aoun-Barakat
• Malini Harigopal
• Maricar Malinis
• Marie-Louise Landry
• Marwan Mikheal Azar
• Micha Sam Brickman Raredon
• Michael Chiorazzi
• Miyu Moriyama
• Naftali Kaminski
• Orchid Allicock
• Pallavi Singh
• Pei Hui
• Peiwen Lu
• Ping Ren
• Pratap Vydyam
• Richard A Martinello
• Roy S. Herbst
• Rupak Datta
• Ruth R Montgomery
• Saad B. Omer
• Scott Pope
• Scott Roberts
• Serena Spudich
• Seth Guller
• Shaili Gupta
• Shelli Farhadian
• Sidi Chen
• Sten H. Vermund
• Steven Kleinstein
• Tomokazu S Sumida
• Tony Melillo
• Veena Rao
• Verity Hill
• Wade Schulz
• Xiaoyu Zhou
• Xiting Yan
• Yuki Yasumoto
• Yuval Kluger
• Zhenhao Fang

Aedes; Arthropod Vectors; Chikungunya virus; Culex; Dengue Virus; Disease Outbreaks; Epidemiology; Genetics, Microbial; Molecular Sequence Data; RNA Viruses; West Nile virus; Directed Molecular Evolution

Emerging Infectious Diseases; Epidemiology Methods; Evolution; Genetics, Genomics, Epigenetics; Global Health; Infectious Diseases; Vector Biology; Mosquito-borne Diseases; COVID-19

• Towards a global virus genomic surveillance networkHill V, Githinji G, Vogels C, Bento A, Chaguza C, Carrington C, Grubaugh N. Towards a global virus genomic surveillance network Cell Host & Microbe 2023 PMID: 36921604, PMCID: PMC9986120, DOI: 10.1016/j.chom.2023.03.003.
• Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approachDu H, Dong E, Badr H, Petrone M, Grubaugh N, Gardner L. Incorporating variant frequencies data into short-term forecasting for COVID-19 cases and deaths in the USA: a deep learning approach EBioMedicine 2023, 89: 104482. PMID: 36821889, PMCID: PMC9943054, DOI: 10.1016/j.ebiom.2023.104482.
• Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster doseFilardi B, Monteiro V, Schwartzmann P, do Prado Martins V, Zucca L, Baiocchi G, Malik A, Silva J, Hahn A, Chen N, Pham K, Pérez-Then E, Miric M, Brache V, Cochon L, Larocca R, Della Rosa Mendez R, Silveira D, Pinto A, Croda J, Yildirim I, Omer S, Ko A, Vermund S, Grubaugh N, Iwasaki A, Lucas C, Initiative Y, Vogels C, Breban M, Koch T, Chaguza C, Tikhonova I, Castaldi C, Mane S, De Kumar B, Ferguson D, Kerantzas N, Peaper D, Landry M, Schulz W. Age-dependent impairment in antibody responses elicited by a homologous CoronaVac booster dose Science Translational Medicine 2023, 15: eade6023. PMID: 36791210, DOI: 10.1126/scitranslmed.ade6023.
• Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineagesOliveira G, Vogels C, Zolfaghari A, Saraf S, Klitting R, Weger-Lucarelli J, P Leon K, Ontiveros C, Agarwal R, Tsetsarkin K, Harris E, Ebel G, Wohl S, Grubaugh N, Andersen K. Genomic and phenotypic analyses suggest moderate fitness differences among Zika virus lineages PLOS Neglected Tropical Diseases 2023, 17: e0011055. PMID: 36753510, PMCID: PMC9907835, DOI: 10.1371/journal.pntd.0011055.
• Routine saliva testing for SARS-CoV-2 in children: Methods for partnering with community childcare centersRayack E, Askari H, Zirinsky E, Lapidus S, Sheikha H, Peno C, Kazemi Y, Yolda-Carr D, Liu C, Grubaugh N, Ko A, Wyllie A, Spatz E, Oliveira C, Bei A. Routine saliva testing for SARS-CoV-2 in children: Methods for partnering with community childcare centers Frontiers In Public Health 2023, 11: 1003158. PMID: 36817891, PMCID: PMC9936085, DOI: 10.3389/fpubh.2023.1003158.
• Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA - Volume 29, Number 2—February 2023 - Emerging Infectious Diseases journal - CDCHart C, Hassett E, Vogels C, Shapley D, Grubaugh N, Thangamani S. Powassan Virus Lineage I in Field-Collected Dermacentor variabilis Ticks, New York, USA - Volume 29, Number 2—February 2023 - Emerging Infectious Diseases journal - CDC Emerging Infectious Diseases 2023, 29: 415-417. PMID: 36692472, PMCID: PMC9881768, DOI: 10.3201/eid2902.220410.
• Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infectionChaguza C, Hahn A, Petrone M, Zhou S, Ferguson D, Breban M, Pham K, Peña-Hernández M, Castaldi C, Hill V, Initiative Y, Billig K, Earnest R, Fauver J, Kalinch C, Kerantzas N, Koch T, De Kumar B, Landry M, Ott I, Peaper D, Tikhonova I, Vogels C, Schulz W, Swanstrom R, Roberts S, Grubaugh N. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection Cell Reports Medicine 2023, 4: 100943. PMID: 36791724, PMCID: PMC9906997, DOI: 10.1016/j.xcrm.2023.100943.
• Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection studyCheemarla N, Hanron A, Fauver J, Bishai J, Watkins T, Brito A, Zhao D, Alpert T, Vogels C, Ko A, Schulz W, Landry M, Grubaugh N, van Dijk D, Foxman E. Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study The Lancet Microbe 2023, 4: e38-e46. PMID: 36586415, PMCID: PMC9835789, DOI: 10.1016/s2666-5247(22)00296-8.
• Identification and characterization of novel lineage 1 Powassan virus strains in New York StateLange R, Dupuis A, Prusinski M, Maffei J, Koetzner C, Ngo K, Backenson B, Oliver J, Vogels C, Grubaugh N, Kramer L, Ciota A. Identification and characterization of novel lineage 1 Powassan virus strains in New York State Emerging Microbes & Infections 2022, 12: 2155585. PMID: 36503411, PMCID: PMC9788702, DOI: 10.1080/22221751.2022.2155585.
• Daily Rapid Antigen Exit Testing to Tailor University COVID-19 Isolation Policy - Volume 28, Number 12—December 2022 - Emerging Infectious Diseases journal - CDCEarnest R, Chen C, Chaguza C, Hahn A, Grubaugh N, Wilson M, . Daily Rapid Antigen Exit Testing to Tailor University COVID-19 Isolation Policy - Volume 28, Number 12—December 2022 - Emerging Infectious Diseases journal - CDC Emerging Infectious Diseases 2022, 28: 2455-2462. PMID: 36417936, PMCID: PMC9707582, DOI: 10.3201/eid2812.220969.
• 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 RepublicPaulino-Ramírez R, Pham K, Breban M, Peguero A, Jabier M, Sánchez N, Eustate I, Ruiz I, Grubaugh N, Hahn A. 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 Announcements 2022, 12: e01113-22. PMID: 36448812, PMCID: PMC9872639, DOI: 10.1128/mra.01113-22.
• Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic AssaysGarrigues J, Hemarajata P, Lucero B, Alarcón J, Ransohoff H, Marutani A, Kim M, Marlowe E, Realegeno S, Kagan R, Montero C, Chen N, Grubaugh N, Vogels C, Green N. Identification of Human Monkeypox Virus Genome Deletions That Impact Diagnostic Assays Journal Of Clinical Microbiology 2022, 60: e01655-22. PMID: 36445125, PMCID: PMC9769645, DOI: 10.1128/jcm.01655-22.
• Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort studyHay J, Kissler S, Fauver J, Mack C, Tai C, Samant R, Connolly S, Anderson D, Khullar G, MacKay M, Patel M, Kelly S, Manhertz A, Eiter I, Salgado D, Baker T, Howard B, Dudley J, Mason C, Nair M, Huang Y, DiFiori J, Ho D, Grubaugh N, Grad Y. Quantifying the impact of immune history and variant on SARS-CoV-2 viral kinetics and infection rebound: A retrospective cohort study ELife 2022, 11: e81849. PMID: 36383192, PMCID: PMC9711520, DOI: 10.7554/elife.81849.
• Global disparities in SARS-CoV-2 genomic surveillanceBrito A, Semenova E, Dudas G, Hassler G, Kalinich C, Kraemer M, Ho J, Tegally H, Githinji G, Agoti C, Matkin L, Whittaker C, Howden B, Sintchenko V, Zuckerman N, Mor O, Blankenship H, de Oliveira T, Lin R, Siqueira M, Resende P, Vasconcelos A, Spilki F, Aguiar R, Alexiev I, Ivanov I, Philipova I, Carrington C, Sahadeo N, Branda B, Gurry C, Maurer-Stroh S, Naidoo D, von Eije K, Perkins M, van Kerkhove M, Hill S, Sabino E, Pybus O, Dye C, Bhatt S, Flaxman S, Suchard M, Grubaugh N, Baele G, Faria N. Global disparities in SARS-CoV-2 genomic surveillance Nature Communications 2022, 13: 7003. PMID: 36385137, PMCID: PMC9667854, DOI: 10.1038/s41467-022-33713-y.
• Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniquesBaaijens J, Zulli A, Ott I, Nika I, van der Lugt M, Petrone M, Alpert T, Fauver J, Kalinich C, Vogels C, Breban M, Duvallet C, McElroy K, Ghaeli N, Imakaev M, Mckenzie-Bennett M, Robison K, Plocik A, Schilling R, Pierson M, Littlefield R, Spencer M, Simen B, Hanage W, Grubaugh N, Peccia J, Baym M. Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques Genome Biology 2022, 23: 236. PMID: 36348471, PMCID: PMC9643916, DOI: 10.1186/s13059-022-02805-9.
• Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidencePoterek ML, Vogels CBF, Grubaugh ND, Ebel GD, Perkins T, Cavany SM. Interactions between seasonal temperature variation and temporal synchrony drive increased arbovirus co-infection incidence Royal Society Open Science 2022, 9: 220829. PMID: 36277835, PMCID: PMC9579765, DOI: 10.1098/rsos.220829.
• Multi-site validation of an amplicon-based sequencing approach for human monkeypox virus.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 PA, 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 : The Preprint Server For Health Sciences 2022 PMID: 36299420, PMCID: PMC9603838, DOI: 10.1101/2022.10.14.22280783.
• Bivalent mRNA vaccine booster induces robust antibody immunity against Omicron lineages BA.2, BA.2.12.1, BA.2.75 and BA.5Fang Z, Monteiro VS, Hahn AM, Grubaugh ND, 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 2022, 8: 108. PMID: 36220819, PMCID: PMC9552143, DOI: 10.1038/s41421-022-00473-4.
• Heterotypic vaccination responses against SARS-CoV-2 Omicron BA.2Fang 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, Grubaugh N, Wilen C, Chen S. Heterotypic vaccination responses against SARS-CoV-2 Omicron BA.2 Cell Discovery 2022, 8: 69. PMID: 35853867, PMCID: PMC9295082, DOI: 10.1038/s41421-022-00435-w.
• Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection.Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MedRxiv : The Preprint Server For Health Sciences 2022 PMID: 35794895, PMCID: PMC9258298, DOI: 10.1101/2022.06.29.22276868.
• SARS-CoV-2 Outbreak at a College with High COVID-19 Vaccination Coverage—Connecticut, August–September 2021M. S, Curtiss CC, Earnest R, Lobe-Costonis R, Peterson H, McWilliams C, Billig K, Hadler JL, 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 2022, 75: ciac422-. PMID: 35675696, PMCID: PMC9214140, DOI: 10.1093/cid/ciac422.
• Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2Fang 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 2022, 13: 3250. PMID: 35668119, PMCID: PMC9169595, DOI: 10.1038/s41467-022-30878-4.
• Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Marrero Rolon R, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, , Rhoads DD. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1 Journal Of Clinical Microbiology 2022, 60: e00600-22. PMID: 35582905, PMCID: PMC9199403, DOI: 10.1128/jcm.00600-22.
• Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and IotaPetrone 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 ND. Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 variants Alpha and Iota Communications Biology 2022, 5: 439. PMID: 35545661, PMCID: PMC9095641, DOI: 10.1038/s42003-022-03347-3.
• Application of phylodynamic tools to inform the public health response to COVID-19: a qualitative analysis of expert opinions.Rich S, Richards V, Mavian C, Rife Magalis B, Grubaugh N, Rasmussen S, Dellicour S, Vrancken B, Carrington C, Fisk-Hoffman R, Danso-Odei D, Chacreton D, Shapiro J, Seraphin M, Hepp C, Black A, Dennis A, Trovao N, Vandamme A, Rasmussen A, Lauzardo M, Dean N, Salemi M, Prosperi M. Application of phylodynamic tools to inform the public health response to COVID-19: a qualitative analysis of expert opinions. JMIR Formative Research 2022 PMID: 36848460, DOI: 10.2196/39409.
• Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1.Rodino KG, Peaper DR, Kelly BJ, Bushman F, Marques A, Adhikari H, Tu ZJ, Rolon RM, Westblade LF, Green DA, Berry GJ, Wu F, Annavajhala MK, Uhlemann AC, Parikh BA, McMillen T, Jani K, Babady NE, Hahn AM, Koch RT, Grubaugh ND, Rhoads DD. Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1. MedRxiv : The Preprint Server For Health Sciences 2022 PMID: 35547854, PMCID: PMC9094110, DOI: 10.1101/2022.04.25.22274187.
• Rapid emergence of SARS-CoV-2 Omicron variant is associated with an infection advantage over Delta in vaccinated personsChaguza 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 JL, 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 2022, 3: 325-334.e4. PMID: 35399324, PMCID: PMC8983481, DOI: 10.1016/j.medj.2022.03.010.
• Translating virus evolution into epidemiologyGrubaugh ND. Translating virus evolution into epidemiology Cell Host & Microbe 2022, 30: 444-448. PMID: 35421340, DOI: 10.1016/j.chom.2022.03.006.
• Insights into the limited global spread of the immune evasive SARS-CoV-2 variant Mu.Petrone ME, Lucas C, Menasche B, Breban MI, Yildirim I, Campbell M, Omer SB, Ko AI, Grubaugh ND, Iwasak A, Wilen CB, Vogels CBF, Fauver JR. Insights into the limited global spread of the immune evasive SARS-CoV-2 variant Mu. MedRxiv : The Preprint Server For Health Sciences 2022 PMID: 35378749, PMCID: PMC8978943, DOI: 10.1101/2022.03.28.22273077.
• Evaluation of saliva self-collection devices for SARS-CoV-2 diagnosticsAllicock OM, Petrone ME, Yolda-Carr D, Breban M, 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 2022, 22: 284. PMID: 35337266, PMCID: PMC8953967, DOI: 10.1186/s12879-022-07285-7.
• Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USAEarnest 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 HB, Kales S, Berenzy D, Carpenter-Azevedo K, King E, Huard RC, Novitsky V, Howison M, Darpolor J, Manne A, Kantor R, Smole SC, Brown CM, Fink T, Lang AS, Gallagher GR, Pitzer VE, Sabeti PC, Gabriel S, MacInnis BL, Team N, Altajar A, DeJesus A, Brito A, Watkins A, Muyombwe A, Blumenstiel B, Neal C, Kalinich C, Liu C, Loreth C, Castaldi C, Pearson C, Bernard C, Nolet C, Ferguson D, Buzby E, Laszlo E, Reagan F, Vicente G, Rooke H, Munger H, Johnson H, Tikhonova I, Ott I, Razeq J, Meldrim J, Brown J, Wang J, Vostok J, Beauchamp J, Grimsby J, Hall J, Messer K, Larkin K, Vernest K, Madoff L, Green L, Webber L, Gagne L, Ulcena M, Ray M, Fisher M, Barter M, Lee M, DeFelice M, Cipicchio M, Smith N, Lennon N, Fitzgerald N, Kerantzas N, Hui P, Harrington R, Downing R, Haye R, Lynch R, Anderson S, Hennigan S, English S, Cofsky S, Clancy S, Mane S, Ash S, Baez S, Fleming S, Murphy S, Chaluvadi S, Alpert T, Rivard T, Schulz W, Mandese Z, Tewhey R, Adams M, Park D, Lemieux J, Grubaugh N. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA Cell Reports Medicine 2022, 3: 100583. PMID: 35480627, PMCID: PMC8913280, DOI: 10.1016/j.xcrm.2022.100583.
• Assessment of Clinical Effectiveness of BNT162b2 COVID-19 Vaccine in US AdolescentsOliveira CR, Niccolai LM, Sheikha H, Elmansy L, Kalinich CC, Grubaugh ND, Shapiro ED, Billig K, Breban M, Brito A, Earnest R, Fauver J, Koch T, Ott I, Petrone M, Vogels C, Pham K, Tikhonova I, Castaldi C, Mane S, Bilguvar K, De Kumar B, Ferguson D, Kerantzas N, Landry M, Peaper D, Schulz W. Assessment of Clinical Effectiveness of BNT162b2 COVID-19 Vaccine in US Adolescents JAMA Network Open 2022, 5: e220935. PMID: 35238933, PMCID: PMC8895259, DOI: 10.1001/jamanetworkopen.2022.0935.
• Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2.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. BioRxiv : The Preprint Server For Biology 2022 PMID: 35194606, PMCID: PMC8863141, DOI: 10.1101/2022.02.14.480449.
• Clinical effectiveness of additional primary SARS‐CoV‐2 vaccine doses for solid organ transplant recipientsRadcliffe 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 2022, 36: e14601. PMID: 35064939, DOI: 10.1111/ctr.14601.
• An outbreak of SARS‐CoV‐2 on a transplant unit in the early vaccination eraRoberts SC, Palacios C, Grubaugh ND, Alpert T, Ott IM, Breban MI, Initiative Y, Martinello RA, Smith C, Davis MW, Mcmanus D, Tirmizi S, Topal JE, Azar MM, Malinis M. An outbreak of SARS‐CoV‐2 on a transplant unit in the early vaccination era Transplant Infectious Disease 2022, 24: e13782. PMID: 34969164, DOI: 10.1111/tid.13782.
• Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, 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, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason L, Ko A, Montgomery R, Farhadian S, Iwasaki A, Shaw A, van Dijk D, Zhao H, Kleinstein S, Hafler D, Kaminski N, Dela Cruz C. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19 Nature Communications 2022, 13: 440. PMID: 35064122, PMCID: PMC8782894, DOI: 10.1038/s41467-021-27716-4.
• Neutralizing antibodies against the SARS-CoV-2 Delta and Omicron variants following heterologous CoronaVac plus BNT162b2 booster vaccinationPérez-Then E, Lucas C, Monteiro VS, Miric M, Brache V, Cochon L, Vogels CBF, Malik AA, 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 2022, 28: 481-485. PMID: 35051990, PMCID: PMC8938264, DOI: 10.1038/s41591-022-01705-6.
• Sequencing SARS-CoV-2 Genomes from SalivaAlpert T, Vogels CBF, Breban MI, Petrone ME, Team Y, Wyllie A, Grubaugh N, Fauver J. Sequencing SARS-CoV-2 Genomes from Saliva Virus Evolution 2022, 8: veab098-. PMID: 35542310, PMCID: PMC9074962, DOI: 10.1093/ve/veab098.
• Of variants and vaccinesGrubaugh ND, Cobey S. Of variants and vaccines Cell 2021, 184: 6222-6223. PMID: 34942096, PMCID: PMC8693473, DOI: 10.1016/j.cell.2021.11.013.
• COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective AnalysisLee M, Sallah YH, Petrone M, Ringer M, Cosentino D, Vogels CBF, Fauver JR, Alpert TD, Grubaugh ND, Gupta S. COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis JMIRx Med 2021, 2: e31503. PMID: 35014989, PMCID: PMC8722526, DOI: 10.2196/31503.
• Authors' Response to Peer Reviews of “COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis”Lee M, Sallah Y, Petrone M, Ringer M, Cosentino D, Vogels C, Fauver J, Alpert T, Grubaugh N, Gupta S. Authors' Response to Peer Reviews of “COVID-19 Outcomes and Genomic Characterization of SARS-CoV-2 Isolated From Veterans in New England States: Retrospective Analysis” JMIRx Med 2021, 2: e35515. DOI: 10.2196/35515.
• Global disparities in SARS-CoV-2 genomic surveillance.Brito AF, Semenova E, Dudas G, Hassler GW, Kalinich CC, Kraemer MUG, Ho J, Tegally H, Githinji G, Agoti CN, Matkin LE, Whittaker C, Howden BP, Sintchenko V, Zuckerman NS, Mor O, Blankenship HM, de Oliveira T, Lin RTP, Siqueira MM, Resende PC, Vasconcelos ATR, Spilki FR, Aguiar RS, Alexiev I, Ivanov IN, Philipova I, 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. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 34462754, PMCID: PMC8404891, DOI: 10.1101/2021.08.21.21262393.
• 301. Detection of Pneumococcal Pneumonia During SARS-CoV-2 InfectionWatkins A, Yolda-Carr D, Ott I, Nakahata M, Moore A, Muenker M, Tokuyama M, Vogels C, Campbell M, Datta R, Cruz C, Farhadian S, Iwasaki A, Ko A, Grubaugh N, Alexander-Parrish R, Arguedas A, Gessner B, Weinberger D, Wyllie A. 301. Detection of Pneumococcal Pneumonia During SARS-CoV-2 Infection Open Forum Infectious Diseases 2021, 8: s257-s257. PMCID: PMC8644655, DOI: 10.1093/ofid/ofab466.503.
• 362. Saliva as a Reliable Sample Type for Mass SARS-CoV-2 Testing StrategiesWyllie A, Vogels C, Allicock O, Watkins A, Petrone M, Yolda-Carr D, Harden C, Brackney D, Kalinich C, Breban M, Ott I, Sikka R, Kadiri L, Grubaugh N. 362. Saliva as a Reliable Sample Type for Mass SARS-CoV-2 Testing Strategies Open Forum Infectious Diseases 2021, 8: s284-s284. PMCID: PMC8644416, DOI: 10.1093/ofid/ofab466.563.
• Viral Dynamics of SARS-CoV-2 Variants in Vaccinated and Unvaccinated PersonsKissler SM, Fauver JR, Mack C, Tai CG, Breban MI, Watkins AE, Samant RM, Anderson DJ, Metti J, Khullar G, Baits R, MacKay M, Salgado D, Baker T, Dudley JT, Mason CE, Ho DD, Grubaugh ND, Grad YH. Viral Dynamics of SARS-CoV-2 Variants in Vaccinated and Unvaccinated Persons New England Journal Of Medicine 2021, 385: 2489-2491. PMID: 34941024, PMCID: PMC8693673, DOI: 10.1056/nejmc2102507.
