Research

I obtained my MD at the University of Toronto, and my PhD in Experimental Medicine from the University of British Columbia and the BC Centre for Excellence in HIV/AIDS.

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Ph.D. Dissertation: "Deep sequencing of HIV-1 envelope determines coreceptor usage and predicts virologic responses to antiretroviral treatment with CCR5 antagonist medication". 

Curriculum Vitae, January 2016

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Risk of Breast Cancer with CXCR4-Using HIV Defined by V3 Loop Sequencing.

Goedert JJ, Swenson LC, Napolitano L, Haddad M, Anastos K, Minkoff H, Young M, Levine A, Adeyemi O, Seaberg EC, Aouizerat B, Rabkin CS, Harrigan PR, Hessol NA. 
Journal of Acquired Human Immune Deficiency Syndromes 2015; 68(1): 30-35.
 

HIV drug resistance detected during low-level viraemia is associated with subsequent virologic failure   

Swenson LC, Min JE, Woods CK, Cai E, Li JZ, Montaner JS, Harrigan PR, Gonzalez-Serna A. 
AIDS 2014; 28(8): 1125-1134.

Comparative performance of HIV-1 RNA load assays at low viral load levels: Results of an international collaboration

Swenson LC, Cobb B, Geretti AM, Harrigan PR, Poljak M, Seguin-Devaux C, Verhofstede C, Wirden M, Amendola A, Boni J, Bourlet T, Huder JB, Karasi JC, Zidovec Lepej S, Lunar MM, Mukabayire O, Schuurman R, Tomazic J, Van Laethem K, Vandekerckhove L, Wensing AM for the International Viral Load Assay Collaboration. 
Journal of Clinical Microbiology 2014; 52(2): 517-523.    .

Performance of HIV-1 Drug Resistance Testing at Low Level Viraemia and Its Ability to Predict Future Virological Outcomes and Viral Evolution in Treatment-Naïve Individuals

Gonzalez-Serna A, Min JE, Woods C, Chan D, Lima VD, Montaner JSG, Harrigan PR, Swenson LC. 
Clinical Infectious Diseases 2014; 58(8): 1165-1173.

Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing

Liang RH, Mo T, Dong W, Lee GQ, Swenson LC, McCloskey RM, Woods CK, Brumme CJ, Ho CKY, Schinkel J, Joy JB, Harrigan PR, Poon AFY. 
Nucleic Acids Research 2014, 42(12): e98.

Genotypic Analysis of the HIV V3 Region in Virologic Non-Responders to Maraviroc-containing Regimens Reveals Distinct Patterns of Failure

Swenson LC, Chui CKS, Brumme CJ, Chan D, Woods CK, Mo T, Dong W, Chapman D, Lewis M, Demarest JF, James I, Portsmouth S, Goodrich J, Heera J, Valdez H, Harrigan PR. 
Antimicrobial Agents and Chemotherapy 2013; 57(12): 6122-6130.

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Use of Cellular HIV DNA to Predict Virologic Response to Maraviroc: Performance of Population-Based and Deep Sequencing

Swenson LC, Dong WWY, Mo T, Demarest J, Chapman D, Ellery S, Heera J, Valdez H, Poon AF, Harrigan PR. 
Clinical Infectious Diseases 2013; 56(11): 1659-1666.

Results of the External Quality Assurance (EQA) for Proviral DNA Testing of HIV Tropism in the Maraviroc Switch Collaborative Study (MARCH)

Tu E, Swenson LC, Land S, Pett S, Emery S, Marks K, Kelleher A, Kaye S, Kaiser R, Schuelter E, Harrigan PR, on 5 behalf of the MARCH laboratory group and the MARCH study group. 
Journal of Clinical Microbiology 2013; 51(7): 2063-2071.

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Reply to "Issues on Results of the External Quality Assessment for Proviral DNA Testing of HIV-1 Tropism in the Maraviroc Switch Collaborative Study

Tu E, Swenson LC, Land S, Pett S, Emery S, Marks K, Kelleher A, Kaye S, Kaiser R, Schuelter E, Harrigan PR. 
Journal of Clinical Microbiology 2013; 51(12): 4287.

Development of a Novel Codon-Specific PCR for the detection of CXCR4-Utilizing HIV-1 Subtype B

McLaughlin S, Swenson LC, Hu S, Hughes P, Harrigan PR, Coombs RW, Frenkel LM. 
AIDS Research and Human Retroviruses 2013; 29(5): 814-825.    

Next-Generation Sequencing to Assess HIV Tropism 

Swenson LC, Däumer M, Paredes R. 
Current Opinion in HIV and AIDS 2012; 7(5): 478-485.

