Hongshuo Song, MD, PhD

Contact Info

• Academic Email: hongshuosong@usf.edu

Education

Biography

The research in our lab focuses on the interface of HIV-1 genetic evolution, phenotype, and pathogenesis. We are particularly interested in the fundamental aspects of HIV-1 transmissibility, immunopathogenesis, and persistence. Our long-term goal is to translate knowledge into approaches toward effective HIV prevention and functional cure (long-term ART-free HIV-1 remission). Our group elucidated the evolutionary process of coreceptor switch of the transmitted founder (T/F) HIV-1 in natural infection (eBioMedicine 2023). Based on the finding that coreceptor switch is triggered by immune escape mutations, we propose an innovative concept termed “escape by shifting”. The central hypothesis is that, for viruses with entry pathway flexibility, entry pathway alteration functions as a molecular mechanism of immune evasion (R01AI181601). Our lab also identified a highly pathogenic CXCR4 tropic T/F HIV-1 which does not have CCR5-using capacity (eBioMedicine 2024). This finding demonstrates that CXCR4 tropic HIV-1 is transmissible through the mucosal route in people with wild-type CCR5 gene and preferentially target the central memory and naïve CD4+ T cell subsets in vivo. More recent studies in our group identified unique genetic signature in the highly virulent B HIV-1 that are responsible for immune escape from broadly neutralizing antibodies (iScience 2025). We also discovered that CCR5 tropic HIV-1 viruses, which mainly target the memory CD4+ T cells, have distinct memory CD4+ T cell subset targeting in vivo (ASM Case Report 2025)

Research Interests

• Current research in our lab covers broad topics on HIV-1 transmissibility and immunopathogenesis, such as, 1) the co-evolution of HIV-1 entry pathway and antigenicity. 2) the root cause of chronic immune activation in HIV-1 infection. 3) the CD4+ T cell subset-specific fitness of HIV-1 in determining transmissibility, virulence, reservoir landscape, and immune dysfunction. 4) epigenetic regulation of CCR5 and CXCR4 genes expression.

Awards/Honors

• Young Investigator Award (Center for HIV/AIDS Vaccine Immunology (CHAVI) - 2012)
• Young Investigator Award (20th Conference on Retroviruses and Opportunistic Infections (CROI), Atlanta - 2013)
• Young Investigator Award (21th Conference on Retroviruses and Opportunistic Infections (CROI), Boston - 2014)

