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tep in the progression to aids a number of studies with subtype b infected individuals have determined that between 40 and 50 percent of aids patients can harbour viruses of the si and it is presumed the x4 phenotypes 56 57 hiv 2 is much less pathogenic than hiv 1 and is restricted in its worldwide distribution to west africa the adoption of accessory genes by hiv 2 and its more promiscuous pattern of co receptor usage including cd4 independence may assist the virus in its adaptation to avoid innate restriction factors present in host cells adaptation to use normal cellular machinery to enable transmission and productive infection has also aided the establishment of hiv 2 replication in humans a survival strategy for any infectious agent is not to kill its host but ultimately become a commensal organism having achieved a low pathogenicity over time variants that are more successful at transmission will be selected 58 replication cycle this section needs to be updated please help update this article to reflect recent events or newly available information february 2025 the hiv replication cycle entry to the cell mechanism of viral entry 1 initial interaction between gp120 and cd4 2 conformational change in gp120 allows for secondary interaction with cxcr4 3 the distal tips of gp41 are inserted into the cellular membrane 4 gp41 undergoes significant conformational change folding in half and forming coiled coils this process pulls the viral and cellular membranes together fusing them the hiv virion enters macrophages and cd4 t cells by the adsorption of glycoproteins on its surface to receptors on the target cell followed by fusion of the viral envelope with the target cell membrane and the release of the hiv capsid into the cell 59 60 entry to the cell begins through interaction of the trimeric envelope complex gp160 spike on the hiv viral envelope and both cd4 and a chemokine co receptor generally either ccr5 or cxcr4 but others are known to interact on the target cell surface 59 60 gp120 binds to integrin α 4 β 7 activating lfa 1 the central integrin involved in the establishment of virological synapses which facilitate efficient cell to cell spreading of hiv 1 61 the gp160 spike contains binding domains for both cd4 and chemokine receptors 59 60 the first step in fusion involves the high affinity attachment of the cd4 binding domains of gp120 to cd4 once gp120 is bound with the cd4 protein the envelope complex undergoes a structural change exposing the chemokine receptor binding domains of gp120 and allowing them to interact with the target chemokine receptor 59 60 this allows for a more stable two pronged attachment which allows the n terminal fusion peptide gp41 to penetrate the cell membrane 59 60 repeat sequences in gp41 hr1 and hr2 then interact causing the collapse of the extracellular portion of gp41 into a hairpin shape this loop structure brings the virus and cell membranes close together allowing fusion of the membranes and subsequent entry of the viral capsid 59 60 hiv can infect dendritic cells dcs by this cd4 ccr5 route but another route using mannose specific c type lectin receptors such as dc sign can also be used 62 dcs are one of the first cells encountered by the virus during sexual transmission they are currently thought to play an important role by transmitting hiv to t cells when the virus is captured in the mucosa by dcs 62 the presence of fez 1 which occurs naturally in neurons is believed to prevent the infection of cells by hiv 63 clathrin mediated endocytosis hiv 1 entry as well as entry of many other retroviruses has long been believed to occur exclusively at the plasma membrane more recently however productive infection by ph independent clathrin mediated endocytosis of hiv 1 has also been reported and was recently suggested to constitute the only route of productive entry 64 65 66 67 68 replication and transcription reverse transcription of the hiv genome into double stranded dna shortly after the viral capsid enters the cell an enzyme called reverse transcriptase liberates the positive sense single stranded rna genome from the attached viral proteins and copies it into a complementary dna cdna molecule 69 the process of reverse transcription is extremely error prone and the resulting mutations may cause drug resistance or allow the virus to evade the body s immune system the reverse transcriptase also has ribonuclease activity that degrades the viral rna during the synthesis of cdna as well as dna dependent dna polymerase activity that creates a sense dna from the antisense cdna 70 together the cdna and its complement form a double stranded viral dna that is then transported into the cell nucleus the integration of the viral dna into the host cell s genome is carried out by another viral enzyme called integrase 69 the integrated viral dna may then lie dormant in the latent stage of hiv infection 69 to actively produce the virus certain cellular