Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.

Deep sequencing technologies have the potential to transform the study of highly variable viral pathogens by providing a rapid and cost-effective approach to sensitively characterize rapidly evolving viral quasispecies. Here, we report on a high-throughput whole HIV-1 genome deep sequencing platform that combines 454 pyrosequencing with novel assembly and variant detection algorithms. In one subject we combined these genetic data with detailed immunological analyses to comprehensively evaluate viral evolution and immune escape during the acute phase of HIV-1 infection. The majority of early, low frequency mutations represented viral adaptation to host CD8+ T cell responses, evidence of strong immune selection pressure occurring during the early decline from peak viremia. CD8+ T cell responses capable of recognizing these low frequency escape variants coincided with the selection and evolution of more effective secondary HLA-anchor escape mutations. Frequent, and in some cases rapid, reversion of transmitted mutations was also observed across the viral genome. When located within restricted CD8 epitopes these low frequency reverting mutations were sufficient to prime de novo responses to these epitopes, again illustrating the capacity of the immune response to recognize and respond to low frequency variants. More importantly, rapid viral escape from the most immunodominant CD8+ T cell responses coincided with plateauing of the initial viral load decline in this subject, suggestive of a potential link between maintenance of effective, dominant CD8 responses and the degree of early viremia reduction. We conclude that the early control of HIV-1 replication by immunodominant CD8+ T cell responses may be substantially influenced by rapid, low frequency viral adaptations not detected by conventional sequencing approaches, which warrants further investigation. These data support the critical need for vaccine-induced CD8+ T cell responses to target more highly constrained regions of the virus in order to ensure the maintenance of immunodominant CD8 responses and the sustained decline of early viremia.

Highly sensitive and specific detection of rare variants in mixed viral populations from massively parallel sequence data.

Viruses diversify over time within hosts, often undercutting the effectiveness of host defenses and therapeutic interventions. To design successful vaccines and therapeutics, it is critical to better understand viral diversification, including comprehensively characterizing the genetic variants in viral intra-host populations and modeling changes from transmission through the course of infection. Massively parallel sequencing technologies can overcome the cost constraints of older sequencing methods and obtain the high sequence coverage needed to detect rare genetic variants (< 1%) within an infected host, and to assay variants without prior knowledge. Critical to interpreting deep sequence data sets is the ability to distinguish biological variants from process errors with high sensitivity and specificity. To address this challenge, we describe V-Phaser, an algorithm able to recognize rare biological variants in mixed populations. V-Phaser uses covariation (i.e. phasing) between observed variants to increase sensitivity and an expectation maximization algorithm that iteratively recalibrates base quality scores to increase specificity. Overall, V-Phaser achieved > 97% sensitivity and > 97% specificity on control read sets. On data derived from a patient after four years of HIV-1 infection, V-Phaser detected 2,015 variants across the -10 kb genome, including 603 rare variants (< 1% frequency) detected only using phase information. V-Phaser identified variants at frequencies down to 0.2%, comparable to the detection threshold of allele-specific PCR, a method that requires prior knowledge of the variants. The high sensitivity and specificity of V-Phaser enables identifying and tracking changes in low frequency variants in mixed populations such as RNA viruses.

A holistic approach for suppression of COVID-19 spread in workplaces and universities.

As society has moved past the initial phase of the COVID-19 crisis that relied on broad-spectrum shutdowns as a stopgap method, industries and institutions have faced the daunting question of how to return to a stabilized state of activities and more fully reopen the economy. A core problem is how to return people to their workplaces and educational institutions in a manner that is safe, ethical, grounded in science, and takes into account the unique factors and needs of each organization and community. In this paper, we introduce an epidemiological model (the "Community-Workplace" model) that accounts for SARS-CoV-2 transmission within the workplace, within the surrounding community, and between them. We use this multi-group deterministic compartmental model to consider various testing strategies that, together with symptom screening, exposure tracking, and nonpharmaceutical interventions (NPI) such as mask wearing and physical distancing, aim to reduce disease spread in the workplace. Our framework is designed to be adaptable to a variety of specific workplace environments to support planning efforts as reopenings continue. Using this model, we consider a number of case studies, including an office workplace, a factory floor, and a university campus. Analysis of these cases illustrates that continuous testing can help a workplace avoid an outbreak by reducing undetected infectiousness even in high-contact environments. We find that a university setting, where individuals spend more time on campus and have a higher contact load, requires more testing to remain safe, compared to a factory or office setting. Under the modeling assumptions, we find that maintaining a prevalence below 3% can be achieved in an office setting by testing its workforce every two weeks, whereas achieving this same goal for a university could require as much as fourfold more testing (i.e., testing the entire campus population twice a week). Our model also simulates the dynamics of reduced spread that result from the introduction of mitigation measures when test results reveal the early stages of a workplace outbreak. We use this to show that a vigilant university that has the ability to quickly react to outbreaks can be justified in implementing testing at the same rate as a lower-risk office workplace. Finally, we quantify the devastating impact that an outbreak in a small-town college could have on the surrounding community, which supports the notion that communities can be better protected by supporting their local places of business in preventing onsite spread of disease.

