Human Immunodeficiency Virus 1 Capsid Uncoating in the Nucleus Progresses Through Defect Formation in the Capsid Lattice

The HIV-1 core consists of a cone-shaped capsid shell made of [~]250 capsid protein (CA) hexamers and 12 pentamers encapsulating the viral genome. HIV-1 capsid disassembly, referred to as uncoating, is a highly regulated process that is important for productive infection, however, the location, timing, and regulation of uncoating remain controversial. Here, we employ amber codon suppression to directly label CA and visualize capsid trafficking and uncoating in live cells. In addition to direct CA labeling, a fluid phase fluorescent probe is incorporated into the viral core to detect the formation of small defects in the capsid lattice. This double-labeling strategy does not significantly impact HIV-1 infectivity, maturation, nuclear import, or capsid stability. Single virus tracking reveals nuclear import of intact cores defined as complexes containing both the fluid phase marker and robust CA signal. Subsequent uncoating of HIV-1 cores in the nucleus is manifested by a sequential loss of both fluorescent markers. This two-step uncoating - release of the core content marker followed by loss of CA - is observed in different cells, including a macrophage line. Importantly, the lag between the two steps of uncoating ([~]30 min) appears independent of the cell type and is much longer than upon uncoating of cell-free viruses. These data suggest that HIV- 1 uncoating in the nucleus is initiated through a localized defect in the capsid lattice that precedes a global loss of CA. Our results imply that intact HIV-1 cores enter the cell nucleus and uncoat in a stepwise fashion, before integrating into the host genome.