Step-by-step explanation:
Human immunodeficiency virus type 1 (HIV-1) enters target cells by first binding to the primary receptor CD4 and then to a coreceptor, generally one of the chemokine receptors CCR5 and CXCR4 (4). CD4 binding induces structural changes in the envelope (Env) glycoprotein that form and expose the coreceptor binding site. There are two main interactions between Env and coreceptor (13, 14, 25, 50, 51): the base of the third variable loop (V3) engages the N terminus of the coreceptor, while the crown of the V3 loop that includes the highly conserved GPGR/Q arch motif binds to the extracellular loops of the coreceptor, with the second extracellular loop of the coreceptor being particularly important (16, 25, 35, 48, 62). Although some HIV-1 strains are able to use a variety of different G protein-coupled receptors to gain entry into CD4+ cell lines, the great majority of these viruses use CCR5 and/or CXCR4 as coreceptors to infect primary cells (3, 4, 10, 23, 47, 66). CCR3, GPR15, APJ, and FPRL-1 are among the most frequently used alternative coreceptors when overexpressed on cell lines (11, 26, 43, 47, 57). Rare cases of HIV-1 strains that are able to use FPRL-1 and GPR1, but not CCR5 or CXCR4, have been reported (57); however, their in vivo relevance remains unknown.
To characterize the biological processes underlying HIV/simian immunodeficiency virus (SIV) transmission, we recently developed an experimental strategy that permits the identification, enumeration, and molecular cloning of transmitted/founder (T/F) viruses (28, 53). This strategy, which employs single-genome amplification (SGA) and direct amplicon sequencing of HIV/SIV RNA or DNA from the plasma or infected cells, makes it possible to infer the nucleotide sequence of the viral strain(s) that initiated productive infection weeks earlier (1, 28, 29, 37, 53, 58, 67). An important prediction of this approach has been that inferred T/F viruses are fully functional and encode all proteins necessary to establish a new infection. Indeed, this prediction has been borne out in numerous studies, which have shown that T/F viral genes as well as full-length genomes are biologically active. Sets of T/F Envs have been shown to mediate efficient virus entry in single-round infection assays, and they invariably use CCR5 as a coreceptor (28, 34). Similarly, T/F infectious molecular clones (IMCs) of HIV-1, SIVmac and SIVagm all produce replication competent virus that grow to high titers in primary CD4+ T cells (22, 38, 54).
MATERIALS AND METHODS
Amplification of the HIV-1 env gene. Serial plasma samples collected from an acutely infected plasma donor, ZP6248, were purchased from ZeptoMetrix. A total of seven plasma samples were collected between 12 February and 9 March 1997, and viral loads (VLs) were determined by the COBAS Amplicor HIV-1 monitor test.
Sequence analysis. All SGA amplicons were sequenced directly by cycle sequencing and dye terminator methods using an ABI 3730xl genetic analyzer (Applied Biosystems, Foster City, CA). Individual sequences were assembled and edited using the Sequencher program 4.7 (Gene Codes, Ann Arbor, MI). The env sequences were aligned using CLUSTAL W (60), and manual adjustment for optimal alignment was done using MASE (20).