1. Novitsky, V., C. Arnold, and J. P. Clewley. 1996. Heteroduplex mobility assay for subtyping HIV-1: improved methodology and comparison with phylogenetic analysis of sequence data. J Virol Methods 59:61-72.

2. Novitsky VA, Montano MA, Essex M. Molecular epidemiology of an HIV-1 subtype A subcluster among injection drug users in the Southern Ukraine. AIDS Res Hum Retro. 1998;14:1079-85.

3. Montano, MA, VA Novitsky, JT Blackard, NL Cho, DA Katzenstein, and M Essex. 1997. Divergent transcriptional regulation among expanding human immunodeficiency virus type 1 subtypes. J. Virol. 71:8657-65.

4. Novitsky VA, Montano MA, McLane MF, Renjifo B, Vannberg F, Foley BT, Ndung’u TP, Rahman M, Makhema MJ, Marlink R, Essex M. Molecular cloning and phylogenetic analysis of human immunodeficiency virus type 1 subtype C: a set of 23 full-length clones from Botswana. J Virol. 1999;73:4427-32.

5. Novitsky VA, Gaolekwe S, McLane MF, Ndung’u TP, Foley BT, Vannberg F, Marlink R, Essex M. HIV-1 A/J recombinant with a pronounced pol gene mosaicism. AIDS Res Hum Retro. 2000;16:1015-20.

6. Ndung’u T, Renjifo B, Novitsky V, McLane MF, Gaolekwe S, Essex M. Molecular cloning and biological characterization of full-length HIV-1 subtype C from Botswana. Virology. 2000;278:390-9.

7. Montano, M. A., C. P. Nixon, T. Ndung’u, H. Bussmann, V. A. Novitsky, D. Dickman, and M. Essex. 2000. Elevated tumor necrosis factor-alpha activation of human immunodeficiency virus type 1 subtype C in Southern Africa is associated with an NF-kappaB enhancer gain-of-function. J Infect Dis 181:76-81.

8. Gilbert PB, Novitsky VA, Montano MA, Essex M. An efficient test for comparing sequence diversity between two populations. J Comput Biol. 2001;8:123-39.

9. Novitsky V, Flores-Villanueva PO, Chigwedere P, Gaolekwe S, Bussmann H, Sebetso G, Marlink R, Yunis EJ, Essex M. Identification of most frequent HLA class I antigen specificities in Botswana: relevance for HIV vaccine design. Hum Immunol. 2001;62:146-56.

10. Novitsky V, Rybak N, McLane MF, Gilbert P, Chigwedere P, Klein I, Gaolekwe S, Chang SY, Peter T, Thior I, Ndung’u T, Vannberg F, Foley BT, Marlink R, Lee TH, Essex M. Identification of human immunodeficiency virus type 1 subtype C Gag-, Tat-, Rev-, and Nef-specific elispot-based cytotoxic T-lymphocyte responses for AIDS vaccine design. J Virol. 2001;75:9210-28.

11. Ndung’u, T., Y. Lu, B. Renjifo, N. Touzjian, N. Kushner, V. Pena-Cruz, V. A. Novitsky, T.-H. Lee, and M. Essex. 2001. Infectious Simian/Human Immunodeficiency Virus with Human Immunodeficiency Virus Type 1 Subtype C from an African Isolate: Rhesus Macaque Model. J. Virol. 75:11417-11425.

12. Rivera-Morales, L. G., V. A. Novitsky, J. R. Trujillo, C. Lavalle-Montalvo, C. Cano-Dominguez, J. Ramos-Jimenez, E. Jimenez-Rios, L. Flores-Flores, P. Lopez-Guillen, P. Gilbert, F. Vannberg, R. Tamez-Guerra, C. Rodriguez-Padilla, and M. Essex. 2001. The Molecular Epidemiology of HIV Type 1 of Men in Mexico. AIDS Res Hum Retroviruses 17:87-92.

13. Gaschen B, Taylor J, Yusim K, Foley B, Gao F, Lang D, Novitsky V, Haynes B, Hahn BH, Bhattacharya T, Korber B. Diversity considerations in HIV-1 vaccine selection. Science. 2002;296(5577):2354-60.

14. Novitsky V, Smith UR, Gilbert P, McLane MF, Chigwedere P, Williamson C, Ndung’u T, Klein I, Chang SY, Peter T, Thior I, Foley BT, Gaolekwe S, Rybak N, Gaseitsiwe S, Vannberg F, Marlink R, Lee TH, Essex M.  HIV-1 subtype C molecular phylogeny: consensus sequence for an AIDS vaccine design. J Virol. 2002;76:5435-51.

