Chapter 2 : Human Immunodeficiency Virus

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Since AIDS was first reported 26 years ago, more scientific effort at both the national and international levels has been focused on human immunodeficiency virus (HIV) than on any other virus in modern history. There is still no vaccine available for prevention of HIV infection, but multiple antiretroviral (ARV) drugs are available for combination therapy to control the infection. Many laboratory technologies, including conventional or rapid immunological and molecular methods, have been developed and used for diagnosis of HIV infection, surveillance, epidemiology, and monitoring of therapy. Tests for initial diagnosis of infection include enzyme immunoassay (EIA) or enzyme-linked immunosorbent assay (ELISA), Western blotting (WB) and other confirmatory assays, rapid immunoassay, quantitative viral RNA detection assays (commonly known as viral load [VL] assays), and qualitative proviral DNA assays. Tests for determining prognosis and for monitoring of ARV therapy include VL assays, genotyping, and phenotyping assays. The current HIV-1 VL assays offer reliable testing with excellent sensitivity and specificity. While genotypic testing is an indirect measure of drug susceptibility, it is the primary methodology for the analysis of HIV drug resistance. Currently, the report and interpretation are based on HIV-1 mutations that are known to be associated with drug resistance. In summary, there have been many achievements in diagnostic microbiology for patients who are immunocompromised because of HIV infection. Newer immunological and molecular technologies will continue to lead the way in laboratory diagnosis of infection caused by HIV.

Citation: (Wayne) Wang Y, Eaton M, Schuetz A, Nesheim S. 2009. Human Immunodeficiency Virus, p 47-68. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch2
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Image of Figure 1.
Figure 1.

Schematic of HIV infection. RNA*, HIV-1 RNA or proviral DNA in the newborn. (Modified with permission from references , and .)

Citation: (Wayne) Wang Y, Eaton M, Schuetz A, Nesheim S. 2009. Human Immunodeficiency Virus, p 47-68. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch2
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Image of Figure 2.
Figure 2.

Algorithm for screening, confirmation, and rapid tests for diagnosing HIV infection. *, possibly repeat with second different rapid assay or even third different assay for rapid confirmation. **, if positive, confirmed HIV-1 infection; if negative, repeat serology in 1 to 3 months.

Citation: (Wayne) Wang Y, Eaton M, Schuetz A, Nesheim S. 2009. Human Immunodeficiency Virus, p 47-68. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch2
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Image of Figure 3.
Figure 3.

Algorithm for monitoring HIV-1 infection and ARV therapy. CD4 measurement is not listed here because it is not HIV specific.

