HIV
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2008-07-15T07:34:15Z
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{{Taxobox | color=violet
| name = ''Human immunodeficiency virus''
| image = HIV-budding-Color.jpg
| image_width = 180px
| image_caption = Scanning electron micrograph of HIV-1 (in green) budding from cultured lymphocyte. Multiple round bumps on cell surface represent sites of assembly and budding of virions.
| virus_group = vi
| familia = ''[[Retroviridae]]''
| genus = ''[[Lentivirus]]''
| subdivision_ranks = Species
| subdivision =
* '''''Human immunodeficiency virus 1'''''
* '''''Human immunodeficiency virus 2'''''
}}
{{DiseaseDisorder infobox |
Name = International Statistical Classification of Diseases and Related Health Problems Codes |
ICD10 = B20-B24 |
ICD9 = {{ICD9|042}}-{{ICD9|044}} |
}}
'''Human immunodeficiency virus''' ('''HIV''') is a [[lentivirus]] (a member of the [[retrovirus]] family) that can lead to ''[[AIDS|acquired immunodeficiency syndrome]]'' (AIDS), a condition in [[human]]s in which the [[immune system]] begins to fail, leading to life-threatening [[opportunistic infection]]s. Previous names for the [[virus]] include '''human T-lymphotropic virus-III''' ('''HTLV-III'''), '''lymphadenopathy-associated virus''' ('''LAV'''), and '''AIDS-associated retrovirus''' ('''ARV''').<ref>{{cite web| author=Rick Sowadsky| year=1999 |date = 1999-02-24 |url=http://www.thebody.com/Forums/AIDS/safesex/Archive/origins/Q8777.html |title=What is HTLV-III?| accessdate=2008-04-03}}</ref><ref name=Coffin>{{cite journal
| author=Coffin, J., Haase, A., Levy, J. A., Montagnier, L., Oroszlan, S., Teich, N., Temin, H., Toyoshima, K., Varmus, H., Vogt, P. and Weiss, R. A. | title=What to call the AIDS virus? | journal=Nature | year=1986 | pages=10 | volume=321 | issue=6065 | pmid=3010128| doi=10.1038/321010a0}}</ref>
Infection with HIV occurs by the transfer of [[blood]], [[semen]], [[vaginal fluid]], [[pre-ejaculate]], or [[breast milk]]. Within these bodily fluids, HIV is present as both free virus particles and virus within infected immune cells. The four major routes of transmission are [[unprotected sex|unprotected sexual intercourse]], contaminated needles, breast milk, and transmission from an infected mother to her baby at [[childbirth|birth]]. Screening of blood products for HIV has largely eliminated transmission through blood transfusions or infected blood products in the [[developed world]].
HIV infection in humans is now [[pandemic]]. As of January 2006, the [[Joint United Nations Programme on HIV/AIDS]] (UNAIDS) and the [[World Health Organization]] (WHO) estimate that AIDS has killed more than 25 million people since it was first recognized on [[December 1]], [[1981]], making it one of the most destructive [[AIDS pandemic|pandemics]] in recorded history. It is estimated that about 0.6% of the world's population is infected with HIV.<ref name=UNAIDS2006>{{cite book
| author =[[Joint United Nations Programme on HIV/AIDS]]
| year = 2006
| title = 2006 Report on the global AIDS epidemic
| chapter = Overview of the global AIDS epidemic
| chapterurl = http://data.unaids.org/pub/GlobalReport/2006/2006_GR_CH02_en.pdf
| accessdate = 2006-06-08
| format= [[Portable Document Format|PDF format]]
}}</ref>{{update after|2007|12|01}} In 2005 alone, AIDS claimed an estimated 2.4–3.3 million lives, of which more than 570,000 were children. A third of these deaths are occurring in sub-Saharan [[Africa]], retarding [[economic growth]] and increasing poverty.<ref name=Greener>{{cite book
| author =Greener, R.
| year = 2002
| title = State of The Art: AIDS and Economics
| chapter = AIDS and macroeconomic impact
| chapterurl = http://www.popline.org/docs/285428
| editor = S, Forsyth (ed.)
| edition =
| pages = 49-55
| publisher = IAEN
}}</ref> According to current estimates, HIV is set to infect 90 million people in [[Africa]], resulting in a minimum estimate of 18 million [[orphan]]s.<ref name=UNAIDS>{{cite web
| author=[[Joint United Nations Programme on HIV/AIDS]]
| publisher=
| publishyear= 2005
| url=http://www.unaids.org/epi/2005/doc/EPIupdate2005_pdf_en/epi-update2005_en.pdf
| title=AIDS epidemic update, 2005
| accessdate=2006-02-28|format=[[Portable Document Format|PDF format]]
}}</ref> [[antiretroviral drug|Antiretroviral]] treatment reduces both the [[Mortality rate|mortality]] and the [[morbidity]] of HIV infection, but routine access to antiretroviral medication is not available in all countries.<ref name=Palella>{{cite journal
| author=Palella, F. J. Jr, Delaney, K. M., Moorman, A. C., Loveless, M. O., Fuhrer, J., Satten, G. A., Aschman and D. J., Holmberg, S. D.
| title=Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection. HIV Outpatient Study Investigators
| journal=N. Engl. J. Med
| year=1998
| pages=853–860
| volume=338
| issue=13
| pmid=9516219
| doi=10.1056/NEJM199803263381301
}}</ref>
HIV primarily infects vital cells in the [[human]] [[immune system]] such as [[helper T cell]]s (specifically CD4<SUP>+</SUP> T cells), [[macrophage]]s and [[dendritic cell]]s. HIV infection leads to low levels of CD4<SUP>+</SUP> T cells through three main mechanisms: firstly, direct viral killing of infected cells; secondly, increased rates of [[apoptosis]] in infected cells; and thirdly, killing of infected CD4<SUP>+</SUP> T cells by [[CD8 cytotoxic lymphocyte]]s that recognize infected cells. When CD4<SUP>+</SUP> T cell numbers decline below a critical level, [[cell-mediated immunity]] is lost, and the body becomes progressively more susceptible to [[opportunistic infection]]s.
Eventually most HIV-infected individuals develop [[AIDS|AIDS (Acquired Immunodeficiency Syndrome)]]. These individuals mostly die from [[opportunistic infection]]s or [[malignancies]] associated with the progressive failure of the immune system.<ref name=Lawn>{{
cite journal
| author=Lawn SD
| title=AIDS in Africa: the impact of coinfections on the pathogenesis of HIV-1 infection
| journal=J. Infect. Dis. | year=2004 | pages=1–12 | volume=48 | issue=1
| pmid=14667787
}}</ref> About 9 out of every 10 persons with HIV will progress to AIDS after 10-15 years.<ref name=Buchbinder>{{cite journal
| author=Buchbinder SP, Katz MH, Hessol NA, O'Malley PM, Holmberg SD.
| title=Long-term HIV-1 infection without immunologic progression.
| journal=AIDS
| year=1994
| pages=1123–1128
| volume=8
| issue=8
| pmid=7986410
| doi=10.1097/00002030-199408000-00014
}}</ref> Treatment with anti-retrovirals, where available, increases the life expectancy of people infected with HIV. After the diagnosis of AIDS is made, the current average survival time with antiretroviral therapy (as of 2005) is estimated to be more than 5 years.<ref name=Schneider>{{
cite journal
| author=Schneider MF, Gange SJ, Williams CM, Anastos K, Greenblatt RM, Kingsley L, Detels R, Munoz A
| title=Patterns of the hazard of death after AIDS through the evolution of antiretroviral therapy: 1984–2004
| journal=AIDS | year=2005 | pages=2009–2018 | volume=19 | issue=17
| pmid=16260908
}}</ref> Without antiretroviral therapy, death normally occurs within a year.<ref name=Morgan2>{{
cite journal
| author=Morgan D, Mahe C, Mayanja B, Okongo JM, Lubega R, Whitworth JA
| title=HIV-1 infection in rural Africa: is there a difference in median time to AIDS and survival compared with that in industrialized countries?
| journal=AIDS | year=2002 | pages=597–632 | volume=16 | issue=4 | pmid=11873003
}}</ref> It is hoped that current and future treatments may allow HIV-infected individuals to achieve a life expectancy approaching that of the general public.
==Classification==
HIV is a member of the genus [[Lentivirus]],<ref name=ICTV61.0.6>{{cite web
| author=[[International Committee on Taxonomy of Viruses]]
| publisher=[[National Institutes of Health]]
| publishyear=2002
| url=http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/61060000.htm
| title=61.0.6. Lentivirus
| accessdate=2006-02-28
}}</ref> part of the family of [[Retroviridae]].<ref name=ICTV61.>{{cite web
| author=[[International Committee on Taxonomy of Viruses]]
| publisher=[[National Institutes of Health]]
| publishyear=2002
| url=http://www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/61000000.htm
| title=61. Retroviridae
| accessdate=2006-02-28
}}</ref> Lentiviruses have many common morphologies and biological properties. Many species are infected by lentiviruses, which are characteristically responsible for long-duration illnesses with a long incubation period.<ref name=Levy>{{cite journal
| author=Lévy, J. A.
| title=HIV pathogenesis and long-term survival
| journal=AIDS
| year=1993
| pages=1401–1410
| volume=7
| issue=11
| pmid=8280406
| doi=10.1097/00002030-199311000-00001
}}</ref> Lentiviruses are transmitted as single-stranded, positive-[[Sense (molecular biology)|sense]], enveloped [[RNA virus]]es. Upon entry of the target cell, the viral RNA [[genome]] is converted to double-stranded [[DNA]] by a virally encoded [[reverse transcriptase]] that is present in the virus particle. This viral DNA is then integrated into the cellular DNA by a virally encoded [[integrase]], along with host cellular co-factors,<ref name="JASmith">{{cite journal | author= Smith, Johanna A.; Daniel, René (Division of Infectious Diseases, Center for Human Virology, Thomas Jefferson University, Philadelphia) |title= Following the path of the virus: the exploitation of host DNA repair mechanisms by retroviruses |journal=ACS Chem Biol|volume=1|issue=4 |pages= 217–26 | year= 2006 |pmid= 17163676 |doi= |url= http://www.ncbi.nlm.nih.gov/pubmed/17163676?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum}}</ref> so that the genome can be [[Transcription (genetics)|transcribed]]. Once the virus has infected the cell, two pathways are possible: either the virus becomes [[Incubation period|latent]] and the infected cell continues to function, or the virus becomes active and replicates, and a large number of virus particles are liberated that can then infect other cells.
Two species of HIV infect humans: HIV-1 and HIV-2. HIV-1 is the virus that was initially discovered and termed LAV. It is more virulent, relatively easily transmitted, and is the cause of the majority of HIV infections globally. HIV-2 is less transmittable than HIV-1 and is largely confined to [[West Africa]].<ref name=Reeves>{{cite journal
| author=Reeves, J. D. and Doms, R. W
| title=Human Immunodeficiency Virus Type 2
| journal=J. Gen. Virol. | year=2002 | pages=1253–1265 | volume=83 | issue=Pt 6
| pmid=12029140
}}</ref>
{|class="wikitable"
|+Comparison of HIV species
|-
! Species !! [[Virulence]] !! Transmittability !! Prevalence !! Purported origin
|-
! HIV-1
| High || High || Global || [[Common Chimpanzee]]
|-
! HIV-2
| Lower || Low || West Africa || [[Sooty Mangabey]]
|}
==Discovery==
Controversy surrounding the discovery of the Human Immunodeficiency Virus (HIV) was intense after American researcher Robert Gallo and French scientist Luc Montagnier both claimed to have discovered it. The dispute was settled on a political level with both teams receiving equal credit.
