Sensitive and Specific Detection of SARS-CoV-2 Antibodies Using a High-Throughput, Fully Automated Liquid-Handling Robotic System.

As of July 22, 2020, more than 14.7 million infections of SARS-CoV-2, the virus responsible for Coronavirus Disease 2019 (COVID-19), have been confirmed globally. Serological assays are essential for community screening, assessing infection prevalence, aiding identification of infected patients, and enacting appropriate treatment and quarantine protocols in the battle against this rapidly expanding pandemic. Antibody detection by agglutination-PCR (ADAP) is a pure solution phase immunoassay that generates a PCR amplifiable signal when patient antibodies agglutinate DNA-barcoded antigen probes into a dense immune complex. Here, we present an ultrasensitive and high-throughput automated liquid biopsy assay based on the Hamilton Microlab ADAP STAR automated liquid-handling platform, which was developed and validated for the qualitative detection of total antibodies against spike protein 1 (S1) of SARS-CoV-2 that uses as little as 4 µL of serum. To assess the clinical performance of the ADAP assay, 57 PCR-confirmed COVID-19 patients and 223 control patients were tested. The assay showed a sensitivity of 98% (56/57) and a specificity of 99.55% (222/223). Notably, the SARS-CoV-2-negative control patients included individuals with other common coronaviral infections, such as CoV-NL63 and CoV-HKU, which did not cross-react. In addition to high performance, the hands-free automated workstation enabled high-throughput sample processing to reduce screening workload while helping to minimize analyst contact with biohazardous samples. Therefore, the ADAP STAR liquid-handling workstation can be used as a valuable tool to address the COVID-19 global pandemic.

Use of the Bio-Rad Geenius HIV-1/2 supplemental assay for the testing of oral fluids for the presence of HIV antibody.

There is currently an absence of products which are cleared by the FDA to provide supplemental testing for oral fluid for HIV antibody. We created a procedure for the use of the BioRad Geenius HIV-1/2 as a supplemental antibody test for oral fluid specimens. The modified procedure was evaluated for its ability to detect HIV-1 antibody in oral fluid in specimens that were found to be repeatedly reactive for HIV-1 antibody by way of the Avioq HIV-1 enzyme immunoassay (EIA). Evaluated were oral fluid specimens analyzed at a local public health laboratory which were stored frozen and oral fluid specimens collected prospectively. Prospectively collected specimens were from patients whose HIV status was subsequently assessed through blood-based testing. For retrospective specimens found repeatedly EIA reactive, and positive by Western blot, the modified Geenius was found positive in 37/38 instances (97.4 %). Those specimens with a mean EIA signal-to-cutoff (S/CO) greater than 3.00 were found to be positive by Geenius in 34/34 (100 %) of instances. For specimens found repeated reactive by EIA and positive by Western blot with mean S/CO less than or equal to 3.00, the Geenius was positive in 4/5 instances (80 %) of instances. For prospectively collected specimens, the Geenius accurately confirmed infection in 22/24 cases (92 %) while prospective specimens found repeatedly reactive by EIA without supplemental Geenius testing were confirmed positive in 29/37 instances (78 %). A modified usage of the Geenius HIV-1/2 Supplemental Assay antibody test may provide utility in the supplementation of testing of oral fluid for the presence of HIV-1 antibody.

Antibody detection by agglutination-PCR (ADAP) enables early diagnosis of HIV infection by oral fluid analysis.

Oral fluid (OF) is a highly effective substrate for population-based HIV screening efforts, as it is noninfectious and significantly easier to collect than blood. However, anti-HIV antibodies are found at far lower concentrations in OF compared with blood, leading to poor sensitivity and a longer period of time from infection to detection threshold. Thus, despite its inherent advantages in sample collection, OF is not widely used for population screening. Here we report the development of an HIV OF assay based on Antibody Detection by Agglutination-PCR (ADAP) technology. This assay is 1,000-10,000 times more analytically sensitive than clinical enzyme-linked immunoassays (EIAs), displaying both 100% clinical sensitivity and 100% specificity for detecting HIV antibodies within OF samples. We show that the enhanced analytical sensitivity enables this assay to correctly identify HIV-infected individuals otherwise missed by current OF assays. We envision that the attributes of this improved HIV OF assay can increase testing rates of at-risk individuals while enabling diagnosis and treatment at an earlier time point.

