课题组目前开展几方面研究工作：

1、围绕单纯疱疹病毒（HSV-1/HSV-2）、登革热病毒（DENV）开展系统的病原学和免疫学研究，包括病毒的感染致病机制和抗病毒靶点的筛选及验证。

2、开展单纯疱疹病毒（HSV-1/HSV-2）、登革热病毒（DENV）的新型疫苗研发。

3、基孔肯雅病毒和新型冠状病毒等高致病性病原体防控研究。

作为负责人或骨干主持以下科研项目：

1、甲型肝炎病毒利用细胞的miR-149-3p拮抗β干扰素产生的分子机制（31500724）国家自然科学基金委  2016.1-2018.12  24万  主持

2、AAV载体递送无ADE效应的登革广谱中和抗体构建及功能研究（2017FB115） 云南省科技厅  2017.5-2020.4  10万  主持

3、腺病毒递送无ADE效应的登革广谱中和抗体构建及功能研究（3332016113） 北京协和医学院  2016.4-2018.4  15万   主持

4、 新型疫苗佐剂关键技术平台建立及应用（2017-12M-3-022）中国医学科学院  2017.1-2020.12 160万 骨干

5、云南省卫生高层人才-医学学科带头人培养计划，云南省医学学科带头人（D-2017008） 云南省卫计委  2019.01-2021.12  15万  主持

6、 云南省中青年学术技术带头人后备人才（2019HB043） 云南省科学技术厅  2019.01-2023.12  12万   主持

7、 云南省万人计划青年拔尖人才中共云南省委组织部  2019.01-2023.12   50万  主持

8、 云南省基础研究重点项目“SV40病毒T抗原基因反向剪接成环机制及功能研究”云南省科技厅  2020.06-2023.05   50万  主持

9、 中央级公益性科研院所基本科研业务费“标准化、数字化和可视化高等级病原微生物模拟实验室生物安全培训体系建设提升” 中国医学科学院 2022.7-2023.9  200万  主持

10. 中国医学科学院医学与健康科技创新工程 “应对新发突发传染病应急防控生物安全保障关键技术研究” 子课题“有输入风险的高致病性病毒防控储备技术研究”  360万  骨干

11. 云南省基础研究重点项目“芳香烃受体AhR促进Ⅰ型单纯疱疹病毒裂解感染的机制及作为抗病毒治疗靶点研究”云南省科技厅  2024.03-2027.02 50万  主持

12. 云南省重大科技专项计划生物医药专项“新型重组生殖器疱疹疫苗（Sf9细胞）1类新药临床前预研究”  2025-01-01至2027-12-31  79万  主持

13. 云南省高层次卫生健康技术人才培养项目 “医学高端人才” 2025-01-01至2027-12-31  50万  主持

14. 中央级公益性科研院所基本科研业务费“高等级病原微生物实验室智慧化管理系统建设” 中国医学科学院 2025-01至2025-12  100万  主持

部分代表性文章：（＃表示并列一作，*表示通讯作者）

【23】Pan X, Guo X, Shi J*. Design of a novel multiepitope vaccine with CTLA-4 extracellular domain against Mycoplasma pneumoniae: A vaccine-immunoinformatics approach. Vaccine. 2024 Jul 11;42(18):3883-3898. doi: 10.1016/j.vaccine.2024.04.098. Epub 2024 May 21. PMID: 38777697.

【22】Ma Y, Lei M, Chen H, Huang P, Sun J, Sun Q, Hu Y, Shi J*. Susceptibility of bovine to SARS-CoV-2 variants of concern: insights from ACE2, AXL, and NRP1 receptors. Virol J. 2023 Nov 27;20(1):276. doi: 10.1186/s12985-023-02222-9. PMID: 38012648; PMCID: PMC10680262.

【21】Guo X, Pan X, Sun Q, Hu Y, Shi J*. Design of a novel multiepitope vaccine against Chlamydia pneumoniae using the extracellular protein as a target. Sci Rep. 2023 Sep 12;13(1):15070. doi: 10.1038/s41598-023-42222-x. PMID: 37700027; PMCID: PMC10497608.

【20】Lei M, Ma Y, Chen H, Huang P, Sun J, Wang X, Sun Q, Hu Y, Shi J*. Emerging SARS-CoV-2 variants of concern potentially expand host range to chickens: insights from AXL, NRP1 and ACE2 receptors. Virol J. 2023 Aug 29;20(1):196. doi: 10.1186/s12985-023-02123-x. PMID: 37644471; PMCID: PMC10466743.

【19】 Shi J＃, Du T, Wang J, Tang C, Lei M, Yu W, Yang Y, Ma Y, Huang P, Chen H, Wang X, Sun J, Wang H, Zhang Y, Luo F, Huang Q, Li B, Lu S, Hu Y, Peng X. Aryl hydrocarbon receptor is a proviral host factor and a candidate pan-SARS-CoV-2 therapeutic target. Sci Adv. 2023 Jun 2;9(22):eadf0211. doi: 10.1126/sciadv.adf0211. Epub 2023 May 31. PMID: 37256962.

【18】 Huang P, Wang X, Lei M, Ma Y, Chen H, Sun J, Hu Y, Shi J*. Metabolomics Profiles Reveal New Insights of Herpes Simplex Virus Type 1 Infection. Int J Mol Sci. 2023 Jan 12;24(2):1521. doi: 10.3390/ijms24021521. PMID: 36675052; PMCID: PMC9862159.

【17】Zhu X＃, Chen W＃, Ma C, Wang X, Sun J, Nie J,  Shi J*, Hu Y*. Whole genome analysis identifies intra-serotype recombinants and positive selection sites of dengue virus in mainland China from 2015 to 2020. Virus Res. 2022 Apr 2;311:198705. doi: 10.1016/j.virusres.2022.198705. Epub 2022 Feb 1. PMID: 35121087.