==Transmission==
{| class="prettytable" style="float:right; font-size:85%; margin-left:15px;"
|- bgcolor="#efefef"
! colspan=5 style="border-right:0px;";| Estimated per act risk for acquisition<br/>of HIV-1 by exposure route<ref name=MMWR>{{cite journal | author=Smith, D. K., Grohskopf, L. A., Black, R. J., Auerbach, J. D., Veronese, F., Struble, K. A., Cheever, L., Johnson, M., Paxton, L. A., Onorato, I. A. and Greenberg, A. E. | title=Antiretroviral Postexposure Prophylaxis After Sexual, Injection-Drug Use, or Other Nonoccupational Exposure to HIV in the United States | journal=MMWR | year=2005 | pages=1–20 | volume=54 | issue=RR02 | url=http://www.cdc.gov/mmwr/preview/mmwrhtml/rr5402a1.htm#tab1}}</ref>
|- bgcolor="#efefef"
| align="center" style="width: 100px"|'''Exposure Route'''
| align="center" style="width: 130px"|'''Estimated infections<br/>per 10,000 exposures<br/>to an infected source'''
|-
| Blood Transfusion
| align="center" | 9,000<ref name=Donegan>{{cite journal
| author=Donegan, E., Stuart, M., Niland, J. C., Sacks, H. S., Azen, S. P., Dietrich, S. L., Faucett, C., Fletcher, M. A., Kleinman, S. H., Operskalski, E. A., et al.
| title=Infection with human immunodeficiency virus type 1 (HIV-1) among recipients of antibody-positive blood donations
| journal=Ann. Intern. Med.
| year=1990
| pages=733–739
| volume=113
| issue=10
| pmid=2240875
}}</ref>
|-
| Childbirth
| align="center" | 2,500<ref name=Coovadia>{{cite journal
| author=Coovadia, H.
| title=Antiretroviral agents—how best to protect infants from HIV and save their mothers from AIDS | journal=N. Engl. J. Med.
| year=2004
| pages=289–292
| volume=351
| issue=3
| pmid=15247337
| doi=10.1056/NEJMe048128
}}</ref>
|-
| Needle-sharing injection drug use
| align="center" | 67<ref name=Kaplan>{{cite journal | author=Kaplan, E. H. and Heimer, R. | title=HIV incidence among New Haven needle exchange participants: updated estimates from syringe tracking and testing data | journal=J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. | year=1995 | pages=175–176 | volume=10 | issue=2
| pmid=7552482 }}</ref>
|-
| Receptive anal intercourse<sup>*</sup>
| align="center" | 50<ref name=ESG>{{cite journal | author=European Study Group on Heterosexual Transmission of HIV | title=Comparison of female to male and male to female transmission of HIV in 563 stable couples | journal=BMJ. | year=1992 | pages=809–813 | volume=304 | issue=6830 | pmid=1392708}}</ref><ref name=Varghese>{{cite journal | author=Varghese, B., Maher, J. E., Peterman, T. A., Branson, B. M. and Steketee, R. W. | title=Reducing the risk of sexual HIV transmission: quantifying the per-act risk for HIV on the basis of choice of partner, sex act, and condom use | journal=Sex. Transm. Dis. | year=2002 | pages=38–43 | volume=29 | issue=1 | pmid=11773877}}</ref>
|-
| Percutaneous needle stick
| align="center" | 30<ref name=Bell>{{
cite journal | author=Bell, D. M. | title=Occupational risk of human immunodeficiency virus infection in healthcare workers: an overview. | journal=Am. J. Med. | year=1997 | pages=9-15 | volume=102 | issue=5B | pmid=9845490
}}</ref>
|-
| Receptive penile-vaginal intercourse<sup>*</sup>
| align="center" | 10<ref name=ESG /><ref name=Varghese /><ref name=Leynaert>{{
cite journal | author=Leynaert, B., Downs, A. M. and de Vincenzi, I. | title=Heterosexual transmission of human immunodeficiency virus: variability of infectivity throughout the course of infection. European Study Group on Heterosexual Transmission of HIV | journal=Am. J. Epidemiol. | year=1998 | pages=88-96 | volume=148 | issue=1 | pmid=9663408
}}</ref>
|-
| Insertive anal intercourse<sup>*</sup>
| align="center" | 6.5<ref name=ESG /><ref name=Varghese />
|-
| Insertive penile-vaginal [[sexual intercourse|intercourse]]<sup>*</sup>
| align="center" | 5<ref name=ESG /><ref name=Varghese />
|-
| Receptive [[fellatio]]<sup>*</sup>
| align="center" | 1<ref name=Varghese />
|-
| Insertive fellatio<sup>*</sup>
| align="center" | 0.5<ref name=Varghese />
|- bgcolor="#efefef"
! colspan=5 style="border-right:0px;";| <sup>*</sup> assuming no condom use </br>
|}
Since the beginning of the [[pandemic]], three main transmission routes for HIV have been identified:
*'''Sexual route.''' The majority of HIV infections are acquired through unprotected sexual relations. Sexual transmission can occur when infected sexual secretions of one partner come into contact with the genital, oral, or rectal [[mucous membranes]] of another.
*'''Blood or blood product route.''' This transmission route can account for infections in intravenous drug users, [[hemophiliac]]s and recipients of [[blood transfusion]]s (though most transfusions are checked for HIV in the developed world) and blood products. It is also of concern for persons receiving medical care in regions where there is prevalent substandard hygiene in the use of injection equipment, such as the reuse of needles in Third World countries. HIV can also be spread through the sharing of needles. Health care workers such as nurses, laboratory workers, and doctors, have also been infected, although this occurs more rarely. People who give and receive tattoos, piercings, and [[Scarification#Scarification_as_a_body_modification|scarification]] procedures can also be at risk of infection.
*'''Mother-to-child transmission''' (MTCT). The transmission of the virus from the mother to the child can occur ''in utero'' during pregnancy and ''intrapartum'' at childbirth. In the absence of treatment, the transmission rate between the mother and child is around 25%.<ref name=Coovadia /> However, where combination [[antiretroviral]] drug treatment and [[Cesarian section]] are available, this risk can be reduced to as low as 1%.<ref name=Coovadia /> Breast feeding also presents a risk of infection for the baby.
HIV-2 is transmitted much less frequently by the MTCT and sexual route than HIV-1.
HIV has been found at low concentrations in the [[saliva]], [[tears]] and [[urine]] of infected individuals, but there are no recorded cases of infection by these secretions and the potential risk of transmission is negligible.<ref name="pmid2963151">{{cite journal
|author=Lifson AR
|title=Do alternate modes for transmission of human immunodeficiency virus exist? A review
|journal=JAMA
|volume=259
|issue=9
|pages=1353–6
|year=1988
|pmid=2963151
|doi=
}}</ref> The use of physical barriers such as the [[latex]] [[condom]] is widely advocated to reduce the sexual transmission of HIV. [[Spermicide]], when used alone or with vaginal contraceptives like a [[diaphragm (contraceptive)|diaphragm]], actually increases the male to female transmission rate due to inflammation of the vagina; it should not be considered a barrier to infection.<ref name="spermicide">{{cite web |url=http://www.fda.gov/oashi/aids/condom.html#should |title=Should spermicides be used with condoms? |accessdate=2006-10-23 |work=Condom Brochure, FDA OSHI HIV STDs }}</ref>
A meta-analysis of twenty-seven observational studies conducted prior to 1999 in sub-Saharan Africa indicated that male [[circumcision]] reduces the risk of HIV infection.<ref>{{cite journal |last=Weiss |first=H.A. |authorlink= |coauthors=M.A. Quigley, R.J. Hayes |year=2000 |month= |title=Male circumcision and risk of HIV infection in sub-Saharan Africa: A systematic review and meta-analysis |journal=AIDS |volume=14 |issue=15 |pages=2361–2370 |pmid=11089625 |quote=|doi=10.1097/00002030-200010200-00018 }}</ref> However, a subsequent review indicated that the correlation between circumcision and HIV in these observational studies may have been due to [[Confounding variable|confounding factors]].<ref name=Siegfred>{{cite journal
| author=Siegfried, N., Muller, M., Deeks, J., Volmink, J., Egger, M., Low, N., Walker, S. and Williamson, P. | title=HIV and male circumcision--a systematic review with assessment of the quality of studies | journal=Lancet Infect. Dis. | year=2005 | pages=165–173 | volume=5 | issue=3 | pmid=15766651}}</ref> Later trials, in which [[Circumcision|uncircumcised]] men were randomly assigned to be medically circumcised in sterile conditions and given counseling and other men were not circumcised, have been conducted in South Africa,<ref name=Williams>{{
cite journal
| author=Williams BG, Lloyd-Smith JO, Gouws E, Hankins C, Getz WM, Hargrove J, de Zoysa I, Dye C, Auvert B.
| title=The Potential Impact of Male Circumcision on HIV in Sub-Saharan Africa.
| journal=PLoS Med | year=2006 | pages=e262 | volume=3 | issue=7
| pmid=16822094
}}</ref> Kenya<ref>{{cite journal |author=Bailey RC, Moses S, Parker CB, ''et al'' |title=Male circumcision for HIV prevention in young men in Kisumu, Kenya: a randomised controlled trial |journal=Lancet |volume=369 |issue=9562 |pages=643–56 |year=2007 |pmid=17321310 |doi=10.1016/S0140-6736(07)60312-2}}</ref> and Uganda<ref>{{cite journal
| quotes =
| author = Gray RH et al
| date = [[24 February]] [[2007]]
| year = 2007
| month = February
| title = Male circumcision for HIV prevention in men in Rakai, Uganda: a randomised trial.
