Preprint Article Version 1 This version is not peer-reviewed

# Defining Kinetic Properties of HIV-Specific CD8+ T-cell Responses in Acute Infection

Version 1 : Received: 5 January 2019 / Approved: 8 January 2019 / Online: 8 January 2019 (11:22:41 CET)

A peer-reviewed article of this Preprint also exists.

Yang, Y.; Ganusov, V.V. Defining Kinetic Properties of HIV-Specific CD8+ T-Cell Responses in Acute Infection. Microorganisms 2019, 7, 69. Yang, Y.; Ganusov, V.V. Defining Kinetic Properties of HIV-Specific CD8+ T-Cell Responses in Acute Infection. Microorganisms 2019, 7, 69.

Journal reference: Microorganisms 2019, 7, 69
DOI: 10.3390/microorganisms7030069

## Abstract

Multiple lines of evidence indicate that CD8$^+$ T cells are important in the control of HIV-1 (HIV) replication. However, CD8$^+$ T cells induced by natural infection cannot eliminate the virus or reduce viral loads to acceptably low levels in most infected individuals. Understanding the basic quantitative features of CD8$^+$ T-cell responses induced during the course of HIV infection may therefore inform us about the limits that HIV vaccines, which aim to induce protective CD8$^+$ T-cell responses, must exceed. Using previously published experimental data from a cohort of HIV-infected individuals with sampling times from acute to chronic infection we defined the quantitative properties of CD8$^+$ T-cell responses to the whole HIV proteome. In contrast with a commonly held view, we found that the relative number of HIV-specific CD8$^+$ T-cell responses (response breadth) changed little over the course of infection (first 400 days post-infection), with moderate but statistically significant changes occurring only during the first 35 symptomatic days. This challenges the idea that a change in the T-cell response breadth over time is responsible for the slow speed of viral escape from CD8$^+$ T cells in the chronic infection. The breadth of HIV-specific CD8$^+$ T-cell responses was not correlated with the average viral load for our small cohort of patients. Metrics of relative immunodominance of HIV-specific CD8$^+$ T-cell responses such as Shannon entropy or the Evenness index were also not significantly correlated with the average viral load. Our mathematical-model-driven analysis suggested extremely slow expansion kinetics for the majority of HIV-specific CD8$^+$ T-cell responses and the presence of intra- and interclonal competition between multiple CD8$^+$ T-cell responses; such competition may limit the magnitude of CD8$^+$ T-cell responses, specific to different epitopes, and the overall number of T-cell responses induced by vaccination. Further understanding of mechanisms underlying interactions between the virus and virus-specific CD8$^+$ T-cell response will be instrumental in determining which T-cell-based vaccines will induce T-cell responses providing durable protection against HIV infection.

## Subject Areas

acute HIV infection; vaccines; CD8$^+$ T cells; immune response; multiple epitopes; competition; mathematical model