Hezhao Ji

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

Education

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

Awards

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

https://doi.org/10.3390/pathogens11070739

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

https://doi.org/10.3390/pathogens11070724

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

https://doi.org/10.3390/pathogens11060693

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

https://doi.org/10.3390/v14061152

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

https://doi.org/10.1038/s41467-022-30913-4

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.

https://doi.org/10.1097/QAD.0000000000002829

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

https://doi.org/10.3390/v12121456

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

https://doi.org/10.3390/v12070694

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

https://doi.org/10.3390/v12060666

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

https://doi.org/10.3390/v12050627

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

https://doi.org/10.3390/v12050617

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

https://doi.org/10.3390/v12060586

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

https://doi.org/10.3390/v12050556

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

https://doi.org/10.3390/v12050550

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.

https://doi.org/10.1038/s41598-020-58544-z

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.

https://doi.org/10.1101/733238

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.

https://doi.org/10.1038/s41598-019-45328-3

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.

https://doi.org/10.1002/jia2.25193

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

https://doi.org/10.2174/1570162X16666180626152252

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.

https://doi.org/10.1097/QAI.0000000000001649

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.

https://doi.org/10.1155/2017/4979252

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.

https://doi.org/10.1016/S2352-3018(16)30119-9

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.

https://doi.org/10.1371/journal.pone.0157340

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.

https://doi.org/10.1016/j.virol.2014.12.037

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.

https://doi.org/10.1371/journal.pone.0056170

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.

https://doi.org/10.1016/j.jviromet.2012.10.018

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

https://doi.org/10.3851/IMP1839

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.

https://doi.org/10.1371/journal.pone.0009263

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.

https://doi.org/10.3109/00365540903496536.

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.

https://doi.org/10.1080/10425170701606177

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)

https://doi.org/10.1097/QAD.0b013e3280ef6ae1

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.

https://doi.org/10.1007/s10038-004-0185-9

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.

https://doi.org/10.1084/jem.193.8.935

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.

https://doi.org/10.1023/a:1026531506202

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.

https://doi.org/10.1084/jem.191.9.1525