Impact of GeneXpert MTB/RIF on patients and tuberculosis programs in a low-burden setting. a hypothetical trial.

RATIONALE: Guidelines recommend routine nucleic-acid amplification testing in patients with presumed tuberculosis (TB), but these tests have not been widely adopted. GeneXpert MTB/RIF (Xpert), a novel, semiautomated TB nucleic-acid amplification test, has renewed interest in this technology, but data from low-burden countries are limited. OBJECTIVES: We sought to estimate Xpert's potential clinical and public health impact on empiric treatment, contact investigation, and housing in patients undergoing TB evaluation. METHODS: We performed a prospective, cross-sectional study with 2-month follow-up comparing Xpert with standard strategies for evaluating outpatients for active pulmonary TB at the San Francisco Department of Public Health TB Clinic between May 2010 and June 2011. We calculated the diagnostic accuracy of standard algorithms for initial empiric TB treatment, contact investigation, and housing in reference to three Mycobacterium tuberculosis sputum cultures, as compared with that of a single sputum Xpert test. We estimated the incremental diagnostic value of Xpert, and the hypothetical reductions in unnecessary treatment, contact investigation, and housing if Xpert were adopted to guide management decisions. MEASUREMENTS AND MAIN RESULTS: A total of 156 patients underwent Xpert testing. Fifty-nine (38%) received empiric TB treatment. Thirteen (8%) had culture-positive TB. Xpert-guided management would have hypothetically decreased overtreatment by 94%, eliminating a median of 44 overtreatment days (interquartile range, 43-47) per patient and 2,169 total overtreatment days (95% confidence interval, 1,938-2,400) annually, without reducing early detection of TB patients. We projected similar benefits for contact investigation and housing. CONCLUSIONS: Xpert could greatly reduce the frequency and impact of unnecessary empiric treatment, contact investigation, and housing, providing substantial patient and programmatic benefits if used in management decisions.

A new trend in the HIV epidemic among men who have sex with men, San Francisco, 2004-2011.

BACKGROUND: In San Francisco, men who have sex with men (MSM) have historically comprised 90% of the HIV epidemic. It has been suggested that given the ongoing HIV transmission among this population, there is the possibility of a high-level endemic of HIV into the future. We report on the possibility of another phase in the HIV epidemic among MSM in San Francisco. METHODS: Behavioral surveillance systems monitor HIV prevalence, HIV incidence, and behaviors among populations at high risk for HIV infection. Among MSM, time-location sampling is used to obtain samples for standardized behavioral surveys, HIV-antibody and incidence testing. We analyzed National HIV Behavioral Surveillance data from MSM sampled in 2004, 2008, and 2011. RESULTS: Three hundred eighty-six, 521, and 510 MSM were enrolled in each of the waves. Only slight changes were seen in demographics over time. We detected significant declines in unrecognized HIV infection and methamphetamine use, a significant increase in HIV testing in the past 6 months, and no changes in HIV prevalence, history of gonorrhea infection, or having multiple sex partners. Among HIV-infected men, current antiretroviral treatment (ART) use seems to have risen from 2008 to 2011. CONCLUSIONS: The trends of the last 7 years point to stable HIV prevalence as rising ART coverage results in improving survival coupled with decreasing incidence as ART use achieves viral load suppression at levels more than sufficient to offset ongoing sexual risk behavior. "Treatment as prevention" may be occurring among MSM in San Francisco.

Evaluation of an IgM/IgG sensitive enzyme immunoassay and the utility of index values for the screening of syphilis infection in a high-risk population.

