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Mutation of the Rev-binding loop in the human immunodeficiency virus 1 leader causes a replication defect characterized by altered RNA trafficking and packaging

¹ Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge CB2 2QQ, UK
² Center for Human Virology, Division of Infectious Diseases, Thomas Jefferson University, Philadelphia, PA 19107-5587, USA
³ Christian Doppler Laboratory for Gene Therapeutic Vectors, Research Institute of Virology and Biomedicine, University for Veterinary Sciences, Vienna, Austria

Correspondence
Jane S. Greatorex
jg10018{at}mole.bio.cam.ac.uk
Andrew M. L. Lever
amll1{at}mole.bio.cam.ac.uk

An internal RNA loop, located within the packaging signal of human immunodeficiency virus 1, that resembles the Rev-responsive element (RRE) closely was identified previously. Subsequent in vitro studies confirmed that the loop, termed loop A, could bind Rev protein specifically. Its proximity to the major splice donor has suggested a role for Rev–loop A interaction supplementary to or preceding that of the Rev–RRE interaction. To investigate this further in a replication-competent provirus, loop A was mutated to decrease its affinity for Rev. Impairing the Rev–loop A interaction led to reduced nuclear export of viral genomic RNA. RNA packaging decreased by approximately 30 %. Viral protein production and export of virus particles appeared normal; however, the virus was severely replication-deficient. The loop A sequence, which is 98 % conserved amongst viral isolates, is implicated in several cis-acting functions critical to virus viability.