15. Lee TH, Novitsky V. HIV vaccines: design and development. In: Essex M, Mboup S, Kanki PJ, Marlink RG, Tlou SD, editors. AIDS in Africa. 2nd ed. New York: Kluwer Academic / Plenum; 2002:594-611.

16. Novitsky V, Cao H, Rybak N, Gilbert P, McLane MF, Gaolekwe S, Peter T, Thior I, Ndung’u T, Marlink R, Lee TH, Essex M. Magnitude and frequency of cytotoxic T-lymphocyte responses: identification of immunodominant regions of human immunodeficiency virus type 1 subtype C. J Virol. 2002;76:10155-68.

17. Novitsky V, Gilbert P, Peter T, McLane MF, Gaolekwe S, Rybak N, Thior I, Ndung’u T, Marlink R, Lee TH, Essex M. Association between virus-specific T-cell responses and plasma viral load in human immunodeficiency virus type 1 subtype C infection. J Virol. 2003;77:882-90.

18. Jones, N., D. Agrawal, M. Elrefaei, A. Hanson, V. Novitsky, J. T. Wong, and H. Cao. 2003. Evaluation of antigen-specific responses using in vitro enriched T cells. J Immunol Methods 274:139-47.

19. Novitsky V, Shapiro R, Essex M. Human Retroviruses. In Gorbach SL, Bartlett JG, Blacklow NR, editors. Infectious diseases. 3rd ed. Philadelphia: Saunders; 2004:2082-105.

20. McKinney DM, Skvoretz R, Livingston BD, Wilson CC, Anders M, Chesnut RW, Sette A, Essex M, Novitsky V, Newman MJ. Recognition of variant HIV-1 epitopes from diverse viral subtypes by vaccine-induced CTL. J Immunol. 2004;173:1941-50.

21. Doualla-Bell, F., S. Gaseitsiwe, T. Ndung’u, M. Modukanele, T. Peter, V. Novitsky, N. Ndwapi, T. Gaolathe, A. Avalos, W. Wester, H. Bussmann, P. Cardiello, R. Marlink, H. Moffat, I. Thior, M. A. Wainberg, and M. Essex. 2004. Mutations and polymorphisms associated with antiretroviral drugs in HIV-1C-infected African patients. Antiviral Chem Chemother. 15:21-32.

22. Bussmann H, Novitsky V, Wester W, Peter T, Masupu K, Gabaitiri L, Kim S, Gaseitsiwe S, Ndung’u T, Marlink R, Thior I, Essex M. HIV-1 subtype C drug-resistance background among ARV-naïve adults in Botswana. Antiviral Chem Chemother. 2005;16:103-15.

23. Ndung’u T, Gaseitsiwe S, Sepako E, Doualla-Bell F, Peter T, Kim S, Thior I, Novitsky VA, Essex M. MHC class II (HLA-DRB and DQB) allele frequencies in Botswana: association with HIV-1 infection. Clin Diag Lab Immunol. 2005;12:1020-8.

24. Ndung’u T, Sepako E, McLane MF, Chand F, Bedi K, Gaseitsiwe S, Doualla-Bell F, Peter T, Thior I, Moyo SM, Gilbert PB, Novitsky VA, Essex M. HIV-1 Subtype C in vitro Growth and Coreceptor Utilization. Virology. 2006;347:247-60.

25. Novitsky VA, Gilbert PB, Shea K, McLane MF, Rybak N, Klein I, Thior I, Ndung’u T, Lee TH & Essex ME. Interactive association of proviral load and IFN-gamma-secreting T cell responses in HIV-1C infection. Virology. 2006; 349:142-55.

26. O’Neill, E., L. L. Baugh, V. A. Novitsky, M. E. Essex, and J. V. Garcia. 2006. Intra- and Intersubtype Alternative Pak2-Activating Structural Motifs of Human Immunodeficiency Virus Type 1 Nef. J. Virol. 80:8824-8829.

27. Shapiro, R. L., I. Thior, P. B. Gilbert, S. Lockman, C. Wester, L. M. Smeaton, L. Stevens, S. J. Heymann, T. Ndung’u, S. Gaseitsiwe, V. Novitsky, J. Makhema, S. Lagakos, and M. Essex. Maternal single-dose nevirapine versus placebo as part of an antiretroviral strategy to prevent mother-to-child HIV transmission in Botswana. AIDS 2006; 20:1281-8.

