By Professor Miles Davenport

Preprints

Docken SS; Macairan A; Schlub TE; Fennessey CM; Varco-Merth B; Picker LJ; Okoye AA; Immonen TT; Cromer D; Keele BF; Davenport MP, 2025, Dissecting the steps in early Simian Immunodeficiency Virus dissemination following mucosal and intravenous infection of rhesus macaques, http://dx.doi.org/10.1101/2025.03.24.644849

Pampena MB; Samer S; Viox EG; Nguyen K; Deleage C; Kuri-Cervantes L; Regan J; Wu VH; Docken S; Safrit JT; Bar KJ; Keele BF; Davenport MP; Paiardini M; Betts MR, 2025, Therapeutic CD8+T cell tissue retention and immunomodulation during ART interruption fails to prevent SIV rebound, http://dx.doi.org/10.1101/2025.03.17.643755

Tabilas C; Venturi V; Kean C; Minervina A; Thomas PG; Grimson A; Grenier JK; Davenport MP; Smith NL; Rudd BD, 2025, Single-cell multiomics reveals the distinct properties of neonatal and adult recent thymic emigrants, http://dx.doi.org/10.1101/2025.02.26.640106

Hilt ZT; Reynaldi A; Steinhilber M; Zhang S; Wesnak SP; Smith NL; Davenport MP; Rudd BD, 2025, Recent thymic emigrants are preferentially recruited into the memory pool during persistent infection., http://dx.doi.org/10.1101/2025.02.06.636722

Abayasingam A; Gupta M; Wu B-R; Underwood AP; Young C; Rodrigo C; Walker MR; Agapiou D; Eltahla AA; Li H; Keoshkerian E; Su S; Brasher NA; Reynaldi A; Burnett D; Davenport M; Luciani F; Tedla N; Maher L; Lloyd AR; Bull RA, 2024, Affinity of the Transmitted Founder Virus Drives Early Emergence of Hepatitis C Virus Specific Neutralising Antibodies, http://dx.doi.org/10.2139/ssrn.4935049

Kent S; Li S; Amarasena T; Reynaldi A; Lee WS; Leeming M; O’Connor D; Nguyen J; Kent H; Caruso F; Juno J; Wheatley A; Davenport M; Ju Y, 2024, Blood Distribution of SARS-CoV-2 Lipid Nanoparticle mRNA Vaccine in Humans, http://dx.doi.org/10.1101/2024.07.25.24311039

Berry M; MacIntyre R; Cromer D; Hacker A; Davenport M; Khoury D, 2024, Optimal deployment of limited vaccine supplies to combat mpox, http://dx.doi.org/10.1101/2024.11.03.24316551

Conway E; Walker C; Lydeamore M; Golding N; Ryan G; Mavec D; Oates J; Kabashima G; Price D; Shearer F; Cromer D; Davenport M; McCaw J; Eriksson E; Hodgkin P; Wu L; Le T; Baker C; Mueller I; McVernon J, 2024, Optimal timing of booster doses in a highly vaccinated population with minimal natural exposure to COVID-19, http://dx.doi.org/10.1101/2024.05.14.24307386

Ashley C; Bloul M; Alca S; Smith L; Jin W; Khoury D; Counoupas C; Davenport M; Triccas J; Steain M, 2024, Optimisation of a multiplexed, high throughput assay to measure neutralising antibodies against SARS-CoV-2 variants, http://dx.doi.org/10.1101/2024.09.01.610733

Cromer D; Reynaldi A; Hie A; Schlub T; Juno J; Wheatley A; Kent S; Khoury D; Davenport M, 2024, Predicting COVID-19 booster immunogenicity against future SARS-CoV-2 variants and the benefits of vaccine updates, http://dx.doi.org/10.1101/2024.02.08.24302032

Lee WS; Tan H-X; Reynaldi A; Esterbauer R; Koutsakos M; Nguyen J; Amarasena T; Kent H; Aggarwal A; Turville S; Taiaroa G; Kinsella P; Liew KC; Tran T; Williamson D; Cromer D; Davenport M; Kent S; Juno J; Khoury D; Wheatley A, 2023, Durable reprogramming of neutralising antibody responses following breakthrough Omicron infection, http://dx.doi.org/10.1101/2023.02.19.23286159