| journal = Lancet
| volume = 369
| issue = 9562
| pages = 657–66
| pmid = 17321311
| doi = 10.1016/S0140-6736(07)60313-4
| id =
| url = http://www.ncbi.nlm.nih.gov/pubmed/17321311?dopt=abstractplus
| language = English
| format =
| accessdate = 2007-04-17
| laysummary =
| laysource =
| laydate =
| quote =
}}</ref> showing reductions in HIV transmission for heterosexual sex of 60%, 53%, and 51% respectively. As a result, a panel of experts convened by WHO and the UNAIDS Secretariat has "recommended that male circumcision now be recognized as an additional important intervention to reduce the risk of heterosexually acquired HIV infection in men."<ref name=WHOUNAIDScircum>{{
cite web
| author=WHO | publisher=WHO.int | year=2007
| url=http://www.who.int/hiv/mediacentre/news68/en/index.html
| title=WHO and UNAIDS announce recommendations from expert consultation on male circumcision for HIV prevention
| accessdate=2007-07-13
}}</ref> Research is clarifying whether there is a historical relationship between rates of male circumcision and rates of HIV in differing social and cultural contexts. Some South African medical experts have expressed concern that the repeated use of unsterilized blades in the [[Circumcision#Cultures and religions|ritual]] (not medical) circumcision of adolescent boys may be spreading HIV.<ref name=Kaisercircum>{{
cite web
| author=Various | publisher=Kaisernetwork.org | year=2005
| url=http://www.kaisernetwork.org/daily_reports/rep_index.cfm?DR_ID=31199
| title=Repeated Use of Unsterilized Blades in Ritual Circumcision Might Contribute to HIV Spread in S. Africa, Doctors Say
| accessdate=2006-03-28
}}</ref>
==Structure and genome==
{{main|HIV structure and genome}}
[[Image:HIV Viron.png|thumb|300px|Diagram of HIV]]
HIV is different in structure from other retroviruses. It roughly spherical<ref name=McGovern>{{
cite journal | author=McGovern SL, Caselli E, Grigorieff N, Shoichet BK | title=A common mechanism underlying promiscuous inhibitors from virtual and high-throughput screening | journal=J Med Chem | year=2002 | pages=1712-22 | volume=45 | issue=8
| pmid=11931626
}}</ref>
with a diameter of about 120 [[Nanometre|nm]], around 60 times smaller than a red blood cell, yet large for a virus<ref name=Microbiology3> Compared with overview in: {{cite book |author=Fisher, Bruce; Harvey, Richard P.; Champe, Pamela C. |title=Lippincott's Illustrated Reviews: Microbiology (Lippincott's Illustrated Reviews Series) |publisher=Lippincott Williams & Wilkins |location=Hagerstown, MD |year= |pages= |isbn=0-7817-8215-5 |oclc= |doi=}} Page 3 </ref>. It is composed of two copies of positive single-stranded [[RNA]] that codes for the virus's nine [[gene]]s enclosed by a conical [[capsid]] composed of 2,000 copies of the viral protein [[HIV structure and genome|p24]].<ref name=compendia>{{
cite book
| author = Various
| year = 2008
| title = HIV Sequence Compendium 2008 Introduction | url = http://www.hiv.lanl.gov/content/sequence/HIV/COMPENDIUM/2008/frontmatter.pdf
| format= [[Portable Document Format|PDF format]]
}}</ref> The single-stranded RNA is tightly bound to nucleocapsid proteins, p7 and enzymes needed for the development of the virion such as [[reverse transcriptase]], [[aspartyl protease|proteases]], [[ribonuclease]] and [[integrase]]. A matrix composed of the viral protein p17 surrounds the capsid ensuring the integrity of the virion particle.<ref name=compendia/> This is, in turn, surrounded by the viral envelope which is composed of two layers of fatty molecules called [[phospholipid]]s taken from the membrane of a human cell when a newly formed virus particle buds from the cell. Embedded in the viral envelope are proteins from the host cell and about 70 copies of a complex HIV protein that protrudes through the surface of the virus particle.<ref name=compendia/> This protein, known as Env, consists of a cap made of three molecules called [[gp120|glycoprotein (gp) 120]], and a stem consisting of three [[gp41]] molecules that anchor the structure into the viral envelope.<ref name=Chan>{{
cite journal
| author=Chan, DC., Fass, D., Berger, JM., Kim, PS. | title=Core Structure of gp41 from the HIV Envelope Glycoprotein | journal=Cell | year=1997 | pages=263–273 | volume=89 | pmid=9108481 |format=pdf |url=http://www.its.caltech.edu/~chanlab/PDFs/Chan_Cell_1997.pdf
}}</ref> This glycoprotein complex enables the virus to attach to and fuse with target cells to initiate the infectious cycle.<ref name=Chan>{{
cite journal
| author=Chan, DC., Fass, D., Berger, JM., Kim, PS. | title=Core Structure of gp41 from the HIV Envelope Glycoprotein | journal=Cell | year=1997 | pages=263–273 | volume=89 | pmid=9108481 |format=pdf |url=http://www.its.caltech.edu/~chanlab/PDFs/Chan_Cell_1997.pdf
}}</ref>
Both these surface proteins, especially gp120, have been considered as targets of future treatments or vaccines against HIV.<ref name=nih1998>{{
cite news
| author=National Institute of Health | title=Crystal Structure of Key HIV Protein Reveals New Prevention, Treatment Targets | date=[[June 17]], [[1998]] |url=http://www3.niaid.nih.gov/news/newsreleases/1998/hivprotein.htm | accessdate = 2006-09-14
}}</ref>
The RNA genome consists of at least 7 structural landmarks (LTR, TAR, RRE, PE, SLIP, CRS, INS) and nine genes (''gag'', ''pol'', and ''env'', ''tat'', ''rev'', ''nef'', ''vif'', ''vpr'', ''vpu'', and ''tev'') encoding 19 proteins. Three of these genes, ''gag'', ''pol'', and ''env'', contain information needed to make the structural proteins for new virus particles.<ref name=compendia/> For example, ''env'' codes for a protein called gp160 that is broken down by a viral enzyme to form gp120 and gp41. The six remaining genes, ''tat'', ''rev'', ''nef'', ''vif'', ''vpr'', and ''vpu'' (or ''vpx'' in the case of HIV-2), are regulatory genes for proteins that control the ability of HIV to infect cells, produce new copies of virus (replicate), or cause disease.<ref name=compendia/> The two Tat proteins (p16 and p14) are [[Activator (genetics)|transcriptional transactivators]] for the LTR promoter acting by binding the TAR RNA element. The [[HIV_structure_and_genome#Rev|Rev]] protein (p19) is involved in shuttling RNAs from the nucleus and the cytoplasm by binding to the RRE RNA element. The Vif protein (p23) prevents the action of [[APOBEC3G]] (a cell protein which deaminates DNA:RNA hybrids and/or interferes with the Pol protein). The Vpr protein (p14) arrests cell divsiion at G2/M. The Nef protein (p27) downregulates [[CD4]] the major viral receptor and [[MHC class I]] molecules. Nef also interacts with SH3 domains. The Vpu protein (p16) influences the release of new virus particles from infected cells.<ref name=compendia/> The ends of each strand of HIV RNA contain an RNA sequence called the [[long terminal repeat]] (LTR). Regions in the LTR act as switches to control production of new viruses and can be triggered by proteins from either HIV or the host cell. The [[Retroviral Psi packaging element|Psi element]] is involved in viral genome packaging and recognized by Gag and Rev proteins. The SLIP element (TTTTTT) is involved in the frameshift in the Gag-Pol reading frame required to make functional Pol. <ref name=compendia/>
==Tropism==
{{Main|HIV tropism}}
The term [[viral tropism]] refers to which cell types HIV infects. HIV can infect a variety of immune cells such as [[Helper T cell|CD4<SUP>+</SUP> T cells]], [[macrophage]]s, and [[microglial cell]]s. HIV-1 entry to macrophages and CD4<SUP>+</SUP> T cells is mediated through interaction of the virion envelope glycoproteins (gp120) with the CD4 molecule on the target cells and also with [[chemokine]] coreceptors.<ref name=Chan/>
Macrophage (M-tropic) strains of HIV-1, or non-[[syncitia]]-inducing strains (NSI) use the ''β''-chemokine receptor [[CCR5]] for entry and are thus able to replicate in macrophages and CD4<SUP>+</SUP> T cells.<ref name=Coakley>{{
cite journal
| author=Coakley, E., Petropoulos, C. J. and Whitcomb, J. M. | title=Assessing ch vbgemokine co-receptor usage in HIV | journal=Curr. Opin. Infect. Dis. | year=2005 | pages=9-15 | volume=18 | issue=1 | pmid=15647694 |format=
}}</ref> This CCR5 coreceptor is used by almost all primary HIV-1 isolates regardless of viral genetic subtype. Indeed, macrophages play a key role in several critical aspects of HIV infection. They appear to be the first cells infected by HIV and perhaps the source of HIV production when CD4<SUP>+</SUP> cells become depleted in the patient. Macrophages and microglial cells are the cells infected by HIV in the [[central nervous system]]. In tonsils and [[adenoids]] of HIV-infected patients, macrophages fuse into multinucleated giant cells that produce huge amounts of virus.
T-tropic isolates, or [[syncitia]]-inducing (SI) strains replicate in primary CD4<SUP>+</SUP> T cells as well as in macrophages and use the ''α''-chemokine receptor, [[CXCR4]], for entry.<ref name=Coakley /><ref name=Deng>
{{cite journal
| author=Deng H, Liu R, Ellmeier W, Choe S, Unutmaz D, Burkhart M, Di Marzio P, Marmon S, Sutton RE, Hill CM, Davis CB, Peiper SC, Schall TJ, Littman DR, Landau NR. | title=Identification of a major co-receptor for primary isolates of HIV-1. | journal=Nature | year=1996 | pages=661–666 | volume=381 | issue=6584 | pmid=8649511 | doi=10.1038/381661a0
}}</ref><ref name=Feng>
{{cite journal
| author=Feng Y, Broder CC, Kennedy PE, Berger EA. | title=HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor. | journal=Science | year=1996 | pages=872–877 | volume=272 | issue=5263 | pmid=8629022 | doi=10.1126/science.272.5263.872
}}</ref> Dual-tropic HIV-1 strains are thought to be transitional strains of the HIV-1 virus and thus are able to use both CCR5 and CXCR4 as co-receptors for viral entry.
The ''α''-chemokine, SDF-1, a ligand for CXCR4, suppresses replication of T-tropic HIV-1 isolates. It does this by down-regulating the expression of CXCR4 on the surface of these cells. HIV that use only the CCR5 receptor are termed [[HIV tropism|R5]], those that only use CXCR4 are termed [[HIV tropism|X4]], and those that use both, X4R5. However, the use of coreceptor alone does not explain viral tropism, as not all R5 viruses are able to use CCR5 on macrophages for a productive infection<ref name=Coakley /> and HIV can also infect a subtype of [[myeloid dendritic cells]],<ref name=Knight>
{{cite journal
| author=Knight, S. C., Macatonia, S. E. and Patterson, S. | title=HIV I infection of dendritic cells | journal=Int. Rev. Immunol. | year=1990 | pages=163–175 | volume=6 | issue=2-3 | pmid=2152500 | doi=10.3109/08830189009056627
}}</ref> which probably constitute a reservoir that maintains infection when CD4<SUP>+</SUP> T cell numbers have declined to extremely low levels.
Some people are resistant to certain strains of HIV.<ref name=Tang>{{
cite journal
| author=Tang, J. and Kaslow, R. A.
| title=The impact of host genetics on HIV infection and disease progression in the era of highly active antiretroviral therapy
| journal=AIDS | year=2003 | pages=S51-S60 | volume=17 | issue=Suppl 4
| pmid=15080180
}}</ref> One example of how this occurs is people with the [[CCR5-Δ32]] mutation; these people are resistant to infection with R5 virus as the mutation stops HIV from binding to this coreceptor, reducing its ability to infect target cells.
