Sequencing of a bulk polymerase chain reaction (PCR) product to identify drug resistance mutations informs antiretroviral therapy selection but has limited sensitivity for minority variants. ...Alternatively, deep sequencing is capable of detecting minority variants but is subject to sequencing errors and PCR resampling due to low input templates. We screened for resistance mutations among 184 HIV-1-infected, therapy-naive subjects using the 454 sequencing platform to sequence two amplicons spanning HIV-1 reverse transcriptase codons 34-245. Samples from 19 subjects were also analyzed using the MiSeq sequencing platform for comparison. Errors and PCR resampling were addressed by tagging each HIV-1 RNA template copy (i.e., cDNA) with a unique sequence tag (Primer ID), allowing a consensus sequence to be constructed for each original template from resampled sequences. In control reactions, Primer ID reduced 454 and MiSeq errors from 71 to 2.6 and from 24 to 1.2 errors/10,000 nucleotides, respectively. MiSeq also allowed accurate sequencing of codon 65, an important drug resistance position embedded in a homopolymeric run that is poorly resolved by the 454 platform. Excluding homopolymeric positions, 14% of subjects had evidence of ≥1 resistance mutation among Primer ID consensus sequences, compared to 2.7% by bulk population sequencing. When calls were restricted to mutations that appeared twice among consensus sequence populations, 6% of subjects had detectable resistance mutations. The use of Primer ID revealed 5-15% template utilization on average, limiting the depth of deep sequencing sampling and revealing sampling variation due to low template utilization. Primer ID addresses important limitations of deep sequencing and produces less biased estimates of low-level resistance mutations in the viral population.
COVID-19 convalescent plasma (CCP) was an early and widely adopted putative therapy for severe COVID-19. Results from randomized control trials and observational studies have failed to demonstrate a ...clear therapeutic role for CCP for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Underlying these inconclusive findings is a broad heterogeneity in the concentrations of neutralizing antibodies (nAbs) between different CCP donors. We conducted this study to evaluate the effectiveness and safety of nAb titer-defined CCP in adults admitted to an academic referral hospital. Patients positive by a SARS-CoV-2 nucleic acid amplification test and with symptoms for <10 days were eligible. Participants received either CCP with nAb titers of >1:640 (high-titer group) or ≥1:160 to 1:640 (standard-titer group) in addition to standard of care treatments. The primary clinical outcome was time to hospital discharge, with mortality and respiratory support evaluated as secondary outcomes. Adverse events were contrasted by CCP titer. Between 28 August and 4 December 2020, 316 participants were screened, and 55 received CCP, with 14 and 41 receiving high- versus standard-titer CCP, respectively. Time to hospital discharge was shorter among participants receiving high- versus standard-titer CCP, accounting for death as a competing event (hazard ratio, 1.94; 95% confidence interval CI, 1.05 to 3.58; Gray's
= 0.02). Severe adverse events (SAEs) (≥grade 3) occurred in 4 (29%) and 23 (56%) of participants receiving the high versus standard titer, respectively, by day 28 (risk ratio, 0.51; 95% CI, 0.21 to 1.22; Fisher's
= 0.12). There were no observed treatment-related AEs. (This study has been registered at ClinicalTrials.gov under registration no. NCT04524507).
In this study, in a high-risk population of patients admitted for COVID-19, we found an earlier time to hospital discharge among participants receiving CCP with nAb titers of >1:640 compared with participants receiving CCP with a lower nAb titer and no CCP-related AEs. The significance of our research is in identifying a dose response of CCP and clinical outcomes based on nAb titer. Although limited by a small study size, these findings support further study of high-nAb-titer CCP defined as >1:640 in the treatment of COVID-19.
Adherence to antiretroviral (ARV) therapy is critical for achieving HIV RNA suppression in people living with HIV and for preventing HIV infection in uninfected individuals using preexposure ...prophylaxis. However, a high level of adherence can be challenging to achieve for people living with HIV on lifelong ARVs and for HIV-negative individuals using daily preexposure prophylaxis who are not at daily risk for HIV infection. Current biological measures of adherence are invasive and use bioanalytical methods that do not allow for real-time feedback during a clinic visit. This study was designed to test the feasibility and acceptability of using MedViewer, a novel, minimally invasive, hair-based assay that measures longitudinal ARV drug adherence in real time and provides an output for provider-patient discussion.
The primary objectives were to investigate the feasibility of delivering the MedViewer results as planned, the acceptability of participation in a discussion of the MedViewer results, and the appropriateness of using MedViewer for adherence counseling. The secondary objectives were to investigate additional dimensions of feasibility, acceptability, and appropriateness of using the MedViewer test during a routine clinic visit for people with HIV.
