Human Immunodeficiency Viruses*

Bernard M. Branson; S. Michele Owen

doi:10.1128/9781555817381.ch82

Chapter 82 : Human Immunodeficiency Viruses*

Authors: Bernard M. Branson, S. Michele Owen

Content Type: Reference

Publication Year: 2015

Category: Clinical Microbiology

Book DOI: 10.1128/9781555817381

Chapter DOI: 10.1128/9781555817381.ch82

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:

Human Immunodeficiency Viruses*, Page 1 of 2

< Previous page | Next page > /docserver/preview/fulltext/10.1128/9781555817381/9781555817381.ch82-1.gif /docserver/preview/fulltext/10.1128/9781555817381/9781555817381.ch82-2.gif

Abstract:

HIV is the etiologic agent of AIDS. HIV virions are enveloped positive-strand RNA retroviruses and are classified based on their degree of phylogenetic relatedness into types (HIV-1 and HIV-2), groups, subtypes, sub-subtypes, and recombinant forms. Approximately 75 million people worldwide have become infected with HIV. In the United States, the CDC estimates that 1.1 million persons are living with HIV. Previously, diagnosis was most often made by detection of antibody against HIV. HIV infection can now be expeditiously and more accurately identified during its highly infectious acute phase using a diagnostic algorithm. The algorithm employs an initial HIV-1/2 antibody/p24 antigen combination immunoassay followed by an antibody assay that differentiates HIV-1 from HIV-2 and, if necessary, a nucleic acid test to identify HIV RNA before antibodies develop. Chemiluminescent immunoassays that allow rapid processing on random-access analyzers are now available. Single-use rapid point-of-care antibody and antibody/p24 antigen combination assays that can be used with finger-stick whole blood or with oral fluids facilitate testing outside traditional laboratories. Qualitative DNA and RNA assays can diagnose acute HIV infection before seroconversion and also in infants born to HIV-infected mothers, in whom antibody tests are unreliable because of maternal antibody reactivity. Effective antiretroviral therapy delays progression of HIV disease, improves survival, and reduces infectiousness. Genotypic and phenotypic resistance assays guide the selection of antiretroviral regimens, and quantitative viral load assays that can detect fewer than 50 viral copies per ml are useful for prognosis and for monitoring response to therapy.

Citation: Branson B, Owen S. 2015. Human Immunodeficiency Viruses*, p 1436-1457. In Jorgensen J, Pfaller M, Carroll K, Funke G, Landry M, Richter S, Warnock D (ed), Manual of Clinical Microbiology, Eleventh Edition. ASM Press, Washington, DC. doi: 10.1128/9781555817381.ch82

Highlighted Text: Show | Hide

Full text loading...

Figures

Human Immunodeficiency Viruses*

[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817381.mcm11.ch82-1,webId=/content/author/10.1128/9781555817381.mcm11.ch82-1,properties={foaf_givenname=Bernard M., foaf_name=Bernard M. Branson, foaf_surname=Branson}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555817381.mcm11.ch82-2,webId=/content/author/10.1128/9781555817381.mcm11.ch82-2,properties={foaf_givenname=S. Michele, foaf_name=S. Michele Owen, foaf_surname=Owen}]]

/content/10.1128/9781555817381.mcm11.ch82.ch82.fig001

FIGURE 1

Schematic representation of a mature HIV virion showing the localization of viral proteins. doi:10.1128/9781555817381.ch82.f1

10.1128/9781555817381/9781555817381.ch82.f1_thmb.gif

10.1128/9781555817381/9781555817381.ch82.f1.gif

FIGURE 1

Schematic representation of a mature HIV virion showing the localization of viral proteins. doi:10.1128/9781555817381.ch82.f1

/content/10.1128/9781555817381.mcm11.ch82.ch82.fig002

FIGURE 2

Time course of appearance of laboratory markers for HIV-1 infection. Units for vertical axis not noted because their magnitude differs for RNA, p24 antigen, and antibody. Adapted data from reference 90 and updated with data from references 29 , 97 , and 107 . doi:10.1128/9781555817381.ch82.f2

10.1128/9781555817381/9781555817381.ch82.f2_thmb.gif

10.1128/9781555817381/9781555817381.ch82.f2.gif

FIGURE 2

/content/10.1128/9781555817381.mcm11.ch82.ch82.fig003

FIGURE 3

Diagnostic HIV testing algorithm showing sequence of follow-up testing. doi:10.1128/9781555817381.ch82.f3

10.1128/9781555817381/9781555817381.ch82.f3_thmb.gif

10.1128/9781555817381/9781555817381.ch82.f3.gif

FIGURE 3

Diagnostic HIV testing algorithm showing sequence of follow-up testing. doi:10.1128/9781555817381.ch82.f3

References

/content/book/10.1128/9781555817381.mcm11.ch82

1. Masur H,, Michelis MA,, Greene JB,, Onorato I,, Stouwe RA,, Holzman RS,, Wormser G,, Brettman L,, Lange M,, Murray HW,, Cunningham-Rundles S. 1981. An outbreak of community-acquired Pneumocystis carinii pneumonia: initial manifestation of cellular immune dysfunction. N Engl J Med 305: 1431– 1438.

2. Barre-Sinoussi F,, Chermann JC,, Rey F,, Nugeyre MT,, Chamaret S,, Gruest J,, Dauguet C,, Axler-Blin C,, Vezinet-Brun F,, Rouzioux C,, Rozenbaum W,, Montagnier L. 1983. Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science 220: 868– 871.

3. Gallo RC,, Salahuddin SZ,, Popovic M,, Shearer GM,, Kaplan M,, Haynes BF,, Palker TJ,, Redfield R,, Oleske J,, Safai B,, White G,, Foster P,, Markham PD. 1984. Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS. Science 224: 500– 503.

4. Levy JA,, Hoffman AD,, Kramer SM,, Landis JA,, Shimabukuro JM,, Oshiro LS. 1984. Isolation of lymphocytopathic retroviruses from San Francisco patients with AIDS. Science 225: 840– 842.

5. Coffin J,, Haase A,, Levy JA,, Montagnier L,, Oroszlan S,, Teich N,, Temin H,, Toyoshima K,, Varmus H,, Vogt P, , et al. 1986. What to call the AIDS virus? Nature 321: 10.

6. Clavel F Gu,, Tard D,, Brun V,, Zinet F,, Chamaret S,, Rey MA,, Santos-Ferreira MO,, Laurent AG,, Dauguet C,, Katlama C,, Rouzioux C,, Klatzmann D,, Champalimaud JL,, Montagnier L. 1986. Isolation of a new human retrovirus from west African patients with AIDS. Science 233: 343– 346.

7. Hahn BH,, Shaw GM,, De Cock KM,, Sharp PM. 2000. AIDS as a zoonosis: scientific and public health implications. Science 287: 607– 614.

8. Sharp PM,, Bailes E,, Robertson DL,, Gao F,, Hahn BH. 1999. Origins and evolution of AIDS viruses. Biol Bull 196: 338– 342.

9. Zhu T,, Korber BT,, Nahmias AJ,, Hooper E,, Sharp PM,, Ho DD. 1998. An African HIV-1 sequence from 1959 and implications for the origin of the epidemic. Nature 391: 594– 597.