Sexual intercourse is the major mode of HIV transmission. Both X4 and R5 HIV are present in the [[seminal fluid]] which is passed from a male to his sexual partner. The virions can then infect numerous cellular targets and disseminate into the whole organism. However, a selection process leads to a predominant transmission of the R5 virus through this pathway.<ref name=Zhu1993>
{{cite journal
| author=Zhu T, Mo H, Wang N, Nam DS, Cao Y, Koup RA, Ho DD. | title=Genotypic and phenotypic characterization of HIV-1 patients with primary infection | journal=Science | year=1993 | pages=1179–1181 | volume=261 | issue=5125 | pmid=8356453 | doi=10.1126/science.8356453
}}</ref><ref name=Wout>
{{cite journal
| author=van’t Wout AB, Kootstra NA, Mulder-Kampinga GA, Albrecht-van Lent N, Scherpbier HJ, Veenstra J, Boer K, Coutinho RA, Miedema F, Schuitemaker H. | title=Macrophage-tropic variants initiate human immunodeficiency virus type 1 infection after sexual, parenteral, and vertical transmission | journal=J Clin Invest | year=1994 | pages=2060–2067 | volume=94 | issue=5 | pmid=7962552 | doi=10.1172/JCI117560
}}</ref><ref name=Zhu1996>
{{cite journal
| author=Zhu T, Wang N, Carr A, Nam DS, Moor-Jankowski R, Cooper DA, Ho DD. | title=Genetic characterization of human immunodeficiency virus type 1 in blood and genital secretions: evidence for viral compartmentalization and selection during sexual transmission | journal=J Virol | year=1996 | pages=3098–3107 | volume=70 | issue=5 | pmid=8627789
}}</ref> How this selective process works is still under investigation, but one model is that [[spermatozoa]] may selectively carry R5 HIV as they possess both CCR3 and CCR5 but not CXCR4 on their surface<ref name=Muciaccia>
{{cite journal
| author=Muciaccia B, Padula F, Vicini E, Gandini L, Lenzi A, Stefanini M. | title=Beta-chemokine receptors 5 and 3 are expressed on the head region of human spermatozoon | journal=FASEB J | year=2005 | pages=2048–2050 | volume=19 | issue=14 | pmid=16174786
}}</ref> and that genital [[epithelial cell]]s preferentially sequester X4 virus.<ref name=Berlier>
{{cite journal
| author=Berlier W, Bourlet T, Lawrence P, Hamzeh H, Lambert C, Genin C, Verrier B, Dieu-Nosjean MC, Pozzetto B, Delezay O. | title=Selective sequestration of X4 isolates by human genital epithelial cells: Implication for virus tropism selection process during sexual transmission of HIV | journal=J Med Virol. | year=2005 | pages=465–474 | volume=77 | issue=4 | pmid=16254974 | doi=10.1002/jmv.20478
}}</ref> In patients infected with subtype B HIV-1, there is often a co-receptor switch in late-stage disease and T-tropic variants appear that can infect a variety of T cells through CXCR4.<ref name=Clevestig>
{{cite journal
| author=Clevestig P, Maljkovic I, Casper C, Carlenor E, Lindgren S, Naver L, Bohlin AB, Fenyo EM, Leitner T, Ehrnst A. | title=The X4 phenotype of HIV type 1 evolves from R5 in two children of mothers, carrying X4, and is not linked to transmission | journal=AIDS Res Hum Retroviruses | year=2005 | pages=371–378 | volume=5 | issue=21 | pmid=15929699 | doi=10.1089/aid.2005.21.371
}}</ref> These variants then replicate more aggressively with heightened virulence that causes rapid T cell depletion, immune system collapse, and opportunistic infections that mark the advent of AIDS.<ref name=Moore>
{{cite journal
| author=Moore JP.| title=Coreceptors: implications for HIV pathogenesis and therapy | journal=Science | year=1997 | pages=51–52 | volume=276 | issue=5309 | pmid=9122710 | doi=10.1126/science.276.5309.51
}}</ref> Thus, during the course of infection, viral adaptation to the use of CXCR4 instead of CCR5 may be a key step in the progression to AIDS. A number of studies with subtype B-infected individuals have determined that between 40 and 50% of AIDS patients can harbour viruses of the SI, and presumably the X4, phenotype.<ref name=Karlsson>
{{cite journal
| author=Karlsson A, Parsmyr K, Aperia K, Sandstrom E, Fenyo EM, Albert J.| title=MT-2 cell tropism of human immunodeficiency virus type 1 isolates as a marker for response to treatment and development of drug resistance | journal=J Infect Dis. | year=1994 | pages=1367–1375 | volume=170 | issue=6 | pmid=7995974
}}</ref><ref name=Koot>
{{cite journal
| author=Koot M, van 't Wout AB, Kootstra NA, de Goede RE, Tersmette M, Schuitemaker H.| title=Relation between changes in cellular load, evolution of viral phenotype, and the clonal composition of virus populations in the course of human immunodeficiency virus type 1 infection | journal=J Infect Dis. | year=1996 | pages=349–354 | volume=173 | issue=2 | pmid=8568295
}}</ref>
==Replication cycle==
[[Image:HIV gross cycle only.png|right|thumb|300px|The HIV replication cycle]]
===Entry to the cell===
HIV enters macrophages and CD4<SUP>+</SUP> T cells by the [[adsorption]] of [[glycoprotein]]s on its surface to receptors on the target cell followed by fusion of the viral envelope with the cell membrane and the release of the HIV capsid into the cell.<ref name=Chan2>{{cite journal |author=Chan D, Kim P |title=HIV entry and its inhibition |journal=Cell |volume=93 |issue=5 |pages=681–4 |year=1998 |pmid=9630213 |doi=10.1016/S0092-8674(00)81430-0}}</ref><ref name=Wyatt>{{cite journal |author=Wyatt R, Sodroski J |title=The HIV-1 envelope glycoproteins: fusogens, antigens, and immunogens |journal=Science |volume=280 |issue=5371 |pages=1884–8 |year=1998 | doi=10.1126/science.280.5371.1884 |pmid=9632381}}</ref>
Entry to the cell begins through interaction of the trimeric envelope complex ([[gp160]] spike) and both [[CD4]] and a chemokine receptor (generally either [[CCR5]] or [[CXCR4]], but others are known to interact) on the cell surface.<ref name=Chan2/><ref name=Wyatt/> gp120 binds to [[integrin]] α<sub>4</sub>β<sub>7</sub> activating [[LFA-1]] the central integrin involved in the establishment of virological synapses, which facilitate efficient cell-to-cell spreading of HIV-1.<ref name=Arthos>{{cite journal |author=Arthos J, Cicala C, Martinelli E, Macleod K, Van Ryk D, Wei D, Xiao Z, Veenstra TD, Conrad TP, Lempicki RA, McLaughlin S, Pascuccio M, Gopaul R, McNally J, Cruz CC, Censoplano N, Chung E, Reitano KN, Kottilil S, Goode DJ, Fauci AS. |title=HIV-1 envelope protein binds to and signals through integrin alpha(4)beta(7), the gut mucosal homing receptor for peripheral T cells |journal=Nature Immunol. |volume=In Press |issue= |pages= 301|year=2008|pmid=18264102 |doi=10.1038/ni1566}}</ref> The gp160 spike contains binding domains for both CD4 and chemokine receptors.<ref name=Chan2/><ref name=Wyatt/> 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 binding domains of gp120 and allowing them to interact with the target chemokine receptor.<ref name=Chan2/><ref name=Wyatt/> This allows for a more stable two-pronged attachment, which allows the N-terminal fusion peptide gp41 to penetrate the cell membrane.<ref name=Chan2/><ref name=Wyatt/> Repeat sequences in gp41, HR1 and HR2 then interact, causing the collapse of the extracellular portion of gp41 into a hairpin. This loop structure brings the virus and cell membranes close together, allowing fusion of the membranes and subsequent entry of the viral capsid.<ref name=Chan2/><ref name=Wyatt/>
Once HIV has bound to the target cell, the HIV [[RNA]] and various [[enzyme]]s, including reverse transcriptase, integrase, ribonuclease and protease, are injected into the cell.<ref name=Chan2/>
During the microtubule based transport to the nucleus, the viral single strand RNA genome is transcribed into double strand DNA, which is then integrated into a host chromosome.
HIV can infect [[dendritic cell]]s (DCs) by this CD4-CCR5 route, but another route using mannose-specific C-type lectin receptors such as [[DC-SIGN]] can also be used.<ref name=Pope_2003>{{cite journal |author=Pope M, Haase A |title=Transmission, acute HIV-1 infection and the quest for strategies to prevent infection |journal=Nat Med |volume=9 |issue=7 |pages=847–52 |year=2003 |pmid=12835704 |doi=10.1038/nm0703-847}}</ref> 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 once the virus has been captured in the [[mucosa]] by DCs.<ref name=Pope_2003 />
===Replication and transcription===
Once the viral capsid enters the cell, an [[enzyme]] called ''[[reverse transcriptase]]'' liberates the single-stranded (+)[[RNA]] from the attached viral proteins and copies it into a complementary [[DNA]].<ref name=Zheng>{{cite journal
| author=Zheng, Y. H., Lovsin, N. and Peterlin, B. M. | title=Newly identified host factors modulate HIV replication | journal=Immunol. Lett. | year=2005 | pages=225–234 | volume=97 | issue=2 | pmid=15752562 | doi=10.1016/j.imlet.2004.11.026}}</ref> This process of reverse transcription is extremely error-prone and it is during this step that mutations may occur. Such mutations may cause [[Resistance to antiviral drugs|drug resistance]]. The reverse transcriptase then makes a complementary DNA strand to form a double-stranded viral DNA intermediate (vDNA). This vDNA 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]]''.<ref name=Zheng/>
[[Image:Reverse Transcription.png|thumb|right|300px|Reverse transcription of the HIV genome into double strand DNA]]
This integrated viral DNA may then lie dormant, in the latent stage of HIV infection.<ref name=Zheng/> To actively produce the virus, certain cellular [[transcription factor]]s need to be present, the most important of which is [[NF-κB|NF-''κ''B]] (NF kappa B), which is upregulated when T cells become activated.<ref name=Hiscott>{{cite journal
| author=Hiscott J, Kwon H, Genin P. | title=Hostile takeovers: viral appropriation of the NF-kappaB pathway | journal=J Clin Invest. | year=2001 | pages=143–151 | volume=107 | issue=2 | pmid=11160127 | doi=10.1172/JCI11918
}}</ref> This means that those cells most likely to be killed by HIV are those currently fighting infection.
In this replication process, the integrated [[provirus]] is copied to [[Messenger RNA|mRNA]] which is then [[Splicing (genetics)|spliced]] into smaller pieces. These small pieces produce the regulatory proteins [[HIV structure and genome#Tat|Tat]] (which encourages new virus production) and [[HIV structure and genome#Rev|Rev]]. As Rev accumulates it gradually starts to inhibit [[Messenger RNA|mRNA]] splicing.<ref name=Pollard>
{{cite journal
| author=Pollard, V. W. and Malim, M. H. | title=The HIV-1 Rev protein | journal=Annu. Rev. Microbiol. | year=1998 | pages=491–532 | volume=52 | issue= | pmid=9891806 | doi=10.1146/annurev.micro.52.1.491
}}</ref> At this stage, the structural proteins Gag and Env are produced from the full-length mRNA. The full-length RNA is actually the virus genome; it binds to the Gag protein and is packaged into new virus particles.
HIV-1 and HIV-2 appear to package their RNA differently; HIV-1 will bind to any appropriate RNA whereas HIV-2 will preferentially bind to the mRNA which was used to create the Gag protein itself. This may mean that HIV-1 is better able to mutate (HIV-1 infection progresses to AIDS faster than HIV-2 infection and is responsible for the majority of global infections).
