Epidemiology of the 2022 Mpox Outbreak in the US Veterans Health Administration.

BACKGROUND: In May 2022, mpox cases were reported in nonendemic countries, including the United States. We examined mpox infections in the Veterans Health Administration (VHA). METHODS: Mpox diagnostic and whole genome sequencing (WGS) results, demographics, risk factors, hospitalizations, exposures, deaths, and pharmacy and immunization data were obtained from VHA data sources (23 May 2022-31 May 2023). RESULTS: Of 1144 Veterans tested, 251 (21.9%) were presumptive positive for nonvariola orthopoxvirus (NVO) or confirmed positive for NVO and Monkeypox virus (MPXV). Incidence rate was 7.5 per 100 000 Veterans in care, with the highest rate observed in Veterans aged 25-34 years (13.83 cases per 100 000). Higher odds of NVO or NVO/MPXV positivity was associated with male sex; non-Hispanic Black race/ethnicity; syphilis or human immunodeficiency virus (HIV) positivity; or genital/rectal sample site, whereas older age and vaccination with JYNNEOS or vaccinia (smallpox) had lower odds. Among 209 with confirmatory testing, 90.4% reported intimate contact and/or an epidemiological link, 84.5% were men who have sex with men (MSM), 24.2% received tecovirimat, and 8.1% were hospitalized with 1 death. Eighty-six sequenced samples had evaluable WGS results. All were clade IIb, representing 10 different lineages from 20 states and the District of Columbia. CONCLUSIONS: Mpox affected younger, MSM, non-Hispanic Black, and HIV/syphilis-positive men among US Veterans. Viral diversity was noted across geographic regions. At-risk Veterans would benefit from vaccination and risk reduction strategies for mpox and other sexually transmitted infections.

Companion and complementary diagnostics for infectious diseases.

INTRODUCTION: Companion diagnostics (CDx) are important in oncology therapeutic decision-making, but specific regulatory-approved CDx for infectious disease treatment are officially lacking. While not approved as CDx, several ID diagnostics are used as CDx. The diagnostics community, manufacturers, and regulatory agencies have made major efforts to ensure that diagnostics for new antimicrobials are available at or near release of new agents. AREAS COVERED: This review highlights the status of Complementary and companion diagnostic (c/CDx) in the infectious disease literature, with a focus on genotypic antimicrobial resistance testing against pathogens as a class of diagnostic tests. EXPERT OPINION: CRISPR, sepsis markers, and narrow spectrum antimicrobials, in addition to current and emerging technologies, present opportunities for infectious disease c/CDx. Challenges include slow guideline revision, high costs for regulatory approval, lengthy buy in by agencies, discordant pharmaceutical/diagnostic partnerships, and higher treatment costs. The number of patients and available medications used to treat different infectious diseases is well suited to support competing diagnostic tests. However, newer approaches to treatment (for example, narrow spectrum antibiotics), may be well suited for a small number of patients, i.e. a niche market in support of a CDx. The current emphasis is rapid and point-of-care (POC) diagnostic platforms as well as changes in treatment.

Analysis of multiple cell reservoirs expressing unspliced HIV-1 gag-pol mRNA in patients on antiretroviral therapy.

AIMS: Longitudinal percentage change of eight HIV-1 gag-pol mRNA cellular reservoirs from HIV-infected subjects on antiretroviral therapy was ascertained by simultaneous ultrasensitive subpopulation staining/hybridization in situ (SUSHI). MATERIALS #ENTITYSTARTX00026; METHODS: Serial peripheral blood mononuclear cells were taken from three subjects with treatment success, limited response and viral breakthrough plasma viral load (PVL) profiles. SUSHI was carried out on monocytes, macrophages, CD4(+) cells and naive, memory and activated T-cell reservoirs followed with broad light scatter flow cytometry. RESULTS: All gag-pol(+) reservoirs declined in the treatment success patient and similar to PVL. Only some gag-pol(+) reservoirs responded similarly to PVL for the limited treatment patient, and most gag-pol(+) reservoirs increased 16 weeks prior to PVL breakthrough in the viral breakthrough patient. CONCLUSION: SUSHI measures changes in a wide range of gag-pol(+) reservoirs in response to antiretroviral therapy.