Selva KJ; Ramanathan P; Haycroft ER; Reynaldi A; Cromer D; Tan CW; Wang L-F; Wines B; Hogarth M; Downie L; Davis S; Purcell RA; Kent H; Juno J; Wheatley A; Davenport M; Kent SJ; Chung A, 2023, Lasting first impression: Pre-existing immunity restricts mucosal antibody responses during Omicron breakthrough, http://dx.doi.org/10.1101/2023.03.28.23287848

Wagstaffe H; Thwaites R; Reynaldi A; Sidhu J; McKendry R; Ascough S; Papargyris L; Collins A; Xu J; Lemm N-M; Siggins M; Chain B; Killingley B; Kalinova M; Mann A; Catchpole A; Davenport M; Openshaw PJM; Chiu C, 2023, Mucosal and Systemic Immune Correlates of Viral Control following SARS-CoV-2 Infection Challenge in Seronegative Adults, http://dx.doi.org/10.1101/2023.07.21.23292994

Berry M; Khan S; Schlub T; Notaras A; Kunasekaran M; Grulich A; MacIntyre R; Davenport M; Khoury D, 2023, Predicting vaccine effectiveness in Mpox, http://dx.doi.org/10.1101/2023.11.23.23298850

Elias K; Khan S; Stadler E; Schlub T; Cromer D; Polizzotto M; Kent S; Turner T; Davenport M; Khoury D, 2023, Viral clearance as a surrogate of clinical efficacy for COVID-19 therapies in outpatients: A systematic review and meta-analysis, http://dx.doi.org/10.1101/2023.06.18.23291566

Stadler E; Cromer D; Ogunlade S; Ongoiba A; Doumbo S; Kayentao K; Traore B; Crompton P; Portugal S; Davenport M; Khoury D, 2022, A role for super-spreaders in carrying malaria parasites across the months-long dry season, http://dx.doi.org/10.1101/2022.04.28.22274398

Bauer A; Lindemuth E; Joy J; Marino FE; Docken S; Krause R; Mallick S; McCormick K; Holt C; Georgiev I; Felber B; Keele B; Veazey R; Davenport M; Li H; Shaw G; Bar K, 2022, Adaptation of a transmitted/founder simian-human immunodeficiency virus for enhanced replication in rhesus macaques, http://dx.doi.org/10.1101/2022.12.12.520031

Khoury D; Schlub T; Cromer D; Steain M; Fong Y; Gilbert P; Subbarao K; Triccas J; Kent S; Davenport M, 2022, Correlates of protection, thresholds of protection, and immunobridging in SARS-CoV-2 infection, http://dx.doi.org/10.1101/2022.06.05.22275943

Stadler E; Chai KL; Schlub T; Cromer D; Polizzotto M; Kent S; Beecher C; White H; White H; Turner T; Skoetz N; Skoetz N; Estcourt L; McQuilten Z; Wood E; Khoury D; Davenport M, 2022, Determinants of passive antibody efficacy in SARS-CoV-2 infection, http://dx.doi.org/10.1101/2022.03.21.22272672

Watson N; Patel R; Oyesola O; Laniewski N; Grenier J; Wang J; Tabilas C; Yee Mon K; Peng S; Wesnak S; Nzingha K; Smith N; Davenport M; Tait Wojno E; Scheible K; Grimson A; Rudd B, 2022, Lin28b specifies an innate-like lineage of CD8+ T cells in early life, http://dx.doi.org/10.1101/2022.02.14.480406

Stadler E; Burgess M; Schlub T; Chai KL; McQuilten Z; Wood E; Polizzotto M; Kent S; Cromer D; Davenport M; Khoury D, 2022, Monoclonal antibody levels and protection from COVID-19, http://dx.doi.org/10.1101/2022.11.22.22282199

Cromer D; Steain M; Reynaldi A; Schlub T; Sasson S; Kent S; Khoury D; Davenport MP, 2022, Neutralising antibodies predict protection from severe COVID-19, http://dx.doi.org/10.1101/2022.06.09.22275942

