Publications

Casto AM; Song H; Xie H; Selke S; Roychoudhury P; Wu MC; Wald A; Greninger AL; Johnston C, 2024. Viral genomic variation and the severity of genital HSV-2 infection as quantified by shedding rate: a viral genome-wide association study. J Infect Dis.

Rasmussen AL; Gronvall GK; Lowen AC; Goodrum F; Alwine J; Andersen KG; Anthony SJ; Baines J; Banerjee A; Broadbent AJ; Brooke CB; Campos SK; Caposio P; Casadevall A; Chan GC; Cliffe AR; Collins-McMillen D; Connell N; Damania B; Daugherty MD; Debbink K; Dermody TS; DiMaio D; Duprex WP; Emerman M; Galloway DA; Garry RF; Goldstein SA; Greninger AL; Hartman AL; Hogue BG; Horner SM; Hotez PJ; Jung JU; Kamil JP; Karst SM; Laimins L; Lakdawala SS; Landais I; Letko M; Lindenbach B; Liu S-L; Luftig M; McFadden G; Mehle A; Morrison J; Moscona A; Mühlberger E; Munger J; Münger K; Murphy E; Neufeldt CJ; Nikolich JZ; O'Connor CM; Pekosz A; Permar SR; Pfeiffer JK; Popescu SV; Purdy JG; Racaniello VR; Rice CM; Runstadler JA; Sapp MJ; Scott RS; Smith GA; Sorrell EM; Speranza E; Streblow D; Tibbetts SA; Toth Z; Van Doorslaer K; Weiss SR; White EA; White TM; Wobus CE; Worobey M; Yamaoka S; Yurochko A, 2024. Correction for Rasmussen et al., "Virology-the path forward". J Virol 98(3):e0007424

Lieberman NAP; Avendaño CC; Bakhash SAKM; Nunley E; Xie H; Giacani L; Berzkalns A; Soge OO; Reid TB; Golden MR; Greninger AL, 2024. Genomic Epidemiology of Treponema pallidum and Circulation of Strains With Diminished tprK Antigen Variation Capability in Seattle, 2021-2022. J Infect Dis 229(3):866-875

Makhsous N; Goya S; Avendaño CC; Rupp J; Kuypers J; Jerome KR; Boeckh M; Waghmare A; Greninger AL, 2024. Within-Host Rhinovirus Evolution in Upper and Lower Respiratory Tract Highlights Capsid Variability and Mutation-Independent Compartmentalization. J Infect Dis 229(2):403-412

Ford ES; Mayer-Blackwell K; Jing L; Laing KJ; Sholukh AM; St Germain R; Bossard EL; Xie H; Pulliam TH; Jani S; Selke S; Burrow CJ; McClurkan CL; Wald A; Greninger AL; Holbrook MR; Eaton B; Eudy E; Murphy M; Postnikova E; Robins HS; Elyanow R; Gittelman RM; Ecsedi M; Wilcox E; Chapuis AG; Fiore-Gartland A; Koelle DM, 2024. Repeated mRNA vaccination sequentially boosts SARS-CoV-2-specific CD8(+) T cells in persons with previous COVID-19. Nat Immunol 25(1):166-177

Reed J; Kwak G; Piliper EA; Degli-Angeli EJ; Goecker EA; Greninger AL, 2024. Validation of digital droplet PCR assays for cell-associated HIV-1 DNA, HIV-1 2-LTR circle, and HIV-1 unspliced RNA for clinical studies in HIV-1 cure research. J Clin Virol 170:105632

Powell EA; Greninger AL; Marlowe EM; Naccache SN; Doern CD, 2024. Proceedings of the Clinical Microbiology Open 2023: discussions about pandemic preparedness. J Clin Microbiol.

Ubals M; Nadal-Baron P; Arando M; Rivero Á; Mendoza A; Descalzo Jorro V; Ouchi D; Pérez-Mañá C; Álvarez M; Alemany A; Hoyos-Mallecot Y; Nunley E; Lieberman NAP; Greninger AL; Galván-Casas C; Suñer C; G-Beiras C; Paredes R; Rodríguez-Gascón A; Canut A; García-Patos V; Farré M; Marks M; Giacani L; Vall-Mayans M; Mitjà O, 2024. Oral linezolid compared with benzathine penicillin G for treatment of early syphilis in adults (Trep-AB Study) in Spain: a prospective, open-label, non-inferiority, randomised controlled trial. Lancet Infect Dis 24(4):404-416

Kachikis A; Pike M; Eckert LO; Roberts E; Frank Y; Young AL; Goecker E; Gravett MG; Greninger AL; Englund JA, 2024. Timing of Maternal COVID-19 Vaccine and Antibody Concentrations in Infants Born Preterm. JAMA Netw Open 7(1):e2352387

LaCourse SM; Wetzler EA; Aurelio MC; Escudero JN; Selke SS; Greninger AL; Goecker EA; Barnes SR; Arnould IS; Pérez-Osorio AC; Richardson BA; Kachikis A; Englund JA; Drake AL, 2024. Hybrid Immunity to Severe Acute Respiratory Syndrome Coronavirus 2 During Pregnancy Provides More Durable Infant Antibody Responses Compared to Natural Infection or Vaccination Alone. J Infect Dis 229(4):1241-1243

Golden MR; Soge OO; Mills M; Berzkalns A; Cannon C; Ramchandani M; Dombrowski JC; Karmarkar EN; Chow EJ; Gov JP; Swenson P; Greninger AL, 2024. Asymptomatic and Subclinical Mpox: An Association With Modified Vaccinia Ankara Vaccine. Sex Transm Dis 51(5):342-347

Cox RM; Wolf JD; Lieberman NA; Lieber CM; Kang HJ; Sticher ZM; Yoon JJ; Andrews MK; Govindarajan M; Krueger RE; Sobolik EB; Natchus MG; Gewirtz AT; deSwart RL; Kolykhalov AA; Hekmatyar K; Sakamoto K; Greninger AL; Plemper RK, 2024. Therapeutic mitigation of measles-like immune amnesia and exacerbated disease after prior respiratory virus infections in ferrets. Nat Commun 15(1):1189

Lieber CM; Kang HJ; Aggarwal M; Lieberman NA; Sobolik EB; Yoon JJ; Natchus MG; Cox RM; Greninger AL; Plemper RK, 2024. Influenza A virus resistance to 4'-fluorouridine coincides with viral attenuation in vitro and in vivo. PLoS Pathog 20(2):e1011993

Babu TM; Shen X; McClelland RS; Wang Z; Selke S; Wilkens C; Hauge KA; McClurkan CL; Goecker E; Laing KJ; Koelle DM; Greninger AL; Nussenzweig MC; Montefiori DC; Corey L; Wald A, 2024. Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Subvariant Neutralization Following a Primary Vaccine Series of NVX-CoV2373 and BNT162b2 Monovalent Booster Vaccine. Open Forum Infect Dis 11(2):ofad673

Boonyaratanakornkit J; Wang Q; Nader A; Kimball L; Stevens-Ayers T; Levkova M; Blazevic R; Nguyen J; Wright J; Castor J; Greninger AL; Ford E; Mielcarek M; Fordred S; Han J; Boeckh M; Waghmare A, 2024. The effect of gastrointestinal graft-versus-host disease and diarrhea on the pharmacokinetic profile of sotrovimab in hematopoietic stem cell transplant recipients. J Infect Dis.

Reid TB; Godornes C; Campbell VL; Laing KJ; Tantalo LC; Gomez A; Pholsena TN; Lieberman NAP; Krause TM; Cegielski VI; Culver LA; Nguyen N; Tong DQ; Hawley KL; Greninger AL; Giacani L; Cameron CE; Dombrowski JC; Wald A; Koelle DM, 2024. Treponema pallidum periplasmic and membrane proteins are recognized by circulating and skin CD4+ T cells. bioRxiv.

Magaret CA; Li L; deCamp AC; Rolland M; Juraska M; Williamson BD; Ludwig J; Molitor C; Benkeser D; Luedtke A; Simpkins B; Heng F; Sun Y; Carpp LN; Bai H; Dearlove BL; Giorgi EE; Jongeneelen M; Brandenburg B; McCallum M; Bowen JE; Veesler D; Sadoff J; Gray GE; Roels S; Vandebosch A; Stieh DJ; Le Gars M; Vingerhoets J; Grinsztejn B; Goepfert PA; de Sousa LP; Silva MST; Casapia M; Losso MH; Little SJ; Gaur A; Bekker LG; Garrett N; Truyers C; Van Dromme I; Swann E; Marovich MA; Follmann D; Neuzil KM; Corey L; Greninger AL; Roychoudhury P; Hyrien O; Gilbert PB, 2024. Quantifying how single dose Ad26.COV2.S vaccine efficacy depends on Spike sequence features. Nat Commun 15(1):2175

Paredes MI; Perofsky AC; Frisbie L; Moncla LH; Roychoudhury P; Xie H; Bakhash SAM; Kong K; Arnould I; Nguyen TV; Wendm ST; Hajian P; Ellis S; Mathias PC; Greninger AL; Starita LM; Frazar CD; Ryke E; Zhong W; Gamboa L; Threlkeld M; Lee J; Stone J; McDermot E; Truong M; Shendure J; Oltean HN; Viboud C; Chu H; Müller NF; Bedford T, 2024. Local-scale phylodynamics reveal differential community impact of SARS-CoV-2 in a metropolitan US county. PLoS Pathog 20(3):e1012117

Kubinski HC; Despres HW; Johnson BA; Schmidt MM; Jaffrani SA; Mills MG; Lokugamage K; Dumas CM; Shirley DJ; Estes LK; Pekosz A; Crothers JW; Roychoudhury P; Greninger AL; Jerome KR; Di Genova BM; Walker DH; Ballif BA; Ladinsky MS; Bjorkman PJ; Menachery VD; Bruce EA, 2024. Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation. bioRxiv.

Wagner C; Kistler KE; Perchetti GA; Baker N; Frisbie LA; Torres LM; Aragona F; Yun C; Figgins M; Greninger AL; Cox A; Oltean HN; Roychoudhury P; Bedford T, 2024. Positive selection underlies repeated knockout of ORF8 in SARS-CoV-2 evolution. Nat Commun 15(1):3207

Singh K; Rubenstein K; Callier V; Shaw-Saliba K; Rupert A; Dewar R; Laverdure S; Highbarger H; Lallemand P; Huang ML; Jerome KR; Sampoleo R; Mills MG; Greninger AL; Juneja K; Porter D; Benson CA; Dempsey W; El Sahly HM; Focht C; Jilg N; Paules CI; Rapaka RR; Uyeki TM; Lane HC; Beigel J; Dodd LE, 2024. SARS-CoV-2 RNA and nucleocapsid antigen are blood biomarkers associated with severe disease outcomes that improve in response to remdesivir. J Infect Dis.

Nimgaonkar I; Yoke LH; Roychoudhury P; Flaherty PW; Oshima MU; Weixler A; Gauthier J; Greninger AL; Mielcarek M; Boeckh M; Liu C; Hill JA, 2024. Outcomes in Hematopoietic Cell Transplant and Chimeric Antigen Receptor T Cell Therapy Recipients with Pre-Cellular Therapy SARS-CoV-2 Infection. Clin Infect Dis.

Crawford KHD; Selke S; Pepper G; Goecker E; Sobel A; Wald A; Johnston C; Greninger AL, 2024. Performance characteristics of highly automated HSV-1 and HSV-2 IgG testing. J Clin Microbiol.

Choudhary MC; Deo R; Evering TH; Chew KW; Giganti MJ; Moser C; Ritz J; Regan J; Flynn JP; Crain CR; Wohl DA; Currier JS; Eron JJ; Margolis D; Zhu Q; Zhon L; Ya L; Greninger AL; Hughes MD; Smith D; Daar ES; Li JZ, 2024. Characterization of treatment resistance and viral kinetics in the setting of single- versus dual-active monoclonal antibodies against SARS-CoV-2. J Infect Dis.

Heldman MR; Greninger AL; Hill JA, 2024. The iciHHV-6 sense: sensing the source and relevance of human herpesvirus 6 (HHV-6) DNA in the transplant recipient with inherited chromosomally integrated HHV-6. J Infect Dis.

Deo R; Choudhary MC; Moser C; Ritz J; Daar ES; Wohl DA; Greninger AL; Eron JJ; Currier JS; Hughes MD; Smith DM; Chew KW; Li JZ, 2023. Symptom and Viral Rebound in Untreated SARS-CoV-2 Infection. Ann Intern Med 176(3):348-354

Hao L; Hsiang TY; Dalmat RR; Ireton R; Morton JF; Stokes C; Netland J; Hale M; Thouvenel C; Wald A; Franko NM; Huden K; Chu HY; Sigal A; Greninger AL; Tilles S; Barrett LK; Van Voorhis WC; Munt J; Scobey T; Baric RS; Rawlings DJ; Pepper M; Drain PK; Gale M Jr, 2023. Dynamics of SARS-CoV-2 VOC Neutralization and Novel mAb Reveal Protection against Omicron. Viruses 15.

Romeis E; Lieberman NAP; Molini B; Tantalo LC; Chung B; Phung Q; Avendaño C; Vorobieva A; Greninger AL; Giacani L, 2023. Treponema pallidum subsp. pallidum with an Artificially impaired TprK antigenic variation system is attenuated in the Rabbit model of syphilis. PLoS Pathog 19(3):e1011259

Cheng GS; Crothers K; Aliberti S; Bergeron A; Boeckh M; Chien JW; Cilloniz C; Cohen K; Dean N; Dela Cruz CS; Dickson RP; Greninger AL; Hage CA; Hohl TM; Holland SM; Jones BE; Keane J; Metersky M; Miller R; Puel A; Ramirez J; Restrepo MI; Sheshadri A; Staitieh B; Tarrand J; Winthrop KL; Wunderink RG; Evans SE, 2023. Immunocompromised Host Pneumonia: Definitions and Diagnostic Criteria: An Official American Thoracic Society Workshop Report. Ann Am Thorac Soc 20(3):341-353

Goya S; Sereewit J; Pfalmer D; Nguyen TV; Bakhash SAKM; Sobolik EB; Greninger AL, 2023. Genomic Characterization of Respiratory Syncytial Virus during 2022-23 Outbreak, Washington, USA. Emerg Infect Dis 29(4):865-868

Drain PK; Dalmat RR; Hao L; Bemer MJ; Budiawan E; Morton JF; Ireton RC; Hsiang TY; Marfatia Z; Prabhu R; Woosley C; Gichamo A; Rechkina E; Hamilton D; Montaño M; Cantera JL; Ball AS; Golez I; Smith E; Greninger AL; McElrath MJ; Thompson M; Grant BD; Meisner A; Gottlieb GS; Gale M Jr, 2023. Duration of viral infectiousness and correlation with symptoms and diagnostic testing in non-hospitalized adults during acute SARS-CoV-2 infection: A longitudinal cohort study. J Clin Virol 161:105420

Moser CB; Chew KW; Giganti MJ; Li JZ; Aga E; Ritz J; Greninger AL; Javan AC; Daar ES; Currier JS; Eron JJ; Smith DM; Hughes MD, 2023. Statistical Challenges when Analyzing SARS-CoV-2 RNA Measurements Below the Assay Limit of Quantification in COVID-19 Clinical Trials. medRxiv.

Pettit R; Peng B; Yu P; Matos PG; Greninger AL; McCashin J; Amos CI, 2023. Optimized workplace risk mitigation measures for SARS-CoV-2 in 2022. Sci Rep 13(1):2779

Rao A; Westbrook A; Bassit L; Parsons R; Fitts E; Greenleaf M; McLendon K; Sullivan JA; O'Sick W; Baugh T; Bowers HB; Frank F; Wang E; Le M; Frediani J; Roychoudhury P; Greninger AL; Jerris R; Pollock NR; Ortlund EA; Roback JD; Lam WA; Piantadosi A, 2023. Sensitivity of Rapid Antigen Tests Against SARS-CoV-2 Omicron and Delta Variants. medRxiv.