Molecular epidemiology of HIV-1 subtypes and drug resistant strains in Taiwan.

The Taiwanese government has provided free highly active antiretroviral therapy since April 1997. Previously, we have reported on the molecular epidemiology of HIV-1 in Taiwan from 1988 to 1998. In addition, an outbreak of circulating recombinant form (CRF) 07_BC among intravenous drug users was noted in 2004. Therefore, the purposes of this study were to elucidate the distribution of HIV-1 subtypes among different high-risk groups in Taiwan from 1999 to 2000 and to conduct surveillance on drug resistance among treatment naïve patients from 1997 to 2000. Blood samples from 239 HIV-1/AIDS patients and their subtypes were examined using DNA sequencing and phylogenetic analysis. The results showed that among 226 male patients, 213 (94.2%) had subtype B, 11 (4.9%) had CRF01_AE, 1 had unique recombinant strain related to both CRF07_BC and CRF08_BC (strain T12-99TW) and 1 had CRF08_BC (strain L9312-00TW). The patients infected with T12-99TW and L9312-00TW were intravenous drug users and had needle-sharing experiences in Yunnan Province, China. Of the 13 HIV-1-infected females, 7 (53.8%) had subtype B, 5 (38.5%) had CRF01_AE, and 1 (7.7%) had subtype C. Phylogenetic analysis demonstrated that the neither strain T12-99TW nor L9312-00TW clustered with CRF07_BC strains isolated from Taiwanese intravenous drug users in 2004. In addition, 126 treatment naïve patients were selected for genotypic DR analysis and the results showed that 4.3% (2/47) homosexual males had M184V mutations. This is the first report on the identification of CRF08_BC and a unique recombinant strain related to both CRF07_BC and CRF08_BC in Taiwan.

Cost assessment of the automated VERSANT 440 Molecular System versus the semi-automated System 340 bDNA Analyzer platforms.

Labor, supply and waste were evaluated for HIV-1 and HCV bDNA on the semi-automated System 340 bDNA Analyzer and the automated VERSANT 440 Molecular System (V440). HIV-1 sample processing was evaluated using a 24- and 48-position centrifuge rotor. Vigilance time (hands-on manipulations plus incubation time except initial target hybridization) and disposables were approximately 37 and 12% lower for HIV-1, and 64 and 31% lower for HCV bDNA, respectively, with V440. Biohazardous solid waste was approximately twofold lower for both assays and other waste types were the same for either assay on both platforms. HIV-1 sample processing vigilance time for the 48-position rotor was reduced by 2 h. V440 provides cost savings and improved workflow.

HIV-1 and HCV viral load cost models for bDNA: 440 Molecular System versus real-time PCR AmpliPrep/TaqMan test.

Comparative cost models were developed to assess cost-per-reportable result and annual costs for HIV-1 and HCV bDNA and AmpliPrep/TaqMan Test (PCR). Model cost components included kit, disposables, platform and related equipment, equipment service plan, equipment maintenance, equipment footprint, waste and labor. Model assessment was most cost-effective when run by bDNA with 36 or more clinical samples and PCR with 30 or fewer clinical samples. Lower costs are attained with maximum samples (84-168) run daily. Highest cost contributors include kit, platform and PCR proprietary disposables. Understanding component costs and the most economic use of HIV-1 and HCV viral load will aid in attaining lowest costs through selection of the appropriate assay and effective negotiations.

Evaluation of the VACUTAINER PPT Plasma Preparation Tube for use with the Bayer VERSANT assay for quantification of human immunodeficiency virus type 1 RNA.

