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Hongshuo Song, PhD

Academic Title:

Assistant Professor

Primary Appointment:



Institute of Human Virology

Phone (Primary):


Education and Training

Education and Training:

2002-2007: Bachelor of Medicine (MD equivalent), Peking University

2007-2010: PhD, Peking University (thesis advisor: Prof. Hui Zhuang)

2010-2015: Postdoctoral Associate, Duke University  



The research in my laboratory focuses on the interface of HIV genetic evolution, phenotypic property and pathogenesis. We combine conventional approaches in virology and novel technologies such as next-generation sequencing to address fundamental questions relevant to HIV treatment and prevention. We are particularly interested in the following areas:

The global phenotypic diversity of HIV-1. The extensive genetic diversity of HIV-1 in the global epidemic has been well demonstrated. However, how such genetic-level variation translates into diverse phenotypic traits, and in turn influences the outcomes of the disease and treatment and prevention strategies remains poorly understood. One of our long-term goals is to better characterize the global phenotypic diversity of HIV-1. The motivation comes from our recent observation that distinct phylogenetic clusters within the same clade can have different CD4 virulence (Song, PNAS, 2019). We hope the knowledge obtained can help to more precisely inform therapeutic and preventative approaches in different regions of the world where distinct HIV-1 subtypes/CRFs predominate.

The driving force and evolutionary dynamics of HIV-1 coreceptor switching. The mechanism of HIV-1 coreceptor switching is an old, yet unresolved question. To date, most of our knowledge on HIV-1 coreceptor switching is derived from subtype B HIV-1, for which CXCR4-using viruses emerge in a subset of infections during relatively late infection stage. Our recent study on certain CRF01_AE clusters identified an unexpectedly high frequency of CXCR4-using viruses among relatively early infections (Song, PNAS, 2019). This means that HIV-1 coreceptor switching, a process associated with faster disease progression, is not simply a late-infection-stage event as previously thought, and prompted us to revisit this process in the context of subtype diversity. We are currently trying to decipher the driving force of HIV-1 coreceptor switching and the mechanism of subtype difference from a perspective of virus-host coevolution.

Role of HIV fitness in viral load rebound dynamics. An important goal in HIV vaccine development is to target highly conserved epitopes with high fitness constraint. In collaboration with the US Military HIV Research Program (MHRP), we will investigate the correlation between HIV replication fitness and the dynamics of viral load rebound in a therapeutic vaccine trial among acutely treated individuals (RV405). The long-term goal is to translate knowledge of HIV vulnerabilities into optimizing future vaccine strategies towards the goal of ART-free remission.

Our major collaborators include scientists from the U.S. Military HIV Research Program, Duke University and the Los Alamos National Laboratory.

We are currently inviting highly motivated individuals to join the team at the levels of postdoctoral fellow, graduate student, and research assistant (please contact Dr. Song at: 






Research/Clinical Keywords

Molecular virology, HIV, Viral fitness, Coreceptor switching, Evolution dynamics, Therapeutic vaccine

Highlighted Publications

Song H#, Bose M, Pinyakorn S, Sanders-Buell E, O'Sullivan AM, Silas D, Trichavaroj R, Nuntapinit B, Pham P, Akapirat S, Kroon E, de Souza M, Gramzinski R, Michael NL, Robb ML, Vasan S, Tovanabutra S, Ananworanich J, on behalf of the RV254/SEARCH010 Study Group. Dynamics of HIV-1 genetic diversification during acute infection. Open Forum Infectious Diseases. In press. (#Corresponding author)

Colby DJ,  Sarnecki M, Barouch DH, Tipsuk S, Stieh DJ, Kroon E, Schuetz A, Intasan J, Sacdalan C, Pinyakorn S, Grandin P, Song H, Tovanabutra S, Shubin Z, Kim D, Paquin-Proulx D, Eller MA, Thomas R, Souza M, Wieczorek L, Polonis VR, Pagliuzza A, Chomont N, Peter L, Nkolola JP, Vingerhoets J, Truyers C, Pau MG, Schuitemaker H, Phanuphak N, Michael NL, Robb ML, Tomaka FL, Ananworanich J and the HTX1001/RV405 Study Team. Safety and Immunogenicity of Ad26, MVA vaccines in acutely treated HIV and effect on viral rebound after ART interruption. Nature Medicine. 26(4):498-501. 2020. 