• A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in miceMao T, Israelow B, Lucas C, Vogels CBF, Gomez-Calvo ML, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Alpert T, Anderson F, Earnest R, Fauver J, Kalinich C, Munyenyembe K, Ott I, Petrone M, Rothman J, Watkins A, Wilen C, Landry M, Grubaugh N, Pyle A, Iwasaki A. A stem-loop RNA RIG-I agonist protects against acute and chronic SARS-CoV-2 infection in mice Journal Of Experimental Medicine 2021, 219: e20211818. PMID: 34757384, PMCID: PMC8590200, DOI: 10.1084/jem.20211818.
• Early Release - Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016–2017 - Volume 27, Number 11—November 2021 - Emerging Infectious Diseases journal - CDCSantiago 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. Early Release - Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016–2017 - Volume 27, Number 11—November 2021 - Emerging Infectious Diseases journal - CDC Emerging Infectious Diseases 2021, 27: 2971-2973. PMID: 34670646, PMCID: PMC8544999, DOI: 10.3201/eid2711.211575.
• Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant RecipientKlein 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, Dela Cruz C, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B, Iwasaki A, Azar MM, Team F. Longitudinal Immune Profiling of a Severe Acute Respiratory Syndrome Coronavirus 2 Reinfection in a Solid Organ Transplant Recipient The Journal Of Infectious Diseases 2021, 225: 374-384. PMID: 34718647, PMCID: PMC8807168, DOI: 10.1093/infdis/jiab553.
• Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunityLucas C, Vogels CBF, Yildirim I, Rothman JE, Lu P, Monteiro V, Gehlhausen JR, Campbell M, Silva J, Tabachnikova A, Peña-Hernandez MA, Muenker MC, Breban MI, Fauver JR, Mohanty S, Huang J, Shaw A, Ko A, Omer S, Grubaugh N, Iwasaki A. Impact of circulating SARS-CoV-2 variants on mRNA vaccine-induced immunity Nature 2021, 600: 523-529. PMID: 34634791, PMCID: PMC9348899, DOI: 10.1038/s41586-021-04085-y.
• Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA.Earnest R, Uddin R, Matluk N, Renzette N, Siddle KJ, Loreth C, Adams G, Tomkins-Tinch CH, Petrone ME, Rothman JE, Breban MI, Koch RT, Billig K, Fauver JR, Vogels CBF, Turbett S, 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, Tewhey R, Adams MD, Park DJ, Lemieux JE, Grubaugh ND. Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 34642698, PMCID: PMC8509091, DOI: 10.1101/2021.10.06.21264641.
• Reply to: A finding of sex similarities rather than differences in COVID-19 outcomesTakahashi T, Ellingson MK, Wong P, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang EY, Casanovas-Massana A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Shaw A, Fournier JB, Odio CD, Farhadian S, Dela Cruz C, Grubaugh ND, Schulz WL, Ring AM, Ko AI, Omer SB, Iwasaki A. Reply to: A finding of sex similarities rather than differences in COVID-19 outcomes Nature 2021, 597: e10-e11. PMID: 34552250, DOI: 10.1038/s41586-021-03645-6.
• COVID-19 vaccines: Keeping pace with SARS-CoV-2 variantsCevik M, Grubaugh ND, Iwasaki A, Openshaw P. COVID-19 vaccines: Keeping pace with SARS-CoV-2 variants Cell 2021, 184: 5077-5081. PMID: 34534444, PMCID: PMC8445744, DOI: 10.1016/j.cell.2021.09.010.
• Zika Virus Non-Structural Protein 1 Antigen-Capture ImmunoassayBeddingfield B, Hartnett J, Wilson R, Kulakosky P, Andersen K, Robles-Sikisaka R, Grubaugh N, Aybar A, Nunez M, Fermin C, Garry R. Zika Virus Non-Structural Protein 1 Antigen-Capture Immunoassay Viruses 2021, 13: 1771. PMID: 34578352, PMCID: PMC8473068, DOI: 10.3390/v13091771.
• Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.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, Hanage WP, Grubaugh ND, Peccia J, Baym M. Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 34494031, PMCID: PMC8423229, DOI: 10.1101/2021.08.31.21262938.
• SARS-CoV-2 Reinfection: A Case Series from a 12-Month Longitudinal Occupational CohortMack 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 2021, 74: ciab738-. PMID: 34453431, DOI: 10.1093/cid/ciab738.
• Influenza Antigens NP and M2 Confer Cross Protection to BALB/c Mice against Lethal Challenge with H1N1, Pandemic H1N1 or H5N1 Influenza A VirusesMytle 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 2021, 13: 1708. PMID: 34578289, PMCID: PMC8473317, DOI: 10.3390/v13091708.
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• Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategiesKissler 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 YH. Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies PLOS Biology 2021, 19: e3001333. PMID: 34252080, PMCID: PMC8297933, DOI: 10.1371/journal.pbio.3001333.
• Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics.Allicock OM, Petrone ME, Yolda-Carr D, Breban M, Walsh H, Watkins AE, Rothman JE, Farhadian SF, Grubaugh ND, Wyllie AL. Evaluation of saliva self-collection devices for SARS-CoV-2 diagnostics. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33564787, PMCID: PMC7872382, DOI: 10.1101/2021.02.01.21250946.
• Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages.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 lineages. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 34230938, PMCID: PMC8259915, DOI: 10.1101/2021.07.01.21259859.
• Sequencing SARS-CoV-2 Genomes from Saliva.Alpert T, Vogels CBF, Breban MI, Petrone ME, Wyllie AL, Grubaugh ND, Fauver JR. Sequencing SARS-CoV-2 Genomes from Saliva. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 34230934, PMCID: PMC8259911, DOI: 10.1101/2021.06.21.21259289.
• Evidence for SARS-CoV-2 Spike Protein in the Urine of COVID-19 Patients.George S, Pal AC, 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 V, Campbell M, Farhadian SF, Grubaugh ND, Dela Cruz CS, Ko AI, Berna Perez AZ, Akaho EH, Moledina DG, Testani J, John AR, Ledizet M, Mamoun CB. Evidence for SARS-CoV-2 Spike Protein in the Urine of COVID-19 Patients. Kidney360 2021, 2: 924-936. PMID: 35373072, PMCID: PMC8791366, DOI: 10.34067/kid.0002172021.
• Author Correction: Delayed production of neutralizing antibodies correlates with fatal COVID-19Lucas C, Klein J, Sundaram ME, 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 CH, Casanovas-Massana A, Moore AJ, Zell J, Fournier JB, Wyllie A, Campbell M, Lee A, Chun H, Grubaugh N, Schulz W, Farhadian S, Dela Cruz C, Ring A, Shaw A, Wisnewski A, Yildirim I, Ko A, Omer S, Iwasaki A. Author Correction: Delayed production of neutralizing antibodies correlates with fatal COVID-19 Nature Medicine 2021, 27: 1309-1309. PMID: 34145437, PMCID: PMC8212078, DOI: 10.1038/s41591-021-01416-4.
• A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice.Mao T, Israelow B, Lucas C, Vogels CBF, Fedorova O, Breban MI, Menasche BL, Dong H, Linehan M, Wilen CB, Landry ML, Grubaugh ND, Pyle AM, Iwasaki A. A stem-loop RNA RIG-I agonist confers prophylactic and therapeutic protection against acute and chronic SARS-CoV-2 infection in mice. BioRxiv : The Preprint Server For Biology 2021 PMID: 34159330, PMCID: PMC8219094, DOI: 10.1101/2021.06.16.448754.