Khoury D; Docken S; Subbarao K; Kent S; Davenport M; Cromer D, 2022, Predicting the efficacy of variant-modified COVID-19 vaccine boosters, http://dx.doi.org/10.1101/2022.08.25.22279237

Koutsakos M; Reynaldi A; Lee WS; Nguyen J; Amarasena T; Taiaroa G; Kinsella P; Liew KC; Tran T; Kent H; Tan H-X; Rowntree L; Nguyen T; Thomas P; Kedzierska K; Petersen J; Rossjohn J; Williamson D; Khoury D; Davenport M; Kent S; Wheatley A; Juno J, 2022, Rapid Recall and de novo T Cell Responses During SARS-CoV-2 Breakthrough Infection, http://dx.doi.org/10.2139/ssrn.4311124

Koutsakos M; Reynaldi A; Lee WS; Nguyen J; Amarasena T; Taiaroa G; Kinsella P; Liew KC; Tran T; Kent H; Tan H-X; Rowntree L; Nguyen T; Thomas P; Kedzierska K; Petersen J; Rossjohn J; Williamson D; Khoury D; Davenport M; Kent S; Wheatley A; Juno J, 2022, Rapid recall andde novoT cell responses during SARS-CoV-2 breakthrough infection, http://dx.doi.org/10.1101/2022.12.19.521129

Stadler E; Cromer D; Mehra S; Adekunle A; Flegg J; Anstey N; Watson J; Chu C; Mueller I; Robinson L; Schlub T; Davenport M; Khoury D, 2022, Risk of Plasmodium vivax recurrences follows a 30-70 rule and indicates relapse heterogeneity in the population, http://dx.doi.org/10.1101/2022.05.18.22275180

Goel RR; Painter MM; Apostolidis SA; Mathew D; Meng W; Rosenfeld AM; Lundgreen KA; Reynaldi A; Khoury DS; Pattekar A; Gouma S; Kuri-Cervantes L; Hicks P; Dysinger S; Hicks A; Sharma H; Herring S; Korte S; Baxter AE; Oldridge DA; Giles JR; Weirick ME; McAllister CM; Awofolaju M; Tanenbaum N; Drapeau EM; Dougherty J; Long S; D'Andrea K; Hamilton JT; McLaughlin M; Williams JC; Adamski S; Kuthuru O; UPenn COVID Processing Unit ; Frank I; Betts MR; Vella LA; Grifoni A; Weiskopf D; Sette A; Hensley SE; Davenport MP; Bates P; Luning Prak ET; Greenplate AR; Wherry EJ, 2021, mRNA Vaccination Induces Durable Immune Memory to SARS-CoV-2 with Continued Evolution to Variants of Concern., http://dx.doi.org/10.1101/2021.08.23.457229

Golfinos AE; Gellerup DD; Schweigert H; Mathiaparanam J; Balgeman AJ; Weiler AM; Friedrich TC; Keele BF; Davenport MP; Venturi V; O'Connor SL, 2021, The Mucosal Barrier and Anti-Viral Immune Responses can Eliminate Portions of the Viral Population during Transmission and Early Viral Growth, http://dx.doi.org/10.20944/preprints202105.0206.v1

Moriarty RV; Fesser N; Sutton MS; Venturi V; Davenport MP; Schlub T; O'Connor SL, 2021, Validation of multiplex PCR sequencing assay of SIV, http://dx.doi.org/10.21203/rs.3.rs-35062/v2

Khoury D; Steain M; Triccas J; Sigal A; Davenport M; Cromer D, 2021, A meta-analysis of Early Results to predict Vaccine efficacy against Omicron, http://dx.doi.org/10.1101/2021.12.13.21267748

Koutsakos M; Lee WS; Reynaldi A; Tan H-X; Gare G; Kinsella P; Liew KC; Williamson D; Kent H; Stadler E; Cromer D; Khoury D; Wheatley A; Juno J; Davenport M; Kent S, 2021, Dynamics of immune recall following SARS-CoV-2 vaccination or breakthrough infection, http://dx.doi.org/10.1101/2021.12.23.21268285