28. Thior, I., S. Lockman, L. M. Smeaton, R. L. Shapiro, C. Wester, S. J. Heymann, P. B. Gilbert, L. Stevens, T. Peter, S. Kim, E.van Widenfelt, C. Moffat, P. Ndase, P. Arimi, P. Kebaabetswe, P. Mazonde, J. Makhema, K. McIntosh, V. Novitsky, T. H. Lee, R. Marlink, S. Lagakos, and M. Essex. Breastfeeding plus infant zidovudine prophylaxis for 6 months vs formula feeding plus infant zidovudine for 1 month to reduce mother-to-child HIV transmission in Botswana: a randomized trial: the Mashi Study. JAMA 2006; 296:794-805.

29. Da’Dara, A. A., N. Lautsch, T. Dudek, V. Novitsky, T. H. Lee, M. Essex, and D. A. Harn. 2006. Helminth infection suppresses T-cell immune response to HIV-DNA-based vaccine in mice. Vaccine 24:5211-9.

30. Gupta, S. B., C. T. Mast, N. D. Wolfe, V. Novitsky, S. A. Dubey, E. G. Kallas, M. Schechter, B. Mbewe, E. Vardas, P. Pitisuttithum, D. Burke, D. Freed, R. Mogg, P. M. Coplan, J. H. Condra, R. S. Long, K. Anderson, D. R. Casimiro, J. W. Shiver, and W. L. Straus. 2006. Cross-clade reactivity of HIV-1-specific T-cell responses in HIV-1-infected individuals from Botswana and Cameroon. J Acquir Immune Defic Syndr 42:135-9.

31. Doualla-Bell, F., A. Avalos, T. Gaolathe, M. Mine, S. Gaseitsiwe, N. Ndwapi, V. A. Novitsky, B. Brenner, M. Oliveira, D. Moisi, H. Moffat, I. Thior, M. Essex, and M. A. Wainberg. 2006. Impact of Human Immunodeficiency Virus Type 1 Subtype C on Drug Resistance Mutations in Patients from Botswana Failing a Nelfinavir-Containing Regimen. Antimicrob. Agents Chemother. 50:2210-2213.

32. Wester, C. W., O. A. Okezie, A. M. Thomas, H. Bussmann, S. Moyo, T. Muzenda, J. Makhema, E. van Widenfelt, R. Musonda, V. Novitsky, T. Gaolathe, N. Ndwapi, M. Essex, D. R. Kuritzkes, V. Degruttola, and R. G. Marlink. 2007. Higher-than-expected rates of lactic acidosis among highly active antiretroviral therapy-treated women in Botswana: preliminary results from a large randomized clinical trial. J Acquir Immune Defic Syndr 46:318-22.

33. Novitsky, V., C.W. Wester, V. DeGruttola, H. Bussmann, S. Gaseitsiwe, A. Thomas, S. Moyo, R. Musonda, E. Widenfelt, R.G. Marlink, and M. Essex. 2007. The Reverse Transcriptase 67N 70R 215Y Genotype Is the Predominant TAM Pathway Associated with Virologic Failure among HIV-1C-Infected Adults Treated with ZDV/ddI-Containing HAART in Southern Africa. AIDS Res Hum Retroviruses 23:868-78

34. Novitsky, V., T. Gaolathe, E. Woldegabriel, J. Makhema, and M. Essex. 2007. A seronegative case of HIV-1 subtype C infection in Botswana. Clin Infect Dis 45:e68-71.

35.  Lockman, S., R. L. Shapiro, L. M. Smeaton, C. Wester, I. Thior, L. Stevens, F. Chand, J. Makhema, C. Moffat, A. Asmelash, P. Ndase, P. Arimi, E. van Widenfelt, L. Mazhani, V. Novitsky, S. Lagakos, and M. Essex. 2007. Response to antiretroviral therapy after a single, peripartum dose of nevirapine. N Engl J Med 356:135-47.

36. Novitsky, V., E. Woldegabriel, C. Wester, E. McDonald, R. Rossenkhan, M. Ketunuti, J. Makhema, G. R. Seage, 3rd, and M. Essex. 2008. Identification of primary HIV-1C infection in Botswana. AIDS Care 20:806-11.

37. Novitsky, V., E. Woldegabriel, L. Kebaabetswe, R. Rossenkhan, B. Mlotshwa, C. Bonney, M. Finucane, R. Musonda, S. Moyo, C. Wester, E. van Widenfelt, J. Makhema, S. Lagakos, and M. Essex. 2009. Viral Load and CD4+ T Cell Dynamics in Primary HIV-1 Subtype C Infection. J Acquir Immune Defic Syndr 50:65-76.

38. Novitsky, V., S. Lagakos, M. Herzig, C. Bonney, L. Kebaabetswe, R. Rossenkhan, D. Nkwe, L. Margolin, R. Musonda, S. Moyo, E. Woldegabriel, E. van Widenfelt, J. Makhema, and M. Essex. 2009. Evolution of proviral gp120 over the first year of HIV-1 subtype C infection. Virology  383:47-59.