===Assembly and release===
The final step of the viral cycle, assembly of new HIV-1 virons, 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|Golgi]] complex where it is cleaved by [[HIV-1 protease|protease]] and processed into the two HIV envelope glycoproteins gp41 and gp120. These are transported to the [[plasma membrane]] of the host cell where gp41 anchors the 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. Maturation either occurs in the forming bud or in the immature virion after it buds from the host cell. During maturation, HIV proteases cleave the polyproteins into individual functional HIV proteins and enzymes. The various structural components then assemble to produce a mature HIV virion.<ref name=Gelderblom>{{cite book
| last = Gelderblom | first = H. R | year = 1997 | title = '''HIV Sequence Compendium''' | chapter = Fine structure of HIV and SIV | chapterurl = http://www.hiv.lanl.gov/content/sequence/HIV/COMPENDIUM/1997/partIII/Gelderblom.pdf | editor = Los Alamos National Laboratory (ed.) | edition = | pages = 31-44 | publisher = [[Los Alamos National Laboratory]] | location = [[Los Alamos, New Mexico]] | format = [[Portable Document Format|PDF format]]}}</ref> This cleavage step can be inhibited by protease inhibitors. The mature virus is then able to infect another cell.
==Genetic variability==
{{See|Subtypes of HIV}}
[[Image:HIV-SIV-phylogenetic-tree.svg|thumb|300px|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 [[HIV#Life cycle of HIV|replication cycle]], with the generation of 10<sup>9</sup> to 10<sup>10</sup> virions every day, coupled with a high mutation rate of approximately 3 x 10<sup>-5</sup> per nucleotide base per cycle of replication and [[Genetic recombination|recombinogenic]] properties of reverse transcriptase.<ref name=RobertsonDL>
{{cite journal
| author=Robertson DL, Hahn BH, Sharp PM. | title=Recombination in AIDS viruses | journal=J Mol Evol. | year=1995 | pages=249–259 | volume=40 | issue=3 | pmid=7723052 | doi=10.1007/BF00163230
}}</ref> This complex scenario leads to the generation of many variants of HIV in a single infected patient in the course of one day.<ref name=RobertsonDL/> 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.<ref name=RobertsonDL/> This recombination is most obvious when it occurs between subtypes.<ref name=RobertsonDL/>
The closely related [[simian immunodeficiency virus]] (SIV) exhibits a somewhat different behavior: in its natural hosts, [[African green monkey]]s and [[sooty mangabey]]s, the retrovirus is present in high levels in the blood, but evokes only a mild immune response,<ref>{{cite journal |author=Holzammer S, Holznagel E, Kaul A, Kurth R, Norley S |title=High virus loads in naturally and experimentally SIVagm-infected African green monkeys |journal=Virology |volume=283 |issue=2 |pages=324–31 |year=2001 |pmid=11336557 |doi=10.1006/viro.2001.0870}}</ref> does not cause the development of simian AIDS,<ref>Kurth, R. and Norley, S. (1996) Why don't the natural hosts of SIV develop simian AIDS?, ''J. NIH Res.'' '''8''', 33-37.</ref> and does not undergo the extensive mutation and recombination typical of HIV.<ref>{{cite journal |author=Baier M, Dittmar MT, Cichutek K, Kurth R |title=Development of vivo of genetic variability of simian immunodeficiency virus |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=88 |issue=18 |pages=8126–30 |year=1991 |pmid=1896460 |doi=}}</ref> By contrast, infection of heterologous hosts (rhesus or cynomologus macaques) with SIV results in the generation of genetic diversity that is on the same order as HIV in infected humans; these heterologous hosts also develop simian AIDS.<ref>{{cite journal |author=Daniel MD, King NW, Letvin NL, Hunt RD, Sehgal PK, Desrosiers RC |title=A new type D retrovirus isolated from macaques with an immunodeficiency syndrome |journal=Science |volume=223 |issue=4636 |pages=602–5 |year=1984 |pmid=6695172 |doi=10.1126/science.6695172}}</ref> The relationship, if any, between genetic diversification, immune response, and disease progression is unknown.
Three groups of HIV-1 have been identified on the basis of differences in ''env'': M, N, and O.<ref name=Thomson>
{{cite journal
| author=Thomson, M. M., Perez-Alvarez, L. and Najera, R. | title=Molecular epidemiology of HIV-1 genetic forms and its significance for vaccine development and therapy | journal=Lancet Infect. Dis. | year=2002 | pages=461–471 | volume=2 | issue=8 | pmid=12150845 | doi=10.1016/S1473-3099(02)00343-2
}}</ref> Group M is the most prevalent and is subdivided into eight subtypes (or [[clade]]s), based on the whole genome, which are geographically distinct.<ref name=Carr>{{cite book
| last = Carr | first = J. K. | coauthors = Foley, B. T., Leitner, T., Salminen, M., Korber, B. and McCutchan, F. | year = 1998 | title = '''HIV Sequence Compendium''' | chapter = Reference Sequences Representing the Principal Genetic Diversity of HIV-1 in the Pandemic | chapterurl = http://www.hiv.lanl.gov/content/sequence/HIV/COMPENDIUM/1998/III/Carr.pdf | editor = Los Alamos National Laboratory (ed.) | edition = | pages = 10-19 | publisher = [[Los Alamos National Laboratory]] | location = [[Los Alamos, New Mexico]] | format=[[Portable Document Format|PDF format]]}}</ref> The most prevalent are subtypes B (found mainly in North America and Europe), A and D (found mainly in Africa), and C (found mainly in Africa and Asia); these subtypes form branches in the phylogenetic tree representing the lineage of the M group of HIV-1. Coinfection with distinct subtypes gives rise to circulating recombinant forms (CRFs). In 2000, the last year in which an analysis of global subtype prevalence was made, 47.2% of infections worldwide were of subtype C, 26.7% were of subtype A/CRF02_AG, 12.3% were of subtype B, 5.3% were of subtype D, 3.2% were of CRF_AE, and the remaining 5.3% were composed of other subtypes and CRFs.<ref name=Osmanov>
{{cite journal
| author=Osmanov S, Pattou C, Walker N, Schwardlander B, Esparza J; WHO-UNAIDS Network for HIV Isolation and Characterization. | title=Estimated global distribution and regional spread of HIV-1 genetic subtypes in the year 2000 | journal=Acquir. Immune. Defic. Syndr. | year=2002 | pages=184–190 | volume=29 | issue=2 | pmid=11832690
}}</ref> Most HIV-1 research is focused on subtype B; few laboratories focus on the other subtypes.<ref name=Perrin>
{{cite journal
| author=Perrin L, Kaiser L, Yerly S. | title=Travel and the spread of HIV-1 genetic variants | journal=Lancet Infect Dis. | year=2003 | pages=22–27 | volume=3 | issue=1 | pmid=12505029 | doi=10.1016/S1473-3099(03)00484-5
}}</ref>
The genetic sequence of HIV-2 is only partially homologous to HIV-1 and more closely resembles that of SIV than HIV-1.
==The clinical course of infection==
[[Image:Hiv-timecourse.png|300px|thumb|right|A generalized graph of the relationship between HIV copies (viral load) and CD4 counts over the average course of untreated HIV infection; any particular individual's disease course may vary considerably.
{{legend-line|blue solid 2px|CD4<sup>+</sup> T cell count (cells per µL)}}
{{legend-line|red solid 2px|HIV RNA copies per mL of plasma}}
]]
Infection with HIV-1 is associated with a progressive decrease of the CD4<SUP>+</SUP> T cell count and an increase in [[viral load]]. The stage of infection can be determined by measuring the patient's CD4<SUP>+</SUP> T cell count, and the level of HIV in the blood.
HIV infection has basically four stages: incubation period, acute infection, latency stage and AIDS. The initial [[incubation period]] upon infection is [[asymptomatic]] and usually lasts between two and four weeks. The second stage, acute infection, which lasts an average of 28 days and can include symptoms such as [[fever]], [[lymphadenopathy]] (swollen lymph nodes), [[pharyngitis]] (sore throat), [[rash]], [[myalgia]] (muscle pain), [[malaise]], and mouth and esophageal sores. The latency stage, which occurs third, shows few or no symptoms and can last anywhere from two weeks to twenty years and beyond. AIDS, the fourth and final stage of HIV infection shows as symptoms of various [[opportunistic infection]]s.
===Acute HIV infection===
{{Main|Acute HIV infection}}
The initial infection with HIV generally occurs after transfer of body fluids from an infected person to an uninfected one. The first stage of infection, the primary, or acute infection, is a period of rapid viral replication that immediately follows the individual's exposure to HIV leading to an abundance of virus in the peripheral blood with levels of HIV commonly approaching several million viruses per mL.<ref name=Piatak>
{{cite journal | author=Piatak, M., Jr, Saag, M. S., Yang, L. C., Clark, S. J., Kappes, J. C., Luk, K. C., Hahn, B. H., Shaw, G. M. and Lifson, J.D. | title=High levels of HIV-1 in plasma during all stages of infection determined by competitive PCR | journal=Science | year=1993 | pages=1749–1754 | volume=259 | issue=5102 | pmid=8096089 | doi=10.1126/science.8096089}}
</ref> This response is accompanied by a marked drop in the numbers of circulating CD4<sup>+</sup> T cells. This acute viremia is associated in virtually all patients with the activation of [[cytotoxic T cell|CD8<sup>+</sup> T cells]], which kill HIV-infected cells, and subsequently with antibody production, or [[seroconversion]]. The CD8<sup>+</sup> T cell response is thought to be important in controlling virus levels, which peak and then decline, as the CD4<sup>+</sup> T cell counts rebound to around 800 cells per mL (the normal [[blood value]] is 1200 cells per mL ). A good CD8<sup>+</sup> T cell response has been linked to slower disease progression and a better prognosis, though it does not eliminate the virus.<ref name=Pantaleo1998>
{{cite journal
| author=Pantaleo G, Demarest JF, Schacker T, Vaccarezza M, Cohen OJ, Daucher M, Graziosi C, Schnittman SS, Quinn TC, Shaw GM, Perrin L, Tambussi G, Lazzarin A, Sekaly RP, Soudeyns H, Corey L, Fauci AS. | title=The qualitative nature of the primary immune response to HIV infection is a prognosticator of disease progression independent of the initial level of plasma viremia | journal=Proc Natl Acad Sci U S A. | year=1997 | pages=254–258 | volume=94 | issue=1 | pmid=8990195 | doi=10.1073/pnas.94.1.254
}}</ref> During this period (usually 2-4 weeks post-exposure) most individuals (80 to 90%) develop an influenza or mononucleosis-like illness called [[acute HIV infection]], the most common symptoms of which may include [[fever]], [[lymphadenopathy]], [[pharyngitis]], [[rash]], [[myalgia]], [[malaise]], mouth and esophagal sores, and may also include, but less commonly, [[headache]], [[nausea]] and [[vomiting]], enlarged liver/spleen, [[weight loss]], [[Candidiasis|thrush]], and neurological symptoms. Infected individuals may experience all, some, or none of these symptoms. The duration of symptoms varies, averaging 28 days and usually lasting at least a week.<ref name=Kahn>
{{cite journal
| author=Kahn, J. O. and Walker, B. D. | title=Acute Human Immunodeficiency Virus type 1 infection | journal=N. Engl. J. Med. | year=1998 | pages=33–39 | volume=331 | issue=1 | pmid=9647878 | doi=10.1056/NEJM199807023390107
}}</ref> Because of the nonspecific nature of these symptoms, they are often not recognized as signs of HIV infection. Even if patients go to their doctors or a hospital, they will often be misdiagnosed as having one of the more common infectious diseases with the same symptoms. Consequently, these primary symptoms are not used to diagnose HIV infection as they do not develop in all cases and because many are caused by other more common diseases. However, recognizing the syndrome can be important because the patient is much more infectious during this period.<ref name="pmid11187417">{{cite journal |author=Daar ES, Little S, Pitt J, ''et al'' |title=Diagnosis of primary HIV-1 infection. Los Angeles County Primary HIV Infection Recruitment Network |journal=Ann. Intern. Med. |volume=134 |issue=1 |pages=25–9 |year=2001 |pmid=11187417 |doi=}}</ref>
===Latency stage===
A strong immune defense reduces the number of viral particles in the blood stream, marking the start of the infection's ''clinical latency'' stage. Clinical latency can vary between two weeks and 20 years. During this early phase of infection, HIV is active within [[Lymphatic system|lymphoid organs]], where large amounts of virus become trapped in the follicular [[dendritic cell]]s (FDC) network.<ref name=burton>
{{cite journal
| author=Burton GF, Keele BF, Estes JD, Thacker TC, Gartner S. | title=Follicular dendritic cell contributions to HIV pathogenesis | journal=Semin Immunol. | year=2002 | pages=275–284 | volume=14 | issue=4 | pmid=12163303 | doi=10.1016/S1044-5323(02)00060-X
}}</ref> The surrounding tissues that are rich in CD4<SUP>+</SUP> T cells may also become infected, and viral particles accumulate both in infected cells and as free virus. Individuals who are in this phase are still infectious. During this time, [[Helper T cell|CD4<SUP>+</SUP> CD45RO<SUP>+</SUP> T cells]] carry most of the proviral load.<ref name=clapham>
{{cite journal
| author=Clapham PR, McKnight A. | title=HIV-1 receptors and cell tropism | journal=Br Med Bull. | year=2001 | pages=43–59 | volume=58 | issue=4 | pmid=11714623 | doi=10.1093/bmb/58.1.43
}}</ref>
===AIDS===
{{Main|AIDS}}
:''For more details on this topic, see [[AIDS#Diagnosis|AIDS Diagnosis]], [[AIDS#Symptoms|AIDS Symptoms]] and [[WHO Disease Staging System for HIV Infection and Disease]]''
When CD4<sup>+</sup> T cell numbers decline below a critical level, cell-mediated immunity is lost, and infections with a variety of opportunistic microbes appear. The first symptoms often include moderate and unexplained weight loss, recurring respiratory tract infections (such as [[sinusitis]], [[bronchitis]], [[otitis media]], [[pharyngitis]]), [[prostatitis]], skin rashes, and oral ulcerations. Common opportunistic infections and tumors, most of which are normally controlled by robust CD4<sup>+</sup> T cell-mediated immunity then start to affect the patient. Typically, resistance is lost early on to oral Candida species and to ''Mycobacterium tuberculosis'', which leads to an increased susceptibility to [[oral candidiasis]] (thrush) and [[tuberculosis]]. Later, reactivation of latent [[Herpesviridae|herpes viruses]] may cause worsening recurrences of [[herpes simplex]] eruptions, [[shingles]], [[Epstein-Barr virus]]-induced B-cell lymphomas, or [[Kaposi's sarcoma]], a [[tumor]] of [[endothelial cell]]s that occurs when HIV proteins such as Tat interact with [[Kaposi's sarcoma-associated herpesvirus|Human Herpesvirus-8]]. Pneumonia caused by the fungus ''[[Pneumocystis jirovecii]]'' is common and often fatal. In the final stages of AIDS, infection with [[cytomegalovirus]] (another herpes virus) or [[Mycobacterium avium complex]] is more prominent. Not all patients with AIDS get all these infections or tumors, and there are other tumors and infections that are less prominent but still significant.
