Hezhao Ji

Image Sarah London
Research Scientist & Head of Viral Genetics Unit

Research focusing on HIV drug resistance and molecular epidemiology.

Current research and/or projects

Dr. Ji’s work focuses on HIV Drug resistance, HIV Genetics, HIV viral evolution, Molecular HIV epidemiology, and Next generation sequencing.

Research and/or project statements

  • Development and implementation of next generation sequencing (NGS)-based HIV drug resistance (HIVDR) testing technologies
  • Development of a universal, full-length genome sequencing protocol for HCV and HIV based on oligonucleotide capture enrichment and next-generation sequencing
  • Revolution of molecular viral characterization strategies in support of enhanced viral disease outbreak investigation and surveillance in the next generation sequencing era
  • A key initiator and the organizing committee chair of the international symposium for NGS-based HIV drug resistance testing series since 2017.
    • contributes greatly to the standardization and operationalization of such assays for frontline HIVDR lab testing for both research, surveillance and patient care purposes

Professional activities / interests

Supervised graduate students, co-op students and postdoctoral fellows.

Education and awards


Ph.D. Medical Microbiology & Infectious Diseases, University of Manitoba, 2007

M.Sc.  Medical Immunology, Hebei Medical University, 1996

Bachelor of Medicine (MD equivalent), Zhangjiakou Medical College, 1993


Scientific Excellence Award, Infectious Disease Prevention and Control Branch, PHAC, 2019

International experience and/or work

Member of International AIDS society

Member of WHO Global HIV Drug Resistance Network “Research and Innovation Working Group”

Hosted three international training workshops (2015,2016 and 2017) on NGS HIVDR technologies with trainees from regional or national HIVDR reference labs from Mexico, Brazil, Puerto Rico (USA), Chile, Martinique, Argentina, Colombia, Panama and Uganda

Initiated and chaired the 1st  (2018) and the 2nd  (2019) International Symposia on NGS-based HIV Drug Resistance Testing  in Winnipeg, Canada, with expert delegates from across the world.

Key publications

Ji H and Sandstrom P.  Overview of the Analytes Applied in Genotypic HIV Drug Resistance Testing. Pathogens, 2022, 11(7):739  


Chua R, Capina R and Ji H.  Point-of-care tests for HIV drug resistance monitoring: advances and potentials. Pathogens, 2022, 11(7):724  


Munyuza C, Ji H. and Lee ER.  Probe Capture Enrichment Methods for HIV and HCV Genome 2
Sequencing and Drug Resistance Genotyping. Pathogens, 2022, 11(6), 693


 Li K, Lowey C, Sandstrom P and Ji H.  CAVES: A Novel Tool for Comparative Analysis of Variant Epitope Sequences. Viruses, 2022, 14(6) 1152


Ssemaganda A, Nguyen C, Nuhu F, Jahan J, Card CM, Kiazyk  S, Severeni G, Keynan Y, Su R, Ji H, McLaren PJ, Ball TB, Bullard J, Caeseele PV, Stein D, and McKinnon LR. Expansion of cytotoxic, tissue-resident CD8+ T cells and CCR6+ CD161+ CD4+ T cells in the nasal mucosa following mRNA COVID-19 vaccination. Nature Communications, 2022,13:3357


Gebrebrhav H, Kambaran C, Sivro A, Adhiambo W, Siele N, Becker M, Li J, Choi S, Mwatelah R, Reyes NV, Akolo M, Njogu P, Choletter F, Ho J,Kim J, Peterson SW, Martin I, Sandstrom P, Mehta S, Lorway RR, Ball TB, Kimani J, McLaren P, Ji H and McKinnon L. Rectal microbiota diversity in Kenyan men who have sex with men (MSM) is inversely associated with frequency of receptive anal sex, independent of HIV status. AIDS, 2021, 35(7):1091-1101.


