Average Pairwise Difference Research Articles

Human Brain Ancestral Barcodes.

Dynamic CpG methylation "barcodes" were read from 15,000 to 21,000 single cells from three human male brains. To overcome sparse sequencing coverage, the barcode had ~31,000 rapidly fluctuating X-chromosome CpG sites (fCpGs), with at least 500 covered sites per cell and at least 30 common sites between cell pairs (average of ~48). Barcodes appear to start methylated and record mitotic ages because excitatory neurons and glial cells that emerge later in development were less methylated. Barcodes are different between most cells, with average pairwise differences (PWDs) of ~0.5 between cells. About 10 cell pairs per million were more closely related with PWDs < 0.05. Barcodes appear to record ancestry and reconstruct trees where more related cells had similar phenotypes, albeit some pairs had phenotypic differences. Inhibitory neurons showed more evidence of tangential migration than excitatory neurons, with related cells in different cortical regions. fCpG barcodes become polymorphic during development and can distinguish between thousands of human cells.

Patterns of the Predicted Mutation Burden in 19,778 Domesticated Barley Accessions Conserved Ex Situ.

Long-term conservation of more than 7 million plant germplasm accessions in 1750 genebanks worldwide is a challenging mission. The extent of deleterious mutations present in conserved germplasm and the genetic risk associated with accumulative mutations are largely unknown. This study took advantage of published barley genomic data to predict sample-wise mutation burdens for 19,778 domesticated barley (Hordeum vulgare L.) accessions conserved ex situ. It was found that the conserved germplasm harbored 407 deleterious mutations and 337 (or 82%) identified deleterious alleles were present in 20 (or 0.1%) or fewer barley accessions. Analysis of the predicted mutation burdens revealed significant differences in mutation burden for several groups of barley germplasm (landrace > cultivar (or higher burden estimate in landrace than in cultivar); winter barley > spring barley; six-rowed barley > two-rowed barley; and 1000-accession core collection > non-core germplasm). Significant differences in burden estimate were also found among seven major geographical regions. The sample-wise predicted mutation burdens were positively correlated with the estimates of sample average pairwise genetic difference. These findings are significant for barley germplasm management and utilization and for a better understanding of the genetic risk in conserved plant germplasm.

Leveraging a Previously Published Population Pharmacokinetic Model to Predict Rivaroxaban Exposure in Real-World Patients.

Population pharmacokinetic (PK)/pharmacodynamic models are commonly used to inform drug dosing; however, often real-world patients are not well represented in the clinical trial population. We sought to determine how well dosing recommended in the rivaroxaban drug label results in exposure for real-world patients within a reference area under the concentration-time curve (AUC) range. To accomplish this, we assessed the utility of a prior published rivaroxaban population PK model to predict exposure in real-world patients. We used the model to predict rivaroxaban exposure for 230 real-world patients using 3 methods: (1) using patient phenotype information only, (2) using individual post hoc estimates of clearance from the prior model based on single PK samples of rivaroxaban collected at steady state without refitting of the prior model, and (3) using individual post hoc estimates of clearance from the prior model based on PK samples of rivaroxaban collected at steady state after refitting of the prior model. We compared the results across 3 software packages (NONMEM, Phoenix NLME, and Monolix). We found that while the average patient-assigned dosing per the drug label will likely result in the AUC falling within the reference range, AUC for most individual patients will be outside the reference range. When comparing post hoc estimates, the average pairwise percentage differences were all &lt;10% when comparing the software packages, but individual pairwise estimates varied as much as 50%. This study demonstrates the use of a prior published rivaroxaban population PK model to predict exposure in real-world patients.

Covariance of pairwise differences on a multi-species coalescent tree and implications for FST.

The multi-species coalescent (MSC) provides a theoretical foundation for modern phylogenetics and comparative population genetics. Its theoretical properties have been heavily studied but there are still aspects of the MSC that are largely unknown, including the covariances in pairwise coalescence times, which are fundamental for understanding the properties of statistics that combine data from multiple species, such as the fixation index (FST). The major contribution of this study is the derivation and implementation of exact expressions for the covariances of pairwise coalescence times under phylogenetic models with piecewise constant changes in population size, assuming no gene flow after species divergence. We use these expressions to derive the variance in average pairwise differences within and between populations. We then derive approximations for the expectation and bias of a sequence-based estimator of FST, a commonly used genetic measurement of population differentiation, when it is applied to a non-recombining region of the genome. We show that the estimator of FST is generally biased downward. A freely available software package is provided, STCov, to calculate the mean, variances and covariances in coalescence times presented here under user-defined piecewise-constant species trees.This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.