10. McCutchan FE. 2006. Global epidemiology of HIV. J Med Virol 78( suppl 1): S7– S12.

11. McCutchan FE. 2000. Understanding the genetic diversity of HIV-1. AIDS 14: S31– S34.

12. Plantier JC,, Leoz M,, Dickerson JE,, De Oliveira F,, Cordonnier F,, Lemee V,, Damond F,, Robertson DL,, Simon F. 2009. A new human immunodeficiency virus derived from gorillas. Nat Med 15: 871– 872.

13. Robertson DL,, Anderson JP,, Bradac JA,, Carr JK,, Foley B,, Funkhouser RK,, Gao F,, Hahn BH,, Kalish ML,, Kuiken C,, Learn GH,, Leitner T,, McCutchan F,, Osmanov S,, Peeters M,, Pieniazek D,, Salminen M,, Sharp PM,, Wolinsky S,, Korber B. 2000. HIV-1 nomenclature proposal. Science 288: 55– 56.

14. Perelson AS,, Neumann AU,, Markowitz M,, Leonard JM,, Ho DD. 1996. HIV-1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation time. Science 271: 1582– 1586.

15. Feng Y,, Broder CC,, Kennedy PE,, Berger EA. 1996. HIV-1 entry cofactor: functional cDNA cloning of a seven-transmembrane, G protein-coupled receptor. Science 272: 872– 877.

16. Choe H,, Farzan M,, Sun Y,, Sullivan N,, Rollins B,, Ponath PD,, Wu L,, Mackay CR,, Larosa G,, Newman W,, Gerard N,, Gerard C,, Sodroski J. 1996. The beta-chemokine receptors CCR3 and CCR5 facilitate infection by primary HIV-1 isolates. Cell 85: 1135– 1148.

17. Campbell-Yesufu OT,, Gandhi RT. 2011. Update on human immunodeficiency virus (HIV)-2 infection. Clin Infect Dis 52: 780– 787.

18. UNAIDS. 23 September 2013, posting date. 2013 Global Fact Sheet. http://www.unaids.org/sites/default/files/en/media/unaids/contentassets/documents/epidemiology/2013/gr2013/20130923_FactSheet_Global_en.pdf

19. Centers for Disease Control and Prevention. 2012. Monitoring selected national HIV prevention and care objectives by using HIV surveillance data—United States and 6 U.S. dependent areas—2010. HIV Surveill Suppl Rep 17, Atlanta, Georgia.

20. Centers for Disease Control and Prevention. 2012. Estimated HIV incidence in the United States, 2007–2010. HIV Surveill Suppl Rep 17:1–26, Atlanta, Georgia.

21. Royce RA,, Sena A,, Cates W Jr.,, Cohen MS. 1997. Sexual transmission of HIV. N Engl J Med 336: 1072– 1078.

22. Bell DM. 1997. Occupational risk of human immunodeficiency virus infection in healthcare workers: an overview. Am J Med 102: 9– 15.

23. Cardo DM,, Culver DH,, Ciesielski CA,, Srivastava PU,, Marcus R,, Abiteboul D,, Heptonstall J,, Ippolito G,, Lot F,, McKibben PS,, Bell DM. 1997. A case-control study of HIV seroconversion in health care workers after percutaneous exposure. Centers for Disease Control and Prevention Needlestick Surveillance Group. N Engl J Med 337: 1485– 1490.

24. Kuhar DT,, Henderson DK,, Struble KA,, Heneine W,, Thomas V,, Cheever LW,, Gomaa A,, Panlilio AL. 2013. Updated US Public Health Service guidelines for the management of occupational exposures to human immunodeficiency virus and recommendations for postexposure prophylaxis. Infect Control Hosp Epidemiol 34: 875– 892.

25. Montano M,, Russell M,, Gilbert P,, Thior I,, Lockman S,, Shapiro R,, Chang SY,, Lee TH,, Essex M. 2003. Comparative prediction of perinatal human immunodeficiency virus type 1 transmission, using multiple virus load markers. J Infect Dis 188: 406– 413.

26. Cooper ER,, Chaurat M,, Mofenson L. 2002. Combination antiretroviral strategies for the treatment of pregnant HIV-1-infected women and prevention of perinatal HIV-1 transmission. J Acquir Immune Defic Syndr 29: 484– 494.

27. Keele BF,, Giorgi EE,, Salazar-Gonzalez JF,, Decker JM,, Pham KT,, Salazar MG,, Sun C,, Grayson T,, Wang S,, Li H,, Wei X,, Jiang C,, Kirchherr JL,, Gao F,, Anderson JA,, Ping LH,, Swanstrom R,, Tomaras GD,, Blattner WA,, Goepfert PA,, Kilby JM,, Saag MS,, Delwart EL,, Busch MP,, Cohen MS,, Montefiori DC,, Haynes BF,, Gaschen B,, Athreya GS,, Lee HY,, Wood N,, Seoighe C,, Perelson AS,, Bhattacharya T,, Korber BT,, Hahn BH,, Shaw GM. 2008. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A 105: 7552– 7557.

28. Lee HY,, Giorgi EE,, Keele BF,, Gaschen B,, Athreya GS,, Salazar-Gonzalez JF,, Pham KT,, Goepfert PA,, Kilby JM,, Saag MS,, Delwart EL,, Busch MP,, Hahn BH,, Shaw GM,, Korber BT,, Bhattacharya T,, Perelson AS. 2009. Modeling sequence evolution in acute HIV-1 infection. J Theor Biol 261: 341– 360.

29. Fiebig EW,, Wright DJ,, Rawal BD,, Garrett PE,, Schumacher RT,, Peddada L,, Heldebrant C,, Smith R,, Conrad A,, Kleinman SH,, Busch MP. 2003. Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS 17: 1871– 1879.

30. Daar EC,, Little S,, Pitt J,, Santangelo J,, Ho P,, Harawa N,, Kerndt P,, Giorgi JV,, Bai J,, Gaut P,, Richman DD,, Mandel S,, Nichols S. 2001. Diagnosis of primary HIV-1 infection. Annals of Internal Medicine 134: 25– 29.

31. Daar ES,, Pilcher CD,, Hecht FM. 2008. Clinical presentation and diagnosis of primary HIV-1 infection. Current opinion in HIV and AIDS 3: 10– 15.

32. Hecht FM,, Busch MP,, Rawal B,, Webb M,, Rosenberg E,, Swanson M,, Chesney M,, Anderson J,, Kahn JO. 2002. Use of laboratory tests and clinical symptoms for identification of primary HIV infection. AIDS 16: 1119– 1129.

33. Kahn JO,, Walker BD. 1998. Acute human immunodeficiency virus type 1 infection. New England Journal of Medicine 339: 33– 39.

34. Mellors JW,, Munoz A,, Giorgi JV,, Margolick JB,, Tassoni CJ,, Gupta P,, Kingsley LA,, Todd JA,, Saah AJ,, Detels R,, Phair JP,, Rinaldo CR. 1997. Plasma viral load and CD4+ lymphocytes as prognostic markers of HIV-1 infection. Annals of Internal Medicine 126: 946– 954.

35. Mellors JW,, Rinaldo CR,, Gupta P,, White RM,, Todd JA,, Kingsley LA. 1996. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272: 1167– 1170.

36. Pantaleo G,, Graziosi C,, Demarest JF,, Butini L,, Montroni M,, Fox CH,, Orenstein JM,, Kotler DP,, Fauci AS. 1993. HIV infection is active and progressive in lymphoid tissue during the clinically latent stage of disease. Nature 362: 355– 358.