Citation: (Wayne) Wang Y, Eaton M, Schuetz A, Nesheim S. 2009. Human Immunodeficiency Virus, p 47-68. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch2
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1. American Academy of Pediatrics. 2006. Human immunodeficiency virus infection, p. 378–401. In Red Book: Report of the Committee on Infectious Diseases, 27th ed. American Academy of Pediatrics, Elk Grove Village, IL.
2. Beealert, G.,, G. Vercauteren,, K. Fransen,, M. Mangelschots,, M. De Rooy,, S. Garcia-Ribas, and, G. van der Groen. 2002. Comparative evaluation of eight commercial enzyme linked immunoabsorbent assays and 14 simple assays for detection of antibodies to HIV. J. Virol. Methods 105: 197206.
3. Berger, A.,, L. Scherzed,, M. Sturmer,, W. Preiser,, H. W. Doerr, and, H. F. Rabenau. 2005. Comparative evaluation of the Cobas Amplicor HIV-1 Monitor ultrasensitive test, the new Cobas AmpliPrep/Cobas Amplicor HIV-1 Monitor ultrasensitive test and the Versant HIV RNA 3.0 assays for quantitation of HIV-1 RNA in plasma samples. J. Clin. Virol. 33: 4351.
4. Bulterys, M.,, D. J. Jamieson,, M. J. O’Sullivan,, M. H. Cohen,, R. Maupin,, S. Nesheim,, M. P. Webber,, R. Van Dyke,, J. Wiener,, B. M. Branson, et al. 2004. Rapid HIV-1 testing during labor: a multicenter study. JAMA 292: 219223.
5. Busch, M.P.,, L. L. Lee,, G. A. Satten,, D. R. Henrard,, H. Farzadegan,, K. E. Nelson,, S. Read,, R. Y. Dodd, and, L. R. Peterson. 1995. Time course of detection of viral and serologic markers preceding human immunodeficiency virus type 1 seroconversion: implications for screening of blood and tissue donors. Transfusion 35: 9197.
6. Busch, M. P.,, and G. A. Satten. 1997. Time course of viremia and antibody seroconversion following human immunodeficiency virus exposure. Am. J. Med. 102: 117124.
7. Busch, M. P.,, S. H. Kleinman,, B. Jackson,, S. L. Stramer,, I. Hewlett, and, S. Preston. 2000. Committee report. Nucleic acid amplification testing of blood donors for transfusion-transmitted infectious diseases: report of the Interorganizational Task Force on Nucleic Acid Amplification Testing of Blood Donors. Transfusion 40: 143159.
8. Busch, M. P.,, S. A. Glynn,, D. J. Wright,, D. Hirschkorn,, M. E. Laycock,, J. McAuley,, Y. Tu,, C. Giachetti,, J. Gallarda,, J. Heitman,, S. H. Kleinman, et al. 2005. Relative sensitivities of licensed nucleic acid amplification tests for detection of viremia in early human immunodeficiency virus and hepatitis C virus infection. Transfusion 45: 18531863.
9. Call, S. A.,, M. S. Saag,, A. O. Westfall,, J. L. Raper,, S. V. Pham,, J. M. Tolson,, N. S. Hellmann,, G. A. Cloud, and, V. A. Johnson. 2001. Phenotypic drug susceptibility testing predicts long-term virologic suppression better than treatment history in patients with human immunodeficiency virus infection. J. Infect. Dis. 183: 401408.
10. Centers for Disease Control (CDC). 1981. Pneumocystis pneumonia—Los Angeles. MMWR Morb. Mortal. Wkly. Rep. 30: 250252.
11. Centers for Disease Control (CDC). 1981. Kaposi’s sarcoma and Pneumocystis pneumonia among homosexual men—New York City and California. MMWR Morb. Mortal. Wkly. Rep. 30: 305308.
12. Centers for Disease Control (CDC). 2006. Revised recommendations for HIV testing of adults, adolescents, and pregnant women in health-care settings. MMWR Morb. Mortal. Wkly. Rep. 55: 116.
13. Chearskul, P.,, C. Rongkavilit,, H. Al-Tatari, and, B. Asmar. 2006. New antiretroviral drugs in clinical use. Indian J. Pediatr. 73: 335341.
14. Chun, T. W.,, D. C. Nickle,, J. S. Justement,, D. Large,, A. Semerjian,, M. E. Curlin,, M. A. O’Shea,, C. W. Hallahan,, M. Daucher,, D. J. Ward,, S. Moir,, J. I. Mullins,, C. Kovacs, and, A. S. Fauci. 2005. HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir. J. Clin. Investig. 115: 32503255.
15. Church, J. D.,, D. Jones,, T. Flys,, D. Hoover,, N. Marlowe,, S. Chen,, C. Shi,, J. R. Eshleman,, L. A. Guay,, J. B. Jackson,, N. Kumwenda,, T. E. Taha, and, S. H. Eshleman. 2006. Sensitivity of the ViroSeq HIV-1 genotyping system for detection of the K103N resistance mutation in HIV-1 subtypes A, C, and D. J. Mol. Diagn. 8: 430432.
16. Claassen, M.,, G. U. van Zyl,, S. N. J. Korsman,, L. Smit,, M. F. Cotton, and, W. Preiser. 2006. Pitfalls with rapid HIV antibody testing in HIV-infected children in the Western Cape, South Africa. J. Clin. Virol. 37: 6871.
17. Cohen, M. S.,, J. A. Anderson, and, R. Swanstrom. 2005. Acute HIV infection: implications for HIV spread, disease progression, and vaccine development. HIV Mol. Immun. 2005: 2131.
18. Constantine, N. T.,, A. M. Sill,, N. Jack,, K. Kreisel,, J. Edwards,, T. Cafarella,, H. Smith,, C. Bartholomew,, F. R. Cleghorn, and, W. A. Blattner. 2003. Improved classification of recent HIV-1 infection by employing a two-stage sensitive/less-sensitive test strategy. J. Acquir. Immune Defic. Syndr. 32: 94103.
19. Constantine, N. T.,, and H. Zink. 2005. HIV testing technologies after two decades of evolution. Indian J. Med. Res. 121: 519538.
20. Cunningham, C. K.,, T. T. Charbonneau, and, K. Song. 1999. Comparison of human immunodeficiency virus 1 DNA polymerase chain reaction and qualitative and quantitative RNA polymerase chain reaction in human immunodeficiency virus 1-exposed infants. Pediatr. Infect. Dis. J. 18: 3035.
21. Daar, E.,, S. Little,, J. Pitt,, J. Santangelo,, P. Ho,, N. Harawa,, P. Kempt,, J. Giorgi,, J. Bai,, P. Gaut,, D. Richman,, S. Mandel, and, S. Nichols. 2001. Diagnosis of primary HIV-1 infection. Ann. Intern. Med. 134: 2529.
