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2022

Worobey M, Levy JI, Serrano LM, Crits-Christoph A, Pekar JE, Goldstein SA, Rasmussen AL, Kraemer MUG, Newman C, Koopmans MPG, Suchard MA, Wertheim JO, Lemey P, Robertson DL, Garry RF, Holmes EC, Rambaut A, Andersen KG.
The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic.
Science. 2022 Jul 26:abp8715.  Epub ahead of print.

Pekar JE, Magee A, Parker E, Moshiri N, Izhikevich K, Havens JL, Gangavarapu K, Malpica Serrano LM, Crits-Christoph A, Matteson NL, Zeller M, Levy JI, Wang JC, Hughes S, Lee J, Park H, Park MS, Ching KZY, Lin RTP, Mat Isa MN, Noor YM, Vasylyeva TI, Garry RF, Holmes EC, Rambaut A, Suchard MA, Andersen KG, Worobey M, Wertheim JO.
The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2. Science. 2022 Jul 26:eabp8337. Epub ahead of print.

Hughes L, Gangavarapu K, Latif AA, Mullen J, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves C, Zaiets K, Cano M, Zhou J, Qian Z, Sattler R, Matteson N, Levy J, Lee R, Freitas L, Maurer-Stroh S, Suchard M, Wu C, Su A, Andersen K.
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.
Research square, [Preprint]. 2022 Jun 28:rs.3.rs-1723829.

Arizti-Sanz J, Bradley A, Zhang YB, Boehm CK, Freije CA, Grunberg ME, Kosoko-Thoroddsen TF, Welch NL, Pillai PP, Mantena S, Kim G, Uwanibe JN, John OG, Eromon PE, Kocher G, Gross R, Lee JS, Hensley LE, MacInnis BL, Johnson J, Springer M, Happi CT, Sabeti PC, Myhrvold C.
Simplified Cas13-based assays for the fast identification of SARS-CoV-2 and its variants. Nature biomedical engineering. 2022 May 30.  Epub ahead of print.

Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C.
Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants.
Nature Medicine,28(5):1083-1094.

Melnik LI, Garry RF.
Enterotoxigenic Escherichia coli Heat-Stable Toxin and Ebola Virus Delta Peptide: Similarities and Differences.
Pathogens, 11(2):170.

Siddle KJ, Krasilnikova LA, Moreno GK, Schaffner SF, Vostok J, Fitzgerald NA, Lemieux JE, Barkas N, Loreth C, Specht I, Tomkins-Tinch CH, Paull JS, Schaeffer B, Taylor BP, Loftness B, Johnson H, Schubert PL, Shephard HM, Doucette M, Fink T, Lang AS, Baez S, Beauchamp J, Hennigan S, Buzby E, Ash S, Brown J, Clancy S, Cofsky S, Gagne L, Hall J, Harrington R, Gionet GL, DeRuff KC, Vodzak ME, Adams GC, Dobbins ST, Slack SD, Reilly SK, Anderson LM, Cipicchio MC, DeFelice MT, Grimsby JL, Anderson SE, Blumenstiel BS, Meldrim JC, Rooke HM, Vicente G, Smith NL, Messer KS, Reagan FL, Mandese ZM, Lee MD, Ray MC, Fisher ME, Ulcena MA, Nolet CM, English SE, Larkin KL, Vernest K, Chaluvadi S, Arvidson D, Melchiono M, Covell T, Harik V, Brock-Fisher T, Dunn M, Kearns A, Hanage WP, Bernard C, Philippakis A, Lennon NJ, Gabriel SB, Gallagher GR, Smole S, Madoff LC, Brown CM, Park DJ, MacInnis BL, Sabeti PC.
Transmission from vaccinated individuals in a large SARS-CoV-2 Delta variant outbreak.
Cell, 185(3):485-492.e10

Lagerborg KA, Normandin E, Bauer MR, Adams G, Figueroa K, Loreth C, Gladden-Young A, Shaw BM, Pearlman LR, Berenzy D, Dewey HB, Kales S, Dobbins ST, Shenoy ES, Hooper D, Pierce VM, Zachary KC, Park DJ, MacInnis BL, Tewhey R, Lemieux JE, Sabeti PC, Reilly SK, Siddle KJ. Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows.
Nature Microbiology, 7(1):108-119.

Melnik LI, Guha S, Ghimire J, Smither AR, Beddingfield BJ, Hoffmann AR, Sun L, Ungerleider NA, Baddoo MC, Flemington EK, Gallaher WR, Wimley WC, Garry RF.
Ebola virus delta peptide is an enterotoxin
Cell Reports, 4;38(1):110172.

Kolls JK, Garry RF.
Role of the T cell vitamin D receptor in severe COVID-19
Nature Immunology, 23(1):5-6.

2021

Oluniyi PE, Ajogbasile F, Oguzie J, et al.
VGEA: an RNA viral assembly toolkit.
PeerJ. 2021;9:e12129.

Borrega R, Nelson DKS, Koval AP, Bond NG, Heinrich ML, Rowland MM, Lathigra R, Bush DJ, Aimukanova I, Phinney WN, Koval SA, Hoffmann AR, Smither AR, Bell-Kareem AR, Melnik LI, Genemaras KJ, Chao K, Snarski P, Melton AB, Harrell JE, Smira AA, Elliott DH, Rouelle JA, Sabino-Santos G Jr, Drouin AC, Momoh M, Sandi JD, Goba A, Samuels RJ, Kanneh L, Gbakie M, Branco ZL, Shaffer JG, Schieffelin JS, Robinson JE, Fusco DN, Sabeti PC, Andersen KG, Grant DS, Boisen ML, Branco LM, Garry RF.
Cross-Reactive Antibodies to SARS-CoV-2 and MERS-CoV in Pre-COVID-19 Blood Samples from Sierra Leoneans
Viruses. 2021 Nov 21;13(11):2325.

Beddingfield BJ, Hartnett JN, Wilson RB, Kulakosky PC, Andersen KG, Robles-Sikisaka R, Grubaugh ND, Aybar A, Nunez MZ, Fermin CD, Garry RF.
Zika Virus Non-Structural Protein 1 Antigen-Capture Immunoassay
Viruses. 2021 Sep 5;13(9):1771.

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 G Jr, 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. 2021 Sep 16;184(19):4939-4952.e15.

Holmes EC, Goldstein SA, Rasmussen AL, Robertson DL, Crits-Christoph A, Wertheim JO, Anthony SJ, Barclay WS, Boni MF, Doherty PC, Farrar J, Geoghegan JL, Jiang
The origins of SARS-CoV-2: A critical review
Cell. 2021 Sep 16;184(19):4848-4856.

Koch MR, Kanneh L, Wise PH, Kurina LM, Alhasan F, Garry RF, Schieffelin JS, Shaffer JG, Grant DS.
Health seeking behavior after the 2013-16 Ebola epidemic: Lassa fever as a metric of persistent changes in Kenema District, Sierra Leone
PLoS Neglected Tropical Diseases. 2021 Jul 14;15(7):e0009576.

Happi AN, Ogunsanya OA, Oguzie JU, Oluniyi PE, Olono AS, Heeney JL, Happi CT. Microbial metagenomic approach uncovers the first rabbit haemorrhagic disease virus genome in Sub-Saharan Africa. Scientific Reports.  2021 Jul 1;11(1):13689.

Gaye A, Ndiaye T, Sy M, Deme AB, Thiaw AB, Sene A, Ndiaye C, Diedhiou Y, Mbaye AM, Ndiaye I, Tomkins-Tinch C, Gomis JF, Badiane AS, MacInnis B, Park DJ, Ndiaye M, Sy N, Sabeti PC, Siddle KJ, Ndiaye D.
Genomic investigation of a dengue virus outbreak in Thiès, Senegal, in 2018.
Scientific Reports. 2021 May 14;11(1):10321.