37. Okulicz JF,, Marconi VC,, Landrum ML,, Wegner S,, Weintrob A,, Ganesan A,, Hale B,, Crum-Cianflone N,, Delmar J,, Barthel V,, Quinnan G,, Agan BK,, Dolan MJ. 2009. Clinical outcomes of elite controllers, viremic controllers, and long-term nonprogressors in the US Department of Defense HIV natural history study. J Infect Dis 200: 1714– 1723.

38. Ho DD,, Neumann AU,, Perelson AS,, Chen W,, Leonard JM,, Markowitz M. 1995. Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection. Nature 373: 123– 126.

39. Siliciano JD,, Kajdas J,, Finzi D,, Quinn TC,, Chadwick K,, Margolick JB,, Kovacs C,, Gange SJ,, Siliciano RF. 2003. Long-term follow-up studies confirm the stability of the latent reservoir for HIV-1 in resting CD4+ T cells. Nat Med 9: 727– 728.

40. Clifford DB,, Ances BM. 2013. HIV-associated neurocognitive disorder. Lancet Infect Dis 13: 976– 986.

41. Haynes BF,, Liao HX,, Tomaras GD. 2010. Is developing an HIV-1 vaccine possible? Current opinion in HIV and AIDS 5: 362– 367.

42. Taylor BS,, Sobieszczyk ME,, McCutchan FE,, Hammer SM. 2008. The challenge of HIV-1 subtype diversity. N Engl J Med 358: 1590– 1602.

43. Griffith BP,, Rigsby MO,, Garner RB,, Gordon MM,, Chacko TM. 1997. Comparison of the Amplicor HIV-1 monitor test and the nucleic acid sequence-based amplification assay for quantitation of human immunodeficiency virus RNA in plasma, serum, and plasma subjected to freeze-thaw cycles. J Clin Microbiol 35: 3288– 3291.

44. Griffith BP,, Mayo DR. 2006. Increased levels of HIV RNA detected in samples with viral loads close to the detection limit collected in Plasma Preparation Tubes (PPT). J Clin Virol 35: 197– 200.

45. Salimnia H,, Moore EC,, Crane LR,, Macarthur RD,, Fairfax MR. 2005. Discordance between viral loads determined by Roche COBAS AMPLICOR human immunodeficiency virus type 1 monitor (version 1.5) Standard and ultrasensitive assays caused by freezing patient plasma in centrifuged becton-dickinson vacutainer brand plasma preparation tubes. J Clin Microbiol 43: 4635– 4639.

46. Ginocchio CC,, Wang XP,, Kaplan MH,, Mulligan G,, Witt D,, Romano JW,, Cronin M,, Carroll R. 1997. Effects of specimen collection, processing, and storage conditions on stability of human immunodeficiency virus type 1 RNA levels in plasma. J Clin Microbiol 35: 2886– 2893.

47. Lew J,, Reichelderfer P,, Fowler M,, Bremer J,, Carrol R,, Cassol S,, Chernoff D,, Coombs R,, Cronin M,, Dickover R,, Fiscus S,, Herman S,, Jackson B,, Kornegay J,, Kovacs A,, McIntosh K,, Meyer W,, Michael N,, Mofenson L,, Moye J,, Quinn T,, Robb M,, Vahey M,, Weiser B,, Yeghiazarian T. 1998. Determinations of levels of human immunodeficiency virus type 1 RNA in plasma: reassessment of parameters affecting assay outcome. TUBE Meeting Workshop Attendees. Technology Utilization for HIV-1 Blood Evaluation and Standardization in Pediatrics. J Clin Microbiol 36: 1471– 1479.

48. Stramer SL,, Glynn SA,, Kleinman SH,, Strong DM,, Caglioti S,, Wright DJ,, Dodd RY,, Busch MP. 2004. Detection of HIV-1 and HCV infections among antibody-negative blood donors by nucleic acid-amplification testing. New England Journal of Medicine 351: 760– 768.

49. Fransen K,, Mertens G,, Stynen D,, Goris A,, Nys P,, Nkengasong J,, Heyndrickx L,, Janssens W,, Van Der Groen G. 1997. Evaluation of a newly developed HIV antigen test. J Med Virol 53: 31– 35.

50. Goudsmit J,, De Wolf F,, Paul DA,, Epstein LG,, Lange JM,, Krone WJ,, Speelman H,, Wolters EC,, Van Der Noordaa J,, Oleske JM, Et Al. 1986. Expression of human immunodeficiency virus antigen (HIV-Ag) in serum and cerebrospinal fluid during acute and chronic infection. Lancet 2: 177– 180.

51. Bollinger RC,, Kline RL,, Francis HL,, Moss MW,, Bartlett JG,, Quinn TC. 1992. Acid dissociation increases the sensitivity of p24 antigen detection for the evaluation of antiviral therapy and disease progression in asymptomatic human immunodeficiency virus infected persons. J Infect Dis 165: 913– 916.

52. Schupbach J,, Tomasik Z,, Knuchel M,, Opravil M,, Gunthard HF,, Nadal D,, Boni J,, Swiss HIVCS,, Swiss HIVMCCS. 2006. Optimized virus disruption improves detection of HIV-1 p24 in particles and uncovers a p24 reactivity in patients with undetectable HIV-1 RNA under long-term HAART. J Med Virol 78: 1003– 1010.

53. Pokriefka RA,, Manzor O,, Markowitz NP,, Saravolatz LD,, Kvale P,, Donovan RM. 1993. Increased detection of human immunodeficiency virus antigenemia after dissociation of immune complexes at low pH. J Clin Microbiol 31: 1656– 1658.

54. Nadal D,, Boni J,, Kind C,, Varnier OE,, Steiner F,, Tomasik Z,, Schupbach J. 1999. Prospective evaluation of amplification-boosted ELISA for heat-denatured p24 antigen for diagnosis and monitoring of pediatric human immunodeficiency virus type 1 infection. J Infect Dis 180: 1089– 1095.

55. Pascual A,, Cachafeiro A,, Funk ML,, Fiscus SA. 2002. Comparison of an assay using signal amplification of the heat-dissociated p24 antigen with the Roche Monitor human immunodeficiency virus RNA assay. J Clin Microbiol 40: 2472– 2475.

56. Schupbach J. 2002. Measurement of HIV-1 p24 antigen by signal-amplification-boosted ELISA of heat-denatured plasma is a simple and inexpensive alternative to tests for viral RNA. AIDS Rev 4: 83– 92.

57. Respess RA,, Cachafeiro A,, Withum D,, Fiscus SA,, Newman D,, Branson B,, Varnier OE,, Lewis K,, Dondero TJ. 2005. Evaluation of an ultrasensitive p24 antigen assay as a potential alternative to human immunodeficiency virus type 1 RNA viral load assay in resource-limited settings. J Clin Microbiol 43: 506– 508.

58. Cachafeiro A,, Sherman GG,, Sohn AH,, Beck-Sague C,, Fiscus SA. 2009. Diagnosis of human immunodeficiency virus type 1 infection in infants by use of dried blood spots and an ultrasensitive p24 antigen assay. J Clin Microbiol 47: 459– 462.

59. Sherman GG,, Stevens G,, Stevens WS. 2004. Affordable diagnosis of human immunodeficiency virus infection in infants by p24 antigen detection. Pediatr Infect Dis J 23: 173– 176.