22. DeGruttola, V.,, L. Dix,, R. D’Aquila,, D. Holder,, A. Phillips,, M. Ait-Khaled,, J. Baxter,, P. Clevenbergh,, S. Hammer,, R. Harrigan,, D. Katzenstein,, R. Lanier,, M. Miller,, M. Para,, S. Yerly,, A. Zolopa,, J. Murray,, A. Patick,, V. Miller,, S. Castillo,, L. Pedneault, and, J. Mellors. 2000. The relation between baseline HIV drug resistance and response to antiretroviral therapy: re-analysis of retrospective and prospective studies using a standardized data analysis plan. Antivir. Ther. 5: 4148.
23. Delamare, C.,, M. Burgard,, M. J. Mayaux, et al. 1997. HIV-1 RNA detection in plasma for the diagnosis of infection in neonates. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 15: 121125.
24. Delwart, E.,, M. C. Kuhns, and, M. P. Busch. 2006. Surveillance of the genetic variation in incident HIV, HCV, and HBV infections in blood and plasma donors: implications for blood safety, diagnostics, treatment, and molecular epidemiology. J. Med. Virol. 78: S30S35.
25. Dezube, B. J.,, J. Proper,, J. Zhang,, V. J. Choy,, W. Weeden,, J. Morrissey,, E. M. Burns,, J. D. Dixon,, C. O’Loughlin,, L. A. Williams,, P. J. Pickering,, C. S. Crumpacker, and, F. B. Gelder. 2003. A passive immunotherapy, (PE)HRG214, in patients infected with human immunodeficiency virus: a phase I study. J. Infect. Dis. 187: 500503.
26. Dunn, D. T.,, C. D. Brandt,, A. Krivine,, S. A. Cassol,, P. Roques,, W. Borkowsky,, A. De Rossi,, E. Denamur,, A. Ehrnst, and, C. Loveday. 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: F7F11.
27. Dunn, D. T.,, R. J. Simonds,, M. Bulterys,, L. A. Kalish,, J. Moyer, Jr.,, A. de Maria,, C. Kind,, C. Rudin,, E. Denamur,, A. Krivine,, C. Loveday, and, M. L. Newell. 2000. Interventions to prevent vertical transmission of HIV-1: effect on viral detection rate in early infant samples. AIDS 14: 14211428.
28. Dunne, A. L.,, F. M. Mitchell,, S. K. Coherly,, N. S. Hellmann,, J. Hoy,, A. Mijch,, C. J. Petropoulos,, J. Mills, and, S. M. Crowe. 2001. Comparison of genotyping and phenotyping methods for determining susceptibility of HIV-1 to antiretroviral drugs. AIDS 15: 14711475.
29. Erali, M.,, S. Page,, L. G. Reimer, and, D. R. Hillyard. 2001. Human immunodeficiency virus type 1 drug resistance testing: a comparison of three sequence-based methods. J. Clin. Microbiol. 39: 21572165.
30. Erice, A.,, D. Brambilla,, J. Bremer,, J. B. Jackson,, R. Kokka,, B. Yen-Lieberman, and, R. W. Coombs. 2000. Performance characteristics of the QUANTIPLEX HIV-1 RNA 3.0 assay for detection and quantitation of human immunodeficiency virus type 1 RNA in plasma. J. Clin. Microbiol. 38: 28372845.
31. Fiebig, E. W.,, D. J. Wright,, B. D. Rawal,, P. E. Garrett,, R. T. Schumacher,, L. Peddada,, C. Heldebrant,, R. Smith,, A. Conrad,, S. Kleinman, and, M. P. Busch. 2003. Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS 17: 18711879.
32. Fiebig, E. W.,, C. M. Heldebrant,, R. I. Smith,, A. J. Conrad,, E. L. Delwart, and, M. P. Busch. 2005. Intermittent low-level viremia in very early primary HIV-1 infection. J. Acquir. Immune Defic. Syndr. 39: 133137.
33. Franco-Paredes, C.,, I. Tellez, and, C. del Rio. 2006. Rapid HIV testing: a review of the literature and implications for the clinician. Curr. HIV/AIDS Rep. 3: 169175.
34. Gallego, O.,, L. Martin-Carbonero,, J. Aguero,, C. de Mendoza,, A. Corral, and, V. Soriano. 2004. Correlation between rules-based interpretation and virtual phenotype interpretation of HIV-1 genotypes for predicting drug resistance in HIV-infected individuals. J. Virol. Methods 121: 115118.
35. Gibellini, D.,, F. Vitone,, E. Gori,, M. La Placa, and, M. C. Re. 2004. Quantitative detection of human immunodeficiency virus type 1 (HIV-1) viral load by SYBR green real-time RTPCR technique in HIV-1 seropositive patients. J. Virol. Methods 115: 183189.
36. Gleaves, C. A.,, J. Welle,, M. Campbell,, T. Elbeik,, V. Ng,, P. E. Taylor,, K. Kuramoto,, S. Aceituno,, E. Lewalski,, B. Joppa,, L. Sawyer,, C. Schaper,, D. McNairn, and, T. Quinn. 2002. Multicenter evaluation of the Bayer VERSANT HIV-1 RNA 3.0 assay: analytical and clinical performance. J. Clin. Virol. 25: 205216.
37. Gottlieb, M. S. 2001. AIDS—past and future. N. Engl. J. Med. 344: 17881791.
38. Granade, T. C. 2005. Use of rapid HIV antibody testing for controlling the HIV pandemic. Expert Rev. Anti Infect. Ther. 3: 957969.
39. Greenwald, J. L.,, G. R. Burstein,, J. Pincus, and, B. Branson. 2006. A rapid review of rapid HIV antibody tests. Curr. Infect. Dis. Rep. 8: 125131.
40. Gueudin, M.,, J.-C. Platier,, F. Damond,, P. Rouques,, P. Mauclere, and, F. Simon. 2003. Plasma viral RNA assay in HIV-1 group O infection by real-time PCR. J. Virol. Methods 113: 4349.
41. Hanna, G. J.,, and R. T. D’Aquila. 2001. Clinical use of genotypic and phenotypic drug resistance testing to monitor anti-retroviral chemotherapy. Clin. Infect. Dis. 32: 774782.
42. Hirsch, M. S.,, F. Brun-Vezinet,, B. Clotet,, B. Conway,, D. R. Kuritzkes,, R. T. D’Aquila,, L. M. Demeter,, S. M. Hammer,, V. A. Johnson,, C. Loveday,, J. W. Mellors,, D. M. Jacobsen, and, D. D. Richman. 2003. Antiretroviral drug resistance testing in adults infected with human immunodeficiency virus type 1: 2003 recommendations of an international AIDS society—USA panel. Clin. Infect. Dis. 37: 113128.