• Diverse functional autoantibodies in patients with COVID-19Wang EY, Mao T, Klein J, Dai Y, Huck JD, Jaycox JR, Liu F, Zhou T, Israelow B, Wong P, Coppi A, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Zheng NS, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Dela Cruz C, Farhadian S, Schulz W, Ma S, Grubaugh N, Ko A, Iwasaki A, Ring A. Diverse functional autoantibodies in patients with COVID-19 Nature 2021, 595: 283-288. PMID: 34010947, DOI: 10.1038/s41586-021-03631-y.
• Lying in wait: the resurgence of dengue virus after the Zika epidemic in BrazilBrito AF, Machado LC, Oidtman RJ, Siconelli MJL, Tran QM, Fauver JR, Carvalho RDO, Dezordi FZ, Pereira MR, de Castro-Jorge LA, Minto ECM, Passos LMR, Kalinich CC, Petrone ME, Allen E, España GC, Huang AT, Cummings DAT, Baele G, Franca RFO, da Fonseca BAL, Perkins TA, Wallau GL, Grubaugh ND. Lying in wait: the resurgence of dengue virus after the Zika epidemic in Brazil Nature Communications 2021, 12: 2619. PMID: 33976183, PMCID: PMC8113494, DOI: 10.1038/s41467-021-22921-7.
• COVID-19 one year into the pandemic: from genetics and genomics to therapy, vaccination, and policyNovelli 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 2021, 15: 27. PMID: 33966626, PMCID: PMC8107019, DOI: 10.1186/s40246-021-00326-3.
• Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2Vogels CBF, Breban MI, Ott IM, Alpert T, Petrone ME, Watkins AE, Kalinich CC, Earnest R, Rothman JE, Goes de Jesus J, Morales Claro I, Magalhães Ferreira G, Crispim MAE, , Singh L, Tegally H, Anyaneji UJ, , 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 JR, Grubaugh ND. Multiplex qPCR discriminates variants of concern to enhance global surveillance of SARS-CoV-2 PLOS Biology 2021, 19: e3001236. PMID: 33961632, PMCID: PMC8133773, DOI: 10.1371/journal.pbio.3001236.
• Delayed production of neutralizing antibodies correlates with fatal COVID-19Lucas C, Klein J, Sundaram ME, 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 CH, Casanovas-Massana A, Moore AJ, Zell J, Fournier JB, Wyllie A, Campbell M, Lee A, Chun H, Grubaugh N, Schulz W, Farhadian S, Dela Cruz C, Ring A, Shaw A, Wisnewski A, Yildirim I, Ko A, Omer S, Iwasaki A. Delayed production of neutralizing antibodies correlates with fatal COVID-19 Nature Medicine 2021, 27: 1178-1186. PMID: 33953384, PMCID: PMC8785364, DOI: 10.1038/s41591-021-01355-0.
• Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient.Klein J, Brito A, Trubin P, Lu P, Wong P, Alpert T, Pena-Hernandez M, Haynes W, Kamath K, Liu F, Vogels C, Fauver J, Lucas C, Oh JE, Mao T, Silva J, Wyllie A, Muenker MC, Casanovas-Massana A, Moore A, Petrone M, Kalinich C, Cruz CD, Farhadian S, Ring A, Shon J, Ko A, Grubaugh N, Goldman-Israelow B, Iwasaki A, Azar M. Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient. Research Square 2021 PMID: 34013255, PMCID: PMC8132249, DOI: 10.21203/rs.3.rs-405958/v1.
• Divergent and self-reactive immune responses in the CNS of COVID-19 patients with neurological symptomsSong E, Bartley CM, Chow RD, Ngo TT, Jiang R, Zamecnik CR, Dandekar R, Loudermilk RP, Dai Y, Liu F, Sunshine S, Liu J, Wu W, Hawes IA, Alvarenga BD, Huynh T, McAlpine L, Rahman NT, Geng B, Chiarella J, Goldman-Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander JR, Gallego JA, Lencz T, Walsh H, Wapniarski AE, Mohanty S, Lucas C, Klein J, Mao T, Oh J, Ring A, Spudich S, Ko AI, Kleinstein SH, Pak J, 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 2021, 2: 100288. PMID: 33969321, PMCID: PMC8091032, DOI: 10.1016/j.xcrm.2021.100288.
• Diverse Functional Autoantibodies that Underlie Immune Perturbations in COVID-19Mao T, Wang E, Klein J, Dai Y, Huck J, Liu F, Zheng N, Zhou T, Goldman-Israelow B, Wong P, Lucas C, Silva J, Oh J, Song E, Perotti E, Fischer S, Campbell M, Fournier J, Wyllie A, Vogels C, Ott I, Kalinich C, Petrone M, Watkins A, Cruz C, Farhadian S, Schulz W, Grubaugh N, Ko A, Iwasaki A, Ring A. Diverse Functional Autoantibodies that Underlie Immune Perturbations in COVID-19 The Journal Of Immunology 2021, 206: 114.04-114.04. DOI: 10.4049/jimmunol.206.supp.114.04.
• Maternal respiratory SARS-CoV-2 infection in pregnancy is associated with a robust inflammatory response at the maternal-fetal interfaceLu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, 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, Team Y, 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 2021, 2: 591-610.e10. PMID: 33969332, PMCID: PMC8084634, DOI: 10.1016/j.medj.2021.04.016.
• Early introductions and transmission of SARS-CoV-2 variant B.1.1.7 in the United StatesAlpert 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 2021, 184: 2595-2604.e13. PMID: 33891875, PMCID: PMC8018830, DOI: 10.1016/j.cell.2021.03.061.
• Stability of SARS-CoV-2 RNA in Nonsupplemented Saliva - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDCOtt 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, Dela Cruz CS, Farhadian SF, Ko AI, Iwasaki A, Grubaugh ND, Wilen CB, Wyllie AL, . Stability of SARS-CoV-2 RNA in Nonsupplemented Saliva - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDC Emerging Infectious Diseases 2021, 27: 1146-1150. PMID: 33754989, PMCID: PMC8007305, DOI: 10.3201/eid2704.204199.
• Increased SARS-CoV-2 Testing Capacity with Pooled Saliva Samples - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDCWatkins AE, Fenichel EP, Weinberger DM, Vogels CBF, Brackney DE, Casanovas-Massana A, Campbell M, Fournier J, Bermejo S, Datta R, Dela Cruz CS, Farhadian SF, Iwasaki A, Ko AI, Grubaugh ND, Wyllie AL, . Increased SARS-CoV-2 Testing Capacity with Pooled Saliva Samples - Volume 27, Number 4—April 2021 - Emerging Infectious Diseases journal - CDC Emerging Infectious Diseases 2021, 27: 1184-1187. PMID: 33755009, PMCID: PMC8007323, DOI: 10.3201/eid2704.204200.
• Case Study: Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient.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, Cruz CD, Farhadian S, Ring A, Shon J, Ko AI, Grubaugh ND, Israelow B, Iwasaki A, Azar MM. Case Study: Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33791729, PMCID: PMC8010761, DOI: 10.1101/2021.03.24.21253992.