String-pulling in the Greater Vasa parrot (Coracopsis vasa): A replication of capacity, findings of longitudinal retention, and evidence for a species-level general insight factor across five physical cognition tasks

Spontaneous solving of an insight-based means-end reasoning task (the string-pulling problem) is observed in an adult male captive bred Greater Vasa parrot (Coracopsis vasa Shaw, 1812), with an efficiency of 66%, replicating previous work in a singleton context. This case report adds to the existing literature on this species by also demonstrating longitudinal retention, specifically the same bird was found to be able to re-solve the simple form of the problem after a period of seven years (the bird was first tested in 2013, and re-tested in 2020), with an efficiency of 43% (the difference between efficiencies was not significant, χ2 = 0.991, p = .319). In a second analysis, species-level data across five patterned string-pulling tasks involving 14 parrot species were reanalysed, revealing that the Greater Vasa parrot exhibited the greatest general competence among those evaluated. A ‘general insight factor’ (GIF) was also found across taxa, the loadings onto which exhibit positive and large-magnitude associations with the correlation between fission-fusion flocking intensity and indicator level performance (r = 0.831), and also positive small and modest-magnitude associations with the correlation between relative brain size and indicator-level performance, and the magnitude of average pair-wise species differences in performance across indicators (r = 0.219 and 0.365 respectively). Finally, the theoretical implications of these findings are discussed.

Genetic variation and demographic history analysis of Pestalotiopsis, Pseudopestalotiopsis, and Neopestalotiopsis fungi associated with tea (Camellia sinensis) inferred from the internal transcribed spacer region of the nuclear ribosomal DNA

AbstractTo elucidate the demographic history within and among the genera Pseudopestalotiopsis, Neopestalotiopsis, and Pestalotiopsis and their genetic diversity, we studied internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA (nrDNA) with no saturation effects in 172 Pestalotiopsis‐like fungal accessions isolated from Camellia sinensis planted in nine provinces in China (64 from Yunnan, 4 from Guangxi, 2 from Guizhou, 42 from Jiangxi, 3 from Sichuan, 3 from Zhejiang, 1 from Henan, 18 from Fujian, 12 from Chongqing, and 18 from other provinces) and in Japan (1), France (1), Turkey (1), and Thailand (2). Among these, 44 Pestalotiopsis‐like isolates from Yunnan in this study formed a clade in phylogenetic trees with Pestalotiopsis accessions in GenBank, despite their cultural characteristics on potato dextrose agar displaying no genus specificity. Based on estimated sequence polymorphism parameters of average pairwise differences (K), haplotype diversity (Hd), nucleotide diversity (Pi), θ (per site) from η, and recombination event rate (Rm), we identified moderate genetic variation in these three genera. Molecular evolution analysis with neutrality tests and mismatch distribution demonstrated that Pseudopestalotiopsis and Pestalotiopsis ribosomal ITS sequences evolved under a neutral model. However, the recent demographic expansion of the three genera promoted geographical isolation but showed no clear geographical structure. Pairwise genetic divergences between haplotypes and a median‐joining network revealed Yunnan or Jiangxi as a possible centre of origin, and that Pseudopestalotiopsis and Neopestalotiopsis may derive from Pestalotiopsis.

Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel.

For the adoption of massively parallel sequencing (MPS) systems by forensic laboratories, validation studies on specific workflows are needed to support the feasibility of implementation and the reliability of the data they produce. As such, the whole mitochondrial genome sequencing methodology—Precision ID mtDNA Whole Genome Panel, Ion Chef, Ion S5, and Converge—has been subjected to a variety of developmental validation studies. These validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines and assessed reproducibility, repeatability, accuracy, sensitivity, specificity to human DNA, and ability to analyze challenging (e.g., mixed, degraded, or low quantity) samples. Intra- and inter-run replicates produced an average maximum pairwise difference in variant frequency of 1.2%. Concordance with data generated with traditional Sanger sequencing and an orthogonal MPS platform methodology was used to assess accuracy, and generation of complete and concordant haplotypes at DNA input levels as low as 37.5 pg of nuclear DNA or 187.5 mitochondrial genome copies illustrated the sensitivity of the system. Overall, data presented herein demonstrate that highly accurate and reproducible results were generated for a variety of sample qualities and quantities, supporting the reliability of this specific whole genome mitochondrial DNA MPS system for analysis of forensic biological evidence.