43. Ho, D. D.,, T. Moudgil, and, M. Alam. 1989. Quantitation of human immunodeficiency virus type 1 infection. N. Engl. J. Med. 132: 16211625.
44. Hughes, M. D.,, V. A. Johnson,, M. S. Hirsch,, J. W. Bremer,, T. Elbeik,, A. Erice,, D. R. Kuritzkes,, W. A. Scott,, S. A. Spector,, N. Basgoz,, M. A. Fischl, and, R. T. D’Aquila for the ACTG 241 Protocol Virology Substudy Team. 1997. Monitoring plasma HIV-1 RNA levels in addition to CD4 + lymphocyte count improves assessment of antiretroviral therapeutic response. Ann. Intern. Med. 126: 929938.
45. Jackson, J. B.,, K. Smith,, C. Knott,, A. Korpela,, A. Simmons,, E. Piwowar-Manning,, S. McDonough,, L. Mimms, and, J. M. Vargo. 2002. Sensitivity of the Procleix HIV-1/HCV assay for detection of human immunodeficiency virus type 1 and hepatitis C virus RNA in a high-risk population. J. Clin. Microbiol. 40: 23872391.
46. Jackson, J. B.,, E. Piwowar-Manning,, L. Johnson-Lewis,, R. Bassett,, L. M. Demeter, and, D. Brambilla. 2004. Comparison of versions 1.0 and 1.5 of the UltraSensitive AM-PLICOR HIV-1 MONITOR test for subjects with low viral load. J. Clin. Microbiol. 42: 27742776.
47. Janssen, R. S.,, G. A. Satten,, S. L. Stramer,, B. D. Rawal,, T. R. O’Brien,, B. J. Weiblen,, F. M. Hecht,, N. Jack,, F. R. Cleghorn,, J. O. Kahn,, M. A. Chesney, and, M. P. Busch. 1998. New testing strategy to detect early HIV-1 infection for use in incidence estimates and for clinical and prevention purposes. JAMA 280: 4248.
48. Johnson, V. A.,, F. Brun-Vezinet,, B. Clotet,, D. R. Kuritzkes,, D. Pillay,, J. M. Schapiro, and, D. D. Richman. 2006. Update of the drug resistance mutations in HIV-1: fall 2006. Top. HIV Med. 14: 125130.
49. Kahn, J. O.,, and B. D. Walker. 1996. Acute human immunodeficiency type 1 infection. N. Engl. J. Med. 339: 3339.
50. Kandathil, A. J.,, S. Ramalingam,, R. Kannangai,, S. David, and, G. Sridharan. 2005. Molecular epidemiology of HIV. Indian J. Med. Res. 121: 333344.
51. Kantor, R.,, D. A. Katzenstein,, B. Efron,, A. P. Carvalho,, B. Wynhoven,, P. Cane,, J. Clarke,, S. Sirivichayakul,, M. A. Soares,, J. Snoeck,, C. Pillay,, H. Rudich,, R. Rodrigues,, A. Holguin,, K. Ariyoshi,, M. B. Bouzas,, P. Cahn,, W. Sugiura,, V. Soriano,, L. F. Brigido,, Z. Grossman,, L. Morris,, A.-M. Vandamme,, A. Tanuri,, P. Phanuphak,, J. N. Weber,, D. Pillay,, P. R. Harrigan,, R. Camacho,, J. M. Schapiro, and, R. W. Shafer. 2005. Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. PLoS Med. 2: e113. http://www.plosmedicine.org.
52. Keenan, P. A.,, J. M. Keenan, and, B. M. Branson. 2005. Rapid HIV testing: wait time reduced from days to minutes. Postgrad. Med. 117: 4752.
53. Khurana, S.,, J. Needham,, S. Park,, B. Mathieson,, M. P. Busch,, G. Nemo,, P. Nyambi,, S. Zolla-Pazner,, S. Laal,, J. Mulenga,, E. Chomba,, E. Hunter,, S. Allen,, J. McIntyre,, I. Hewlett,, S. Lee,, S. Tang,, E. Cowan,, C. Beyrer,, M. Altfeld,, X. G. Yu,, A. Tounkara,, O. Koita,, A. Kamali,, N. Nguyen,, B. S. Graham,, D. Todd,, P. Mugenyi,, O. Anzala,, E. Sanders,, N. Ketter,, P. Fast, and, H. Golding. 2006. Novel approach for differential diagnosis of HIV infections in the face of vaccinegenerated antibodies: utility for detection of diverse HIV-1 subtypes. J. Acquir. Immune Defic. Syndr. 43: 304312.
54. Kitchen, C. M.,, S. G. Kitchen,, J. A. Dubin, and, M. S. Gottlieb. 2001. Initial virological and immunologic response to highly active antiretroviral therapy predicts long-term clinical outcome. Clin. Infect. Dis. 33: 466472.
55. Klein, D. 2002. Quantification using real-time PCR technology: applications and limitations. Trends Mol. Med. 8: 257260.
56. Kline, M.,, D. Lewis, and, B. Hollinger. 1994. A comparative study of HIV culture, polymerase chain reaction and anti-HIV immunoglobulin A antibody detection in the diagnosis during early infancy of vertically acquired human immunodeficiency virus infection. Pediatr. Infect. Dis. J. 13: 9094.
57. Knuchel, M. C.,, Z. Tomasik,, R. F. Speck,, R. Lüthy, and, J. Schüpbach. 2006. Ultrasensitive quantitative HIV-1 p24 antigen assay adapted to dried plasma spots to improve treatment monitoring in low-resource settings. J. Clin. Virol. 36: 6467.
58. Kovacs, A.,, J. Xu, and, S. Rasheed. 1995. Comparison of a rapid nonisotopic polymerase chain reaction assay with four commonly used methods for the early diagnosis of human immunodeficiency virus type 1 infection in neonates and children. Pediatr. Infect. Dis. J. 14: 948954.
59. Kuritzkes, D. R.,, R. M. Grant,, P. Feorino,, M. Griswold,, M. Hoover,, R. Young,, S. Day,, R. M. Lloyd, Jr.,, C. Reid,, G. F. Morgan, and, D. L. Winslow. 2003. Performance characteristics of the TRUGENE HIV-1 genotyping kit and the open gene DNA sequencing system. J. Clin. Microbiol. 41: 15941599.
60. Lal, R. B.,, S. Chakrabarti, and, C. Yang. 2005. Impact of genetic diversity of HIV-1 on diagnosis, antiretroviral therapy and vaccine development. Indian J. Med. Res. 121: 287314.
61. Lambert, J. S.,, D. R. Harris, and, E. R. Stiehm. 2003. Performance characteristics of HIV-1 culture and HIV-1 DNA and RNA amplification assays for early diagnosis of perinatal HIV-1 infection. J. Acquir. Immune Defic. Syndr. 34: 512519.
62. Lelie, P. N.,, H. A. J. van Drimmelen,, H. T. M. Cuypers,, S. J. Best,, S. L. Stramer,, C. Hyland,, J.-P. Allain,, P. Moncharmont,, C. Defer,, M. Nübling,, A. Glauser,, M. da Silva Cardoso,, J.-F. Viret,, M. H. Lankinen,, L. Grillner,, U. Wirthmüller,, J. Coste,, V. Schottstedt,, B. Masecar, and, E. M. Dax. 2002. Sensitivity of HCV RNA and HIV RNA blood screening assays. Transfusion 42: 527.