Jennings C, Parkin N, Zaccaro DJ, Capina R, Sandstrom P, Ji H, Brambilla DJ and Bremer JW. Application of a Sanger-based external quality assurance strategy for the transition of HIV-1 drug resistance assays to next generation sequencing. Viruses, 2020, 12(12): 1456


Parkin N, Zaccaro D,  Avila-Rios S, Brumme CJ, Hunt G, Ji H, (...), Zhou S and Jennings C. Multi-Laboratory Comparison of Next-Generation to Sanger-Based Sequencing for HIV-1 Drug Resistance Genotyping.  Viruses. 2020, 12(7): 694


Noguera-Julian M,  Lee ER, Trevors S, Shafer R, Kantor R, and Ji H. Dry panels supporting external quality assessment programs for Next Generation Sequencing-Based HIV drug resistance testing. Viruses. 2020, 12(6): 666


Becker M, Liang D, Cooper B, (...), Sandstrom P and Ji H. Development and application of performance assessment criteria for next generation sequencing-based HIV drug resistance assays. Viruses. 2020, 12(6): 627


Avila-Rios S, Parkin N, Swanstrom R, (...), Ji H and Kantor R.  Next-generation sequencing for HIV drug resistance testing: laboratory, clinical, and implementation considerations. Viruses. 2020, 12(6): 617


Ji H, Sandstrom P, Paredes R, Harrigan R,  (...), Parkin N, and Kantor R. Are we ready for NGS HIV drug resistance testing? The second ‘Winnipeg Consensus’ Symposium. Viruses, 2020, 12(6): 586


Ji H, Parkin N, Gao F, (...), Sandstrom P and Kantor R. External quality assessment program for next generation sequencing-based HIV drug resistance testing: Logistical considerations. Viruses, 2020, 12(5): 556


Lee ER, Gao F, Sandstrom P and Ji H.    External quality assessment for next-generation sequencing-based HIV drug resistance testing: unique requirements and challenges. Viruses, 2020, 12(5): 550


Lee ER, Parkin N, Jennings C, (...), Sandstrom P and Ji H. Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing. Scientific Reports 2020, 10(1): 1634. 


Marinier E, Enns E, Tran C, (...), Kidwai A, Ji H, and Van Domselaar G. quasitools: A collection of tools for viral quasispecies analysis. BioRxiv, August 2019.


Taylor, T., Lee, E.R., Nykoluk, M., (...), Brooks, J., Ji, H.  A MiSeq-HyDRA platform for enhanced HIV drug resistance genotyping and surveillance. 2019 Scientific Reports, 9(1),8970.


Ji, H., Enns, E., Brumme, C.J., (...), Kantor, R., Noguera-Julian, M. Bioinformatic data processing pipelines in support of next-generation sequencing-based HIV drug resistance testing: the Winnipeg Consensus. 2018 Journal of the International AIDS Society, 21(10),e25193.


Liu, C.C., Ji, H. PCR amplification strategies towards full-length HIV-1 genome sequencing. 2018 Current HIV Research, 16(2), pp. 98-105. 


Ji, H., Patterson, A., Taylor, T., (...), Brooks, J., Sandstrom, P. Prevalence of primary drug resistance against HIV-1 integrase inhibitors in Canada. 2018 Journal of Acquired Immune Deficiency Syndromes, 78(1), pp. E1-E3. 


Gupta, S., Taylor, T., Patterson, A., (...), Van Domselaar, G., Ji, H.  A robust PCR protocol for HIV drug resistance testing on low-level viremia samples. 2017 BioMed Research International, 2017.


Avila-Rios S, Garcia-Morales C, Matias-Florentino M, Romero-Mora KA, Tapia-Trejo D, Quiroz-Morales SV, Ji H, Sandstrom P, Casillas-Rodriguez J, Sierra-Madero J, Leon-Juarez EA, Magis-Rodriguez C, Uribe-Zuñiga P, Reyes-Terán G. HIV pre-treatment drug resistance in Mexico and its impact on first-line antiretroviral treatment effectiveness: A nationally representative 2015 World Health Organization survey using Sanger and next generation sequencing. Lancet HIV. 3(12) e579–e591, December 2016.