• Abstract S03-03: Cancer patients display diminished viral RNA clearance and altered T cell responses during SARS-CoV-2 infectionChiorazzi M, Silva E, Brower K, Wong P, Lucas C, Klein J, Liu F, Nakahata M, Zhao J, Rahman N, Odio C, Bermejo S, Farhadian S, Dela Cruz C, Casanovas-Massana A, Fournier J, Muenker C, Wyllie A, Vogels C, Kalinich C, Petrone M, Ott I, Watkins A, Moore A, Alpert T, Kluger Y, Ring A, Grubaugh N, Iwasaki A, Ko A, Herbst R. Abstract S03-03: Cancer patients display diminished viral RNA clearance and altered T cell responses during SARS-CoV-2 infection Clinical Cancer Research 2021, 27: s03-03-s03-03. DOI: 10.1158/1557-3265.covid-19-21-s03-03.
• PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern.Vogels CBF, Breban MI, Alpert T, Petrone ME, Watkins AE, Ott IM, de Jesus JG, Claro IM, Ferreira GM, Crispim MAE, Singh L, Tegally H, Anyaneji UJ, 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 JR, Grubaugh ND. PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33758901, PMCID: PMC7987060, DOI: 10.1101/2021.01.28.21250486.
• Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States.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, Fauntleroy KA, Peaper DR, Landry ML, Cook PW, Fauver JR, Mason CE, Lauring AS, George KS, MacCannell DR, Grubaugh ND. Early introductions and community transmission of SARS-CoV-2 variant B.1.1.7 in the United States. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33594373, PMCID: PMC7885932, DOI: 10.1101/2021.02.10.21251540.
• Tracking smell loss to identify healthcare workers with SARS-CoV-2 infectionWeiss 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, Moore AJ, Handoko R, Iwasaki A, Martinello RA, Ko AI, Small DM, Farhadian SF, . Tracking smell loss to identify healthcare workers with SARS-CoV-2 infection PLOS ONE 2021, 16: e0248025. PMID: 33657167, PMCID: PMC7928484, DOI: 10.1371/journal.pone.0248025.
• MOG-associated encephalitis following SARS-COV-2 InfectionPeters J, Alhasan S, Vogels CBF, Grubaugh ND, Farhadian S, Longbrake EE. MOG-associated encephalitis following SARS-COV-2 Infection Multiple Sclerosis And Related Disorders 2021, 50: 102857. PMID: 33647592, PMCID: PMC7900751, DOI: 10.1016/j.msard.2021.102857.
• Emergence of an early SARS-CoV-2 epidemic in the United States.Zeller M, Gangavarapu K, Anderson C, Smither AR, Vanchiere JA, Rose R, Dudas G, Snyder DJ, Watts A, Matteson NL, Robles-Sikisaka R, Marshall M, Feehan AK, Sabino-Santos G, Bell-Kareem A, 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 N, 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. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33564781, PMCID: PMC7872376, DOI: 10.1101/2021.02.05.21251235.
• Saliva for Detection of SARS-CoV-2. Reply.Wyllie AL, Vogels CBF, Grubaugh ND. Saliva for Detection of SARS-CoV-2. Reply. New England Journal Of Medicine 2021, 384: e31. PMID: 33534974, DOI: 10.1056/nejmc2032165.
• Diverse Functional Autoantibodies in Patients with COVID-19.Wang EY, Mao T, Klein J, Dai Y, Huck JD, Liu F, Zheng NS, Zhou T, Israelow B, Wong P, Lucas C, Silva J, Oh JE, Song E, Perotti ES, Fischer S, Campbell M, Fournier JB, Wyllie AL, Vogels CBF, Ott IM, Kalinich CC, Petrone ME, Watkins AE, Cruz CD, Farhadian SF, Schulz WL, Grubaugh ND, Ko AI, Iwasaki A, Ring AM. Diverse Functional Autoantibodies in Patients with COVID-19. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33330894, PMCID: PMC7743105, DOI: 10.1101/2020.12.10.20247205.
• Public health actions to control new SARS-CoV-2 variantsGrubaugh ND, Hodcroft EB, Fauver JR, Phelan AL, Cevik M. Public health actions to control new SARS-CoV-2 variants Cell 2021, 184: 1127-1132. PMID: 33581746, PMCID: PMC7846239, DOI: 10.1016/j.cell.2021.01.044.
• SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface.Lu-Culligan A, Chavan AR, Vijayakumar P, Irshaid L, Courchaine EM, Milano KM, 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, Konnikova L, Neugebauer KM, Ring A, Grubaugh ND, Ko AI, Morotti R, Guller S, Kliman HJ, Iwasaki A, Farhadian SF. SARS-CoV-2 infection in pregnancy is associated with robust inflammatory response at the maternal-fetal interface. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33532791, PMCID: PMC7852242, DOI: 10.1101/2021.01.25.21250452.
• Intrahost speciations and host switches played an important role in the evolution of herpesvirusesBrito 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 2021, 7: veab025-. PMID: 33927887, PMCID: PMC8062258, DOI: 10.1093/ve/veab025.
• Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality.Silva J, Lucas C, Sundaram M, Israelow B, Wong P, Klein J, Tokuyama M, Lu P, Venkataraman A, Liu F, Mao T, Oh JE, Park A, Casanovas-Massana A, Vogels CBF, Muenker CM, Zell J, Fournier JB, Campbell M, Chiorazzi M, Ruiz Fuentes E, Petrone M, Kalinich CC, Ott IM, Watkins A, Moore AJ, Nakahata MI, Grubaugh ND, Farhadian S, Dela Cruz C, Ko A, Schulz WL, Ring AM, Ma S, Omer S, Wyllie AL, Iwasaki A. Saliva viral load is a dynamic unifying correlate of COVID-19 severity and mortality. MedRxiv : The Preprint Server For Health Sciences 2021 PMID: 33442706, PMCID: PMC7805468, DOI: 10.1101/2021.01.04.21249236.
• Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican RepublicPetrone 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 2021, 12: 151. PMID: 33420058, PMCID: PMC7794562, DOI: 10.1038/s41467-020-20391-x.
• Multiple Transmission Chains within COVID-19 Cluster, Connecticut, USA, 2020 - Volume 27, Number 10—October 2021 - Emerging Infectious Diseases journal - CDCM. S, 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 - Volume 27, Number 10—October 2021 - Emerging Infectious Diseases journal - CDC Emerging Infectious Diseases 2021, 27: 2669-2672. PMID: 34545794, PMCID: PMC8462310, DOI: 10.3201/eid2710.211196.
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• 456. Implementing an At-Home Smell Test for Early Assessment of COVID-19 in High-Risk Healthcare WorkersWeiss J, Attuquayefio T, White E, Geng B, Handoko R, Herz R, White T, Iwasaki A, Grubaugh N, Datta R, Campbell M, Martinello R, Ko A, Small D, Farhadian S. 456. Implementing an At-Home Smell Test for Early Assessment of COVID-19 in High-Risk Healthcare Workers Open Forum Infectious Diseases 2020, 7: s295-s296. PMCID: PMC7776583, DOI: 10.1093/ofid/ofaa439.649.
• SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacityVogels 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, Team Y, Anastasio K, Askenase M, Batsu M, Bickerton S, Brower K, Bucklin M, Cahill S, Cao Y, Courchaine E, DeIuliis G, Earnest R, Geng B, Goldman-Israelow B, Handoko R, Khoury-Hanold W, Kim D, Knaggs L, Kuang M, Lapidus S, Lim J, Linehan M, Lu-Culligan A, Martin A, Matos I, McDonald D, Minasyan M, Nakahata M, Naushad N, Nouws J, Obaid A, Odio C, Oh J, Omer S, Park A, Park H, Peng X, Petrone M, Prophet S, Rice T, Rose K, Sewanan L, Sharma L, Shaw A, Shepard D, Smolgovsky M, Sonnert N, Strong Y, Todeasa C, Valdez J, Velazquez S, Vijayakumar P, White E, Yang Y, Dela Cruz C, Ko A, Iwasaki A, Krumholz H, Matheus J, Hui P, Liu C, Farhadian S, Sikka R, Wyllie A, Grubaugh N. SalivaDirect: A simplified and flexible platform to enhance SARS-CoV-2 testing capacity Med 2020, 2: 263-280.e6. PMID: 33521748, PMCID: PMC7836249, DOI: 10.1016/j.medj.2020.12.010.