63. Little, S. J.,, S. Holte,, J.-P. Routy,, E. S. Daar,, M. Markowitz,, A. C. Collier,, R. A. Koup,, J. W. Mellors,, E. Connick,, B. Conway,, M. Kilby,, L. Wang,, J. M. Whitcomb,, N. S. Hellmann, and, D. D. Richman. 2002. Antiretroviral-drug resistance among patients recently infected with HIV. N. Engl. J. Med. 347: 385394.
64. Ly, T. D.,, C. Edlinger, and, A. Vabret. 2000. Contribution of combined detection assays of p24 antigen and anti human immunodeficiency virus (HIV) antibodies in diagnosis of primary HIV infection by routine testing. J. Clin. Microbiol. 38: 24592461.
65. Madec, Y.,, F. Boufassa,, K. Porter, and, L. Meyer on behalf of the CASCADE Collaboration. 2005. Spontaneous control of viral load and CD4 cell count progression among HIV-1 seroconverters. AIDS 19: 20012007.
66. Martin, D. 2000. Appropriate laboratory monitoring of HIV. S. Afr. Med. J. 90: 3336.
67. Martinez-Martinez, P.,, E. Martin del Barrio,, J. De Benito, and, R. Landinez. 1999. New lineal immunoenzymatic assay for simultaneous detection of p24 antigen and HIV antibodies. Eur. J. Clin. Microbiol. Infect. Dis. 18: 591594.
68. McCutchan, F. E. 2006. Global epidemiology of HIV. J. Med. Virol. 78: S7S12.
69. McFarland, W.,, M. P. Busch,, T. A. Kellogg,, B. D. Rawal,, G. A. Satten,, M. H. Katz,, J. Dilley, and, R. S. Janssen. 1999. Detection of early HIV infection and estimation of incidence using a sensitive/less-sensitive enzyme immunoassay testing strategy at anonymous counseling and testing sites in San Francisco. J. Acquir. Immune Defic. Syndr. 22: 484489.
70. Mellors, J. W.,, C. R. Rinaldo,, P. Gupta,, R. M. White,, J. A. Todd, and, L. A. Kingsley. 1996. Prognosis in HIV-1 infection predicted by the quantity of virus in plasma. Science 272: 11671170.
71. Mellors, J. W.,, A. Munoz,, J. V. Giorgi,, J. B. Margolick,, C. J. Tassoni,, P. Gupta,, L. A. Kingsley,, J. A. Todd,, A. J. Saah,, R. Detels,, J. P. Phair, and, C. R. Rinaldo, Jr. 1997. Plasma viral load and CD4+ lymphocytes as prognostic markers of HIV-1 infection. Ann. Intern. Med. 126: 946954.
72. Moser, M. J.,, M. Ruckstuhl,, C. A. Larsen,, A. J. Swearingen,, M. Kozlowski,, L. Bassit,, P. L. Sharma,, R. F. Schinazi, and, J. R. Prudent. 2005. Quantifying mixed populations of drug-resistant human immunodeficiency virus type 1. Antimicrob. Agents Chemother. 49: 33343340.
73. Mracna, M.,, G. Becker-Pergola,, J. Dileanis,, L. A. Guay,, S. Cunningham,, J. B. Jackson, and, S. H. Eshleman. 2001. Performance of Applied Biosystems ViroSeq HIV-1 genotyping system for sequence-based analysis of non-subtype B human immunodeficiency virus type 1 from Uganda. J. Clin. Microbiol. 39: 43234327.
74. Munoz, M.,, R. Carmona,, L. Perez-Alvarez,, G. Cilla,, M. D. Suarez,, E. Delgado,, G. Contreras,, J. Corral,, M. J. de Goicoetxea,, L. Medrano,, M. J. Lezaun, and, R. Najera. 2005. Analysis of discrepancies in the interpretation of antiretroviral drug resistance results in HIV-1 infected patients of Basque Country, Spain. J. Clin. Virol. 33: 224229.
75. Nesheim, S.,, F. Lee,, M. L. Kalish,, C. Y. Ou,, M. Sawyer,, L. Meadows,, V. Grimes,, R. J. Simonds, and, A. Nahmias. 1997. Diagnosis of perinatal human immunodeficiency virus infection by polymerase chain reaction and p24 antigen detection after immune complex dissociation in an urban community hospital. J. Infect. Dis. 175: 13331336.
76. Nesheim, S.,, P. Palumbo,, K. Sullivan,, F. Lee,, P. Vink,, E. Abrams, and, M. Bulterys. 2003. Quantitative RNA testing for diagnosis of HIV-infected infants. J. Acquir. Immune Defic. Syndr. 32: 192195.
77. Niu, M. T.,, J. A. Jermano,, P. Reichelderfer, and, S. M. Schnittman. 1993. Summary of the National Institutes of Health workshop on primary human immunodeficiency virus type 1 infection. AIDS Res. Hum. Retrovir. 9: 913924.
78. Nolte, F. S.,, J. Boysza,, C. Thurmond,, W. S. Clark, and, J. L. Lennox. 1998. Clinical comparison of an enhanced-sensitivity branched-DNA assay and reverse transcription-PCR for quantitation of HIV type 1 RNA in plasma. J. Clin. Microbiol. 36: 716720.
79. Osmanov, S.,, C. Pattou,, N. Walker,, B. Schwardlander,, J. Esparza, et al. 2002. Estimated global distribution and regional spread of HIV-1 genetic subtypes in the year 2000. J. Acquir. Immune Defic. Syndr. 29: 184190.
80. Owens, D. K.,, M. Holodniy,, T. W. McDonald,, J. Scott, and, S. Sonnad. 1996. A meta-analytic evaluation of the polymerase chain reaction for the diagnosis of HIV infection in infants. JAMA 275: 13421348.
81. Parekh, B. S.,, M. S. Kennedy,, T. Dobbs,, C. P. Pau,, R. Byers,, T. Green,, D. J. Hu,, S. Vanichseni,, N. L. Young,, K. Choopanya,, T. D. Mastro, and, J. S. McDougal. 2002. Quantitative detection of increasing HIV type 1 antibodies after seroconversion: a simple assay for detecting recent HIV infection and estimating incidence. AIDS Res. Hum. Retrovir. 18: 295307.
82. Parekh, B. S.,, and J. S. McDougal. 2005. Application of laboratory methods for estimation of HIV-1 incidence. Indian J. Med. Res. 121: 510518.
83. Parkin, N. T.,, Y. S. Lie,, N. S. Hellmann,, M. Markowitz,, S. Bonhoeffer,, D. D. Ho, and, C. J. Petropoulos. 1999. Phenotypic changes in drug susceptibility associated with failure of HIV-1 triple combination therapy. J. Infect. Dis. 180: 865870.