Growth from Birth Through Six Months for Infants of Mothers in the “Women First” Preconception Maternal Nutrition Trial

To evaluate whether the fetal linear growth effects of maternal nutrition supplementation would be maintained through 6months postnatal age. The Women First trial was a multicountry, individually randomized clinical trial that compared the impact of maternal nutrition supplementation initiated preconception (Arm 1) vs at ∼11weeks of gestation (Arm 2), vs no supplement (Arm 3); the intervention was discontinued at delivery. Trial sites were in Democratic Republic of Congo, Guatemala, India, and Pakistan. Analysis includes 2421 infants born to 2408 randomized women. Primary outcome was the trajectory of length-for-age z scores (LAZ) by arm, based on assessments at birth and 1, 3, and 6months. We fitted longitudinal models on growth from birth to 6months using generalized estimating equations; maternal intervention effects were evaluated, adjusting for site and baseline maternal covariates. Linear growth for Arms 1 and 2 was statistically greater than for Arm 3 in 3 of the 4 countries, with average pairwise mean differences in LAZ of 0.25 (95% CI 0.15-0.35; P<.001) and 0.19 (95% CI 0.09-0.28; P<.001), respectively. Compared with Arm 3, average overall adjusted relative risks (95% CI) for stunting (LAZ <-2) were lower for Arms 1 and 2: 0.76 (0.66-0.87; P<.001) and 0.77 (0.67-0.88; P<.001), respectively. Improved linear growth in early infancy observed for the 2 intervention arms supports the critical importance of maternal nutrition before conception and in the early phase of gestation. ClinicalTrials.gov: NCT01883193.

Genetic diversity and population structure of small yellow croaker (Larimichthys polyactis) in the Yellow and East China seas based on microsatellites

Small yellow croaker (Larimichthys polyactis), a member of family Sciaenidae, is mainly distributed in the northwestern Pacific Ocean. To assess the genetic diversity and population structure of this species across its range, we genotyped 150 L. polyactisindividuals sampled in five locations along the coast of the Yellow and East China seas using 20 polymorphic microsatellites. A total of 499 alleles were detected at 20 loci across all individuals, and a relatively high level of genetic diversity was observed, with observed heterozygosity (Ho), expected heterozygosity (He) and polymorphic information content (PIC) ranging from 0.233 to 1.000, from 0.438 to 0.955, and from 0.367 to 0.953 per locus-location combination, respectively. Analysis of molecular variance (AMOVA) (FST = 0.00915,P &lt; 0.001), pairwise FST, and corrected average pairwise differences indicated that there was extremely low, but statistically significant genetic differentiation among the studied populations. However, Bayesian assignment analysis revealed a high number of immigrants among populations and no obvious genetic differentiation. The Wilcoxon signed-rank test and mode-shift indicator of allele frequency distribution support the inferrence thatL. polyactishad not experienced a recent genetic bottleneck. Overall, the results suggest that, despite low genetic differentiation in this species, the small yellow croaker forms a single panmictic population with high genetic variation and gene flow in the studied area. This study will provide useful information for conservation and sustainable exploitation of this important aquatic living resource.

Current genetic diversity in eight local Chinese sheep populations.