Separation and storage of plasma within 2 h of phlebotomy is required for the VACUTAINER PPT Plasma Preparation Tube (PPT) versus 4 h for the predecessor VACUTAINER EDTA tube for human immunodeficiency virus type 1 (HIV-1) viral load (HIVL) testing by the VERSANT HIV-1 RNA 3.0 assay (branched DNA). The 2-h limit for PPT imposes time constraints for handling and transporting to the testing laboratory. This study compares HIVL reproducibility from matched blood in EDTA tubes and PPTs and between PPT pairs following processing within 4 h of phlebotomy, stability of plasma HIV-1 RNA at 24- and 72-h room temperature storage in the tube, and comparative labor and supply requirements. Blood from 159 patients was collected in paired tubes (EDTA/PPT or PPT/PPT): 86 paired EDTA tubes and PPTs were processed 4 h following phlebotomy and their HIVLs were compared, 42 paired PPT/PPT pairs were analyzed for intertube HIVL reproducibility, and 31 PPT/PPT pairs were analyzed for HIV-1 RNA stability by HIVL. Labor and supply requirements were compared between PPT and EDTA tubes. PPTs produce results equivalent to standard EDTA tube results when processed 4 h after phlebotomy. PPT intertube analyte results are reproducible. An average decrease of 13% and 37% in HIVL was observed in PPT plasma after 24 and 72 h of room temperature storage, respectively; thus, plasma can be stored at room temperature up to 24 h in the original tube. PPTs offer labor and supply savings over EDTA tubes.

HIV RNA testing in the context of nonoccupational postexposure prophylaxis.

BACKGROUND: The specificity and positive predictive value of human immunodeficiency virus (HIV) RNA assays have not been evaluated in the setting of postexposure prophylaxis (PEP). METHODS: Plasma from subjects enrolled in a nonoccupational PEP study was tested with 2 branched-chain DNA (bDNA) assays, 2 polymerase chain reaction (PCR) assays, and a transcription-mediated amplification (TMA) assay. Assay specificity and positive predictive value were determined for subjects who remained negative for HIV antibody for >or=3 months. RESULTS: In 329 subjects examined, the lowest specificities (90.1%-93.7%) were seen for bDNA testing performed in real time. The highest specificities were seen with batched bDNA version 3.0 (99.1%), standard PCR (99.4%), ultrasensitive PCR (100%), and TMA (99.6%) testing. Only the 2 assays with the highest specificities had positive predictive values >40%. For the bDNA assays, increasing the cutoff point at which a test is called positive (e.g., from 50 copies/mL to 500 copies/mL for version 3.0) increased both specificity and positive predictive values to 100%. CONCLUSIONS: The positive predictive value of HIV RNA assays in individuals presenting for PEP is unacceptably low for bDNA-based testing and possibly acceptable for PCR- and TMA-based testing. Routine use of HIV RNA assays in such individuals is not recommended.

Simultaneous runs of the Bayer VERSANT HIV-1 version 3.0 and HCV bDNA version 3.0 quantitative assays on the system 340 platform provide reliable quantitation and improved work flow.

Branched DNA (bDNA) assays to quantify human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) consist of three distinct steps, including sample processing, hybridization, and detection, and utilize the System 340 platform for plate incubation and washing. Sample processing differs: HIV-1 from 1 ml of plasma is concentrated by high-speed centrifugation, whereas HCV plasma or serum samples are used without concentration. The first step of hybridization involves viral lysis at 63 degrees C: HIV-1 is performed in a heat block, whereas HCV is performed in System 340. The remaining hybridization and detection steps are similar for HIV-1 and HCV and executed on System 340. In the present study, the HIV-1 bDNA assay was adapted for viral lysis in the System 340 platform. The adaptation, test method 2, includes a 20-s vortex of concentrated viral pellet and lysis working solution, transfer of viral lysate to the 96-well capture plate, and transfer to System 340 programmed for HCV assay specifications. With test method 2, specificity and quantification were within assay specifications. HCV bDNA methodology remains unchanged. Hence, an HIV-1 and an HCV bDNA can be run simultaneously on System 340. With simultaneous testing, laboratories can run full plates, as well as combinations of full and partial plates. Also, simultaneous HIV-1 and HCV bDNA permits labor consolidation and improved workflow while maintaining multitasking and rapid patient result turnaround.

Multicenter evaluation of the performance characteristics of the bayer VERSANT HCV RNA 3.0 assay (bDNA).

