Performance of Bio-Rad and Limiting Antigen Avidity Assays in Detecting Recent HIV Infections Using the Quebec Primary HIV-1 Infection Cohort

A systematic review of limiting antigen avidity enzyme immunoassay for detection of recent HIV-1 infection to expand supported applications

Introduction

The need for detection of new and recent HIV infections is essential for surveillance and assessing interventions in controlling the epidemic. HIV recency assays are one way of providing reliable incidence estimates by determining recent versus non-recent infection. The objective of this study was to review the current body of knowledge of the limiting antigen avidity enzyme immunoassay to expand supported applications through an assessment of what is known and the gaps.

Methods

A search for peer-reviewed literature in PubMed, Embase, and Web of Science Core Collection was conducted using the search term “human immunodeficiency virus and avidity”. Non-peer reviewed published reports from the Population-based HIV Impact Assessment Project were also included. These were limited to literature published in English between January 2010 and August 2021.

Results

This search resulted in 2080 publications and 14 reports, with 137 peer-reviewed studies and 14 non-peer reviewed reports that met the inclusion criteria, yielding a total of 151 studies for the final review. There were similar findings among studies that compared the performances of assay manufacturers and sample types. Studies that evaluated various assay algorithms and thresholds were heterogeneous, illustrating the need for context-specific test characteristics for classifying recent infections. Most studies estimated subtype-specific test characteristics for HIV subtypes A, B, C, and D. This was further illustrated when looking only at studies that compared HIV incidence estimates from recency assay algorithms and longitudinal cohorts.

Conclusions

These findings suggest that the current body of knowledge provides important information that contributes towards distinguishing recent and non-recent infection and incidence estimation. However, there are knowledge gaps with respect to factors that influence the test characteristics (e.g., HIV-1 subtype, population characteristics, assay algorithms and thresholds). Further studies are needed to estimate and establish context-specific test characteristics that consider these influencing factors to improve and expand the use of this assay for detection of recent HIV infection.

The related factors of new HIV infection among older men in Sichuan, China: A case-control study

Human immunodeficiency virus (HIV) has been widely prevalent among older men (aged ≥50 years old) in Sichuan Province. The study aimed to discover associated factors with the new HIV infection in older men, and provide a scientific basis for the prevention and control of acquired immunodeficiency syndrome (AIDS) in this group. A cross-sectional survey study of newly reported HIV/AIDS and general male residents aged 50 years and older was conducted between April and June 2019, with a resample of respondents to identify cases and controls, followed by a case–control study. Logistic regression was applied to analyse the association between the selected factors and new HIV infection among older men. At last, 242 cases and 968 controls were included. The results of multiple logistic regression suggested that many factors including living alone/concentrated (OR 1.56, 95% CI 1.20–2.04, P = 0.001), have a history of migrant worker (OR 2.10, 95% CI 1.61–2.73, P < 0.001), have commercial sexual behaviour (OR 1.71, 95% CI 1.32–2.22, P < 0.001), married (OR 0.48, 95% CI 0.37–0.64, P < 0.001), have a history of HIV antibody testing (OR 0.73, 95% CI 0.56–0.96, P = 0.026), HIV-related knowledge (OR 0.55, 95% CI 0.42–0.72, P < 0.001) were associated with new HIV infection among older men. The present study revealed some potential risky/protective factors altogether. The results highlighted the direction of HIV/AIDS prevention and control among older men, and it is a social issue that requires the joint participation of the whole society.

Use of HIV Recency Assays for HIV Incidence Estimation and Other Surveillance Use Cases: Systematic Review

BACKGROUND

HIV assays designed to detect recent infection, also known as "recency assays," are often used to estimate HIV incidence in a specific country, region, or subpopulation, alone or as part of recent infection testing algorithms (RITAs). Recently, many countries and organizations have become interested in using recency assays within case surveillance systems and routine HIV testing services to measure other indicators beyond incidence, generally referred to as "non-incidence surveillance use cases."

OBJECTIVE

This review aims to identify published evidence that can be used to validate methodological approaches to recency-based incidence estimation and non-incidence use cases. The evidence identified through this review will be used in the forthcoming technical guidance by the World Health Organization (WHO) and United Nations Programme on HIV/AIDS (UNAIDS) on the use of HIV recency assays for identification of epidemic trends, whether for HIV incidence estimation or non-incidence indicators of recency.