Hora B, Keating SM, Chen Y, Sanchez AM, Sabino E, Hunt G, Hackett J, Swanson P, Hewlett I, Ragupathy V, Vemula SV, Zeng P, Tee KK, Chow WZ, Ji H, Sandstrom P, Denny TN, Busch MP and Gao F. Genetic characterization of a panel of diverse HIV-1 isolates at seven international sites. PLoS One, 11(6): e0157340.


Ji, H., Kozak, R.A., Biondi, M.J., (...), Sandstrom, P., Brooks, J. Next generation sequencing of the hepatitis C virus NS5B gene reveals potential novel S282 drug resistance mutations. 2015 Virology, 477, pp. 1-9. 


Ji, H., Li, Y., Liang, B., (...), Sandstrom, P., Brooks, J. Pyrosequencing Dried Blood Spots Reveals Differences in HIV Drug Resistance between Treatment Naïve and Experienced Patients. 2013 PLoS ONE, 8(2),e56170.


Ji H, Liang B, Li Y, Van Domselaar G, Graham M, Tyler S, Merks H, Sandstrom P and Brooks J. Low abundance drug resistance variants in transmitted HIV drug resistance surveillance specimens identified using tagged pooled pyrosequencing. J Virol Methods 187 (2013) 314– 320.


Ji H, Li Y, Graham M, Liang B, Pilon R, Tyson S, Peters G, Tyler S, Merks H, Bertagnolio S, Luis Soto-Ramirez L, Sandstrom P and Brooks J. Next Generation Sequencing of Dried Blood Spot Specimens: A Novel Approach to HIV Drug Resistance Surveillance. Antivir Ther 2011;16(6):871-8


Ji H, Massé N, Tyler S, Liang B, Merks H, Graham M, Sandstrom P and Brooks B. HIV Drug Resistance Surveillance Using Pooled Pyrosequencing. PLoS One  Feb 2010. 5(2):e9263.


Ji H, Ball T B, Liang BB, Ao Z, Kimani J, Yao X and Plummer F A. Reduced HIV-1 long terminal repeat transcription in subjects with protective interferon regulatory factor-1 genotype: A potential mechanism mediating resistance to infection by HIV-1. Scand J Infect Dis 2010. 42(5):389~394.


Ji H, Ball T B, Liang B B, Kimani J and Plummer F A. Human Interferon Regulatory Factor-1 gene and its promoter sequences revealed by population-based complete gene sequencing. DNA Seq 2008 Jun; 19 (3):  326-31.


Ball TB*, Ji H*, Kimani J, Hill A, Marlin C and Plummer F. Polymorphisms in IRF-1 associated with resistance to HIV-1 infection in highly exposed uninfected Kenyan sex workers. AIDS 2007; 31;21(9):1091-101. (*Co-first authorship)


Ji H, Ball TB, Kimani J and Plummer F. Novel Interferon Regulatory Factor-1 Polymorphisms in a Kenyan Population Revealed by Complete Gene Sequencing. (2004). J Hum Genet 2004; 49: 528-535.


Zhong G, Fan P, Ji H, et al. Identification of a chlamydia protease-like activity factor responsible for the degradation of host transcription factors. J Exp Med 2001; 193(8): 935-942.


Li L, Hu H, Ji H, et al. Chlamydia pneumoniae infection significantly exacerbates aortic atherosclerosis in an LDLR-/- mouse model within six months. Mol Cell Biochem   2000; 215(1-2): 123-128.


Zhong G, Liu L, Fan T, Fan P and Ji H. Degradation of transcription factor RFX-5 during the inhibition of both constitutive and Interferon -inducible Major Histocompatibility Complex Class I expression in chlamydia-infected cells. J Exp Med  2000; 191(9): 1525-34.



Research facility

1015 Arlington Street
Winnipeg, MB R3E 3M4


Adjunct Professor, Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba