Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control.

We evaluated the fraction of variation in HIV-1 set point viral load attributable to viral or human genetic factors by using joint host/pathogen genetic data from 541 HIV infected individuals. We show that viral genetic diversity explains 29% of the variation in viral load while host factors explain 8.4%. Using a joint model including both host and viral effects, we estimate a total of 30% heritability, indicating that most of the host effects are reflected in viral sequence variation.

Characterizing Human Immunodeficiency Virus Antiretroviral Therapy Interruption and Resulting Disease Progression Using Population-Level Data in British Columbia, 1996-2015.

BACKGROUND: Suboptimal retention is among the biggest challenges to realize the full benefits of combination antiretroviral therapy (ART). We aimed to describe ART interruption patterns and identify determinants of disease progression while off ART in British Columbia, Canada. METHODS: With population-level data on ART utilization and laboratory testing in British Columbia (1996-2015), we described the timing, frequency, and duration of ART interruptions (a gap of ≥90 days in ART dispensation records). A 4-state continuous-time Markov model was implemented to identify determinants of disease progression during individuals' first ART interruption episode. Disease progression was measured according to CD4-based state transitions (cells/µL: ≥500 to 200-499; 200-499 to <200; ≥500 to death; 200-499 to death; and <200 to death). RESULTS: Among individuals initiating ART, 3129 (38.6%) interrupted ART over a median 8-year follow-up (interquartile range [IQR], 4.3-13.5 years). Those interrupting ART had a median of 1 interruption (IQR, 1.0-3.0), with the first interruption occurring 12.8 (IQR, 4.0-36.1) months after ART initiation, lasting for 7.5 (IQR, 4.1-20.3) months. The proportion of individuals interrupting ART within the first year of ART initiation decreased over time; however, the absolute number of individuals interrupting ART remained high. In a multivariable analysis, age, historical plasma viral load, and ART regimen changes prior to interruption were associated with increased hazard of CD4 decline and death. CONCLUSIONS: Our results demonstrate that ART interruptions are common even in a high-resource setting with universal free access to human immunodeficiency virus care. Further efforts are needed to promote ART reengagement and may consider prioritizing individuals with poorer prognostic factors.

Genotypic susceptibility score (GSS) and CD4+ T cell recovery in HIV-1 patients with suppressed viral load.

OBJECTIVES: HIV drug resistance, measured by the genotypic susceptibility score (GSS), has a deleterious effect on the virological outcome of HIV-1-infected patients. However, it is not known if GSS retains any predictive value for CD4 recovery in patients with suppressed viral load. METHODS: Four hundred and six patients on virological failure (>500 copies/mL) with GSS : <6 months prior to switch therapy who achieved undetectable plasma viral load (<50 copies/mL) within 1 year, remained undetectable >1 year on an unchanged regimen and had CD4 data available during entire follow-up were included. Adjusted and unadjusted analyses of all characteristics at switch related to CD4 recovery were made for three time frames: (i) 'switch-suppression'; (ii) 'suppression-1 year'; and (iii) 'switch-1 year'. RESULTS: Higher GSS was associated with a greater CD4 recovery between 'switch' and '1 year' in the unadjusted analysis (P = 0.010); however, the effect of GSS was no longer statistically significant after adjusting for pre-switch clinical (CD4 count and plasma viral load) and demographic variables. Furthermore, only a lower pre-switch CD4 count was associated with increased CD4 recovery in the 'suppression-1 year' period in both unadjusted and adjusted models. The main CD4 recovery occurred in 'switch-suppression' and the variables associated, both unadjusted and adjusted, were CD4 and plasma viral load at switch, maintaining a trend for GSS (P = 0.06). CONCLUSIONS: In individuals who re-suppressed HIV viraemia after switching therapy, regimens having a higher GSS were associated with improved CD4 recovery only during the period from switch to virological suppression, but, once viral load is re-suppressed, the GSS of the new regimen has no further effect on subsequent CD4 recovery.

