Skip to main content
Local News

Understanding the Score: A Dynamic Interrogation of Acute HIV Infection

By March 25, 2020No Comments

Alex Shalek, Ragon associate member, has a new study published today in Nature Medicine, Integrated Single-Cell Analysis of Multicellular Immune Dynamics during Hyper-Acute HIV-1 Infection. This study uses single-cell RNA sequencing to understand immune system dynamics after acute HIV infection, with samples provided from the FRESH (Females Rising through Education, Support, and Health) study in South Africa, which is run by Ragon member Krista Dong. Graduate student Sam Kazer sequenced and analyzed over 59,000 cells from four patients with HIV who provided frequent clinical samples from a non-infected state, through acute infection, and up to two years, nine months post-infection without treatment. These samples, acquired before South Africa’s standard of care included antiretroviral therapy (ART) starting at HIV diagnosis, represent a unique opportunity to closely examine the immune system’s response to acute HIV infection.


Using a single-cell approach, with samples taken over a long period of time, the Shalek lab was able to identify transient transcriptional changes that, taken together, drive the immune system’s dynamic and changing response to acute HIV infection over more than two years. Essentially, they have examined the immune response as if it is a symphony; each cell is an instrument and they are all playing together, sometimes in harmony with each other and sometimes not, briefly or for an entire movement, to create the larger immune response. Hearing the symphony is relatively easy; hearing each individual note of each cell is often much more difficult.