Flora da Área de Proteção Ambiental Bacia do Rio de Janeiro, Bahia: Malpighiaceae Juss.

The present study aimed to conduct the floristic survey and taxonomic treatment of the Malpighiaceae family in the Environmental Protection Area (EPA) of Bacia do Rio de Janeiro, located in the municipalities of Barreiras and Luís Eduardo Magalhães, Extreme Western Bahia. Through collection expeditions and surveys in virtual herbaria, 26 species were identified distributed in six genera: Byrsonima Rich. ex Kunth, with the highest richness (10 spp.), Heteropterys Kunth (seven spp.), Banisteriopsis C.B.Rob. ex Small. (five spp.), Diplopterys A.Juss. (two spp.), and Camarea A.St.-Hil. and Glicophyllum R.F.Almeida, with one species each. This work presents identification keys for genera and species, taxonomic descriptions, comments and images.El objetivo de este estudio fue realizar un relevamiento florístico y tratamiento taxonómico de la familia Malpighiaceae en el Área de Protección Ambiental (APA) de la Cuenca del Río de Janeiro, ubicada en los municipios de Barreiras y Luís Eduardo Magalhães, en el extremo oeste de Bahía. A través de expediciones de colecta y encuestas en herbarios virtuales, fueron identificadas 26 especies, distribuidas en seis géneros: Byrsonima Rich. ex Kunth, con la mayor riqueza (10 spp.), Heteropterys Kunth (siete spp.), Banisteriopsis C.B.Rob. ex Small. (cinco spp.), Diplopterys A.Juss. (dos spp.), y Camarea A.St.-Hil. y Glicophyllum R.F.Almeida, con una especie cada uno. Esta obra presenta claves de identificación de géneros y especies, descripciones taxonómicas, comentarios e imágenes.O presente estudo objetivou realizar o levantamento florístico e tratamento taxonômico da família Malpighiaceae na Área de Proteção Ambiental (APA) Bacia do Rio de Janeiro, localizada nos municípios de Barreiras e Luís Eduardo Magalhães, Extremo Oeste Baiano. Através de expedições de coleta e levantamentos em herbários virtuais foram identificadas 26 espécies distribuídas em seis gêneros: Byrsonima Rich. ex Kunth, com maior riqueza (10 spp.), Heteropterys Kunth (sete spp.), Banisteriopsis C.B.Rob. ex Small. (cinco spp.), Diplopterys A.Juss. (duas spp.), e Camarea A.St.-Hil. e Glicophyllum R.F.Almeida, com uma espécie cada. Neste trabalho são apresentadas chaves de identificação para gêneros e espécies, descrições taxonômicas, comentários e imagens

Diversidade e taxonomia de Melastomataceae na Área de Proteção Ambiental (APA) Bacia do Rio de Janeiro no Oeste da Bahia