==HIV test==
{{main|HIV test}}
Many HIV-positive people are unaware that they are infected with the virus.<ref name=Kumaranayake>
{{cite journal
| author=Kumaranayake, L. and Watts, C. | title=Resource allocation and priority setting of HIV/AIDS interventions: addressing the generalized epidemic in sub-Saharan Africa | journal=J. Int. Dev. | year=2001 | pages=451–466 | volume=13 | issue=4 | doi = 10.1002/jid.797
}}</ref> For example, less than 1% of the sexually active urban population in Africa have been tested and this proportion is even lower in rural populations.<ref name=Kumaranayake /> Furthermore, only 0.5% of pregnant women attending urban health facilities are counselled, tested or receive their test results.<ref name=Kumaranayake/> Again, this proportion is even lower in rural health facilities.<ref name=Kumaranayake/> Since donors may therefore be unaware of their infection, donor blood and blood products used in medicine and medical research are routinely screened for HIV.<ref name=Kleinman>{{
cite web
| author=Kleinman, S. | publisher=Uptodate
| year=2004 |date=September 2004
| url=http://www.uptodate.com/patients/content/topic.do?topicKey=blod_dis/2419
| title=Patient information: Blood donation and transfusion
| accessdate=2008-04-03
}}</ref>
HIV-1 testing consists of initial screening with an [[enzyme-linked immunosorbent assay]] (ELISA) to detect antibodies to HIV-1. Specimens with a nonreactive result from the initial ELISA are considered HIV-negative unless new exposure to an infected partner or partner of unknown HIV status has occurred. Specimens with a reactive ELISA result are retested in duplicate.<ref name=CDC2001>
{{cite journal
| author=Centers for Disease Control and Prevention. | title=Revised guidelines for HIV counseling, testing, and referral | journal=MMWR Recomm Rep. | year=2001 | pages=1–57 | volume=50 | issue=RR-19 | pmid=11718472
}}</ref> If the result of either duplicate test is reactive, the specimen is reported as repeatedly reactive and undergoes confirmatory testing with a more specific supplemental test (e.g., [[Western blot]] or, less commonly, an [[immunofluorescence assay]] (IFA)). Only specimens that are repeatedly reactive by ELISA and positive by IFA or reactive by Western blot are considered HIV-positive and indicative of HIV infection. Specimens that are repeatedly ELISA-reactive occasionally provide an indeterminate Western blot result, which may be either an incomplete antibody response to HIV in an infected person, or nonspecific reactions in an uninfected person.<ref name=celum>
{{cite journal
| author=Celum CL, Coombs RW, Lafferty W, Inui TS, Louie PH, Gates CA, McCreedy BJ, Egan R, Grove T, Alexander S, et al. | title=Indeterminate human immunodeficiency virus type 1 western blots: seroconversion risk, specificity of supplemental tests, and an algorithm for evaluation | journal=J Infect Dis. | year=1991 | pages=656–664 | volume=164 | issue=4 | pmid=1894929
}}</ref> Although IFA can be used to confirm infection in these ambiguous cases, this assay is not widely used. Generally, a second specimen should be collected more than a month later and retested for persons with indeterminate Western blot results. Although much less commonly available, nucleic acid testing (e.g., viral RNA or proviral DNA amplification method) can also help diagnosis in certain situations.<ref name=CDC2001 /> In addition, a few tested specimens might provide inconclusive results because of a low quantity specimen. In these situations, a second specimen is collected and tested for HIV infection.
==Treatment==
<!-- Note that HIV and AIDS are two different pages, so the link to the AIDS treatment section is not simply redirecting here. -->
:''See also [[Antiretroviral drug]].''
[[Image:Abacavir (Ziagen) 300mg.jpg|right|thumb|100px|''[[Abacavir]]'' - a nucleoside analog reverse transcriptase inhibitors (NARTIs or NRTIs)]]
There is currently no [[HIV vaccine|vaccine]] or cure for HIV or AIDS. The only known method of prevention is avoiding exposure to the virus. However, an antiretroviral treatment, known as [[post-exposure prophylaxis]], is believed to reduce the risk of infection if begun directly after exposure.<ref name=Fan>{{cite book
| author = | year = 2005 | title = '''AIDS : science and society''' | chapter = | chapterurl = | editor = Fan, H., Conner, R. F. and Villarreal, L. P. eds | edition = 4th edition | pages = | publisher = Jones and Bartlett Publishers | location = [[Boston, Massachusetts|Boston, MA]] | id = ISBN 0-7637-0086-X}}</ref> Current treatment for HIV infection consists of [[highly active antiretroviral therapy]], or HAART.<ref name=DhhsHivTreatment>{{
cite web
| author=[[Department of Health and Human Services]] | publisher=
| year=January, 2005
| url=http://www.hab.hrsa.gov/tools/HIVpocketguide05/PktGARTtables.htm
| title=A Pocket Guide to Adult HIV/AIDS Treatment January 2005 edition
| accessdate=2006-01-17
}}</ref> This has been highly beneficial to many HIV-infected individuals since its introduction in 1996, when the protease inhibitor-based HAART initially became available.<ref name=Pallelal>{{
cite journal
| author=Palella, F. J., Delaney, K. M., Moorman, A. C., Loveless, M. O., Fuhrer, J., Satten, G. A., Aschman, D. J. and Holmberg, S. D. | title=Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection | journal=N. Engl. J. Med. | year=1998 | pages=853-860 | volume=338 | issue=13 | pmid=9516219
}}</ref>
Current HAART options are combinations (or "cocktails") consisting of at least three drugs belonging to at least two types, or "classes," of [[antiretroviral]] agents. Typically, these classes are two [[nucleoside analogue reverse transcriptase inhibitor]]s (NARTIs or NRTIs) plus either a [[protease inhibitor (pharmacology)|protease inhibitor]] or a [[non-nucleoside reverse transcriptase inhibitor]] (NNRTI). Because AIDS progression in children is more rapid and less predictable than in adults, particularly in young infants, more aggressive treatment is recommended for children than adults.<ref name=2005dhhsHivChildren>{{
cite web
| author=[[Department of Health and Human Services]] Working Group on Antiretroviral Therapy and Medical Management of HIV-Infected Children
| publisher= | date=[[November 3]], [[2005]]
| url=http://www.aidsinfo.nih.gov/ContentFiles/PediatricGuidelines_PDA.pdf
| title=Guidelines for the Use of Antiretroviral Agents in Pediatric HIV Infection
| format= PDF
| accessdate=2006-01-17
}}</ref> In developed countries where HAART is available, doctors assess their patients thoroughly: measuring the [[viral load]], how fast CD4 declines, and patient readiness. They then decide when to recommend starting treatment.<ref name=2005DhhsHivTreatment>{{
cite web
| author=[[Department of Health and Human Services]] Panel on Clinical Practices for Treatment of HIV Infection
| publisher= | date=[[October 6]], [[2005]]
| url=http://aidsinfo.nih.gov/ContentFiles/AdultandAdolescentGL.pdf
| title=Guidelines for the Use of Antiretroviral Agents in HIV-1-Infected Adults and Adolescents
| format= PDF
| accessdate=2006-01-17
}}</ref>
HAART allows the stabilisation of the patient’s symptoms and viremia, but it neither cures the patient, nor alleviates the symptoms; high levels of HIV-1, often HAART resistant, return once treatment is stopped.<ref name=martinez>{{
cite journal
| author=Martinez-Picado, J., DePasquale, M. P., Kartsonis, N., Hanna, G. J., Wong, J., Finzi, D., Rosenberg, E., Gunthard, H. F., Sutton, L., Savara, A., Petropoulos, C. J., Hellmann, N., Walker, B. D., Richman, D. D., Siliciano, R. and D'Aquila, R. T. | title=Antiretroviral resistance during successful therapy of human immunodeficiency virus type 1 infection | journal=Proc. Natl. Acad. Sci. U. S. A. | year=2000 | pages=10948-10953 | volume=97 | issue=20 | pmid=11005867
}}</ref><ref name=Dybul>{{
cite journal
| author=Dybul, M., Fauci, A. S., Bartlett, J. G., Kaplan, J. E., Pau, A. K.; Panel on Clinical Practices for Treatment of HIV.