60. Fiscus SA,, McMillion T,, Nelson JA,, Miller WC. 2013. Validation of the Gen-Probe Aptima qualitative HIV-1 RNA assay for diagnosis of human immunodeficiency virus infection in infants. J Clin Microbiol 51: 4137– 4140.

61. Dunn DT,, Brandt CD,, Krivine A,, Cassol SA,, Roques P,, Borkowsky W,, De Rossi A,, Denamur E,, Ehrnst A,, Loveday C. 1995. The sensitivity of HIV-1 DNA polymerase chain reaction in the neonatal period and the relative contributions of intra-uterine and intra-partum transmission. AIDS 9: 7– 11.

62. Yapo V,, D’Aquin TT,, Desmonde S,, Amani-Bosse C,, Oga M,, Lenaud S,, Menan H,, Timite-Konan M,, Leroy V,, Rouzioux C. 2013. Evaluation of dried blood spot diagnosis using HIV1-DNA and HIV1-RNA Biocentric assays in infants in Abidjan, Cote d’Ivoire. The Pedi-Test DBS ANRS 12183 Study. J Virol Meth 193: 439– 445.

63. Kline NE,, Schwarzwald H,, Kline MW. 2002. False negative DNA polymerase chain reaction in an infant with subtype C human immunodeficiency virus 1 infection. Pediatr Infect Dis J 21: 885– 886.

64. Selik RM,, Mokotoff ED,, Branson B,, Owen SM,, Whitmore S,, Hall IH. 2014. Revised surveillance case definition for HIV infection—United States, 2014. MMWR Recommend Rep 63( No. RR-3) : 1– 10.

65. O’Brien WA,, Hartigan PM,, Martin D,, Esinhart J,, Hill A,, Benoit S,, Rubin M,, Simberkoff MS,, Hamilton JD. 1996. Changes in plasma HIV-1 RNA and CD4+ lymphocyte counts and the risk of progression to AIDS. Veterans Affairs Cooperative Study Group on AIDS. N Engl J Med 334: 426– 431.

66. Novitsky V,, Essex M. 2012. Using HIV viral load to guide treatment-for-prevention interventions. Current opinion in HIV and AIDS 7: 117– 124.

67. Swanson P,, Holzmayer V,, Huang S,, Hay P,, Adebiyi A,, Rice P,, Abravaya K,, Thamm S,, Devare SG,, Hackett J Jr. 2006. Performance of the automated Abbott RealTime HIV-1 assay on a genetically diverse panel of specimens from London: comparison to VERSANT HIV-1 RNA 3.0, AMPLICOR HIV-1 MONITOR v1.5, and LCx HIV RNA Quantitative assays. J Virol Meth 137: 184– 192.

68. Swanson P,, Huang S,, Holzmayer V,, Bodelle P,, Yamaguchi J,, Brennan C,, Badaro R,, Brites C,, Abravaya K,, Devare SG,, Hackett J Jr. 2006. Performance of the automated Abbott RealTime HIV-1 assay on a genetically diverse panel of specimens from Brazil. J Virol Meth 134: 237– 243.

69. Gueudin M,, Plantier JC,, Lemee V,, Schmitt MP,, Chartier L,, Bourlet T,, Ruffault A,, Damond F,, Vray M,, Simon F. 2007. Evaluation of the Roche Cobas TaqMan and Abbott RealTime extraction-quantification systems for HIV-1 subtypes. J Acquir Immune Defic Syndr 44: 500– 505.

70. Schumacher W,, Frick E,, Kauselmann M,, Maier-Hoyle V,, Van Der Vliet R,, Babiel R. 2007. Fully automated quantification of human immunodeficiency virus (HIV) type 1 RNA in human plasma by the COBAS AmpliPrep/COBAS TaqMan system. J Clin Virol 38: 304– 312.

71. Karasi JC,, Dziezuk F,, Quennery L,, Forster S,, Reischl U,, Colucci G,, Schoener D,, Seguin-Devaux C,, Schmit JC. 2011. High correlation between the Roche COBAS(R) AmpliPrep/COBAS(R) TaqMan(R) HIV-1, v2.0 and the Abbott m2000 RealTime HIV-1 assays for quantification of viral load in HIV-1 B and non-B subtypes. J Clin Virol 52: 181– 186.

72. Dewar RL,, Highbarger HC,, Sarmiento MD,, Todd JA,, Vasudevachari MB,, Davey RT Jr.,, Kovacs JA,, Salzman NP,, Lane HC,, Urdea MS. 1994. Application of branched DNA signal amplification to monitor human immunodeficiency virus type 1 burden in human plasma. J Infect Dis 170: 1172– 1179.

73. Lin HJ,, Pedneault L,, Hollinger FB. 1998. Intra-assay performance characteristics of five assays for quantification of human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol 36: 835– 839.

74. Braun J,, Plantier JC,, Hellot MF,, Tuaillon E,, Gueudin M,, Damond F,, Malmsten A,, Corrigan GE,, Simon F. 2003. A new quantitative HIV load assay based on plasma virion reverse transcriptase activity for the different types, groups and subtypes. AIDS 17: 331– 336.

75. Stevens G,, Rekhviashvili N,, Scott LE,, Gonin R,, Stevens W. 2005. Evaluation of two commercially available, inexpensive alternative assays used for assessing viral load in a cohort of human immunodeficiency virus type 1 subtype C-infected patients from South Africa. J Clin Microbiol 43: 857– 861.

76. Schito M,, Peter TF,, Cavanaugh S,, Piatek AS,, Young GJ,, Alexander H,, Coggin W,, Domingo GJ,, Ellenberger D,, Ermantraut E,, Jani IV,, Katamba A,, Palamountain KM,, Essajee S,, Dowdy DW. 2012. Opportunities and challenges for cost-efficient implementation of new point-of-care diagnostics for HIV and tuberculosis. J Infect Dis 205 Suppl 2: S169– 180.

77. Ho DD,, Moudgil T,, Alam M. 1989. Quantitation of human immunodeficiency virus type 1 in the blood of infected persons. N Engl J Med 321: 1621– 1625.

78. Griffith BP. 1987. Principles of laboratory isolation and identification of the human immunodeficiency virus (HIV). Yale J Biol Med 60: 575– 587.

79. Dykes C,, Demeter LM. 2007. Clinical significance of human immunodeficiency virus type 1 replication fitness. Clin Microbiol Rev 20: 550– 578.

80. Hirsch MS,, Brun-Vezinet F,, D’Aquila RT,, Hammer SM,, Johnson VA,, Kuritzkes DR,, Loveday C,, Mellors JW,, Clotet B,, Conway B,, Demeter LM,, Vella S,, Jacobsen DM,, Richman DD. 2000. Antiretroviral drug resistance testing in adult HIV-1 infection: recommendations of an International AIDS Society-USA Panel. JAMA 283: 2417– 2426.

81. Petropoulos CJ,, Parkin NT,, Limoli KL,, Lie YS,, Wrin T,, Huang W,, Tian H,, Smith D,, Winslow GA,, Capon DJ,, Whitcomb JM. 2000. A novel phenotypic drug susceptibility assay for human immunodeficiency virus type 1. Antimicrob Agents Chemother 44: 920– 928.

82. Barbour JD,, Wrin T,, Grant RM,, Martin JN,, Segal MR,, Petropoulos CJ,, Deeks SG. 2002. Evolution of phenotypic drug susceptibility and viral replication capacity during long-term virologic failure of protease inhibitor therapy in human immunodeficiency virus-infected adults. J Virol 76: 11104– 11112.