The proposed study was a single-arm cross-sectional study among patients receiving HIV care and providers of HIV care in a southeastern infectious disease clinic. The study originally planned to implement the MedViewer test with 50 eligible patients who were living with HIV across 2 viral load strata (undetectable or detectable plasma HIV RNA over the previous 2 years), administer brief visit-specific questionnaires to all patient and provider participants, and conduct qualitative in-depth interviews and quantitative end-line questionnaires with a subsample of patient participants (n=30) and all provider participants.
The Establishing Novel Antiretroviral Imaging for Hair to Elucidate Nonadherence study was funded by the National Institute of Allergy and Infectious Diseases and approved by the local institutional review board on November 4, 2019. Provider participant enrollment began on January 17, 2020, and patient participant enrollment began on January 22, 2020. Participant enrollment was halted on March 16, 2020, because of the COVID-19 pandemic (16 providers and 10 patients on study). Study activities resumed on February 2, 2021, with COVID-19 modifications approved by the local institutional review board. Participant enrollment closed on October 8, 2021, and data collection closed on November 15, 2021. In total, 36 unique patient participants, representing 37 samples, and 20 provider participants were enrolled. Data analysis and manuscript writing will take place throughout 2023.
We anticipate that the data collected through this study will provide important insights regarding the feasibility, acceptability, and appropriateness of incorporating new real-time longitudinal, minimally invasive adherence tests into routine clinical care and identify potential barriers to medication adherence among patients.
ClinicalTrials.gov NCT04232540; https://clinicaltrials.gov/ct2/show/NCT04232540.
RR1-10.2196/41188.
In this crossover study of ezetimibe monotherapy in 48 antiretroviral-treated patients with human immunodeficiency virus infection, the mean changes in low-density lipoprotein cholesterol were −5.3% ...(−11 mg/dL) and +5.5% (+4 mg/dL) with ezetimibe treatment and placebo, respectively (P=.04). Ezetimibe was safe and effective in reducing low-density lipoprotein cholesterol and is an option for patients who cannot tolerate treatment with a statin.
Population sexual mixing patterns can be quantified using Newman's assortativity coefficient (r). Suggested methods for estimating the SE for r may lead to inappropriate statistical conclusions in ...situations where intracluster correlation is ignored and/or when cluster size is predictive of the response. We describe a computer-intensive, but highly accessible, within-cluster resampling approach for providing a valid large-sample estimated SE for r and an associated 95% CI.
We introduce needed statistical notation and describe the within-cluster resampling approach. Sexual network data and a simulation study were employed to compare within-cluster resampling with standard methods when cluster size is informative.
For the analysis of network data when cluster size is informative, the simulation study demonstrates that within-cluster resampling produces valid statistical inferences about Newman's assortativity coefficient, a popular statistic used to quantify the strength of mixing patterns. In contrast, commonly used methods are biased with attendant extremely poor CI coverage. Within-cluster resampling is recommended when cluster size is informative and/or when there is within-cluster response correlation.
Within-cluster resampling is recommended for providing valid statistical inferences when applying Newman's assortativity coefficient r to network data.
HIV-1 triple-class antiretroviral drug resistance (TC-DR) may substantially limit therapeutic options and compromise clinical outcomes.
To estimate TC-DR prevalence and incidence, and identify risk ...factors for TC-DR acquisition.
We identified patients in the University of North Carolina HIV Cohort Study with TC-DR HIV-1 variants. Nucleos(t)ide reverse transcriptase inhibitor (NRTI), non-nucleoside reverse transcriptase inhibitor (NNRTI), and major protease inhibitor (PI) mutations, were based on the International AIDS Society - USA guidelines. Prevalence was estimated with the exact binomial distribution, incidence with the exact Poisson distribution, and multivariable analyses were performed using logistic regression.
Of 1587 patients, half initiated therapy with HAART (N = 789), 20% (N = 320) with non-HAART combination therapy, and 30% (N = 478) with one NRTI. The median time on therapy was 5.7 years interquartile range (IQR) 2.9, 8.6, the median number of previous antiretroviral agents was six (IQR 4, 8), and 47% (N = 752) were exposed to at least one NRTI, NNRTI and PI. Assuming patients without genotypes did not harbor TC-DR virus, the prevalence of TC-DR among all antiretroviral-experienced patients was 8% 95% confidence interval (CI) 6%, 9%. The prevalence was 3% (95% CI 2%, 4%) and 12% (95% CI 10%, 15%) among patients treated initially with HAART and non-HAART, respectively. The number of antiretroviral agents received and initiating therapy with non-HAART or an unboosted PI, increased TC-DR risk in multivariable analyses.
The majority of patients with TC-DR have extensive antiretroviral exposure, particularly to non-HAART regimens, whereas HAART initiators are at low risk of acquiring TC-DR during a median of 4 years of follow-up.
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