China has numerous local domestic sheep breeds. In this study, the genetic diversity of eight sheep populations was estimated using 17 microsatellites. Knowledge of such diversity provides novel insight into the degree of breed protection needed and the prediction of hybrid advantage. In total, 17 microsatellites were genotyped in 186 individuals from eight populations. The mean number of alleles (± SD) ranged from 3.71 ± 1.36 in Zhaotong sheep to 11.94 ± 3.58 in small-tailed Han sheep. The observed heterozygote frequency (± SD) within a population ranged from 0.482 ± 0.025 in Zhaotong sheep to 0.664 ± 0.023 in Tibetan sheep. In addition, using pairwise difference (FST) analysis, the highest within-population diversity was observed in Tibetan sheep (πX = 12.8098) and small-tailed Han (πX = 12.67873), and the lowest diversity was observed in Zhaotong sheep (πX = 7.90337). The results for genetic divergence between populations indicated that the populations were significantly different (P < 0.05) based on the average number of pairwise differences between populations (πXY) and the corrected average pairwise differences. Both phylogenetic networks and structure analysis showed that these eight populations were separated into three clusters in accordance with their geographical habitat, except Tibetan and Hu sheep. In short, we genotyped eight local Chinese sheep populations using 17 microsatellites, and the results indicated that their current genetic diversity is decreasing and that new conservation strategies are needed. In addition, significant genetic differences between populations could be used in cross breeding.

Genetic diversity study in Hungarian coldblooded horses

Because of the feeding technology innovation, accelerated transport and communication facilities breeds of high performance breeds replaced local autochone breeds worldwide. These latter species however have an important role in gene conservation. Hungarian cold-blooded horse breeding stock are lacking pedigree, the actual founder breed mares are not known. For this reason, it is an major priority defining the genetic backround of the existing flock, for that breeding could operate with purposeful using of origin maternal founders. In the present study 195 cold-blooded Hungarian mares tail and mane sample were analized. Our analysis was carried out between 15531–15752 base pairs in mithocrondial DNA D-loop region, which reported a total of 222 base pairs. Fourtyone polymorphic sites were determined, which resulted in 39 haplotypes (h=39). The average pairwise differences were k=6.825. High haplotype and nucleotide diversity values were observed (Hd=0.968±0.003, π=0.026±0.003). Based on the previously defined variable positions of haplotypes defined by Jansen et al (2002), we groupped our haplotypes into haplogroups. 23 percent of the studied population (45 mares) belonged to haplogroup F1. Nearly 97% of the analyzed population was classified into one of eight haplogroups defined by Jansen.et al. (2002). This study gives genetic information nearly 25% of the Hungarian population. Another possibility would be patterning more mares or involving more genetic marker in the study which will assuming the possibility of a more comprehensive analysis.

On the use of climate covariates in aquatic species distribution models: are we at risk of throwing out the baby with the bath water?

Species distribution models (SDMs) in river ecosystems can incorporate climate information by using air temperature and precipitation as surrogate measures of instream conditions or by using independent models of water temperature and hydrology to link climate to instream habitat. The latter approach is preferable but constrained by the logistical burden of developing water temperature and hydrology models. We therefore assessed whether regional scale, freshwater SDM predictions are fundamentally different when climate data versus instream temperature and hydrology are used as covariates. Maximum entropy (MaxEnt) SDMs were built for 15 freshwater fishes using one of two covariate sets: 1) air temperature and precipitation (climate variables) in combination with physical habitat variables; or 2) water temperature, hydrology (instream variables) and physical habitat. Three procedures were then used to compare results from climate vs instream models. First, equivalence tests assessed average pairwise differences (site‐specific comparisons throughout each species’ range) among climate and instream models. Second, ‘congruence’ tests determined how often the same stream segments were assigned high habitat suitability by climate and instream models. Third, Schoener's D and Warren's I niche overlap statistics quantified range‐wide similarity in predicted habitat suitability from climate vs instream models. Equivalence tests revealed small, pairwise differences in habitat suitability between climate and instream models (mean pairwise differences in MaxEnt raw scores for all species &lt; 3 × 10–4). Congruence tests showed a strong tendency for climate and instream models to predict high habitat suitability at the same stream segments (median congruence = 68%). D and I statistics reflected a high margin of overlap among climate and instream models (median D = 0.78, median I = 0.96). Overall, we found little support for the hypothesis that SDM predictions are fundamentally different when climate versus instream covariates are used to model fish species’ distributions at the scale of the Columbia Basin.