84. Parkin, N. T.,, S. G. Deeks,, M. T. Wrin,, J. Yap,, R. M. Grant,, K. H. Lee,, D. Heeren,, N. S. Hellmann, and, C. J. Petropoulos. 2000. Loss of antiretroviral drug susceptibility at low viral load during early virological failure in treatment-experienced patients. AIDS 14: 28772887.
85. Perinatal HIV Guidelines Working Group. 12 October 2006, posting date. Public health service task force recommendations for use of antiretroviral drugs in pregnant HIV-1 infected women for maternal health and interventions to reduce perinatal HIV-1 transmission in the United States. http://aidsinfo.nih.gov/ContentFiles/PerinatalGL.pdf.
86. Petropoulos, C. J.,, N. T. Parkin,, K. L. Limoli,, Y. S. Lie,, T. Wrin,, W. Huang,, H. Tian,, D. Smith,, G. A. Winslow,, D. J. Capon, and, J. M. Whitecomb. 2000. A novel phenotypic drug susceptibility assay for human immunodeficiency virus type 1. Antimicrob. Agents Chemother. 44: 920928.
87. Pilcher, C. D.,, S. A. Fiscus,, T. Q. Nguyen,, E. Foust,, L. Wolf,, D. Williams,, R. Ashby,, J. O. O’Dowd,, J. T. McPherson,, B. Stalzer,, L. Hightow,, W. C. Miller,, J. J. Eron, Jr.,, M. S. Cohen, and, P. A. Leone. 2005. Detection of acute infections during HIV testing in North Carolina. N. Engl. J. Med. 352: 18731883.
88. Prasitwattanaseree, S.,, M. Lallemant,, D. Costagliola,, G. Jourdain, and, J. Y. Mary. 2004. Influence of mother and infant zidovudine treatment duration on the age at which HIV infection can be detected by polymerase chain reaction in infants. Antivir. Ther. 9: 179185.
89. Qari, S. H.,, R. Respess,, H. Weinstock,, E. M. Beltrami,, K. Hertogs,, B. A. Larder,, C. J. Petropoulos,, N. Hellmann, and, W. Heneine. 2002. Comparative analysis of two commercial phenotypic assays for drug susceptibility testing of human immunodeficiency virus type 1. J. Clin. Microbiol. 40: 3135.
90. Rawal, B. D.,, A. Degula,, L. Lebedeva,, R. S. Janssen,, F. M. Hecht,, H. W. Sheppard, and, M. P. Busch. 2003. Development of a new less-sensitive enzyme immunoassay for detection of early HIV-1 infection. J. Acquir. Immune Defic. Syndr. 33: 349355.
91. Rich, J. D.,, N. Merriman,, E. Mylonakis,, T. C. Greenough,, T. P. Flanigan,, B. J. Mady, and, C. C. Carpenter. 1999. Misdiagnosis of HIV infection by HIV-1 plasma viral load testing: a case series. Ann. Intern. Med. 130: 3739.
92. Rothman, R. E. 2004. Current centers for disease control and prevention guidelines for HIV counseling, testing, and referral: critical role of and a call to action for emergency physicians. Ann. Emerg. Med. 44: 3142.
93. Rouet, F.,, C. Montcho,, C. Rouzioux,, V. Leroy,, P. Msellati,, J. B. Kottan,, B. You,, I. Viho,, F. Dabis, et al. 2001. Early diagnosis of pediatric HIV-1 infection among African breastfed children using quantitative plasma HIV RNA assay. AIDS 15: 18491856.
94. Rouet, F.,, D. K. Ekouevi,, M.-L. Chaix,, M. Burgard,, A. Inwoley,, T. D’Aquin Tony,, C. Danel,, X. Anglaret,, V. Leroy,, P. Msellati,, F. Dabis, and, C. Rouzioux. 2005. Transfer and evaluation of an automated, low-cost real-time reverse transcription-PCR test for diagnosis and monitoring of human immunodeficiency virus type 1 infection in a West African resource-limited setting. J. Clin. Microbiol. 43: 27092717.
95. Rox, J. M.,, A. M. Eis-Hubinger,, J. Muller,, M. Vogel,, R. Kaiser,, P. Hanfland, and, M. Daumer. 2004. First human immunodeficiency virus-1 group O infection in a European blood donor. Vox Sang. 87: 4445.
96. Ruelle, J.,, B. K. Mukadi,, M. Schutten, and, P. Goubau. 2004. Quantitative real-time PCR on LightCycler for detection of human immunodeficiency virus type 2 (HIV-2). J. Virol. Methods 117: 6774.
97. Saha, B. K.,, B. Tian, and, R. P. Bucy. 2001. Quantitation of HIV-1 by real-time PCR with a unique fluorogenic probe. J. Virol. Methods 93: 3342.
98. Saville, R. D.,, N. T. Constantine,, N. Jack,, C. Bartholomew,, J. Edwards,, P. Gomez, and, W. A. Blattner. 2001. Fourth-generation enzyme-linked immunosorbent assay for the simultaneous detection of human immunodeficiency virus antigen and antibody. J. Clin. Microbiol. 39: 25182524.
99. Schacker, T.,, A. C. Collier,, J. Hughes,, T. Shea, and, L. Corey. 1996. Clinical and epidemiologic features of primary HIV infection. Ann. Intern. Med. 125: 257264.
100. Schochetman, G.,, and M. C. Kuhns. 2006. HIV variations and hepatitis B surface antigen mutants: diagnostic challenges for immunoassays. J. Med. Virol. 78: S3S6.
101. Sherman, G. G.,, G. Stevens,, S. A. Jones,, P. Horsfield, and, W. S. Stevens. 2005. Dried blood spots improve access to HIV diagnosis and care for infants in low-resource settings. J. Acquir. Immune. Defic. Syndr. 38: 615617.
102. Soroka, S. D.,, T. C. Granade,, D. Candal, and, B. S. Parekh. 2005. Modification of rapid human immunodeficiency virus (HIV) antibody assay protocols for detecting recent HIV seroconversion. Clin. Diagn. Lab. Immunol. 12: 918921.
103. Spira, A. I.,, P. A. Marx,, B. K. Patterson,, J. Mahoney,, R. A. Koup,, S. M. Wolinsky, and, D. D. Ho. 1996. Cellular targets of infection and route of viral dissemination after an intravaginal inoculation of simian immunodeficiency virus into rhesus macaques. J. Exp. Med. 183: 215225.
104. Suthon, V.,, R. Archawin,, C. Chanchai,, L. John,, K. Wichuda,, P. Wiroj,, T. Hansa,, S. Pathom,, S. N. Pongnuwat,, P. Silaporn, and, I. Wimala. 2002. Impact of HIV vaccination on laboratory diagnosis: case reports. J. Infect. Dis. 2: 19.