Monitoring for and Characterizing Crizotinib Progression: A Chart Review of ALK-Positive Non-Small Cell Lung Cancer Patients.

INTRODUCTION: Crizotinib is recommended as first-line therapy for ALK-positive non-small cell lung cancer (NSCLC), but within a year of treatment initiation many patients develop resistance. With the recent approval of second-generation ALK inhibitors, this study assessed how physicians monitor for and diagnose progression and how they alter treatment following progression on crizotinib. METHODS: A panel of oncologists from the United States were surveyed regarding their monitoring practices and criteria for diagnosing progression on crizotinib. The physicians also retrospectively provided data (March-June 2016) from the medical charts of their adult patients with locally advanced or metastatic ALK-positive NSCLC who progressed on crizotinib after the approval (April 2014) of the first second-generation ALK inhibitor, ceritinib. RESULTS: A total of 28 physicians responded to the survey. Data was abstracted on 74 patients. In the physician survey, most physicians (71%) reported monitoring for radiographic progression every 3-4 months. When new lesions were detected, physician response varied. Following a symptomatic isolated lesion, most physicians (75%) would add local therapy and resume crizotinib. Following multiple symptomatic lesions, 96% and 64% of physicians would switch to a new therapy depending on whether the lesions were extracranial or isolated to the brain, respectively. For the patient cohort, physician-defined progression on crizotinib was diagnosed after a median of 10 months, and within 30 days of diagnosis, 86% of patients discontinued crizotinib. Among all patients who discontinued crizotinib, 77% switched to ceritinib, 14% to chemotherapy, and 1% to alectinib. The remaining 7% did not receive additional systemic antineoplastic therapy. CONCLUSION: The findings from this physician survey and retrospective chart review study suggest that physician response to the development of new lesions in crizotinib-treated ALK-positive NSCLC patients varies with location and extent of the lesions. Once patients were considered to have progressed, most of them were immediately switched to ceritinib. FUNDING: Novartis Pharmaceuticals Corporation.

Treatment Patterns and Early Outcomes of ALK-Positive Non-Small Cell Lung Cancer Patients Receiving Ceritinib: A Chart Review Study.

INTRODUCTION: This study aimed to provide the first real-world description of the characteristics, treatments, dosing patterns, and early outcomes of patients with ALK-positive non-small cell lung cancer (NSCLC) who received ceritinib in US clinical practice. METHODS: US oncologists provided data from medical charts of adult patients diagnosed with locally advanced or metastatic ALK-positive NSCLC who received ceritinib following crizotinib. Patient characteristics, treatment patterns, ceritinib dosing, early outcomes, and occurrence of gastrointestinal adverse events (AEs) by dose and instructions on food intake were assessed, and Kaplan-Meier analysis was used to describe clinician-defined progression-free survival (PFS) on ceritinib. RESULTS: Medical charts of 58 ALK-positive NSCLC patients treated with ceritinib were reviewed (median age 63 years; 41% male; 21% with prior chemotherapy experience). At ceritinib initiation, 44 patients had multiple distant metastases, most commonly in the liver (60%), bone (53%), and brain (38%). Initial ceritinib dose varied: 71% received 750 mg, 19% 600 mg, and 10% 450 mg. Although median follow-up after ceritinib initiation was short (3.8 months), most patients achieved either a complete or partial response (69%) on ceritinib, regardless of metastatic sites present at initiation or initial dose. Median PFS on ceritinib was 12.9 months. 17% of patients had a gastrointestinal AE reported during follow-up. The majority of events occurred in patients instructed to fast; no patients instructed to take a lower dose of ceritinib with food reported gastrointestinal AEs. CONCLUSION: These early findings of ceritinib use in clinical practice suggest that ceritinib is effective at treating crizotinib-experienced ALK-positive NSCLC patients, regardless of metastatic sites or initial dose, and dosing ceritinib with food may lead to fewer gastrointestinal AEs. Future studies with larger sample size and longer follow-up are warranted, including an ongoing randomized trial to assess the gastrointestinal tolerability of ceritinib 450 and 600 mg with low-fat meals. FUNDING: Novartis Pharmaceutical Corporation.