Aggarwal A; Stella AO; Walker G; Akerman A; Milogiannakis V; Brilot F; Amatayakul-Chantler S; Roth N; Coppola G; Schofield P; Jackson J; Henry J; Mazigi O; Langley D; Lu Y; Forster C; McAllery S; Mathivanan V; Fichter C; Hoppe AC; Munier ML; Jack H-M; Cromer D; Darley D; Matthews G; Christ D; Khoury D; Davenport M; Rawlinson W; Kelleher A; Turville S, 2021, SARS-CoV-2 Omicron: evasion of potent humoral responses and resistance to clinical immunotherapeutics relative to viral variants of concern, http://dx.doi.org/10.1101/2021.12.14.21267772

Lansink LIM; Engel J; Lee HJ; Soon MSF; Williams C; SheelaNair A; Pernold CPS; Laohamonthonkul P; Akter J; Stoll T; Hill M; Talman A; Russell A; Lawniczak M; Davenport M; Khoury D; Haque A, 2021, Systemic host inflammation induces stage-specific transcriptomic modification and slower maturation in malaria parasites, http://dx.doi.org/10.1101/2021.08.18.456784

Moriarty RV; Fesser N; Sutton MS; Venturi V; Davenport MP; Schlub T; O'Connor SL, 2020, Validation of multiplex PCR sequencing assay of SIV, http://dx.doi.org/10.21203/rs.3.rs-35062/v1

Lee WS; Selva KJ; Davis S; Wines B; Reynaldi A; Esterbauer R; Kelly H; Haycroft E; Tan H-X; Juno J; Wheatley A; Hogarth M; Cromer D; Davenport M; Chung A; Kent S, 2020, Decay of Fc-dependent antibody functions after mild to moderate COVID-19, http://dx.doi.org/10.1101/2020.12.13.20248143

Wheatley A; Juno J; Wang J; Selva K; Reynaldi A; Tan H-X; Shi Lee W; Wragg K; Kelly H; Esterbauer R; Davis S; Kent H; Mordant F; Schlub T; Gordon D; Khoury D; Subbarao K; Cromer D; Gordon T; Chung A; Davenport M; Kent S, 2020, Evolution of immunity to SARS-CoV-2, http://dx.doi.org/10.1101/2020.09.09.20191205

Juno J; Tan H-X; Lee WS; Reynaldi A; Kelly H; Wragg K; Esterbauer R; Kent H; Batten J; Mordant F; Gherardin N; Pymm P; Dietrich M; Scott N; Tham W-H; Godfrey D; Subbarao K; Davenport M; Kent S; Wheatley A, 2020, Immunogenic profile of SARS-CoV-2 spike in individuals recovered from COVID-19, http://dx.doi.org/10.1101/2020.05.17.20104869

Soon M; Lee HJ; Engel J; Straube J; Thomas B; Clarke L; Laohamonthonkul P; Pernold C; Haldar R; Williams C; Lansink L; Koufariotis R; Lakis V; Wood S; Chen X; James K; Lönnberg T; Lane S; Davenport M; Khoury D; Svensson V; Teichmann S; Haque A, 2019, Transcriptome Dynamics Reveals Progressive Transition from Effector to Memory in CD4⁺T cells, http://dx.doi.org/10.1101/675967

Cao P; Klonis N; Zaloumis S; Khoury DS; Cromer D; Davenport MP; Tilley L; Simpson JA; McCaw JM, 2017, A mechanistic model quantifies artemisinin-induced parasite growth retardation in blood-stage Plasmodium falciparum infection, http://dx.doi.org/10.48550/arxiv.1701.05302

Aliota M; Dudley D; Newman C; Weger-Lucarelli J; Stewart L; Koenig M; Breitbach M; Weiler A; Semler M; Barry G; Zarbock K; Mohns M; Mohr E; Venturi V; Schultz-Darken N; Peterson E; Newton W; Schotzko M; Simmons H; Mejia A; Hayes J; Capuano S; Davenport M; Friedrich T; Ebel G; O’Connor S; O’Connor D, 2017, Molecularly barcoded Zika virus libraries to probein vivoevolutionary dynamics, http://dx.doi.org/10.1101/221564

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