Margaret IP
Mamie HUI
Zigui CHEN
Christopher KC LAI
Rita WY NG
Siaw Shi BOON
Sishuo WANG
Research, Administrative and Honorary Staff
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Faculty > Zigui CHEN
Personal information
Name Zigui CHEN
Academic / Professional Qualifications B.Sc., Ph.D.
Academic title & affiliations Associate Professor
Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong
Email zigui.chen@cuhk.edu.hk
Current Appointments
(Including honorary appointments)
  • Honorary Associate Professor, Faculty of Dentistry, The University of Hong Kong
  • Member, Papillomaviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV)
  • Scientific Advisor, Papillomavirus Episteme (PaVE), NIAID/NIH
ORCID iD iconorcid.org/0000-0002-8577-1298
Research interest
Microbial evolution and bioinformatics – Using state-of-the-art genetic engineering and bioinformatics to reveal the community dynamics of the microbiome (bacteriome, mycobiome and virome) in human diseases.
Human micro-pathogens in cancer – Using integrative analysis of host-microbiota interactions and in-vitro & in-vivo models to elucidate the causal potential of carcinogenic micro-pathogens in upper aerodigestive tract malignancy.
Emerging respiratory tract infection – Using molecular evolution and multi-omics approaches to understand the genomic heterogenicity and pathogenesis of emerging respiratory infections including COVID-19, seasonal influenza, and bacterial pneumonia.

Understanding evolution of disease-causing microorganisms is the foundation of what we know about origin and adaptation of pathogens to a changing environment. It helps us solve biological problems that impact our health. My laboratory mainly focuses on the carcinogenic potential of tumor bacteria and virus in light of genomic evidence and evolutionary theories. This has been a very successful area delivering fruitful contributions in understanding the heterogeneity and oncogenicity of human papillomaviruses (HPVs) in cervical cancer and oral cancer. Translational research on human microbiome in upper aerodigestive tract cancers using multi-omics approaches represents an increasing extension of our interests, which yields valuable insight into the complex host-microbiota interactions for clinical management and therapeutic intervention. We are actively involving in a multidisciplinary research team on different aspect of human microbiome and diseases, including the emerging infectious diseases such as COVID-19 and Influenza.
Postgraduate students
Information for Postgraduate Study in Department of Microbiology
Research Experience
5/2021 - current Associate Professor
Department of Microbiology, The Chinese University of Hong Kong
5/2015 – 4/2021 Assistant Professor
Department of Microbiology, The Chinese University of Hong Kong
7/2009 – 4/2015 Instructor (Research Assistant Professor)
Department of Paediatrics, Albert Einstein College of Medicine, NY, USA
9/2002 – 6/2009 Research Associate
Department of Microbiology and Immunology, Albert Einstein College of Medicine, NY, USA
9/1997 – 7/2002 PhD, Ocean University of China
9/1993 – 7/1997 Bachelor, Ocean University of China
Association between oral microbiome, HPV and human epigenetic events in head and neck squamous cell carcinoma
General Research Fund (GRF) / University Grants Committee (Hong Kong)
Principle Investigator
Evolutionary dynamics and genetic basis of carcinogenicity of primate papillomaviruses 
Early Career Scheme (ECS) / University Grants Committee (Hong Kong)
Principle Investigator
Characterization of Genomic and Functional Features of Human Microbiome Associated with Oral Cavity Squamous Cell Carcinoma Using Multi-Omics Approaches
Health and Medical Research Fund (HMRF) / Food and Health Bureau (Hong Kong) Principle Investigator
The association between human papillomavirus (HPV) E6 oncoprotein and Aurora B in carcinogenesis – a potential horizon for therapeutic intervention
General Research Fund (GRF) / University Grants Committee (Hong Kong)
Early biomarkers in SARS-CoV-2 infection: correlation with short/medium/long-term clinical outcomes, and implications on acute patient management and long-term medical and health care
Health and Medical Research Fund (HMRF) / Food and Health Bureau (Hong Kong)
Characterizing whole genome stability of the novel coronavirus SARS-CoV-2
Health and Medical Research Fund (HMRF) / Food and Health Bureau (Hong Kong)
Publications (Selected publications relevance to viruses and microbiota)
  1. Long T, Burk RD, Chan PKS, Chen Z*. Non-Human Primate Papillomavirus E6-Mediated p53 Degradation Reveals Ancient Evolutionary Adaptation of Carcinogenic Phenotype to Host Niche. PLoS Pathog. 2022;18(3):e1010444. doi: 10.1371/journal.ppat.1010444.
  2. Chen Z, Ng RWY, Lui G, Ling L, Chow C, Yeung ACM, Boon SS, Wang MH, Chan KCC, Chan RWY, Hui DSC, Chan PKS. Profiling of SARS-CoV-2 subgenomic RNAs in clinical specimens. Microbiol Spectr. 2022:e0018222. doi: 10.1128/spectrum.00182-22.
  3. Cheung MK, Chan JYK, Wong MCS, Wong PY, Lei P, Cai L, Lan L, Ho WCS, Yeung ACM, Chan PKS, Chen Z*. Determinants and Interactions of Oral Bacterial and Fungal Microbiota in Healthy Chinese Adults. Microbiol Spectr. 2022:e0241021. doi: 10.1128/spectrum.02410-21.
  4. Boon SS, Xia C, Wang MH, Yip KL, Luk HY, Li S, Ng RWY, Lai CKC, Chan PKS, Chen Z*. Temporal-Geographical Dispersion of SARS-CoV-2 Spike Glycoprotein Variant Lineages and Their Functional Prediction Using in Silico Approach. mBio. 2021;12(5):e0268721. doi: 10.1128/mBio.02687-21.