BACKGROUND: Increasing interest in the use of enzyme immunoassays (EIA) for syphilis screening has generated a considerable need for data on the performance of such tests. METHODS: We compared the performance of 1 EIA, the TREP-SURE EIA to that of the Venereal Disease Research Laboratory (VDRL) and Treponema pallidum particle agglutination assay (TPPA) in the detection of infection with Treponema pallidum. In total, 674 specimens were tested by VDRL and EIA (356 VDRL-nonreactive and 318 VDRL-reactive). All specimens that were found to be reactive by either the VDRL or EIA were subsequently analyzed by TPPA. RESULTS: We found that the TREP-SURE EIA was marginally less sensitive than the VDRL test for screening, but was significantly more specific. All EIA-TPPA discordant specimens were analyzed by multiple tests, including Immunoglobulin M- and G-specific Western blots and an IgM-specific EIA. Signal-to-cutoff ratios (index values) generated by the TREP-SURE EIA were also investigated. It was found that these values may be instructive regarding the interpretation of test results, as they were found to correlate strongly with the probability of positivity on a TPPA assay. Specimens that reacted positively on the EIA with very high index values were found overwhelmingly to be reactive by TPPA, perhaps obviating the need for the testing of most EIA positive specimens with a secondary treponemal test. CONCLUSIONS: An IgM/IgG sensitive EIA would be an effective alternative to VDRL for syphilis screening. Using the EIA index values may provide additional, helpful information to the diagnostic process.

Differences in HIV burden and immune activation within the gut of HIV-positive patients receiving suppressive antiretroviral therapy.

BACKGROUND: The gut is a major reservoir for human immunodeficiency virus (HIV) in patients receiving antiretroviral therapy (ART). We hypothesized that distinct immune environments within the gut may support varying levels of HIV. METHODS: In 8 HIV-1-positive adults who were receiving ART and had CD4(+) T cell counts of >200 cells/µL and plasma viral loads of <40 copies/mL, levels of HIV and T cell activation were measured in blood samples and endoscopic biopsy specimens from the duodenum, ileum, ascending colon, and rectum. RESULTS: HIV DNA and RNA levels per CD4(+) T cell were higher in all 4 gut sites compared with those in the blood. HIV DNA levels increased from the duodenum to the rectum, whereas the median HIV RNA level peaked in the ileum. HIV DNA levels correlated positively with T cell activation markers in peripheral blood mononuclear cells (PBMCs) but negatively with T cell activation markers in the gut. Multiply spliced RNA was infrequently detected in gut, and ratios of unspliced RNA to DNA were lower in the colon and rectum than in PBMCs, which reflects paradoxically low HIV transcription, given the higher level of T cell activation in the gut. CONCLUSIONS: HIV DNA and RNA are both concentrated in the gut, but the inverse relationship between HIV DNA levels and T cell activation in the gut and the paradoxically low levels of HIV expression in the large bowel suggest that different processes drive HIV persistence in the blood and gut. TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT00884793 (PLUS1).

Assessment of sensitivity and specificity of first, second, and third generation EIA for the detection of antibodies to HIV-1 in oral fluid.

The performances of three blood-based immunoassays test kits were compared with regard to their ability to detect HIV-1 antibody in oral fluid. It was found that these three kits differ in their ability to detect HIV-1 antibody. Notably, a third generation EIA which has been shown to possess superior sensitivity for antibody detection in plasma appears to possess no sensitivity advantage for detecting HIV-1 antibody in oral fluid.

Assessment of rapid tests for detection of human immunodeficiency virus-specific antibodies in recently infected individuals.

We have evaluated four current Food and Drug Administration-cleared rapid tests for human immunodeficiency virus (HIV)-specific antibodies with a panel of specimens from recently infected individuals. Recent infection was detected by RNA-based screening coupled with enzyme immunoassay-based testing. We found that the sensitivities of the various rapid tests vary greatly with regard to their ability to detect HIV-specific antibodies in recently infected individuals.

In situ transduction of target cells on solid surfaces by immobilized viral vectors.

