Dissecting positive selection events and immunological drives during the evolution of adeno-associated virus lineages

by Lirong Li, Runkuan Qin, Yunbo Liu, Yu-Shan Tseng, Weihan Zhang, Lin Yu, Mario Mietzsch, Xinkai Zou, Haizhou Liu, Guangwen Lu, Hongbo Hu, Robert Mckenna, Jinliang Yang, Yuquan Wei, Mavis Agbandje-Mckenna, Jiankun Hu, Lin Yang

Adeno-associated virus (AAV) serotypes from primates are being developed and clinically used as vectors for human gene therapy. However, the evolutionary mechanism of AAV variants is far from being understood, except that genetic recombination plays an important role. Furthermore, little is known about the interaction between AAV and its natural hosts, human and nonhuman primates. In this study, natural AAV capsid genes were subjected to systemic evolutionary analysis with a focus on selection drives during the diversification of AAV lineages. A number of positively selected sites were identified from these AAV lineages with functional relevance implied by their localization on the AAV structures. The selection drives of the two AAV2 capsid sites were further investigated in a series of biological experiments. These observations did not support the evolution of the site 410 of the AAV2 capsid driven by selection pressure from the human CD4⁺ T-cell response. However, positive selection on site 548 of the AAV2 capsid was directly related to host humoral immunity because of the profound effects of mutations at this site on the immune evasion of AAV variants from human neutralizing antibodies at both the individual and population levels. Overall, this work provides a novel interpretation of the genetic diversity and evolution of AAV lineages in their natural hosts, which may contribute to their further engineering and application in human gene therapy.