Population genetic structure and genetic diversity of Chinese pomfret at the coast of the East China Sea and the South China Sea

The Chinese pomfret Pampus chinensis is one of the most economic and ecological important marine fish species in China. In the present study, the population genetic structure and genetic diversity of P. chinensis were evaluated from a total sample size of 180 individuals representing six populations from the East China Sea and the South China Sea using mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 24 variable sites (including 3 singleton sites and 21 parsimony information sites) were observed, and 18 haplotypes were defined. The haplotype diversity (Hd) of the populations ranged from 0.559 to 0.775, and the nucleotide diversity (π) ranged from 0.330 to 1.090%. Analysis of molecular variance (AMOVA) reveals that the main variation (66.02%) was among individuals within populations. The average pairwise differences and ϕST values indicated significant genetic differentiation between Dongxing population and the other populations. The results of the present study are helpful for the sustainable management and utilization of this species.

Mitochondrial DNA D-Loop diversity and evolutionary relationship of wild Punjab Urial sheep (Ovis vignei punjabiensis) with closely related taxa

The taxonomy and systematics of wild sheep is complex with several classifications and revisions proposed on the basis of morphology, geographic distribution and chromosome number. Punjab Urial (O. vignei punjabiensis), an important sub-species of O. vignei is distributed in Pakistan and is classified under vulnerable category. The taxonomic status of this sub-species remains uncertain and the present study is an attempt to assess its mitochondrial DNA diversity and evolutionary relationship with closely related taxa. Analysis of mitochondrial DNA D-Loop of O. vignei punjabiensis revealed wide variations in the number and pattern of tandem repeats as compared to other Moufloniform wild sheep. With the exception of tandem repeat regions, a total of 117 sequences coveringan overlapping region of 748bp from nine wild and domestic sheep populations were analyzed. The nucleotide and haplotype diversity was low to moderate within different sheep populations and Punjab Urial sheep exhibiting a mean of 0.0043 and 0.829 respectively. The average pairwise differences within population varied from 0.67 (O. musimon) to 23.69 (Kachi) while the average differences between Urial sheep and other Moufloniform wild sheep populations was high indicating the distinctness of O. vignei. Bayesian and maximum likelihood phylogeny clearly established the divide between the lineages of O. vignei and O. orientalis populations. Also, the average pairwise differences between O. vignei bochariensis and O. vignei punjabiensis were significantly higher (P<0.01) despite both the populations being classified as sub-species of Urial type sheep. To compare O. vignei punjabiensis with Argaliform and Pachyceriform wild sheep, pairwise FST between populations were utilized to perform principal components analysis (PCA). PCA revealed clustering of Asiatic (O. orientalis), European (O. musimon) and Captive Mouflon type sheep together, while O. nivicola and O. canadensis clustered separately. O. ammon and O. vignei bochariensis were observed to be clustering together while O. vignei punjabiensis was located distinctly. The tests for selective neutrality indicated purifying selection in Punjab Urial sheep while Asiatic Mouflon appears to have experienced a strong population bottleneck in the recent past. Considering the declining population trend and loss in genetic diversity due to possible genetic bottleneck events, there is an urgent need to implement strong conservation measures for O. vignei punjabiensis in the region.

Murine norovirus (MNV-1) exposure in vitro to the purine nucleoside analog Ribavirin increases quasispecies diversity

Ribavirin is a pharmaceutical antiviral used for the treatment of RNA virus infections including norovirus, hepatitis C virus, hepatitis E virus, Lassa virus, respiratory syncytial virus, and rhinovirus. Despite the drug's history and documented efficacy, the antiviral mechanism of Ribavirin remains unclear. Mechanisms proposed include depletion of the intracellular GTP pool, immunomodulatory effects, induction of error catastrophe, inhibition of viral polymerase activity, and/or inhibition of viral capping. In the present study, we leveraged deep sequencing data to demonstrate that Ribavirin increases murine norovirus (MNV-1) viral diversity. By serial passaging MNV-1 in RAW 264.7 cells for twenty generations in the presence of Ribavirin, we demonstrated statistically significant increases in both the number of unique haplotypes and the average pairwise difference (APD). Based on statistically significant differences in the probability of nucleotide mutations based on Roche 454 sequencing, we also demonstrated that single nucleotide substitutions are increased in the presence of Ribavirin. Finally, we demonstrated Ribavirin's impact on statistically significantly reducing the relative proportion of the dominant sequence within the quasispecies.

Quantifying inter-laboratory variability in stable isotope analysis of ancient skeletal remains.

