Purushotham JN, Lutz HL, Parker E, Andersen KG.
Immunological drivers of zoonotic virus emergence, evolution, and endemicity.
Immunity. 2025 Apr 8;58(4):784-796.

Stachler E, Gnirke A, McMahon K, Gomez M, Stenson L, Guevara-Reyes C, Knoll H, Hill T, Hill S, Messer KS, Arizti-Sanz J, Albeez F, Curtis E, Samani P, Wewior N, O’Connor DH, Vuyk W, Khoury SE, Schnizlein MK, Rockey NC, Broemmel Z, Mina M, Madoff LC, Wohl S, O’Connor L, Brown CM, Ozonoff A, Park DJ, MacInnis BL, Sabeti PC.
Establishing Methods to Monitor Influenza (A)H5N1 Virus in Dairy Cattle Milk, Massachusetts, USA.
Emerging Infectious Diseases. 2025 May;31(13):70-75.

Crits-Christoph A, Levy JI, Pekar JE, Goldstein SA, Singh R, Hensel Z, Gangavarapu K, Rogers MB, Moshiri N, Garry RF, Holmes EC, Koopmans MPG, Lemey P, Peacock TP, Popescu S, Rambaut A, Robertson DL, Suchard MA, Wertheim JO, Rasmussen AL, Andersen KG, Worobey M, Débarre F
Genetic Tracing of Market Wildlife and Viruses at the Epicenter of the COVID-19 Pandemic
Cell 187(19):5468-5482

Krasilnikova LA, Tomkins-Tinch CH, Gayton AC, Schaffner SF, Dobbins ST, Gladden-Young A, Siddle KJ, Park DJ, Sabeti PC.
Polyphonia: detecting inter-sample contamination in viral genomic sequencing data.
Bioinformatics. 2024 Nov 28;40(12):btae698.

Mantena S, Pillai PP, Petros BA, Welch NL, Myhrvold C, Sabeti PC, Metsky HC.
Model-directed generation of artificial CRISPR-Cas13a guide RNA sequences improves nucleic acid detection.
Nature Biotechnology. 2024 Oct 11.

Carr CR, Crawford KHD, Murphy M, Galloway JG, Haddox HK, Matsen FA 4th, Andersen KG, King NP, Bloom JD
Deep Mutational Scanning Reveals Functional Constraints and Antibody-Escape Potential of Lassa virus Glycoprotein Complex
Immunity 57(9):2061-2076

Bond NG, Shore KR, Engel EJ, Coonan EE, Al-Hasan F, Gbakie MA, Kamara FK, Kanneh L, Momoh M, Kanneh IM, Sandi JD, Elliott D, Ficenec SC, Smira AR, Fischer WA, Wohl DA, Robinson JE, Shaffer JG, Garry RF, Samuels RJ, Grant DS, Schieffelin JS.
Ebola Virus-Specific Neutralizing Antibody Persists at High Levels in Survivors 2 Years After Resolution of Disease in a Sierra Leonean Cohort.
Journal of Infectious Diseases. 2024 Oct 16;230(4):e929-e937.

Paull JS, Petros BA, Brock-Fisher TM, Jalbert SA, Selser VM, Messer KS, Dobbins ST, DeRuff KC, Deng D, Springer M, Sabeti PC.
Optimisation and evaluation of viral genomic sequencing of SARS-CoV-2 rapid diagnostic tests: a laboratory and cohort-based study.
Lancet Microbe. 2024 May;5(5):e468-e477.

Sandi JD, Levy JI, Tapela K, Zeller M, Yeboah JA, Saka DF, Grant DS, Awandare GA, Quashie PK, Andersen KG, Paemka L
Upper Airway Epithelial Tissue Transcriptome Analysis Reveals Immune Signatures Associated with COVID-19 Severity in GhanaiansJournal of Immunology Research 2024:6668017.

