The National Institutes of Health INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE (INCLUDE) Project: Accelerating research discoveries for people with Down syndrome across the lifespan.

The National Institutes of Health (NIH) has a long-standing history of support for research in Down syndrome (DS). In response to a 2018 congressional directive for a trans-NIH initiative to address medical issues in DS, NIH launched the INCLUDE Project (INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE). Reflecting the three INCLUDE components of basic science research, cohort development, and clinical trials, the Project has published funding opportunities to address conditions such as immune disorders and Alzheimer's disease. Due to a steady expansion in dedicated funding over its first 5 years, INCLUDE has invested $258 M in over 250 new research projects. INCLUDE also supports training initiatives to expand the number and diversity of investigators studying DS. NIH has funded an INCLUDE Data Coordinating Center that is collecting de-identified clinical information and multi-omics data from research participants for broad data sharing and secondary analyses. Through the DS-Connect® registry, INCLUDE investigators can access recruitment support. The INCLUDE Research Plan articulates research goals for the program, with an emphasis on diversity of research participants and investigators. Finally, a new Cohort Development Program is poised to increase the impact of the INCLUDE Project by recruiting a large DS cohort across the lifespan.

Current honey bee stressor investigations and mitigation methods in the United States and Canada.

Honey bees are the most important managed insect pollinators in the US and Canadian crop systems. However, the annual mortality of colonies in the past 15 years has been consistently higher than historical records. Because they are eusocial generalist pollinators and amenable to management, honey bees provide a unique opportunity to investigate a wide range of questions at molecular, organismal, and ecological scales. Here, the American Association of Professional Apiculturists (AAPA) and the Canadian Association of Professional Apiculturists (CAPA) created 2 collections of articles featuring investigations on micro and macro aspects of honey bee health, sociobiology, and management showcasing new applied research from diverse groups studying honey bees (Apis mellifera) in the United States and Canada. Research presented in this special issue includes examinations of abiotic and biotic stressors of honey bees, and evaluations and introductions of various stress mitigation measures that may be valuable to both scientists and the beekeeping community. These investigations from throughout the United States and Canada showcase the wide breadth of current work done and point out areas that need further research.

Analysis of education and previous nursing experience of certified PNPs in the United States.

BACKGROUND: Educational programs to prepare nurse practitioners (NPs) were historically built upon foundational nursing experience. Originally prepared as certificate programs in 1965, the educational requirements for nurse practitioners (NPs) rapidly shifted from certificate programs to the Master's degree (DellaBella, 2015; Fairman, 2008). As Doctor of Nursing Practice (DNP) degree programs increase in number, it is unknown whether this foundational nursing experience has changed, or if it differs by certification type for pediatric nurse practitioners (PNPs). This study aimed to evaluate the educational preparation and prior nursing experience of primary care and acute care certified PNPs. METHODS: A national survey of members of the Pediatric Nurse Practitioner Certification Board (N = 17,530) was completed (Mudd et al., 2022). A sub-analysis of this data was conducted (n = 1974). RESULTS: There was no statistical evidence among either primary or acute care PNPs of an association between previous nursing experience and type of degree preparation (Master's or DNP). There was only a weak association between educational preparation and experience among acute care nurse practitioners. Most respondents were prepared at the Master's level, and 85% of all respondents had >1 year of nursing experience prior to returning for additional PNP education. DISCUSSION: This study adds to the literature as it describes the educational preparation and foundational nursing experience of primary and acute care PNPs. It can serve as a benchmark as the move to the DNP continues for Advanced Practice Registered Nurse preparation.

Resection of NAFLD/NASH-related Hepatocellular Carcinoma (HCC): Clinical Features and Outcomes Compared with HCC Due to Other Etiologies.

BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) are the leading causes of hepatocellular carcinoma (HCC) worldwide. Limited data exist on surgical outcomes for NAFLD/NASH-related HCC compared with other HCC etiologies. We evaluated differences in clinicopathological characteristics and outcomes of patients undergoing surgical resection for NAFLD/NASH-associated HCC compared with other HCC etiologies. METHODS: Demographic, clinicopathological features, and survival outcomes of patients with surgically resected HCC were collected. NAFLD activity score (NAS) and fibrosis score were assessed by focused pathologic review in a subset of patients. RESULTS: Among 492 patients screened, 260 met eligibility (NAFLD/NASH [n = 110], and other etiologies [n = 150]). Median age at diagnosis was higher in the NAFLD/NASH HCC cohort compared with the other etiologies cohort (66.7 vs. 63.4 years, respectively, P = .005), with an increased percentage of female patients (36% vs. 18%, P = .001). NAFLD/NASH-related tumors were more commonly >5 cm (66.0% vs. 45%, P = .001). There were no significant differences in rates of lymphovascular or perineural invasion, histologic grade, or serum AFP levels. The NAFLD/NASH cohort had lower rates of background liver fibrosis, lower AST and ALT levels, and higher platelet counts (P < .01 for all). Median overall survival (OS) was numerically shorter in NAFLD/NASH vs other etiology groups, however, not statistically significant. CONCLUSIONS: Patients with NAFLD/NASH-related HCC more commonly lacked liver fibrosis and presented with larger HCCs compared with patients with HCC from other etiologies. No differences were seen in rates of other high-risk features or survival. With the caveat of sample size and retrospective analysis, this supports a similar decision-making approach regarding surgical resection for NAFLD/NASH and other etiology-related HCCs.

Developing a Virtual Equity Hub: Adapting the Tumor Board Model for Equity in Cancer Care.

We define cancer equity as all people having as the same opportunity for cancer prevention, treatment, and survivorship care. However, marginalized populations continue to experience avoidable and unjust disparities in cancer care, access to clinical trials, and cancer survival. Racial and ethnic minorities, and individuals with low socioeconomic status, Medicaid insurance, limited health literacy, disabilities, and mental health disorders are more likely to experience delays to cancer diagnosis and less likely to receive guideline-concordant cancer care. These disparities are impacted by the social determinants of health including structural discrimination, racism, poverty, and inequities in access to healthcare and clinical trials. There is an urgent need to develop and adapt evidence-based interventions in collaboration with community partners that have potential to address the social determinants of health and build capacity for cancer care for underserved populations. We established the Virtual Equity Hub by developing a collaborative network connecting a comprehensive cancer center, academic safety net hospital, and community health centers and affiliates. The Virtual Equity Hub utilizes a virtual tumor board, an evidence-based approach that increases access to multi-specialty cancer care and oncology subspecialty expertise. We adapted the tumor board model by engaging person-centered teams of multi-disciplinary specialists across health systems, addressing the social determinants of health, and applying community-based research principles with a focus on populations with poor cancer survival. The virtual tumor board included monthly videoconferences, case discussion, sharing of expertise, and a focus on addressing barriers to care and trial participation. Specifically, we piloted virtual tumor boards for breast oncology, neuro-oncology, and individuals with cancer and serious mental illness. The Virtual Equity Hub demonstrated promise at building capacity for clinicians to care for patients with complex needs and addressing barriers to care. Research is needed to measure the impact, reach, and sustainability of virtual equity models for patients with cancer.

Making computed tomography safer for patients with Crohn's disease.