Clinical Outcomes with First-line Endocrine Therapy or Chemotherapy in Postmenopausal HR+/HER2- Metastatic Breast Cancer.

OBJECTIVE: To describe patient profiles and clinical outcomes associated with first-line endocrine monotherapy (ET) and chemotherapy (CT) for postmenopausal HR+/HER2- metastatic breast cancer (mBC) patients. METHODS: This is a retrospective chart review of 139 postmenopausal HR+/HER2- mBC patients initiating first-line ET monotherapy or CT. Overall survival (OS) was described using Kaplan-Meier curves. Exploratory comparative proportional hazards regression was conducted. RESULTS: Patients on first-line CT had significantly more frequent liver metastases than patients on first-line ET monotherapy at baseline. The median OS was 35.5 months [95% confidence interval (CI), 22.7-41.2 months] for patients on first-line ET monotherapy and 22.2 months (95% CI, 13.6-25.9 months) for those on first-line CT (P = 0.021). Adjusting for baseline characteristics, the OS between first-line ET monotherapy and CT was not significantly different. CONCLUSIONS: Patients who were prescribed CT as first-line treatment had evidence of more advanced disease at baseline and shorter OS than those who received ET monotherapy as first-line treatment, suggesting a need for additional safe and effective treatment options for these patients.

Treatment patterns and duration in post-menopausal women with HR+/HER2- metastatic breast cancer in the US: a retrospective chart review in community oncology practices (2004-2010).

BACKGROUND: Clinical guidelines prefer endocrine therapy (ET) as initial treatment for post-menopausal women with hormone receptor positive (HR+)/human epidermal growth factor receptor 2 negative (HER2-) metastatic breast cancer (mBC). Chemotherapy (CT) should be reserved for patients who develop symptomatic visceral disease or have no clinical benefit after three sequential ET regimens. It is unclear if real-world clinical practice reflects these guidelines. OBJECTIVE: To describe treatment patterns and treatment durations by lines of therapy for ET and CT among post-menopausal HR+/HER2- mBC patients. METHODS: Charts were reviewed from a network of community-based oncology practices of eligible patients who had progressed after initiating adjuvant or first-line treatment for mBC between 1 January 2004 and 30 September 2010. Extracted chart data included demographics, treatment histories, and outcomes. Treatment duration was estimated using Kaplan-Meier estimators. RESULTS: A total of 144 patients were studied. Patients received a median of two lines of ET, and <10% had three or more lines of ET before receiving CT. From first line to second line, the median treatment duration was 11.6 to 4.9 months for ET overall; 13.8 to 10.5 months for anastrozole; 18.6 to 7.0 months for letrozole; and 5.1 to 2.9 months for fulvestrant. For CT, the median duration was 5.1 months in the first line and 3.7 months and below in subsequent lines. CONCLUSION: During the study period (1 January 2004 - 30 September 2012), most patients received <3 lines of ET before receiving CT. The drop in median duration of ET from first to second line suggests that single agent ETs might not be as effective beyond the first line. A key limitation of this study was the small sample size. In addition, more research is needed to further investigate the short treatment duration of fulvestrant across early lines of therapy (which could indicate lack of efficacy).

Physician Underestimation of the Risk of Gastrointestinal Stromal Tumor Recurrence After Resection.

