HIV This Week

Designing a genome-based HIV incidence assay with high sensitivity and specificity

Park SY, Love TM, Nelson J, Thurston SW, Perelson AS, Lee HY. AIDS. 2011 Jun 29. [Epub ahead of print]

Considerable inaccuracy in estimates of human immunodeficiency virus (HIV) incidence has been a serious obstacle to the development of efficient HIV prevention interventions. Accurately distinguishing recent or incident infections from chronic infections enables one to monitor epidemics and evaluate the impact of HIV prevention/intervention trials. However, serological testing has not been able to realise these promises due to a number of critical limitations. This study is aimed to design a novel scheme of identifying incident infections in a highly accurate manner, based on the characteristics of HIV gene diversification within an infected individual. Park and colleagues perform a comprehensive meta-analysis on 5596 full envelope HIV genes generated by single genome amplification-direct sequencing from 182 incident and 43 chronic cases. They devise a binary classification test based on the tail characteristics of the Hamming distance distribution of sequences. The authors identify a clear signature of incident infections, the presence of closely related strains in the sampled HIV envelope gene sequences in each HIV infected patient, in both single-variant and multi-variant transmissions. The sequence similarity used as a biomarker is found to have high specificity and sensitivity, greater than 95%, and is robust to viral and host specific factors such as the clade of the viral strain, viral load, and the length and location of sequences in the HIV envelope gene. Because of rapid and continuing improvements in sequencing technology and cost, sequence based incidence assays hold great promise as a means of quantifying HIV incidence from a single blood test.

For abstract access click here

Editor’s note: Current laboratory tests to estimate HIV incidence, such as the STARHS testing algorithm, the BED assay, and the avidity assay, have critical limitations that make interpretation of their results a challenge. They have variable sensitivity, i.e. the proportion of incident infections correctly identified as incident varies from 42-100% (median 89%), and variable specificity, i.e. the proportion of chronic infections correctly identified as chronic varies from 49.5-100% (median 86.8%). Accurately estimating HIV incidence is critical for assessing the effectiveness of HIV prevention programmes and for efficient allocation of resources, both human and financial. The biomarker described here, a genome-based HIV incidence assay, requires only one blood specimen and has high sensitivity and specificity regardless of viral clade and viral load. It measures HIV gene diversification as the Hamming distance, i.e. the number of base differences between a pair of sequences. In incident infections (first year), the Hamming distance is low because there are a fair number of identical or near identical sequences in each lineage of the transmitted founder virus. The HIV population diversifies over time because HIV is a sloppy copier of itself and identical sequences decrease exponentially over time. This genome-based assay has a couple of problems. Although most infections are established by a single founder virus, multi-variant transmission occurs in 36% of anal-sex transmissions and 60% of injecting-related transmissions. The assay picks up the increased Hamming distance diversity and variance and classifies these infections as chronic. In end stage HIV disease, viral diversity declines so this sequencing-based assay might incorrectly identify these people as having incident infections. Nonetheless, this new powerful tool, reporting a sensitivity of 97% and specificity of 100% in this study, is an exciting development for the HIV field.

Host genetics and HIV-1: the final phase?

Fellay J, Shianna KV, Telenti A, Goldstein DB. PLoS Pathog. 2010 Oct 14;6(10):e1001033

This is a crucial transition time for human genetics in general, and for HIV host genetics in particular. After years of equivocal results from candidate gene analyses, several genome-wide association studies have been published that looked at plasma viral load or disease progression. Results from other studies that used various large-scale approaches - small interfering RNA (siRNA) screens, transcriptome or proteome analysis, comparative genomics - have also shed new light on retroviral pathogenesis. However, most of the inter-individual variability in response to HIV-1 infection remains to be explained: genome resequencing and systems biology approaches are now required to progress toward a better understanding of the complex interactions between HIV-1 and its human host.

Abstract

Editors’ note : Highly exposed, yet uninfected, people such as the 5% of men with severe haemophilia born before 1979 who did not become infected, the cohorts of men who have sex with men reporting high exposure levels, and the famous Nairobi sex workers have exceptional resistance to HIV infection. Analysing their genetic make-up improves our understanding of genetic influences on susceptibility, as will comparing the genetic make-up of people with HIV infection with that of uninfected controls. So far, most genetic studies have focused on people with Western European ancestry with the result that we lack information on genetic diversity. Thus far, we have only found variation in CCR5 to be a significant human genetic determinant of HIV acquisition while human leukocyte antigen (HLA) class is the most prominent genetic determinant of differences in viral load set point and CD4 count decline. Because some clinically stable people who become superinfected have very rapid disease progression and because marked differences have been documented in viral load set point between donor and recipients in HIV transmission pairs, the virus itself must be important too. Understanding individual host-virus interaction differences is key to both developing HIV vaccines and anticipating how people living with HIV will respond to treatment. The HIV host genetic research field is using genome analysis and systems biology high throughput quantitative modelling techniques to describe human genetic influences on HIV. This review is an interesting read.