transcription factors need to be present the most important of which is nf κ b nuclear factor kappa b which is upregulated when t cells become activated 71 this means that those cells most likely to be targeted entered and subsequently killed by hiv are those actively fighting infection during viral replication the integrated dna provirus is transcribed into rna the full length genomic rnas grna can be packaged into new viral particles in a pseudodiploid form the selectivity in the packaging is explained by the structural properties of the dimeric conformer of the grna the grna dimer is characterized by a tandem three way junction within the grna monomer in which the sd and aug hairpins responsible for splicing and translation respectively are sequestered and the dis dimerization initiation signal hairpin is exposed the formation of the grna dimer is mediated by a kissing interaction between the dis hairpin loops of the grna monomers at the same time certain guanosine residues in the grna are made available for binding of the nucleocapsid nc protein leading to the subsequent virion assembly 72 the labile grna dimer has been also reported to achieve a more stable conformation following the nc binding in which both the dis and the u5 aug regions of the grna participate in extensive base pairing 73 rna can also be processed to produce mature messenger rnas mrnas in most cases this processing involves rna splicing to produce mrnas that are shorter than the full length genome which part of the rna is removed during rna splicing determines which of the hiv protein coding sequences is translated 74 mature hiv mrnas are exported from the nucleus into the cytoplasm where they are translated to produce hiv proteins including rev as the newly produced rev protein is produced it moves to the nucleus where it binds to full length unspliced copies of virus rnas and allows them to leave the nucleus 75 some of these full length rnas function as mrnas that are translated to produce the structural proteins gag and env gag proteins bind to copies of the virus rna genome to package them into new virus particles 76 hiv 1 and hiv 2 appear to package their rna differently 77 78 hiv 1 will bind to any appropriate rna 79 hiv 2 will preferentially bind to the mrna that was used to create the gag protein itself 80 recombination further information genetic recombination two rna genomes are encapsidated in each hiv 1 particle see structure and genome of hiv upon infection and replication catalyzed by reverse transcriptase recombination between the two genomes can occur 81 82 recombination occurs as the single strand positive sense rna genomes are reverse transcribed to form dna during reverse transcription the nascent dna can switch multiple times between the two copies of the viral rna this form of recombination is known as copy choice recombination events may occur throughout the genome anywhere from two to 20 recombination events per genome may occur at each replication cycle and these events can rapidly shuffle the genetic information that is transmitted from parental to progeny genomes 82 viral recombination produces genetic variation that likely contributes to the evolution of resistance to anti retroviral therapy 83 recombination may also contribute in principle to overcoming the immune defenses of the host yet for the adaptive advantages of genetic variation to be realized the two viral genomes packaged in individual infecting virus particles need to have arisen from separate progenitor parental viruses of differing genetic constitution it is unknown how often such mixed packaging occurs under natural conditions 84 bonhoeffer et al 85 suggested that template switching by reverse transcriptase acts as a repair process to deal with breaks in the single stranded rna genome in addition hu and temin 81 suggested that recombination is an adaptation for repair of damage in the rna genomes strand switching copy choice recombination by reverse transcriptase could generate an undamaged copy of genomic dna from two damaged single stranded rna genome copies this view of the adaptive benefit of recombination in hiv could explain why each hiv particle contains two complete genomes rather than one furthermore the view that recombination is a repair process implies that the benefit of repair can occur at each replication cycle and that this benefit can be realized whether or not the two genomes differ genetically on the view that recombination in hiv is a repair process the generation of recombinational variation would be a consequence but not the cause of the evolution of template switching 85 hiv 1 infection causes chronic inflammation and production of reactive oxygen species 86 thus the hiv genome may be vulnerable to oxidative damage including breaks in the single stranded rna for hiv as well as for viruses in general successful infection depends on overcoming host defense strategies that often include production of genome damaging reactive oxygen species thus michod et