Primary Infection by a Human Immunodeficiency Virus with Atypical Coreceptor Tropism

Abstract

The great majority of human immunodeficiency virus type 1 (HIV-1) strains enter CD4؉ target cells by interacting with one of two coreceptors, CCR5 or CXCR4. Here we describe a transmitted/founder (T/F) virus (ZP6248) that was profoundly impaired in its ability to utilize CCR5 and CXCR4 coreceptors on multiple CD4؉ cell lines as well as primary human CD4 ؉ T cells and macrophages in vitro yet replicated to very high titers (>80 million RNA copies/ml) in an acutely infected individual. Interestingly, the envelope (Env) glycoprotein of this clade B virus had a rare GPEK sequence in the crown of its third variable loop (V3) rather than the consensus GPGR sequence. Extensive sequencing of sequential plasma samples showed that the GPEK sequence was present in virtually all Envs, including those from the earliest time points after infection. The molecularly cloned (single) T/F virus was able to replicate, albeit poorly, in cells obtained from ccr5⌬32 homozygous donors. The ZP6248 T/F virus could also infect cell lines overexpressing the alternative coreceptors GPR15, APJ, and FPRL-1. A single mutation in the V3 crown sequence (GPEK->GPGK) of ZP6248 restored its infectivity in CCR5؉ cells but reduced its ability to replicate in GPR15 ؉ cells, indicating that the V3 crown motif played an important role in usage of this alternative coreceptor. These results suggest that the ZP6248 T/F virus established an acute in vivo infection by using coreceptor(s) other than CCR5 or CXCR4 or that the CCR5 coreceptor existed in an unusual conformation in this individual.

Cloning and Analysis of Sooty Mangabey Alternative Coreceptors That Support Simian Immunodeficiency Virus SIVsmm Entry Independently of CCR5

“…However, a recent report described a transmitter/founder virus from an acutely infected person that was impaired in its ability to use CCR5 and CXCR4 but entered efficiently through GPR15 (29). Allelic variants of CXCR6 have also been associated with disease progression in HIV-1-infected subjects (20,38), although a direct virological mechanism is unclear since most HIV-1 isolates do not utilize CXCR6 for entry.…”

“…If patterns are similar in SIV natural hosts, the exclusion of CXCR6 from less differentiated and self-renewing naïve cells or Tcm cells would be consistent with shifting of viral targets away from subsets critical for T cell homeostasis into potentially more expendable cell targets. While GPR15 is expressed in human blood CD4 ϩ T cells and in lymphoid tissues (17,21,22,29,36), its distribution on specific subsets has not been defined. CXCR6 and GPR15 are also both expressed in human intestinal tissue (17,36), which is an important site for viral replication.…”

Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection

“…cDNA was synthesized using the SuperScript III reverse transcriptase (Invitrogen, Carlsbad, CA) with the primers 07Rev8 5′-CCTARTGGGATG TGTACTTCTGAACTT-3′ (nt5193-5219 in HXB2) for the 5′ half genome, or primer 1.R3.B3R 5′-ACTACTT GAAGCACTCAAGGCAAGCTTTATTG-3′ (nt9611-9 642) for the 3′ half genome. Single genome amplification (SGA) was performed to obtain the 5′ half, 3′ half or near full-length HIV-1 genome as described previously [13,42]. For the 5′ half genome amplification, the first round PCR was carried out using the primers 1.U5.B1F 5′-CCTTGAGTGCTTCAAGTAGTGTGTGCCCGTCTG T-3′ (nt538-571) and 07Rev8 5′-CCTARTGGGATGTGT ACTTCTGAACTT-3′ (nt5193-5219), and the second round PCR with primers Upper1A 5′-AGTGGCGCCCGA ACAGG-3′ (nt634-650) and Rev11 5′-ATCATCACCTGC-CATCTGTTTTCCAT-3′ (nt5041-5066).…”

Transmitted/Founder and Chronic HIV-1 Envelope Proteins Are Distinguished by Differential Utilization of CCR5

“…This has made it possible to seek genotypic and phenotypic differences between T/F Env proteins and those derived from chronically infected individuals (chronic control [CC] Envs). Several phenotypic characteristics are clearly associated with transmission: T/F Envs virtually always use CCR5 rather than CXCR4 or other noncanonical coreceptors (2,(16)(17)(18) and generally infect T cells but not macrophages (2,13,15,19) as a result of requiring relatively high levels of CD4 to mediate virus entry (20)(21)(22)(23)(24)(25). Other phenotypic and genotypic traits that have been linked to transmission are less well defined: Envs isolated from acute infection have sometimes been reported to be more neutralization sensitive (19), have on average fewer putative N-linked glycosylation sites (1,26), and have shorter variable loops (1,(27)(28)(29) compared to Envs isolated from chronically infected individuals.…”