Translational HIV-1 research: from routine diagnostics to new virology insights in Amsterdam, the Netherlands during 1983-2013

Abstract

An HIV-1 diagnostic laboratory was established in the Academic Medical Center (AMC) of the University of Amsterdam after the discovery of human immunodeficiency virus (HIV) as the cause of the acquired immunodeficiency syndrome (AIDS). The first AIDS patients were diagnosed here in 1981 and since 1983 we have tested the samples of 50992 patients using a variety of assays that greatly improved over the years. We will describe some of the basic results from this diagnostic laboratory and then focus on the spin-off in terms of the development of novel virus assays to detect super-infections and ultra-sensitive assays to measure the intracellular HIV-1 RNA load. We also review several original research findings in the field of HIV-1 virology that stem from initial observations made in the diagnostic unit. This includes the study of genetic defects in the HIV-1 genome and time trends of the replication fitness over 30 years of viral evolution, but also the description of novel HIV-1 variants in difficult-to-diagnose clinical specimen.

Figure 1

HIV antibody-tests at the AMC. A. Numbers of individuals tested for HIV-infection using serology at the AMC (Amsterdam, the Netherlands) from 1983-2012. The introduction of antiretroviral treatment (AZT/zidovudine and cART) is indicated by arrows. Between 1984 and 1992/1993, patient data were mainly recorded in written documents and not always filed later in databases. Therefore, the number of tests in those years is probably an underestimation as not all data could be retrieved. B. Numbers of HIV positive patients tested in the AMC in Amsterdam from 1983-2012 according to the most likely route of HIV transmission.

Figure 2

Numbers of HIV-assays performed at the AMC. A. Numbers of HIV-1/HIV-2 antibody assays performed in the AMC (Amsterdam, the Netherlands) from 1996-2012. Confirmation assays include Western blots and INNO-LIA (Innogenetics NV, Gent, Belgium). B. Numbers of HIV-1 plasma viral load assays performed in the AMC (Amsterdam, the Netherlands) from 1996-2012. C. Number of genotyping assays performed in the AMC (Amsterdam, the Netherlands) from 1996-2012. In-house assays were used for IN and ENV-V3, and for PR/RT until a commercial assay became available for the latter genomic region in 2001 (Applied Biosystems ViroSeq HIV-1 Genotyping System).

Figure 3

HIV drug resistance testing in the AMC. A. Percentage of key drug resistance mutations PR/RT in sequences from 1995-2012. Percentages of A (green), C (blue), U (red) and G (black) nucleotides are also shown. B. The number of key drug resistance mutations in PR from 1995-2012. The size of the circles is correlated with the number of sequences in that category. C. The number of key drug resistance mutations in RT per sequence from 1995-2012. The size of the circles is correlated with the number of sequences in that category; colours were added for clarity.

Figure 4

HIV-1 subtype distribution in the AMC. A. Numbers of HIV-1 non-B subtypes detected in patients visiting the AMC (Amsterdam, the Netherlands) from 1996-2012. “Unknown” consists of circulating recombinant forms (CRFs) other than CRF01_AE and CRF02_AG as well as difficult to type, complex mosaic strains and possible new subtypes. B. Percentages of HIV-1 B and non-B subtypes in the patient population according to the transmission risk group of HIV-1 that could be retrieved from the database. The total number of sequences (N) analysed in each group is indicated.