  5. Chan JYK, Ng CWK, Lan L, Fung S, Li JW, Cai L, Lei P, Mou Q, Meehan K, Lau EHL, Yeung Z, Chan KCA, Wong EWY, Chan PKS, Chen Z*. Restoration of the Oral Microbiota After Surgery for Head and Neck Squamous Cell Carcinoma Is Associated With Patient Outcomes. Front Oncol. 2021;11:737843. doi: 10.3389/fonc.2021.737843.
  6. Chen Z, Chong KC, Wong MCS, Boon SS, Huang J, Wang MH, Ng RWY, Lai CKC, Chan PKS. A global analysis of replacement of genetic variants of SARS-CoV-2 in association with containment capacity and changes in disease severity. Clin Microbiol Infect. 2021. doi: 10.1016/j.cmi.2021.01.018.
  7. Chen Z*, Wong PY, Ng CWK, Lan L, Fung S, Li JW, Cai L, Lei P, Mou Q, Wong SH, Wu WKK, Li RJ, Meehan K, Lui VWY, Chow C, Lo KW, Chan ABW, Boon SS, Lau EHL, Yeung Z, Chan KCA, Wong EWY, Cheng ASL, Yu J, Chan PKS, Chan JYK. The Intersection between Oral Microbiota, Host Gene Methylation and Patient Outcomes in Head and Neck Squamous Cell Carcinoma. Cancers (Basel). 2020;12(11). doi: 10.3390/cancers12113425.
  8. Yeoh YK, Chen Z, Wong MCS, Hui M, Yu J, Ng SC, Sung JJY, Chan FKL, Chan PKS. Southern Chinese populations harbour non-nucleatum Fusobacteria possessing homologues of the colorectal cancer-associated FadA virulence factor. Gut. 2020;69(11):1998-2007. doi: 10.1136/gutjnl-2019-319635.
  9. Chen Z*, Long T, Wong PY, Ho WCS, Burk RD, Chan PKS. Non-human Primate Papillomaviruses Share Similar Evolutionary Histories and Niche Adaptation as the Human Counterparts. Front Microbiol. 2019;10(2093):2093. doi: 10.3389/fmicb.2019.02093.
  10. Chen Z*, Hui PC, Hui M, Yeoh YK, Wong PY, Chan MCW, Wong MCS, Ng SC, Chan FKL, Chan PKS. Impact of Preservation Method and 16S rRNA Hypervariable Region on Gut Microbiota Profiling. mSystems. 2019;4(1). doi: 10.1128/mSystems.00271-18.
  11. Chen Z*, DeSalle R, Schiffman M, Herrero R, Wood CE, Ruiz JC, Clifford GM, Chan PKS, Burk RD. Niche adaptation and viral transmission of human papillomaviruses from archaic hominins to modern humans. PLoS Pathog. 2018;14(11):e1007352. doi: 10.1371/journal.ppat.1007352.
  12. Wong MCS, Vlantis AC, Liang M, Wong PY, Ho WCS, Boon SS, Sze RKH, Leung C, Chan PKS, Chen Z*. Prevalence and Epidemiologic Profile of Oral Infection with Alpha, Beta, and Gamma Papillomaviruses in an Asian Chinese Population. J Infect Dis. 2018;218(3):388-97. doi: 10.1093/infdis/jiy160.
  13. Goldman DL, Chen Z#, Shankar V, Tyberg M, Vicencio A, Burk R. Lower airway microbiota and mycobiota in children with severe asthma. J Allergy Clin Immunol. 2018;141(2):808-11 e7. doi: 10.1016/j.jaci.2017.09.018.
  14. Chen Z, Ho WCS, Boon SS, Law PTY, Chan MCW, DeSalle R, Burk RD, Chan PKS. Ancient Evolution and Dispersion of Human Papillomavirus 58 Variants. J Virol. 2017;91(21). doi: 10.1128/JVI.01285-17.
  15. The Cancer Genome Atlas Research Network. Integrated genomic and molecular characterization of cervical cancer. Nature. 2017;543(7645):378-84. doi: 10.1038/nature21386.
  16. Chen Z, DeSalle R, Schiffman M, Herrero R, Burk RD. Evolutionary dynamics of variant genomes of human papillomavirus types 18, 45, and 97. J Virol. 2009;83(3):1443-55. doi: 10.1128/JVI.02068-08.
  17. Wood CE, Chen Z, Cline JM, Miller BE, Burk RD. Characterization and experimental transmission of an oncogenic papillomavirus in female macaques. J Virol. 2007;81(12):6339-45. doi: 10.1128/JVI.00233-07.
  18. Chen Z*, Fu L, Herrero R, Schiffman M, Burk RD. Identification of a novel human papillomavirus (HPV97) related to HPV18 and HPV45. Int J Cancer. 2007;121(1):193-8. doi: 10.1002/ijc.22632.
  19. Narechania A, Chen Z, DeSalle R, Burk RD. Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses. J Virol. 2005;79(24):15503-10. doi: 10.1128/JVI.79.24.15503-15510.2005.
  20. Chen Z, Terai M, Fu L, Herrero R, DeSalle R, Burk RD. Diversifying selection in human papillomavirus type 16 lineages based on complete genome analyses. J Virol. 2005;79(11):7014-23. doi: 10.1128/JVI.79.11.7014-7023.2005.