METHODS

To identify the best methodological and field implementation practices for the use of recency assays to estimate HIV incidence and trends in recent infections for specific populations or geographic areas, we conducted a systematic review of the literature to (1) understand the use of recency testing for surveillance in programmatic and laboratory settings, (2) review methodologies for implementing recency testing for both incidence estimation and non-incidence use cases, and (3) assess the field performance characteristics of commercially available recency assays.

RESULTS

Among the 167 documents included in the final review, 91 (54.5%) focused on assay or algorithm performance or methodological descriptions, with high-quality evidence of accurate age- and sex-disaggregated HIV incidence estimation at national or regional levels in general population settings, but not at finer geographic levels for prevention prioritization. The remaining 76 (45.5%) described the field use of incidence assays including field-derived incidence (n=45), non-incidence (n=25), and both incidence and non-incidence use cases (n=6). The field use of incidence assays included integrating RITAs into routine surveillance and assisting with molecular genetic analyses, but evidence was generally weaker or only reported on what was done, without validation data or findings related to effectiveness of using non-incidence indicators calculated through the use of recency assays as a proxy for HIV incidence.

CONCLUSIONS

HIV recency assays have been widely validated for estimating HIV incidence in age- and sex-specific populations at national and subnational regional levels; however, there is a lack of evidence validating the accuracy and effectiveness of using recency assays to identify epidemic trends in non-incidence surveillance use cases. More research is needed to validate the use of recency assays within HIV testing services, to ensure findings can be accurately interpreted to guide prioritization of public health programming.

Diagnosis delays in the UK according to pre or postmigration acquisition of HIV

OBJECTIVES

The aim of this study was to evaluate whether infection occurred pre or postmigration and the associated diagnosis delay in migrants diagnosed with HIV in the UK.

DESIGN

We analyzed a cohort of individuals diagnosed with HIV in the UK in 2014-2016 born in Africa or elsewhere in Europe. Inclusion criteria were arrival within 15 years before diagnosis, availability of HIV pol sequence, and viral subtype shared by at least 10 individuals.

METHODS

We examined phylogenies for evidence of infection after entry into the UK and incorporated this information into a Bayesian analysis of timing of infection using biomarkers of CD4+ cell count, avidity assays, proportion of ambiguous nucleotides in viral sequences, and last negative test dates where available.

RESULTS

One thousand, two hundred and fifty-six individuals were included. The final model indicated that HIV was acquired postmigration for most MSM born in Europe (posterior expectation 65%, 95% credibility interval 64-67%) or Africa (65%, 62-69%), whereas a minority (20-30%) of men and women with heterosexual transmission acquired HIV postmigration. Estimated diagnosis delays were lower for MSM than for those with heterosexual transmission, and were lower for those with postmigration infection across all subgroups. For MSM acquiring HIV postmigration, the estimated mean time to diagnosis was less than one year, but for those who acquired HIV premigration, the mean time from infection to diagnosis was more than five years for all subgroups.

CONCLUSION

Acquisition of HIV postmigration is common, particularly among MSM, calling for prevention efforts aimed at migrant communities. Delays in diagnosis reinforce the need for targeted testing initiatives.

Short Communication: Validation of the Asante HIV-1 Rapid Recency Assay for Detection of Recent HIV-1 Infections in Uganda