Over the past forty years, stable isotope analysis of bone (and tooth) collagen and hydroxyapatite has become a mainstay of archaeological and paleoanthropological reconstructions of paleodiet and paleoenvironment. Despite this method's frequent use across anthropological subdisciplines (and beyond), the present work represents the first attempt at gauging the effects of inter-laboratory variability engendered by differences in a) sample preparation, and b) analysis (instrumentation, working standards, and data calibration). Replicate analyses of a 14C-dated ancient human bone by twenty-one archaeological and paleoecological stable isotope laboratories revealed significant inter-laboratory isotopic variation for both collagen and carbonate. For bone collagen, we found a sizeable range of 1.8‰ for δ13Ccol and 1.9‰ for δ15Ncol among laboratories, but an interpretatively insignificant average pairwise difference of 0.2‰ and 0.4‰ for δ13Ccol and δ15Ncol respectively. For bone hydroxyapatite the observed range increased to a troublingly large 3.5‰ for δ13Cap and 6.7‰ for δ18Oap, with average pairwise differences of 0.6‰ for δ13Cap and a disquieting 2.0‰ for δ18Oap. In order to assess the effects of preparation versus analysis on isotopic variability among laboratories, a subset of the samples prepared by the participating laboratories were analyzed a second time on the same instrument. Based on this duplicate analysis, it was determined that roughly half of the isotopic variability among laboratories could be attributed to differences in sample preparation, with the other half resulting from differences in analysis (instrumentation, working standards, and data calibration). These findings have serious implications for choices made in the preparation and extraction of target biomolecules, the comparison of results obtained from different laboratories, and the interpretation of small differences in bone collagen and hydroxyapatite isotope values. To address the issues arising from inter-laboratory comparisons, we devise a novel measure we term the Minimum Meaningful Difference (MMD), and demonstrate its application.

PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data

Estimating viral diversity in infected patients can provide insight into pathogen evolution and emergence of drug resistance. With the widespread adoption of deep sequencing, it is important to develop tools to accurately calculate population diversity from very large datasets. Current methods for estimating diversity that are based on multiple alignments are not practical to apply to such data.In this study, the authors report a novel method (Pairwise Alignment Positional Nucleotide Counting, PAPNC) for estimating population diversity from 454 sequence data. The diversity measurements determined using this method were comparable to those calculated by average pairwise difference (APD) of multiply aligned sequences using MEGA5. Diversities were estimated for 9 patient plasma HIV samples sequenced with Titanium 454 technology and by single-genome sequencing (SGS). Diversities calculated from deep sequencing using PAPNC ranged from 0.002 to 0.021 while APD measurements calculated from SGS data ranged proximately from 0.001 to 0.018, with the difference being attributable to PCR error (contributing background diversity of 0.0016 in a control sample). Comparison of APDs estimated from 100 sets of sequences drawn at random from 454 generated data and from corresponding SGS data showed very close correlation between the two methods with R2 of 0.96, and differing on average by about 1% (after correction for PCR error).The authors have developed a novel method that is good for calculating genetic diversities for large scale datasets from next generation sequencing. It can be implemented easily as a function in available variation calling programs like SAMtools or haplotype reconstruction software for nucleotide genetic diversity calculation.A Perl script implementing this method is available upon request.

Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy

A better understanding of changes in HIV-1 population genetics with combination antiretroviral therapy (cART) is critical for designing eradication strategies. We therefore analyzed HIV-1 genetic variation and divergence in patients' plasma before cART, during suppression on cART, and after viral rebound. Single-genome sequences of plasma HIV-1 RNA were obtained from HIV-1 infected patients prior to cART (N = 14), during suppression on cART (N = 14) and/or after viral rebound following interruption of cART (N = 5). Intra-patient population diversity was measured by average pairwise difference (APD). Population structure was assessed by phylogenetic analyses and a test for panmixia. Measurements of intra-population diversity revealed no significant loss of overall genetic variation in patients treated for up to 15 years with cART. A test for panmixia, however, showed significant changes in population structure in 2/10 patients after short-term cART (<1 year) and in 7/10 patients after long-term cART (1–15 years). The changes consisted of diverse sets of viral variants prior to cART shifting to populations containing one or more genetically uniform subpopulations during cART. Despite these significant changes in population structure, rebound virus after long-term cART had little divergence from pretherapy virus, implicating long-lived cells infected before cART as the source for rebound virus. The appearance of genetically uniform virus populations and the lack of divergence after prolonged cART and cART interruption provide strong evidence that HIV-1 persists in long-lived cells infected before cART was initiated, that some of these infected cells may be capable of proliferation, and that on-going cycles of viral replication are not evident.