Ford ES; Simmons W; Karmarkar EN; Yoke LH; Braimah AB; Orozco JJ; Ghiuzeli CM; Barnhill S; Sack CL; Benditt JO; Roychoudhury P; Greninger AL; Shapiro AE; Hammond JL; Rusnak JM; Dolsten M; Boeckh M; Liu C; Cheng GS; Corey L, 2023. Successful Treatment of Prolonged, Severe Coronavirus Disease 2019 Lower Respiratory Tract Disease in a B cell Acute Lymphoblastic Leukemia Patient With an Extended Course of Remdesivir and Nirmatrelvir/Ritonavir. Clin Infect Dis 76(5):926-929

Marcink TC; Zipursky G; Cheng W; Stearns K; Stenglein S; Golub K; Cohen F; Bovier F; Pfalmer D; Greninger AL; Porotto M; des Georges A; Moscona A, 2023. Subnanometer structure of an enveloped virus fusion complex on viral surface reveals new entry mechanisms. Sci Adv 9(6):eade2727

Roychoudhury P; Sereewit J; Xie H; Nunley E; Bakhash SM; Lieberman NAP; Greninger AL, 2023. Genomic Analysis of Early Monkeypox Virus Outbreak Strains, Washington, USA. Emerg Infect Dis 29(3):644-646

Romeis E; Lieberman NAP; Molini B; Tantalo LC; Chung B; Phung Q; Avendaño C; Vorobieva A; Greninger AL; Giacani L, 2023. Treponema pallidum subsp. pallidum with an Artificially Impaired TprK Antigenic Variation System is Attenuated in the Rabbit Model of Syphilis. bioRxiv.

Perchetti GA; Biernacki MA; Xie H; Castor J; Joncas-Schronce L; Ueda Oshima M; Kim Y; Jerome KR; Sandmaier BM; Martin PJ; Boeckh M; Greninger AL; Zamora D, 2023. Cytomegalovirus breakthrough and resistance during letermovir prophylaxis. Bone Marrow Transplant 58(4):430-436

Taiwo BO; Chew KW; Moser C; Wohl DA; Daar ES; Li JZ; Greninger AL; Bausch C; Luke T; Hoover K; Neytman G; Giganti MJ; Olefsky M; Javan AC; Fletcher CV; Eron JJ; Currier JS; Hughes MD; Smith DM, 2023. Phase 2 Safety and Antiviral Activity of SAB-185, a Novel Polyclonal Antibody Therapy for Nonhospitalized Adults With COVID-19. J Infect Dis 228(2):133-142

Mills MG; Juergens KB; Gov JP; McCormick CJ; Sampoleo R; Kachikis A; Amory JK; Fang FC; Pérez-Osorio AC; Lieberman NAP; Greninger AL, 2023. Evaluation and clinical validation of monkeypox (mpox) virus real-time PCR assays. J Clin Virol 159:105373

Oltean HN; Allen KJ; Frisbie L; Lunn SM; Torres LM; Manahan L; Painter I; Russell D; Singh A; Peterson JM; Grant K; Peter C; Cao R; Garcia K; Mackellar D; Jones L; Halstead H; Gray H; Melly G; Nickerson D; Starita L; Frazar C; Greninger AL; Roychoudhury P; Mathias PC; Kalnoski MH; Ting CN; Lykken M; Rice T; Gonzalez-Robles D; Bina D; Johnson K; Wiley CL; Magnuson SC; Parsons CM; Chapman ED; Valencia CA; Fortna RR; Wolgamot G; Hughes JP; Baseman JG; Bedford T; Lindquist S, 2023. Sentinel Surveillance System Implementation and Evaluation for SARS-CoV-2 Genomic Data, Washington, USA, 2020-2021. Emerg Infect Dis 29(2):242-251

Ujjani C; Gooley TA; Spurgeon SE; Stephens DM; Lai C; Broome CM; O'Brien S; Zhu H; Laing KJ; Winter AM; Pongas G; Greninger AL; Koelle DM; Siddiqi T; Davids MS; Rogers KA; Danilov AV; Sperling A; Tu B; Sorensen T; Launchbury K; Burrow CJ; Quezada G; Hill JA; Shadman M; Thompson PA, 2023. Diminished humoral and cellular responses to SARS-CoV-2 vaccines in patients with chronic lymphocytic leukemia. Blood Adv 7(17):4728-4737

Graf SA; Lynch RC; Ujjani CS; Gooley TA; Rasmussen H; Coffey DG; Cowan AJ; Smith SD; Shadman M; Warren EH; Libby EN; Greninger AL; Fromm JR; Gopal AK, 2023. Efficacy, safety, and molecular response predictors of oral ixazomib and short-course rituximab in untreated iNHL. Blood Adv 7(5):687-696

Bender Ignacio RA; Chew KW; Moser C; Currier JS; Eron JJ; Javan AC; Giganti MJ; Aga E; Gibbs M; Tchouakam Kouekam H; Johnsson E; Esser MT; Hoover K; Neytman G; Newell M; Daar ES; Fischer W; Fletcher CV; Li JZ; Greninger AL; Coombs RW; Hughes MD; Smith D; Wohl DA, 2023. Safety and Efficacy of Combined Tixagevimab and Cilgavimab Administered Intramuscularly or Intravenously in Nonhospitalized Patients With COVID-19: 2 Randomized Clinical Trials. JAMA Netw Open 6(4):e2310039

Gonzalez MA; Bhatti AM; Fitzpatrick K; Boonyaratanakornkit J; Huang ML; Campbell VL; Hecht J; Ibrahimi S; Wanner SN; Green DJ; Maloney DG; Gauthier J; Cowan AJ; Greninger AL; Krantz EM; Koelle DM; Hill JA, 2023. Humoral and cellular responses to SARS-CoV-2 vaccines before and after chimeric antigen receptor-modified T-cell therapy. Blood Adv 7(9):1849-1853

Tu YP; Green C; Hao L; Greninger AL; Morton JF; Sights HA; Gale M Jr; Drain PK, 2023. COVID-19 Antigen Results Correlate with the Quantity of Replication-Competent SARS-CoV-2 in a Cross-Sectional Study of Ambulatory Adults during the Delta Wave. Microbiol Spectr 11(3):e0006423

Despres HW; Mills MG; Schmidt MM; Gov J; Perez Y; Jindrich M; Crawford AML; Kohl WT; Rosenblatt E; Kubinski HC; Simmons BC; Nippes MC; Goldenberg AJ; Murtha KE; Nicoloro S; Harris MJ; Feeley AC; Gelinas TK; Cronin MK; Frederick RS; Thomas M; Johnson ME; Murphy J; Lenzini EB; Carr PA Jr; Berger DH; Mehta SP; Floreani CJ; Koval AC; Young AL; Fish JH; Wallace J; Chaney E; Ushay G; Ross RS; Vostal EM; Thisner MC; Gonet KE; Deane OC; Pelletiere KR; Rockafeller VC; Waterman M; Barry TW; Goering CC; Shipman SD; Shiers AC; Reilly CE; Duff AM; Shirley DJ; Jerome KR; Pérez-Osorio AC; Greninger AL; Fortin N; Mosher BA; Bruce EA, 2023. Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA. bioRxiv.

Áñez G; Dunkle LM; Gay CL; Kotloff KL; Adelglass JM; Essink B; Campbell JD; Cloney-Clark S; Zhu M; Plested JS; Roychoudhury P; Greninger AL; Patel N; McGarry A; Woo W; Cho I; Glenn GM; Dubovsky F, 2023. Safety, Immunogenicity, and Efficacy of the NVX-CoV2373 COVID-19 Vaccine in Adolescents: A Randomized Clinical Trial. JAMA Netw Open 6(4):e239135

Moser CB; Chew KW; Giganti MJ; Li JZ; Aga E; Ritz J; Greninger AL; Javan AC; Bender Ignacio R; Daar ES; Wohl DA; Currier JS; Eron JJ; Smith DM; Hughes MD, 2023. Statistical Challenges When Analyzing SARS-CoV-2 RNA Measurements Below the Assay Limit of Quantification in COVID-19 Clinical Trials. J Infect Dis 228(Suppl 2):S101-S110

Welsh FC; Eguia RT; Lee JM; Haddox HK; Galloway J; Chau NVV; Loes AN; Huddleston J; Yu TC; Le MQ; Nhat NTD; Thanh NTL; Greninger AL; Chu HY; Englund JA; Bedford T; Matsen FA 4th; Boni MF; Bloom JD, 2023. Age-dependent heterogeneity in the antigenic effects of mutations to influenza hemagglutinin. bioRxiv.

LaCourse SM; Wetzler EA; Aurelio MC; Escudero JN; Selke SS; Greninger AL; Goecker EA; Barnes SR; Arnould IS; Pérez-Osorio AC; Richardson BA; Kachikis A; Englund JA; Drake AL, 2023. Hybrid immunity to SARS-CoV-2 during pregnancy provides more durable infant antibody responses compared to natural infection alone. J Infect Dis.

Dionne JA; Giacani L; Tamhane A; Workowski K; Lieberman NAP; Greninger AL; Perlowski C; Newman L; Hook EW 3rd, 2023. Prevalence and Predictors of Oral Treponema pallidum Detection by qPCR in Early Syphilis. J Infect Dis.

Lieber CM; Kang HJ; Aggarwal M; Lieberman NA; Sobolik EB; Yoon JJ; Natchus MG; Cox RM; Greninger AL; Plemper RK, 2023. Influenza A virus resistance to 4'-fluorouridine coincides with viral attenuation in vitro and in vivo. bioRxiv.

Sasidharan A; Selvarangan R; Konrad K; Faron ML; Shakir SM; Hillyard D; McCall RK; McHardy IH; Goldberg DC; Dunn JJ; Greninger AL; Lansang C; Bogh R; Remillard CV, 2023. Multi-center clinical evaluation of the Panther Fusion SARS-CoV-2/Flu A/B/RSV assay in nasopharyngeal swab specimens from symptomatic individuals. J Clin Microbiol 61(11):e0082723

Tantalo LC; Lieberman NAP; Pérez-Mañá C; Suñer C; Vall Mayans M; Ubals M; González-Beiras C; Rodríguez-Gascón A; Canut A; González-Candelas F; Mueller J; Tapia K; Greninger AL; Giacani L; Mitjà O, 2023. Antimicrobial susceptibility of Treponema pallidum subspecies pallidum: an in-vitro study. Lancet Microbe 4(12):e994-e1004

Lewinski MA; Alby K; Babady NE; Butler-Wu SM; Bard JD; Greninger AL; Hanson K; Naccache SN; Newton D; Temple-Smolkin RL; Nolte F, 2023. Exploring the Utility of Multiplex Infectious Disease Panel Testing for Diagnosis of Infection in Different Body Sites: A Joint Report of the Association for Molecular Pathology, American Society for Microbiology, Infectious Diseases Society of America, and Pan American Society for Clinical Virology. J Mol Diagn 25(12):857-875

Rao A; Westbrook A; Bassit L; Parsons R; Fitts E; Greenleaf M; McLendon K; Sullivan JA; O'Sick W; Baugh T; Bowers HB; Frank F; Wang E; Le M; Frediani J; Roychoudhury P; Greninger AL; Jerris R; Pollock NR; Ortlund EA; Roback JD; Lam WA; Piantadosi A, 2023. Sensitivity of rapid antigen tests against SARS-CoV-2 Omicron and Delta variants. J Clin Microbiol 61(10):e0013823

Despres HW; Mills MG; Schmidt MM; Gov J; Perez Y; Jindrich M; Crawford AML; Kohl WT; Rosenblatt E; Kubinski HC; Simmons BC; Nippes MC; Goldenberg AJ; Murtha KE; Nicoloro S; Harris MJ; Feeley AC; Gelinas TK; Cronin MK; Frederick RS; Thomas M; Johnson ME; Murphy J; Lenzini EB; Carr PA Jr; Berger DH; Mehta SP; Floreani CJ; Koval AC; Young AL; Fish JH; Wallace J; Chaney E; Ushay G; Ross RS; Vostal EM; Thisner MC; Gonet KE; Deane OC; Pelletiere KR; Rockafeller VC; Waterman M; Barry TW; Goering CC; Shipman SD; Shiers AC; Reilly CE; Duff AM; Madruga SL; Shirley DJ; Jerome KR; Pérez-Osorio AC; Greninger AL; Fortin N; Mosher BA; Bruce EA, 2023. Surveillance of Vermont wildlife in 2021-2022 reveals no detected SARS-CoV-2 viral RNA. Sci Rep 13(1):14683

Ramirez SI; Lopez PG; Faraji F; Parikh UM; Heaps A; Ritz J; Moser C; Eron JJ; Wohl DA; Currier JS; Daar ES; Greninger AL; Klekotka P; Grifoni A; Weiskopf D; Sette A; Peters B; Hughes MD; Chew KW; Smith DM; Crotty S, 2023. Early antiviral CD4 and CD8 T cell responses are associated with upper respiratory tract clearance of SARS-CoV-2. bioRxiv.

Ribeiro RM; Choudhary MC; Deo R; Giganti MJ; Moser C; Ritz J; Greninger AL; Regan J; Flynn JP; Wohl DA; Currier JS; Eron JJ; Hughes MD; Smith DM; Chew KW; Daar ES; Perelson AS; Li JZ, 2023. Variant-Specific Viral Kinetics in Acute COVID-19. J Infect Dis 228(Suppl 2):S136-S143

Makhsous N; Goya S; Avendaño C; Rupp J; Kuypers J; Jerome KR; Boeckh M; Waghmare A; Greninger AL, 2023. Within-host rhinovirus evolution in upper and lower respiratory tract highlights capsid variability and mutation-independent compartmentalization. bioRxiv.

Drake AL; Escudero JN; Aurelio MC; Wetzler EA; Ellington SR; Zapata LB; Galang RR; Snead MC; Yamamoto K; Salerno CC; Richardson BA; Greninger AL; Kachikis AB; Englund JA; LaCourse SM, 2023. Severe acute respiratory syndrome coronavirus 2 seroprevalence and longitudinal antibody response following natural infection in pregnancy: A prospective cohort study. Womens Health (Lond) 19:17455057231190955

Glasgow HL; Zhu H; Xie H; Kenkel EJ; Lee C; Huang ML; Greninger AL, 2023. Genotypic testing improves detection of antiviral resistance in human herpes simplex virus. J Clin Virol 167:105554

Cox RM; Lieber CM; Wolf JD; Karimi A; Lieberman NAP; Sticher ZM; Roychoudhury P; Andrews MK; Krueger RE; Natchus MG; Painter GR; Kolykhalov AA; Greninger AL; Plemper RK, 2023. Comparing molnupiravir and nirmatrelvir/ritonavir efficacy and the effects on SARS-CoV-2 transmission in animal models. Nat Commun 14(1):4731

Hedskog C; Rodriguez L; Roychoudhury P; Huang ML; Jerome KR; Hao L; Ireton RC; Li J; Perry JK; Han D; Camus G; Greninger AL; Gale M Jr; Porter DP, 2023. Viral Resistance Analyses From the Remdesivir Phase 3 Adaptive COVID-19 Treatment Trial-1 (ACTT-1). J Infect Dis 228(9):1263-1273

McCulloch DJ; Rogers JH; Wang Y; Chow EJ; Link AC; Wolf CR; Uyeki TM; Rolfes MA; Mosites E; Sereewit J; Duchin JS; Sugg NK; Greninger AL; Boeckh MJ; Englund JA; Shendure J; Hughes JP; Starita LM; Roychoudhury P; Chu HY, 2023. Respiratory syncytial virus and other respiratory virus infections in residents of homeless shelters - King County, Washington, 2019-2021. Influenza Other Respir Viruses 17(6):e13166

Jilg N; Chew KW; Giganti MJ; Daar ES; Wohl DA; Javan AC; Kantor A; Moser C; Coombs RW; Neytman G; Hoover K; Jana A; Hart PA; Greninger AL; Szurgot B; Eron JJ; Currier JS; Hughes MD; Smith DM; Li JZ, 2023. One Week of Oral Camostat Versus Placebo in Nonhospitalized Adults With Mild-to-Moderate Coronavirus Disease 2019: A Randomized Controlled Phase 2 Trial. Clin Infect Dis 77(7):941-949

Li Y; Moser C; Aga E; Currier JS; Wohl DA; Daar ES; Ritz J; Greninger AL; Sieg S; Parikh UM; Coombs RW; Hughes MD; Eron JJ; Smith DM; Chew KW; Li JZ, 2023. Immune Status and SARS-CoV-2 Viral Dynamics. J Infect Dis 228(Suppl 2):S111-S116

Aldrete S; Kroft SH; Romeis E; Lieberman NAP; Greninger AL; Giacani L; Kron MA, 2023. Whole Genome Sequence of a Treponema pallidum Strain From a Formalin-Fixed, Paraffin-Embedded Fine Needle Aspirate of a Cervical Lymph Node. Sex Transm Dis 50(8):550-552

Letendre SL; Chen H; McKhann A; Roa J; Vecchio A; Daar ES; Berzins B; Hunt PW; Marra CM; Campbell TB; Coombs RW; Ma Q; Swaminathan S; Macatangay BJC; Morse GD; Miller T; Rusin D; Greninger AL; Ha B; Alston-Smith B; Robertson K; Paul R; Spudich S, 2023. Antiretroviral Therapy Intensification for Neurocognitive Impairment in Human Immunodeficiency Virus. Clin Infect Dis 77(6):866-874

Lieber CM; Cox RM; Sourimant J; Wolf JD; Juergens K; Phung Q; Saindane MT; Natchus MG; Painter GR; Sakamoto K; Greninger AL; Plemper RK, 2022. SARS-CoV-2 variant of concern type and biological sex affect efficacy of molnupiravir in dwarf hamster model of severe COVID-19. bioRxiv.

