Publications

For the complete, continuously updated record, see my Google Scholar profile ( ) and my ORCID. The list below highlights papers where I am (co-)first or senior author, together with co-authored papers in selected journals.

2026

• Haogao Gu^*†, Jifan Li^*, Wanying Sun, Mengting Li, Kathy Leung, Joseph T. Wu, Hsiang-Yu Yuan, Maggie H. Wang, Bingyi Yang, Matthew R. McKay, Ning Ning, Leo L. M. Poon^†. Optimizing global genomic surveillance for early detection of emerging SARS-CoV-2 variants. Nature Communications. (2026)
• Haogao Gu, Mengting Li, Ruixuan Wang, L. K. Lee, W. Y. Tam, Alex Y. M. Ho, Miranda C. Y. Yau, K. T. Yip, River C. W. Wong, Barry K. C. Wong, Kristine S. Luk, Jimmy Y. W. Lam, T. L. Que, Viola C. Y. Chow, Sandy K. Y. Chau, Sebastian Duchene, Gilman K. H. Siu, Leo L. M. Poon. Genomic Epidemiology of Hospital-Associated SARS-CoV-2 Clusters in Hong Kong During a Period of Relaxed Visitation (May–August 2022). Influenza and Other Respiratory Viruses, 20(3), e70249. (2026)
• Yongtao Ye, Huiping Shuai, Yi Song, Marcus Ho-Hin Shum, David K. Smith, Haogao Gu, Huachen Zhu, Joseph T. Wu, Nicola S. Lewis, Francesco Bonfante, Edward C. Holmes, Malik Peiris, Leo Lit-Man Poon, Yi Guan, Tommy Tsan-Yuk Lam. Genomic features associated with sustained mammalian transmission of avian influenza A viruses. Nature Microbiology, s41564-025-02257-4. (2026)
• Nigeer Te, Alex Wing Hong Chin, Haogao Gu, Janice Zhirong Jia, Yi Huang, Samuel Mo Sheung Cheng, Chee Wah Tan, Jincun Zhao, Kenrie Pui Yan Hui, Michael Chi Wai Chan, Bo Feng, Ahmed Abdul Quadeer, Matthew R McKay, Linfa Wang, Sophie A Valkenburg, Malik Peiris, Leo Lit Man Poon. Broad beta-CoV immunity and transmission blockade by a single-dose live-attenuated vaccine with atypical codon usage. Proceedings of the National Academy of Sciences, 123(4), e2518645123. (2026)

2025

• Wanying Sun, Ka Tim Choy, Ka Man Cheng, Christopher J Brackman, Samuel MS Cheng, Thomas HC Sit, CN Anne, Leslie D Sims, Haogao Gu, Amy WY Tang, Andrew NC Wong, Andrew TL Tsang, Joe CT Koo, Leo LH Luk, Hui-Ling Yen, Malik Peiris, Leo LM Poon. Detection and characterisation of high pathogenicity avian influenza virus (H5N1/H5N8) clade 2.3.4.4b, Hong Kong SAR, China, 2021 to 2024. Eurosurveillance, 2400839. (2025)
• Yi Cao, Alex WH Chin, Haogao Gu, Mengting Li, Yuner Gu, Sylvia PN Lau, Kenrie PY Hui, Michael CW Chan, Leo LM Poon. An interferon-stimulated long non-coding RNA USP30-AS1 as an immune modulator in influenza A virus infection. PLOS Pathogens, e1012854. (2025)

2024

• Chase Nelson, Leo L.M. Poon, Haogao Gu. Reply to: Population genetic considerations regarding the interpretation of within-patient SARS-CoV-2 polymorphism data. Nature Communications, 15, 3239. (2024)
• Janice Jia^*, Carolyn Cohen^*, Haogao Gu^*, Milla McLean, Raghavan Varadarajan, Nisha Bhandari, Malik Peiris, Gabriel Leung, Leo Poon, Amy Chung, Benjamin Cowling , Nancy Leung , Tim Tsang, Sophie Valkenburg. Influenza antibody breadth and effector functions are immune correlates from acquisition of pandemic infection of children. Nature Communications, 15, 3210. (2024)