105. Svarovskaia, E. S.,, M. J. Moser,, A. S. Bae,, J. R. Prudent,, M. D. Miller, and, K. Borroto-Esoda. 2006. MultiCode-RTx real-time PCR system for detection of subpopulations of K65R human immunodeficiency virus type 1 reverse transcriptase mutant viruses in clinical samples. J. Clin. Microbiol. 44: 42374241.
106. Taylor, P.,, G. Pickard,, A. Gammie, and, M. Atkins. 2004. Comparison of the ADVIA Centaur and Abbott AxSYM immunoassay systems for a routine diagnostic virology laboratory. J. Clin. Virol. 30 (Suppl. 1) : S11S15.
107. UNAIDS. 2006. Report on the global AIDS epidemic: executive summary. A UNAIDS 10th anniversary special edition. UNAIDS, Geneva, Switzerland. http://www.unaids.org.
108. U.S. Department of Health and Human Services Panel on Antiretroviral Guidelines for Adults and Adolescents. 29 January 2008, posting date. Guidelines for the use of antiretroviral agents in HIV-1-infected adults and adolescents. U.S. Department of Health and Human Services, Washington, DC. http://aidsinfo.nih.gov/ContentFiles/AdultandAdolescentGL.pdf.
109. Van Binsbergen, J.,, A. Siebelink,, A. Jacobs,, W. Keuer,, F. Bruynis,, M. van de Graaf,, J. van der Heijden,, D. Kambel, and, J. Toonen. 1999. Improved performance of seroconversion with a 4th generation HIV antigen/antibody assay. J. Virol. Methods 82: 7784.
110. Vandamme, A. M.,, A. Sönnerborg,, M. Ait-Khaled,, J. Albert,, B. Asjo,, L. Bacheler,, D. Banhegyi,, C. Boucher,, F. Brun-Vézinet,, R. Camacho,, P. Clevenbergh,, N. Clumeck,, N. Dedes,, A. De Luca,, H. W. Doerr,, J.-L. Faudon,, G. Gatti,, J. Gerstoft,, W. W. Hall,, A. Hatzakis,, N. Hellmann,, A. Horban,, J. D. Lundgren,, D. Kempf,, M. Miller,, V. Miller,, T. W. Myers,, C. Nielsen,, M. Opravil,, L. Palmisano,, C. F. Perno,, A. Phillips,, D. Pillay,, T. Pumarola,, L. Ruiz,, M. Salminen,, J. Schapiro,, B. Schmidt,, J.-C. Schmit,, R. Schuurman,, E. Shulse,, V. Soriano,, S. Staszewski,, S. Vella,, M. Youle,, R. Ziermann, and, L. Perrin. 2004. Updated European recommendations for the clinical use of HIV drug resistance testing. Antivir. Ther. 9: 829848.
111. Vanhems, P.,, C. Dassa,, J. Lambert,, D. A. Cooper,, L. Perrin,, J. Vizzard,, B. Hirschel,, S. K. Loes,, A. Carr, and, R. Allard. 1999. Comprehensive classification of symptoms and signs reported among 218 patients with acute HIV-1 infection. J. Acquir. Immune Defic. Syndr. Hum. Retrovir. 21: 99106.
112. Wang, Y. F. 2006. Advanced antibody detection, p. 42–62. In Y. W. Tang and, C. W. Stratton (ed.), Advanced Techniques in Diagnostic Microbiology. Springer, New York, NY.
113. Wang, Y. F. 2006. Signal amplification techniques, p. 228–242. In Y. W. Tang and, C. W. Stratton (ed.), Advanced Techniques in Diagnostic Microbiology. Springer, New York, NY.
114. Weber, B.,, A. Berger,, H. Rabenau, and, H. W. Doerr. 2002. Evaluation of a new combined antigen and antibody human immunodeficiency virus screening assay, VIDAS HIV DUO Ultra. J. Clin. Microbiol. 40: 14201426.
115. Weber, B.,, R. Thorstensson,, S. Tanprasert,, U. Schmitt, and, W. Melchior. 2003. Reduction of the diagnostic window in three cases of human immunodeficiency-1 subtype E primary infection with fourth-generation HIV screening assays. Vox Sang. 85: 7379.
116. Weber, B. 2006. Screening of HIV infection: role of molecular and immunological assays. Expert Rev. Mol. Diagn. 6: 399411.
117. Weber, B.,, B. Orazi,, A. Raineri,, R. Thorstensson,, P. Burgisser,, A. Muhlbacher,, C. Areal,, A. Eiras,, R. Villaescusa,, R. Camacho,, I. Diogo,, H. J. Roth,, I. Zahn,, J. Bartel,, V. Bossi,, F. Piro,, K. Atamasirikul,, P. Permpikul,, L. Webber, and, S. Singh. 2006. Multicenter evaluation of a new 4th generation HIV screening assay Elecsys HIV combi. Clin. Lab. 52: 463473.
118. Wilson, J. W.,, and P. Bean. 2000. A physician’s primer to antiretroviral drug resistance testing. AIDS Read. 10: 469473, 476–478.
119. Wong, J. K.,, M. Hezareh,, H. F. Gunthard,, D. V. Havlir,, C. C. Ignacio,, C. A. Spina, and, D. D. Richman. 1997. Recovery of replication-competent HIV despite prolonged suppression of plasma viremia. Science 278: 12911295.
120. Working Group on Antiretroviral Therapy and Medical Management of HIV-Infected Children. 28 February 2008, posting date. Guidelines for the use of antiretroviral agents in pediatric HIV infection. http://aidsinfo.nih.gov/ContentFiles/PediatricGuidelines.pdf.
121. Yeni, P. G.,, S. M. Hammer,, C. C. J. Carpenter,, D. A. Cooper,, M. A. Fischl,, J. M. Gatell,, B. G. Gazzard,, M. S. Hirsch,, D. M. Jacobsen,, D. A. Katzenstein,, J. S. G. Montaner,, D. D. Richman,, M. S. Saag,, M. Schechter,, R. T. Schooley,, M. A. Thompson,, S. Vella, and, P. A. Volberding. 2002. Antiretroviral treatment for adult HIV infection in 2002. Updated recommendations of the International AIDS Society—-USA panel. JAMA 288: 222235.
122. Young, N. L.,, N. Shaffer, and, T. Chaowanachan. 2000. Early diagnosis of HIV-1-infected infants in Thailand using RNA and DNA PCR assays sensitive to non-B subtypes. J. Acquir. Immune. Defic. Syndr. 24: 401407.
123. Zhang, J.,, S. Y. Rhee,, J. Taylor, and, R. W. Shafer. 2005. Comparison of the precision and sensitivity of the Anti-virogram and PhenoSense HIV drug susceptibility assays. J. Acquir. Immune. Defic. Syndr. 38: 439444.
124. Zhang, M.,, and J. Versalovic. 2002. HIV update. Diagnostic tests and markers of disease progression and response to therapy. Am. J. Clin. Pathol. 118: S26S32.


