Genetic Variation in Clinical Varicella-Zoster Virus Isolates Collected in Ireland Between 2002 and 2003

Analysis of genetic variation in 16 varicella-zoster virus (VZV) isolates selected at random and circulating in the Irish population between March 2002 and February 2003 was carried out. A 919 bp fragment of the glycoprotein E gene (open reading frame 68) encompassing codon 150, at which a non-synonymous mutation defines the escape mutant VZV-MSP, and including two other epitope regions e1 and c1, was sequenced. No new single nucleotide polymorphisms (SNPs) were detected, indicating stability of these epitopes in clinical isolates of VZV. However, when four informative polymorphic markers consisting of defined regions from genes 1, 21, 50, and 54 were sequenced 14 variable nucleotide positions were identified. Phylogenetic analysis showed the presence of three highly supported clades A, B, and C circulating in the Irish population. Approximately one third (6/16; 37.5%) of the Irish VZV isolates in this study belonged to genotype C, 4/16 (25%) to genotype A, and 4/16 (25%) to genotype B. A smaller number 2/16 (12.5%) belonged to genotype J1. This indicates remarkable heterogeneity in the Irish population given the small sample size. No evidence was found to suggest any of the 16 isolates was a recombinant. These findings have implications for the model of geographic isolation of VZV clades to certain regions as the circulating Irish VZV population appears to comprise approximately equal numbers of each of the main genotypes. This data is inconsistent with a model of strict geographical separation of VZV genotypes and suggests that VZVdiversity ismorepronounced in certain areas than had been thought previously

Genetic Variation in Clinical Varicella-Zoster Virus Isolates Collected in Ireland Between 2002 and 2003

Analysis of genetic variation in 16 varicella-zoster virus (VZV) isolates selected at random and circulating in the Irish population between March 2002 and February 2003 was carried out. A 919 bp fragment of the glycoprotein E gene (open reading frame 68) encompassing codon 150, at which a non-synonymous mutation defines the escape mutant VZV-MSP, and including two other epitope regions e1 and c1, was sequenced. No new single nucleotide polymorphisms (SNPs) were detected, indicating stability of these epitopes in clinical isolates of VZV. However, when four informative polymorphic markers consisting of defined regions from genes 1, 21, 50, and 54 were sequenced 14 variable nucleotide positions were identified. Phylogenetic analysis showed the presence of three highly supported clades A, B, and C circulating in the Irish population. Approximately one third (6/16; 37.5%) of the Irish VZV isolates in this study belonged to genotype C, 4/16 (25%) to genotype A, and 4/16 (25%) to genotype B. A smaller number 2/16 (12.5%) belonged to genotype J1. This indicates remarkable heterogeneity in the Irish population given the small sample size. No evidence was found to suggest any of the 16 isolates was a recombinant. These findings have implications for the model of geographic isolation of VZV clades to certain regions as the circulating Irish VZV population appears to comprise approximately equal numbers of each of the main genotypes. This data is inconsistent with a model of strict geographical separation of VZV genotypes and suggests that VZVdiversity ismorepronounced in certain areas than had been thought previously

Chronic Obstructive Pulmonary Disease: Thoracic CT Texture Analysis and Machine Learning to Predict Pulmonary Ventilation

Background Fixed airflow limitation and ventilation heterogeneity are common in chronic obstructive pulmonary disease (COPD). Conventional noncontrast CT provides airway and parenchymal measurements but cannot be used to directly determine lung function. Purpose To develop, train, and test a CT texture analysis and machine-learning algorithm to predict lung ventilation heterogeneity in participants with COPD. Materials and Methods In this prospective study

Applying a SNP-based tool for conservation of wild and managed black bees in Ireland

Apis mellifera mellifera (Amm) is threatened over much of its natural range. However, in Ireland microsatellite and mitochondrial data have shown that a significant population of this subspecies exists in pure form and is spread over a large geographical region on the Island. Black bees have been managed and protected by beekeepers on the island, some of whom formed the Native Irish Honeybee Society (NIHBS)in 2012 and a breeding programme was initiated for Amm in 2014/2015. The application of a SNP panel that detects hybridization between M and C lineages clearly supports other data showing that the majority of beekeepers included in the breeding programme indeed have bees with very low to no introgression from the C lineage. Furthermore, SNP data has also been applied to the first feral bee colonies located in Ireland subsequent to the introduction of Varroa. Here we will present on the use of molecular data as an aid to manage and conserve honeybees in Ireland, and to elucidate patterns in colour variation and honeybee subspecies purity in wild and managed bees with a view towards improving conservation approaches in the face of a potential hybridization threat.info:eu-repo/semantics/publishedVersio