Stability of the parainfluenza virus 5 genome revealed by deep sequencing of strains isolated from different hosts and following passage in cell culture.

ABSTRACTThe strain diversity of a rubulavirus, parainfluenza virus 5 (PIV5), was investigated by comparing 11 newly determined and 6 previously published genome sequences. These sequences represent 15 PIV5 strains, of which 6 were isolated from humans, 1 was from monkeys, 2 were from pigs, and 6 were from dogs. Strain diversity is remarkably low, regardless of host, year of isolation, or geographical origin; a total of 7.8% of nucleotides are variable, and the average pairwise difference between strains is 2.1%. Variation is distributed unevenly across the PIV5 genome, but no convincing evidence of selection for antibody-mediated evasion in hemagglutinin-neuraminidase was found. The finding that some canine and porcine, but not primate, strains are mutated in the SH gene, and do not produce SH, raised the possibility that dogs (or pigs) may not be the natural host of PIV5. The genetic stability of PIV5 was also demonstrated during serial passage of one strain (W3) in Vero cells at a high multiplicity of infection, under conditions of competition with large proportions of defective interfering genomes. A similar observation was made for a strain W3 mutant (PIV5VΔC) lacking V gene function, in which the dominant changes were related to pseudoreversion in this gene. The mutations detected in PIV5VΔC during pseudoreversion, and also those characterizing the SH gene in canine and porcine strains, predominantly involved U-to-C transitions. This suggests an important role for biased hypermutation via an adenosine deaminase, RNA-specific (ADAR)-like activity.IMPORTANCE Here we report the sequence variation of 16 different isolates of parainfluenza virus 5 (PIV5) that were isolated from a number of species, including humans, monkeys, dogs, and pigs, over 4 decades. Surprisingly, strain diversity was remarkably low, regardless of host, year of isolation, or geographical origin. Variation was distributed unevenly across the PIV5 genome, but no convincing evidence of immune or host selection was found. This overall genome stability of PIV5 was also observed when the virus was grown in the laboratory, and the genome stayed remarkably constant even during the selection of virus mutants. Some of the canine isolates had lost their ability to encode one of the viral proteins, termed SH, suggesting that although PIV5 commonly infects dogs, dogs may not be the natural host for PIV5.

Multisoftware Reproducibility Study of Stress and Rest Myocardial Blood Flow Assessed with 3D Dynamic PET/CT and a 1-Tissue-Compartment Model of 82Rb Kinetics

Routine quantification of myocardial blood flow (MBF) requires robust and reproducible processing of dynamic image series. The goal of this study was to evaluate the reproducibility of 3 highly automated software programs commonly used for absolute MBF and flow reserve (stress/rest MBF) assessment with (82)Rb PET imaging. Dynamic rest and stress (82)Rb PET scans were selected in 30 sequential patient studies performed at 3 separate institutions using 3 different 3-dimensional PET/CT scanners. All 90 scans were processed with 3 different MBF quantification programs, using the same 1-tissue-compartment model. Global (left ventricle) and regional (left anterior descending, left circumflex, and right coronary arteries) MBF and flow reserve were compared among programs using correlation and Bland-Altman analyses. All scans were processed successfully by the 3 programs, with minimal operator interactions. Global and regional correlations of MBF and flow reserve all had an R(2) of at least 0.92. There was no significant difference in flow values at rest (P = 0.68), stress (P = 0.14), or reserve (P = 0.35) among the 3 programs. Bland-Altman coefficients of reproducibility (1.96 × SD) averaged 0.26 for MBF and 0.29 for flow reserve differences among programs. Average pairwise differences were all less than 10%, indicating good reproducibility for MBF quantification. Global and regional SD from the line of perfect agreement averaged 0.15 and 0.17 mL/min/g, respectively, for MBF, compared with 0.22 and 0.26, respectively, for flow reserve. The 1-tissue-compartment model of (82)Rb tracer kinetics is a reproducible method for quantification of MBF and flow reserve with 3-dimensional PET/CT imaging.