Background and aims: Computed tomography (CT), often more accessible than magnetic resonance imaging (MRI), remains widely used though radiation exposure is an obvious disadvantage. We previously showed that modern CT technology can achieve over 70% reduction in radiation-dose without loss of accuracy. Here, we compare low- versus conventional-dose CT in patients with known Crohn's disease to assess clinical confidence and accuracy of the low-dose procedure in the semi-acute setting.Methods: A comparative study of low-dose CT with full iterative reconstruction (IR) versus conventional-dose CT was conducted in 50 consecutive outpatients with Crohn's disease. Clinicians were provided with the low-dose images and reports, whereas conventional-dose images were reviewed after 4 weeks.Results: The clinical question was adequately addressed with low-dose IR imaging in all cases. Complications of Crohn's were detected in 37/50 (74%) with no disagreement between low- and conventional-dose imaging. The effective radiation dose reduction was 76.5% (low-dose mean 2.15 mSv versus conventional-dose CT 6.99 mSv).Conclusion: Low-dose IR CT is safe and accurate for evaluating distribution and complications of known Crohn's disease in the outpatient setting. We propose that low-dose radiation imaging should be adopted as standard-of-care for the evaluation of Crohn's disease and an acceptable alternative to MR particularly in the acute setting. ClinicalTrials.gov: NCT03140306.

Diagnostic accuracy of ultrasonography-guided core needle biopsy of parotid gland neoplasms: A large, single-institution experience in United Kingdom.

Salivary gland tumours present a pleomorphic and complex morphology and, apart from the most common neoplasms with well-established histopathological criteria, may create diagnostic difficulty for histopathologists. The majority of salivary gland tumours occur in the parotid gland and the use of ultrasound guided parotid biopsy (US-PB) has increased. US-PB in contrast with fine needle aspiration (FNA), which is an easy and relatively painless technique, is performed under local anaesthesia, usually by radiologists. US-PB offers some advantages over the FNA such as tumour grading and the possibility of performing immunohistochemistry. We report our experience of the diagnostic value of US-PB in a large, referral centre in the United Kingdom.

The older prisoner health and social care assessment and plan (OHSCAP) versus treatment as usual: a randomised controlled trial.

BACKGROUND: Older people are the fastest-growing demographic group among prisoners in England and Wales and they have complex health and social care needs. Their care is frequently ad hoc and uncoordinated. No previous research has explored how to identify and appropriately address the needs of older adults in prison. We hypothesised that the Older prisoner Health and Social Care Assessment and Plan (OHSCAP) would significantly increase the proportion of met health and social care needs 3 months after prison entry, compared to treatment as usual (TAU). METHODS: The study was a parallel randomised controlled trial (RCT) recruiting male prisoners aged 50 and over from 10 prisons in northern England. Participants received the OHSCAP or TAU. A clinical trials unit used minimisation with a random element as the allocation procedure. Data analysis was conducted blind to allocation status. The intervention group had their needs assessed using the OHSCAP tool and care plans were devised; processes that lasted approximately 30 min in total per prisoner. TAU included the standard prison health assessment and care. The intention to treat principle was followed. The trial was registered with the UK Clinical Research Network Portfolio (ISRCTN ID: 11841493) and was closed on 30 November 2016. RESULTS: Data were collected between 28 January 2014 and 06 April 2016. Two hundred and forty nine older prisoners were assigned TAU of which 32 transferred prison; 12 were released; 2 withdrew and 1 was deemed unsafe to interview. Two hundred and fifty three 3 prisoners were assigned the OHSCAP of which 33 transferred prison; 11 were released; 6 withdrew and 1 was deemed unsafe to interview. Consequently, data from 202 participants were analysed in each of the two groups. There were no significant differences in the number of unmet needs as measured by the Camberwell Assessment of Needs - Forensic Short Version (CANFOR-S). The mean number of unmet needs for the OHSCAP group at follow-up was 2.03 (SD = 2.07) and 2.06 (SD = 2.11) for the TAU group (mean difference = 0.088; 95% CI - 0.276 to 0.449, p = 0.621). No adverse events were reported. CONCLUSION: The OHSCAP was fundamentally not implemented as planned, partly due to the national prison staffing crisis that ensued during the study period. Therefore, those receiving the OHSCAP did not experience improved outcomes compared to those who received TAU. TRIAL REGISTRATION: Current Controlled Trials: ISRCTN11841493 , 25/10/2012.

Baseline Screening MRI Uptake and Findings in Women with ≥ 20% Lifetime Risk of Breast Cancer.