al 87 suggested that recombination by viruses is an adaptation for repair of genome damage and that recombinational variation is a byproduct that may provide a separate benefit assembly and release hiv assembling on the surface of an infected macrophage the hiv virions have been marked with a green fluorescent tag and then viewed under a fluorescent microscope the final step of the viral cycle assembly of new hiv 1 virions begins at the plasma membrane of the host cell the env polyprotein gp160 goes through the endoplasmic reticulum and is transported to the golgi apparatus where it is cleaved by furin resulting in the two hiv envelope glycoproteins gp41 and gp120 88 these are transported to the plasma membrane of the host cell where gp41 anchors gp120 to the membrane of the infected cell the gag p55 and gag pol p160 polyproteins also associate with the inner surface of the plasma membrane along with the hiv genomic rna as the forming virion begins to bud from the host cell the budded virion is still immature as the gag polyproteins still need to be cleaved into the actual matrix capsid and nucleocapsid proteins this cleavage is mediated by the packaged viral protease and can be inhibited by antiretroviral drugs of the protease inhibitor class the various structural components then assemble to produce a mature hiv virion 89 only mature virions are then able to infect another cell spread within the body animation demonstrating cell free spread of hiv the classical process of infection of a cell by a virion can be called cell free spread to distinguish it from a more recently recognized process called cell to cell spread 90 in cell free spread see figure virus particles bud from an infected t cell enter the blood or extracellular fluid and then infect another t cell following a chance encounter 90 hiv can also disseminate by direct transmission from one cell to another by a process of cell to cell spread for which two pathways have been described firstly an infected t cell can transmit virus directly to a target t cell via a virological synapse 61 91 secondly an antigen presenting cell apc such as a macrophage or dendritic cell can transmit hiv to t cells by a process that either involves productive infection in the case of macrophages or capture and transfer of virions in trans in the case of dendritic cells 92 whichever pathway is used infection by cell to cell transfer is reported to be much more efficient than cell free virus spread 93 a number of factors contribute to this increased efficiency including polarised virus budding towards the site of cell to cell contact close apposition of cells which minimizes fluid phase diffusion of virions and clustering of hiv entry receptors on the target cell towards the contact zone 91 cell to cell spread is thought to be particularly important in lymphoid tissues where cd4 t cells are densely packed and likely to interact frequently 90 intravital imaging studies have supported the concept of the hiv virological synapse in vivo 94 the many dissemination mechanisms available to hiv contribute to the virus ongoing replication in spite of anti retroviral therapies 90 95 genetic variability further information subtypes of hiv the phylogenetic tree of the siv and hiv hiv differs from many viruses in that it has very high genetic variability this diversity is a result of its fast replication cycle with the generation of about 10 10 virions every day coupled with a high mutation rate of approximately 3 10 5 per nucleotide base per cycle of replication and recombinogenic properties of reverse transcriptase 96 97 98 some estimates put hiv s mutation rate as high as 4 1 10 3 substitutions per base pair making hiv the microbe with the highest mutation rate known by far 99 a 2014 study estimated that about 15 20 of all hiv mutations are due to recombination numbering roughly 1 35 10 3 recombination events per nucleotide repn per replication cycle 100 this complex scenario leads to the generation of many variants of hiv in a single infected patient in the course of one day 96 this variability is compounded when a single cell is simultaneously infected by two or more different strains of hiv when simultaneous infection occurs the genome of progeny virions may be composed of rna strands from two different strains this hybrid virion then infects a new cell where it undergoes replication as this happens the reverse transcriptase by jumping back and forth between the two different rna templates will generate a newly synthesized retroviral dna sequence that is a recombinant between the two parental genomes 96 this recombination is most obvious when it occurs between subtypes 96 the closely related simian immunodeficiency virus siv has evolved into many strains classified by the natural host species siv strains of the african green monkey sivagm and sooty mangabey sivsmm are thought to have a long evolutionary history with their hosts these hosts have adapted 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