An Unusual Case of Alternating Ventricular Morphology on the 12-Lead Electrocardiogram.

BACKGROUND: One of the principal tasks of an emergency physician is identifying potentially life-threatening conditions in the undifferentiated patient; cardiac dysrhythmia is an example of such a condition. A systematic approach to a patient with atypical dysrhythmia enables proper identification of such-life threatening conditions. CASE REPORT: We describe a 31-year-old man presenting to the emergency department with an undifferentiated dysrhythmia after naloxone reversal of an opiate overdose. A systematic approach to the electrocardiogram led to the rare diagnosis of Wolff-Parkinson-White (WPW) alternans. We review the differential diagnosis of this dysrhythmia and the initial evaluation of a patient with the WPW pattern present on their electrocardiogram. WHY SHOULD AN EMERGENCY PHYSICIAN BE AWARE OF THIS?: Emergency physicians should be prepared to use a systematic approach to an undifferentiated dysrhythmia to identify potentially life-threatening conditions.

Maraviroc, as a Switch Option, in HIV-1-infected Individuals With Stable, Well-controlled HIV Replication and R5-tropic Virus on Their First Nucleoside/Nucleotide Reverse Transcriptase Inhibitor Plus Ritonavir-boosted Protease Inhibitor Regimen: Week 48 Results of the Randomized, Multicenter MARCH Study.

BACKGROUND: Alternative combination antiretroviral therapies in virologically suppressed human immunodeficiency virus (HIV)-infected patients experiencing side effects and/or at ongoing risk of important comorbidities from current therapy are needed. Maraviroc (MVC), a chemokine receptor 5 antagonist, is a potential alternative component of therapy in those with R5-tropic virus. METHODS: The Maraviroc Switch Study is a randomized, multicenter, 96-week, open-label switch study in HIV type 1-infected adults with R5-tropic virus, virologically suppressed on a ritonavir-boosted protease inhibitor (PI/r) plus double nucleoside/nucleotide reverse transcriptase inhibitor (2 N(t)RTI) backbone. Participants were randomized 1:2:2 to current combination antiretroviral therapy (control), or replacing the protease inhibitor (MVC + 2 N(t)RTI arm) or the nucleoside reverse transcriptase inhibitor backbone (MVC + PI/r arm) with twice-daily MVC. The primary endpoint was the difference (switch minus control) in proportion with plasma viral load (VL) <200 copies/mL at 48 weeks. The switch arms were judged noninferior if the lower limit of the 95% confidence interval (CI) for the difference in the primary endpoint was < -12% in the intention-to-treat (ITT) population. RESULTS: The ITT population comprised 395 participants (control, n = 82; MVC + 2 N(t)RTI, n = 156; MVC + PI/r, n = 157). Baseline characteristics were well matched. At week 48, noninferior rates of virological suppression were observed in those switching away from a PI/r (93.6% [95% CI, -9.0% to 2.2%] and 91.7% [95% CI, -9.6% to 3.8%] with VL <200 and <50 copies/mL, respectively) compared to the control arm (97.6% and 95.1% with VL <200 and <50 copies/mL, respectively). In contrast, MVC + PI/r did not meet noninferiority bounds and was significantly inferior (84.1% [95% CI, -19.8% to -5.8%] and 77.7% [95% CI, -24.9% to -8.4%] with VL <200 and <50 copies/mL, respectively) to the control arm in the ITT analysis. CONCLUSIONS: These data support MVC as a switch option for ritonavir-boosted PIs when partnered with a 2-N(t)RTI backbone, but not as part of N(t)RTI-sparing regimens comprising MVC with PI/r. CLINICAL TRIALS REGISTRATION: NCT01384682.

Heat Stroke-Induced Sinoatrial Node Dysfunction.

