Margaret IP
Mamie HUI
Zigui CHEN
Christopher KC LAI
Rita WY NG
Siaw Shi BOON
Yun Kit YEOH
Chiu Yeung CHAN
Research, Administrative and Honorary Staff
Elite Alumni Microbiologists
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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)
  • Member, Papillomaviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV)
  • Scientific Advisor, Papillomavirus Episteme (PaVE), NIAID/NIH
  • Editorial Board Membership – Pathogens
  • Editorial Board Membership – Journal of Virology Methods
ORCID iD iconorcid.org/0000-0002-8577-1298
Research interest
Microbial evolution and bioinformatics – Using big dataset and bioinformatics to elucidate the community dynamics and host-microorganism interaction of human microbiome, mycobiome and virome.
Human micro-pathogens in cancer – Using molecular evolution and in-vitro cell models to understand the genomics diversity and carcinogenic potential of human papillomaviruses (HPV) and human microbiome in cervical cancer and head and neck squamous cell carcinoma.
Emerging respiratory tract infection – Using bioinformatics and omics approaches to study the molecular genomics, epidemiology 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 genetic basis, gene origins, and the adaptation of pathogens to a changing environment. It helps us solve biological problems that impact our health. Our group devotes to the studies of human microbial and viral evolution, genomics and epigenetics using analytic tools of systems biology and advanced bioinformatics pipeline. We have collaborated with several scientists and made fruitful contributions to identifying the genetic heterogeneity of human papillomaviruses (HPVs) causing cervical cancer. With the quick facilitation of Next-Generation Sequencing (NGS) and big dataset analysis, we are expanding our research interests in the complex ecological community of human microbiome interacting with human cancers and disease outcomes. Our mission is to develop and apply evolutionary and bioinformatics approaches to characterize and interpret the host-pathogen causality.
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
SARS-Co V-2 global and local variant characterization in associate with clinical and public impacts
CUHK RC's One-off Project Impact Enhancement Fund
Principle Investigator
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)
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)
Publications (Selected publications relevance to viruses and microbiota)
  1. Chen Z, Chong KC, Wong MCS, Boon SS, Huang J, Wang MH, Ng RWY, Lai CKC, Chan PKS. A global analysis on replacement of genetic variants of SARS-CoV-2 in associate with containment capacity and changes in disease severity. Clin Microbiol Infect. 2021. Epub 2021/02/02. doi: 10.1016/j.cmi.2021.01.018. PubMed PMID: 33524589. [IF=6.425]
  2. 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) Epub 2020/11/22. doi: 10.3390/cancers12113425. PubMed PMID: 33218162 [IF=6.126]
  3. Lai CKC, Chen Z, Lui G, Ling L, Li T, Wong MCS, Ng RWY, Tso EYK, Ho T, Fung KSC, Ng ST, Wong BKC, Boon SS, Hui DSC, Chan PKS. Prospective study comparing deep-throat saliva with other respiratory tract specimens in the diagnosis of novel coronavirus disease (COVID-19). J Infect Dis. 2020. Epub 2020/08/02. doi: 10.1093/infdis/jiaa487. PubMed PMID: 32738137. [IF=5.186] (co-first author)
  4. Wong MC, Vlantis AC, Liang M, Wong PY, Ho WC, Boon SS, Leung C, Chan PK, Chen Z. Persistence and clearance of oral human papillomavirus infections: a prospective population-based cohort study. J Med Virol. 2020. Epub 2020/06/04. doi: 10.1002/jmv.26130. PubMed PMID: 32492214. [IF=2.021]