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Table 1.

Global epidemiology of HIV variants

Citation: (Wayne) Wang Y, Eaton M, Schuetz A, Nesheim S. 2009. Human Immunodeficiency Virus, p 47-68. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch2
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Table 2.

Methods of screening and confirmation, including rapid methods

Citation: (Wayne) Wang Y, Eaton M, Schuetz A, Nesheim S. 2009. Human Immunodeficiency Virus, p 47-68. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch2
Generic image for table
Table 3.

NAAT methods for HIV-1

Citation: (Wayne) Wang Y, Eaton M, Schuetz A, Nesheim S. 2009. Human Immunodeficiency Virus, p 47-68. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch2
Generic image for table
Table 4.

The FDA-approved ARV drugs for HIV

Citation: (Wayne) Wang Y, Eaton M, Schuetz A, Nesheim S. 2009. Human Immunodeficiency Virus, p 47-68. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch2
Generic image for table
Table 5.

Genotyping and phenotyping methods for HIV-1

Citation: (Wayne) Wang Y, Eaton M, Schuetz A, Nesheim S. 2009. Human Immunodeficiency Virus, p 47-68. In Hayden R, Carroll K, Tang Y, Wolk D (ed), Diagnostic Microbiology of the Immunocompromised Host. ASM Press, Washington, DC. doi: 10.1128/9781555815455.ch2

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