Melastomataceae is the fifth most diverse family of angiosperms in Brazil, distributed over all Brazilian territory. It represents one of the families that most needs botanical studies in cerrado, where a great diversity of this group and few studies are performed. This study presents a survey and the taxonomic treatment of the family Melastomataceae in the Área de Proteção Ambiental (APA) do Rio de Janeiro, located in Barreiras and Luís Eduardo Magalhães, Bahia. By bibliographical consults, virtual surveys in herbarium, technical visits to national herbarium, and field collections, it was possible to survey the species and elaborate the taxonomic treatment. In the area, Melastomataceae is represented by 13 genera and 22 species, Miconia is the most representative genera. Among these species we highlighted Cambessedesia membranacea subsp. membranacea, Graffenrieda weddellii e Microlicia euphorbioides as new occurrences for Bahia state.Melastomataceae es la quinta familia más diversa de angiospermas en Brasil, distribuyéndose por todo el territorio brasileño. Representa una de las familias que requiere más estudios botánicos en el cerrado Baiano, donde se encuentra en gran diversidad y con pocos estudios realizados. Este trabajo presenta un levantamiento y tratamiento taxonómico de la familia Melastomataceae en el Área de Protección Ambiental (APA) de la Cuenca del Río de Janeiro, ubicada en los municipios de Barreiras y Luís Eduardo Magalhães, Bahía. A través de consultas bibliográficas, investigaciones virtuales en herbarios, visitas técnicas a herbarios nacionales y expediciones de recolección, fue posible realizar el levantamiento y tratamiento taxonómico de la familia. En el área, Melastomataceae está representada por 13 géneros y 22 especies, siendo Miconia el género más representativo. Entre las especies, destacamos Cambessedesia membranacea subsp. membranacea, Graffenriedaweddellii y Microlicia euphorbioides como nuevas ocurrencias para el estado de Bahía.Melastomataceae é a quinta família mais diversa de angiospermas no Brasil, distribuindo-se por todo o território brasileiro. Representa uma das famílias que mais necessita de estudos botânicos no cerrado, onde ocorre em grande diversidade e com poucos estudos realizados. Esse trabalho apresenta um levantamento e o tratamento taxonômico da família Melastomataceae na Área de Proteção Ambiental (APA) do Rio de Janeiro, localizada nos municípios de Barreiras e em Luís Eduardo Magalhães, Bahia. Por meio de consultas bibliográficas, levantamentos virtuais em herbários, visitas técnicas para herbários nacionais e expedições de coletas, foi possível realizar o levantamento e o tratamento taxonômico da família. Na área, Melastomataceae está representada por 13 gêneros e 22 espécies, sendo Miconia o gênero mais representativo. Dentre as espécies destacamos Cambessedesia membranacea subsp. membranacea, Graffenrieda weddellii e Microlicia euphorbioides como novas ocorrências para o estado da Bahia

Flora da Serra do Cipó, Minas Gerais: Leguminosae – “Caesalpinioideae”

”). O estudo da subfamília “Caesalpinioideae” é parte do levantamento da Flora da Serra do Cipó, Minas Gerais, Brasil. Esta subfamília está representada na área pelos seguintes gêneros, com o respectivo número de espécies: Apuleia (1), Bauhinia (4), Cassia (1), Chamaecrista (36), Copaifera (2), Hymenaea (2), Melanoxylon (1), Peltophorum (1), Schnella (1), Senna (12) e Tachigali (4). São apresentadas chaves para gêneros e espécies, descrições e ilustrações das mesmas, além de comentários sobre sua distribuição geográfica, fenologia e variabilidade

Listagem das Leguminosae - Caesalpinioideae no Parque Estadual da Serra de Caldas Novas, Goiás, Brasil

Although the Leguminosae is the family with the greatest richness in the Cerrado, the family remains only partially documented in many parts of this biome including many parks and hilly areas. An example is the Parque Estadual da Serra de Caldas Novas (PESCAN), a conservation area located south of Goias, a region with many different habitats. Contributing to the documentation of the Leguminosae from the Cerrado, our study lists the representatives of the Caesalpinioideae occurring in PESCAN and shows one key to identify the species. To this end, we collected all fertile individuals found in this area for 12 months. We found 27 species in eight genera. This study represents the most complete list of species of Caesalpinioideae for PESCAN.Leguminosae é a família de maior riqueza florística no Cerrado. Entretanto, esforços para o mapeamento dos representantes desta família neste bioma ainda são necessários, pois muitos de seus parques e serras têm sua flora pouco conhecida. Um exemplo é o Parque Estadual da Serra de Caldas Novas (PESCAN), uma Unidade de Conservação, localizada a sul do estado de Goiás, que abriga diferentes fisionomias. Visando contribuir com o mapeamento das Leguminosae ocorrentes no Cerrado, o presente estudo teve por objetivo listar os representantes de Leguminosae, subfamília Caesalpinioideae, ocorrentes no PESCAN e apresentar uma chave para identificação das espécies. Para tanto, foram coletados todos os indivíduos férteis encontrados nesta área durante 12 meses. Foram encontradas 27 espécies distribuídas em oito gêneros. Este estudo representa a lista mais completa de espécies de Leguminosae – Caesalpinioideae já apresentada para o PESCAN

Precipitation is the main axis of tropical phylogenetic turnover across space and time