39. Shapiro, R. L., L. Smeaton, S. Lockman, I. Thior, R. Rossenkhan, C. Wester, L. Stevens, C. Moffat, P. Arimi, P. Ndase, A. Asmelash, J. Leidner, V. Novitsky, J. Makhema, and M. Essex. 2009. Risk factors for early and late transmission of HIV via breast-feeding among infants born to HIV-infected women in a randomized clinical trial in Botswana. J Infect Dis 199:414-8.

40. Novitsky, V., R. Wang, L. Kebaabetswe, J. Greenwald, R. Rossenkhan, S. Moyo, R. Musonda, E. Woldegabriel, S. Lagakos, and M. Essex. Better Control of Early Viral Replication Is Associated with Slower Rate of Elicited Antiviral Antibodies in the Detuned EIA during Primary HIV-1C Infection. J Acquir Immune Defic Syndr. 2009 52: 265-272.

41. Bussmann, H., C. W. Wester, A. Thomas, V. Novitsky, R. Okezie, T. Muzenda, T. Gaolathe, N. Ndwapi, N. Mawoko, E. Widenfelt, S. Moyo, R. Musonda, M. Mine, J. Makhema, H. Moffat, M. Essex, V. Degruttola, and R. G. Marlink. 2009. Response to zidovudine/didanosine-containing combination antiretroviral therapy among HIV-1 subtype C-infected adults in Botswana: two-year outcomes from a randomized clinical trial. J Acquir Immune Defic Syndr 51:37-46.

42. Novitsky, V., R. Wang, L. Margolin, J. Baca, L. Kebaabetswe, R. Rossenkhan, C. Bonney, M. Herzig, D. Nkwe, S. Moyo, R. Musonda, E. Woldegabriel, E. van Widenfelt, J. Makhema, S. Lagakos, and M. Essex. 2009. Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection. PLoS One 4:e7727.

43. Rossenkhan, R., T. Ndung’u, T. K. Sebunya, J. E. Hagan, R. Shapiro, V. Novitsky, S. M. Moyo, I. Thior, S. Lockman, R. Mitchell, S. Kim, R. Musonda, E. van Widenfelt, J. Makhema, and M. Essex. 2009. Temporal reduction of HIV type 1 viral load in breast milk by single-dose nevirapine during prevention of MTCT. AIDS Res Hum Retroviruses 25:1261-4.

44. Mast, T. C., L. Kierstead, S. B. Gupta, A. A. Nikas, E. G. Kallas, V. Novitsky, B. Mbewe, P. Pitisuttithum, M. Schechter, E. Vardas, N. D. Wolfe, M. Aste-Amezaga, D. R. Casimiro, P. Coplan, W. L. Straus, and J. W. Shiver. 2010. International epidemiology of human pre-existing adenovirus (Ad) type-5, type-6, type-26 and type-36 neutralizing antibodies: correlates of high Ad5 titers and implications for potential HIV vaccine trials. Vaccine 28:950-7.

45. Wester, C. W., A. M. Thomas, H. Bussmann, S. Moyo, J. M. Makhema, T. Gaolathe, V. Novitsky, M. Essex, V. deGruttola, and R. G. Marlink. 2010. Non-nucleoside reverse transcriptase inhibitor outcomes among combination antiretroviral therapy-treated adults in Botswana. AIDS 24 Suppl 1:S27-36.

46. Novitsky, V., R. Wang, S. Lagakos, and M. Essex. 2010. HIV-1 Subtype C Phylodynamics in the Global Epidemic. Viruses 2:33-54.

47. Novitsky, V., R. Wang, H. Bussmann, S. Lockman, M. Baum, R. Shapiro, I. Thior, C. Wester, C. W. Wester, A. Ogwu, A. Asmelash, R. Musonda, A. Campa, S. Moyo, E. van Widenfelt, M. Mine, C. Moffat, M. Mmalane, J. Makhema, R. Marlink, P. Gilbert, G. R. Seage, 3rd, V. DeGruttola, and M. Essex. 2010. HIV-1 subtype C-infected individuals maintaining high viral load as potential targets for the “test-and-treat” approach to reduce HIV transmission. PLoS One 5:e10148.

48. Novitsky, V., R. Wang, L. Margolin, J. Baca, S. Moyo, R. Musonda, and M. Essex. 2010. Dynamics and timing of in vivo mutations at Gag residue 242 during primary HIV-1 subtype C infection. Virology 403:37-46.