Washington NL, Gangavarapu K, Zeller M, Bolze A, Cirulli ET, Schiabor Barrett KM, Larsen BB, Anderson C, White S, Cassens T, Jacobs S, Levan G, Nguyen J, Ramirez JM 3rd, Rivera-Garcia C, Sandoval E, Wang X, Wong D, Spencer E, Robles-Sikisaka R, Kurzban E, Hughes LD, Deng X, Wang C, Servellita V, Valentine H, De Hoff P, Seaver P, Sathe S, Gietzen K, Sickler B, Antico J, Hoon K, Liu J, Harding A, Bakhtar O, Basler T, Austin B, MacCannell D, Isaksson M, Febbo PG, Becker D, Laurent M, McDonald E, Yeo GW, Knight R, Laurent LC, de Feo E, Worobey M, Chiu CY, Suchard MA, Lu JT, Lee W, Andersen KG
Emergence and Rapid Transmission of SARS-CoV-2 B.1.1.7 in the United States
Cell [Epub ahead of print]

Landeras-Bueno S, Wasserman H, Oliveira G, VanAernum ZL, Busch F, Salie ZL, Wysocki VH, Andersen K, Saphire EO
Cellular mRNA Triggers Structural Transformation of Ebola virus Matrix Protein VP40 to Its Essential Regulatory Form
Cell Reports 35(2):108986

Gunn BM, Lu R, Slein MD, Ilinykh PA, Huang K, Atyeo C, Schendel SL, Kim J, Cain C, Roy V, Suscovich TJ, Takada A, Halfmann PJ, Kawaoka Y, Pauthner MG, Momoh M, Goba A, Kanneh L, Andersen KG, Schieffelin JS, Grant D, Garry RF, Saphire EO, Bukreyev A, Alter G
A Fc Engineering Approach to Define Functional Humoral Correlates of Immunity Against Ebola virus
Immunity 54(4):815-828.e5

Kinganda-Lusamaki E, Black A, Mukadi DB, Hadfield J, Mbala-Kingebeni P, Pratt CB, Aziza A, Diagne MM, White B, Bisento N, Nsunda B, Akonga M, Faye M, Faye O, Edidi-Atani F, Matondo-Kuamfumu M, Mambu-Mbika F, Bulabula J, Di Paola N, Pauthner MG, Andersen KG, Palacios G, Delaporte E, Sall AA, Peeters M, Wiley MR, Ahuka-Mundeke S, Bedford T, Tamfum JM
Integration of Genomic Sequencing Into the Response to the Ebola virus Outbreak in Nord Kivu, Democratic Republic of the Congo
Nature Medicine 27(4):710-716

Shaffer JG, Schieffelin JS, Momoh M, Goba A, Kanneh L, Alhasan F, Gbakie M, Engel EJ, Bond NG, Hartnett JN, Nelson DKS, Bush DJ, Boisen ML, Heinrich ML, Rowland MM, Branco LM, Samuels RJ, Garry RF, Grant DS, The Viral Hemorrhagic Fever Consortium
Space-Time Trends in Lassa Fever in Sierra Leone by ELISA Serostatus, 2012-2019
Microorganisms 9(3):586

Bond NG, Grant DS, Himmelfarb ST, Engel EJ, Al-Hasan F, Gbakie M, Kamara F, Kanneh L, Mustapha I, Okoli A, Fischer W, Wohl D, Garry RF, Samuels R, Shaffer JG, Schieffelin JS
Post-Ebola Syndrome Presents With Multiple Overlapping Symptom Clusters: Evidence From an Ongoing Cohort Study in Eastern Sierra Leone
Clinical Infectious Diseases [Epub ahead of print]