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• Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement.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 NT, Geng B, Chiarella J, Israelow B, Vogels CBF, Grubaugh ND, Casanovas-Massana A, Phinney BS, Salemi M, Alexander J, Gallego JA, 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. Exploratory neuroimmune profiling identifies CNS-specific alterations in COVID-19 patients with neurological involvement. BioRxiv : The Preprint Server For Biology 2020 PMID: 32935102, PMCID: PMC7491516, DOI: 10.1101/2020.09.11.293464.
• 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 VectorsLemos D, Stuart JB, Louie W, Singapuri A, Ramírez AL, Watanabe J, Usachenko J, Keesler RI, Martin CS, Li T, Martyn C, Oliveira G, Saraf S, Grubaugh ND, Andersen KG, Thissen J, Allen J, Borucki M, Tsetsarkin KA, Pletnev AG, Chiu CY, Van Rompay KKA, 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 2020, 94: e01605-20. PMID: 32999034, PMCID: PMC7925200, DOI: 10.1128/jvi.01605-20.
• Epidemiological hypothesis testing using a phylogeographic and phylodynamic frameworkDellicour 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 2020, 11: 5620. PMID: 33159066, PMCID: PMC7648063, DOI: 10.1038/s41467-020-19122-z.
• Detection of SARS-CoV-2 RNA by multiplex RT-qPCRKudo 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, , 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 2020, 18: e3000867. PMID: 33027248, PMCID: PMC7571696, DOI: 10.1371/journal.pbio.3000867.
• Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamicsPeccia J, Zulli A, Brackney DE, Grubaugh ND, Kaplan EH, Casanovas-Massana A, Ko AI, Malik AA, Wang D, Wang M, Warren JL, Weinberger DM, Arnold W, Omer SB. Measurement of SARS-CoV-2 RNA in wastewater tracks community infection dynamics Nature Biotechnology 2020, 38: 1164-1167. PMID: 32948856, PMCID: PMC8325066, DOI: 10.1038/s41587-020-0684-z.
• Tracking Smell Loss to Identify Healthcare Workers with SARS-CoV-2 Infection.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, Martinello RA, Ko AI, Small DM, Farhadian SF. Tracking Smell Loss to Identify Healthcare Workers with SARS-CoV-2 Infection. MedRxiv : The Preprint Server For Health Sciences 2020 PMID: 32935121, PMCID: PMC7491536, DOI: 10.1101/2020.09.07.20188813.
• Pooling saliva to increase SARS-CoV-2 testing capacity.Watkins AE, Fenichel EP, Weinberger DM, Vogels CBF, Brackney DE, Casanovas-Massana A, Campbell M, Fournier J, Bermejo S, Datta R, Dela Cruz CS, Farhadian SF, Iwasaki A, Ko AI, Grubaugh ND, Wyllie AL. Pooling saliva to increase SARS-CoV-2 testing capacity. MedRxiv : The Preprint Server For Health Sciences 2020 PMID: 32909003, PMCID: PMC7480055, DOI: 10.1101/2020.09.02.20183830.
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• Sex differences in immune responses that underlie COVID-19 disease outcomesTakahashi T, Ellingson MK, Wong P, Israelow B, Lucas C, Klein J, Silva J, Mao T, Oh JE, Tokuyama M, Lu P, Venkataraman A, Park A, Liu F, Meir A, Sun J, Wang EY, Casanovas-Massana A, Wyllie AL, Vogels CBF, Earnest R, Lapidus S, Ott IM, Moore AJ, Shaw A, Fournier J, Odio C, Farhadian S, Dela Cruz C, Grubaugh N, Schulz W, Ring A, Ko A, Omer S, Iwasaki A. Sex differences in immune responses that underlie COVID-19 disease outcomes Nature 2020, 588: 315-320. PMID: 32846427, PMCID: PMC7725931, DOI: 10.1038/s41586-020-2700-3.
• Real-time public health communication of local SARS-CoV-2 genomic epidemiologyKalinich 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 2020, 18: e3000869. PMID: 32822393, PMCID: PMC7467297, DOI: 10.1371/journal.pbio.3000869.
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• Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices.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, Dela Cruz CS, Farhadian SF, Ko AI, Iwasaki A, Grubaugh ND, Wilen CB, Wyllie AL. Simply saliva: stability of SARS-CoV-2 detection negates the need for expensive collection devices. MedRxiv : The Preprint Server For Health Sciences 2020 PMID: 32793924, PMCID: PMC7418742, DOI: 10.1101/2020.08.03.20165233.
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• Sampling bias and incorrect rooting make phylogenetic network tracing of SARS-COV-2 infections unreliableMavian C, Pond SK, Marini S, Magalis BR, Vandamme AM, Dellicour S, Scarpino SV, Houldcroft C, Villabona-Arenas J, Paisie TK, Trovão NS, Boucher C, Zhang Y, Scheuermann RH, Gascuel O, Lam TT, Suchard MA, Abecasis A, Wilkinson E, de Oliveira T, Bento AI, Schmidt HA, Martin D, Hadfield J, Faria N, 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 Proceedings Of The National Academy Of Sciences Of The United States Of America 2020, 117: 12522-12523. PMID: 32381734, PMCID: PMC7293693, DOI: 10.1073/pnas.2007295117.
• Why does Japan have so few cases of COVID‐19?Iwasaki A, Grubaugh ND. Why does Japan have so few cases of COVID‐19? EMBO Molecular Medicine 2020, 12: e12481. PMID: 32275804, PMCID: PMC7207161, DOI: 10.15252/emmm.202012481.
• Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology.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 I, Quick J, Loman NJ, Neugebauer KM, Greninger AL, Jerome KR, Roychoundhury P, Xie H, Shrestha L, Huang ML, Pitzer VE, Iwasaki A, Omer SB, Khan K, Bogoch I, Martinello RA, Foxman EF, Landry ML, Neher RA, Ko AI, Grubaugh ND. Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology. MedRxiv : The Preprint Server For Health Sciences 2020 PMID: 32511630, PMCID: PMC7276058, DOI: 10.1101/2020.03.25.20043828.
• We shouldn’t worry when a virus mutates during disease outbreaksGrubaugh ND, Petrone ME, Holmes EC. We shouldn’t worry when a virus mutates during disease outbreaks Nature Microbiology 2020, 5: 529-530. PMID: 32071422, PMCID: PMC7095397, DOI: 10.1038/s41564-020-0690-4.
• Genomic Epidemiology as a Public Health Tool to Combat Mosquito-Borne Virus Outbreaks.Pollett S, Fauver JR, Maljkovic Berry I, 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. The Journal Of Infectious Diseases 2019, 221: s308-s318. PMID: 31711190, DOI: 10.1093/infdis/jiz302.
• Twenty years of West Nile virus spread and evolution in the Americas visualized by NextstrainHadfield 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 2019, 15: e1008042. PMID: 31671157, PMCID: PMC6822705, DOI: 10.1371/journal.ppat.1008042.
• Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning EpidemicGrubaugh 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, Network G, Gardner LM, Perkins TA, Baele G, Khan K, Morrison A, Isern S, Michael SF, Andersen KG. Travel Surveillance and Genomics Uncover a Hidden Zika Outbreak during the Waning Epidemic Cell 2019, 178: 1057-1071.e11. PMID: 31442400, PMCID: PMC6716374, DOI: 10.1016/j.cell.2019.07.018.