DeepWings: a machine learning tool for identification of honey bee subspecies

DeepWings© is a software that uses Machine Learning for fully automated identification of Apis mellifera subspecies based on wing geometric morphometrics (WGM). Here, we examined the performance of DeepWings© under realistic conditions by processing 14,782 wing images with varying quality and produced by different operators. These images represented 2,593 colonies covering the native ranges of A. m. iberiensis (Portugal, Spain and historical introduction in the Azores), A. m. mellifera (Belgium, France, Ireland, Poland, Russia, Sweden, Switzerland, UK) and A. m. carnica (Croatia, Hungary, Romania). The classification probability obtained for the colonies was contrasted with the endemic subspecies distribution. Additionally, the association between WGM classification and that inferred from microsatellites and SNPs was evaluated for 1,214 colonies. As much as 94.4% of the wings were accepted and classified by DeepWings©. In the Iberian honey bee native range, 92,6% of the colonies were classified as A. m. iberiensis with a median probability of 91.88 (IQR = 22.52). In the Azores, 85.7% of colonies were classified as A. m. iberiensis, with a median probability of 84.16 (32.40). In the Dark honey bee native range, 41.1 % of the colonies were classified as A. m mellifera with a median probability of 99.36 (8.02). The low percentage of colonies matching the native subspecies was mainly due to the low values registered in Avignon (20.0%), Poland (32.9%), and Wales (41.2%). In contrast, most of the colonies analyzed in other locations of the native range of A. m. mellifera matched this subspecies: Belgium (100.0%), Groix (63.9%), Ouessant (72.7%), Ireland (78.0%), Russia (96.2%), Sweden (84.2%) and Switzerland (55.6%). In the colonies from Croatia, Hungary, and Romania, 88.0% of the samples were classified as A. m. carnica, with a median probability of 98.49 (6.76). The association between WGM and molecular data was highly significant but not very strong (Spearman r = 0.31, p < 0.0001). A good agreement between morphological and molecular methods was registered in samples originating from highly conserved M-lineage populations whereas in populations with historical records of foreign queen importations the agreement was weaker. In general, DeepWings© showed good performance when tested under realistic conditions. It is a valuable tool that can be used not only for honey bee breeding and conservation but also for research purposes.info:eu-repo/semantics/publishedVersio

Pulmonary Imaging Biomarkers of Gas Trapping and Emphysema in COPD: (3)He MR Imaging and CT Parametric Response Maps

PURPOSE: To directly compare magnetic resonance (MR) imaging and computed tomography (CT) parametric response map (PRM) measurements of gas trapping and emphysema in ex-smokers both with and without chronic obstructive pulmonary disease (COPD). MATERIALS AND METHODS: Participants provided written informed consent to a protocol that was approved by a local research ethics board and Health Canada and was compliant with the HIPAA (Institutional Review Board Reg. #00000940). The prospectively planned study was performed from March 2014 to December 2014 and included 58 ex-smokers (mean age, 73 years ± 9) with (n = 32; mean age, 74 years ± 7) and without (n = 26; mean age, 70 years ± 11) COPD. MR imaging (at functional residual capacity plus 1 L), CT (at full inspiration and expiration), and spirometry or plethysmography were performed during a 2-hour visit to generate ventilation defect percent (VDP), apparent diffusion coefficient (ADC), and PRM gas trapping and emphysema measurements. The relationships between pulmonary function and imaging measurements were determined with analysis of variance (ANOVA), Holm-Bonferroni corrected Pearson correlations, multivariate regression modeling, and the spatial overlap coefficient (SOC). RESULTS: VDP, ADC, and PRM gas trapping and emphysema (ANOVA, P \u3c .001) measurements were significantly different in healthy ex-smokers than they were in ex-smokers with COPD. In all ex-smokers, VDP was correlated with PRM gas trapping (r = 0.58, P \u3c .001) and with PRM emphysema (r = 0.68, P \u3c .001). VDP was also significantly correlated with PRM in ex-smokers with COPD (gas trapping: r = 0.47 and P = .03; emphysema: r = 0.62 and P \u3c .001) but not in healthy ex-smokers. In a multivariate model that predicted PRM gas trapping, the forced expiratory volume in 1 second normalized to the forced vital capacity (standardized coefficients [βS] = -0.69, P = .001) and airway wall area percent (βS = -0.22, P = .02) were significant predictors. PRM emphysema was predicted by the diffusing capacity for carbon monoxide (βS = -0.29, P = .03) and VDP (βS = 0.41, P = .001). Helium 3 ADC values were significantly elevated in PRM gas-trapping regions (P \u3c .001). The spatial relationship for ventilation defects was significantly greater with PRM gas trapping than with PRM emphysema in patients with mild (for gas trapping, SOC = 36% ± 28; for emphysema, SOC = 1% ± 2; P = .001) and moderate (for gas trapping, SOC = 34% ± 28; for emphysema, SOC = 7% ± 15; P = .006) COPD. For severe COPD, the spatial relationship for ventilation defects with PRM emphysema (SOC = 64% ± 30) was significantly greater than that for PRM gas trapping (SOC = 36% ± 18; P = .01). CONCLUSION: In all ex-smokers, ADC values were significantly elevated in regions of PRM gas trapping, and VDP was quantitatively and spatially related to both PRM gas trapping and PRM emphysema. In patients with mild to moderate COPD, VDP was related to PRM gas trapping, whereas in patients with severe COPD, VDP correlated with both PRM gas trapping and PRM emphysema