| title=Guidelines for using antiretroviral agents among HIV-infected adults and adolescents
| journal=Ann. Intern. Med. | year=2002 | pages=381-433 | volume=137 | issue=5 Pt 2
| pmid=12617573
}}</ref> Moreover, it would take more than a lifetime for HIV infection to be cleared using HAART.<ref name=blankson>{{
cite journal
| author=Blankson, J. N., Persaud, D., Siliciano, R. F. | title=The challenge of viral reservoirs in HIV-1 infection | journal=Annu. Rev. Med. | year=2002 | pages=557-593 | volume=53 | issue= | pmid=11818490
}}</ref> Despite this, many HIV-infected individuals have experienced remarkable improvements in their general health and quality of life, which has led to a large reduction in HIV-associated [[morbidity]] and mortality in the developed world.<ref name=Pallelal>{{
cite journal
| author=Palella, F. J., Delaney, K. M., Moorman, A. C., Loveless, M. O., Fuhrer, J., Satten, G. A., Aschman, D. J. and Holmberg, S. D. | title=Declining morbidity and mortality among patients with advanced human immunodeficiency virus infection | journal=N. Engl. J. Med. | year=1998 | pages=853-860 | volume=338 | issue=13 | pmid=9516219
}}</ref><ref name=Wood>{{
cite journal
| author=Wood, E., Hogg, R. S., Yip, B., Harrigan, P. R., O'Shaughnessy, M. V. and Montaner, J. S.
| title=Is there a baseline CD4 cell count that precludes a survival response to modern antiretroviral therapy?
| journal=AIDS | year=2003 | pages=711-720 | volume=17 | issue=5
| pmid=12646794
}}</ref><ref name=Chene>{{
cite journal
| author=Chene, G., Sterne, J. A., May, M., Costagliola, D., Ledergerber, B., Phillips, A. N., Dabis, F., Lundgren, J., D'Arminio Monforte, A., de Wolf, F., Hogg, R., Reiss, P., Justice, A., Leport, C., Staszewski, S., Gill, J., Fatkenheuer, G., Egger, M. E. and the Antiretroviral Therapy Cohort Collaboration.
| title=Prognostic importance of initial response in HIV-1 infected patients starting potent antiretroviral therapy: analysis of prospective studies
| journal=Lancet | year=2003 | pages=679-686 | volume=362 | issue=9385
| pmid=12957089
}}</ref> One study suggests the average life expectancy of an HIV infected individual is 32 years from the time of infection if treatment is started when the CD4 count is 350/µL.<ref name=schack> A computer based study in 2006, following the 2004 United States treatment guidelines: {{
cite journal
| author=Schackman BR, Gebo KA, Walensky RP, Losina E, Muccio T, Sax PE, Weinstein MC, Seage GR 3rd, Moore RD, Freedberg KA.
| title=The lifetime cost of current HIV care in the United States
| journal=Med Care | year=2006 | pages=990-997 | volume=44 | issue=11
| pmid=17063130
}}</ref> The study predicting this was, however, limited as it did not take into account possible future treatments and the projection has not been confirmed within a clinical cohort setting. In the absence of HAART, progression from HIV infection to AIDS has been observed to occur at a [[median]] of between nine to ten years and the median survival time after developing AIDS is only 9.2 months.<ref name=Morgan2 /> However, HAART sometimes achieves far less than optimal results, in some circumstances being effective in less than fifty percent of patients. This is due to a variety of reasons such as medication intolerance/side effects, prior ineffective antiretroviral therapy and infection with a drug-resistant strain of HIV. However, non-adherence and non-persistence with antiretroviral therapy is the major reason most individuals fail to benefit from HAART.<ref name=becker>{{
cite journal
| author=Becker SL, Dezii CM, Burtcel B, Kawabata H, Hodder S. | title=Young HIV-infected adults are at greater risk for medication nonadherence | journal=MedGenMed. | year=2002 | pages=21 | volume=4| issue=3 | pmid=12466764
}}</ref> The reasons for non-adherence and non-persistence with HAART are varied and overlapping. Major psychosocial issues, such as poor access to medical care, inadequate social supports, psychiatric disease and drug abuse contribute to non-adherence. The complexity of these HAART regimens, whether due to pill number, dosing frequency, meal restrictions or other issues along with side effects that create intentional non-adherence also contribute to this problem.<ref name=Nieuwkerk>{{
cite journal
| author=Nieuwkerk, P., Sprangers, M., Burger, D., Hoetelmans, R. M., Hugen, P. W., Danner, S. A., van Der Ende, M. E., Schneider, M. M., Schrey, G., Meenhorst, P. L., Sprenger, H. G., Kauffmann, R. H., Jambroes, M., Chesney, M. A., de Wolf, F., Lange, J. M. and the ATHENA Project. | title=Limited Patient Adherence to Highly Active Antiretroviral Therapy for HIV-1 Infection in an Observational Cohort Study | journal=Arch. Intern. Med. | year=2001 | pages=1962-1968 | volume=161 | issue=16 | pmid=11525698
}}</ref><ref name=Kleeberger>{{
cite journal
| author=Kleeberger, C., Phair, J., Strathdee, S., Detels, R., Kingsley, L. and Jacobson, L. P. | title=Determinants of Heterogeneous Adherence to HIV-Antiretroviral Therapies in the Multicenter AIDS Cohort Study| journal=J. Acquir. Immune Defic. Syndr. | year=2001 | pages=82-92 | volume=26 | issue=1 | pmid=11176272
}}</ref><ref name=heath>{{
cite journal
| author=Heath, K. V., Singer, J., O'Shaughnessy, M. V., Montaner, J. S. and Hogg, R. S. | title=Intentional Nonadherence Due to Adverse Symptoms Associated With Antiretroviral Therapy | journal=J. Acquir. Immune Defic. Syndr. | year=2002 | pages=211-217 | volume=31 | issue=2 | pmid=12394800
}}</ref> The side effects include [[lipodystrophy]], [[dyslipidemia]], [[insulin resistance]], an increase in [[cardiovascular]] risks and [[birth defect]]s.<ref name=Montessori>{{
cite journal |
author=Montessori, V., Press, N., Harris, M., Akagi, L., Montaner, J. S. |
title=Adverse effects of antiretroviral therapy for HIV infection. |
journal=CMAJ | year=2004 | pages=229-238 | volume=170 | issue=2 | pmid=14734438
}}</ref><ref name=Saitoh>{{
cite journal
| author=Saitoh, A., Hull, A. D., Franklin, P. and Spector, S. A.
| title=Myelomeningocele in an infant with intrauterine exposure to efavirenz
| journal=J. Perinatol. | year=2005 | pages=555-556 | volume=25 | issue=8
| pmid=16047034
}}</ref>
The timing for starting HIV treatment is still debated. There is no question that treatment should be started before the patient's CD4 count falls below 200, and most national guidelines say to start treatment once the CD4 count falls below 350; but there is some evidence from cohort studies that treatment should be started before the CD4 count falls below 350.<ref name="Wang2004">{{
cite journal
| author=Wang C, Vlahov D, Galai N, ''et al.''
| title=Mortality in HIV-seropositive versus seronegative persons in the era of highly active antiretroviral therapy.
| journal=J. Infect. Dis. | year=2004 | volume=190 | pages=1046–54
| pmid=15319852
}}</ref><ref name="Wood">{{
cite journal
| author=Wood E, HoggRS, Harrigan PR, Montaner JS.
| title=When to initial antiretroviral therapy in HIV-1-infected adults: a review for clinicians and patients
| journal=Lancet Infect. Dis.
| year=2005
| volume=5
| pages=407–14
}}</ref> In those countries where CD4 counts are not available, patients with WHO stage III or IV disease<ref name="WHO">{{
cite web
| author=World Health Organisation
| title=WHO case definitions of HIV for surveillance and revised clinical staging and immunological classification
| year=2006
| url=http://www.who.int/hiv/pub/guidelines/WHO%20HIV%20Staging.pdf
| accessdate=2006-12-27
|format=PDF}}</ref> should be offered treatment.
Anti-retroviral drugs are expensive, and the majority of the world's infected individuals do not have access to medications and treatments for HIV and AIDS.<ref name=Ferrantelli>{{
cite journal
| author=Ferrantelli F, Cafaro A, Ensoli B. | title=Nonstructural HIV proteins as targets for prophylactic or therapeutic vaccines | journal=Curr Opin Biotechnol. | year=2004 | pages=543-556 | volume=15 | issue=6
| pmid=15560981
}}</ref> Research to improve current treatments includes decreasing side effects of current drugs, further simplifying drug regimens to improve adherence, and determining the best sequence of regimens to manage drug resistance. Unfortunately, only a vaccine is thought to be able to halt the pandemic. This is because a vaccine would cost less, thus being affordable for developing countries, and would not require daily treatment.<ref name=Ferrantelli/> However, after over 20 years of research, HIV-1 remains a difficult target for a vaccine.<ref name=Ferrantelli/> A region on HIV's surface is a potential target for a vaccine.<ref name="HIV weak spot"> The National Institute of Allergy and Infectious Diseases, February 2007: {{
cite web
| author=BBC News
| title=Scientists expose HIV weak spot
| year=2007
| url=http://news.bbc.co.uk/2/hi/health/6357287.stm
| accessdate=2007-04-20
}}</ref>
Promising new treatments include [[Cre recombinase]]<ref name="Cre recombinase">Researchers at the Heinrich Pette Institute of Experimental Virology and Immunology at Hamburg:{{cite web
| author=Paternity Testing Labs
| title=German scientists “cure” HIV-infected human lymphocytes
| year=2007
| url=http://www.theblogofscience.com/german-scientists-cure-hiv-infected-human-lymphocytes/
| accessdate=2008-04-03
}}</ref> and the enzyme [[Tre recombinase]],<ref name="Tre recombinase"> scientists at the Max Planck Institute for Molecular Cell Biology and Genetics in Dresden: {{
cite web
| author=Terra Daily
| title=Another Potential Cure For HIV Discovered
| year=2007
| url=http://www.terradaily.com/reports/Another_Potential_Cure_For_HIV_Discovered_999.html
| accessdate=2007-06-29
}}</ref> both of which are able to remove HIV from an infected cell. These enzymes promise a treatment in which a patient's [[stem cells]] are extracted, cured, and reinjected to promulgate the enzyme into the body. The carried enzyme then finds and removes the virus.
==Epidemiology==
{{main|AIDS pandemic}}
[[Image:HIV Epidem.png|300px|thumb|right|Estimated prevalence of HIV among young adults (15-49) per country at the end of 2005.]]
UNAIDS and the WHO estimate that AIDS has killed more than 25 million people since it was first recognized in 1981, making it one of the most destructive pandemics in recorded history. Despite recent improved access to antiretroviral treatment and care in many regions of the world, the AIDS pandemic claimed an estimated 2.8 million (between 2.4 and 3.3 million) lives in 2005 of which more than half a million (570,000) were children.<ref name=UNAIDS2006 />
Globally, between 33.4 and 46 million people currently live with HIV.<ref name=UNAIDS2006 /> In 2005, between 3.4 and 6.2 million people were newly infected and between 2.4 and 3.3 million people with AIDS died, an increase from 2004 and the highest number since 1981.