83. Armstrong KL,, Lee TH,, Essex M. 2009. Replicative capacity differences of thymidine analog resistance mutations in subtype B and C human immunodeficiency virus type 1. J Virol 83: 4051– 4059.

84. Hsieh SM,, Pan SC,, Chang SY,, Hung CC,, Sheng WH,, Chen MY,, Chang SC. 2013. Differential impact of resistance-associated mutations to protease inhibitors and nonnucleoside reverse transcriptase inhibitors on HIV-1 replication capacity. AIDS Res Hum Retroviruses 29: 1117– 1122.

85. Miura T,, Brumme ZL,, Brockman MA,, Rosato P,, Sela J,, Brumme CJ,, Pereyra F,, Kaufmann DE,, Trocha A,, Block BL,, Daar ES,, Connick E,, Jessen H,, Kelleher AD,, Rosenberg E,, Markowitz M,, Schafer K,, Vaida F,, Iwamoto A,, Little S,, Walker BD. 2010. Impaired replication capacity of acute/early viruses in persons who become HIV controllers. J Virol 84: 7581– 7591.

86. Centers for Disease Control. 1989. Interpretation and use of the Western blot assay for serodiagnosis of human immunodeficiency virus type 1 infections. MMWR Morb Mortal Wkly Rep 38: 1– 7.

87. Brenner BG,, Roger M,, Routy JP,, Moisi D,, Ntemgwa M,, Matte C,, Baril JG,, Thomas R,, Rouleau D,, Bruneau J,, Leblanc R,, Legault M,, Tremblay C,, Charest H,, Wainberg MA. 2007. High rates of forward transmission events after acute/early HIV-1 infection. J Infect Dis 195: 951– 959.

88. Hogan CM,, Degruttola V,, Sun X,, Fiscus SA,, Del Rio C,, Hare CB,, Markowitz M,, Connick E,, Macatangay B,, Tashima KT,, Kallungal B,, Camp R,, Morton T,, Daar ES,, Little S. 2012. The setpoint study (ACTG A5217): effect of immediate versus deferred antiretroviral therapy on virologic set point in recently HIV-1-infected individuals. J Infect Dis 205: 87– 96.

89. Forsgren A,, Nordstrom K. 1974. Protein A from Staphylococcus aureus: the biological significance of its reaction with IgG. Ann N Y Acad Sci 236: 252– 266.

90. Busch MP,, Satten GA. 1997. Time course of viremia and antibody seroconversion following human immunodeficiency virus exposure. Am J Med 102( 5B): 117– 124.

91. Louie B,, Pandori MW,, Wong E,, Klausner JD,, Liska S. 2006. Use of an acute seroconversion panel to evaluate a third-generation enzyme-linked immunoassay for detection of human immunodeficiency virus-specific antibodies relative to multiple other assays. J Clin Microbiol 44: 1856– 1858.

92. Patel P,, Mackellar D,, Simmons P,, Uniyal A,, Gallagher K,, Bennett B,, Sullivan TJ,, Kowalski A,, Parker MM,, Lalota M,, Kerndt P,, Sullivan PS. 2010. Detecting acute human immunodeficiency virus infection using 3 different screening immunoassays and nucleic acid amplification testing for human immunodeficiency virus RNA, 2006–2008. Arch Intern Med 170: 66– 74.

93. Ly TD,, Ebel A,, Faucher V,, Fihman V,, Laperche S. 2007. Could the new HIV combined p24 antigen and antibody assays replace p24 antigen specific assays? J Virol Meth 143: 86– 94.

94. Masciotra S,, McDougal JS,, Feldman J,, Sprinkle P,, Wesolowski L,, Owen SM. 2011. Evaluation of an alternative HIV diagnostic algorithm using specimens from seroconversion panels and persons with established HIV infections. J Clin Virol 52( Suppl 1): S17– 22.

95. Nasrullah M,, Wesolowski LG,, Meyer WA 3rd,, Owen SM,, Masciotra S,, Vorwald C,, Becker WJ,, Branson BM. 2013. Performance of a fourth-generation HIV screening assay and an alternative HIV diagnostic testing algorithm. AIDS 27: 731– 737.

96. Centers for Disease Control and Prevention, Association of Public Health Laboratories. 22 Septermber 2014, posting date. Laboratory Testing for Diagnosis of HIV infection: updated recommendations. http://stacks.cdc .gov/view/cdc/23447.

97. Owen SM,, Yang C,, Spira T,, Ou CY,, Pau CP,, Parekh BS,, Candal D,, Kuehl D,, Kennedy MS,, Rudolph D,, Luo W,, Delatorre N,, Masciotra S,, Kalish ML,, Cowart F,, Barnett T,, Lal R,, McDougal JS. 2008. Alternative algorithms for human immunodeficiency virus infection diagnosis using tests that are licensed in the United States. J Clin Microbiol 46: 1588– 1595.

98. Centers for Disease Control and Prevention. 1998. Update: HIV counseling and testing using rapid tests—United States, 1995. MMWR Morb Mortal Wkly Rep 47: 211– 215.

99. Branson BM,, Handsfield HH,, Lampe MA,, Janssen RS,, Taylor AW,, Lyss SB,, Clark JE. 2006. Revised recommendations for HIV testing of adults, adolescents, and pregnant women in health-care settings. MMWR Recommend Rep 55( RR-14): 1– 17.

100. Branson BM. 2003. Point of care rapid tests for HIV antibodies. J Lab Med 27: 288– 295.

101. Granade TC,, Parekh BS,, Phillips SK,, McDougal JS. 2004. Performance of the OraQuick and Hema-Strip rapid HIV antibody detection assays by non-laboratorians. J Clin Virol 30: 229– 232.

102. Gray RH,, Makumbi F,, Serwadda D,, Lutalo T,, Nalugoda F,, Opendi P,, Kigozi G,, Reynolds SJ,, Sewankambo NK,, Wawer MJ. 2007. Limitations of rapid HIV-1 tests during screening for trials in Uganda: diagnostic test accuracy study. BMJ (Clin Res Ed) 335: 188.

103. Campbell S,, Fedoriw Y. 2009. HIV testing near the patient: changing the face of HIV testing. Clinics Lab Med 29: 491– 501.

104. Delaney KP,, Branson BM,, Uniyal A,, Phillips S,, Candal D,, Owen SM,, Kerndt PR. 2011. Evaluation of the performance characteristics of 6 rapid HIV antibody tests. Clin Infect Dis 52: 257– 263.

105. Stekler JD,, O’Neal JD,, Lane A,, Swanson F,, Maenza J,, Stevens C,, Coombs RW,, Dragavon J,, Swenson PD,, Golden M,, Branson BM. 2013. Relative accuracy of serum, whole blood, and oral fluid HIV tests among Seattle men who have sex with men. J Clin Virol 58( Suppl 1): e119– e122.

106. Pilcher CD,, Louie B,, Facente S,, Keating S,, Hackett J Jr.,, Vallari A,, Hall C,, Dowling T,, Busch MP,, Klausner JD,, Hecht FM,, Liska S,, Pandori MW. 2013. Performance of rapid point-of-care and laboratory tests for acute and established HIV Infection in San Francisco. PLoS One 8: e80629. 10.1371/journal.pone.0080629.