Reverse transcriptase drug resistance mutations in HIV-1 subtype C infected patients on ART in Karonga District, Malawi

<p>Abstract</p> <p>Background</p> <p>Drug resistance testing before initiation of, or during, antiretroviral therapy (ART) is not routinely performed in resource-limited settings. High levels of viral resistance circulating within the population will have impact on treatment programs by increasing the chances of transmission of resistant strains and treatment failure. Here, we investigate Drug Resistance Mutations (DRMs) from blood samples obtained at regular intervals from patients on ART (Baseline-22 months) in Karonga District, Malawi. One hundred and forty nine reverse transcriptase (RT) consensus sequences were obtained via nested PCR and automated sequencing from blood samples collected at three-month intervals from 75 HIV-1 subtype C infected individuals in the ART programme.</p> <p>Results</p> <p>Fifteen individuals showed DRMs, and in ten individuals DRMs were seen from baseline samples (reported to be ART naïve). Three individuals in whom no DRMs were observed at baseline showed the emergence of DRMs during ART exposure. Four individuals who did show DRMs at baseline showed additional DRMs at subsequent time points, while two individuals showed evidence of DRMs at baseline and either no DRMs, or different DRMs, at later timepoints. Three individuals had immune failure but none appeared to be failing clinically.</p> <p>Conclusion</p> <p>Despite the presence of DRMs to drugs included in the current regimen in some individuals, and immune failure in three, no signs of clinical failure were seen during this study. This cohort will continue to be monitored as part of the Karonga Prevention Study so that the long-term impact of these mutations can be assessed. Documenting proviral population is also important in monitoring the emergence of drug resistance as selective pressure provided by ART compromises the current plasma population, archived viruses can re-emerge</p

Conservation of European M-lineage honey bees using abdominal colour as an indicator of subspecies purity has pitfalls

There are 31 honey bee (Apis mellifera) recognized subspecies, which have been grouped into four main lineages. Two of these lineages occur naturally in Europe: M in western and northern Europe and C in southeastern Europe. In Europe, M-lineage groups only two subspecies, Apis mellifera mellifera and Apis mellifera iberiensis, both being black in colour. C-Lineage groups have instead eight subspecies, including one of the beekeepers-favored and phenotypically distinct, the yellow Apis mellifera ligustica from Italy. M-lineage honey bees’ distribution has been changing and in some countries, the native bee is being replaced or hybridised with C-lineage subspecies. Honey bee abdominal pigmentation is one of the most recognisable traits and it has been used by beekeepers as an indicator of subspecies identity. However, this approach may negatively impact population diversity and is futile if there is no association between tergite colour patterns and genetic background. To test this approach, we calculated the introgression level of A. m. mellifera (N=162) and A. m. iberiensis individuals (N=559) with different colour phenotypes and from a wide geographical range using informative SNPs. In this study, many A. m. mellifera samples showed high levels of C-lineage introgression. The individuals collected in Iberia were revealed to be pure. Introgressed A. m. iberiensis individuals were all from the Azores, where a high frequency of C-lineage mitotypes exists in several islands. Our results showed that for both subspecies, it is not possible to directly identify introgressed individuals from observed colour patterns, as we found black honey bees with a considerable amount of introgression and honey bees with yellow banding that were pure or marginally introgressed. With this study, we hope to increase awareness among stakeholders of the need to use other tools to select honey bees for conservation and breeding purposes.This work was financed by the Native Irish Honeybee Society (NIHBS), Federation of Irish Beekeeping Associations (FIBKA) and FEDER (Fundo Europeu de Desenvolvimento Regional) through the program COMPETE 2020–POCI (Programa Operacional para a Competividade e Internacionalização) and by the Portuguese funds through FCT (Fundação para a Ciência e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871). FCT provided financial support by national funds (FCT/MCTES) to CIMO (UIDB/00690/2020). Dora Henriques is funded by BeeHappy and MEDIBEES which is part of the PRIMA programme supported by the European Union.info:eu-repo/semantics/publishedVersio