Recent Publications

• Manukumar Marichannegowda, Yasmine Farah, Meera Bose, Eric Sanders-Buell, David King, Leilani Francisco, Leigh Anne Eller, Abdur Rashid, Sodsai Tovanabutra, Nelson L Michael, Merlin L Robb, Hongshuo Song Distinct memory CD4 subset tropism of two CCR5-tropic HIV-1 in a rapid progressor American Society for Microbiology Case Report. , 2025.
• Manukumar Marichannegowda, Georgina Agyekum, Cinthya Zelaya Aparicio, Aslonso Heredia, Yin Wang, Hongshuo Song Genetic signatures in the highly virulent subtype B HIV-1 conferring resistance to broadly neutralizing antibodies iScience. 28(7) : 112847, 2025.
• Manukumar Marichannegowda, Saini Setua, Meera Bose, Eric Sanders-Buell, David King, Michelle Zemil, Lindsay Wieczorek, Felisa Diaz-Mendez, Nicolas Chomont, Rasmi Thomas, Leilani Francisco, Leigh Anne Eller, Victoria Polonis, Sodsai Tovanabutra, Alonso Heredia, Yutaka Tagaya, Nelson L Michael, Merlin L Robb, Hongshuo Song Transmission of highly virulent CXCR4 tropic HIV-1 through the mucosal route in an individual with a wild-type CCR5 genotype EBioMedicine. 109, 2024.
• Manukumar Honnayakanahalli Marichannegowda, Michelle Zemil, Lindsay Wieczorek, Eric Sanders-Buell, Meera Bose, Anne Marie O'Sullivan, David King, Leilani Francisco, Felisa Diaz-Mendez, Saini Setua, Nicolas Chomont, Nittaya Phanuphak, Jintanat Ananworanich, Denise Hsu, Sandhya Vasan, Nelson L Michael, Leigh Anne Eller, Sodsai Tovanabutra, Yutaka Tagaya, Merlin L Robb, Victoria R Polonis, Hongshuo Song Tracking coreceptor switch of the transmitted/founder HIV-1 identifies co-evolution of HIV-1 antigenicity, coreceptor usage and CD4 subset targeting: the RV217 acute infection cohort study EBioMedicine. 98, 2023.
• Manukumar Honnayakanahalli Marichannegowda, Hongshuo Song Immune escape mutations selected by neutralizing antibodies in natural HIV-1 infection can alter coreceptor usage repertoire of the transmitted/founder virus Virology. 568: 72-76, 2022.
• Hélène Le Buanec, Valérie Schiavon, Marine Merandet, Alexandre How-Kit, Hongshuo Song, David Bergerat, Céline Fombellida-Lopez, Armand Bensussan, Jean-David Bouaziz, Arsène Burny, Gilles Darcis, Mohammad M Sajadi, Shyamasundaran Kottilil, Daniel Zagury, Robert C Gallo IFNα induces CCR5 in CD4+ T cells of HIV patients causing pathogenic elevation Communications Medicine. 4(1) : 52, 2024.
• Hongshuo Song, Meera Bose, Suteeraporn Pinyakorn, Eric Sanders-Buell, Anne Marie O'Sullivan, Daniel Silas, Rapee Trichavaroj, Bessara Nuntapinit, Phuc Pham, Siriwat Akapirat, Eugène Kroon, Mark de Souza, Robert Gramzinski, Nelson L Michael, Merlin L Robb, Sandhya Vasan, Sodsai Tovanabutra, Jintanat Ananworanich, on behalf of the RV254/SEARCH010 Study Group Dynamics of HIV-1 genetic diversification during acute infection Open Forum Infectious Diseases. 12(7) , 2022.
• Donn J Colby, Michal Sarnecki, Dan H Barouch, Somporn Tipsuk, Daniel J Stieh, Eugène Kroon, Alexandra Schuetz, Jintana Intasan, Carlo Sacdalan, Suteeraporn Pinyakorn, Pornsuk Grandin, Hongshuo Song, Sodsai Tovanabutra, Zhanna Shubin, Dohoon Kim, Dominic Paquin-Proulx, Michael A Eller, Rasmi Thomas, Mark de Souza, Lindsay Wieczorek, Victoria R Polonis, Amélie Pagliuzza, Nicolas Chomont, Lauren Peter, Joseph P Nkolola, Johan Vingerhoets, Carla Truyers, Maria G Pau, Hanneke Schuitemaker, Nittaya Phanuphak, Nelson L Michael, Merlin L Robb, Frank L Tomaka, Jintanat Ananworanich Safety and immunogenicity of Ad26 and MVA vaccines in acutely treated HIV and effect on viral rebound after antiretroviral therapy interruption Nature Medicine. 26(4) : 498-501, 2020.
• Hongshuo Song, Weidong Ou, Yi Feng, Junli Zhang, Fan Li, Jing Hu, Hong Peng, Hui Xing, Liying Ma, Qiuxiang Tan, Dongliang Li, Lijuan Wang, Beili Wu, Yiming Shao Disparate impact on CD4 T cell count by two distinct HIV-1 phylogenetic clusters from the same clade PNAS. 116(1) : 239-244, 2019.
• Hongshuo Song, Elena E Giorgi, Vitaly V Ganusov, Fangping Cai, Gayathri Athreya, Hyejin Yoon, Oana Carja, Bhavna Hora, Peter Hraber, Ethan Romero-Severson, Chunlai Jiang, Xiaojun Li, Shuyi Wang, Hui Li, Jesus F Salazar-Gonzalez, Maria G Salazar, Nilu Goonetilleke, Brandon F Keele, David C Montefiori, Myron S Cohen, George M Shaw, Beatrice H Hahn, Andrew J McMichael, Barton F Haynes, Bette Korber, Tanmoy Bhattacharya, Feng Gao Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection Nature communications. 9(1) : 1928, 2018.