Jiaqi (Jackie) Chen

Jiaqi (Jackie) Chen

PhD student at the University of Hong Kong

Publications

Predicting the Time-Varying Population Immunity and Importation Risk and Their Impact on Co-Circulation of Influenza and COVID-19 in Hong Kong

Manuscript under submission  ·  target: Nature Human Behaviour  ·  2026

First AuthorManuscript Under Submission  ·  target: Nature Human Behaviour — Benchmarks three Bayesian transmission models — fully mechanistic, semi-mechanistic, and purely statistical — against multi-source surveillance data to reconstruct 15 years of subtype-specific influenza immunity in Hong Kong and quantify a durable post-pandemic regime change in influenza–COVID-19 co-circulation.

Recommended citation: Chen, J., Wang, H., Wang, D., Lau, Y. C., Hossain, M. P., Ryu, S., Wu, P., Opatowski, L., Cowling, B. J., & Ali, S. T. (2026). "Predicting the time-varying population immunity and importation risk and their impact on co-circulation of influenza and COVID-19 in Hong Kong." Manuscript under submission.

Collective Interactions, Human Mobility and Viral Evolution Shaped the SARS-CoV-2 Transmission in Mainland China

Preprint  ·  medRxiv  ·  2025

Co-AuthormedRxiv preprint (Under Revision) — A spatial higher-order modeling framework integrating human mobility, viral evolution, and collective interactions to explain SARS-CoV-2 transmission heterogeneity across mainland China.

Recommended citation: Wang, D., Wang, Y., Gressani, O., Chen, J., Tao, Y., Wang, H., Li, S., Chen, D., Lau, E. H. Y., Zhao, Y., Wu, P., Zhang, Q., Cowling, B. J., & Ali, S. T. (2025). "Collective Interactions, Human Mobility and Viral Evolution Shaped the SARS-CoV-2 Transmission in Mainland China." medRxiv preprint.
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Unraveling the Impact of Non-Pharmaceutical Interventions on Pathogen Mutation

Under review at Nature Communications  ·  2024

First AuthorNature Communications (Under Review)IF: 16.6 · Rank #8/135 in Multidisciplinary Sciences — A novel Bayesian machine learning framework linking macroscopic public health policies to microscopic pathogen evolutionary dynamics.

Recommended citation: Chen, J., Wang, D., Wu, P., Cowling, B. J., & Ali, S. T. (2024). "Unraveling the Impact of Non-Pharmaceutical Interventions on Pathogen Mutation." Nature Communications (Under Review).

Modeling and Analysis of COVID-19 Spreading Dynamics Based on Complex Network Theory

Submitted to Europhysics Letters  ·  2023

Co-AuthorEurophysics Letters (Submitted)IF: 1.8 · Rank #49/110 in Physics, Multidisciplinary — A comprehensive review of network-based mathematical modeling approaches for COVID-19 spreading dynamics.

Recommended citation: Gu, C., Chen, J., Ruan, Z., & Tang, M. (2023). "Modeling and Analysis of COVID-19 Spreading Dynamics Based on Complex Network Theory." Europhysics Letters (Submitted).

Competition of SARS-CoV-2 Variants on the Pandemic Transmission Dynamics

Published in Chaos, Solitons and Fractals, 2023

First AuthorChaos, Solitons and Fractals (2023)IF: 9.9 · Citations: 30 · Rank #1/81 in Mathematical Physics — ODE-based multi-variant competition model that outperforms deep learning baselines in predicting COVID-19 transmission dynamics.

Recommended citation: Chen, J., Gu, C., Ruan, Z., & Tang, M. (2023). "Competition of SARS-CoV-2 Variants on the Pandemic Transmission Dynamics." Chaos, Solitons and Fractals, 169, 113193.
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Conference Presentations

EPIDEMICS 10 10th International Conference on Infectious Disease Dynamics

📍 San Diego, USA  ·  📅 30 Nov – 03 Dec 2025

🎤 Oral Presentations

Unraveling the Impact of Non-Pharmaceutical Interventions on Pathogen Mutation for SARS-CoV-2

First Author   Presenter

Bayesian machine learning framework linking macroscopic NPI policies to microscopic pathogen mutation dynamics. Submitted to Nature Communications (IF: 16.6, Rank #8/135).  [View slides]

Social Reinforcements and Spatiotemporal Characteristics for Capturing the Impacts of Population Heterogeneity in the Transmission Dynamics of SARS-CoV-2 in Mainland China

Presenter

Higher-order network modeling framework integrating mobility, viral evolution, and collective interaction dynamics. Related preprint: medRxiv 2025.12.17.

📋 Poster Presentations

Assessment of Transmission Dynamics and Projecting Associated Risk of XDV.1 and NB.1.8.1 Variants of the SARS-CoV-2 Virus in Hong Kong, 2025

First Author   Presenter

Real-time epidemiological risk assessment of emerging SARS-CoV-2 subvariants XDV.1 and NB.1.8.1 in Hong Kong using genomic surveillance and transmission modeling.  [View poster]

Disentangling the Multifaceted Drivers of Disease Transmission: A Bayesian Hierarchical Model of Contact Patterns and Other Extrinsic Factors in Hong Kong

First Author   Presenter

A Bayesian hierarchical modeling framework decomposing the joint effects of age-structured contact patterns, environmental conditions, and behavioral factors on respiratory disease transmission in Hong Kong.  [View poster]

Prediction of Co-Circulation and Combined Burden of Multiple Respiratory Pathogens by Inferring Time-Varying Population Immunity and Importation Risk in Hong Kong

Co-First Author

A multi-pathogen modeling framework inferring time-varying population immunity and cross-border importation risk to predict co-circulation dynamics and combined disease burden in Hong Kong.  [View paper]