Biomarkers of immune dysfunction in HIV

Nixon DE, Landay AL. Curr Opin HIV AIDS. 2010 Nov;5(6):498-503

HIV infection is characterized by chronic immune system activation and inflammatory cytokine production. This review highlights recent developments using plasma and cellular biomarkers of immune system activation and dysfunction to predict mortality and opportunistic disease in HIV-infected individuals. HIV infection results in features characteristic of early aging of the immune system or 'immune senescence', driven by chronic antigen exposure and immune system activation. Microbial translocation of gut bacterial components is associated with chronic immune activation and possibly systemic inflammation. Antiretroviral therapy may not fully normalize this condition. Baseline elevations of certain biomarkers of inflammation or coagulopathy, notably interleukin-6, C-reactive protein, and D-dimer, have been associated with mortality or opportunistic disease, after adjustment for appropriate variables, in several large randomized clinical trials. It is not known if elevated interleukin-6 or C-reactive protein causes this morbidity and mortality or if they are simply surrogate markers of a global inflammatory state. Several inflammatory biomarkers appear to add to our ability to predict mortality or opportunistic disease in HIV-infected individuals. Before biomarkers will be useful, it will be necessary to identify interventions that moderate biomarker levels, and then determine if this moderation attenuates disease outcomes.

Abstract

Editors’ note: There are some striking similarities between biomarker changes seen in the immune system during the aging process and those seen in HIV infection. In fact, the ongoing inflammation associated with aging is described as ‘inflamm-aging’. Inflammation plays a role in cancer, cardiovascular disease, metabolic, bone, kidney, and liver disease in the general population so it is not surprising that people living with HIV who have chronic immune system activation are more at risk of these diseases. This review is an excellent summary of the state of our knowledge on the role of each biomarker: plasma or serum biomarkers as well as cellular markers of immune dysfunction. Antiretroviral therapy does reduce one biomarker, D-dimer, and the START (Strategic Timing of Antiretroviral Therapy) study may help validate the concept of ‘biomarker-guided’ antiretroviral therapy.

HIV-1 long-term non-progressors: the viral, genetic, and immunological basis for disease non-progression.

Poropatich K, Sullivan DJ Jr. J Gen Virol. 2010 Nov 24

A small subset of Human Immunodeficiency Virus type 1 (HIV-1)-infected, therapy-naive individuals-referred to as long-term non-progressors (LTNPs)-maintain a favourable course of infection, often being asymptomatic for several years with high CD4+ and CD8+ T cell counts (>500 cells/μL) and low plasma HIV-RNA levels (<10,000 copies/mL). Research in the field has undergone considerable development in recent years and long term non-progressors offer a missing piece to the puzzle of understanding the ways that persons can naturally control HIV-1 infection. Their method of control is based on viral, genetic and immunological components. With respect to virological features, genomic sequencing has shown that some long term non-progressors are infected with attenuated strains of HIV-1 and harbor mutant nef, vpr, vif, or rev genes that contain single nuclear polymorphisms, or less frequently, large deletions, in conserved domains. Studies have also shown that some long term non-progressors have unique genetic advantages including heterozygosity for the CCR5-Δ32 polymorphism, and have been found with activatory mutations that upregulate the production of the chemokines that competitively inhibit HIV-1 binding to CCR5 or CXCR4. Lastly, immunologic factors are crucial for providing long term non-progressors with a natural form of control, the most importantly being robust HIV-specific CD4+ and CD8+ T cell responses that correlate to lower viral loads. Many long term non-progressors carry the HLA class I B57 allele that enhances presentation of antigenic peptides on the surface of infected-CD4+ cells to cytotoxic CD8+ T cells. For these reasons, long term non-progressors serve as an ideal model for HIV-1 vaccine development due to their natural control of HIV-1 infection.

For abstract access click here:

Editors’ note: This excellent review of the scientific literature on long-term non-progressors examines the characteristics of their natural responses to HIV that could provide insights for the design of efficacious HIV vaccines. Long-term non-progressors are people who maintain low levels of virus in the blood and elevated CD4 levels for many years after becoming infected without being on antiretroviral treatment. An estimated 2-5% of people living with HIV are considered to be long-term non-progressors and a small subset of them (less than 1%), called elite controllers, have undetectable viral loads but generally lower CD4 counts than other long-term non-progressors. Sorting out whether the virus infecting non-progressors including elite controllers is different from the virus infecting those who progress more rapidly is the first step. Evidence to date is contradictory suggesting that attenuating viral gene mutations are likely not enough to explain control of infection. The review examines the known host genetic factors that inhibit progression, such as chemokine receptor polymorphisms (e.g. CCR5-delta32) and examines the role of innate immunity (toll-like receptors, mannose-binding lectin, natural killer cells) and adaptive immunity (HLA class I alleles, differences in CD8 cell responses, and broadly neutralising antibodies). It concludes that the most realistic approach to developing an HIV vaccine would be to aim not to prevent HIV infection in the first place but to provide partial immune control against viral replication to prevent clinical disease.