BACKGROUND: The American Cancer Society recommends screening magnetic resonance imaging (MRI) for patients with a ≥ 20% lifetime breast cancer risk. This study assesses the outcomes of baseline MRI screens in women from a high-risk breast clinic (HRBC). METHODS: We retrospectively reviewed patients from our institution's HRBC, excluding those with prior breast cancer and predisposing genetic mutations. Screening MRI was recommended for a lifetime risk of ≥ 20% using the Tyrer-Cuzick model. We determined baseline MRI results, biopsy rates, and frequency of MRI-detected high-risk lesions (HRLs) and breast cancers. RESULTS: Overall, 319 women attended our HRBC; median age was 48 years and 4.7% had prior atypia/lobular carcinoma in situ. Screening MRI was recommended for 282 patients, of whom 196 (69.5%) completed a baseline screen. A Breast Imaging-Reporting and Data System (BIRADS) 3 or 4 finding occurred in 19.6% of patients; 23 (12.3%) required 6-month follow-up MRI, 16 (8.6%) underwent core biopsy, and 4 (2.1%) underwent excisional biopsy after initial core. An additional 7 (3.7%) patients had a non-breast incidental finding. An HRL was identified in 2 (1.1%) patients (atypical ductal and lobular hyperplasia, respectively), and 2 (1.1%) were diagnosed with T1N0 breast cancers. CONCLUSIONS: In the setting of an HRBC, 70% of women with a ≥ 20% lifetime risk of breast cancer pursued screening MRI when recommended. On baseline screen, the rate of MRI-detected breast cancer was low (1%); however, malignancies were mammographically occult and identified at an early stage. Despite a low cancer rate, nearly one in four women required additional diagnostic investigation. Prescreening counselling should include a discussion of this possibility, and longer-term follow-up of screening MRI is needed in this high-risk population.

Pathogenicity of a glucokinase gene mutation and description of its clinical phenotype.

Glucokinase gene (GCK) mutations comprise approximately 10% of cases of maturity-onset diabetes of the young (MODY). Over 800 different mutations in GCK have been reported in the Human Gene Mutation Database, the vast majority of which result in MODY type 2. The missense mutation p.Leu122Val is listed in that database as "disease-causing;" however, the National Center for Biotechnology Information ClinVar database (Variation ID 585919) reports that this mutation is of "uncertain significance." Both databases reference the same Italian pediatric patient reported by Massa et al in 2001, but no phenotypic description of the patient is included in the original article. We report a pedigree of three patients over two generations affected with GCK mutation c.364C > G (p.Leu122Val) to support the clinical significance of this mutation and to provide the first phenotypic description of patients with this particular mutation.

Fine structure of the subitaneous eggshell of the sessile rotifer Stephanoceros millsii (Monogononta) with observations on vesicle trafficking in the integument during ontogeny.

Rotifers that engage in cyclical parthenogenesis produce two types of eggs: subitaneous eggs that hatch as clonal females and meiotic eggs that hatch as haploid males, or if fertilized, as females after a period of diapause (resting eggs). The ultrastructure of resting eggshells is known for some motile species, but there are limited data on subitaneous eggshells, and no data on any eggshells of sessile rotifers. Here, we investigated the ultrastructure of the subitaneous eggshell of the sessile rotifer Stephanoceros millsii and its potential origins of secretion, the maternal vitellarium and embryonic integument. We also explored secretory activity in the larval and adult integuments to determine whether activity changes during ontogeny. The eggshell consists of a single layer with two sublayers: an external granular sublayer apparently derived from the maternal vitellarium, and an internal flocculent sublayer secreted by the embryonic integument that may form a hatching membrane or glycocalyx. Secretory activity remains high in both the larva and adult and appears to be the source of the thickening glycocalyx. Altogether, the subitaneous eggshell of S. millsii is the thinnest among monogonont rotifers. Thin eggshells may have evolved in response to the added protection provided by the mother's extracorporeal tube.