Hannon WW; Roychoudhury P; Xie H; Shrestha L; Addetia A; Jerome KR; Greninger AL; Bloom JD, 2022. Narrow transmission bottlenecks and limited within-host viral diversity during a SARS-CoV-2 outbreak on a fishing boat. bioRxiv.

Gandhi S; Klein J; Robertson AJ; Peña-Hernández MA; Lin MJ; Roychoudhury P; Lu P; Fournier J; Ferguson D; Mohamed Bakhash SAK; Catherine Muenker M; Srivathsan A; Wunder EA Jr; Kerantzas N; Wang W; Lindenbach B; Pyle A; Wilen CB; Ogbuagu O; Greninger AL; Iwasaki A; Schulz WL; Ko AI, 2022. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: a case report. Nat Commun 13(1):1547

Elyanow R; Snyder TM; Dalai SC; Gittelman RM; Boonyaratanakornkit J; Wald A; Selke S; Wener MH; Morishima C; Greninger AL; Gale M Jr; Hsiang TY; Jing L; Holbrook MR; Kaplan IM; Zahid HJ; May DH; Carlson JM; Baldo L; Manley T; Robins HS; Koelle DM, 2022. T cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibodies and disease severity. JCI Insight 7.

Laitman AM; Lieberman JA; Hoffman NG; Roychoudhury P; Mathias PC; Greninger AL, 2022. The SARS-CoV-2 Omicron Variant Does Not Have Higher Nasal Viral Loads Compared to the Delta Variant in Symptomatic and Asymptomatic Individuals. J Clin Microbiol 60(4):e0013922

Wu X; Roberto JB; Knupp A; Greninger AL; Truong CD; Hollingshead N; Kenerson HL; Tuefferd M; Chen A; Koelle DM; Horton H; Jerome KR; Polyak SJ; Yeung RS; Crispe IN, 2022. Response of Human Liver Tissue to Innate Immune Stimuli. Front Immunol 13:811551

Lin MJ; Rachleff VM; Xie H; Shrestha L; Lieberman NAP; Peddu V; Addetia A; Casto AM; Breit N; Mathias PC; Huang ML; Jerome KR; Greninger AL; Roychoudhury P, 2022. Host-pathogen dynamics in longitudinal clinical specimens from patients with COVID-19. Sci Rep 12(1):5856

Zhang JZ; Yeh HW; Walls AC; Wicky BIM; Sprouse KR; VanBlargan LA; Treger R; Quijano-Rubio A; Pham MN; Kraft JC; Haydon IC; Yang W; DeWitt M; Bowen JE; Chow CM; Carter L; Ravichandran R; Wener MH; Stewart L; Veesler D; Diamond MS; Greninger AL; Koelle DM; Baker D, 2022. Thermodynamically coupled biosensors for detecting neutralizing antibodies against SARS-CoV-2 variants. Nat Biotechnol 40(9):1336-1340

Roychoudhury P; Luo S; Hayashibara K; Hajian P; Mills MG; Lozach J; Cassens T; Wendm ST; Arnould I; Becker D; Wesselman T; Davis-Turak J; Creager R; Lai E; Jerome KR; Basler T; Dei Rossi A; Lee W; Greninger AL, 2022. Identification of Omicron-Delta Coinfections Using PCR-Based Genotyping. Microbiol Spectr 10(3):e0060522

Phung Q; Lin MJ; Xie H; Greninger AL, 2022. Fragment Size-Based Enrichment of Viral Sequences in Plasma Cell-Free DNA. J Mol Diagn 24(5):476-484

Bershteyn A; Dahl AM; Dong TQ; Deming ME; Celum CL; Chu HY; Kottkamp AC; Greninger AL; Hoffman RM; Jerome KR; Johnston CM; Kissinger PJ; Landovitz RJ; Laufer MK; Luk A; Neuzil KM; Paasche-Orlow MK; Pitts RA; Schwartz MD; Stankiewicz Karita HC; Thorpe LE; Wald A; Zheng CY; Wener MH; Barnabas RV; Brown ER, 2022. Self-Assessed Severity as a Determinant of Coronavirus Disease 2019 Symptom Specificity: A Longitudinal Cohort Study. Clin Infect Dis 75(1):e1180-e1183

Despres HW; Mills MG; Shirley DJ; Schmidt MM; Huang ML; Roychoudhury P; Jerome KR; Greninger AL; Bruce EA, 2022. Measuring infectious SARS-CoV-2 in clinical samples reveals a higher viral titer:RNA ratio for Delta and Epsilon vs. Alpha variants. Proc Natl Acad Sci U S A 119.

Deming ME; Dong TQ; Agrawal V; Mills MG; Huang MLW; Greninger AL; Jerome KR; Wener MH; Paasche-Orlow MK; Kissinger P; Luk A; Hoffman RM; Stewart J; Kottkamp AC; Bershteyn A; Chu HY; Stankiewicz Karita HC; Johnston CM; Wald A; Barnabas R; Brown ER; Neuzil KM, 2022. Detection and Kinetics of Subgenomic Severe Acute Respiratory Syndrome Coronavirus 2 RNA Viral Load in Longitudinal Diagnostic RNA-Positive Samples. J Infect Dis 226(5):788-796

Montaño MA; Bemer MJ; Heller KB; Meisner A; Marfatia Z; Rechkina EA; Padgett LR; Ahls CL; Rains D; Hao L; Hsiang TY; Cangelosi GA; Greninger AL; Cantera JL; Golden A; Peck RB; Boyle DS; Gale M Jr; Drain PK, 2022. Performance of anterior nares and tongue swabs for nucleic acid, Nucleocapsid, and Spike antigen testing for detecting SARS-CoV-2 against nasopharyngeal PCR and viral culture. Int J Infect Dis 117:287-294

Stalter RM; Atluri V; Xia F; Thomas KK; Lan KF; Greninger AL; Patel RC, 2022. Elucidating Pathways Mediating the Relationship Between Male Sex and COVID-19 Severity. Clin Epidemiol 14:115-125

Wong TY; Horspool AM; Russ BP; Ye C; Lee KS; Winters MT; Bevere JR; Miller OA; Rader NA; Cooper M; Kieffer T; Sourimant J; Greninger AL; Plemper RK; Denvir J; Cyphert HA; Barbier M; Torrelles JB; Martinez I; Martinez-Sobrido L; Damron FH, 2022. Evaluating Antibody Mediated Protection against Alpha, Beta, and Delta SARS-CoV-2 Variants of Concern in K18-hACE2 Transgenic Mice. J Virol 96(6):e0218421

Stankiewicz Karita HC; Dong TQ; Johnston C; Neuzil KM; Paasche-Orlow MK; Kissinger PJ; Bershteyn A; Thorpe LE; Deming M; Kottkamp A; Laufer M; Landovitz RJ; Luk A; Hoffman R; Roychoudhury P; Magaret CA; Greninger AL; Huang ML; Jerome KR; Wener M; Celum C; Chu HY; Baeten JM; Wald A; Barnabas RV; Brown ER, 2022. Trajectory of Viral RNA Load Among Persons With Incident SARS-CoV-2 G614 Infection (Wuhan Strain) in Association With COVID-19 Symptom Onset and Severity. JAMA Netw Open 5(1):e2142796

Dunkle LM; Kotloff KL; Gay CL; Áñez G; Adelglass JM; Barrat Hernández AQ; Harper WL; Duncanson DM; McArthur MA; Florescu DF; McClelland RS; Garcia-Fragoso V; Riesenberg RA; Musante DB; Fried DL; Safirstein BE; McKenzie M; Jeanfreau RJ; Kingsley JK; Henderson JA; Lane DC; Ruíz-Palacios GM; Corey L; Neuzil KM; Coombs RW; Greninger AL; Hutter J; Ake JA; Smith K; Woo W; Cho I; Glenn GM; Dubovsky F, 2022. Efficacy and Safety of NVX-CoV2373 in Adults in the United States and Mexico. N Engl J Med 386(6):531-543

Bruce EA; Mills MG; Sampoleo R; Perchetti GA; Huang ML; Despres HW; Schmidt MM; Roychoudhury P; Shirley DJ; Jerome KR; Greninger AL; Botten JW, 2022. Predicting infectivity: comparing four PCR-based assays to detect culturable SARS-CoV-2 in clinical samples. EMBO Mol Med 14(2):e15290

Juergens KB; Huckabee J; Greninger AL, 2022. Two Novel Iflaviruses Discovered in Bat Samples in Washington State. Viruses 14.

Ujjani C; Greninger AL; Shadman M; Hill JA; Lynch RC; Warren EH; Gopal AK, 2022. Heterologous SARS-CoV-2 vaccinations in patients with B-cell lymphoid malignancies. Am J Hematol 97(2):E67-E69

Greninger AL; Dien Bard J; Colgrove RC; Graf EH; Hanson KE; Hayden MK; Humphries RM; Lowe CF; Miller MB; Pillai DR; Rhoads DD; Yao JD; Lee FM, 2022. Clinical and Infection Prevention Applications of Severe Acute Respiratory Syndrome Coronavirus 2 Genotyping: An Infectious Diseases Society of America/American Society for Microbiology Consensus Review Document. Clin Infect Dis 74(8):1496-1502

Greninger AL; Dien Bard J; Colgrove RC; Graf EH; Hanson KE; Hayden MK; Humphries RM; Lowe CF; Miller MB; Pillai DR; Rhoads DD; Yao JD; Lee FM, 2022. Clinical and Infection Prevention Applications of Severe Acute Respiratory Syndrome Coronavirus 2 Genotyping: an Infectious Diseases Society of America/American Society for Microbiology Consensus Review Document. J Clin Microbiol 60(1):e0165921

McEwen AE; Cohen S; Bryson-Cahn C; Liu C; Pergam SA; Lynch J; Schippers A; Strand K; Whimbey E; Mani NS; Zelikoff AJ; Makarewicz VA; Brown ER; Bakhash SAM; Baker NR; Castor J; Livingston RJ; Huang ML; Jerome KR; Greninger AL; Roychoudhury P, 2022. Variants of Concern Are Overrepresented Among Postvaccination Breakthrough Infections of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) in Washington State. Clin Infect Dis 74(6):1089-1092

Waghmare A; Krantz EM; Baral S; Vasquez E; Loeffelholz T; Chung EL; Pandey U; Kuypers J; Duke ER; Jerome KR; Greninger AL; Reeves DB; Hladik F; Cardozo-Ojeda EF; Boeckh M; Schiffer JT, 2022. Reliability of Self-Sampling for Accurate Assessment of Respiratory Virus Viral and Immunologic Kinetics. J Infect Dis 226(2):278-286

Sereewit J; Lieberman NAP; Xie H; Bakhash SAKM; Nunley BE; Chung B; Mills MG; Roychoudhury P; Greninger AL, 2022. ORF-Interrupting Mutations in Monkeypox Virus Genomes from Washington and Ohio, 2022. Viruses 14.

Avetyan D; Hakobyan S; Nikoghosyan M; Ghukasyan L; Khachatryan G; Sirunyan T; Muradyan N; Zakharyan R; Chavushyan A; Hayrapetyan V; Hovhannisyan A; Mohamed Bakhash SA; Jerome KR; Roychoudhury P; Greninger AL; Niazyan L; Davidyants M; Melik-Andreasyan G; Sargsyan S; Nersisyan L; Arakelyan A, 2022. Molecular Analysis of SARS-CoV-2 Lineages in Armenia. Viruses 14.

Heldman MR; Wight DJ; Aiewsakun P; Aswad A; Fang M; Roychoudhury P; Stevens-Ayers T; Jerome KR; Zerr DM; Greninger AL; Kaufer BB; Boeckh M; Hill JA, 2022. Chromosome-Specific Human Herpesvirus 6 Integration and Hematologic Malignancies. J Virol 96(17):e0093722

Goldman JD; Wang K; Röltgen K; Nielsen SCA; Roach JC; Naccache SN; Yang F; Wirz OF; Yost KE; Lee JY; Chun K; Wrin T; Petropoulos CJ; Lee I; Fallen S; Manner PM; Wallick JA; Algren HA; Murray KM; Hadlock J; Chen D; Dai CL; Yuan D; Su Y; Jeharajah J; Berrington WR; Pappas GP; Nyatsatsang ST; Greninger AL; Satpathy AT; Pauk JS; Boyd SD; Heath JR, 2022. Reinfection with SARS-CoV-2 and Waning Humoral Immunity: A Case Report. Vaccines (Basel) 11.

Paredes MI; Perofsky AC; Frisbie L; Moncla LH; Roychoudhury P; Xie H; Mohamed Bakhash SA; Kong K; Arnould I; Nguyen TV; Wendm ST; Hajian P; Ellis S; Mathias PC; Greninger AL; Starita LM; Frazar CD; Ryke E; Zhong W; Gamboa L; Threlkeld M; Lee J; Stone J; McDermot E; Truong M; Shendure J; Oltean HN; Viboud C; Chu H; Müller NF; Bedford T, 2022. Local-Scale phylodynamics reveal differential community impact of SARS-CoV-2 in metropolitan US county. medRxiv.

Cox RM; Lieber CM; Wolf JD; Karimi A; Lieberman NAP; Sticher ZM; Roychoudhury P; Andrews MK; Krueger RE; Natchus MG; Painter GR; Kolykhalov AA; Greninger AL; Plemper RK, 2022. Paxlovid-like nirmatrelvir/ritonavir fails to block SARS-CoV-2 transmission in ferrets. bioRxiv.

Lieberman NAP; Mathias PC; Bradley BT; Greninger AL, 2022. Clinical Performance and Trends during the First Two Months of Monkeypox Virus PCR Testing at Two United States Reference Labs. J Clin Microbiol 60(12):e0137122

Reynard O; Gonzalez C; Dumont C; Iampietro M; Ferren M; Le Guellec S; Laurie L; Mathieu C; Carpentier G; Roseau G; Bovier FT; Zhu Y; Le Pennec D; Montharu J; Addetia A; Greninger AL; Alabi CA; Moscona A; Vecellio L; Porotto M; Horvat B, 2022. Nebulized fusion inhibitory peptide protects cynomolgus macaques from measles virus infection. Res Sq.