BACKGROUND: For both in vitro and in vivo gene transfer applications, recombinant viral vectors have almost always been used free in solution. Some site-specificity of the delivery of viral vectors can be achieved by applying a solution containing viral particles specifically to the site of interest. However, such site-specificity is seriously limited since viral vectors can diffuse freely in solution after application. RESULTS: We have developed a novel strategy for in situ transduction of target cells on solid surfaces by viral vectors. In this strategy, adenoviral vectors are attached stably to solid surfaces by using the extremely tight interaction between (strept)avidin and biotin, while maintaining the infectivity of the viral vectors. Target cells are cultured directly on such virus-coated solid surfaces, resulting in the transduction of the cells, in situ, on the solid surface. When compared using an equal number of viral particles present in each well (either immobilized or free), the efficiencies of such in situ transduction on solid surfaces were equivalent to those seen with the adenoviral vectors used free in solution. Since viral particles can be attached at desired locations on solid surfaces in any sizes, shapes, and patterns, the ultimate spatial arrangements of transduced cells on solid surfaces can be predetermined at the time of the preparation of the virus-coated solid surfaces. CONCLUSIONS: We have devised a method of immobilizing adenoviral vectors, tightly and stably, on solid surfaces, while maintaining their ability to infect cells. Such immobilized viral vectors can infect target cells, in situ, on solid surfaces. This strategy should be very useful for the development of a variety of both in vitro and in vivo applications, including the creation of cell-based expression arrays for proteomics and drug discovery and highly site-specific delivery of transgenes for gene therapy and tissue engineering.

Adenovirus-microbead conjugates possess enhanced infectivity: a new strategy for localized gene delivery.

We have created a novel method for coupling adenoviral vectors to solid microbeads in a way that does not adversely affect the infectivity of the attached virions. This method utilizes the extremely tight interaction between the protein streptavidin and its ligand biotin as a means of tethering viral particles to microbeads. The adenovirus-microbead conjugates that were created functioned as fully infectious entities and possessed several functional advantages over free, unmodified viral particles. The adenovirus-microbead conjugates possessed enhanced ability to transduce target cells in culture. For target cells of a highly permissive nature, this increase in infectivity was modest. However for target cells of moderate to low permissivity, the enhancement of transduction efficiency was substantial. Adenoviral vectors, previously incapable of infecting a particular colon cancer cell line, were made fully infectious on the same cell line when delivered as solid-phase conjugates. Additionally, solid-phase adenovirus-microbead conjugates showed highly limited diffusion in solution, allowing for focused delivery of viral vectors only to cells that come into contact with the conjugates. When the solid phase to which the viral particles were attached had paramagnetic properties, the location of viral infections was tightly controllable by magnetic force through the use of strategically placed magnets.

Photochemical control of the infectivity of adenoviral vectors using a novel photocleavable biotinylation reagent.

We have explored a novel strategy for controlling the infectivity of adenoviral vectors. This strategy involves a method whereby the infectivity of adenoviral vectors is neutralized by treatment of viral particles with a water-soluble, photocleavable biotinylation reagent. These modified viral vectors possess little to no infectivity for target cells. Exposure of these modified viral vectors to 365 nm light induces a reversal of the neutralizing, chemical modification, resulting in restoration of infectivity to the viral vectors. The light-directed transduction of target cells by photoactivatable adenoviral vectors was demonstrated successfully both in vitro and in vivo. This photochemical infectivity trigger possesses great potential, both as a research tool and as a novel tactic for the delivery of gene-transfer agents, since the infectivity of adenoviral vectors can be controlled externally in a versatile manner.

A chimera of a gelatinase inhibitor peptide with streptavidin as a bifunctional tumor targeting reagent.

A chimeric protein, consisting of streptavidin fused to a cyclic decapeptide with potent inhibitory activity for matrix metalloproteinases (MMP), has been produced in Escherichia coli and purified. The purified chimera formed a tetramer and showed full biotin-binding ability. The chimera was also capable of both binding to MMP-2 and inhibiting its activity. Thus, both the streptavidin moiety and the decapeptide of the chimera are fully functional. This bifunctional nature of the chimera should facilitate the application of the decapeptide since the streptavidin moiety can be used as a specific conjugation site for almost any materials upon biotinylation.