• Endless Forms: Within-Host Variation in the Structure of the West Nile Virus RNA Genome during Serial Passage in Bird HostsScroggs SLP, 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 2019, 4: e00291-19. PMID: 31243074, PMCID: PMC6595145, DOI: 10.1128/msphere.00291-19.
• Small RNA responses of Culex mosquitoes and cell lines during acute and persistent virus infectionRückert C, Prasad AN, Garcia-Luna SM, Robison 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 2019, 109: 13-23. PMID: 30959110, PMCID: PMC6516063, DOI: 10.1016/j.ibmb.2019.04.008.
• Misperceived Risks of Zika-related Microcephaly in IndiaGrubaugh ND, Ishtiaq F, Setoh YX, Ko AI. Misperceived Risks of Zika-related Microcephaly in India Trends In Microbiology 2019, 27: 381-383. PMID: 30826180, DOI: 10.1016/j.tim.2019.02.004.
• Precision epidemiology for infectious disease controlLadner JT, Grubaugh ND, Pybus OG, Andersen KG. Precision epidemiology for infectious disease control Nature Medicine 2019, 25: 206-211. PMID: 30728537, PMCID: PMC7095960, DOI: 10.1038/s41591-019-0345-2.
• Arbovirus coinfection and co-transmission: A neglected public health concern?Vogels CBF, Rückert C, Cavany SM, Perkins TA, Ebel GD, Grubaugh ND. Arbovirus coinfection and co-transmission: A neglected public health concern? PLOS Biology 2019, 17: e3000130. PMID: 30668574, PMCID: PMC6358106, DOI: 10.1371/journal.pbio.3000130.
• An amplicon-based sequencing framework for accurately measuring intrahost virus diversity using PrimalSeq and iVarGrubaugh 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 2019, 20: 8. PMID: 30621750, PMCID: PMC6325816, DOI: 10.1186/s13059-018-1618-7.
• Tracking virus outbreaks in the twenty-first centuryGrubaugh ND, Ladner JT, Lemey P, Pybus OG, Rambaut A, Holmes EC, Andersen KG. Tracking virus outbreaks in the twenty-first century Nature Microbiology 2018, 4: 10-19. PMID: 30546099, PMCID: PMC6345516, DOI: 10.1038/s41564-018-0296-2.
• Common PIEZO1 Allele in African Populations Causes RBC Dehydration and Attenuates Plasmodium InfectionMa 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 2018, 173: 443-455.e12. PMID: 29576450, PMCID: PMC5889333, DOI: 10.1016/j.cell.2018.02.047.
• Genomic Insights into Zika Virus Emergence and SpreadGrubaugh ND, Faria NR, Andersen KG, Pybus OG. Genomic Insights into Zika Virus Emergence and Spread Cell 2018, 172: 1160-1162. PMID: 29522736, DOI: 10.1016/j.cell.2018.02.027.
• Inferring the risk factors behind the geographical spread and transmission of Zika in the AmericasGardner 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 2018, 12: e0006194. PMID: 29346387, PMCID: PMC5790294, DOI: 10.1371/journal.pntd.0006194.
• Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samplesQuick J, Grubaugh ND, Pullan ST, Claro IM, Smith AD, Gangavarapu K, Oliveira G, Robles-Sikisaka R, Rogers TF, Beutler NA, Burton DR, Lewis-Ximenez LL, de Jesus JG, Giovanetti M, Hill SC, Black A, Bedford T, Carroll MW, Nunes M, Alcantara LC, Sabino EC, Baylis SA, Faria NR, 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 2017, 12: 1261-1276. PMID: 28538739, PMCID: PMC5902022, DOI: 10.1038/nprot.2017.066.
• Genomic epidemiology reveals multiple introductions of Zika virus into the United StatesGrubaugh ND, Ladner JT, Kraemer MUG, Dudas G, Tan AL, Gangavarapu K, Wiley MR, White S, Thézé J, Magnani DM, Prieto K, Reyes D, Bingham AM, 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, Luo 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 MJ, 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 2017, 546: 401-405. PMID: 28538723, PMCID: PMC5536180, DOI: 10.1038/nature22400.
• Zika virus evolution and spread in the AmericasMetsky 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, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, 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 L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC. Zika virus evolution and spread in the Americas Nature 2017, 546: 411-415. PMID: 28538734, PMCID: PMC5563848, DOI: 10.1038/nature22402.
• Establishment and cryptic transmission of Zika virus in Brazil and the AmericasFaria NR, Quick J, Claro IM, Thézé J, de Jesus JG, Giovanetti M, Kraemer MUG, Hill SC, Black A, da Costa AC, Franco LC, Silva SP, Wu C, Raghwani 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, Chiu CY, Muñoz-Medina JE, Gonzalez-Bonilla CR, Arias CF, 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, França RF, Magalhães T, Marques ET, Jaenisch T, Wallau GL, de Lima MC, Nascimento V, de Cerqueira EM, de Lima MM, Mascarenhas DL, Neto JPM, 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 NJ, Pybus OG. Establishment and cryptic transmission of Zika virus in Brazil and the Americas Nature 2017, 546: 406-410. PMID: 28538727, PMCID: PMC5722632, DOI: 10.1038/nature22401.
• Mosquitoes Transmit Unique West Nile Virus Populations during Each Feeding EpisodeGrubaugh 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 2017, 19: 709-718. PMID: 28445723, PMCID: PMC5465957, DOI: 10.1016/j.celrep.2017.03.076.
• Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013–2016 EpidemicDiehl 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 2016, 167: 1088-1098.e6. PMID: 27814506, PMCID: PMC5115602, DOI: 10.1016/j.cell.2016.10.014.
• Transmission bottlenecks and RNAi collectively influence tick-borne flavivirus evolutionGrubaugh 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 2016, 2: vew033. PMID: 28058113, PMCID: PMC5210029, DOI: 10.1093/ve/vew033.
• Genetic Drift during Systemic Arbovirus Infection of Mosquito Vectors Leads to Decreased Relative Fitness during Host SwitchingGrubaugh 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 2016, 19: 481-492. PMID: 27049584, PMCID: PMC4833525, DOI: 10.1016/j.chom.2016.03.002.
• Isolation of a Novel Insect-Specific Flavivirus from Culiseta melanura in the Northeastern United StatesMisencik 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 2016, 16: 181-190. PMID: 26807512, PMCID: PMC4779966, DOI: 10.1089/vbz.2015.1889.
• Experimental Evolution of an RNA Virus in Wild Birds: Evidence for Host-Dependent Impacts on Population Structure and Competitive FitnessGrubaugh 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 2015, 11: e1004874. PMID: 25993022, PMCID: PMC4439088, DOI: 10.1371/journal.ppat.1004874.
• Xenosurveillance: A Novel Mosquito-Based Approach for Examining the Human-Pathogen LandscapeGrubaugh ND, Sharma S, Krajacich BJ, Fakoli LS, Bolay FK, Diclaro 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 2015, 9: e0003628. PMID: 25775236, PMCID: PMC4361501, DOI: 10.1371/journal.pntd.0003628.
• Detection and characterization of novel flaviviruses from Southeast Asia: their potential role in human healthLee J, Grubaugh N, Pisarcik S, McMenamy S, Barnes S, Kengluecha A, Jaichapor B, Ponlawat A, O’Guinn M. Detection and characterization of novel flaviviruses from Southeast Asia: their potential role in human health International Journal Of Infectious Diseases 2012, 16: e264. DOI: 10.1016/j.ijid.2012.05.911.