IMPORTANCE: Patients with resectable gastrointestinal stromal tumors (GISTs) might not receive the recommended duration of adjuvant therapy if their risk of recurrence is underestimated, which can have an impact on their recurrence-free survival (RFS). OBJECTIVE: To determine the extent of physician underestimation of risk of recurrence after complete primary GIST resection, the impact of underestimation on planned adjuvant treatment duration, and the association among high-risk patients of planned adjuvant treatment duration and RFS. DESIGN, SETTING, AND PARTICIPANTS: This was a retrospective observational medical record review reported by participating oncologists in 2013. US patients with complete primary GIST resection after 2010 were grouped as underestimated or not if their oncologists' charted risk assessments were lower than assessments based on the Revised National Institutes of Health Consensus Criteria or not. Patients were followed by general community oncologists until death or the end of follow-up. MAIN OUTCOMES AND MEASURES: Fisher exact tests compared planned adjuvant treatment duration between groups. Cox proportional-hazards models estimated the impact of planned adjuvant treatment duration on RFS. RESULTS: A total of 109 oncologists reported information on 506 patients with GIST after primary resection (65.8% were high-risk and 8.7% were intermediate-risk). Physicians underestimated risk for 190 patients (37.5%); 30.1% of tumors with an intermediate-level mitotic count (6-10 per 50 high-powered fields) and an intermediate tumor size (6-10 cm) were correctly recognized as high-risk, as were 7.5% of nongastric tumors with an intermediate-level mitotic count and a tumor size of 2 to 5 cm. A smaller proportion of high-risk patients in the underestimated vs not-underestimated groups had at least 3 years of planned adjuvant therapy (36.1% vs 65.9%; P < .001). Planned adjuvant treatment of at least 3 years vs less than 3 years among high-risk patients conferred a lower hazard of recurrence and/or death (adjusted hazard ratio, 0.29; P < .001; 95% CI, 0.14-0.59). CONCLUSIONS AND RELEVANCE: Overall, physicians tended to underestimate the risk of recurrence for many patients with GIST, especially for patients with tumors of intermediate size, intermediate-level mitotic count, and nongastric location, which had an impact on planned adjuvant therapy duration. Patients with at least 3 years of planned adjuvant treatment had longer RFS. Improved education on postresection risk assessment and risk reduction is needed.

ALK rearrangement testing and treatment patterns for patients with ALK-positive non-small cell lung cancer.

INTRODUCTION: Approximately 2-8% of non-small cell lung cancer (NSCLC) patients have rearrangements in the anaplastic lymphoma kinase gene (ALK). ALK-targeted therapy is available to patients with tumors known to be ALK+. This chart review study described characteristics of patients with ALK+ NSCLC, patterns of ALK testing and subsequent treatments, and oncologists' experience with ALK testing in the US. METHODS: US oncologists provided information in September and October of 2013 on patients from their practice diagnosed with ALK+ locally advanced or metastatic NSCLC, including the timing of ALK testing and treatment received after testing. Participating oncologists were also surveyed about their experience with ALK testing. RESULTS: 27 oncologists provided data on 273 ALK+ NSCLC patients. Patients' median age was 67 years upon NSCLC diagnosis. Smoking history varied, with 33% nonsmokers, 33% light smokers, and 33% heavy smokers. Patients were racially diverse: 59% White, 18% Black, 13% Asian, and 10% other. Upon diagnosis of advanced/metastatic NSCLC, patients who were either not tested (19%) or initially tested negative/inconclusive (1%) all received first-line chemotherapy; the other 219 patients (80%) tested positive, with 133 (61%) receiving an ALK inhibitor and 78 (29%) receiving chemotherapy as first-line treatment. Many oncologists stated being more likely to test for ALK rearrangements among Asians, nonsmokers, and light smokers. CONCLUSIONS: In this sample, ALK+ NSCLC patients were racially diverse with mixed smoking history. One in five patients were not tested before first-line therapy. Oncologists reported being more likely to consider ALK testing for patients with particular smoking and race characteristics.

The epidemiology and targeted therapies for relapsed and refractory CD30+ lymphomas.

BACKGROUND: Hodgkin lymphoma (HL) and systemic anaplastic large cell lymphoma (sALCL) both have consistent expression of CD30, a cytokine receptor that is expressed by activated T and B cells but is largely absent from normal tissue. METHODS: A literature search was conducted via PubMed, Google Scholar, and UpToDate to identify relevant peer-reviewed original research or review articles on HL, sALCL, and CD30 targeted therapies. RESULTS: These lymphomas are both more common among males, young adults and the elderly. Although many patients with HL and sALCL can achieve long-term remission after standard first-line therapy, up to a third of these patients are refractory to or relapse after initial therapy. Among these relapsed/refractory patients, many experience disease progression and/or death despite subsequent treatment, and treatment-related adverse events and mortality are not uncommon. To address the need for safer and more effective therapies for these relapsed/refractory patients, researchers have developed therapies that specifically target CD30-expressing cells. Brentuximab vedotin, an antibody-drug conjugate that selectively delivers a toxic microtubule-disrupting agent to malignant cells with CD30 expression, is the first such therapy to be approved in the US and Europe. In clinical trials, brentuximab vedotin has demonstrated efficacy and safety in patients with HL after failure of autologous stem cell transplantation (ASCT), or after failure of at least two prior multi-agent chemotherapy regimens in patients who are not ASCT candidates, and in patients with sALCL after failure of at least one prior multi-agent chemotherapy regimen. CONCLUSION: HL and sALCL are both CD30+ lymphomas, and therapies like brentuximab vedotin that target cells expressing CD30 hold promise for the treatment of these diseases.