Factors influencing the sensitivity and specificity of conventional sequencing in Human Immunodeficiency Virus-1 tropism testing

Knapp D, McGovern R, Dong W, Poon A, Swenson LC, Zhong X, Woods C, Harrigan PR. 
Journal of Clinical Microbiology 2013; 51(2): 444-451.   

Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data

Poon AFY, Swenson LC, Bunnik EM, Edo-Matas D, Schuitemaker H, van ‘t Wout AB, Harrigan PR. 
PLoS Computational Biology 2012; Nov;8(11):e1002753.

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Prolonged and Substantial Discordance in Prevalence of Raltegravir-resistant HIV-1 in Plasma versus PBMC Samples Revealed by 454 "Deep" Sequencing

Lee GQ, Swenson LC, Poon AFY, Martin JN, Hatano H, Deeks SG, Harrigan PR. 
PLoS ONE 2012, 7(9): e46181.

Deep V3 Sequencing for HIV Type 1 Tropism in Treatment-Naïve Patients: A Reanalysis of the MERIT Trial of Maraviroc

Swenson LC, Mo T, Dong WWY, Zhong X, Woods CK, Thielen A, Jensen MA, Knapp DJHF, Chapman D, Portsmouth S, Lewis M, James I, Heera J, Valdez H, Harrigan PR. 
Clinical Infectious Diseases 2011; 53(7): 732-742.

Detection of Inferred CCR5- and CXCR4-Using HIV-1 Variants and Evolutionary Intermediates Using Ultra-Deep Pyrosequencing

Bunnik EM, Swenson LC, Edo-Matas D, Huang W, Dong W, Frantzell A, et al. 
PLoS Pathogens. 2011 Jun 23;7(6):e1002106.

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Reply to Abbate et al

Luke C Swenson & P Richard Harrigan. Journal of Infectious Diseases 2011;204(6): 973-974.

“Dynamic Range” of Inferred Phenotypic HIV Drug Resistance Values in Clinical Practice

Luke C. Swenson, Graham Pollock, Brian Wynhoven,Theresa Mo, Winnie Dong, Robert S. Hogg, Julio S. G. Montaner, P. Richard Harrigan. 
PLoS ONE 6(2): e17402. 
doi:10.1371/journal.pone.0017402

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Mutations in gp41 are correlated with coreceptor tropism but do not improve prediction methods substantially

Thielen A, Lengauer T, Swenson LC, Dong WW, McGovern RA, Lewis M, James I, Heera J, Valdez H, Harrigan PR. 
Antiviral Therapy 2011;16(3):319-28.
 

Genotypic Inference of HIV-1 Tropism Using Population-based Sequencing of V3 (Video Article)

McGovern RA, Harrigan PR, Swenson LC. 
Journal of Visualized Experiments 2010;48: http://www.jove.com/details.stp?id=2531, doi: 10.3791/2531.

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Deep Sequencing to Infer HIV-1 Co-Receptor Usage: Application to Three Clinical Trials of Maraviroc in Treatment-Experienced Patients

Swenson LC, Mo T, Dong WWY, Zhong X, Woods CK, Jensen MA, Thielen A, Chapman D, Lewis M, James I, Heera J, Valdez H, Harrigan PR. 
Journal of Infectious Diseases 2011; 203(2): 237-245

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Improved Detection of CXCR4-Using HIV by V3 Genotyping: Application of Population-Based and "Deep" Sequencing to Plasma RNA and Proviral DNA

Swenson LC, Moores A, Low AJ, Thielen A, Dong W, Woods C, Jensen MA, Wynhoven B, Chan D, Glascock C, Harrigan PR. 
Journal of Acquired Immune Deficiency Syndromes 2010; 54(5): 506-510.

Phylogenetic Analysis of Population-Based and Deep Sequencing Data to Identify Coevolving Sites in the nef Gene of HIV-1

Poon AFY, Swenson LC, Dong WWY, Deng W, Kosakovsky Pond SL, Brumme ZL, Mullins JI, Richman DD, Harrigan PR, Frost SDW. 
Molecular Biology and Evolution 2010; 27: 819 - 832.

Genotypic determination of HIV-1 tropism in the clinical setting

Swenson LC, Boehme R, Thielen A, McGovern RA, Harrigan PR. 
HIV Therapy 2010; 4(3): 293-303.

HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins 

Brumme ZL, John M, Carlson JM, Brumme CJ, Chan D, Brockman MA, Swenson LC, Tao I, Szeto S, Rosato P, Sela J, Kadie CM, Frahm N, Brander C, Haas DW, Riddler SA, Haubrich R, Walker BD, Harrigan PR, Heckerman D, Mallal S. 
PLoS ONE 2009; 4(8): E6687.

HIV co-receptor phenotyping in the clinical setting

Low AJ, Swenson LC, Harrigan PR. 
AIDS Reviews 2008; 10 (3):143-51.