Cariotipo del tití gris (saguinus leucopus) mediante bandas r-replicativas

Colombia es considerado un país megabiodiverso, ostentando varias especies endémicas como Saguinus leucopus. El Tití gris, como es vulgarmente llamado, habita bosques tropicales, es omnívoro y de hábitos diurnos, y se destaca como dispersor de semillas. Morfológicamente se caracteriza por su reducido tamaño, pelaje café y dorso plateado. Se organiza en grupos familiares formados por la pareja y su descendencia, con una hembra dominante, la cual es la única que cría. Debido a factores fundamentalmente de origen antrópico, se encuentra catalogada como especies en peligro de extinción por la UICN y está registrado en el apéndice I del CITES. Aun cuando se han realizados estudios sobre su biología básica, son pocos los reporte sobre la evaluación citogenética y ninguno sobre cariotipo con bandas R–Replicativa. En esta investigación se realizó el cariotipo y el idiograma, con bandas R-Replicativas, mediante la incorporación de 5’-bromo-2’-deoxiuridina (BrdU) en sangre periférica estimulada con fitohemaglutinina de S. leucopus. Los resultados mostraron un cariotipo 2n = 46, con un número fundamental (NF) de 76. Los cromosomas se organizaron en cinco grupos de acuerdo con su forma y tamaño. El grupo A, es conformado por 3 pares de cromosomas grandes submetacéntricos; el grupo B, por 5 pares de cromosomas de tamaño medio metacéntricos o submetacéntricos; el grupo C, por 6 pares acrocéntricos y el grupo D, por 8 pares subtelocéntricos y el par sexual XX/XY. El cromosoma “X” es de tamaño medio submetacéntrico y el “Y” es metacéntrico, y de los más pequeños del genoma. Finalmente, se propone un idiograma con bandas R- Replicativa con base en mitosis en estadio III de replicación

Laurent inversion

There are well-understood methods, going back to Givental and Hori--Vafa, that to a Fano toric complete intersection X associate a Laurent polynomial f that corresponds to X under mirror symmetry. We describe a technique for inverting this process, constructing the toric complete intersection X directly from its Laurent polynomial mirror f. We use this technique to construct a new four-dimensional Fano manifold

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

Genome sequences from evolving infectious pathogens allow quantification of case introductions and local transmission dynamics. We sequenced 11,357 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from Switzerland in 2020 - the sixth largest effort globally. Using a representative subset of these data, we estimated viral introductions to Switzerland and their persistence over the course of 2020. We contrasted these estimates with simple null models representing the absence of certain public health measures. We show that Switzerland's border closures de-coupled case introductions from incidence in neighboring countries. Under a simple model, we estimate an 86-98% reduction in introductions during Switzerland's strictest border closures. Furthermore, the Swiss 2020 partial lockdown roughly halved the time for sampled introductions to die out. Last, we quantified local transmission dynamics once introductions into Switzerland occurred, using a phylodynamic model. We found that transmission slowed 35-63% upon outbreak detection in summer 2020, but not in fall. This finding may indicate successful contact tracing over summer before overburdening in fall. The study highlights the added value of genome sequencing data for understanding transmission dynamics

Geographical and temporal distribution of SARS-CoV-2 clades in the WHO European Region, January to June 2020

We show the distribution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic clades over time and between countries and outline potential genomic surveillance objectives. We applied three genomic nomenclature systems to all sequence data from the World Health Organization European Region available until 10 July 2020. We highlight the importance of real-time sequencing and data dissemination in a pandemic situation, compare the nomenclatures and lay a foundation for future European genomic surveillance of SARS-CoV-2

CARIOTIPO DEL TITÍ GRIS (Saguinus leucopus) MEDIANTE BANDAS R-REPLICATIVAS KARYOTYPE OF TITÍ GREY (Saguinus leucopus) THROUGH R-REPLICATIVE BANDS

