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1.
Trop Med Health ; 52(1): 50, 2024 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-39090702

RESUMO

The number of dengue cases has increased dramatically in recent years. In Latin America, the number of cases and deaths in 2023 was the highest ever recorded. We report on a patient who had been infected with dengue virus during his stay in Costa Rica in September 2023, and developed the disease after returning to Japan. Plasma obtained from the patient was used for diagnosis and dengue virus serotyping by real-time PCR. The nucleotide sequence of the envelope region of dengue virus was then determined by the direct sequencing method, and this sequence was used for phylogenetic analyses. The patient was found to be infected with dengue virus type 3 genotype III. The sequence from the present case was more homologous with sequences registered in Florida, USA, associated with travel to Cuba in 2022 than with sequences registered in Costa Rica 10 years ago. The Pan American Health Organization reported that only dengue virus type 1 and 2 cases were reported in Costa Rica in 2019-2021, whereas dengue virus type 3 and 4 cases started being reported in 2022. In 2023, the reported numbers of cases with dengue virus types 3 and 4 exceeded those of dengue virus types 1 and 2. In addition, regional differences in endemic strains have been observed in Costa Rica. Our findings suggest that the dengue virus type 3 that infected the patient was more likely an influx of a strain that had been circulating in Caribbean countries such as Cuba in recent years, rather than a re-emergence of an indigenous virus in Costa Rica. The serotypes of dengue virus prevalent in Costa Rica have been changing since 2022. All four serotypes were prevalent in 2023, with a particularly sharp increase in the number of cases of dengue virus types 3 and 4. Future monitoring and surveillance are essential because changes in endemic serotypes can cause antibody-dependent enhancement, which can lead to severe dengue disease presentations.

2.
Trop Med Infect Dis ; 9(7)2024 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-39058182

RESUMO

The persistence of the human papillomavirus type 16 (HPV16) infection on the cervical epithelium contributes to the progression of cervical cancer. Studies have demonstrated that HPV16 genetic variants may be associated with different risks of developing cervical cancer. However, the E5 oncoprotein of HPV16, which is related to several cellular mechanisms in the initial phases of the infection and thus contributes to carcinogenesis, is still little studied. Here we investigate the HPV16 E5 oncogene variants to assess the effects of different mutations on the biological function of the E5 protein. We detected and analyzed the HPV16 E5 oncogene polymorphisms and their phylogenetic relationships. After that, we proposed a tertiary structure analysis of the protein variants, preferential codon usage, and functional activity of the HPV16 E5 protein. Intra-type variants were grouped in the lineages A and D using in silico analysis. The mutations in E5 were located in the T-cell epitopes region. We therefore analyzed the interference of the HPV16 E5 protein in the NF-kB pathway. Our results showed that the variants HPV16E5_49PE and HPV16E5_85PE did not increase the potential of the pathway activation capacity. This study provides additional knowledge about the mechanisms of dispersion of the HPV16 E5 variants, providing evidence that these variants may be relevant to the modulation of the NF-κB signaling pathway.

3.
Microorganisms ; 12(7)2024 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-39065086

RESUMO

Leishmania (Viannia) spp. can harbor a double-stranded RNA virus known as Leishmania RNA virus 1 (LRV-1), whose presence has been reported in nine countries across the Americas and seven Leishmania species. Here, we studied 100 Leishmania (Viannia) isolates from patients with cutaneous leishmaniasis collected from different endemic areas in Panama from 2016 to 2022. We identified L. (V.) panamensis, L. (V.) guyanensis, L. (V.) braziliensis/guyanensis hybrid, and L. (V.) panamensis sp.1. (genetic variant). LRV-1 was detected by RT-PCR in 9% of L. (Viannia) isolates (eight cases in L. (V.) panamensis, and one in L. (V.) guyanensis). Phylogenetic analysis based on sequencing data classified all LRV-1 isolates within genotype A, suggesting that LRV phylogenetic proximity is closely aligned with geographical distribution or to the phylogenetic proximity of the Leishmania host in the case of the L. (V.) panamensis and L. (V.) guyanensis in Panama.

4.
Fungal Biol ; 128(5): 1907-1916, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-39059846

RESUMO

The rubber tree (Hevea brasiliensis) is one of the major domesticated crops planted commercially for the production of natural rubber (NR) worldwide. In recent years, rubber trees in the Southern states of India and other rubber-producing countries have experienced a severe leaf spot disease, characterized by the appearance of several brown circular spots in the initial stage, which later spread all over the lamina of fully matured leaves, leading to yellowing and defoliation. The causal organism of this Circular Leaf Spot (CLS) disease has not been conclusively identified in any previous studies. In this study, we collected infected leaf samples from various locations in the South Indian states. We aimed to identify the actual fungal pathogen that causes the CLS disease on rubber trees. Based on the morphological and molecular analysis of the most frequently isolated fungi from infected leaf samples were identified as Colletotrichum siamense and Colletotrichum fructicola. Pathogenicity tests also confirmed the involvement of isolated Colletotrichum spp. in the development of CLS disease. These findings provide valuable insights into understanding the CLS disease and its impact on rubber cultivation. To our knowledge, it is the first report of C. siamense and C. fructicola associated with CLS disease of rubber trees in India.