107. Masciotra S,, Luo W,, Youngpairoj AS,, Kennedy MS,, Wells S,, Ambrose K,, Sprinkle P,, Owen SM. 2013. Performance of the Alere Determine HIV-1/2 Ag/Ab Combo Rapid Test with specimens from HIV-1 seroconverters from the US and HIV-2 infected individuals from Ivory Coast. J Clin Virol 58( Suppl 1): e54– e58.

108. Laperche S,, Leballais L,, Ly TD,, Plantier JC. 2012. Failures in the detection of HIV p24 antigen with the Determine HIV-1/2 Ag/Ab Combo rapid test. J Infect Dis 206: 1946– 1947. (Author reply 206:1949–1950.)

109. Granade TC,, Phillips SK,, Parekh B,, Gomez P,, Kitson-Piggott W,, Oleander H,, Mahabir B,, Charles W,, Lee-Thomas S. 1998. Detection of antibodies to human immunodeficiency virus type 1 in oral fluids: a large-scale evaluation of immunoassay performance. Clin Diagn Lab Immunol 5: 171– 175.

110. Luo W,, Masciotra S,, Delaney KP,, Charurat M,, Croxton T,, Constantine N,, Blattner W,, Wesolowski L,, Owen SM. 2013. Comparison of HIV oral fluid and plasma results during early infection in a longitudinal Nigerian cohort. J Clin Virol 8( Suppl 1): e113– 118.

111. Wesolowski LG,, Sanchez T,, Mackellar DA,, Branson BM,, Ethridge SF,, Constantine N,, Ketema F,, Sullivan PS. 2009. Evaluation of oral fluid enzyme immunoassay for confirmation of a positive rapid human immunodeficiency virus test result. Clin Vaccine Immunol 16: 1091– 1092.

112. Jafa K,, Patel P,, Mackellar DA,, Sullivan PS,, Delaney KP,, Sides TL,, Newman AP,, Paul SM,, Cadoff EM,, Martin EG,, Keenan PA,, Branson BM. 2007. Investigation of false positive results with an oral fluid rapid HIV-1/2 antibody test. PLoS One 2: e185. 10.1371/journal.pone.0000185

113. Parry JV,, Mortimer PP,, Nicoll AG. 1992. Performance assessment of neonatal dried blood spot testing for HIV antibody. Communicable disease report. CDR Rev 2: R128– 130.

114. Sullivan TJ,, Antonio-Gaddy MS,, Richardson-Moore A,, Styer LM,, Bigelow-Saulsbery D,, Parker MM. 2013. Expansion of HIV screening to non-clinical venues is aided by the use of dried blood spots for Western blot confirmation. J Clin Virol 58( Suppl 1): e123– 126.

115. Lofgren SM,, Morrissey AB,, Chevallier CC,, Malabeja AI,, Edmonds S,, Amos B,, Sifuna DJ,, Von Seidlein L,, Schimana W,, Stevens WS,, Bartlett JA,, Crump JA. 2009. Evaluation of a dried blood spot HIV-1 RNA program for early infant diagnosis and viral load monitoring at rural and remote healthcare facilities. AIDS 23: 2459– 2466.

116. Smit PW,, Sollis KA,, Fiscus S,, Ford N,, Vitoria M,, Essajee S,, Barnett D,, Cheng B,, Crowe SM,, Denny T,, Landay A,, Stevens W,, Habiyambere V,, Perriens JH,, Peeling RW. 2014. Systematic review of the use of dried blood spots for monitoring HIV viral load and for early infant diagnosis. PLoS One 9: e86461. 10.1371/journal.pone.0086461.

117. Urnovitz HB,, Sturge JC,, Gottfried TD. 1997. Increased sensitivity of HIV-1 antibody detection. Nat Med 3: 1258.

118. Pyne MT,, Hackett J Jr.,, Holzmayer V,, Hillyard DR. 2013. Large-scale analysis of the prevalence and geographic distribution of HIV-1 non-B variants in the United States. J Clin Microbiol 51: 2662– 2669.

119. Brennan CA,, Yamaguchi J,, Devare SG,, Foster GA,, Stramer SL. 2010. Expanded evaluation of blood donors in the United States for human immunodeficiency virus type 1 non-B subtypes and antiretroviral drug-resistant strains: 2005 through 2007. Transfusion 50: 2707– 2712.

120. Lee S,, Hu J,, Tang S,, Wood O,, Francis K,, Machuca A,, Rios M,, Daniel S,, Vockley C,, Awazi B,, Zekeng L,, Hewlett I. 2006. Evaluation of FDA licensed HIV assays using plasma from Cameroonian blood donors. J Med Virol 78( Suppl 1): S22– 23.

121. Reynolds SJ,, Ndongala LM,, Luo CC,, Mwandagalirwa K,, Losoma AJ,, Mwamba KJ,, Bazepeyo E,, Nzilambi NE,, Quinn TC,, Bollinger RC. 2002. Evaluation of a rapid test for the detection of antibodies to human immunodeficiency virus type 1 and 2 in the setting of multiple transmitted viral subtypes. Int J STD AIDS 13: 171– 173.

122. Plantier JC,, Djemai M,, Lemee V,, Reggiani A,, Leoz M,, Burc L,, Vessiere A,, Rousset D,, Poveda JD,, Henquell C,, Gautheret-Dejean A,, Barin F. 2009. Census and analysis of persistent false-negative results in serological diagnosis of human immunodeficiency virus type 1 group O infections. J Clin Microbiol 47: 2906– 2911.

123. Styer LM,, Sullivan TJ,, Parker MM. 2011. Evaluation of an alternative supplemental testing strategy for HIV diagnosis by retrospective analysis of clinical HIV testing data. J Clin Virol 52( Suppl 1): S35– 40.

124. Pandori MW,, Westheimer E,, Gay C,, Moss N,, Fu J,, Hightow-Weidman LB,, Craw J,, Hall L,, Giancotti FR,, Mak MD,, Madayag C,, Tsoi BW,, Louie B,, Patel P,, Owen SM,, Peter PJ. 2013. The Multispot rapid HIV-1/HIV-2 differentiation assay is comparable with the Western blot and an immunofluorescence assay at confirming HIV infection an a prospective study in three regions of the United States. J Clin Virol 58( Suppl 1): e92– e96.

125. Centers for Disease Control and Prevention. 2011. HIV-2 Infection Surveillance—United States, 1987–2009. MMWR Morb Mortal Wkly Rep 60: 985– 988.

126. Torian LV,, Eavey JJ,, Punsalang AP,, Pirillo RE,, Forgione LA,, Kent SA,, Oleszko WR. 2010. HIV type 2 in New York City, 2000–2008. Clin Infect Dis 51: 1334– 1342.

127. Tsang VC,, Peralta JM,, Simons AR. 1983. Enzyme-linked immunoelectrotransfer blot techniques (EITB) for studying the specificities of antigens and antibodies separated by gel electrophoresis. Methods Enzymol 92: 377– 391.

128. O’Brien TR,, George JR,, Epstein JS,, Holmberg SD,, Schochetman G. 1992. Testing for antibodies to human immunodeficiency virus type 2 in the United States. MMWR Recommend Rep 41: 1– 9.

129. Mingle JA. 1997. Differentiation of dual seropositivity to HIV 1 and HIV 2 in Ghanaian sera using line immunoassay (INNOLIA). West Afr J Med 16: 71– 74.