  5. 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. Epub 2020/02/14. doi: 10.1136/gutjnl-2019-319635. PubMed PMID: 32051205. [IF=17.943]
  6. 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. Frontiers in Microbiology. 2019;10(2093):2093. Epub 2019/09/26. doi: 10.3389/fmicb.2019.02093. PubMed PMID: 31552003. [IF=4.235]
  7. 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). Epub 2019/03/06. doi: 10.1128/mSystems.00271-18. PubMed PMID: 30834331. [IF=6.280]
  8. 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. Epub 2018/11/02. doi: 10.1371/journal.ppat.1007352. PubMed PMID: 30383862. [IF=6.158]
  9. Chen Z, Yeoh YK, Hui M, Wong PY, Chan MCW, Ip M, Yu J, Burk RD, Chan FKL, Chan PKS. Diversity of macaque microbiota compared to the human counterparts. Scientific Reports. 2018;8(1):15573. Epub 2018/10/24. doi: 10.1038/s41598-018-33950-6. PubMed PMID: 30349024. [IF=4.122]
  10. 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. Epub 2018/07/10. doi: 10.1093/infdis/jiy160. PubMed PMID: 29982800. [IF=6.273]
  11. Chen Z, Schiffman M, Herrero R, DeSalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Chan PKS, Burk RD. Classification and evolution of human papillomavirus genome variants: Alpha-5 (HPV26, 51, 69, 82), Alpha-6 (HPV30, 53, 56, 66), Alpha-11 (HPV34, 73), Alpha-13 (HPV54) and Alpha-3 (HPV61). Virology. 2018;516:86-101. Epub 2018/01/15. https://doi: 10.1016/j.virol.2018.01.002. PubMed PMID: 29331867. [IF=3.351]
  12. Chen Z, Ho WCS, Boon SS, Law PTY, Chan MCW, DeSalle R, Burk RD, Chan PKS. Ancient Evolution and Dispersion of Human Papillomavirus Type 58 Variants. J Virol. 2017. Epub 2017/08/11. PubMed PMID: 28794033. https://doi.org/10.1128/JVI.01285-17. [IF=4.663]
  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. 2017. Epub 2017/10/17. PubMed PMID: 29031597. https://doi.org/10.1016/j.jaci.2017.09.018. [IF=12.485] (co-first author)
  14. Agalliu I, Gapstur S, Chen Z, Wang T, Anderson RL, Teras L, Kreimer AR, Hayes RB, Freedman ND, Burk RD. Associations of Oral alpha-, beta-, and gamma-Human Papillomavirus Types With Risk of Incident Head and Neck Cancer. JAMA Oncol. 2016. Epub 2016/01/23. PubMed PMID: 26794505. https://doi.org/10.1001/jamaoncol.2015.5504. [IF= 16.559]
  15. Chen Z, Schiffman M, Herrero R, DeSalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Burk RD. Evolution and taxonomic classification of alphapapillomavirus 7 complete genomes: HPV18, HPV39, HPV45, HPV59, HPV68 and HPV70. PLoS ONE. 2013;8(8):e72565. Epub 2013/08/27. PubMed PMID: 23977318. https://doi.org/10.1371/journal.pone.0072565. [IF=3.534]
  16. Chen Z, Schiffman M, Herrero R, Desalle R, Anastos K, Segondy M, Sahasrabuddhe VV, Gravitt PE, Hsing AW, Burk RD. Evolution and taxonomic classification of human papillomavirus 16 (HPV16)-related variant genomes: HPV31, HPV33, HPV35, HPV52, HPV58 and HPV67. PLoS ONE. 2011;6(5):e20183. Epub 2011/06/16. PubMed PMID: 21673791. https://doi.org/10.1371/journal.pone.0020183. [IF=4.092]
  17. Bernard HU, Burk RD, Chen Z, van Doorslaer K, zur Hausen H, de Villiers EM. Classification of papillomaviruses (PVs) based on 189 PV types and proposal of taxonomic amendments. Virology. 2010;401(1):70-9. Epub 2010/03/09. PubMed PMID: 20206957. https://doi.org/10.1016/j.virol.2010.02.002. [IF=3.305]
  18. 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. Epub 2008/11/28. PubMed PMID: 19036820. https://doi.org/10.1128/JVI.02068-08. [IF= 5.308]
  19. 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. Epub 2007/03/14. PubMed PMID: 17351898. https://doi.org/10.1002/ijc.22632. [IF=7.36]
  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. Epub 2005/05/14. PubMed PMID: 15890941. https://doi.org/10.1128/JVI.79.11.7014-7023.2005. [IF= 5.308]