In this multicenter evaluation, the VERSANT HCV RNA 3.0 Assay (bDNA) (Bayer Diagnostics, Tarrytown, N.Y.) was shown to have excellent reproducibility, linearity, and analytical sensitivity across specimen collection matrices (serum, EDTA, ACD-A), and hepatitis C virus (HCV) genotypes 1 to 6. The VERSANT HCV bDNA Assay has a reportable range of 615 to 7690000 (7.69 x 10(6)) IU/ml. The total coefficient of variation (CV) ranged from 32.4% at 615 IU/ml to 17% at 6.8 x 10(6) IU/ml. The assay was linear across the reportable range. Analytical specificity of 98.8% was determined by testing 999 specimens from volunteer blood donors. Evaluation of HCV genotypes using RNA transcripts of representative clones of 1a, 1b, 2a, 2b, 2c, 3a, 4a, 5a, and 6a and patient specimens showed that the largest difference between genotype 1, upon which the assay is standardized, and non-1 genotypes was within 1.5-fold. Testing of potentially interfering endogenous substances and exogenous substances and conditions found no interference in HCV-positive or HCV-negative specimens except for unconjugated bilirubin at concentrations of >or=20 mg/dl and protein at concentrations of >or=9 g/dl. Biological variability was estimated from 29 clinically stable individuals not on HCV therapy who were tested weekly over an 8-week period. The combined estimate of total (biologic plus assay) variability was 0.15 log(10) standard deviation (CV, 36.1%), a fold change of 2.6. Thus, the observed fold change between any two consecutive HCV RNA measures is expected to be less than 2.6-fold (equivalent to 0.41 log(10) IU/ml) 95% of the time in clinically stable individuals.

Short-term effects of cannabinoids in patients with HIV-1 infection: a randomized, placebo-controlled clinical trial.

BACKGROUND: Cannabinoid use could potentially alter HIV RNA levels by two mechanisms: immune modulation or cannabinoid-protease inhibitor interactions (because both share cytochrome P-450 metabolic pathways). OBJECTIVE: To determine the short-term effects of smoked marijuana on the viral load in HIV-infected patients. DESIGN: Randomized, placebo-controlled, 21-day intervention trial. SETTING: The inpatient General Clinical Research Center at the San Francisco General Hospital, San Francisco, California. PARTICIPANTS: 67 patients with HIV-1 infection. INTERVENTION: Participants were randomly assigned to a 3.95%-tetrahydrocannabinol marijuana cigarette, a 2.5-mg dronabinol (delta-9-tetrahydrocannabinol) capsule, or a placebo capsule three times daily before meals. MEASUREMENTS: HIV RNA levels, CD4+ and CD8+ cell subsets, and pharmacokinetic analyses of the protease inhibitors. RESULTS: 62 study participants were eligible for the primary end point (marijuana group, 20 patients; dronabinol group, 22 patients; and placebo group, 20 patients). Baseline HIV RNA level was less than 50 copies/mL for 36 participants (58%), and the median CD4+ cell count was 340 x 109 cells/L. When adjusted for baseline variables, the estimated average effect versus placebo on change in log10 viral load from baseline to day 21 was -0.07 (95% CI, -0.30 to 0.13) for marijuana and -0.04 (CI, -0.20 to 0.14) for dronabinol. The adjusted average changes in viral load in marijuana and dronabinol relative to placebo were -15% (CI, -50% to 34%) and -8% (CI, -37% to 37%), respectively. Neither CD4+ nor CD8+ cell counts appeared to be adversely affected by the cannabinoids. CONCLUSIONS: Smoked and oral cannabinoids did not seem to be unsafe in people with HIV infection with respect to HIV RNA levels, CD4+ and CD8+ cell counts, or protease inhibitor levels over a 21-day treatment.

Global cost modeling analysis of HIV-1 and HCV viral load assays.