Song H, Ou W, Feng Y, Zhang J, Li F, Hu J, Peng H, Xing H, Ma L, Tan Q, Li D, Wang L, Wu B, Shao Y. Disparate impact on CD4 T cell count by two distinct HIV-1 phylogenetic clusters from the same clade. Proc Natl Acad Sci U S A. 116(1):239-244. 2019. 

Song H*, Giorgi EE*, Ganusov VV, Cai F, Athreya G, Yoon H, Carja O, Hora B, Hraber P, Romero-Severson E, Jiang C, Li X, Wang S, Li H, Salazar-Gonzalez JF, Salazar MG, Goonetilleke N, Keele BF, Montefiori DC, Cohen MS, Shaw GM, Hahn BH, McMichael AJ, Haynes BF, Korber BT, Bhattacharya T, Gao F. Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection. Nature Communications. 9(1):1928. 2018 (*equal contribution).

Williams WB, Liao HX, Moody MA, Kepler TB, Gao F, Wiehe K, Trama AM, Jones K, Zhang R, Song H, Marshall DJ, Whitesides JF, Sawatzki K, Hua A, Liu P, Tay MZ, Seaton K, Shen X, Foulger A, Lloyd KE, Parks R, Alam SM, Pollara J, Ferrari G, Vandergrift N, Montefiori DC, Sobieszczyk ME, Hammer S, Karuna S, Gilbert P, Grove D, Grunenberg N, McElrath J, Mascola JR, Koup R, Corey L, Nabel GB, Morgan C, Churchyard G, Maenza J, Keefer M, Graham BS, Baden LR, Tomaras GD, Haynes BF. Diversion of HIV-1 Vaccine-induced Immunity by gp41-Intestinal Microbiota Crossreactive Antibodies. Science. 349(6249):aab1253. 2015. 

Gao F, Bonsignori M, Liao HX, Kumar A, Xia SM, Lu X, Cai F, Hwang KK, Song H, Zhou T, Lynch RM, Alam SM, Moody MA, Ferrari G, Berrong M, Kelsoe G, Shaw GM, Hahn BH, Montefiori DC, Kamanga G, Cohen MS, Hraber P, Kwong PD, Korber BT, Mascola JR, Kepler TB, Haynes BF. Cooperation of B cell lineages in induction of HIV-1-broadly neutralizing antibodies. Cell. 158(3):481-491. 2014.

Song H, Pavlicek JW, Cai F, Bhattacharya T, Li H, Iyer SS, Bar KJ, Decker JM, Goonetilleke N, Liu MK, Berg A, Hora B, Drinker MS, Eudailey J, Pickeral J, Moody MA, Ferrari G, McMichael A, Perelson AS, Shaw GM, Hahn BH, Haynes BF, Gao F. Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome. Retrovirology. 9:89. 2012. 


Additional Publication Citations

Awards and Affiliations

2012: Young Investigator Award, Center for HIV/AIDS Vaccine Immunology (CHAVI)

2013: Young Investigator Award, 20th Conference on Retroviruses and Opportunistic Infections (CROI), Atlanta, GA

2014: Young Investigator Award, 21th Conference on Retroviruses and Opportunistic Infections (CROI), Boston, MA

Grants and Contracts

Active Grant:

07/08/19 - 06/30/21 (Role: PI)

NIH R21: Genetic imprints of therapeutic Ad26/MVA mosaic vaccine in rebound HIV-1 genome from acutely treated individuals