Reynard O; Gonzalez C; Dumont C; Iampietro M; Ferren M; Le Guellec S; Laurie L; Mathieu C; Carpentier G; Roseau G; Bovier FT; Zhu Y; Le Pennec D; Montharu J; Addetia A; Greninger AL; Alabi CA; Brisebard E; Moscona A; Vecellio L; Porotto M; Horvat B, 2022. Nebulized fusion inhibitory peptide protects cynomolgus macaques from measles virus infection. Nat Commun 13(1):6439

Choudhary MC; Chew KW; Deo R; Flynn JP; Regan J; Crain CR; Moser C; Hughes MD; Ritz J; Ribeiro RM; Ke R; Dragavon JA; Javan AC; Nirula A; Klekotka P; Greninger AL; Fletcher CV; Daar ES; Wohl DA; Eron JJ; Currier JS; Parikh UM; Sieg SF; Perelson AS; Coombs RW; Smith DM; Li JZ, 2022. Emergence of SARS-CoV-2 escape mutations during Bamlanivimab therapy in a phase II randomized clinical trial. Nat Microbiol 7(11):1906-1917

Lieberman NAP; Armstrong TD; Chung B; Pfalmer D; Hennelly CM; Haynes A; Romeis E; Wang QQ; Zhang RL; Kou CX; Ciccarese G; Conte ID; Cusini M; Drago F; Nakayama SI; Lee K; Ohnishi M; Konda KA; Vargas SK; Eguiluz M; Caceres CF; Klausner JD; Mitja O; Rompalo A; Mulcahy F; Hook EW 3rd; Hoffman IF; Matoga MM; Zheng H; Yang B; Lopez-Medina E; Ramirez LG; Radolf JD; Hawley KL; Salazar JC; Lukehart SA; Seña AC; Parr JB; Giacani L; Greninger AL, 2022. High-throughput nanopore sequencing of Treponema pallidum tandem repeat genes arp and tp0470 reveals clade-specific patterns and recapitulates global whole genome phylogeny. Front Microbiol 13:1007056

Áñez G; Dunkle LM; Gay CL; Kotloff KL; Adelglass JM; Essink B; Campbell JD; Cloney-Clark S; Zhu M; Plested JS; Roychoudhury P; Greninger AL; Patel N; McGarry A; Woo W; Cho I; Glenn GM; Dubovsky F, 2022. Safety, Immunogenicity and Efficacy of NVX-CoV2373 in Adolescents in PREVENT-19: A Randomized, Phase 3 Trial. medRxiv.

Chow EJ; Casto AM; Sampoleo R; Mills MG; Han PD; Xie H; Pfau B; Nguyen TV; Sereewit J; Rogers JH; Cox SN; Rolfes MA; Ogokeh C; Mosites E; Uyeki TM; Greninger AL; Hughes JP; Shim MM; Sugg N; Duchin JS; Starita LM; Englund JA; Roychoudhury P; Chu HY, 2022. Human Parainfluenza Virus in Homeless Shelters before and during the COVID-19 Pandemic, Washington, USA. Emerg Infect Dis 28(11):2343-2347

Hardt K; Vandebosch A; Sadoff J; Le Gars M; Truyers C; Lowson D; Van Dromme I; Vingerhoets J; Kamphuis T; Scheper G; Ruiz-Guiñazú J; Faust SN; Spinner CD; Schuitemaker H; Van Hoof J; Douoguih M; Struyf F, 2022. Efficacy, safety, and immunogenicity of a booster regimen of Ad26.COV2.S vaccine against COVID-19 (ENSEMBLE2): results of a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Infect Dis 22(12):1703-1715

Bolze A; Basler T; White S; Dei Rossi A; Wyman D; Dai H; Roychoudhury P; Greninger AL; Hayashibara K; Beatty M; Shah S; Stous S; McCrone JT; Kil E; Cassens T; Tsan K; Nguyen J; Ramirez J; Carter S; Cirulli ET; Schiabor Barrett K; Washington NL; Belda-Ferre P; Jacobs S; Sandoval E; Becker D; Lu JT; Isaksson M; Lee W; Luo S, 2022. Evidence for SARS-CoV-2 Delta and Omicron co-infections and recombination. Med 3(12):848-859.e4

Deo R; Choudhary MC; Moser C; Ritz J; Daar ES; Wohl DA; Greninger AL; Eron JJ; Currier JS; Hughes MD; Smith DM; Chew KW; Li JZ, 2022. Viral and Symptom Rebound in Untreated COVID-19 Infection. medRxiv.

Chang A; Sholukh AM; Wieland A; Jaye DL; Carrington M; Huang ML; Xie H; Jerome KR; Roychoudhury P; Greninger AL; Koff JL; Cohen JB; Koelle DM; Corey L; Flowers CR; Ahmed R, 2022. Herpes simplex virus lymphadenitis is associated with tumor reduction in a patient with chronic lymphocytic leukemia. J Clin Invest 132.

Chow EJ; Casto AM; Roychoudhury P; Han PD; Xie H; Pfau B; Nguyen TV; Sereewit J; Rogers JH; Cox SN; Wolf CR; Rolfes MA; Mosites E; Uyeki TM; Greninger AL; Hughes JP; Shim MM; Sugg N; Duchin JS; Starita LM; Englund JA; Chu HY, 2022. The Clinical and Genomic Epidemiology of Rhinovirus in Homeless Shelters-King County, Washington. J Infect Dis 226(Suppl 3):S304-S314

Lai E; Kennedy EB; Lozach J; Hayashibara K; Davis-Turak J; Becker D; Brzoska P; Cassens T; Diamond E; Gandhi M; Greninger AL; Hajian P; Leonetti NA; Nguyen JM; O'Donovan KMC; Peck T; Ramirez JM 3rd; Roychoudhury P; Sandoval E; Wesselman C; Wesselman T; White S; Williams S; Wong D; Yu Y; Creager RS, 2022. A Method for Variant Agnostic Detection of SARS-CoV-2, Rapid Monitoring of Circulating Variants, and Early Detection of Emergent Variants Such as Omicron. J Clin Microbiol 60(7):e0034222

Mills MG; Hajian P; Bakhash SM; Xie H; Mantzke D; Zhu H; Perchetti GA; Huang ML; Pepper G; Jerome KR; Roychoudhury P; Greninger AL, 2022. Rapid and accurate identification of SARS-CoV-2 Omicron variants using droplet digital PCR (RT-ddPCR). J Clin Virol 154:105218

Boucau J; Chew KW; Choudhary MC; Deo R; Regan J; Flynn JP; Crain CR; Hughes MD; Ritz J; Moser C; Dragavon JA; Javan AC; Nirula A; Klekotka P; Greninger AL; Coombs RW; Fischer WA 2nd; Daar ES; Wohl DA; Eron JJ; Currier JS; Smith DM; Li JZ; Barczak AK, 2022. Monoclonal antibody treatment drives rapid culture conversion in SARS-CoV-2 infection. Cell Rep Med 3(7):100678

Nguyen Quoc B; Saingam P; RedCorn R; Carter JA; Jain T; Candry P; Gattuso M; Huang MW; Greninger AL; Meschke JS; Bryan A; Winkler MKH, 2022. Case Study: Impact of Diurnal Variations and Stormwater Dilution on SARS-CoV-2 RNA Signal Intensity at Neighborhood Scale Wastewater Pumping Stations. ACS ES T Water 2(11):1964-1975

Shrestha L; Lin MJ; Xie H; Mills MG; Mohamed Bakhash SA; Gaur VP; Livingston RJ; Castor J; Bruce EA; Botten JW; Huang ML; Jerome KR; Greninger AL; Roychoudhury P, 2022. Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes. J Mol Diagn 24(9):963-976

Lieber CM; Cox RM; Sourimant J; Wolf JD; Juergens K; Phung Q; Saindane MT; Smith MK; Sticher ZM; Kalykhalov AA; Natchus MG; Painter GR; Sakamoto K; Greninger AL; Plemper RK, 2022. SARS-CoV-2 VOC type and biological sex affect molnupiravir efficacy in severe COVID-19 dwarf hamster model. Nat Commun 13(1):4416

Hawman DW; Meade-White K; Clancy C; Archer J; Hinkley T; Leventhal SS; Rao D; Stamper A; Lewis M; Rosenke R; Krieger K; Randall S; Khandhar AP; Hao L; Hsiang TY; Greninger AL; Gale M Jr; Berglund P; Fuller DH; Rosenke K; Feldmann H; Erasmus JH, 2022. Replicating RNA platform enables rapid response to the SARS-CoV-2 Omicron variant and elicits enhanced protection in naïve hamsters compared to ancestral vaccine. EBioMedicine 83:104196

Kumbhakar R; Neradilek M; Barnabas RV; Stewart J; Stankiewicz Karita HC; Landovitz RJ; Kissinger PJ; Jerome KR; Paasche-Orlow MK; Bershteyn A; Chu HY; Neuzil KM; Greninger AL; Luk A; Wald A; Brown ER; Johnston C, 2022. Using time-weighted average change from baseline of SARS-CoV-2 viral load to assess impact of hydroxychloroquine as postexposure prophylaxis and early treatment for COVID-19. J Med Virol 94(12):6091-6096

Chandler CM; Bourassa L; Mathias PC; Greninger AL, 2021. Estimating the False-Positive Rate of Highly Automated SARS-CoV-2 Nucleic Acid Amplification Testing. J Clin Microbiol 59(8):e0108021

Müller NF; Wagner C; Frazar CD; Roychoudhury P; Lee J; Moncla LH; Pelle B; Richardson M; Ryke E; Xie H; Shrestha L; Addetia A; Rachleff VM; Lieberman NAP; Huang ML; Gautom R; Melly G; Hiatt B; Dykema P; Adler A; Brandstetter E; Han PD; Fay K; Ilcisin M; Lacombe K; Sibley TR; Truong M; Wolf CR; Boeckh M; Englund JA; Famulare M; Lutz BR; Rieder MJ; Thompson M; Duchin JS; Starita LM; Chu HY; Shendure J; Jerome KR; Lindquist S; Greninger AL; Nickerson DA; Bedford T, 2021. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. Sci Transl Med 13.

Peng B; Zhou W; Pettit RW; Yu P; Matos PG; Greninger AL; McCashin J; Amos CI, 2021. Optimal test-assisted quarantine strategies for COVID-19. medRxiv.

Tordoff DM; Greninger AL; Roychoudhury P; Shrestha L; Xie H; Jerome KR; Breit N; Huang ML; Famulare M; Herbeck JT, 2021. Phylogenetic estimates of SARS-CoV-2 introductions into Washington State. medRxiv.

Addetia A; Lieberman NAP; Phung Q; Hsiang TY; Xie H; Roychoudhury P; Shrestha L; Loprieno MA; Huang ML; Gale M Jr; Jerome KR; Greninger AL, 2021. SARS-CoV-2 ORF6 Disrupts Bidirectional Nucleocytoplasmic Transport through Interactions with Rae1 and Nup98. mBio 12.

Eguia RT; Crawford KHD; Stevens-Ayers T; Kelnhofer-Millevolte L; Greninger AL; Englund JA; Boeckh MJ; Bloom JD, 2021. A human coronavirus evolves antigenically to escape antibody immunity. PLoS Pathog 17(4):e1009453

Addetia A; Phung Q; Bradley BT; Lin MJ; Zhu H; Xie H; Huang ML; Greninger AL, 2021. In Vivo Generation of BK and JC Polyomavirus Defective Viral Genomes in Human Urine Samples Associated with Higher Viral Loads. J Virol 95.

Greninger AL; Addetia A; Tao Y; Adler A; Qin X, 2021. Inactivation of genes in oxidative respiration and iron acquisition pathways in pediatric clinical isolates of Small colony variant Enterobacteriaceae. Sci Rep 11(1):7457

Yang S; Jerome KR; Greninger AL; Schiffer JT; Goyal A, 2021. Endogenously Produced SARS-CoV-2 Specific IgG Antibodies May Have a Limited Impact on Clearing Nasal Shedding of Virus during Primary Infection in Humans. Viruses 13.

Elyanow R; Snyder TM; Dalai SC; Gittelman RM; Boonyaratanakornkit J; Wald A; Selke S; Wener MH; Morishima C; Greninger AL; Holbrook MR; Kaplan IM; Zahid HJ; Carlson JM; Baldo L; Manley T; Robins HS; Koelle DM, 2021. T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity. medRxiv.

Johnston C; Brown ER; Stewart J; Karita HCS; Kissinger PJ; Dwyer J; Hosek S; Oyedele T; Paasche-Orlow MK; Paolino K; Heller KB; Leingang H; Haugen HS; Dong TQ; Bershteyn A; Sridhar AR; Poole J; Noseworthy PA; Ackerman MJ; Morrison S; Greninger AL; Huang ML; Jerome KR; Wener MH; Wald A; Schiffer JT; Celum C; Chu HY; Barnabas RV; Baeten JM, 2021. Hydroxychloroquine with or without azithromycin for treatment of early SARS-CoV-2 infection among high-risk outpatient adults: A randomized clinical trial. EClinicalMedicine 33:100773

Child SJ; Greninger AL; Geballe AP, 2021. Rapid adaptation to human protein kinase R by a unique genomic rearrangement in rhesus cytomegalovirus. PLoS Pathog 17(1):e1009088

Nakamichi K; Shen JZ; Lee CS; Lee A; Roberts EA; Simonson PD; Roychoudhury P; Andriesen J; Randhawa AK; Mathias PC; Greninger AL; Jerome KR; Van Gelder RN, 2021. Hospitalization and mortality associated with SARS-CoV-2 viral clades in COVID-19. Sci Rep 11(1):4802

Phan IQ; Subramanian S; Kim D; Murphy M; Pettie D; Carter L; Anishchenko I; Barrett LK; Craig J; Tillery L; Shek R; Harrington WE; Koelle DM; Wald A; Veesler D; King N; Boonyaratanakornkit J; Isoherranen N; Greninger AL; Jerome KR; Chu H; Staker B; Stewart L; Myler PJ; Van Voorhis WC, 2021. In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19. Sci Rep 11(1):4290

Bosch DE; Mathias PC; Krumm N; Bryan A; Fang FC; Greninger AL, 2021. Elevated White Blood Cell Count Does Not Predict Clostridium difficile Nucleic Acid Testing Results. Clin Infect Dis 73(4):699-705

Crawford KHD; Dingens AS; Eguia R; Wolf CR; Wilcox N; Logue JK; Shuey K; Casto AM; Fiala B; Wrenn S; Pettie D; King NP; Greninger AL; Chu HY; Bloom JD, 2021. Dynamics of Neutralizing Antibody Titers in the Months After Severe Acute Respiratory Syndrome Coronavirus 2 Infection. J Infect Dis 223(2):197-205

Long DR; Gombar S; Hogan CA; Greninger AL; O'Reilly-Shah V; Bryson-Cahn C; Stevens B; Rustagi A; Jerome KR; Kong CS; Zehnder J; Shah NH; Weiss NS; Pinsky BA; Sunshine JE, 2021. Occurrence and Timing of Subsequent Severe Acute Respiratory Syndrome Coronavirus 2 Reverse-transcription Polymerase Chain Reaction Positivity Among Initially Negative Patients. Clin Infect Dis 72(2):323-326

Aswad A; Aimola G; Wight D; Roychoudhury P; Zimmermann C; Hill J; Lassner D; Xie H; Huang ML; Parrish NF; Schultheiss HP; Venturini C; Lager S; Smith GCS; Charnock-Jones DS; Breuer J; Greninger AL; Kaufer BB, 2021. Evolutionary History of Endogenous Human Herpesvirus 6 Reflects Human Migration out of Africa. Mol Biol Evol 38(1):96-107

Stone D; Long KR; Loprieno MA; De Silva Feelixge HS; Kenkel EJ; Liley RM; Rapp S; Roychoudhury P; Nguyen T; Stensland L; Colón-Thillet R; Klouser LM; Weber ND; Le C; Wagoner J; Goecker EA; Li AZ; Eichholz K; Corey L; Tyrrell DL; Greninger AL; Huang ML; Polyak SJ; Aubert M; Sagartz JE; Jerome KR, 2021. CRISPR-Cas9 gene editing of hepatitis B virus in chronically infected humanized mice. Mol Ther Methods Clin Dev 20:258-275

Perchetti GA; Pepper G; Shrestha L; LaTurner K; Yae Kim D; Huang ML; Jerome KR; Greninger AL, 2021. Performance characteristics of the Abbott Alinity m SARS-CoV-2 assay. J Clin Virol 140:104869

Li Y; Gordon E; Shean RC; Idle A; Deng X; Greninger AL; Delwart E, 2021. CrAssphage and its bacterial host in cat feces. Sci Rep 11(1):815

Perchetti GA; Huang ML; Mills MG; Jerome KR; Greninger AL, 2021. Analytical Sensitivity of the Abbott BinaxNOW COVID-19 Ag Card. J Clin Microbiol 59.