Kotliar D, Raju S, Tabrizi S, Odia I, Goba A, Momoh M, Sandi JD, Nair P, Phelan E, Tariyal R, Eromon PE, Mehta S, Robles-Sikisaka R, Siddle KJ, Stremlau M, Jalloh S, Gire SK, Winnicki S, Chak B, Schaffner SF, Pauthner M, Karlsson EK, Chapin SR, Kennedy SG, Branco LM, Kanneh L, Vitti JJ, Broodie N, Gladden-Young A, Omoniwa O, Jiang PP, Yozwiak N, Heuklom S, Moses LM, Akpede GO, Asogun DA, Rubins K, Kales S, Happi AN, Iruolagbe CO, Dic-Ijiewere M, Iraoyah K, Osazuwa OO, Okonkwo AK, Kunz S, McCormick JB, Khan SH, Honko AN, Lander ES, Oldstone MBA, Hensley L, Folarin OA, Okogbenin SA, Günther S, Ollila HM, Tewhey R, Okokhere PO, Schieffelin JS, Andersen KG, Reilly SK, Grant DS, Garry RF, Barnes KG, Happi CT, Sabeti PC
Genome-wide Association Study Identifies Human Genetic Variants Associated with Fatal Outcome from Lassa fever
Nature Microbiology 9(3):751-762

Onoja BA, Oguzie JU, George UE, Asoh KE, Ajayi P, Omofaye TF, Igeleke IO, Eromon P, Harouna S, Parker E, Adeniji AJ, Happi CT
Whole genome sequencing unravels cryptic circulation of divergent dengue virus lineages in the rainforest region of Nigeria
Emerg Microbes Infect 13(1):2307511

Levine ZC, Sene A, Mkandawire W, Deme AB, Ndiaye T, Sy M, Gaye A, Diedhiou Y, Mbaye AM, Ndiaye IM, Gomis J, Ndiop M, Sene D, Faye Paye M, MacInnis BL, Schaffner SF, Park DJ, Badiane AS, Colubri A, Ndiaye M, Sy N, Sabeti PC, Ndiaye D, Siddle KJ
Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing
Nature Communications 15(1):747

Barnes KG, Levy JI, Gauld J, Rigby J, Kanjerwa O, Uzzell CB, Chilupsya C, Anscombe C, Tomkins-Tinch C, Mbeti O, Cairns E, Thole H, McSweeney S, Chibwana MG, Ashton PM, Jere KC, Meschke JS, Diggle P, Cornick J, Chilima B, Jambo K, Andersen KG, Kawalazira G, Paterson S, Nyirenda TS, Feasey N
Utilizing River and Wastewater as a SARS-CoV-2 Surveillance Tool in Settings with Limited Formal Sewage Systems
Nature Communications 14(1):7883

Hastie KM, Melnik LI, Cross RW, Klitting RM, Andersen KG, Saphire EO, Garry RF
The Arenaviridae Family: Knowledge Gaps, Animal Models, Countermeasures, and Prototype Pathogens
The Journal of Infectious Diseases 228(Supplement_6):S359-S375

George U, George O, Oguzie J, Osasona O, Motayo B, Kamani J, Eromon P, Folarin O, Happi A, Komolafe I, Happi C.
Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria.
Virus Research. 334:199174.

Lemieux JE, Huang W, Hill N, Cerar T, Freimark L, Hernandez S, Luban M, Maraspin V, Bogovič P, Ogrinc K, Ruzič-Sabljič E, Lapierre P, Lasek-Nesselquist E, Singh N, Iyer R, Liveris D, Reed KD, Leong JM, Branda JA, Steere AC, Wormser GP, Strle F, Sabeti PC, Schwartz I, Strle K.
Whole genome sequencing of human Borrelia burgdorferi isolates reveals linked blocks of accessory genome elements located on plasmids and associated with human dissemination.
PLoS Pathogens. 19(8):e1011243.

Cross RW, Heinrich ML, Fenton KA, Borisevich V, Agans KN, Prasad AN, Woolsey C, Deer DJ, Dobias NS, Rowland MM, Lathigra R, Borrega R, Geisbert JB, Garry RF, Branco LM, Geisbert TW
A human monoclonal antibody combination rescues nonhuman primates from advanced disease caused by the major lineages of Lassa virus
Proceedings of the National Academy of Sciences U S A. 120(34)

Oguzie JU, Petros BA, Oluniyi PE, Mehta SB, Eromon PE, Nair P, Adewale-Fasoro O, Ifoga PD, Odia I, Pastusiak A, Gbemisola OS, Aiyepada JO, Uyigue EA, Edamhande AP, Blessing O, Airende M, Tomkins-Tinch C, Qu J, Stenson L, Schaffner SF, Oyejide N, Ajayi NA, Ojide K, Ogah O, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Okogbenin S, Okokhere PO, Park DJ, Folarin OA, Komolafe I, Ihekweazu C, Frost SDW, Jackson EK, Siddle KJ, Sabeti PC, Happi CT
Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria
Nature Communications 14(1):4693

Pandit JA, Radin JM, Chiang DC, Spencer EG, Pawelek JB, Diwan M, Roumani L, Mina MJ.
The Coronavirus Disease 2019 Rebound Study: A Prospective Cohort Study to Evaluate Viral and Symptom Rebound Differences in Participants Treated With Nirmatrelvir Plus Ritonavir Versus Untreated Controls.
Clinical Infectious Diseases 77(1):25-31.