Resumen. Colombia es considerado un país megabiodiverso, ostentando varias especies endémicas como Saguinus leucopus. El Tití gris, como es vulgarmente llamado, habita bosques tropicales, es omnívoro y de hábitos diurnos, y se destaca como dispersor de semillas. Morfológicamente se caracteriza por su reducido tamaño, pelaje café y dorso plateado. Se organiza en grupos familiares formados por la pareja y su descendencia, con una hembra dominante, la cual es la única que cría. Debido a factores fundamentalmente de origen antrópico, se encuentra catalogada como especies en peligro de extinción por la UICN y está registrado en el apéndice I del CITES. Aun cuando se han realizados estudios sobre su biología básica, son pocos los reporte sobre la evaluación citogenética y ninguno sobre cariotipo con bandas R-Replicativa. En esta investigación se realizó el cariotipo y el idiograma, con bandas R-Replicativas, mediante la incorporación de 5'-bromo-2'-deoxiuridina (BrdU) en sangre periférica estimulada con fitohemaglutinina de S. leucopus. Los resultados mostraron un cariotipo 2n = 46, con un número fundamental (NF) de 76. Los cromosomas se organizaron en cinco grupos de acuerdo con su forma y tamaño. El grupo A, es conformado por 3 pares de cromosomas grandes submetacéntricos; el grupo B, por 5 pares de cromosomas de tamaño medio metacéntricos o submetacéntricos; el grupo C, por 6 pares acrocéntricos y el grupo D, por 8 pares subtelocéntricos y el par sexual XX/XY. El cromosoma "X" es de tamaño medio submetacéntrico y el "Y" es metacéntrico, y de los más pequeños del genoma. Finalmente, se propone un idiograma con bandas R- Replicativa con base en mitosis en estadio III de replicación.Abstract. Colombia is considered a mega-biodiverse country, boasting several endemic species such as Saguinus leucopus. The Marmoset gray, as is commonly called, inhabits tropical forests, is omnivorous and diurnal, and stands as seed dispersers. Morphologically characterized by small size, brown fur and silver back. It is organized in family groups formed by the couple and their offspring, with a dominant female, which is the only breeding. Due mainly to anthropogenic factors, is listed as endangered species by IUCN and is registered in Appendix I of CITES. Although studies have been conducted on the basic biology of S. leucopus, there are few reports on the cytogenetic evaluation and none on banded karyotype R - Replicative. In this research was performed the karyotype and ideogram with replicating R-bands by incorporating 5'-bromo-2'-deoxyuridine (BrdU) in peripheral blood stimulated with phytohemaglutinine of S. leucopus. The results showed a karyotype 2n = 46, with a fundamental number (NF) of 76. Chromosomes are organized into five groups according to their shape and size. Group A, is made up of three pairs of large submetacentric chromosomes; group B for 5 pairs of chromosomes metacentric or submetacentric average size; group C for 6 acrocentric pairs; and group D by 8 pairs subtelocentric and sexual pair XX/XY. The "X" chromosome is medium submetacentric, and the "Y" is metacentric and the smallest genome. Finally, we propose an R-banded ideogram based Replicative mitosis stage III replication

Comparing mutational pathways to lopinavir resistance in HIV-1 subtypes B versus C

Although combination antiretroviral therapies seem to be effective at controlling HIV-1 infections regardless of the viral subtype, there is increasing evidence for subtype-specific drug resistance mutations. The order and rates at which resistance mutations accumulate in different subtypes also remain poorly understood. Most of this knowledge is derived from studies of subtype B genotypes, despite not being the most abundant subtype worldwide. Here, we present a methodology for the comparison of mutational networks in different HIV-1 subtypes, based on Hidden Conjunctive Bayesian Networks (H-CBN), a probabilistic model for inferring mutational networks from cross-sectional genotype data. We introduce a Monte Carlo sampling scheme for learning H-CBN models for a larger number of resistance mutations and develop a statistical test to assess differences in the inferred mutational networks between two groups. We apply this method to infer the temporal progression of mutations conferring resistance to the protease inhibitor lopinavir in a large cross-sectional cohort of HIV-1 subtype C genotypes from South Africa, as well as to a data set of subtype B genotypes obtained from the Stanford HIV Drug Resistance Database and the Swiss HIV Cohort Study. We find strong support for different initial mutational events in the protease, namely at residue 46 in subtype B and at residue 82 in subtype C. The inferred mutational networks for subtype B versus C are significantly different sharing only five constraints on the order of accumulating mutations with mutation at residue 54 as the parental event. The results also suggest that mutations can accumulate along various alternative paths within subtypes, as opposed to a unique total temporal ordering. Beyond HIV drug resistance, the statistical methodology is applicable more generally for the comparison of inferred mutational networks between any two groups

V-pipe: a computational pipeline for assessing viral genetic diversity from high-throughput data