Mbala-Kingebeni P, Pratt C, Mutafali-Ruffin M, Pauthner MG, Bile F, Nkuba-Ndaye A, Black A, Kinganda-Lusamaki E, Faye M, Aziza A, Diagne MM, Mukadi D, White B, Hadfield J, Gangavarapu K, Bisento N, Kazadi D, Nsunda B, Akonga M, Tshiani O, Misasi J, Ploquin A, Epaso V, Sana-Paka E, N’kasar YTT, Mambu F, Edidi F, Matondo M, Bula Bula J, Diallo B, Keita M, Belizaire MRD, Fall IS, Yam A, Mulangu S, Rimion AW, Salfati E, Torkamani A, Suchard MA, Crozier I, Hensley L, Rambaut A, Faye O, Sall A, Sullivan NJ, Bedford T, Andersen KG, Wiley MR, Ahuka-Mundeke S, Muyembe Tamfum JJ
Ebola Virus Transmission Initiated by Relapse of Systemic Ebola Virus Disease
The New England Journal of Medicine 384(13):1240-1247

Happi AN, Ugwu CA, Happi CT
Tracking the Emergence of New SARS-CoV-2 Variants in South Africa
Nature Medicine 27(3):372-373

Botti-Lodovico Y, Rosenberg E, Sabeti PC
Testing in a Pandemic – Improving Access, Coordination, and Prioritization
New England Journal of Medicine 21;384(3):197-199

Mina MJ, Andersen KG
COVID-19 Testing: One Size Does Not Fit All
Science 371(6525):126-127

Smither AR, Bell-Kareem AR.
Ecology of Lassa Virus.
Current Topics in Microbiology and Immunology. [Epub ahead of print]

Olagunju A, Fowotade A, Olagunoye A, Ojo TO, Adefuye BO, Fagbamigbe AF, Adebiyi AO, Olagunju OI, Ladipo OT, Akinloye A, Adeagbo BA, Onayade A, Bolaji OO, Happi C, Rannard S, Owen A.
Efficacy and safety of nitazoxanide plus atazanavir/ritonavir for the treatment of moderate to severe COVID-19 (NACOVID): A structured summary of a study protocol for a randomised controlled trial.
Trials, 22(1):3.

2020

Arizti-Sanz J, Freije CA, Stanton AC, Petros BA, Boehm CK, Siddiqui S, Shaw BM, Adams G, Kosoko-Thoroddsen TF, Kemball ME, Uwanibe JN, Ajogbasile FV, Eromon PE, Gross R, Wronka L, Caviness K, Hensley LE, Bergman NH, MacInnis BL, Happi CT, Lemieux JE, Sabeti PC, Myhrvold C.
Streamlined inactivation, amplification, and Cas13-based detection of SARS-CoV-2. Nature communications, 11(1), 5921.

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(1), 5620.

Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O’Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA.
Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2.
Nature Communications,11(1):5110.

Tessema SK, Inzaule SC, Christoffels A, Kebede Y, de Oliveira T, Ouma AEO, Happi CT, Nkengasong JN.
Accelerating genomics-based surveillance for COVID-19 response in Africa
Lancet Microbe, 1(6):e227-e228.

Heinrich ML, Boisen ML, Nelson DKS, Bush DJ, Cross RW, Koval AP, Hoffmann AR, Beddingfield BJ, Hastie KM, Rowland MM, Aimukanova I, Koval S, Lathigra R, Borisevich V, Momoh M, Sandi JD, Goba A, Odia L, Baimba F, Aiyepada JO, Ebo B, Eromon P, Ugwu C, Folarin O, Olumade T, Onyechi MN, Etafo J, Adeyemi R, Ella EE, Aminu M, Gomerep SS, Eke MA, Ogunsanya O, Akpede GO, Asogun DO, Okogbenin SA, Okokhere PO, Holst J, Shaffer JG, Schieffelin JS, Geisbert TW, Saphire EO, Happi CT, Grant DS, Garry RF, Branco LM.
Antibodies from Sierra Leonean and Nigerian Lassa fever survivors cross-react with recombinant proteins representing Lassa viruses of divergent lineages.
Scientific Reports,10(1):16030.