Barnabas RV; Brown ER; Bershteyn A; Stankiewicz Karita HC; Johnston C; Thorpe LE; Kottkamp A; Neuzil KM; Laufer MK; Deming M; Paasche-Orlow MK; Kissinger PJ; Luk A; Paolino K; Landovitz RJ; Hoffman R; Schaafsma TT; Krows ML; Thomas KK; Morrison S; Haugen HS; Kidoguchi L; Wener M; Greninger AL; Huang ML; Jerome KR; Wald A; Celum C; Chu HY; Baeten JM, 2021. Hydroxychloroquine as Postexposure Prophylaxis to Prevent Severe Acute Respiratory Syndrome Coronavirus 2 Infection : A Randomized Trial. Ann Intern Med 174(3):344-352

Corcorran MA; Olin S; Rani G; Nasenbeny K; Constantino-Shor C; Holmes C; Quinnan-Hostein L; Solan W; Snoeyenbos Newman G; Roxby AC; Greninger AL; Jerome KR; Neme S; Lynch JB; Dellit TH; Cohen SA, 2021. Prolonged persistence of PCR-detectable virus during an outbreak of SARS-CoV-2 in an inpatient geriatric psychiatry unit in King County, Washington. Am J Infect Control 49(3):293-298

Mathieu C; Ferren M; Harder O; Bovier FT; Marcink TC; Predella C; Angius F; Drew-Bear J; Dorrello NV; Greninger AL; Moscona A; Niewiesk S; Horvat B; Porotto M, 2021. Single-chain variable fragment antibody constructs neutralize measles virus infection in vitro and in vivo. Cell Mol Immunol 18(7):1835-1837

Boonyaratanakornkit J; Morishima C; Selke S; Zamora D; McGuffin S; Shapiro AE; Campbell VL; McClurkan CL; Jing L; Gross R; Liang J; Postnikova E; Mazur S; Lukin VV; Chaudhary A; Das MK; Fink SL; Bryan A; Greninger AL; Jerome KR; Holbrook MR; Gernsheimer TB; Wener MH; Wald A; Koelle DM, 2021. Clinical, laboratory, and temporal predictors of neutralizing antibodies against SARS-CoV-2 among COVID-19 convalescent plasma donor candidates. J Clin Invest 131.

Mathieu C; Bovier FT; Ferren M; Lieberman NAP; Predella C; Lalande A; Peddu V; Lin MJ; Addetia A; Patel A; Outlaw V; Corneo B; Dorrello NV; Briese T; Hardie D; Horvat B; Moscona A; Greninger AL; Porotto M, 2021. Molecular Features of the Measles Virus Viral Fusion Complex That Favor Infection and Spread in the Brain. mBio 12(3):e0079921

Pettit R; Peng B; Yu P; Matos PG; Greninger AL; McCashin J; Amos CI, 2021. Optimized Post-Vaccination Strategies and Preventative Measures for SARS-CoV-2. medRxiv.

Mayfield JJ; Chatterjee NA; Noseworthy PA; Poole JE; Ackerman MJ; Stewart J; Kissinger PJ; Dwyer J; Hosek S; Oyedele T; Paasche-Orlow MK; Paolino K; Friedman PA; Waters C; Moreno J; Leingang H; Heller KB; Morrison SA; Krows ML; Barnabas RV; Baeten J; Johnston C; Sridhar AR, 2021. Implementation of a fully remote randomized clinical trial with cardiac monitoring. Commun Med (Lond) 1:62

Rijsbergen LC; Schmitz KS; Begeman L; Drew-Bear J; Gommers L; Lamers MM; Greninger AL; Haagmans BL; Porotto M; de Swart RL; Moscona A; de Vries RD, 2021. Modeling Infection and Tropism of Human Parainfluenza Virus Type 3 in Ferrets. mBio 13(1):e0383121

Boucau J; Chew KW; Choudhary M; Deo R; Regan J; Flynn JP; Crain CR; Hughes MD; Ritz J; Moser C; Dragavon JA; Javan AC; Nirula A; Klekotka P; Greninger AL; Coombs RW; Fischer WA 2nd; Daar ES; Wohl DA; Eron JJ; Currier JS; Smith DM; Li JZ; Barczak AK, 2021. Monoclonal antibody treatment drives rapid culture conversion in SARS-CoV-2 infection. medRxiv.

Greninger AL; Zerr DM, 2021. NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology. J Pediatric Infect Dis Soc 10(Supplement_4):S88-S95

Lieberman NAP; Lin MJ; Xie H; Shrestha L; Nguyen T; Huang ML; Haynes AM; Romeis E; Wang QQ; Zhang RL; Kou CX; Ciccarese G; Dal Conte I; Cusini M; Drago F; Nakayama SI; Lee K; Ohnishi M; Konda KA; Vargas SK; Eguiluz M; Caceres CF; Klausner JD; Mitjà O; Rompalo A; Mulcahy F; Hook EW 3rd; Lukehart SA; Casto AM; Roychoudhury P; DiMaio F; Giacani L; Greninger AL, 2021. Treponema pallidum genome sequencing from six continents reveals variability in vaccine candidate genes and dominance of Nichols clade strains in Madagascar. PLoS Negl Trop Dis 15(12):e0010063

Gandhi S; Klein J; Robertson A; Peña-Hernández MA; Lin MJ; Roychoudhury P; Lu P; Fournier J; Ferguson D; Mohamed Bakhash SA; Catherine Muenker M; Srivathsan A; Wunder EA; Kerantzas N; Wang W; Lindenbach B; Pyle A; Wilen CB; Ogbuagu O; Greninger AL; Iwasaki A; Schulz WL; Ko AI, 2021. De novo emergence of a remdesivir resistance mutation during treatment of persistent SARS-CoV-2 infection in an immunocompromised patient: A case report. medRxiv.

Cox RM; Wolf JD; Lieber CM; Sourimant J; Lin MJ; Babusis D; DuPont V; Chan J; Barrett KT; Lye D; Kalla R; Chun K; Mackman RL; Ye C; Cihlar T; Martinez-Sobrido L; Greninger AL; Bilello JP; Plemper RK, 2021. Oral prodrug of remdesivir parent GS-441524 is efficacious against SARS-CoV-2 in ferrets. Nat Commun 12(1):6415

Lownik JC; Farrar JS; Way GW; McKay A; Roychoudhury P; Greninger AL; Martin RK, 2021. Fast SARS-CoV-2 Variant Detection Using Snapback Primer High-Resolution Melting. Diagnostics (Basel) 11.

Greninger AL; Rybkina K; Lin MJ; Drew-Bear J; Marcink TC; Shean RC; Makhsous N; Boeckh M; Harder O; Bovier F; Burstein SR; Niewiesk S; Rima BK; Porotto M; Moscona A, 2021. Human parainfluenza virus evolution during lung infection of immunocompromised individuals promotes viral persistence. J Clin Invest 131.

Ferren M; Favède V; Decimo D; Iampietro M; Lieberman NAP; Weickert JL; Pelissier R; Mazelier M; Terrier O; Moscona A; Porotto M; Greninger AL; Messaddeq N; Horvat B; Mathieu C, 2021. Hamster organotypic modeling of SARS-CoV-2 lung and brainstem infection. Nat Commun 12(1):5809

Greninger AL, 2021. Test it earlier, result it faster, makes us stronger: how rapid viral diagnostics enable therapeutic success. Curr Opin Virol 49:111-116

Despres HW; Mills MG; Shirley DJ; Schmidt MM; Huang ML; Jerome KR; Greninger AL; Bruce EA, 2021. Quantitative measurement of infectious virus in SARS-CoV-2 Alpha, Delta and Epsilon variants reveals higher infectivity (viral titer:RNA ratio) in clinical samples containing the Delta and Epsilon variants. medRxiv.

Hill JA; Ujjani CS; Greninger AL; Shadman M; Gopal AK, 2021. Immunogenicity of a heterologous COVID-19 vaccine after failed vaccination in a lymphoma patient. Cancer Cell 39(8):1037-1038

Bradley BT; Bryan A; Fink SL; Goecker EA; Roychoudhury P; Huang ML; Zhu H; Chaudhary A; Madarampalli B; Lu JYC; Strand K; Whimbey E; Bryson-Cahn C; Schippers A; Mani NS; Pepper G; Jerome KR; Morishima C; Coombs RW; Wener M; Cohen S; Greninger AL, 2021. Anti-SARS-CoV-2 Antibody Levels Measured by the AdviseDx SARS-CoV-2 Assay Are Concordant with Previously Available Serologic Assays but Are Not Fully Predictive of Sterilizing Immunity. J Clin Microbiol 59(9):e0098921

Perchetti GA; Zhu H; Mills MG; Shrestha L; Wagner C; Bakhash SM; Lin MJ; Xie H; Huang ML; Mathias P; Bedford T; Jerome KR; Greninger AL; Roychoudhury P, 2021. Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State. J Med Virol 93(10):5931-5941

Bourassa L; Perchetti GA; Phung Q; Lin MJ; Mills MG; Roychoudhury P; Harmon KG; Reed JC; Greninger AL, 2021. A SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance. J Clin Virol 141:104900

Yoke LH; Lee JM; Krantz EM; Morris J; Marquis S; Bhattacharyya P; So L; Riedo FX; Simmons J; Khaki AR; Cheng GS; Greninger AL; Pergam SA; Waghmare A; Ogimi C; Liu C, 2021. Clinical and Virologic Characteristics and Outcomes of Coronavirus Disease 2019 at a Cancer Center. Open Forum Infect Dis 8(6):ofab193

Peng B; Zhou W; Pettit RW; Yu P; Matos PG; Greninger AL; McCashin J; Amos CI, 2021. Reducing COVID-19 quarantine with SARS-CoV-2 testing: a simulation study. BMJ Open 11(7):e050473

Ye C; Chiem K; Park JG; Silvas JA; Morales Vasquez D; Sourimant J; Lin MJ; Greninger AL; Plemper RK; Torrelles JB; Kobie JJ; Walter MR; de la Torre JC; Martinez-Sobrido L, 2021. Analysis of SARS-CoV-2 infection dynamic in vivo using reporter-expressing viruses. Proc Natl Acad Sci U S A 118.

Greninger AL, 2021. Unbiased Pandemic Pathogen Detection and the Federal Register. J Clin Microbiol 59(10):e0134621

Berg MG; Zhen W; Lucic D; Degli-Angeli EJ; Anderson M; Forberg K; Olivo A; Sheikh F; Toolsie D; Greninger AL; Cloherty GA; Coombs RW; Berry GJ, 2021. Development of the RealTime SARS-CoV-2 quantitative Laboratory Developed Test and correlation with viral culture as a measure of infectivity. J Clin Virol 143:104945

Lin MJ; Haynes AM; Addetia A; Lieberman NAP; Phung Q; Xie H; Nguyen TV; Molini BJ; Lukehart SA; Giacani L; Greninger AL, 2021. Longitudinal TprK profiling of in vivo and in vitro-propagated Treponema pallidum subsp. pallidum reveals accumulation of antigenic variants in absence of immune pressure. PLoS Negl Trop Dis 15(9):e0009753

Chiem K; Morales Vasquez D; Silvas JA; Park JG; Piepenbrink MS; Sourimant J; Lin MJ; Greninger AL; Plemper RK; Torrelles JB; Walter MR; de la Torre JC; Kobie JK; Ye C; Martinez-Sobrido L, 2021. A Bifluorescent-Based Assay for the Identification of Neutralizing Antibodies against SARS-CoV-2 Variants of Concern In Vitro and In Vivo. J Virol 95(22):e0112621

Choudhary MC; Chew KW; Deo R; Flynn JP; Regan J; Crain CR; Moser C; Hughes M; Ritz J; Ribeiro RM; Ke R; Dragavon JA; Javan AC; Nirula A; Klekotka P; Greninger AL; Fletcher CV; Daar ES; Wohl DA; Eron JJ; Currier JS; Parikh UM; Sieg SF; Perelson AS; Coombs RW; Smith DM; Li JZ, 2021. Emergence of SARS-CoV-2 Resistance with Monoclonal Antibody Therapy. medRxiv.

Buckner FS; McCulloch DJ; Atluri V; Blain M; McGuffin SA; Nalla AK; Huang ML; Greninger AL; Jerome KR; Cohen SA; Neme S; Green ML; Chu HY; Kim HN, 2020. Clinical Features and Outcomes of 105 Hospitalized Patients With COVID-19 in Seattle, Washington. Clin Infect Dis 71(16):2167-2173

Perchetti GA; Nalla AK; Huang ML; Zhu H; Wei Y; Stensland L; Loprieno MA; Jerome KR; Greninger AL, 2020. Validation of SARS-CoV-2 detection across multiple specimen types. J Clin Virol 128:104438

Perchetti GA; Huang ML; Peddu V; Jerome KR; Greninger AL, 2020. Stability of SARS-CoV-2 in Phosphate-Buffered Saline for Molecular Detection. J Clin Microbiol 58.

Roxby AC; Greninger AL; Hatfield KM; Lynch JB; Dellit TH; James A; Taylor J; Page LC; Kimball A; Arons M; Munanga A; Stone N; Jernigan JA; Reddy SC; Lewis J; Cohen SA; Jerome KR; Duchin JS; Neme S, 2020. Outbreak Investigation of COVID-19 Among Residents and Staff of an Independent and Assisted Living Community for Older Adults in Seattle, Washington. JAMA Intern Med 180(8):1101-1105

Casto AM; Huang ML; Nalla A; Perchetti GA; Sampoleo R; Shrestha L; Wei Y; Zhu H; Greninger AL; Jerome KR, 2020. Comparative Performance of SARS-CoV-2 Detection Assays using Seven Different Primer/Probe Sets and One Assay Kit. medRxiv.

Lieberman JA; Mays JA; Wells C; Cent A; Bell D; Bankson DD; Greninger AL; Jerome KR; Limaye AP, 2020. Expedited SARS-CoV-2 screening of donors and recipients supports continued solid organ transplantation. Am J Transplant 20(11):3106-3112

Mays JA; Greninger AL; Jerome KR; Lynch JB; Mathias PC, 2020. Preprocedural Surveillance Testing for SARS-CoV-2 in an Asymptomatic Population in the Seattle Region Shows Low Rates of Positivity. J Clin Microbiol 58.

Degli-Angeli E; Dragavon J; Huang ML; Lucic D; Cloherty G; Jerome KR; Greninger AL; Coombs RW, 2020. Validation and verification of the Abbott RealTime SARS-CoV-2 assay analytical and clinical performance. J Clin Virol 129:104474

Bruce EA; Huang ML; Perchetti GA; Tighe S; Laaguiby P; Hoffman JJ; Gerrard DL; Nalla AK; Wei Y; Greninger AL; Diehl SA; Shirley DJ; Leonard DGB; Huston CD; Kirkpatrick BD; Dragon JA; Crothers JW; Jerome KR; Botten JW, 2020. DIRECT RT-qPCR DETECTION OF SARS-CoV-2 RNA FROM PATIENT NASOPHARYNGEAL SWABS WITHOUT AN RNA EXTRACTION STEP. bioRxiv.

Randhawa AK; Fisher LH; Greninger AL; Li SS; Andriesen J; Corey L; Jerome KR, 2020. Changes in SARS-CoV-2 Positivity Rate in Outpatients in Seattle and Washington State, March 1-April 16, 2020. JAMA 323(22):2334-2336

Joung J; Ladha A; Saito M; Segel M; Bruneau R; Huang MW; Kim NG; Yu X; Li J; Walker BD; Greninger AL; Jerome KR; Gootenberg JS; Abudayyeh OO; Zhang F, 2020. Point-of-care testing for COVID-19 using SHERLOCK diagnostics. medRxiv.

Long DR; Gombar S; Hogan CA; Greninger AL; OReilly Shah V; Bryson-Cahn C; Stevens B; Rustagi A; Jerome KR; Kong CS; Zehnder J; Shah NH; Weiss NS; Pinsky BA; Sunshine J, 2020. Occurrence and Timing of Subsequent SARS-CoV-2 RT-PCR Positivity Among Initially Negative Patients. medRxiv.