[[AIDS pandemic#Sub-Saharan Africa|Sub-Saharan Africa]] remains by far the worst-affected region, with an estimated 21.6 to 27.4 million people currently living with HIV. Two million [1.5–3.0 million] of them are children younger than 15 years of age. More than 64% of all people living with HIV are in sub-Saharan Africa, as are more than three quarters of all women living with HIV. In 2005, there were 12.0 million [10.6–13.6 million] AIDS orphans living in sub-Saharan Africa 2005.<ref name=UNAIDS2006 /> [[AIDS pandemic#South and South-East Asia|South & South East Asia]] are second-worst affected with 15% of the total. AIDS accounts for the deaths of 500,000 children in this region. [[South Africa]] has the largest number of HIV patients in the world followed by [[Nigeria]].<ref>{{cite news |first=Donald |last=McNeil, Jr. |authorlink= |coauthors= |title= U.N. Agency to Say It Overstated Extent of H.I.V. Cases by Millions |url=http://query.nytimes.com/gst/fullpage.html?res=9C01EEDF103BF933A15752C1A9619C8B63&n |work= |publisher=''The New York Times'' |date=[[November 20]], [[2007]] |accessdate=2008-01-16 }}</ref> India has an estimated 2.5 million infections (0.23% of population), making India the country with the third largest population of HIV patients. In the 35 African nations with the highest prevalence, average [[life expectancy]] is 48.3 years—6.5 years less than it would be without the disease.<ref name=UNAIDS2001>{{
cite web
| author=UNAIDS | publisher= | year=2001
| url=http://data.unaids.org/Publications/External-Documents/GAS26-rt3_en.pdf
| title=Special Session of the General Assembly on HIV/AIDS Round table 3 Socio-economic impact of the epidemic and the strengthening of national capacities to combat HIV/AIDS
| accessdate=2006-06-15
| format= [[Portable Document Format|PDF format]]
}}</ref>
The latest evaluation report of the [[World Bank Group|World Bank's]] Operations Evaluation Department assesses the development effectiveness of the World Bank's country-level HIV/AIDS assistance defined as policy dialogue, analytic work, and lending with the explicit objective of reducing the scope or impact of the AIDS epidemic.<ref name=Worldbank>{{
cite web
| author=[[World Bank Group|World Bank]] | publisher= | year=2005
| url=http://www.worldbank.org/oed/aids/main_report.html
| title=Evaluating the World Bank's Assistance for Fighting the HIV/AIDS Epidemic
| accessdate=2006-01-17
}}</ref> This is the first comprehensive evaluation of the World Bank's HIV/AIDS support to countries, from the beginning of the epidemic through mid-2004. Because the Bank aims to assist in implementation of national government programmes, their experience provides important insights on how national AIDS programmes can be made more effective.
The development of [[HAART]] as effective therapy for HIV infection and AIDS has substantially reduced the death rate from this disease in those areas where these drugs are widely available. This has created the misperception that the disease has vanished. In fact, as the life expectancy of persons with AIDS has increased in countries where HAART is widely used, the number of persons living with AIDS has increased substantially. In the United States, the number of persons with AIDS increased from about 35,000 in 1988 to over 220,000 in 1996 and 312,000 in 2002<ref name=CDC2002>{{
cite journal |
author=[[Centers for Disease Control and Prevention]] |
title=Cases of HIV Infection and AIDS in the United States, 2002 |
journal=HIV/AIDS Surveillance Report |year = 2002| url=http://www.cdc.gov/hiv/topics/surveillance/resources/reports/2002report/table1.htm
}}</ref>
In Africa, the number of MTCT and the prevalence of AIDS is beginning to reverse decades of steady progress in child survival. Countries such as Uganda are attempting to curb the MTCT epidemic by offering VCT (voluntary counselling and testing), PMTCT (prevention of mother-to-child transmission) and ANC (ante-natal care) services, which include the distribution of antiretroviral therapy.
==History==
===Origin===
{{Main|AIDS origin}}
HIV is thought to have originated in non-human [[primate]]s in sub-Saharan Africa and transferred to humans during the 20th century. The epidemic officially began on [[5 June]] [[1981]].<ref name=MMWR2>{{cite web |url=http://www.cdc.gov/MMWR/preview/mmwrhtml/00043494.htm |title=Pneumocystis Pneumonia -- Los Angeles |format= |work= |accessdate=2008-05-05}}</ref>
Two species of HIV infect humans: HIV-1 and HIV-2. Both species of the virus are believed to have originated in West-Central Africa and jumped species ([[zoonosis]]) from a non-human primate to humans.
HIV-1 is thought to have originated in southern [[Cameroon]] after jumping from wild [[chimpanzee]]s (''Pan troglodytes troglodytes'') to humans during the twentieth century.<ref name=Gao>{{cite journal
| author=Gao, F., Bailes, E., Robertson, D. L., Chen, Y., Rodenburg, C. M., Michael, S. F., Cummins, L. B., Arthur, L. O., Peeters, M., Shaw, G. M., Sharp, P. M., and Hahn, B. H.
| title=Origin of HIV-1 in the Chimpanzee Pan troglodytes troglodytes
| journal=Nature
| year=1999
| pages=436–441
| volume=397
| issue=6718
| pmid=9989410
| doi=10.1038/17130
}}</ref><ref name=Keele>{{cite journal
| author=Keele, B. F., van Heuverswyn, F., Li, Y. Y., Bailes, E., Takehisa, J., Santiago, M. L., Bibollet-Ruche, F., Chen, Y., Wain, L. V., Liegois, F., Loul, S., Mpoudi Ngole, E., Bienvenue, Y., Delaporte, E., Brookfield, J. F. Y., Sharp, P. M., Shaw, G. M., Peeters, M., and Hahn, B. H.
| title=Chimpanzee Reservoirs of Pandemic and Nonpandemic HIV-1
| journal=Science | year=2006 | pages= 523| volume=Online [[2006-05-25]] | issue=
| url= http://www.sciencemag.org/cgi/content/abstract/1126531
| doi = 10.1126/science.1126531
| format=
| pmid=16728595
}}
</ref> It evolved from a [[Simian Immunodeficiency Virus]] (SIV<sub><small>cpz</small></sub>)<ref>[http://www.nature.com/nature/journal/v397/n6718/abs/397436a0_fs.html http://www.nature.com/nature/journal/v397/n6718/abs/397436a0_fs.html]</ref>
HIV-2, on the other hand, may have originated from the [[Sooty Mangabey]] (''Cercocebus atys''), an Old World monkey of [[Guinea-Bissau]], [[Gabon]], and [[Cameroon]].<ref name=Reeves>{{cite journal
| author=Reeves, J. D. and Doms, R. W
| title=Human Immunodeficiency Virus Type 2
| journal=J. Gen. Virol. | year=2002 | pages=1253–1265 | volume=83 | issue=Pt 6
| pmid= 12029140
}}</ref>
===Early history===
:''See [[AIDS origin#History of known cases and spread|History of known cases and spread]] for early cases of HIV / AIDS''
==AIDS denialism==
{{main|AIDS denialism}}
Individuals, including several scientists who are not recognized experts on HIV, question the connection between HIV and AIDS,<ref name=Duesberg>{{cite journal
| author=Duesberg, P. H.
| title=HIV is not the cause of AIDS
| journal=Science | year=1988 | pages=514, 517 | volume=241 | issue=4865
| pmid=3399880 | doi=10.1126/science.3399880
}}</ref> the existence of HIV itself,<ref name=Papadopulos>{{
cite journal
| author=Papadopulos-Eleopulos, E., Turner, V. F., Papadimitriou, J., Page, B., Causer, D., Alfonso, H., Mhlongo, S., Miller, T., Maniotis, A. and Fiala, C.
| title=A critique of the Montagnier evidence for the HIV/AIDS hypothesis
| journal=Med Hypotheses | year=2004 | pages=597–601 | volume=63 | issue=4
| pmid=15325002
}}</ref> or the validity of current testing and treatment methods. These claims have been examined and rejected as having no validity,<ref name=consensus> For evidence that HIV is the cause of AIDS, see (for example):
*{{cite journal |author= ,|title=The Durban Declaration |journal=Nature |volume=406 |issue=6791 |pages=15–6 |year=2000 |pmid=10894520 |doi=10.1038/35017662}} - full text [http://www.nature.com/nature/journal/v406/n6791/full/406015a0.html here].
*{{cite journal
| author=Cohen, J.
| title=The Controversy over HIV and AIDS
| journal=Science | year=1994 | pages=1642–1649 | volume=266 | issue=5191
| url=http://www.sciencemag.org/feature/data/cohen/266-5191-1642a.pdf
| format = PDF}}
*{{cite web
| author=Various
| publisher=[[National Institute of Allergy and Infectious Diseases]] | year=
| url=http://www3.niaid.nih.gov/news/focuson/hiv/resources/
| title=Focus on the HIV-AIDS Connection: Resource links
| accessdate = 2006-09-07
}}
*{{cite journal |author=O'Brien SJ, Goedert JJ |title=HIV causes AIDS: Koch's postulates fulfilled |journal=Curr. Opin. Immunol. |volume=8 |issue=5 |pages=613–8 |year=1996 |pmid=8902385 |doi=}}
*{{cite journal |author=Galéa P, Chermann JC |title=HIV as the cause of AIDS and associated diseases |journal=Genetica |volume=104 |issue=2 |pages=133–42 |year=1998 |pmid=10220906 |doi=}}</ref> although they have had a political impact, particularly in [[South Africa]], where governmental acceptance of AIDS denialism has been blamed for an ineffective response to that country's AIDS epidemic.<ref>{{cite journal |author=Watson J |title=Scientists, activists sue South Africa's AIDS 'denialists' |journal=Nat. Med. |volume=12 |issue=1 |pages=6 |year=2006 |pmid=16397537 |doi=10.1038/nm0106-6a}}</ref><ref>{{cite journal |author=Baleta A |title=S Africa's AIDS activists accuse government of murder |journal=Lancet |volume=361 |issue=9363 |pages=1105 |year=2003 |pmid=12672319 |doi=10.1016/S0140-6736(03)12909-1}}</ref><ref>{{cite journal |author=Cohen J |title=South Africa's new enemy |journal=Science |volume=288 |issue=5474 |pages=2168–70 |year=2000 |pmid=10896606 |doi=10.1126/science.288.5474.2168}}</ref>
==Notes and references==
{{reflist|2}}
==See also==
*[[HIV Superinfection]]
==External links==
{{Sisterlinks|b=Sexual Health/Sexually Transmitted Diseases#HIV|commons=Category:HIV|n=Category:AIDS}}
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* {{Dmoz|Health/Conditions_and_Diseases/Immune_Disorders/Immune_Deficiency/AIDS/|HIV/AIDS}}
* {{cite web
|url=http://aidsinfo.nih.gov/
|title=AIDSinfo - HIV/AIDS Treatment Information
|accessdate=2008-03-21
|publisher=US Department of Health and Human Services
|format=
|work=
}}
* {{cite web
|url=http://www.unaids.org/en/
|title=UNAIDS: The Joint United Nations Programme on HIV/AIDS
|accessdate=2008-03-21
|publisher=UNAIDS
|format=
|work=
}}
* {{cite web
|url=http://www.AIDS.gov
|title=AIDS.gov: Portal to all Federal HIV/AIDS information
|accessdate=2008-05-20
|publisher=AIDS.gov
|format=
|work=
}}
{{AIDS}}
{{STD/STI}}
[[Category:HIV/AIDS]]
[[Category:Retroviruses]]
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