Humoral immune system targets clonotypic antibody-associated hepatitis C virus.

Hypervariable region 1 (HVR1) is one of the potential neutralization domains in the E2 glycoprotein of hepatitis C virus (HCV). Point mutations of the HVR1 can lead to humoral immune escape in HCV-infected patients. In this study, we segregated the chronically infected viraemic sera from HCV-infected patients into populations of antibody-free virus and antibody-associated virus (AAV) and mapped potential epitopes within the E1E2 gene junction of AAV sequences (residues 364-430). Furthermore, we generated HCV pseudoparticles (HCVpp) derived from AAV sequences to assess their infectivity. We studied the neutralization potential of virus-free Fab obtained from antibody-virus complexes, in the HCVpp system. We observed selective targeting of clonotypic HCV variants from the quasispecies pool. Moreover, we identified potential neutralizing epitopes within the HVR1 and an additional epitope that overlapped with a broadly neutralizing AP33 epitope (amino acid 412-423 in E2). We observed a marked difference in the infectivity of HCVpp generated using E1E2 sequences isolated from AAV. We document reduction in the infectivity of HCVpp-H77 and HCVpp derived from AAV sequences when challenged with virus-free Fab. Our results provide novel insights into the complexities of engagement between HCV and the humoral immune system.

Trace-metal contamination in the glacierized Rio Santa watershed, Peru.

The objective of this research is to characterize the variability of trace metals in the Rio Santa watershed based on synoptic sampling applied at a large scale. To that end, we propose a combination of methods based on the collection of water, suspended sediments, and riverbed sediments at different points of the watershed within a very limited period. Forty points within the Rio Santa watershed were sampled between June 21 and July 8, 2013. Forty water samples, 36 suspended sediments, and 34 riverbed sediments were analyzed for seven trace metals. The results, which were normalized using the USEPA guideline for water and sediments, show that the Rio Santa water exhibits Mn concentrations higher than the guideline at more than 50% of the sampling points. As is the second highest contaminating element in the water, with approximately 10% of the samples containing concentrations above the guideline. Sediments collected in the Rio Santa riverbed were heavily contaminated by at least four of the tested elements at nearly 85% of the sample points, with As presenting the highest normalized concentration, at more than ten times the guideline. As, Cd, Fe, Pb, and Zn present similar concentration trends in the sediment all along the Rio Santa.The findings indicate that care should be taken in using the Rio Santa water and sediments for purposes that could affect the health of humans or the ecosystem. The situation is worse in some tributaries in the southern part of the watershed that host both active and abandoned mines and ore-processing plants.

Are there biological differences between screen-detected and interval colorectal cancers in the English Bowel Cancer Screening Programme?

BACKGROUND: We measured biomarkers of tumour growth and vascularity in interval and screen-detected colorectal cancers (CRCs) in the English Bowel Cancer Screening Programme in order to determine whether rapid tumour growth might contribute to interval CRC (a CRC diagnosed between a negative guaiac stool test and the next scheduled screening episode). METHODS: Formalin-fixed, paraffin-embedded sections from 71 CRCs (screen-detected 43, interval 28) underwent immunohistochemistry for CD31 and Ki-67, in order to measure the microvessel density (MVD) and proliferation index (PI), respectively, as well as microsatellite instability (MSI) testing. RESULTS: Interval CRCs were larger (P=0.02) and were more likely to exhibit venous invasion (P=0.005) than screen-detected tumours. There was no significant difference in MVD or PI between interval and screen-detected CRCs. More interval CRCs displayed MSI-high (14%) compared with screen-detected tumours (5%). A significantly (P=0.005) higher proportion (51%) of screen-detected CRC resection specimens contained at least one polyp compared with interval CRC (18%) resections. CONCLUSIONS: We found no evidence of biological differences between interval and screen-detected CRCs, consistent with the low sensitivity of guaiac stool testing as the main driver of interval CRC. The contribution of synchronous adenomas to occult blood loss for screening requires further investigation.