Point of care rapid recency testing for HIV-1 may be a cost-effective tool to identify recently infected individuals for incidence estimation, and focused HIV prevention through intensified contact tracing. We validated the Asante™ HIV-1 rapid recency^® assay for use in Uganda. Archived specimens (serum/plasma), collected from longitudinally observed HIV-1 recently and long-term infected participants, were tested with the Asante HIV-1 rapid recency assay per manufacturer's instructions. Previously identified antiretroviral therapy (ART)-naive samples with known seroconversions within 6 months of follow-up were tested in independent laboratories: the Rakai Health Sciences Program (RHSP) and the Uganda Virus Research Institute HIV Reference Laboratory (UVRI-HRL). In addition, samples from participants who seroconverted within 6-18 months and samples from individuals with chronic HIV-1 infection of at least 18 months duration were classified into three categories: ART naive, ART exposed with suppressed viral loads, and ART exposed with detectable viremia. Of the 85 samples seroconverting in ≤6 months, 27 and 42 samples were identified as "recent" by the Asante HIV-1 rapid recency test at the RHSP laboratory and UVRI-HRL, corresponding to sensitivities of 32% and 49%, respectively. There was 72% agreement between the laboratories (Cohen's kappa = 0.481, 95% CI = 0.317-0.646, p < .0001). Specificity was 100% (200/200) among chronically infected ART-naive samples. The Asante HIV-1 rapid recency assay had low sensitivity for detection of recent HIV-1 infections in Uganda, with substantial interlaboratory variability due to differential interpretation of the test strip bands. Specificity was excellent. Assessment of assay performance in other settings is needed to guide decisions on test utility.

HIV-1 Envelope Glycoprotein Amino Acids Signatures Associated with Clade B Transmitted/Founder and Recent Viruses

Background: HIV-1 transmitted/founder viruses (TF) are selected during the acute phase of infection from a multitude of virions present during transmission. They possess the capacity to establish infection and viral dissemination in a new host. Deciphering the discrete genetic determinant of infectivity in their envelope may provide clues for vaccine design. Methods: One hundred twenty-six clade B HIV-1 consensus envelope sequences from untreated acute and early infected individuals were compared to 105 sequences obtained from chronically infected individuals using next generation sequencing and molecular analyses. Results: We identified an envelope amino acid signature associated with TF viruses. They are more likely to have an isoleucine (I) in position 841 instead of an arginine (R). This mutation of R to I (R841I) in the gp41 cytoplasmic tail (gp41CT), specifically in lentivirus lytic peptides segment 1 (LLP-1), is significantly enriched compared to chronic viruses (OR = 0.2, 95% CI (0.09, 0.44), p = 0.00001). Conversely, a mutation of lysine (K) to isoleucine (I) located in position six (K6I) of the envelope signal peptide was selected by chronic viruses and compared to TF (OR = 3.26, 95% CI (1.76–6.02), p = 0.0001). Conclusions: The highly conserved gp41 CT_ LLP-1 domain plays a major role in virus replication in mediating intracellular traffic and Env incorporation into virions in interacting with encoded matrix protein. The presence of an isoleucine in gp41 in the TF viruses’ envelope may sustain its role in the successful establishment of infection during the acute stage.

A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses

The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum samples of recently (n = 106) and chronically (n = 156) HIV-1-infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance of ≤10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering. Ninety-eight distinct consensus envelope sequences were subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small TCs while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's kappa (κ) coefficient of 0.59, p < .00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, odds ratio (OR) = 0.25, 95% confidence interval (CI, 0.04-0.66), p = .002 and OR: 0.17, 95% CI (0.10-0.61), p = .011, respectively. The present study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.

Evaluation of the Bio-Rad Geenius HIV 1/2 Assay as Part of a Confirmatory HIV Testing Strategy for Quebec, Canada: Comparison with Western Blot and Inno-Lia Assays

The rapid confirmatory Bio-Rad Geenius HIV 1/2 assay was evaluated as an alternative to the HIV-1 Western blot (WB) confirmatory assay. A total of 370 retrospective samples collected from 356 patients were tested.

The rapid confirmatory Bio-Rad Geenius HIV 1/2 assay was evaluated as an alternative to the HIV-1 Western blot (WB) confirmatory assay. A total of 370 retrospective samples collected from 356 patients were tested. Sensitivity of the Geenius assay to detect HIV-1 and HIV-2 infections was 100% and 97%, respectively, and that of the WB assay was 86% and 39%, respectively. Geenius reduced the number of indeterminate results by 85% and exhibited a differentiation capacity for HIV-1 and HIV-2 of 100% and 89%, respectively. Three of 10 patients presenting with an early HIV infection (1 to 2 weeks before seroconversion by WB) were positive using Geenius. None of the HIV-negative samples were positive using Geenius or WB. However, 7% and 10% of them were indeterminate with Geenius and WB, respectively, leading to a specificity rate of 93% for Geenius and 90% for WB. Ninety cadaveric samples (54 negative, 23 HIV-1 positive, and 3 HIV-1 indeterminate) were tested with Geenius, leading to a sensitivity of 100%, a specificity of 96%, and an indeterminate rate of 4%. Our results indicate that the Bio-Rad Geenius HIV 1/2 rapid test exhibits better sensitivity to detect HIV-1 infections and better performance than WB to confirm and differentiate between HIV-1 and HIV-2 infections. The performance of this new confirmatory assay to detect early infections, to reduce the rate of indeterminate status, and to confirm HIV-1 infection in cadaveric blood samples makes Geenius a potent reliable alternative to the WB.