Early natural historians – Compte de Buffon, von Humboldt and De Candolle – established ecology and geography as two principal axes determining the distribution of groups of organisms, laying the foundations for biogeography over the subsequent 200 years, yet the relative importance of these two axes remains unresolved. Leveraging phylogenomic and global species distribution data for Mimosoid legumes, an pantropical plant clade of 3,400 species, we show that the water availability gradient from deserts to rainforests dictates turnover of lineages within continents across the tropics. We demonstrate that 95% of speciation occurs within a precipitation niche, showing profound phylogenetic niche conservatism, and that lineage turnover boundaries coincide with isohyets of precipitation. We reveal similar patterns on different continents, implying that evolution and dispersal follow universal processes.Fil: Ringelberg, Jens J. University of Zurich. Department of Systematic and Evolutionary Botany; SuizaFil: Koenen, Erik J.M. University of Zurich. Department of Systematic and Evolutionary Botany; Suiza. Université Libre de Bruxelles. Faculté des Sciences. Evolutionary Biology & Ecology; BélgicaFil: Sauter, Benjamín. University of Zurich. Department of Systematic and Evolutionary Botany; SuizaFil: Aebli, Anahita. University of Zurich. Department of Systematic and Evolutionary Botany; Suiza. Abteling Umweltschutz und Energie. Departement Bau und Umwelt; SuizaFil: Rando, Juliana G. Universidade Federal do Oeste da Bahia. Centro das Ciências Biológicas e da Saúde. Programa de Pós Graduação em Ciências Ambientais; BrasilFil: Iganci, João R. Universidade Federal de Pelotas. Campus Universitário Capão do Leão. Instituto de Biologia; Brasil. Universidade Federal do Rio Grande do Sul. Programa de Pós-Graduação em Botânica; BrasilFil: de Queiroz, Luciano P. Universidade Estadual de Feira de Santana. Departamento Ciências Biológicas; BrasilFil: Murphy, Daniel J. Royal Botanic Gardens Victoria: AustraliaFil: Gaudeul, Myriam. Institut de Systématique, Evolution, Biodiversité (ISYEB), MNHN-CNRS-SU-EPHE-UA: FranciaFil: Bruneau, Anne. Université de Montréal. Institut de Recherche en Biologie Végétale and Département de Sciences Biologiques; CanadáFil: Luckow, Melissa. Cornell University. School of Integrative Plant Science. Plant Biology Section; Estados UnidosFil: Morales, Matias. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Recursos Biológicos; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad de Morón. Facultad de Agronomía y Ciencias Agroalimentarias; Argentin

Naturally occurring SARS-CoV-2 gene deletions close to the spike S1/S2 cleavage site in the viral quasispecies of COVID19 patients

Altres ajuts: This study was partially supported by the Direcció General de Recerca i Innovació en Salut (DGRIS) Catalan Health Ministry Generalitat de Catalunya through Vall d'Hebron Institut de Recerca (VHIR) and Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business, grant number IDI-20200297.The SARS-CoV-2 spike (S) protein, the viral mediator for binding and entry into the host cell, has sparked great interest as a target for vaccine development and treatments with neutralizing antibodies. Initial data suggest that the virus has low mutation rates, but its large genome could facilitate recombination, insertions, and deletions, as has been described in other coronaviruses. Here, we deep-sequenced the complete SARS-CoV-2 S gene from 18 patients (10 with mild and 8 with severe COVID-19), and found that the virus accumulates deletions upstream and very close to the S1/S2 cleavage site (PRRAR/S), generating a frameshift with appearance of a stop codon. These deletions were found in a small percentage of the viral quasispecies (2.2%) in samples from all the mild and only half the severe COVID-19 patients. Our results suggest that the virus may generate free S1 protein released to the circulation. We suggest that natural selection has favoured a "Don't burn down the house" strategy, in which free S1 protein may compete with viral particles for the ACE2 receptor, thus reducing the severity of the infection and tissue damage without losing transmission capability

Genomic evolution of human respiratory syncytial virus during a decade (2013–2023): bridging the path to monoclonal antibody surveillance

Evolution; Human respiratory syncytial virus; Monoclonal antibodiesEvolución; Virus respiratorio sincitial humano; Anticuerpos monoclonicosEvolució; Virus respiratori sincitial humà; Anticossos monoclonalsObjectives This study investigated the prevalence, genetic diversity, and evolution of human respiratory syncytial virus (HRSV) in Barcelona from 2013 to 2023. Methods Respiratory specimens from patients with RTI suspicion at Hospital Universitari Vall d′Hebron were collected from October 2013 to May 2023 for laboratory-confirmation of respiratory viruses. Next-generation sequencing was performed in randomly-selected samples with Illumina technology. Phylogenetic analyses of whole genome sequences were performed with BEAST v1.10.4. Signals of selection and evolutionary pressures were inferred by population dynamics and evolutionary analyses. Mutations in major surface proteins were genetic and structurally characterised, emphasizing those within antigenic epitopes. Results Analyzing 139,625 samples, 5.3% were HRSV-positive (3008 HRSV-A, 3882 HRSV-B, 56 HRSV-A and -B, and 495 unsubtyped HRSV), with a higher prevalence observed in the paediatric population. Pandemic-related shifts in seasonal patterns returned to normal in 2022–2023. A total of 198 whole-genome sequences were obtained for HRSV-A (6.6% of the HRSV-A positive samples) belonging to GA2.3.5 lineage. For HRSV-B, 167 samples were sequenced (4.3% of the HRSV-B positive samples), belonging to GB5.0.2, GB5.0.4a and GB5.0.5a. HRSV-B exhibited a higher evolution rate. Post-SARS-CoV-2 pandemic, both subtypes showed increased evolutionary rates and decreased effective population size initially, followed by a sharp increase. Analyses indicated negative selective pressure on HRSV. Mutations in antigenic epitopes, including S276N and M274I in palivizumab-targeted site II, and I206M, Q209R, and S211N in nirsevimab-targeted site Ø, were identified. Discussion Particularly in the context of the large-scale use in 2023–2024 season of nirsevimab, continuous epidemiological and genomic surveillance is crucial.This study was supported by the European Development Regional Fund (ERDF) “A way to achieve Europe”, Spanish Ministry of Economy and Competitiveness [Grant FIS PI18/00685], and by CIBER -Consorcio Centro de Investigación Biomédica en Red- (CB 2021), CIBERINFEC, Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación and Unión Europea – NextGenerationEU

Host-dependent editing of SARS-CoV-2 in COVID-19 patients

SARS-CoV-2; Mutacions; QuasiespècieSARS-CoV-2; Mutaciones; CuasiespecieSARS-CoV-2; Mutations; QuasispeciesA common trait among RNA viruses is their high capability to acquire genetic variability due to viral and host mechanisms. Next-generation sequencing (NGS) analysis enables the deep study of the viral quasispecies in samples from infected individuals. In this study, the viral quasispecies complexity and single nucleotide polymorphisms of the SARS-CoV-2 spike gene of coronavirus disease 2019 (COVID-19) patients with mild or severe disease were investigated using next-generation sequencing (Illumina platform). SARS-CoV-2 spike variability was higher in patients with long-lasting infection. Most substitutions found were present at frequencies lower than 1%, and had an A → G or T → C pattern, consistent with variants caused by adenosine deaminase acting on RNA-1 (ADAR1). ADAR1 affected a small fraction of replicating genomes, but produced multiple, mainly non-synonymous mutations. ADAR1 editing during replication rather than the RNA-dependent RNA polymerase (nsp12) was the predominant mechanism generating SARS-CoV-2 genetic variability. However, the mutations produced are not fixed in the infected human population, suggesting that ADAR1 may have an antiviral role, whereas nsp12-induced mutations occurring in patients with high viremia and persistent infection are the main source of new SARS-CoV-2 variants.This study was supported by the Direcció General de Recerca i Innovació en Salut (DGRIS) of the Catalan Health Ministry, Generalitat de Catalunya, through the Vall d’Hebron Institut de Recerca (VHIR); the European Regional Development Fund (ERDF) “A way to achieve Europe” by the Spanish Network for Research in Infectious Diseases [grant number REIPI RD16/0016/0003]; Instituto de Salud Carlos III [grant number FIS PI19/00301]; and Centro para el Desarrollo Tecnologico Industrial (CDTI) from the Ministry of Economic Affairs and Digital Transformation [grant number IDI-20200297]

Host-dependent editing of SARS-CoV-2 in COVID-19 patients

A common trait among RNA viruses is their high capability to acquire genetic variability due to viral and host mechanisms. Next-generation sequencing (NGS) analysis enables the deep study of the viral quasispecies in samples from infected individuals. In this study, the viral quasispecies complexity and single nucleotide polymorphisms of the SARS-CoV-2 spike gene of coronavirus disease 2019 (COVID-19) patients with mild or severe disease were investigated using next-generation sequencing (Illumina platform). SARS-CoV-2 spike variability was higher in patients with long-lasting infection. Most substitutions found were present at frequencies lower than 1%, and had an A → G or T → C pattern, consistent with variants caused by adenosine deaminase acting on RNA-1 (ADAR1). ADAR1 affected a small fraction of replicating genomes, but produced multiple, mainly non-synonymous mutations. ADAR1 editing during replication rather than the RNA-dependent RNA polymerase (nsp12) was the predominant mechanism generating SARS-CoV-2 genetic variability. However, the mutations produced are not fixed in the infected human population, suggesting that ADAR1 may have an antiviral role, whereas nsp12-induced mutations occurring in patients with high viremia and persistent infection are the main source of new SARS-CoV-2 variants

The frequency of defective genomes in Omicron differs from that of the Alpha, Beta and Delta variants

Evolution; Genetics; Molecular biologyEvolució; Genètica; Biologia molecularEvolución; Genética; Biología molecularThe SARS-CoV-2 Omicron variant emerged showing higher transmissibility and possibly higher resistance to current COVID-19 vaccines than other variants dominating the global pandemic. In March 2020 we performed a study in clinical samples, where we found that a portion of genomes in the SARS-CoV-2 viral population accumulated deletions immediately before the S1/S2 cleavage site (furin-like cleavage site, PRRAR/S) of the spike gene, generating a frameshift and appearance of a premature stop codon. The main aim of this study was to determine the frequency of defective deletions in prevalent variants from the first to sixth pandemic waves in our setting and discuss whether the differences observed might support epidemiological proposals. The complete SARS-CoV-2 spike gene was deeply studied by next-generation sequencing using the MiSeq platform. More than 90 million reads were obtained from respiratory swab specimens of 78 COVID-19 patients with mild infection caused by the predominant variants circulating in the Barcelona city area during the six pandemic waves: B.1.5, B.1.1, B.1.177, Alpha, Beta, Delta, and Omicron. The frequency of defective genomes found in variants dominating the first and second waves was similar to that seen in Omicron, but differed from the frequencies seen in the Alpha, Beta and Delta variants. The changing pattern of mutations seen in the various SARS-CoV-2 variants driving the pandemic waves over time can affect viral transmission and immune escape. Here we discuss the putative biological effects of defective deletions naturally occurring before the S1/S2 cleavage site during adaption of the virus to human infection.This study was partially supported by Pla Estratègic de Recerca i Innovació en Salut (PERIS) – Direcció General de Recerca i Innovació en Salut (DGRIS), Catalan Health Ministry, Generalitat de Catalunya; the Spanish Network for the Research in Infectious Diseases (REIPI RD16/0016/0003) from the European Regional Development Fund (ERDF); Centro para el Desarrollo Tecnológico Industrial (CDTI) from the Spanish Ministry of Economy and Business, grant number IDI-20200297; Grant PI19/00301 from Instituto de Salud Carlos III cofinanced by the European Regional Development Fund (ERDF), and Gilead’s biomedical research project GLD21/00006. We gratefully acknowledge the authors, originating and submitting laboratories of the sequences from GISAID’s EpiCov Database on which this research is based