【16】 Yang M＃, Qi M＃, Xu L＃, Huang P＃, Wang X, Sun J, Shi J*, Hu Y*. Differential host circRNA expression profiles in human lung epithelial cells infected with SARS-CoV-2. Infect Genet Evol. 2021 May 15:104923. doi: 10.1016/j.meegid.2021.104923. Epub ahead of print. PMID: 34004360; PMCID: PMC8123525.

【15】Qi M, Yang M, Xu L, Ma C, Huang P, Sun J, Shi J*, Hu Y*. Complete genome analysis identifies recombinant events and positive selection sites of hepatitis C virus from mainland China during 2010-2019. Virus Res. 2021;296:198354.

【14】Xu L, Qi M, Ma C, Yang M, Huang P, Sun J, Shi J*, Hu Y*. Natural intertypic and intratypic recombinants of enterovirus 71 from mainland China during 2009-2018: a complete genome analysis. Virus Genes. 2021;57(2):172-180.

【13】 Mo, Ling; Zeng, Zhaoping; Deng, Rongzhen; Li, Zhiyuan; Sun, Jing; Hu,Ningzhu; Shi, Jiandong*; Hu, Yunzhang*; Hepatitis A virus-induced hsa-miR-146a-5p attenuates IFN-β signaling by targeting adaptor protein TRAF6. Archives of Virology, 2021, 166(3): 789-799.

【12】 Jiandong Shi*; Jing Sun; Yunzhang Hu*; Enteric involvement of SARS-CoV-2: Implications for the COVID-19 management, transmission, and infection control. Virulence, 2020, 11(1): 941-944.

【11】  Shi J*, Sun J, Hu N, Hu Y*. Phylogenetic and genetic analyses of the emerging Nipah virus from bats to humans. Infect Genet Evol. 2020;85:104442.

【10】Shi J, Hu N, Li J, Zeng Z, Mo L, Sun J, Wu M, Hu Y. Unique expression signatures of circular RNAs in response to DNA tumor virus SV40 infection. Oncotarget. 2017 Oct 9;8(58):98609-98622. doi: 10.18632/oncotarget.21694. PMID: 29228714; PMCID: PMC5716754.

【9】 Zeng Z＃, Shi J＃, Guo X, Mo L, Hu N, Sun J, Wu M, Zhou H*, Hu Y*. Full-length genome and molecular characterization of dengue virus serotype 2 isolated from an  imported patient from Myanmar. Virology Journal. 2018 Aug 20;15(1):131. doi: 10.1186/s12985-018-1043-2. PMID: 30126417; PMCID: PMC6102819.

【8】Mo L＃, Shi J＃, Guo X, Zeng Z, Hu N, Sun J, Wu M, Zhou H*, Hu Y*. Molecular characterization and phylogenetic analysis of a dengue virus serotype 3 isolated from a Chinese traveler returned from Laos. Virology Journal. 2018 Jul 24;15(1):113. doi: 10.1186/s12985-018-1016-5. PMID: 30041666; PMCID: PMC6057004.

【7】Shi J, Hu N, Mo L, Zeng Z, Sun J, Hu Y. Deep RNA Sequencing Reveals a Repertoire of Human Fibroblast Circular RNAs Associated with Cellular Responses to Herpes Simplex Virus 1 Infection. Cell Physiol Biochem. 2018;47(5):2031-2045. doi: 10.1159/000491471. Epub 2018 Jul 4. PMID: 29972822.

【6】 Shi J, Sun J, Wu M, Hu N, Hu Y. Hepatitis A virus-encoded miRNAs attenuate the accumulation of viral genomic RNAs in infected cells. Virus Genes. 2016;52(3):317-24.

【5】 Shi J, Sun J, Wu M, Wang H, Hu N, Hu Y. Comprehensive profiling and characterization of cellular miRNAs in response to hepatitis A virus infection in human fibroblasts. Infect Genet Evol. 2016;45:176-186.

【4】 Shi J, Sun J, Wu M, Hu N, Li J, Li Y, Wang H, Hu Y. Inferring Protective CD8+ T-Cell Epitopes for NS5 Protein of Four Serotypes of Dengue Virus Chinese Isolates Based on HLA-A, -B and -C Allelic Distribution: Implications for Epitope-Based Universal Vaccine Design. PLoS One. 2015;10(9):e0138729.

【3】  Shi, Jiandong; Zhang, Jing; Li, Sijin; Sun, Jing; Teng, Yumei; Wu,Meini; Li, Jianfan; Li, Yanhan; Hu, Ningzhu; Wang, Haixuan; Hu, Yunzhang*; Epitope-Based Vaccine Target Screening against Highly Pathogenic MERS-CoV: An In Silico Approach Applied to Emerging Infectious Diseases. PLos One, 2015, 10(12): 0-e0144475.

【2】  Shi, Jiandong; Sun, Jing; Wang, Bin; Wu, Meini; Zhang, Jing; Duan,Zhiqing; Wang, Haixuan; Hu, Ningzhu; Hu, Yunzhang*; Novel microRNA-like viral small regulatory RNAs arising during human hepatitis A virus infection.The FASEB Journal, 2014, 28(10): 4381-4393.

【1】 Shi, Jiandong; Duan, Zhiqing; Sun, Jing; Wu, Meini; Wang, Bin; Zhang, Jing; Wang, Haixuan; Hu, Ningzhu; Hu, Yunzhang*; Identification and validation of a novel microRNA-like molecule derived from a cytoplasmic RNA virus antigenome by bioinformatics and experimental approaches. Virology Journal, 2014, 11: 121-121.