BACKGROUND: Heat stroke has been associated with stress-induced cardiomyopathy and electrocardiogram ST segment elevation and depression. Laboratory studies with dogs have demonstrated heat stroke-induced sinoatrial node dysfunction in the setting of hyperkalemia. No prior case report has described heat stroke-induced complete sinoatrial node dysfunction that resolved in the emergency department. CASE REPORT: An 87-year-old female presented to the emergency department with heat stroke and severe bradycardia. Initial electrocardiogram demonstrated complete sinoatrial node dysfunction. The bradycardia responded to external cardiac pacing and the sinoatrial node dysfunction resolved with aggressive cooling. Emergency physicians should be aware that heat stroke can cause complete sinoatrial node dysfunction and that this bradydysthrmia can be treated with aggressive cooling.

Lateral canthotomy and cantholysis: emergency management of orbital compartment syndrome.

BACKGROUND: Orbital compartment syndrome is a sight-threatening emergency. Vision may be preserved when timely intervention is performed. OBJECTIVE: To present a case of orbital compartment syndrome caused by traumatic retrobulbar hemorrhage and the procedure of lateral canthotomy and cantholysis, reviewed with photographic illustration. DISCUSSION: Lateral canthotomy and cantholysis are readily performed at the bedside with simple instruments. The procedure may prevent irreversible blindness in cases of acute orbital compartment syndrome. CONCLUSIONS: Emergency physicians should be familiar with lateral canthotomy and cantholysis in the management of orbital compartment syndrome to minimize the chance of irreversible visual loss.

Temporal trends in the discontinuation of first-line antiretroviral therapy.

OBJECTIVES: The aim of this study was to describe the rates and predictors of discontinuing first-line antiretroviral therapy in the different eras of treatment over a nearly 20 year period initiated in British Columbia between 1992 and 2010. METHODS: All naive adults who started antiretroviral therapy (first-line antiretroviral therapy) at any hospital or clinic in British Columbia (Canada) in 1992-2010 were included in this population-based retrospective cohort study. We were primarily interested in whether the era of treatment (1992-95, 1996-2000, 2001-05 and 2006-10) was associated with discontinuation (stopping or switching of initial treatment) within 3 years of starting therapy. Weibull survival analysis was used to model the era of treatment and its association with time to discontinuation. RESULTS: The study included 7901 patients. Overall, the probability of discontinuing at 12, 24 and 36 months of treatment was 52%, 68% and 76%, respectively. In the adjusted model, variables associated with discontinuing were earlier treatment era, younger age, low adherence and lower baseline CD4 count. Regarding the 2006-10 period, the probability of discontinuing at 12, 24 and 36 months was 36%, 47% and 53%, respectively. In the adjusted model, the variables associated with discontinuation were younger age, female gender, AIDS-defining illnesses at baseline, low adherence and a protease inhibitor (PI)-based regimen. CONCLUSIONS: Discontinuation rates of first-line therapy have decreased over time, but are still quite high even for the latest drug combinations. In the most recent era, younger women on a PI regimen and those not achieving optimal adherence had the highest risk of discontinuing first-line antiretroviral therapy.

RECall for automated genotypic tropism testing.

Standardization of sequence chromatogram analysis is required for consistent genotypic tropism determination across laboratories. A freely available, fast, and automated chromatogram analysis tool (RECall) provided tropism interpretations equivalent to those of manual sequence editing of 521 V3 loop HIV-1 population sequences, suggesting that RECall can be useful in standardizing genotypic tropism testing across laboratories.

Results of external quality assessment for proviral DNA testing of HIV tropism in the Maraviroc Switch collaborative study.