Fauver JR; Petrone ME; Hodcroft EB; Shioda K; Ehrlich HY; Watts AG; Vogels CBF; Brito AF; Alpert T; Muyombwe A; Razeq J; Downing R; Cheemarla NR; Wyllie AL; Kalinich CC; Ott IM; Quick J; Loman NJ; Neugebauer KM; Greninger AL; Jerome KR; Roychoudhury P; Xie H; Shrestha L; Huang ML; Pitzer VE; Iwasaki A; Omer SB; Khan K; Bogoch II; Martinello RA; Foxman EF; Landry ML; Neher RA; Ko AI; Grubaugh ND, 2020. Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States. Cell 181(5):990-996.e5

Barrett SLR; Holmes EA; Long DR; Shean RC; Bautista GE; Ravishankar S; Peddu V; Cookson BT; Singh PK; Greninger AL; Salipante SJ, 2020. Cell free DNA from respiratory pathogens is detectable in the blood plasma of Cystic Fibrosis patients. Sci Rep 10(1):6903

Bryan A; Pepper G; Wener MH; Fink SL; Morishima C; Chaudhary A; Jerome KR; Mathias PC; Greninger AL, 2020. Performance Characteristics of the Abbott Architect SARS-CoV-2 IgG Assay and Seroprevalence in Boise, Idaho. J Clin Microbiol 58.

Peddu V; Bradley BT; Casto AM; Shree R; Colbert BG; Xie H; Santo TK; Huang ML; Cheng EY; Konnick E; Salipante SJ; Jerome KR; Lockwood CM; Greninger AL, 2020. High-resolution profiling of human cytomegalovirus cell-free DNA in human plasma highlights its exceptionally fragmented nature. Sci Rep 10(1):3734

Casto AM; Roychoudhury P; Xie H; Selke S; Perchetti GA; Wofford H; Huang ML; Verjans GMGM; Gottlieb GS; Wald A; Jerome KR; Koelle DM; Johnston C; Greninger AL, 2020. Large, Stable, Contemporary Interspecies Recombination Events in Circulating Human Herpes Simplex Viruses. J Infect Dis 221(8):1271-1279

Greninger AL; Addetia A; Starr K; Cybulski RJ; Stewart MK; Salipante SJ; Bryan AB; Cookson B; Gaudreau C; Bekal S; Fang FC, 2020. International Spread of Multidrug-Resistant Campylobacter coli in Men Who Have Sex With Men in Washington State and Québec, 2015-2018. Clin Infect Dis 71(8):1896-1904

Casto AM; Stout SC; Selvarangan R; Freeman AF; Newell BD; Stahl ED; Ahmed AA; Greninger AL; Yin DE, 2020. Evaluation of Genotypic Antiviral Resistance Testing as an Alternative to Phenotypic Testing in a Patient with DOCK8 Deficiency and Severe HSV-1 Disease. J Infect Dis 221(12):2035-2042

Paul GR; Leber A; Nemastil CJ; Novak KJ; Brady M; Stack-Simone S; Greninger AL; Antonara S, 2020. Identification of Mycobacterium porcinum in patients with cystic Fibrosis: Pathogen or contaminant? J Cyst Fibros 19(4):580-586

Marcink TC; Yariv E; Rybkina K; Más V; Bovier FT; des Georges A; Greninger AL; Alabi CA; Porotto M; Ben-Tal N; Moscona A, 2020. Hijacking the Fusion Complex of Human Parainfluenza Virus as an Antiviral Strategy. mBio 11.

Pandey U; Greninger AL; Levin GR; Jerome KR; Anand VC; Dien Bard J, 2020. Pathogen or Bystander: Clinical Significance of Detecting Human Herpesvirus 6 in Pediatric Cerebrospinal Fluid. J Clin Microbiol 58.

Jing L; Ott M; Church CD; Kulikauskas RM; Ibrani D; Iyer JG; Afanasiev OK; Colunga A; Cook MM; Xie H; Greninger AL; Paulson KG; Chapuis AG; Bhatia S; Nghiem P; Koelle DM, 2020. Prevalent and Diverse Intratumoral Oncoprotein-Specific CD8(+) T Cells within Polyomavirus-Driven Merkel Cell Carcinomas. Cancer Immunol Res 8(5):648-659

Peddu V; Shean RC; Xie H; Shrestha L; Perchetti GA; Minot SS; Roychoudhury P; Huang ML; Nalla A; Reddy SB; Phung Q; Reinhardt A; Jerome KR; Greninger AL, 2020. Metagenomic Analysis Reveals Clinical SARS-CoV-2 Infection and Bacterial or Viral Superinfection and Colonization. Clin Chem 66(7):966-972

Bhatraju PK; Ghassemieh BJ; Nichols M; Kim R; Jerome KR; Nalla AK; Greninger AL; Pipavath S; Wurfel MM; Evans L; Kritek PA; West TE; Luks A; Gerbino A; Dale CR; Goldman JD; O'Mahony S; Mikacenic C, 2020. Covid-19 in Critically Ill Patients in the Seattle Region - Case Series. N Engl J Med 382(21):2012-2022

Addetia A; Tantalo LC; Lin MJ; Xie H; Huang ML; Marra CM; Greninger AL, 2020. Comparative genomics and full-length Tprk profiling of Treponema pallidum subsp. pallidum reinfection. PLoS Negl Trop Dis 14(4):e0007921

Nalla AK; Casto AM; Huang MW; Perchetti GA; Sampoleo R; Shrestha L; Wei Y; Zhu H; Jerome KR; Greninger AL, 2020. Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit. J Clin Microbiol 58.

Roxby AC; Greninger AL; Hatfield KM; Lynch JB; Dellit TH; James A; Taylor J; Page LC; Kimball A; Arons M; Schieve LA; Munanga A; Stone N; Jernigan JA; Reddy SC; Lewis J; Cohen SA; Jerome KR; Duchin JS; Neme S, 2020. Detection of SARS-CoV-2 Among Residents and Staff Members of an Independent and Assisted Living Community for Older Adults - Seattle, Washington, 2020. MMWR Morb Mortal Wkly Rep 69(14):416-418

Waghmare A; Krantz EM; Baral S; Vasquez E; Loeffelholz T; Chung EL; Pandey U; Kuypers J; Duke ER; Jerome KR; Greninger AL; Reeves DB; Hladik F; Cardozo-Ojeda EF; Boeckh M; Schiffer JT, 2020. Reliability of self-sampling for accurate assessment of respiratory virus viral and immunologic kinetics. medRxiv.

Lieberman JA; Pepper G; Naccache SN; Huang ML; Jerome KR; Greninger AL, 2020. Comparison of Commercially Available and Laboratory-Developed Assays for In Vitro Detection of SARS-CoV-2 in Clinical Laboratories. J Clin Microbiol 58.

Deng X; Gu W; Federman S; du Plessis L; Pybus OG; Faria N; Wang C; Yu G; 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; Chan C; Yu AT; Chai SJ; Villarino E; Bonin B; Wadford DA; Chiu CY, 2020. A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage. medRxiv.

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, 2020. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California. Science 369(6503):582-587

Bedford T; Greninger AL; Roychoudhury P; Starita LM; Famulare M; Huang ML; Nalla A; Pepper G; Reinhardt A; Xie H; Shrestha L; Nguyen TN; Adler A; Brandstetter E; Cho S; Giroux D; Han PD; Fay K; Frazar CD; Ilcisin M; Lacombe K; Lee J; Kiavand A; Richardson M; Sibley TR; Truong M; Wolf CR; Nickerson DA; Rieder MJ; Englund JA; Hadfield J; Hodcroft EB; Huddleston J; Moncla LH; Müller NF; Neher RA; Deng X; Gu W; Federman S; Chiu C; Duchin J; Gautom R; Melly G; Hiatt B; Dykema P; Lindquist S; Queen K; Tao Y; Uehara A; Tong S; MacCannell D; Armstrong GL; Baird GS; Chu HY; Shendure J; Jerome KR, 2020. Cryptic transmission of SARS-CoV-2 in Washington State. medRxiv.

Addetia A; Crawford KHD; Dingens A; Zhu H; Roychoudhury P; Huang ML; Jerome KR; Bloom JD; Greninger AL, 2020. Neutralizing Antibodies Correlate with Protection from SARS-CoV-2 in Humans during a Fishery Vessel Outbreak with a High Attack Rate. J Clin Microbiol 58.

Bryan A; Fink SL; Gattuso MA; Pepper G; Chaudhary A; Wener MH; Morishima C; Jerome KR; Mathias PC; Greninger AL, 2020. SARS-CoV-2 Viral Load on Admission Is Associated With 30-Day Mortality. Open Forum Infect Dis 7(12):ofaa535

Addetia A; Lin MJ; Phung Q; Xie H; Huang ML; Ciccarese G; Dal Conte I; Cusini M; Drago F; Giacani L; Greninger AL, 2020. Estimation of Full-Length TprK Diversity in Treponema pallidum subsp. pallidum. mBio 11.

Outlaw VK; Bovier FT; Mears MC; Cajimat MN; Zhu Y; Lin MJ; Addetia A; Lieberman NAP; Peddu V; Xie X; Shi PY; Greninger AL; Gellman SH; Bente DA; Moscona A; Porotto M, 2020. Inhibition of Coronavirus Entry In Vitro and Ex Vivo by a Lipid-Conjugated Peptide Derived from the SARS-CoV-2 Spike Glycoprotein HRC Domain. mBio 11.

Boonyaratanakornkit J; Morishima C; Selke S; Zamora D; McGuffin S; Shapiro AE; Campbell VL; McClurkan CL; Jing L; Gross R; Liang J; Postnikova E; Mazur S; Chaudhary A; Das MK; Fink SL; Bryan A; Greninger AL; Jerome KR; Holbrook MR; Gernsheimer TB; Wener MH; Wald A; Koelle DM, 2020. Clinical, laboratory, and temporal predictors of neutralizing antibodies to SARS-CoV-2 after COVID-19. medRxiv.

Addetia A; Lin MJ; Peddu V; Roychoudhury P; Jerome KR; Greninger AL, 2020. Sensitive Recovery of Complete SARS-CoV-2 Genomes from Clinical Samples by Use of Swift Biosciences' SARS-CoV-2 Multiplex Amplicon Sequencing Panel. J Clin Microbiol 59.

Rassoulian Barrett S; Hoffman NG; Rosenthal C; Bryan A; Marshall DA; Lieberman J; Greninger AL; Peddu V; Cookson BT; Salipante SJ, 2020. Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment. J Clin Microbiol 58.

Müller NF; Wagner C; Frazar CD; Roychoudhury P; Lee J; Moncla LH; Pelle B; Richardson M; Ryke E; Xie H; Shrestha L; Addetia A; Rachleff VM; Lieberman NAP; Huang ML; Gautom R; Melly G; Hiatt B; Dykema P; Adler A; Brandstetter E; Han PD; Fay K; Llcisin M; Lacombe K; Sibley TR; Truong M; Wolf CR; Boeckh M; Englund JA; Famulare M; Lutz BR; Rieder MJ; Thompson M; Duchin JS; Starita LM; Chu HY; Shendure J; Jerome KR; Lindquist S; Greninger AL; Nickerson DA; Bedford T, 2020. Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State. medRxiv.

Bruce EA; Huang ML; Perchetti GA; Tighe S; Laaguiby P; Hoffman JJ; Gerrard DL; Nalla AK; Wei Y; Greninger AL; Diehl SA; Shirley DJ; Leonard DGB; Huston CD; Kirkpatrick BD; Dragon JA; Crothers JW; Jerome KR; Botten JW, 2020. Direct RT-qPCR detection of SARS-CoV-2 RNA from patient nasopharyngeal swabs without an RNA extraction step. PLoS Biol 18(10):e3000896

Goldman JD; Wang K; Röltgen K; Nielsen SCA; Roach JC; Naccache SN; Yang F; Wirz OF; Yost KE; Lee JY; Chun K; Wrin T; Petropoulos CJ; Lee I; Fallen S; Manner PM; Wallick JA; Algren HA; Murray KM; Su Y; Hadlock J; Jeharajah J; Berrington WR; Pappas GP; Nyatsatsang ST; Greninger AL; Satpathy AT; Pauk JS; Boyd SD; Heath JR, 2020. Reinfection with SARS-CoV-2 and Failure of Humoral Immunity: a case report. medRxiv.

McAulay K; Bryan A; Greninger AL; Grill F; Lake D; Kaleta EJ; Grys TE, 2020. Retrospective clinical evaluation of 4 lateral flow assays for the detection of SARS-CoV-2 IgG. Diagn Microbiol Infect Dis 98(3):115161

Mohon AN; Oberding L; Hundt J; van Marle G; Pabbaraju K; Berenger BM; Lisboa L; Griener T; Czub M; Doolan C; Servellita V; Chiu CY; Greninger AL; Jerome KR; Pillai DR, 2020. Optimization and clinical validation of dual-target RT-LAMP for SARS-CoV-2. J Virol Methods 286:113972

Joung J; Ladha A; Saito M; Kim NG; Woolley AE; Segel M; Barretto RPJ; Ranu A; Macrae RK; Faure G; Ioannidi EI; Krajeski RN; Bruneau R; Huang MW; Yu XG; Li JZ; Walker BD; Hung DT; Greninger AL; Jerome KR; Gootenberg JS; Abudayyeh OO; Zhang F, 2020. Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing. N Engl J Med 383(15):1492-1494

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; Roychoudhury P; Xie H; Shrestha L; Huang ML; Pitzer VE; Iwasaki A; Omer SB; Khan K; Bogoch II; Martinello RA; Foxman EF; Landry ML; Neher RA; Ko AI; Grubaugh ND, 2020. Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology. medRxiv.

Lieberman NAP; Peddu V; Xie H; Shrestha L; Huang ML; Mears MC; Cajimat MN; Bente DA; Shi PY; Bovier F; Roychoudhury P; Jerome KR; Moscona A; Porotto M; Greninger AL, 2020. In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age. PLoS Biol 18(9):e3000849

Bedford T; Greninger AL; Roychoudhury P; Starita LM; Famulare M; Huang ML; Nalla A; Pepper G; Reinhardt A; Xie H; Shrestha L; Nguyen TN; Adler A; Brandstetter E; Cho S; Giroux D; Han PD; Fay K; Frazar CD; Ilcisin M; Lacombe K; Lee J; Kiavand A; Richardson M; Sibley TR; Truong M; Wolf CR; Nickerson DA; Rieder MJ; Englund JA; Hadfield J; Hodcroft EB; Huddleston J; Moncla LH; Müller NF; Neher RA; Deng X; Gu W; Federman S; Chiu C; Duchin JS; Gautom R; Melly G; Hiatt B; Dykema P; Lindquist S; Queen K; Tao Y; Uehara A; Tong S; MacCannell D; Armstrong GL; Baird GS; Chu HY; Shendure J; Jerome KR, 2020. Cryptic transmission of SARS-CoV-2 in Washington state. Science 370(6516):571-575

Addetia A; Crawford KH; Dingens A; Zhu H; Roychoudhury P; Huang ML; Jerome KR; Bloom JD; Greninger AL, 2020. Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate. medRxiv.

Lieberman NAP; Peddu V; Xie H; Shrestha L; Huang ML; Mears MC; Cajimat MN; Bente DA; Shi PY; Bovier F; Roychoudhury P; Jerome KR; Moscona A; Porotto M; Greninger AL, 2020. In vivo antiviral host response to SARS-CoV-2 by viral load, sex, and age. bioRxiv.