This review addresses hidden costs associated with the Bayer VERSANT assay, Roche AMPLICOR MONITOR test and COBAS AMPLICOR MONITOR test and how these influence the final per reportable cost to a testing laboratory in resource-rich and -poor countries. An in-depth evaluation and recommendation of the most cost-effective approach for these tests is presented. The analyses demonstrate the need for manufacturers to consider labor and supply costs when marketing a kit in resource-poor countries, noting that marketing strategies need to change. In the absence of any proven monitoring alternative, emphasis is placed on increasing market share to promote significant reduction in kit prices to suit the demands of markets in resource-poor countries. Finally, recommendations are made to improve the overall cost structure of viral load testing. This review is intended as a tool to optimize assay usage in attaining the lowest performance costs by assay and is not to endorse any test, as will become apparent.

Multicenter evaluation of the Bayer VERSANT HIV-1 RNA 3.0 assay: analytical and clinical performance.

BACKGROUND: The use of quantitative HIV-1 RNA assays is part of the standard of care for the management of HIV-1-infected individuals. OBJECTIVE: The Bayer VERSANT HIV-1 RNA 3.0 Assay (bDNA) was evaluated for reproducibility, linearity, limits of detection and quantitation, effects of potentially interfering substances and conditions, effects of plasma collection and handling conditions, clinical sensitivity and specificity, and biologic variability. STUDY DESIGN: Anti-HIV-1-positive specimens, patient specimens containing potentially interfering substances, and anti-HIV-negative specimens were collected from several HIV clinics, blood centers, or commercial companies across the United States. Specimen panels used to evaluate nonclinical performance of the assay were prepared at Bayer Diagnostics. Bayer Assay Development personnel performed 2 of the nonclinical studies-effect of freeze-thaw cycles using 'spiked' HIV-1 RNA-positive samples and effect of other disease organisms. All other studies were conducted at 7 external sites. In some of the studies performed, specimens were tested in parallel with the Roche AMPLICOR HIV-1 MONITOR version 1.0 PCR Test. RESULTS/CONCLUSIONS: The results of these studies showed that the Bayer Assay has excellent reproducibility, a broad linear range (75-500,000 HIV-1 RNA copies/ml), throughput of 168 patient results per two-plate run in a 22-h period, and few limitations for use. Because this test is designed for use only in individuals who are known to be HIV-1-positive, the clinical specificity of 97.6% is adequate for its intended use. These characteristics make it an attractive method for general laboratory use of monitoring HIV-1-infected patients.

Health care industries' perspective of viral load assays: the VERSANT HIV-1 RNA 3.0 assay.

This article will compare the VERSANT HIV-1 RNA 3.0 (bDNA 3.0) assay with other HIV-1 viral load assays, particularly the AMPLICOR HIV-1 MONITOR (Amplicor 1.5), the industry standard. The discussion will cover the history of viral load assay development and challenges to the field. It will finish with a description of the evolving markets for viral load assays in the developing world and the impact of variations in the different assays on their ability to reach those markets and patient populations.

Comparative analysis of HIV-1 viral load assays on subtype quantification: Bayer Versant HIV-1 RNA 3.0 versus Roche Amplicor HIV-1 Monitor version 1.5.

Quantification of HIV-1 subtypes is essential for appropriate clinical management. Whereas viral load assays were initially developed to accurately quantify subtype B, the recent worldwide spread of non-B subtypes and the introduction of treatment programs in regions with non-B subtypes have prompted adaptations of these assays. The Bayer Versant HIV-1 RNA 3.0 Assay (branched DNA [bDNA] 3.0) and the Roche Amplicor HIV-1 Monitor version 1.5 (Amplicor 1.5) assays are reported to quantify all subtypes in group M; however, evaluation of performance characteristics remains limited. In this study, we evaluated the accuracy and reliability of bDNA 3.0 and Amplicor 1.5 on multiple serially diluted viral isolates from HIV-1 group M, subtypes A through F. Testing was conducted on both assay systems in two independent laboratories. Comparative pansubtype quantification from regression analysis showed that quantification by bDNA 3.0 was approximately 0.3 log-fold lower than that by Amplicor 1.5. Comparative pansubtype accuracy analysis showed data points more closely distributed about their respective regression lines and thus showing greater reliability by bDNA 3.0 than by Amplicor 1.5.