130. Blumberg RS,, Sandstrom EG,, Paradis TJ,, Neumeyer DN,, Sarngadharan MG,, Hartshorn KL,, Byington RE,, Hirsch MS,, Schooley RT. 1986. Detection of human T-cell lymphotropic virus type III-related antigens and anti-human T-cell lymphotropic virus type III antibodies by anticomplementary immunofluorescence. J Clin Microbiol 23: 1072– 1077.

131. Torian LV,, Forgione LA,, Punsalang AE,, Pirillo RE,, Oleszko WR. 2011. Comparison of Multispot EIA with Western blot for confirmatory serodiagnosis of HIV. J Clin Virol 52( Suppl 1): S41– 44.

132. Ramos EM,, Harb S,, Dragavon J,, Coombs RW. 2013. Clinical performance of the Multispot HIV-1/HIV-2 Rapid Test to correctly differentiate HIV-2 from HIV-1 infection in screening algorithms using third and fourth generation assays and to identify cross reactivity with the HIV-1 Western blot. J Clin Virol 58( Suppl 1): e104– e107.

133. Gottlieb GS,, Sow PS,, Hawes SE,, Ndoye I,, Coll-Seck AM,, Curlin ME,, Critchlow CW,, Kiviat NB,, Mullins JI. 2003. Molecular epidemiology of dual HIV-1/HIV-2 seropositive adults from Senegal, West Africa. AIDS Res Hum Retroviruses 19: 575– 584.

134. Cohen CJ,, Hunt S,, Sension M,, Farthing C,, Conant M,, Jacobson S,, Nadler J,, Verbiest W,, Hertogs K,, Ames M,, Rinehart AR,, Graham NM,, Team VS. 2002. A randomized trial assessing the impact of phenotypic resistance testing on antiretroviral therapy. AIDS 16: 579– 588.

135. Meynard JL,, Vray M,, Morand-Joubert L,, Race E,, Descamps D,, Peytavin G,, Matheron S,, Lamotte C,, Guiramand S,, Costagliola D,, Brun-Vezinet F,, Clavel F,, Girard PM,, Narval Trial G. 2002. Phenotypic or genotypic resistance testing for choosing antiretroviral therapy after treatment failure: a randomized trial. AIDS 16: 727– 736.

136. Weinstein MC,, Goldie SJ,, Losina E,, Cohen CJ,, Baxter JD,, Zhang H,, Kimmel AD,, Freedberg KA. 2001. Use of genotypic resistance testing to guide hiv therapy: clinical impact and cost-effectiveness. Ann Intern Med 134: 440– 450.

137. Snedecor SJ,, Khachatryan A,, Nedrow K,, Chambers R,, Li C,, Haider S,, Stephens J. 2013. The prevalence of transmitted resistance to first-generation non-nucleoside reverse transcriptase inhibitors and its potential economic impact in HIV-infected patients. PLoS One 8: e72784. 10.1371/journal.pone.0072784.

138. Erali M,, Page S,, Reimer LG,, Hillyard DR. 2001. Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods. J Clin Microbiol 39: 2157– 2165.

139. Gunthard HF,, Wong JK,, Ignacio CC,, Havlir DV,, Richman DD. 1998. Comparative performance of high-density oligonucleotide sequencing and dideoxynucleotide sequencing of HIV type 1 pol from clinical samples. AIDS Res Hum Retroviruses 14: 869– 876.

140. Johnson JA,, Li JF,, Wei X,, Lipscomb J,, Irlbeck D,, Craig C,, Smith A,, Bennett DE,, Monsour M,, Sandstrom P,, Lanier ER,, Heneine W. 2008. Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naive populations and associate with reduced treatment efficacy. PLoS Med 5: e158. 10.1371/journal.pmed.00 50158.

141. Johnson JA,, Li JF,, Wei X,, Lipscomb J,, Bennett D,, Brant A,, Cong ME,, Spira T,, Shafer RW,, Heneine W. 2007. Simple PCR assays improve the sensitivity of HIV-1 subtype B drug resistance testing and allow linking of resistance mutations. PLoS One 2: e638. 10.1371.pone.000 0638.

142. Palmer S,, Kearney M,, Maldarelli F,, Halvas EK,, Bixby CJ,, Bazmi H,, Rock D,, Falloon J,, Davey RT Jr.,, Dewar RL,, Metcalf JA,, Hammer S,, Mellors JW,, Coffin JM. 2005. Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J Clin Microbiol 43: 406– 413.

143. Avidor B,, Girshengorn S,, Matus N,, Talio H,, Achsanov S,, Zeldis I,, Fratty IS,, Katchman E,, Brosh-Nissimov T,, Hassin D,, Alon D,, Bentwich Z,, Yust I,, Amit S,, Forer R,, Vulih Shultsman I,, Turner D. 2013. Evaluation of a benchtop HIV ultradeep pyrosequencing drug resistance assay in the clinical laboratory. J Clin Microbiol 51: 880– 886.

144. Ji H,, Liang B,, Li Y,, Van Domselaar G,, Graham M,, Tyler S,, Merks H,, Sandstrom P,, Brooks J. 2013. Low abundance drug resistance variants in transmitted HIV drug resistance surveillance specimens identified using tagged pooled pyrosequencing. J Virol Meth 187: 314– 320.

145. Whitcomb JM,, Huang W,, Fransen S,, Limoli K,, Toma J,, Wrin T,, Chappey C,, Kiss LD,, Paxinos EE,, Petropoulos CJ. 2007. Development and characterization of a novel single-cycle recombinant-virus assay to determine human immunodeficiency virus type 1 coreceptor tropism. Antimicrob Agents Chemother 51: 566– 575.

146. Macarthur RD,, Novak RM. 2008. Reviews of anti-infective agents: maraviroc: the first of a new class of antiretroviral agents. Clin Infect Dis 47: 236– 241.

147. Tsibris AM,, Sagar M,, Gulick RM,, Su Z,, Hughes M,, Greaves W,, Subramanian M,, Flexner C,, Giguel F,, Leopold KE,, Coakley E,, Kuritzkes DR. 2008. In vivo emergence of vicriviroc resistance in a human immunodeficiency virus type 1 subtype C-infected subject. J Virol 82: 8210– 8214.

148. Chikere K,, Chou T,, Gorry PR,, Lee B. 2013. Affinofile profiling: how efficiency of CD4/CCR5 usage impacts the biological and pathogenic phenotype of HIV. Virology 435: 81– 91.

149. Raymond S,, Saliou A,, Nicot F,, Delobel P,, Dubois M,, Carcenac R,, Saune K,, Marchou B,, Massip P,, Izopet J. 2013. Characterization of CXCR4-using HIV-1 during primary infection by ultra-deep pyrosequencing. J Antimicrob Chemother 68: 2875– 2881.

150. Prada N,, Davis B,, Jean-Pierre P,, La Roche M,, Duh FM,, Carrington M,, Poles M,, Mehandru S,, Mohri H,, Markowitz M. 2008. Drug-susceptible HIV-1 infection despite intermittent fixed-dose combination tenofovir/emtricitabine as prophylaxis is associated with low-level viremia, delayed seroconversion, and an attenuated clinical course. J Acquir Immune Defic Syndr 49: 117– 122.

151. Terzi R,, Niero F,, Iemoli E,, Capetti A,, Coen M,, Rizzardini G. 2007. Late HIV seroconversion after non-occupational postexposure prophylaxis against HIV with concomitant hepatitis C virus seroconversion. AIDS 21: 262– 263.