Can introgression in M-lineage honey bees be detected by abdominal colour patterns?

Honey bee abdominal pigmentation is one of the most recognisable traits and it is often used by beekeepers as an indicator of M-lineage subspecies purity. However, this approach may negatively impact population diversity and is futile if there is no association between tergite colour patterns and the genetic background. To assess whether this trait can be used as a proxy for introgression proportions in M-lineage subspecies, we genotyped, with highly informative SNP assays, A. m. mellifera and A. m. iberiensis individuals displaying four different colour phenotypes. The SNP data detected highly introgressed bees exhibiting a black phenotype and, at the same time, pure or marginally introgressed bees with yellow banding patterns, in both subspecies. Despite these observations, contrary to A. m. iberiensis , in A. m. mellifera , introgression proportions revealed to be a significant predictor of abdominal pigmentation. Therefore, abdominal pigmentation could be used by A. m. mellifera conservationists to guide colony selection when genetic tools are unavailable.KAB was funded by Dr. Tony Ryan research scholarship and an Irish Research Council scholarship. This work was financed by the Native Irish Honeybee Society (NIHBS), Federation of Irish Beekeeping Associations (FIBKA) and FEDER (Fundo Europeu de Desenvolvimento Regional) through the program COMPETE 2020–POCI (Programa Operacional para a Competividade e Internacionalização) and by the Portuguese funds through FCT (Fundação para a Ciência e a Tecnologia) in the framework of the project BeeHappy (POCI-01-0145-FEDER-029871).info:eu-repo/semantics/publishedVersio

A molecular tool to detect genetic introgression from Spermatheca content

The genetic integrity of Apis mellifera mellifera is threatened by introgression in many places of its native distribution, after recurrent importations of commercial queens typically belonging to the divergent C-lineage. A growing interest in keeping and protecting A. m. mellifera has motivated the development of conservation programs in many places of Europe. As part of the conservation efforts, isolated mating stations are set to avoid unwanted crosses, but these are not always effective as matings with unwanted drones are frequently reported. An interesting method to monitor the degree of isolation of mating stations could be through genetic analysis of the queen spermatheca contents. While this method implies that queens selected for monitoring are sacrificed, it can be a powerful way of assessing the effectiveness of mating stations because it would allow easy detection of unwanted alleles. Here, we developed an SNP-based tool suited to the analysis of DNA extracted from spermatheca or from pooled DNA of varying sources. To that end, we first designed an SNP panel from whole-genome sequence data generated from 228 drones, of which 148 belonged to the M-lineage (117 A. m. iberiensis and 31 A. m. mellifera) and 80 to the C-lineage (46 A. m. carnica and 34 A. m. ligustica). A total of 5,007 highly differentiated SNPs was found. Based on different criteria, 130 SNPs were selected to be included in the genotyping tool. This tool is based on the NEBNext Direct Genotyping Solution that allows high-throughput, sequence-based target genotyping of single-individual or pooled DNA. To assess the tool’s sensitivity and accuracy, 142 samples (DNA extracted from spermatheca and tissue, as well as known DNA mixtures) were genotyped. After removing the problematic SNPs, 81 were retained and these were able to provide an estimate of the pool introgression level with great accuracy. This tool represents a significant advance in the genetic analysis of honey bee colonies with a variety of applications, including breeding and conservation of A. m. mellifera.info:eu-repo/semantics/publishedVersio