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Matthew Cousins

Class 2009
Education MS, Clemson University

Dr. Susan Eshleman

Current Position Medical School

University of North Carolina Chapel Hill

Research Interests

HIV diversity and incidence testing

HIV diversity generally increases over the course of infection. Genetically diverse HIV variants are generated as a result of the viruses’ high mutation frequency, large population size, and short generation time. These variants are then selected by immune responses and other factors. The ability of HIV to evolve and diversify allows the virus to avoid eradication by the immune system and antiretroviral (ARV) drugs. It is known that HIV diversification is impacted by many factors and does not occur uniformly across the genome; however, the capacity of the virus to diversify and the dynamic patterns of diversification have not been well-studied. In addition to the importance of diversity for its potential clinical correlates, HIV diversity may serve as a marker for the duration of infection. If this is true and HIV diversity can be quantified using a relatively simple assay, HIV diversity may be useful for assessing HIV incidence. Accurate HIV incidence estimates are critical for monitoring the HIV/AIDS epidemic, identifying populations at high risk of HIV acquisition, targeting prevention efforts, and designing and evaluating HIV prevention trials. The goals of my project are to characterize HIV diversity and diversification over the course of HIV disease and to develop and test a new diversity-based method for analysis of HIV incidence.


  • Cousins MM, O Laeyendecker, G Beauchamp, R Brookmeyer, WI Towler, SE Hudelson, L Khaki, B Koblin, M Chesney, RD Moore, GD Kelen, T Coates, C Celum, SP Buchbinder, GR Seage III, TC Quinn, D Donnell, SH Eshleman. 2011. Use of a high resolution melting (HRM) assay to compare gag, pol, and env diversity in adults with different stages of HIV infection. PLoS ONE. 6(11):e27211.
  • Cousins MM, SS Ou, MJ Wawer, S Munshaw, D Swan, CA Magaret, CE Mullis, D Serwadda, SF Porcella, RH Gray, TC Quinn, D Donnell, SH Eshleman, AD Redd. 2012. Comparison of a high resolution melting (HRM) assay to next generation sequencing for analysis of HIV diversity. Journal of Clinical Microbiology. 50(9):3054-3059.
  • James MM, L Wang, D Donnell, MM Cousins, L Barlow-Mosha, JM Fogel, WI Towler, AL Agwu, D Bagenda, M Mubiru, P Musoke, SH Eshleman. 2012. Use of a high resolution melting assay to analyze HIV diversity in HIV-infected Ugandan children. Pediatric Infectious Disease Journal. 31(11): e222-e228.
  • Cousins MM, D Donnell, SH Eshleman. 2012. Impact of mutation type and amplicon characteristics on genetic diversity measures generated using a high resolution melting diversity assay. Journal of Molecular Diagnostics. 15(1):130-137.
  • Cousins MM, Swan D, Magaret CA, Hoover DR, Eshleman SH. 2013. Analysis of HIV using a high resolution melting (HRM) diversity assay: Automation of HRM data analysis enhances the utility of the assay for analysis of HIV incidence. PLoS ONE. 7(12):e51359.
  • Laeyendecker O, R Brookmeyer, MM Cousins, C Mullis, J Konikoff, D Donnell, C Celum, S Buchbinder, G Seage, S Mehta, J Astemborski, L Jacobson, J Margolick, J Brown, T Quinn, S Eshleman. 2013. HIV incidence determination in the United States: A multi-assay approach. Journal of Infectious Diseases. 207(2):232-239.