152. Erickson CP,, McNiff T,, Klausner JD. 2006. Influenza vaccination and false positive HIV results. N Engl J Med 354: 1422– 1423.

153. Araujo PR,, Albertoni G,, Arnoni C,, Almeida K,, Ribeiro J,, Rizzo SR,, Carvalho FO,, Baretto JA,, Mangueira C. 2009. Rubella vaccination and transitory false-positive test results for human immunodeficiency virus Type 1 in blood donors. Transfusion 49: 2516– 2517.

154. Cooper CJ,, Metch B,, Dragavon J,, Coombs RW,, Baden LR. 2010. Vaccine-induced HIV seropositivity/reactivity in noninfected HIV vaccine recipients. JAMA 304: 275– 283.

155. Patel P,, Bennett B,, Sullivan T,, Parker MM,, Heffelfinger JD,, Sullivan PS, for the CDC Acute HIV Infection Study Group. 2012. Rapid HIV screening: missed opportunities for HIV diagnosis and prevention. J Clin Virol 54: 42– 47.

156. Ren A,, Louie B,, Rauch L,, Castro L,, Liska S,, Klausner JD,, Pandori MW. 2008. Screening and confirmation of human immunodeficiency virus type 1 infection solely by detection of RNA. J Med Microbiol 57: 1228– 1233.

157. Clinical and Laboratory Standards Institute. 2011. Criteria for Laboratory Testing and Diagnosis of Human Immunodeficiency Virus Infection; Approved Guideline Clinical and Laboratory Standards Institute. Document M-53-P. Clinical and Laboratory Standards Institute, Wayne, PA.

158. Long EF. 2011. HIV screening via fourth-generation immunoassay or nucleic acid amplification test in the United States: a cost-effectiveness analysis. PLoS One 6: e27625. 10.1371/journal.pone.0027625.

159. Stekler J,, Swenson PD,, Wood RW,, Handsfield HH,, Golden MR. 2005. Targeted screening for primary HIV infection through pooled HIV-RNA testing in men who have sex with men. AIDS 19: 1323– 1325.

160. Lilian RR,, Kalk E,, Bhowan K,, Berrie L,, Carmona S,, Technau K,, Sherman GG. 2012. Early diagnosis of in utero and intrapartum HIV infection in infants prior to 6 weeks of age. J Clin Microbiol 50: 2373– 2377.

161. King SM. 2004. Evaluation and treatment of the human immunodeficiency virus-1–exposed infant. Pediatrics 114: 497– 505.

162. Lopez M. 2013. A multi-step pace towards a cure for HIV: kick, kill, and contain. AIDS Rev 15: 190– 191.

163. Malloch L,, Kadivaar K,, Putz J,, Levett PN,, Tang J,, Hatchette TF,, Kadkhoda K,, Ng D,, Ho J,, Kim J. 2013. Comparative evaluation of the Bio-Rad Geenius HIV-1/2 Confirmatory Assay and the Bio-Rad Multispot HIV-1/2 Rapid Test as an alternative differentiation assay for CLSI M53 algorithm-I. J Clin Virol 58( Suppl 1) : e85– 91.

164. Read JS. 2007. Diagnosis of HIV-1 infection in children younger than 18 months in the United States. Pediatrics 120: e1547– 1562.

165. Deeks SG,, Coleman RL,, White R,, Pachl C,, Schambelan M,, Chernoff DN,, Feinberg MB. 1997. Variance of plasma human immunodeficiency virus type 1 RNA levels measured by branched DNA within and between days. J Infect Dis 176: 514– 517.

166. Aleman S,, Soderbarg K,, Visco-Comandini U,, Sitbon G,, Sonnerborg A. 2002. Drug resistance at low viraemia in HIV-1-infected patients with antiretroviral combination therapy. AIDS 16: 1039– 1044.

167. Nettles RE,, Kieffer TL,, Kwon P,, Monie D,, Han Y,, Parsons T,, Cofrancesco J Jr.,, Gallant JE,, Quinn TC,, Jackson B,, Flexner C,, Carson K,, Ray S,, Persaud D,, Siliciano RF. 2005. Intermittent HIV-1 viremia (Blips) and drug resistance in patients receiving HAART. JAMA 293: 817– 829.

168. Ginocchio CC,, Kemper M,, Stellrecht KA,, Witt DJ. 2003. Multicenter evaluation of the performance characteristics of the NucliSens HIV-1 QT assay used for quantitation of human immunodeficiency virus type 1 RNA. J Clin Microbiol 41: 164– 173.

169. Wojewoda CM,, Spahlinger T,, Harmon ML,, Schnellinger B,, Li Q,, Dejelo C,, Schmotzer C,, Zhou L. 2013. Comparison of Roche Cobas AmpliPrep/Cobas TaqMan HIV-1 test version 2.0 (CAP/CTM v2.0) with other real-time PCR assays in HIV-1 monitoring and follow-up of low-level viral loads. J Virol Meth 187: 1– 5.

170. Naeth G,, Ehret R,, Wiesmann F,, Braun P,, Knechten H,, Berger A. 2013. Comparison of HIV-1 viral load assay performance in immunological stable patients with low or undetectable viremia. Med Microbiol Immunol 202: 67– 75.

171. Hirsch MS,, Gunthard HF,, Schapiro JM,, Brun-Vezinet F,, Clotet B,, Hammer SM,, Johnson VA,, Kuritzkes DR,, Mellors JW,, Pillay D,, Yeni PG,, Jacobsen DM,, Richman DD. 2008. Antiretroviral drug resistance testing in adult HIV-1 infection: 2008 recommendations of an International AIDS Society-USA panel. Clin Infect Dis 47: 266– 285.

172. Montesinos I,, Eykmans J,, Delforge ML. 2014. Evaluation of the Bio-Rad Geenius HIV-1/2 test as a confirmatory assay. J Clin Virol 60: 399– 401.

173. Liu TF,, Shafer RW. 2006. Web resources for HIV type 1 genotype-resistance test interpretation. Clin Infect Dis 4: 1608– 1618.

Tables

Human Immunodeficiency Viruses*

/content/10.1128/9781555817381.mcm11.ch82.ch82.tab001

TABLE 1

Major HIV proteins of diagnostic significance

TABLE 1

Major HIV proteins of diagnostic significance

/content/10.1128/9781555817381.mcm11.ch82.ch82.tab002

TABLE 2

HIV infection stage, based on age-specific CD4+ T-lymphocyte count or CD4+ T-lymphocyte percentage of total lymphocytes

TABLE 2

HIV infection stage, based on age-specific CD4+ T-lymphocyte count or CD4+ T-lymphocyte percentage of total lymphocytes

/content/10.1128/9781555817381.mcm11.ch82.ch82.tab003

TABLE 3

FDA-approved viral load assays and specimen requirements

TABLE 3

FDA-approved viral load assays and specimen requirements

/content/10.1128/9781555817381.mcm11.ch82.ch82.tab004

TABLE 4

FDA-approved conventional laboratory HIV serologic tests

TABLE 4

FDA-approved conventional laboratory HIV serologic tests

/content/10.1128/9781555817381.mcm11.ch82.ch82.tab005

TABLE 5

FDA-approved rapid and point-of-care HIV tests

TABLE 5

FDA-approved rapid and point-of-care HIV tests

/content/10.1128/9781555817381.mcm11.ch82.ch82.tab006

TABLE 6

HIV-1 resistance and tropism assays

TABLE 6

HIV-1 resistance and tropism assays