A single amino acid change in the hypervariable region 1 of hepatitis C virus genotype 4a aids humoral immune escape.

Longitudinal analysis of chronic hepatitis C virus (HCV) infection has shown that the virus has several adaptive strategies that maintain persistence and infectivity over time. We examined four serum samples from the same chronically infected HCV genotype 4a patient for the presence of IgG antibody-associated virus. RNA was isolated from antibody-associated and antibody-free virions. Subsequent to sequence analysis, 27 aa hypervariable region 1 (HVR1) peptides were used to test the humoral immune escape. We demonstrated that differential peptide binding of Fab was associated with a single amino acid change. We provide direct evidence of natural humoral immune escape by HCV within HVR1.

Network Analysis of the Chronic Hepatitis C Virome Defines Hypervariable Region 1 Evolutionary Phenotypes in the Context of Humoral Immune Responses.

UNLABELLED: Hypervariable region 1 (HVR1) of hepatitis C virus (HCV) comprises the first 27 N-terminal amino acid residues of E2. It is classically seen as the most heterogeneous region of the HCV genome. In this study, we assessed HVR1 evolution by using ultradeep pyrosequencing for a cohort of treatment-naive, chronically infected patients over a short, 16-week period. Organization of the sequence set into connected components that represented single nucleotide substitution events revealed a network dominated by highly connected, centrally positioned master sequences. HVR1 phenotypes were observed to be under strong purifying (stationary) and strong positive (antigenic drift) selection pressures, which were coincident with advancing patient age and cirrhosis of the liver. It followed that stationary viromes were dominated by a single HVR1 variant surrounded by minor variants comprised from conservative single amino acid substitution events. We present evidence to suggest that neutralization antibody efficacy was diminished for stationary-virome HVR1 variants. Our results identify the HVR1 network structure during chronic infection as the preferential dominance of a single variant within a narrow sequence space. IMPORTANCE: HCV infection is often asymptomatic, and chronic infection is generally well established in advance of initial diagnosis and subsequent treatment. HVR1 can undergo rapid sequence evolution during acute infection, and the variant pool is typically seen to diverge away from ancestral sequences as infection progresses from the acute to the chronic phase. In this report, we describe HVR1 viromes in chronically infected patients that are defined by a dominant epitope located centrally within a narrow variant pool. Our findings suggest that weakened humoral immune activity, as a consequence of persistent chronic infection, allows for the acquisition and maintenance of host-specific adaptive mutations at HVR1 that reflect virus fitness.

The outcomes of transcatheter aortic valve replacement in a cohort of patients with end-stage renal disease.

OBJECTIVES: To examine whether transcatheter aortic valve replacement (TAVR) is a safe and effective treatment option for aortic stenosis in patients with end-stage renal disease (ESRD). BACKGROUND: Patients with ESRD undergoing surgical aortic valve replacement have an operative mortality approaching 20% and a 10-year survival of approximately 12%. We investigated whether TAVR is a more reasonable option. METHODS: This is a multicenter, retrospective study of all patients with ESRD who underwent TAVR in 8 institutions between 12/2011 and 02/2013. Demographic characteristics, mortality, major, and minor complications were evaluated. Outcomes were stratified by operative approach. RESULTS: Forty-three patients with a mean age 76.2 ± 11.0 years and a mean STS predicted risk of mortality of 15.53 ± 8.70% underwent TAVR. Mean duration of dialysis was 45.2 ± 52.3 months (median 29.5 months). Transfemoral (TF) TAVR was performed in 31/43 (72.1%), transapical in 11/43 (25.6%), and transaortic in 1/43 (2.3%). Operative mortality was 14.0% (6/43) with TF mortality 6.5% (2/31) and 33.3% (4/12) in non-TF patients. Six-month mortality was 11/43 (25.6%: 16.1% TF, 50.0% non-TF). Complications included stroke in 2.3% (1/43) and life-threatening or major bleeding in 14.0% (6/43). Discharge to another healthcare facility was 27.0% (10/37). Readmission within 30 days of procedure for any cause was 18.9% (7/37). CONCLUSIONS: Patients with ESRD who undergo TAVR are at high risk for mortality and complications. TAVR outcomes are comparable to but not substantially better than those with SAVR. Transfemoral TAVR seems to be at least as safe and effective as the current standard SAVR in patients undergoing aortic valve replacement. © 2016 Wiley Periodicals, Inc.

