ABSTRACT
La comprensión de la COVID-19, provocada por el coronavirus de tipo 2 (SARS-CoV-2) causante de síndrome respiratorio agudo severo, utilizando un enfoque multidisciplinario, es esencial para mejorar la toma de decisiones basadas en evidencia. Se estimó el número reproductivo efectivo (Rt) en Perú a partir de 113 genomas completos generados por el Instituto Nacional de Salud (INS) del Perú almacenados en la base de datos pública GISAID. La tendencia mostrada por el Rt durante marzo y abril del 2020 fue similar a otras estimaciones epidemiológicas. El Rt disminuyó considerablemente durante la primera quincena de marzo, alcanzando su menor valor la semana posterior al inicio de la cuarentena, pero aumentó moderadamente desde la quincena de abril. Se discute las implicancias de las medidas tempranas tomadas para mitigar la transmisión. La vigilancia genómica será una herramienta necesaria para conocer la transmisión y evolución del virus, y complementará la información epidemiológica.
The understanding of COVID-19, caused by the SARS-CoV-2, is essential to improve evidence-based public health policies. The effective reproductive number (Rt) in Peru was estimated using information from 113 complete genomes sequenced by the Instituto Nacional de Salud del Perú (INS), available in the GISAID public database. The Rt trend during March and April of 2020 was found to be similar to results from other epidemiological reports. The Rt decreased during the first two weeks of March. Its lowest value was reported during the week after the quarantine began. The Rt increased moderately after the second week of April. The implication of early decisions taken to mitigate the transmission are discussed. Genomic surveillance will be necessary to understand the transmission and evolution of SARS-CoV-2 in Peru, and will complement the epidemiological information.
ABSTRACT
After nearly a century of vaccination and six decades of drug therapy, tuberculosis (TB) kills more people annually than any other infectious disease. Substantial challenges to disease eradication remain among vulnerable and underserved populations. The Guarani-Kaiowá people are an indigenous population in Paraguay and the Brazilian state of Mato Grosso do Sul. This community, marginalized in Brazilian society, experiences severe poverty. Like other South American indigenous populations, their TB prevalence is high, but the disease has remained largely unstudied in their communities. Herein, Mycobacterium tuberculosis isolates from local clinics were whole genome sequenced, and a population genetic framework was generated. Phylogenetics show M. tuberculosis isolates in the Guarani-Kaiowá people cluster away from selected reference strains, suggesting divergence. Most cluster in a single group, further characterized as M. tuberculosis sublineage 4.3.3. Closer analysis of SNPs showed numerous variants across the genome, including in drug resistance-associated genes, and with many unique changes fixed in each group. We report that local M. tuberculosis strains have acquired unique polymorphisms in the Guarani-Kaiowá people, and drug resistance characterization is urgently needed to inform public health to ensure proper care and avoid further evolution and spread of drug-resistant TB
Subject(s)
Humans , Tuberculosis, Multidrug-Resistant/microbiology , Polymorphism, Single Nucleotide/genetics , Mycobacterium tuberculosis/genetics , Phylogeny , Brazil , Drug Resistance, Multiple, Bacterial/genetics , Population Groups , GenotypeABSTRACT
China is rich in the diversified Chinese medicine resources and is notable for the wide and long-term applications of Chinese medicine. However,the lack of genomic information on medicinal taxa leads to problems in relation to resource conservation and the downstream application of traditional Chinese medicine resources,which restricts the modernization process of traditional Chinese medicine. Molecular phylogenetics is an important tool to understand the origin and evolution of the earth's biodiversity and promote the conservation and use of medicinal taxa. With the development of sequencing technology,the combination of genomic data extends the traditional molecular phylogenetics to the research level of phylogenomics,making it more powerfully applied to all aspects of biological research. Undoubtedly,carrying out phylogenomic research on Chinese medicine species will greatly promote their resources conservation,molecular evaluation and identification,and the exploration and utilization of natural pharmacodynamic components,promoting the modernization of traditional Chinese medicine. This article starts with a brief introduction of the developing history and basic research methods of phylogenomics,and then reviews the current research progress in phylogenomics related to traditional Chinese medicine resources. Finally,it discusses the problems existing in the current research and the next direction of phylogenomics research in medicinal taxa. The article will hopefully provide a reference for relevant researches in future.
Subject(s)
China , Conservation of Natural Resources , Drugs, Chinese Herbal , Medicine, Chinese Traditional , Phylogeny , Plants, Medicinal , GeneticsABSTRACT
RNA-Sequencing (RNA-Seq) is a newly developed method to analyze gene function and interaction at the omics level, which is widely used in frontier field in molecular biology and other fields. In recent years, this technology has been intensively used in the research of medicinal plants, and growing number of reports are published. This paper systematically sorted out relevant literatures and summarized applications of RNA-Seq technology in functional gene discovery, gene network analysis, genetic mechanism revelation and development of molecular marker of medicinal plants. Meanwhile, according to the technical characteristics of RNA-Seq and the development needs of medicinal plant research, this article brings the future prospects regarding RNA-seq technology in Chinese medicinal materials, and intending to provide inspirations for researches on Chinese materia medica based on RNA-Seq.
ABSTRACT
Schistosoma mansoni is one of the three main causative agents of human schistosomiasis, a major health problem with a vast socio-economic impact. Recent advances in the proteomic analysis of schistosomes have revealed that peptidases are the main virulence factors involved in the pathogenesis of this disease. In this context, evolutionary studies can be applied to identify peptidase families that have been expanded in genomes over time in response to different selection pressures. Using a phylogenomic approach, we searched for expanded endopeptidase families in the S. mansoni predicted proteome with the aim of contributing to the knowledge of such enzymes as potential therapeutic targets. We found three endopeptidase families that comprise leishmanolysins (metallopeptidase M8 family), cercarial elastases (serine peptidase S1 family) and cathepsin D proteins (aspartic peptidase A1 family). Our results suggest that the Schistosoma members of these families originated from successive gene duplication events in the parasite lineage after its diversification from other metazoans. Overall, critical residues are conserved among the duplicated genes/proteins. Furthermore, each protein family displays a distinct evolutionary history. Altogether, this work provides an evolutionary view of three S. mansoni peptidase families, which allows for a deeper understanding of the genomic complexity and lineage-specific adaptations potentially related to the parasitic lifestyle.