The Maraviroc Switch collaborative study (MARCH) is a study in aviremic patients on stable antiretroviral therapy and utilizes population-based sequencing of proviral DNA to determine HIV tropism and susceptibility to maraviroc. An external quality assessment (EQA) program was implemented to ensure competency in assessing the tropism of clinical samples conducted by MARCH laboratories (n = 14). The MARCH EQA has three prestudy phases assessing V3 loop sequencing and tropism determination using the bioinformatic algorithm geno2pheno, which generates a false-positive rate (FPR). DNA sequences with low FPRs are more likely to be from CXCR4-using (X4) viruses. Phase 1 of the EQA involved chromatogram interpretation. Phases 2, 2/3, and 3 involved patient and clonal samples. Clinical samples used in these phases were from treatment-experienced HIV-infected volunteers; 18/20 had viral loads of <50 copies/ml, and 10/15 were CXCR4-tropic on prior phenotyping. All samples were tested in triplicate, and any replicate with a geno2pheno FPR of <10% was designated X4. Performance was deemed adequate if ≤2 R5 and ≤1 X4 specimens were miscalled. For several clinical samples in the EQA, triplicate testing revealed marked DNA variability (FPR range, 0 to 96.7%). Therefore, a consensus-based approach was employed for each sample, i.e., a median FPR across laboratories was used to define sample tropism. Further sequencing analysis showed mixed viral populations in the clinical samples, explaining the differences in tropism predictions. All laboratories passed the EQA after achieving predefined competence thresholds in either of the phase 2 rounds. The use of clinical samples from patients resembling those who were likely to be screened in the MARCH, coupled with triplicate testing, revealed inherent DNA variability that might have been missed if single or duplicate testing and/or clonal samples alone were used. These data highlight the importance of intensive EQA of tropism laboratories before embarking on clinical studies. (This study has been registered at ClinicalTrials.gov under registration no. NCT01384682 [http://www.clinicaltrials.gov/ct2/show/study/NCT01384682?term=NCT01384682&rank=1].).

An interesting cause of wide complex tachycardia: Ashman's phenomenon in atrial fibrillation.

BACKGROUND: Ashman's phenomenon is an aberrant intraventricular conduction abnormality that occurs in response to a change in QRS cycle length. In atrial fibrillation, Ashman's phenomenon will present as a long RR cycle followed by a short RR cycle, with the subsequent QRS complex manifesting a right bundle branch block morphology. This morphologic variation can create difficulty with electrocardiographic interpretation, and can alter management in patients with this dysrhythmia. OBJECTIVES: This report presents a case, describes the Ashman's phenomenon in atrial fibrillation, and discusses interpretation of this electrocardiographic finding. CASE REPORT: This is a 27-year-old woman who presented with palpitations and chest pain. The patient was symptomatic with a heart rate >200 beats/min and a wide complex tachycardia on electrocardiogram. CONCLUSIONS: Ashman's phenomenon should be suspected in atrial fibrillation when there is a long cycle followed by a short cycle, with the subsequent QRS complex manifesting a right bundle branch block pattern. Emergency physician awareness of this phenomenon may improve diagnostic certainty and have an impact on dysrhythmia management.

Alternative treatments of pneumothorax.

BACKGROUND: Pneumothorax has traditionally been treated in the Emergency Department by tube thoracostomy. However, this is an invasive procedure with high risk of complication and prolonged hospitalization. DISCUSSION: In select settings, there are alternative forms of management of pneumothorax that carry lower risks and may reduce hospital stay. This article reviews the settings in which less invasive treatment, including observation alone, may be indicated. This article also reviews the techniques for simple aspiration and small-bore catheter insertion (by either Seldinger or catheter-over-wire technique) with Heimlich valve, as well as the indications, contraindications, and potential risks and benefits of each. CONCLUSIONS: The practices of observation, simple aspiration, and small-bore catheter insertion with Heimlich valve for selected patients may decrease complications, time, and costs by avoiding invasive procedures and hospital admissions.

Electrocardiographic electrode misplacement, misconnection, and artifact.

BACKGROUND: Electrocardiograms (ECGs) are performed by humans, and thus are subject to human error. An underappreciated source of electrocardiographic abnormality is electrode misconnection, both limb and precordial, and improper placement, which is principally an issue with the precordial electrodes due to anatomic variation. Patterns of abnormality exist; recognition allows the emergency physician to avoid mistaking the resulting electrocardiographic findings for true pathology. OBJECTIVES: The purpose of this clinical review is to describe the patterns of electrocardiographic electrode reversal, misplacement, and artifact and thus make them recognizable to the Emergency Physician. DISCUSSION: Common limb electrode reversals feature distinctive patterns manifesting as unexpected morphologic and frontal plane axis changes in the QRS complexes in the limb and augmented leads. Precordial electrode misplacement (improper positioning of the electrodes on the chest) is common and may mimic a pseudoinfarction pattern, or ST-segment/T-wave changes, which must be recognized as the result of the misplacement rather than true cardiac ischemia. Precordial electrode reversal should be suspected when the normal R/S wave amplitude transition is violated. Electrocardiographic artifact must be distinguished from dysrhythmia to avoid a potentially hazardous progression to unnecessary diagnostics and therapeutics. CONCLUSIONS: The hallmarks of electrode misconnection, misplacement, and electrocardiographic artifact can be easily mastered by the Emergency Physician; recognition of these findings can positively impact patient care by avoiding unnecessary intervention secondary to misattribution of findings on the 12-lead ECG to cardiac pathology.

Missing data on the estimation of the prevalence of accumulated human immunodeficiency virus drug resistance in patients treated with antiretroviral drugs in north america.

Determination of the prevalence of accumulated antiretroviral drug resistance among persons infected with human immunodeficiency virus (HIV) is complicated by the lack of routine measurement in clinical care. By using data from 8 clinic-based cohorts from the North American AIDS Cohort Collaboration on Research and Design, drug-resistance mutations from those with genotype tests were determined and scored using the Genotypic Resistance Interpretation Algorithm developed at Stanford University. For each year from 2000 through 2005, the prevalence was calculated using data from the tested subset, assumptions that incorporated clinical knowledge, and multiple imputation methods to yield a complete data set. A total of 9,289 patients contributed data to the analysis; 3,959 had at least 1 viral load above 1,000 copies/mL, of whom 2,962 (75%) had undergone at least 1 genotype test. Using these methods, the authors estimated that the prevalence of accumulated resistance to 2 or more antiretroviral drug classes had increased from 14% in 2000 to 17% in 2005 (P < 0.001). In contrast, the prevalence of resistance in the tested subset declined from 57% to 36% for 2 or more classes. The authors' use of clinical knowledge and multiple imputation methods revealed trends in HIV drug resistance among patients in care that were markedly different from those observed using only data from patients who had undergone genotype tests.

Impact of cobas PCR Media freezing on SARS-CoV-2 viral RNA integrity and whole genome sequencing analyses.

SARS-CoV-2 whole genome sequencing is a molecular biology tool performed to support many aspects of the response to the pandemic. Freezing of primary clinical nasopharyngeal swabs and shipment to reference laboratories is usually required for sequencing. Cobas PCR Media transport medium facilitates high throughput SARS-CoV-2 RT-PCR analyses on cobas platforms. The manufacturer doesn't recommend freezing this transport medium because of risks of degrading molecular templates and impairing test results. Our objective was to compare the quality and results of SARS-CoV-2 genomic sequencing when performed on fresh or frozen samples in cobas PCR Media. Viral genome sequencing was performed using Oxford Nanopore Technologies MinION platform. Sequencing performance, quality and results did not significantly differ between fresh and frozen samples (n = 10). Freezing of cobas PCR Media does not negatively affect SARS-CoV-2 RNA sequencing results and it is therefore a suitable transport medium for outsourcing sequencing analyses to reference laboratories.

Treatment Experience and Repeat Pregnancy Impact the Effectiveness of Non-Nucleoside Reverse Transcription Inhibitor-Highly Active Antiretroviral Therapy for the Prevention of Mother to Child Transmission of Human Immunodeficiency Virus.

Non-nucleoside reverse transcription inhibitor (NNRTI)-containing antiretroviral therapy (ART) for the prevention of mother to child transmission (PMTCT) of human immunodeficiency virus (HIV) has led to dramatic reductions in perinatal HIV infection in resource-constrained settings. Nonetheless, PMTCT programs are complicated by repeat pregnancies, in which long-term or repeat exposures to PMTCT regimens over time may lead to the acquisition of HIV drug resistance mutations, and consequent treatment failure. In this study, we retrospectively assessed the effectiveness of the NNRTI-based PMTCT protocol from 2008 to 2010 in The Bahamas National HIV/AIDS Program. We show that women who had been in repeat pregnancies and those who were already prescribed ART at conception were at increased risk of virologic failure, relative to treatment-inexperienced women and primigravida, respectively (AOR 3.1, 95% CI: 1.3-7.1, p = .008 and AOR 5.0, 95% CI: 1.8-14.1, p = .002). In addition, women undergoing treatment at conception were more likely to possess HIVDR mutations relative to treatment-naive women (AOR 447.1, 95% CI: 17.9-11,173.5, p = .001). Therefore, individual treatment history is a key metric determining the effectiveness of current and future PMTCT interventions. The implications of this to PMTCT programmatic success in light of the most recent WHO guidelines are discussed.

HIV-1 phylodynamic analysis among people who inject drugs in Pakistan correlates with trends in illicit opioid trade.

Pakistan is considered by the World Health Organization to currently have a "concentrated" HIV-1 epidemic due to a rapid rise in infections among people who inject drugs (PWID). Prevalence among the country's nearly 105,000 PWID is estimated to be 37.8% but has been shown to be higher in several large urban centers. A lack of public health resources, the common use of professional injectors and unsafe injection practices are believed to have fueled the outbreak. Here we evaluate the molecular characteristics of HIV-1 sequences (n = 290) from PWID in several Pakistani cities to examine transmission dynamics and the association between rates of HIV-1 transmission with regards to regional trends in opioid trafficking. Tip-to-tip (patristic) distance based phylogenetic cluster inferences and BEAST2 Bayesian phylodynamic analyses of time-stamped data were performed on HIV-1 pol sequences generated from dried blood spots collected from 1,453 PWID as part of a cross-sectional survey conducted in Pakistan during 2014/2015. Overall, subtype A1 strains were dominant (75.2%) followed by CRF02_AG (14.1%), recombinants/unassigned (7.2%), CRF35_AD (2.1%), G (1.0%) and C (0.3%). Nearly three quarters of the PWID HIV-1 sequences belonged to one of five distinct phylogenetic clusters. Just below half (44.4%) of individuals in the largest cluster (n = 118) did seek help injecting from professional injectors which was previously identified as a strong correlate of HIV-1 infection. Spikes in estimated HIV-1 effective population sizes coincided with increases in opium poppy cultivation in Afghanistan, Pakistan's western neighbor. Structured coalescent analysis was undertaken in order to investigate the spatial relationship of HIV-1 transmission among the various cities under study. In general terms, our analysis placed the city of Larkana at the center of the PWID HIV-1 epidemic in Pakistan which is consistent with previous epidemiological data.

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore.

Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome sequencing (https://www.protocols.io/view/ncov-2019-sequencing-protocol-bbmuik6w) online on January 22, 2020. This approach has rapidly become the most popular method for sequencing SARS-CoV-2 due to its simplicity and cost-effectiveness. Here we present improvements to the original protocol: i) an updated primer scheme with 22 additional primers to improve genome coverage, ii) a streamlined library preparation workflow which improves demultiplexing rate for up to 96 samples and reduces hands-on time by several hours and iii) cost savings which bring the reagent cost down to £10 per sample making it practical for individual labs to sequence thousands of SARS-CoV-2 genomes to support national and international genomic epidemiology efforts.