Intensive temporal mapping of hepatitis C hypervariable region 1 quasispecies provides novel insights into hepatitis C virus evolution in chronic infection.

Hepatitis C virus (HCV) is an RNA virus which exists as swarms of closely related viruses known as quasispecies (QS). A number of studies have demonstrated associations between QS hypervariable region 1 (HVR1) characteristics (diversity and complexity) and treatment success. We investigated HCV QS change in chronic infection over intervals of 2-4 weeks in 23 chronically infected individuals to describe the natural history of virus evolution and establish whether HCV QS characteristics could be used to individualize treatment regimens at a molecular level. HVR1 QS diversity, complexity and divergence continue to change in an unpredictable fashion in chronic infection even where there is little phylogenetic change, which is likely to preclude the use of these features in treatment individualization. Our phylogenetic analysis identified no change in the HVR1 QS in 12 subjects, minor change in four subjects and we describe a time-ordered phylogeny for the first time over a period as short as 16 weeks in seven subjects. We identified the existence of multiple subpopulation infections using partitioned analysis of QS and illustrated how subpopulations were sequentially replaced in a number of subjects. We illustrated marked variation in the nucleotide substitution per codon position between patients with sequence change and those without change in the phylogenetic tree. Analysis of codon-specific selection pressures identified a number of codons under purifying selection, suggesting that these code for structurally conserved amino acids. We also identified sections of the HVR1 under positive selection with marked sequence heterogeneity, suggesting that these may be potential epitope-binding sites.

Analysis of the evolution and structure of a complex intrahost viral population in chronic hepatitis C virus mapped by ultradeep pyrosequencing.

UNLABELLED: Hepatitis C virus (HCV) causes chronic infection in up to 50% to 80% of infected individuals. Hypervariable region 1 (HVR1) variability is frequently studied to gain an insight into the mechanisms of HCV adaptation during chronic infection, but the changes to and persistence of HCV subpopulations during intrahost evolution are poorly understood. In this study, we used ultradeep pyrosequencing (UDPS) to map the viral heterogeneity of a single patient over 9.6 years of chronic HCV genotype 4a infection. Informed error correction of the raw UDPS data was performed using a temporally matched clonal data set. The resultant data set reported the detection of low-frequency recombinants throughout the study period, implying that recombination is an active mechanism through which HCV can explore novel sequence space. The data indicate that polyvirus infection of hepatocytes has occurred but that the fitness quotients of recombinant daughter virions are too low for the daughter virions to compete against the parental genomes. The subpopulations of parental genomes contributing to the recombination events highlighted a dynamic virome where subpopulations of variants are in competition. In addition, we provide direct evidence that demonstrates the growth of subdominant populations to dominance in the absence of a detectable humoral response. IMPORTANCE: Analysis of ultradeep pyrosequencing data sets derived from virus amplicons frequently relies on software tools that are not optimized for amplicon analysis, assume random incorporation of sequencing errors, and are focused on achieving higher specificity at the expense of sensitivity. Such analysis is further complicated by the presence of hypervariable regions. In this study, we made use of a temporally matched reference sequence data set to inform error correction algorithms. Using this methodology, we were able to (i) detect multiple instances of hepatitis C virus intrasubtype recombination at the E1/E2 junction (a phenomenon rarely reported in the literature) and (ii) interrogate the longitudinal quasispecies complexity of the virome. Parallel to the UDPS, isolation of IgG-bound virions was found to coincide with the collapse of specific viral subpopulations.