MOTIVATION High-throughput sequencing technologies are used increasingly, not only in viral genomics research but also in clinical surveillance and diagnostics. These technologies facilitate the assessment of the genetic diversity in intra-host virus populations, which affects transmission, virulence, and pathogenesis of viral infections. However, there are two major challenges in analysing viral diversity. First, amplification and sequencing errors confound the identification of true biological variants, and second, the large data volumes represent computational limitations. RESULTS To support viral high-throughput sequencing studies, we developed V-pipe, a bioinformatics pipeline combining various state-of-the-art statistical models and computational tools for automated end-to-end analyses of raw sequencing reads. V-pipe supports quality control, read mapping and alignment, low-frequency mutation calling, and inference of viral haplotypes. For generating high-quality read alignments, we developed a novel method, called ngshmmalign, based on profile hidden Markov models and tailored to small and highly diverse viral genomes. V-pipe also includes benchmarking functionality providing a standardized environment for comparative evaluations of different pipeline configurations. We demonstrate this capability by assessing the impact of three different read aligners (Bowtie 2, BWA MEM, ngshmmalign) and two different variant callers (LoFreq, ShoRAH) on the performance of calling single-nucleotide variants in intra-host virus populations. V-pipe supports various pipeline configurations and is implemented in a modular fashion to facilitate adaptations to the continuously changing technology landscape. AVAILABILITY V-pipe is freely available at https://github.com/cbg-ethz/V-pipe. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online

Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART

The HIV-1 reservoir is the major hurdle to curing HIV-1. However, the impact of the viral genome on the HIV-1 reservoir, i.e. its heritability, remains unknown. We investigate the heritability of the HIV-1 reservoir size and its long-term decay by analyzing the distribution of those traits on viral phylogenies from both partial-pol and viral near full-length genome sequences. We use a unique nationwide cohort of 610 well-characterized HIV-1 subtype-B infected individuals on suppressive ART for a median of 5.4 years. We find that a moderate but significant fraction of the HIV-1 reservoir size 1.5 years after the initiation of ART is explained by genetic factors. At the same time, we find more tentative evidence for the heritability of the long-term HIV-1 reservoir decay. Our findings indicate that viral genetic factors contribute to the HIV-1 reservoir size and hence the infecting HIV-1 strain may affect individual patients' hurdle towards a cure

Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting

International audienceThe Second Annual Meeting of the European Virus Bioinformatics Center (EVBC), held in Utrecht, Netherlands, focused on computational approaches in virology, with topics including (but not limited to) virus discovery, diagnostics, (meta-)genomics, modeling, epidemiology, molecular structure, evolution, and viral ecology. The goals of the Second Annual Meeting were threefold: (i) to bring together virologists and bioinformaticians from across the academic, industrial, professional, and training sectors to share best practice; (ii) to provide a meaningful and interactive scientific environment to promote discussion and collaboration between students, postdoctoral fellows, and both new and established investigators; (iii) to inspire and suggest new research directions and questions. Approximately 120 researchers from around the world attended the Second Annual Meeting of the EVBC this year, including 15 renowned international speakers. This report presents an overview of new developments and novel research findings that emerged during the meeting

Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies

Recent developments in high-throughput sequencing (HTS) technologies and bioinformatics have drastically changed research in virology, especially for virus discovery. Indeed, proper monitoring of the viral population requires information on the different isolates circulating in the studied area. For this purpose, HTS has greatly facilitated the sequencing of new genomes of detected viruses and their comparison. However, bioinformatics analyses allowing reconstruction of genome sequences and detection of single nucleotide polymorphisms (SNPs) can potentially create bias and has not been widely addressed so far. Therefore, more knowledge is required on the limitations of predicting SNPs based on HTS-generated sequence samples. To address this issue, we compared the ability of 14 plant virology laboratories, each employing a different bioinformatics pipeline, to detect 21 variants of pepino mosaic virus (PepMV) in three samples through large-scale performance testing (PT) using three artificially designed datasets. To evaluate the impact of bioinformatics analyses, they were divided into three key steps: reads pre-processing, virus-isolate identification, and variant calling. Each step was evaluated independently through an original, PT design including discussion and validation between participants at each step. Overall, this work underlines key parameters influencing SNPs detection and proposes recommendations for reliable variant calling for plant viruses. The identification of the closest reference, mapping parameters and manual validation of the detection were recognized as the most impactful analysis steps for the success of the SNPs detections. Strategies to improve the prediction of SNPs are also discussed