Anahtar MN, Shaw B, Slater D, Byrne EH, Botti-Lodovico Y, Adams G, Schaffner SF, Eversley JS, McGrath G, Gogakos T, Lennerz J, Marble HD, Ritterhouse LL, Batten J, Georgantas NZ, Pellerin R, Signorelli S, Thierauf J, Kemball M, Happi C, Grant DS, Ndiaye D, Siddle KJ, Mehta SB, Harris JB, Ryan ET, Pierce VM, LaRocque RC, Lemieux J, Sabeti P, Rosenberg E, Branda J, Turbett SE.
Development of a qualitative real-time RT-PCR assay for the detection of SARS-CoV-2: A guide and case study in setting up an emergency-use, laboratory-developed molecular assay.
MedRxiv [Epub ahead of print]

Barnes KG, Lachenauer AE, Nitido A, Siddiqui S, Gross R, Beitzel B, Siddle KJ, Freije CA, Dighero-Kemp B, Mehta SB, Carter A, Uwanibe J, Ajogbasile F, Olumade T, Odia I, Sandi JD, Momoh M, Metsky HC, Boehm CK, Lin AE, Kemball M, Park DJ, Branco L, Boisen M, Sullivan B, Amare MF, Tiamiyu AB, Parker ZF, Iroezindu M, Grant DS, Modjarrad K, Myhrvold C, Garry RF, Palacios G, Hensley LE, Schaffner SF, Happi CT, Colubri A, Sabeti PC.
Deployable CRISPR-Cas13a diagnostic tools to detect and report Ebola and Lassa virus cases in realtime.
Nature Communications,11(1):4131.

Blanton RE, Mock NB, Hiruy HN, Schieffelin JS, Doumbia S, Happi C, Samuels RJ, Oberhelman RA.
African Resources and the Promise of Resilience against COVID-19.
American Journal of Tropical Medicine,103(2):539-541.

Deng X, Gu W, Federman S, du Plessis L, Pybus OG, Faria NR, Wang C, Yu G, Bushnell B, Pan CY, Guevara H, Sotomayor-Gonzalez A, Zorn K, Gopez A, Servellita V, Hsu E, Miller S, Bedford T, Greninger AL, Roychoudhury P, Starita LM, Famulare M, Chu HY, Shendure J, Jerome KR, Anderson C, Gangavarapu K, Zeller M, Spencer E, Andersen KG, MacCannell D, Paden CR, Li Y, Zhang J, Tong S, Armstrong G, Morrow S, Willis M, Matyas BT, Mase S, Kasirye O, Park M, Masinde G, Chan C, Yu AT, Chai SJ, Villarino E, Bonin B, Wadford DA, Chiu CY.
Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
Science, 369(6503):582-587.

Garry RF.
50 Years of Lassa Fever Research.
Current Topics in Microbiology and Immunology, [Epub ahead of print]

Boisen ML, Uyigue E, Aiyepada J, Siddle KJ, Oestereich L, Nelson DKS, Bush DJ, Rowland MM, Heinrich ML, Eromon P, Kayode AT, Odia I, Adomeh DI, Muoebonam EB, Akhilomen P, Okonofua G, Osiemi B, Omoregie O, Airende M, Agbukor J, Ehikhametalor S, Aire CO, Duraffour S, Pahlmann M, Böhm W, Barnes KG, Mehta S, Momoh M, Sandi JD, Goba A, Folarin OA, Ogbaini-Emovan E, Asogun DA, Tobin EA, Akpede GO, Okogbenin SA, Okokhere PO, Grant DS, Schieffelin JS, Sabeti PC, Günther S, Happi CT, Branco LM, Garry RF.
Field evaluation of a Pan-Lassa rapid diagnostic test during the 2018 Nigerian Lassa fever outbreak.
Scientific Reports, 10(1):8724.

Olawoye IB, Frost SDW, Happi CT.
The Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake.
PeerJ, 8:e10121.