HIV-1 envelope sequence-based diversity measures for identifying recent infections

Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections) env coding regions, including V1-C5 of gp120 and the gp41 ectodomain of HIV-1, were successfully amplified and sequenced by next generation sequencing (NGS) using the Illumina MiSeq platform. The ability of the four sequence-based diversity measures to correctly identify recent HIV infections was evaluated using the frequency distribution curves, median and interquartile range and area under the curve (AUC) of the receiver operating characteristic (ROC). Comparing the median and interquartile range and evaluating the frequency distribution curves associated with the 4 sequence-based diversity measures, we observed that the percent diversity, number of haplotypes and Shannon entropy demonstrated significant potential to discriminate recent from chronic infections (p<0.0001). Using the AUC of ROC analysis, only the Shannon entropy measure within three HIV-1 env segments could accurately identify recent infections at a satisfactory level. The env segments were gp120 C2_1 (AUC = 0.806), gp120 C2_3 (AUC = 0.805) and gp120 V3 (AUC = 0.812). Our results clearly indicate that the Shannon entropy measure represents a useful tool for predicting HIV-1 infection recency.

The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards

HIV incidence is a primary metric for epidemic surveillance and prevention efficacy assessment. HIV incidence assay performance is evaluated via false recency rate (FRR) and mean duration of recent infection (MDRI). We conducted a meta-analysis of 438 incident and 305 chronic specimens' HIV envelope genes from a diverse global cohort. The genome similarity index (GSI) accurately characterized infection stage across diverse host and viral factors. All except one chronic specimen had GSIs below 0.67, yielding a FRR of 0.33 [0-0.98] %. We modeled the incidence assay biomarker dynamics with a logistic link function assuming individual variabilities in a Beta distribution. The GSI probability density function peaked close to 1 in early infection and 0 around two years post infection, yielding MDRI of 420 [361, 467] days. We tested the assay by newly sequencing 744 envelope genes from 59 specimens of 21 subjects who followed from HIV negative status. Both standardized residuals and Anderson-Darling tests showed that the test dataset was statistically consistent with the model biomarker dynamics. This is the first reported incidence assay meeting the optimal FRR and MDRI performance standards. Signatures of HIV gene diversification can allow precise cross-sectional surveillance with a desirable temporal range of incidence detection.

Characterization of Humoral Immune Responses against Capsid Protein p24 and Transmembrane Glycoprotein gp41 of Human Immunodeficiency Virus Type 1 in China

The objective of this study was to extend our previous research and to further characterize the humoral immune responses against HIV-1 p24, gp41 and the specific peptides carrying the immunodominant epitopes (IDEs) that react with human serum samples from HIV-1-infected individuals in China. We found that the majority (90.45%, 180/199) of the samples did not react with any of the three HIV-1 p24 peptides carrying IDEs, but did react with the recombinant full-length p24, suggesting that these samples tested in China were primarily directed against the conformational epitopes of HIV-1 p24. In contrast, 84.54% (164/194) of the samples reacted with at least one HIV-1 linear gp41 peptide, in particular the gp41-p1 peptide (amino acids 560-616). Both recently and long-term HIV-1-infected individuals displayed similar humoral immune responses against the recombinant gp41. However, samples from long-term HIV-1-infected subjects but not from recently infected subjects, showed a very strong reaction against the gp41-p1 peptide. The different response patterns observed for the two groups against the gp41 and the peptide gp41-p1 were statistically significant (P<0.01, Chi-square test). These results have direct relevance and importance for design of improved HIV-1 p24 detection assays and the gp41- based immunoassay that can be used to reliably distinguish recent and long-term HIV-1 infection.