2023

• Ming Z. M. Zheng, Tiong Kit Tan, Fernando Villalon-Letelier, Hilda Lau, Yi-Mo Deng, Svenja Fritzlar, Sophie A. Valkenburg, Haogao Gu, Leo L. M. Poon, Patrick C. Reading, Alain R. Townsend, Linda M. Wakim. Single-cycle influenza virus vaccine generates lung CD8+ Trm that cross react against viral variants and subvert virus escape mutants. Science Advances, 9 (36), eadg3469. (2023)
• Ruopeng Xie, Kimberly M. Edwards, Dillon C. Adam, Kathy S.M. Leung, Tim K. Tsang, Shreya Gurung, Weijia Xiong, Xiaoman Wei, Daisy Y.M. Ng, Gigi Y.Z. Liu, Pavithra Krishnan, Lydia D.J. Chang, Samuel M.S. Cheng, Haogao Gu, Gilman K.H. Siu, Joseph T. Wu, Gabriel M. Leung, Malik Peiris, Benjamin J. Cowling, Leo L.M. Poon, Vijaykrishna Dhanasekaran. Resurgence of Omicron BA.2 in SARS-CoV-2 infection-naive Hong Kong. Nature Communications, 14, 2422. (2023)
• Haogao Gu, Ahmed Abdul Quadeer, Pavithra Krishnan, Lydia Chang, Gigi Liu, Daisy Ng, Samuel Cheng, Tommy Lam, Malik Peiris, Matthew McKay, Leo Poon. Within-host genetic diversity of SARS-CoV-2 lineages in unvaccinated and vaccinated individuals. Nature Communications, 14, 1793. (2023)

2022

• Janice Jia, Chee Wah Tan, Samuel Cheng, Haogao Gu, Aileen Yeoh, Chris Ka Pun Mok, Yanqun Wang, Jincun Zhao, Nancy Leung, Benjamin Cowling, Leo Poon, David Hui, Lin-Fa Wang, Malik Peiris, Sophie Valkenburg. Priming conditions shape breadth of neutralizing antibody responses to sarbecoviruses. Nature Communications, 13, 6285. (2022)
• Kenrie Hui, Ka-Chun Ng, John CW Ho, Hin-Wo Yeung, Rachel HH Ching, Haogao Gu, Joseph CK Chung, Velda LY Chow, Ko-Yung Sit, Michael KY Hsin, Timmy WK Au, Leo Poon, JS Peiris, John Nicholls, Michael Chan. Replication of SARS-CoV-2 Omicron BA. 2 Variant in Ex Vivo Cultures of the Human Upper and Lower Respiratory Tract. eBioMedicine, vol. 83: 104232. (2022)
• Maireid B Bull, Haogao Gu, Fionn Ma, Liyanage Perera, Leo Poon, Sophie Valkenburg. Next Generation T cell-activating vaccination increases influenza virus mutation prevalence. Science Advances, 8(14), eabl5209. (2022)
• Asmaa Hachim, Haogao Gu, Otared Kavian, Masashi Mori, Mike Kwan, Wai Hung Chan, Yat Sun Yau, Susan Chiu, Owen Tsang, David Hui, Chris Mok, Fionn Ma, Eric Lau, Gaya Amarasinghe, Abraham Qavi, Samuel Cheng, Leo Poon, Malik Peiris, Sophie Valkenburg, Niloufar Kavian. SARS-CoV-2 accessory proteins reveal distinct serological signatures in children. Nature Communications, 13: 2951. (2022)
• Hui-Ling Yen, Thomas Sit, Christopher Brackman, Shirley Chuk, Haogao Gu, Karina Tam, Pierra Law, Gabriel Leung, Malik Peiris, Leo Poon^†, Samuel Cheng, Lydia Chang, Pavithra Krishnan, Daisy Ng, Gigi Liu, Mani Hui, Sin Ying Ho, Wen Su, Sin Fun Sia, Ka-Tim Choy, Sammi Cheuk, Sylvia Lau, Amy Tang, Joe Koo, Louise Yung. Transmission of SARS-CoV-2 delta variant (AY. 127) from pet hamsters to humans, leading to onward human-to-human transmission: a case study. The Lancet, 399.10329: 1070–1078. (2022)
• Haogao Gu^*, Ruopeng Xie^*, Dillon Adam^*, Joseph Tsui^*, Daniel Chu^*, Lydia Chang, Sammi Cheuk, Shreya Gurung, Pavithra Krishnan, Daisy Ng, Gigi Liu, Carrie Wan, Samuel Cheng, Kimberly Edwards, Kathy Leung, Joseph Wu, Dominic Tsang, Gabriel Leung, Benjamin Cowling, Malik Peiris, Tommy Lam, Vijaykrishna Dhanasekaran^†, Leo Poon^†. Genomic epidemiology of SARS-CoV-2 under an elimination strategy in Hong Kong. Nature Communications, 13, 736 : 1–10. (2022)
• Kenrie Hui, John Ho, Man-chun Cheung, Ka-chun Ng, Rachel Ching, Ka-ling Lai, Tonia Kam, Haogao Gu, Ko-Yung Sit, Michael Hsin, Timmy Au, Leo Poon, Malik Peiris, John Nicholls, Michael Chan^†. SARS-CoV-2 Omicron variant replication in human respiratory tract ex vivo. Nature, 603: 715–720. (2022)
• Haogao Gu, Daisy Ng, Gigi Liu, Samuel Cheng, Pavithra Krishnan, Lydia Chang, Sammi Cheuk, Mani Hui, Tommy Lam, Malik Peiris, Leo Poon. Recombinant BA. 1/BA. 2 SARS-CoV-2 Virus in Arriving Travelers, Hong Kong, February 2022. Emerging infectious diseases, 28 (6) : 1276. (2022)
• Haogao Gu, Pavithra Krishnan, Daisy Ng, Lydia Chang, Gigi Liu, Samuel Cheng, Mani Hui, Mathew Fan, Jacob Wan, Leo Lau, Benjamin Cowling, Malik Peiris, Leo Poon^†. Probable Transmission of SARS-CoV-2 Omicron Variant in Quarantine Hotel, Hong Kong, China, November 2021. Emerging infectious diseases, 28 (2): 460. (2022)
• Haogao Gu, Samuel Cheng, Pavithra Krishnan, Daisy Ng, Lydia Chang, Gigi Liu, Sammi Cheuk, Mani Hui, Mathew Fan, Jacob Wan, Leo Lau, Daniel Chu, Vijaykrishna Dhanasekaran, Malik Peiris, Leo Poon. Monitoring International Travelers Arriving in Hong Kong for Genomic Surveillance of SARS-CoV-2. Emerging infectious diseases, 28(1): 247–250. (2022)