Fang FC; Naccache SN; Greninger AL, 2020. The Laboratory Diagnosis of Coronavirus Disease 2019- Frequently Asked Questions. Clin Infect Dis 71(11):2996-3001

Perchetti GA; Nalla AK; Huang ML; Jerome KR; Greninger AL, 2020. Multiplexing primer/probe sets for detection of SARS-CoV-2 by qRT-PCR. J Clin Virol 129:104499

Mani NS; Budak JZ; Lan KF; Bryson-Cahn C; Zelikoff A; Barker GEC; Grant CW; Hart K; Barbee CJ; Sandoval MD; Dostal CL; Corcorran M; Ungerleider HM; Gates JO; Olin SV; Bryan A; Hoffman NG; Marquis SR; Harvey ML; Nasenbeny K; Mertens K; Chew LD; Greninger AL; Jerome KR; Pottinger PS; Dellit TH; Liu C; Pergam SA; Neme S; Lynch JB; Kim HN; Cohen SA, 2020. Prevalence of Coronavirus Disease 2019 Infection and Outcomes Among Symptomatic Healthcare Workers in Seattle, Washington. Clin Infect Dis 71(10):2702-2707

Aubert M; Strongin DE; Roychoudhury P; Loprieno MA; Haick AK; Klouser LM; Stensland L; Huang ML; Makhsous N; Tait A; De Silva Feelixge HS; Galetto R; Duchateau P; Greninger AL; Stone D; Jerome KR, 2020. Gene editing and elimination of latent herpes simplex virus in vivo. Nat Commun 11(1):4148

Mitchell SH; Bulger EM; Duber HC; Greninger AL; Ong TD; Morris SC; Chew LD; Haffner TM; Sakata VL; Lynch JB, 2020. Western Washington State COVID-19 Experience: Keys to Flattening the Curve and Effective Health System Response. J Am Coll Surg 231(3):316-324.e1

Greene DN; Dickerson JA; Greninger AL; Schmidt RL, 2020. When To Retest: an Examination of Repeat COVID-19 PCR Patterns in an Ambulatory Population. J Clin Microbiol 58.

Addetia A; Xie H; Roychoudhury P; Shrestha L; Loprieno M; Huang ML; Jerome KR; Greninger AL, 2020. Identification of multiple large deletions in ORF7a resulting in in-frame gene fusions in clinical SARS-CoV-2 isolates. J Clin Virol 129:104523

Cox RM; Sourimant J; Toots M; Yoon JJ; Ikegame S; Govindarajan M; Watkinson RE; Thibault P; Makhsous N; Lin MJ; Marengo JR; Sticher Z; Kolykhalov AA; Natchus MG; Greninger AL; Lee B; Plemper RK, 2020. Orally efficacious broad-spectrum allosteric inhibitor of paramyxovirus polymerase. Nat Microbiol 5(10):1232-1246

McCulloch DJ; Kim AE; Wilcox NC; Logue JK; Greninger AL; Englund JA; Chu HY, 2020. Comparison of Unsupervised Home Self-collected Midnasal Swabs With Clinician-Collected Nasopharyngeal Swabs for Detection of SARS-CoV-2 Infection. JAMA Netw Open 3(7):e2016382

Greninger AL; Jerome KR, 2020. The First Quarter of SARS-CoV-2 Testing: the University of Washington Medicine Experience. J Clin Microbiol 58.

Casto AM; Huang MW; Xie H; Jerome KR; Wald A; Johnston CM; Greninger AL, 2020. Herpes Simplex Virus Mistyping due to HSV-1 × HSV-2 Interspecies Recombination in Viral Gene Encoding Glycoprotein B. Viruses 12.

Perchetti GA; Sullivan KW; Pepper G; Huang ML; Breit N; Mathias P; Jerome KR; Greninger AL, 2020. Pooling of SARS-CoV-2 samples to increase molecular testing throughput. J Clin Virol 131:104570

Creager HM; Cabrera B; Schnaubelt A; Cox JL; Cushman-Vokoun AM; Shakir SM; Tardif KD; Huang ML; Jerome KR; Greninger AL; Drobysheva D; Spaulding U; Rogatcheva M; Bourzac KM; Hinrichs SH; Broadhurst MJ; Fey PD, 2020. Clinical evaluation of the BioFire® Respiratory Panel 2.1 and detection of SARS-CoV-2. J Clin Virol 129:104538

Melendez D; Roberts MC; Greninger AL; Weissman S; No D; Rabinowitz P; Wasser S, 2019. Whole-genome analysis of extraintestinal pathogenic Escherichia coli (ExPEC) MDR ST73 and ST127 isolated from endangered southern resident killer whales (Orcinus orca). J Antimicrob Chemother 74(8):2176-2180

Ramchandani MS; Jing L; Russell RM; Tran T; Laing KJ; Magaret AS; Selke S; Cheng A; Huang ML; Xie H; Strachan E; Greninger AL; Roychoudhury P; Jerome KR; Wald A; Koelle DM, 2019. Viral Genetics Modulate Orolabial Herpes Simplex Virus Type 1 Shedding in Humans. J Infect Dis 219(7):1058-1066

Vasireddy R; Vasireddy S; Brown-Elliott BA; Greninger AL; Davidson RM; Ard KL; Turenne CY; Wallace RJ Jr, 2019. Mycobacterium talmoniae, a Potential Pulmonary Pathogen Isolated from Multiple Patients with Bronchiectasis in the United States, Including the First Case of Clinical Disease in a Patient with Cystic Fibrosis. J Clin Microbiol 57.

Casto AM; Adler AL; Makhsous N; Crawford K; Qin X; Kuypers JM; Huang ML; Zerr DM; Greninger AL, 2019. Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters. Clin Infect Dis 69(6):941-948

Shean RC; Makhsous N; Stoddard GD; Lin MJ; Greninger AL, 2019. VAPiD: a lightweight cross-platform viral annotation pipeline and identification tool to facilitate virus genome submissions to NCBI GenBank. BMC Bioinformatics 20(1):48

Greninger AL, 2019. Societal Implications of the Internet of Pathogens. J Clin Microbiol 57.

Addetia A; Greninger AL; Adler A; Yuan S; Makhsous N; Qin X; Zerr DM, 2019. A Novel, Widespread qacA Allele Results in Reduced Chlorhexidine Susceptibility in Staphylococcus epidermidis. Antimicrob Agents Chemother 63.

Shean RC; Greninger AL, 2019. One future of clinical metagenomic sequencing for infectious diseases. Expert Rev Mol Diagn 19(10):849-851

Hanson DJ; Tsvetkova O; Rerolle GF; Greninger AL; Sette A; Jing L; Campbell VL; Koelle DM, 2019. Genome-Wide Approach to the CD4 T-Cell Response to Human Herpesvirus 6B. J Virol 93.

Greninger AL; Naccache SN, 2019. Metagenomics to Assist in the Diagnosis of Bloodstream Infection. J Appl Lab Med 3(4):643-653

Porotto M; Ferren M; Chen YW; Siu Y; Makhsous N; Rima B; Briese T; Greninger AL; Snoeck HW; Moscona A, 2019. Authentic Modeling of Human Respiratory Virus Infection in Human Pluripotent Stem Cell-Derived Lung Organoids. mBio 10.

Toots M; Yoon JJ; Cox RM; Hart M; Sticher ZM; Makhsous N; Plesker R; Barrena AH; Reddy PG; Mitchell DG; Shean RC; Bluemling GR; Kolykhalov AA; Greninger AL; Natchus MG; Painter GR; Plemper RK, 2019. Characterization of orally efficacious influenza drug with high resistance barrier in ferrets and human airway epithelia. Sci Transl Med 11.

Ikuta K; Roychoudhury P; Xie H; Mcclurkan CL; Walkiewicz M; Makhsous N; Huang ML; Beru Y; Alam M; Shepherd A; Lamotte ED; Patel K; Morris A; Ҫoruh B; Yu L; Bhattacharya R; Cheng R; Walter RB; Limaye AP; Lockwood CM; Holland SM; Rakita RM; Koelle DM; Greninger AL, 2019. Trillions and Trillions: Herpes Simplex Virus-1 Hepatitis in an Immunocompetent Adult. Open Forum Infect Dis 6(11):ofz465

Peddu V; Dubuc I; Gravel A; Xie H; Huang ML; Tenenbaum D; Jerome KR; Tardif JC; Dubé MP; Flamand L; Greninger AL, 2019. Inherited Chromosomally Integrated Human Herpesvirus 6 Demonstrates Tissue-Specific RNA Expression In Vivo That Correlates with an Increased Antibody Immune Response. J Virol 94.

Greninger AL; Naccache SN; Pannaraj P; Jerome KR; Dien Bard J; Ruderman JW, 2019. Closing the Brief Case: Inherited Chromosomally Integrated Human Herpesvirus 6 (HHV-6) in the Age of Multiplex HHV-6 Testing. J Clin Microbiol 57.

Greninger AL; Naccache SN; Pannaraj P; Jerome KR; Dien Bard J; Ruderman JW, 2019. The Brief Case: Inherited Chromosomally Integrated Human Herpesvirus 6 (HHV-6) in the Age of Multiplex HHV-6 Testing. J Clin Microbiol 57.

Starr K; Greninger AL; Makhsous N; Jerome KR; Cook L, 2019. Comparison of Three Adenovirus Quantitative PCR Assays with ATCC Reference Strains and Clinical Samples. J Clin Microbiol 57.

Greninger AL; Knudsen GM; Roychoudhury P; Hanson DJ; Sedlak RH; Xie H; Guan J; Nguyen T; Peddu V; Boeckh M; Huang ML; Cook L; Depledge DP; Zerr DM; Koelle DM; Gantt S; Yoshikawa T; Caserta M; Hill JA; Jerome KR, 2018. Comparative genomic, transcriptomic, and proteomic reannotation of human herpesvirus 6. BMC Genomics 19(1):204

Greninger AL, 2018. A decade of RNA virus metagenomics is (not) enough. Virus Res 244:218-229

Xue KS; Greninger AL; Pérez-Osorio A; Bloom JD, 2018. Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples. mSphere 3.

Thakkar VD; Cox RM; Sawatsky B; da Fontoura Budaszewski R; Sourimant J; Wabbel K; Makhsous N; Greninger AL; von Messling V; Plemper RK, 2018. The Unstructured Paramyxovirus Nucleocapsid Protein Tail Domain Modulates Viral Pathogenesis through Regulation of Transcriptase Activity. J Virol 92.

Gern BH; Greninger AL; Weissman SJ; Stapp JR; Tao Y; Qin X, 2018. Continued in vitro cefazolin susceptibility in methicillin-susceptible Staphylococcus aureus. Ann Clin Microbiol Antimicrob 17(1):5

Greninger AL; Roychoudhury P; Makhsous N; Hanson D; Chase J; Krueger G; Xie H; Huang ML; Saunders L; Ablashi D; Koelle DM; Cook L; Jerome KR, 2018. Copy Number Heterogeneity, Large Origin Tandem Repeats, and Interspecies Recombination in Human Herpesvirus 6A (HHV-6A) and HHV-6B Reference Strains. J Virol 92.

Reeves DB; Magaret AS; Greninger AL; Johnston C; Schiffer JT, 2018. Model-based estimation of superinfection prevalence from limited datasets. J R Soc Interface 15.

Shean RC; Greninger AL, 2018. Private collection: high correlation of sample collection and patient admission date in clinical microbiological testing complicates sharing of phylodynamic metadata. Virus Evol 4(1):vey005

Qin X; Zhou C; Zerr DM; Adler A; Addetia A; Yuan S; Greninger AL, 2018. Heterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients. mSphere 3.

Thornton CS; Rubin JE; Greninger AL; Peirano G; Chiu CY; Pillai DR, 2018. Epidemiological and genomic characterization of community-acquired Clostridium difficile infections. BMC Infect Dis 18(1):443

Yoon JJ; Toots M; Lee S; Lee ME; Ludeke B; Luczo JM; Ganti K; Cox RM; Sticher ZM; Edpuganti V; Mitchell DG; Lockwood MA; Kolykhalov AA; Greninger AL; Moore ML; Painter GR; Lowen AC; Tompkins SM; Fearns R; Natchus MG; Plemper RK, 2018. Orally Efficacious Broad-Spectrum Ribonucleoside Analog Inhibitor of Influenza and Respiratory Syncytial Viruses. Antimicrob Agents Chemother 62.

Greninger AL, 2018. The challenge of diagnostic metagenomics. Expert Rev Mol Diagn 18(7):605-615

Greninger AL; Roychoudhury P; Xie H; Casto A; Cent A; Pepper G; Koelle DM; Huang ML; Wald A; Johnston C; Jerome KR, 2018. Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture. mSphere 3.

Roberts MC; Garland-Lewis G; Trufan S; Meschke SJ; Fowler H; Shean RC; Greninger AL; Rabinowitz PM, 2018. Distribution of Staphylococcus species in dairy cows, workers and shared farm environments. FEMS Microbiol Lett 365.

Goya S; Valinotto LE; Tittarelli E; Rojo GL; Nabaes Jodar MS; Greninger AL; Zaiat JJ; Marti MA; Mistchenko AS; Viegas M, 2018. An optimized methodology for whole genome sequencing of RNA respiratory viruses from nasopharyngeal aspirates. PLoS One 13(6):e0199714

Iketani S; Shean RC; Ferren M; Makhsous N; Aquino DB; des Georges A; Rima B; Mathieu C; Porotto M; Moscona A; Greninger AL, 2018. Viral Entry Properties Required for Fitness in Humans Are Lost through Rapid Genomic Change during Viral Isolation. mBio 9.

Roberts MC; Joshi PR; Greninger AL; Melendez D; Paudel S; Acharya M; Bimali NK; Koju NP; No D; Chalise M; Kyes RC, 2018. The human clone ST22 SCCmec IV methicillin-resistant Staphylococcus aureus isolated from swine herds and wild primates in Nepal: is man the common source? FEMS Microbiol Ecol 94.

Dalmat RR; Makhsous N; Pepper GG; Magaret A; Jerome KR; Wald A; Greninger AL, 2018. Limited Marginal Utility of Deep Sequencing for HIV Drug Resistance Testing in the Age of Integrase Inhibitors. J Clin Microbiol 56.

Medina GN; Knudsen GM; Greninger AL; Kloc A; Díaz-San Segundo F; Rieder E; Grubman MJ; DeRisi JL; de Los Santos T, 2017. Interaction between FMDV L(pro) and transcription factor ADNP is required for optimal viral replication. Virology 505:12-22

Greninger AL; Streithorst J; Golden JA; Chiu CY; Miller S, 2017. Complete genome sequence of sequential Pandoraea apista isolates from the same cystic fibrosis patient supports a model of chronic colonization with in vivo strain evolution over time. Diagn Microbiol Infect Dis 87(1):1-6

Koelle DM; Norberg P; Fitzgibbon MP; Russell RM; Greninger AL; Huang ML; Stensland L; Jing L; Magaret AS; Diem K; Selke S; Xie H; Celum C; Lingappa JR; Jerome KR; Wald A; Johnston C, 2017. Worldwide circulation of HSV-2 × HSV-1 recombinant strains. Sci Rep 7:44084

Shean RC; Makhsous N; Crawford RL; Jerome KR; Greninger AL, 2017. Draft Genome Sequences of Six Novel Picorna-Like Viruses from Washington State Spiders. Genome Announc 5.

Greninger AL; Waghmare A; Adler A; Qin X; Crowley JL; Englund JA; Kuypers JM; Jerome KR; Zerr DM, 2017. Rule-Out Outbreak: 24-Hour Metagenomic Next-Generation Sequencing for Characterizing Respiratory Virus Source for Infection Prevention. J Pediatric Infect Dis Soc 6(2):168-172

Makhsous N; Shean RC; Droppers D; Guan J; Jerome KR; Greninger AL, 2017. Genome Sequences of Three Novel Bunyaviruses, Two Novel Rhabdoviruses, and One Novel Nyamivirus from Washington State Moths. Genome Announc 5.

Bateman AC; Greninger AL; Atienza EE; Limaye AP; Jerome KR; Cook L, 2017. Quantification of BK Virus Standards by Quantitative Real-Time PCR and Droplet Digital PCR Is Confounded by Multiple Virus Populations in the WHO BKV International Standard. Clin Chem 63(3):761-769

Greninger AL; Bateman AC; Atienza EE; Wendt S; Makhsous N; Jerome KR; Cook L, 2017. Copy Number Heterogeneity of JC Virus Standards. J Clin Microbiol 55(3):824-831

Greninger AL; Zerr DM; Qin X; Adler AL; Sampoleo R; Kuypers JM; Englund JA; Jerome KR, 2017. Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections. J Clin Microbiol 55(1):177-182

Greninger AL; Streithorst J; Chiu CY; Miller S, 2017. First Complete Genome Sequence of Corynebacterium riegelii. Genome Announc 5.