Libuit KG, Doughty EL, Otieno JR, Ambrosio F, Kapsak CJ, Smith EA, Wright SM, Scribner MR, Petit Iii RA, Mendes CI, Huergo M, Legacki G, Loreth C, Park DJ, Sevinsky JR.
Accelerating bioinformatics implementation in public health.
Microbial Genomics 9(7):mgen001051.

Happi AN, Ayinla AO, Ogunsanya OA, Sijuwola AE, Saibu FM, Akano K, George UE, Sopeju AE, Rabinowitz PM, Ojo KK, Barrett LK, Van Voorhis WC, Happi CT.
Detection of SARS-CoV-2 in Terrestrial Animals in Southern Nigeria: Potential Cases of Reverse Zoonosis.
Viruses 15(5):1187.

Gangavarapu K, Latif AA, Mullen JL, Alkuzweny M, Hufbauer E, Tsueng G, Haag E, Zeller M, Aceves CM, Zaiets K, Cano M, Zhou X, Qian Z, Sattler R, Matteson NL, Levy JI, Lee RTC, Freitas L, Maurer-Stroh S; GISAID Core and Curation Team; Suchard MA, Wu C, Su AI, Andersen KG, Hughes LD.
Outbreak.info genomic reports: scalable and dynamic surveillance of SARS-CoV-2 variants and mutations.
Nature Methods. 20(4):512-522

Oluniyi PE, Oguzie JU, Uwanibe JN, Kayode TA, Olumade TJ, Ajogbasile FV, Parker E, Eromon PE, Abechi P, Sobajo TA, Ugwu CA, George UE, Ayoade F, Akano K, Oyejide NE, Nosamiefan I, Fred-Akintunwa I, Adedotun-Sulaiman K, Brimmo FB, Adegboyega BB, Philip C, Adeleke RA, Chukwu GC, Ahmed MI, Ope-Ewe OO, Otitoola SG, Ogunsanya OA, Saibu MF, Sijuwola AE, Ezekiel GO, John OG, Akin-John JO, Akinlo OO, Fayemi OO, Ipaye TO, Nwodo DC, Omoniyi AE, Omwanghe IB, Terkuma CA, Okolie J, Ayo-Ale O, Ikponmwosa O, Benevolence E, Naregose GO, Patience AE, Blessing O, Micheal A, Jacqueline A, Aiyepada JO, Ebhodaghe P, Racheal O, Rita E, Rosemary GE, Solomon E, Anieno E, Edna Y, Chris AO, Donatus AI, Ogbaini-Emovon E, Tatfeng MY, Omunakwe HE, Bob-Manuel M, Ahmed RA, Onwuamah CK, Shaibu JO, Okwuraiwe A, Ataga AE, Bock-Oruma A, Daramola F, Yusuf IF, Fajola A, Ntia NA, Ekpo JJ, Moses AE, Moore-Igwe BW, Fakayode OE, Akinola M, Kida IM, Oderinde BS, Wudiri ZW, Adeyemi OO, Akanbi OA, Ahumibe A, Akinpelu A, Ayansola O, Babatunde O, Omoare AA, Chukwu C, Mba NG, Omoruyi EC, Olisa O, Akande OK, Nwafor IE, Ekeh MA, Ndoma E, Ewah RL, Duruihuoma RO, Abu A, Odeh E, Onyia V, Ojide CK, Okoro S, Igwe D, Ogah EO, Khan K, Ajayi NA, Ugwu CN, Ukwaja KN, Ugwu NI, Abejegah C, Adedosu N, Ayodeji O, Liasu AA, Isamotu RO, Gadzama G, Petros BA, Siddle KJ, Schaffner SF, Akpede G, Erameh CO, Baba MM, Oladiji F, Audu R, Ndodo N, Fowotade A, Okogbenin S, Okokhere PO, Park DJ, Mcannis BL, Adetifa IM, Ihekweazu C, Salako BL, Tomori O, Happi AN, Folarin OA, Andersen KG, Sabeti PC, Happi CT
Emergence and Spread of Two SARS-CoV-2 Variants of Interest in Nigeria
Nature Communications 14(1):811