2021

• Haogao Gu, Daniel Chu, Lydia Chang, Sammi Cheuk, Shreya Gurung, Pavithra Krishnan, Daisy Ng, Gigi Liu, Carrie Wan, Ruopeng Xie, Samuel Cheng, Benjamin Cowling, Dominic Tsang, Malik Peiris, Vijaykrishna Dhanasekaran, Leo Poon. Genetic Diversity of SARS-CoV-2 among Travelers Arriving in Hong Kong. Emerging infectious diseases, 27(10): 2666–2668. (2021)
• Daniel Chu^*, Haogao Gu^*, Lydia Chang, Sammi Cheuk, Shreya Gurung, Pavithra Krishnan, Daisy Ng, Gigi Liu, Carrie Wan, Dominic Tsang, Malik Peiris, Leo Poon. SARS-CoV-2 superspread in fitness center, Hong Kong, China, March 2021. Emerging infectious diseases, 27(8): 2230–2232. (2021)

2020

• Haogao Gu, Daniel Chu, Malik Peiris, Leo Poon. Multivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses. Virus Evolution 6, no. 1: veaa032. (2020)

2019

• Haogao Gu, Rebecca Fan, Di Wang, Leo Poon. Dinucleotide evolutionary dynamics in influenza A virus. Virus Evolution 5, no. 2: vez038. (2019)

2016

• Haogao Gu, Ross Ka-Kit Leung, Qinlong Jing, Wangjian Zhang, Zhicong Yang, Jiahai Lu, Yuantao Hao, Dingmei Zhang. Meteorological Factors for Precise Dengue Fever Control and Prevention in South China. International Journal of Environmental Research and Public Health, 13(9), 867. (2016)
• Tianmu Chen^*, Haogao Gu^*, Ross Ka-Kit Leung, Ruchun Liu, Qiuping Chen, Ying Wu, Yaman Li. Evidence-Based interventions of Norovirus outbreaks in China. BMC Public Health, 16(1): 1072. (2016)

2015

• Haogao Gu, Wangjian Zhang, Hao Xu, Pengyuan Li, Luolin Wu, Pi Guo, Yuantao Hao, Jiahai Lu, Dingmei Zhang. Predicating risk area of human infection with avian influenza a (H7N9) virus by using early warning model in China. Chinese Journal of Epidemiology, 36(5): 470–475. (2015)

^* Co-first authors; ^† Corresponding authors.