Comparing nilotinib with dasatinib as second-line therapies in patients with chronic myelogenous leukemia resistant or intolerant to imatinib -- a retrospective chart review analysis.

INTRODUCTION: This study compared progression, progression-free survival (PFS), overall survival (OS), and treatment changes among chronic myelogenous leukemia patients in chronic phase (CML-CP) receiving nilotinib or dasatinib as second-line therapy. PATIENTS AND METHODS: Information on CML-CP patients switched from imatinib to nilotinib or dasatinib as second-line therapy was collected retrospectively from 122 US hematologists and oncologists through an online medical chart review. Progression, PFS, and OS were compared using multivariate Cox proportional hazard models, and treatment changes using chi-square tests. RESULTS: Of 597 imatinib resistant or intolerant patients, 301 initiated nilotinib and 296 dasatinib as second-line therapy. Nilotinib was associated with a lower risk of progression (hazard ratio [HR] = 0.27; p = 0.021) and longer PFS (HR = 0.48; p = 0.030) than dasatinib, with a median follow-up time of 11 months for nilotinib and 10 months for dasatinib. Nilotinib patients had a lower estimated hazard of mortality than dasatinib patients, though not statistically significant (HR = 0.46; p = 0.067). When treatment changes were classified by the physicians' justifications, fewer nilotinib patients had treatment changes due to ineffectiveness (2.0% vs. 5.1%, p = 0.041) or drug holidays due to intolerance (0.0% vs. 1.7%, p = 0.024) than dasatinib patients. CONCLUSIONS: Among CML-CP patients in this retrospective chart review who switched from imatinib to either nilotinib or dasatinib, nilotinib was associated with a significantly lower risk of progression and longer PFS than dasatinib. Nilotinib patients were also less likely than dasatinib patients to subsequently have treatment changes due to ineffectiveness or drug holidays due to intolerance. These findings could be subject to unobserved confounders.

Association between molecular monitoring and long-term outcomes in chronic myelogenous leukemia patients treated with first line imatinib.

OBJECTIVE: Molecular monitoring using quantitative polymerase chain reaction (qPCR) of BCR-ABL mRNA transcripts using the international scale (IS) is recommended by the National Comprehensive Cancer Network and the European LeukemiaNet for patients with chronic myelogenous leukemia in chronic phase (CML-CP). This study assessed the impact of the frequency of qPCR testing on progression-free survival (PFS). RESEARCH DESIGN AND METHODS: This retrospective chart review of 402 CML-CP patients on first line imatinib therapy, performed by 38 community-based US physicians, analyzed the impact of the frequency of molecular monitoring on the risk of progression and PFS. MAIN OUTCOME MEASURES: Time to progression and progression-free survival. RESULTS: Over the 3 year study, 13.2% of patients did not have any qPCR monitoring and 46.3% had 3-4 qPCR tests per year; 5.7% of CML-CP patients progressed to accelerated/blast phase or died. Compared to patients with no qPCR monitoring, those with 3-4 qPCR tests per year had a lower risk of progression (HR = 0.085; p = 0.001) and longer PFS (HR = 0.088; p = 0.001) after adjusting for potential confounders, as did those patients with 1-2 qPCR tests per year (both p < 0.02). Results were consistent after adjusting for Sokal score when available. CONCLUSION: This is the first study to document the clinical impact of frequent molecular monitoring, and the findings underscore the importance of regular molecular monitoring in delivering quality care for CML. These findings could be subject to unobserved confounders.

Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity.

The rapid spread of dengue is a worldwide public health problem. In two clinical studies of dengue in Managua, Nicaragua, we observed an abrupt increase in disease severity across several epidemic seasons of dengue virus serotype 2 (DENV-2) transmission. Waning DENV-1 immunity appeared to increase the risk of severe disease in subsequent DENV-2 infections after a period of cross-protection. The increase in severity coincided with replacement of the Asian/American DENV-2 NI-1 clade with a new virus clade, NI-2B. In vitro analyses of viral isolates from the two clades and analysis of viremia in patient blood samples support the emergence of a fitter virus in later, relative to earlier, epidemic seasons. In addition, the NI-1 clade of viruses was more virulent specifically in children who were immune to DENV-1, whereas DENV-3 immunity was associated with more severe disease among NI-2B infections. Our data demonstrate that the complex interaction between viral genetics and population dynamics of serotype-specific immunity contributes to the risk of severe dengue disease. Furthermore, this work provides insights into viral evolution and the interaction between viral and immunological determinants of viral fitness and virulence.