Garry RF
Lassa fever – the road ahead
Nature Reviews. Microbiology. 21(2):87-96

Levy JI, Andersen KG, Knight R, Karthikeyan S
Wastewater Surveillance for Public Health
Science. 379(6627):26-27

Grant DS, Engel EJ, Roberts Yerkes N, Kanneh L, Koninga J, Gbakie MA, Alhasan F, Kanneh FB, Kanneh IM, Kamara FK, Momoh M, Yillah MS, Foday M, Okoli A, Zeoli A, Weldon C, Bishop CM, Zheng C, Hartnett J, Chao K, Shore K, Melnik LI, Mucci M, Bond NG, Doyle P, Yenni R, Podgorski R, Ficenec SC, Moses L, Shaffer JG, Garry RF, Schieffelin JS
Seroprevalence of anti-Lassa Virus IgG antibodies in three districts of Sierra Leone: A cross-sectional, population-based study
PLoS Neglected Tropical Diseases. 17(2):e0010938

Vasylyeva TI, Fang CE, Su M, Havens JL, Parker E, Wang JC, Zeller M, Yakovleva A, Hassler GW, Chowdhury MA, Andersen KG, Hughes S, Wertheim JO.
Introduction and Establishment of SARS-CoV-2 Gamma Variant in New York City in Early 2021.
Journal Infectious Diseases. 226(12):2142-2149.

Petros BA, Paull JS, Tomkins-Tinch CH, Loftness BC, DeRuff KC, Nair P, Gionet GL, Benz A, Brock-Fisher T, Hughes M, Yurkovetskiy L, Mulaudzi S, Leenerman E, Nyalile T, Moreno GK, Specht I, Sani K, Adams G, Babet SV, Baron E, Blank JT, Boehm C, Botti-Lodovico Y, Brown J, Buisker AR, Burcham T, Chylek L, Cronan P, Dauphin A, Desreumaux V, Doss M, Flynn B, Gladden-Young A, Glennon O, Harmon HD, Hook TV, Kary A, King C, Loreth C, Marrs L, McQuade KJ, Milton TT, Mulford JM, Oba K, Pearlman L, Schifferli M, Schmidt MJ, Tandus GM, Tyler A, Vodzak ME, Krohn Bevill K, Colubri A, MacInnis BL, Ozsoy AZ, Parrie E, Sholtes K, Siddle KJ, Fry B, Luban J, Park DJ, Marshall J, Bronson A, Schaffner SF, Sabeti PC.
Multimodal surveillance of SARS-CoV-2 at a university enables development of a robust outbreak response framework..
Med (New York, N.Y.) 3(12):883-900.e13

Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri AN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang’a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Muhammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JC, Tamfum JM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O’Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR; Africa Pathogen Genomics Initiative (Africa PGI)‡, Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, Wilkinson E.
The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.
Science. 378(6615):eabq5358

Garry RF.
SARS-CoV-2 furin cleavage site was not engineered.
Proceedings of the National Academy of Sciences of the United States of America. 119(40):e2211107119

Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R.
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission
Nature. 609(7925):101-108

Klitting R, Kafetzopoulou LE, Thiery W, Dudas G, Gryseels S, Kotamarthi A, Vrancken B, Gangavarapu K, Momoh M, Sandi JD, Goba A, Alhasan F, Grant DS, Okogbenin S, Ogbaini-Emovo E, Garry RF, Smither AR, Zeller M, Pauthner MG, McGraw M, Hughes LD, Duraffour S, Günther S, Suchard MA, Lemey P, Andersen KG, Dellicour S.
Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades.
Nature Communications. 13(1):5596

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. 377(6609):951-959

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. 377(6609):951-959

Parker E, Anderson C, Zeller M, Tibi A, Havens JL, Laroche G, Benlarbi M, Ariana A, Robles-Sikisaka R, Latif AA, Watts A, Awidi A, Jaradat SA, Gangavarapu K, Ramesh K, Kurzban E, Matteson NL, Han AX, Hughes LD, McGraw M, Spencer E, Nicholson L, Khan K, Suchard MA, Wertheim JO, Wohl S, Côté M, Abdelnour A, Andersen KG, Abu-Dayyeh I.
Regional connectivity drove bidirectional transmission of SARS-CoV-2 in the Middle East during travel restrictions.
Nature Communications. 13(1):4784

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. 6(8):932-943

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.

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.

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

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. 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.

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 184(10):2587-2594

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 73(6):1046-1054

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 440:67-86.

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.

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.

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 440:1-22.

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.