Johnston C; Magaret A; Roychoudhury P; Greninger AL; Reeves D; Schiffer J; Jerome KR; Sather C; Diem K; Lingappa JR; Celum C; Koelle DM; Wald A, 2017. Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: A nested cross-sectional viral genotyping study. PLoS Med 14(12):e1002475

Greninger AL; Hess JR, 2017. Clostridium perfringens sepsis masquerading as a hemolytic transfusion reaction. Transfusion 57(5):1112

Kozyreva VK; Truong CL; Greninger AL; Crandall J; Mukhopadhyay R; Chaturvedi V, 2017. Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory. J Clin Microbiol 55(8):2502-2520

Johnston C; Magaret A; Roychoudhury P; Greninger AL; Cheng A; Diem K; Fitzgibbon MP; Huang ML; Selke S; Lingappa JR; Celum C; Jerome KR; Wald A; Koelle DM, 2017. Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 U(L) and U(S) regions from genital swabs collected from 3 continents. Virology 510:90-98

Ogimi C; Greninger AL; Waghmare AA; Kuypers JM; Shean RC; Xie H; Leisenring WM; Stevens-Ayers TL; Jerome KR; Englund JA; Boeckh M, 2017. Prolonged Shedding of Human Coronavirus in Hematopoietic Cell Transplant Recipients: Risk Factors and Viral Genome Evolution. J Infect Dis 216(2):203-209

Makhsous N; Jensen NL; Haman KH; Batts WN; Jerome KR; Winton JR; Greninger AL, 2017. Isolation and characterization of the fall Chinook aquareovirus. Virol J 14(1):170

Niyonzima N; Lambert AR; Werther R; De Silva Feelixge H; Roychoudhury P; Greninger AL; Stone D; Stoddard BL; Jerome KR, 2017. Tuning DNA binding affinity and cleavage specificity of an engineered gene-targeting nuclease via surface display, flow cytometry and cellular analyses. Protein Eng Des Sel 30(7):503-522

Bateman AC; Perez-Osorio AC; Li Z; Tran M; Greninger AL, 2017. Conservation and Recombination in the Genome Sequence of Haemophilus influenzae Type f WAPHL1. Genome Announc 5.

Bajema KL; Simonson PD; Greninger AL; Çoruh B; Pottinger PS; Bhattacharya R; Liou IW; Jalikis FG; Fligner CL; Rakita RM, 2017. Acute Liver Failure Due to Echovirus 9 Associated With Persistent B-Cell Depletion From Rituximab. Open Forum Infect Dis 4(3):ofx174

Paniz-Mondolfi AE; Greninger AL; Ladutko L; Brown-Elliott BA; Vasireddy R; Jakubiec W; Vasireddy S; Wallace RJ Jr; Simmon KE; Dunn BE; Jackoway G; Vora SB; Quinn KK; Qin X; Campbell S, 2017. Mycobacterium grossiae sp. nov., a rapidly growing, scotochromogenic species isolated from human clinical respiratory and blood culture specimens. Int J Syst Evol Microbiol 67(11):4345-4351

Greninger AL; Pepper G; Shean RC; Cent A; Palileo I; Kuypers JM; Schiffer JT; Jerome KR, 2017. Myeloablation-associated deletion of ORF4 in a human coronavirus 229E infection. NPJ Genom Med 2:30

Soupene E; Kao J; Cheng DH; Wang D; Greninger AL; Knudsen GM; DeRisi JL; Kuypers FA, 2016. Association of NMT2 with the acyl-CoA carrier ACBD6 protects the N-myristoyltransferase reaction from palmitoyl-CoA. J Lipid Res 57(2):288-98

De Silva Feelixge HS; Stone D; Pietz HL; Roychoudhury P; Greninger AL; Schiffer JT; Aubert M; Jerome KR, 2016. Detection of treatment-resistant infectious HIV after genome-directed antiviral endonuclease therapy. Antiviral Res 126:90-8

Greninger AL; Chatterjee SS; Chan LC; Hamilton SM; Chambers HF; Chiu CY, 2016. Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Resistant to Fifth-Generation Cephalosporins Reveals Potential Non-mecA Mechanisms of Resistance. PLoS One 11(2):e0149541

Greninger AL; Messacar K; Dunnebacke T; Naccache SN; Federman S; Bouquet J; Mirsky D; Nomura Y; Yagi S; Glaser C; Vollmer M; Press CA; Kleinschmidt-DeMasters BK; Dominguez SR; Chiu CY, 2016. Erratum to: Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med 8(1):1

Sedlak RH; Liang S; Niyonzima N; De Silva Feelixge HS; Roychoudhury P; Greninger AL; Weber ND; Boissel S; Scharenberg AM; Cheng A; Magaret A; Bumgarner R; Stone D; Jerome KR, 2016. Digital detection of endonuclease mediated gene disruption in the HIV provirus. Sci Rep 6:20064

Greene TT; Tokuyama M; Knudsen GM; Kunz M; Lin J; Greninger AL; DeFilippis VR; DeRisi JL; Raulet DH; Coscoy L, 2016. A Herpesviral induction of RAE-1 NKG2D ligand expression occurs through release of HDAC mediated repression. Elife 5.

Greninger AL; Jerome KR, 2016. Draft Genome Sequence of Goose Dicistrovirus. Genome Announc 4.

Aubert M; Madden EA; Loprieno M; DeSilva Feelixge HS; Stensland L; Huang ML; Greninger AL; Roychoudhury P; Niyonzima N; Nguyen T; Magaret A; Galleto R; Stone D; Jerome KR, 2016. In vivo disruption of latent HSV by designer endonuclease therapy. JCI Insight 1.

Greninger AL; Streithorst J; Chiu CY; Miller S, 2016. First Draft Genome Sequences of Neisseria sp. Strain 83E34 and Neisseria sp. Strain 74A18, Previously Identified as CDC Eugonic Fermenter 4b Species. Genome Announc 4.

Kozyreva VK; Jospin G; Greninger AL; Watt JP; Eisen JA; Chaturvedi V, 2016. Recent Outbreaks of Shigellosis in California Caused by Two Distinct Populations of Shigella sonnei with either Increased Virulence or Fluoroquinolone Resistance. mSphere 1.

Naccache SN; Thézé J; Sardi SI; Somasekar S; Greninger AL; Bandeira AC; Campos GS; Tauro LB; Faria NR; Pybus OG; Chiu CY, 2016. Distinct Zika Virus Lineage in Salvador, Bahia, Brazil. Emerg Infect Dis 22(10):1788-92

Greninger AL; DeRisi JL, 2015. Draft Genome Sequences of Leviviridae RNA Phages EC and MB Recovered from San Francisco Wastewater. Genome Announc 3.

Martínez MA; Soto-Del Río Mde L; Gutiérrez RM; Chiu CY; Greninger AL; Contreras JF; López S; Arias CF; Isa P, 2015. DNA microarray for detection of gastrointestinal viruses. J Clin Microbiol 53(1):136-45

Greninger AL, 2015. Picornavirus--host interactions to construct viral secretory membranes. Prog Mol Biol Transl Sci 129:189-212

Greninger AL; Naccache SN; Messacar K; Clayton A; Yu G; Somasekar S; Federman S; Stryke D; Anderson C; Yagi S; Messenger S; Wadford D; Xia D; Watt JP; Van Haren K; Dominguez SR; Glaser C; Aldrovandi G; Chiu CY, 2015. A novel outbreak enterovirus D68 strain associated with acute flaccid myelitis cases in the USA (2012-14): a retrospective cohort study. Lancet Infect Dis 15(6):671-82

Greninger AL; Chorny I; Knowles S; Ng VL; Chaturvedi V, 2015. Draft Genome Sequences of Four NDM-1-Producing Klebsiella pneumoniae Strains from a Health Care Facility in Northern California. Genome Announc 3.

Greninger AL; Cunningham G; Hsu ED; Yu JM; Chiu CY; Miller S, 2015. Draft Genome Sequence of Mycobacterium obuense Strain UC1, Isolated from Patient Sputum. Genome Announc 3.

Greninger AL; Cunningham G; Yu JM; Hsu ED; Chiu CY; Miller S, 2015. Draft Genome Sequence of Mycobacterium arupense Strain GUC1. Genome Announc 3.

Greninger AL; DeRisi JL, 2015. Draft Genome Sequences of Marine RNA Viruses SF-1, SF-2, and SF-3 Recovered from San Francisco Wastewater. Genome Announc 3.

Greninger AL; DeRisi JL, 2015. Draft Genome Sequences of Ciliovirus and Brinovirus from San Francisco Wastewater. Genome Announc 3.

Greninger AL; Langelier C; Cunningham G; Keh C; Melgar M; Chiu CY; Miller S, 2015. Two Rapidly Growing Mycobacterial Species Isolated from a Brain Abscess: First Whole-Genome Sequences of Mycobacterium immunogenum and Mycobacterium llatzerense. J Clin Microbiol 53(7):2374-7

Greninger AL; Cunningham G; Yu JM; Hsu ED; Chiu CY; Miller S, 2015. Draft Genome Sequence of Mycobacterium elephantis Strain Lipa. Genome Announc 3.

Greninger AL; DeRisi JL, 2015. Draft Genome Sequence of Tombunodavirus UC1. Genome Announc 3.

Greninger AL; DeRisi JL, 2015. Draft Genome Sequence of Laverivirus UC1, a Dicistrovirus-Like RNA Virus Featuring an Unusual Genome Organization. Genome Announc 3.

Greninger AL; Cunningham G; Chiu CY; Miller S, 2015. Draft Genome Sequence of Mycobacterium heraklionense Strain Davo. Genome Announc 3.

Greninger AL; Cunningham G; Chiu CY; Miller S, 2015. Draft Genome Sequence of Mycobacterium heckeshornense Strain RLE. Genome Announc 3.

Greninger AL; Kozyreva V; Truong CL; Longoria R; Chaturvedi V, 2015. Draft Genome Sequence of Kerstersia gyiorum CG1, Isolated from a Leg Ulcer. Genome Announc 3.

Greninger AL; Kozyreva V; Truong CL; Graves M; Chaturvedi V, 2015. Draft Genome Sequence of Turicella otitidis TD1, Isolated from a Patient with Bacteremia. Genome Announc 3.

Greninger AL; Naccache SN; Federman S; Yu G; Mbala P; Bres V; Stryke D; Bouquet J; Somasekar S; Linnen JM; Dodd R; Mulembakani P; Schneider BS; Muyembe-Tamfum JJ; Stramer SL; Chiu CY, 2015. Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med 7:99

Greninger AL; Messacar K; Dunnebacke T; Naccache SN; Federman S; Bouquet J; Mirsky D; Nomura Y; Yagi S; Glaser C; Vollmer M; Press CA; Kleinschmidt-DeMasters BK; Dominguez SR; Chiu CY, 2015. Clinical metagenomic identification of Balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. Genome Med 7:113

Greninger AL; DeRisi JL, 2015. Draft Genome Sequence of Picalivirus D Recovered from San Francisco Wastewater. Genome Announc 3.

Morris JH; Knudsen GM; Verschueren E; Johnson JR; Cimermancic P; Greninger AL; Pico AR, 2014. Affinity purification-mass spectrometry and network analysis to understand protein-protein interactions. Nat Protoc 9(11):2539-54

Naccache SN; Federman S; Veeraraghavan N; Zaharia M; Lee D; Samayoa E; Bouquet J; Greninger AL; Luk KC; Enge B; Wadford DA; Messenger SL; Genrich GL; Pellegrino K; Grard G; Leroy E; Schneider BS; Fair JN; Martínez MA; Isa P; Crump JA; DeRisi JL; Sittler T; Hackett J Jr; Miller S; Chiu CY, 2014. A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples. Genome Res 24(7):1180-92

Coffey LL; Page BL; Greninger AL; Herring BL; Russell RC; Doggett SL; Haniotis J; Wang C; Deng X; Delwart EL, 2014. Enhanced arbovirus surveillance with deep sequencing: Identification of novel rhabdoviruses and bunyaviruses in Australian mosquitoes. Virology 448:146-58

Herman EK; Greninger AL; Visvesvara GS; Marciano-Cabral F; Dacks JB; Chiu CY, 2013. The mitochondrial genome and a 60-kb nuclear DNA segment from Naegleria fowleri, the causative agent of primary amoebic meningoencephalitis. J Eukaryot Microbiol 60(2):179-91

Naccache SN; Greninger AL; Lee D; Coffey LL; Phan T; Rein-Weston A; Aronsohn A; Hackett J Jr; Delwart EL; Chiu CY, 2013. The perils of pathogen discovery: origin of a novel parvovirus-like hybrid genome traced to nucleic acid extraction spin columns. J Virol 87(22):11966-77

Greninger AL; Knudsen GM; Betegon M; Burlingame AL; DeRisi JL, 2013. ACBD3 interaction with TBC1 domain 22 protein is differentially affected by enteroviral and kobuviral 3A protein binding. mBio 4(2):e00098-13

Nelson CS; Fuller CK; Fordyce PM; Greninger AL; Li H; DeRisi JL, 2013. Microfluidic affinity and ChIP-seq analyses converge on a conserved FOXP2-binding motif in chimp and human, which enables the detection of evolutionarily novel targets. Nucleic Acids Res 41(12):5991-6004

Yu G; Greninger AL; Isa P; Phan TG; Martínez MA; de la Luz Sanchez M; Contreras JF; Santos-Preciado JI; Parsonnet J; Miller S; DeRisi JL; Delwart E; Arias CF; Chiu CY, 2012. Discovery of a novel polyomavirus in acute diarrheal samples from children. PLoS One 7(11):e49449

O'Donoghue AJ; Eroy-Reveles AA; Knudsen GM; Ingram J; Zhou M; Statnekov JB; Greninger AL; Hostetter DR; Qu G; Maltby DA; Anderson MO; Derisi JL; McKerrow JH; Burlingame AL; Craik CS, 2012. Global identification of peptidase specificity by multiplex substrate profiling. Nat Methods 9(11):1095-100

Greninger AL; Knudsen GM; Betegon M; Burlingame AL; Derisi JL, 2012. The 3A protein from multiple picornaviruses utilizes the golgi adaptor protein ACBD3 to recruit PI4KIIIβ. J Virol 86(7):3605-16

Greninger AL; Chen EC; Sittler T; Scheinerman A; Roubinian N; Yu G; Kim E; Pillai DR; Guyard C; Mazzulli T; Isa P; Arias CF; Hackett J; Schochetman G; Miller S; Tang P; Chiu CY, 2010. A metagenomic analysis of pandemic influenza A (2009 H1N1) infection in patients from North America. PLoS One 5(10):e13381

Greninger AL; Holtz L; Kang G; Ganem D; Wang D; DeRisi JL, 2010. Serological evidence of human klassevirus infection. Clin Vaccine Immunol 17(10):1584-8

Chiu CY; Greninger AL; Chen EC; Haggerty TD; Parsonnet J; Delwart E; Derisi JL; Ganem D, 2010. Cultivation and serological characterization of a human Theiler's-like cardiovirus associated with diarrheal disease. J Virol 84(9):4407-14

Kistler AL; Smith JM; Greninger AL; Derisi JL; Ganem D, 2010. Analysis of naturally occurring avian bornavirus infection and transmission during an outbreak of proventricular dilatation disease among captive psittacine birds. J Virol 84(4):2176-9

Gancz AY; Kistler AL; Greninger AL; Farnoushi Y; Mechani S; Perl S; Berkowitz A; Perez N; Clubb S; DeRisi JL; Ganem D; Lublin A, 2009. Experimental induction of proventricular dilatation disease in cockatiels (Nymphicus hollandicus) inoculated with brain homogenates containing avian bornavirus 4. Virol J 6:100

Greninger AL; Runckel C; Chiu CY; Haggerty T; Parsonnet J; Ganem D; DeRisi JL, 2009. The complete genome of klassevirus - a novel picornavirus in pediatric stool. Virol J 6:82

Chiu CY; Greninger AL; Kanada K; Kwok T; Fischer KF; Runckel C; Louie JK; Glaser CA; Yagi S; Schnurr DP; Haggerty TD; Parsonnet J; Ganem D; DeRisi JL, 2008. Identification of cardioviruses related to Theiler's murine encephalomyelitis virus in human infections. Proc Natl Acad Sci U S A 105(37):14124-9

Publication list retrieved from NCBI using ImpactPubs