Assuntos
Colletotrichum , Hevea , Doenças das Plantas , Folhas de Planta , Hevea/microbiologia , Colletotrichum/genética , Colletotrichum/isolamento & purificação , Colletotrichum/classificação , Doenças das Plantas/microbiologia , Índia , Folhas de Planta/microbiologia , DNA Fúngico/genética , Filogenia , Análise de Sequência de DNA , Dados de Sequência Molecular
5.
Anat Rec (Hoboken) ; 2024 Jul 11.
Artigo em Inglês | MEDLINE | ID: mdl-38989612

RESUMO

We present the pelvic and hindlimb musculature of the abelisaurid Skorpiovenator bustingorryi, constituting the most comprehensive muscle reconstruction to date in ceratosaur theropods. Using extant phylogenetic bracket method, we reconstructed 39 muscles that can commonly found in extant archosaurs. Through the identification of bone correlates, we recognized thigh and hindlimb muscles including knee extensors, m. iliofibularis, m. flexor tibialis externus, mm. caudofemorales, mm. puboischiofemorales, and crus muscles important in foot extension and flexion (e.g., m. tibialis anterior, mm. gastrocnemii). Also, autopodial intrinsic muscles were reconstructed whose function involve extension (m. extensor digiti 2-4), flexion (mm. flexor digitorum brevis superficialis), interdigital adduction (m. interosseus dorsalis) and abduction (m. interosseous plantaris, m. abductor 4). Abelisaurids like Skorpiovenator show a deep pre- and postacetabular blade of the ilia and enlarged cnemial crests, which would have helped increasing the moment arm of muscles related to hip flexion and hindlimb extension. Also, pedal muscles related to pronation were probably present but reduced (e.g., m. pronator profundus). Despite some gross differences in the autopodial morphology in extant outgroups (e.g., crocodilian metatarsus and avian tarsometatarsus), the present study allows us to hypothesize several pedal muscles in Skorpiovenator. These muscles would not be arranged in tendinous bundles as in Neornithes, but rather the condition would be similar to that of crocodilians with several layers formed by fleshy bellies on the plantar and dorsal aspects of the metatarsus. The musculature of Skorpiovenator is key for future studies concerning abelisaurid biomechanics, including the integration of functional morphology and ichnological data.

6.
Sci Rep ; 14(1): 17219, 2024 07 26.
Artigo em Inglês | MEDLINE | ID: mdl-39060371

RESUMO

Fire plays a key role in grasslands, determining the distribution and evolution of species and boundaries with neighboring ecosystems. Evidence of community-wide responses to fire is largely based on taxonomic and functional descriptors, while the phylogenetic dimension is overlooked. Here we evaluated how the taxonomic and phylogenetic structure of grassland plant communities responded to a time since fire (TSF) gradient. We sampled 12 communities in Southern Brazil under varying TSF and calculated taxonomic species richness (S) and dominance (D), phylogenetic diversity (PD), and mean phylogenetic distances (MPD). We used Structural Equation Models to test the relationships between the environmental gradient and community descriptors. Communities with longer TSF presented higher PD and MPD but lower species richness and increased taxonomic dominance. These sites were dominated by monocots, specifically C4 grasses, but also presented exclusive clades, whereas recently-burned sites presented lower taxonomic dominance and more species distributed in a wider variety of clades. Our results indicate that these scenarios are interchangeable and dependent on fire management. Fire adaptation was not constrained by phylogenetic relatedness, contrasting with previous findings for tropical savannahs and indicating that temperate and tropical non-forest ecosystems from South America respond differently to fire, possibly due to different evolutionary histories.


Assuntos
Biodiversidade , Incêndios , Pradaria , Filogenia , Brasil , Plantas/classificação , Plantas/genética , Poaceae/genética , Poaceae/classificação , Ecossistema
7.
Biol Lett ; 20(7): 20240216, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-39046287

RESUMO

Most described species have not been explicitly included in phylogenetic trees-a problem named the Darwinian shortfall-owing to a lack of molecular and/or morphological data, thus hampering the explicit incorporation of evolution into large-scale biodiversity analyses. We investigate potential drivers of the Darwinian shortfall in tetrapods, a group in which at least one-third of described species still lack phylogenetic data, thus necessitating the imputation of their evolutionary relationships in fully sampled phylogenies. We show that the number of preserved specimens in scientific collections is the main driver of phylogenetic knowledge accumulation, highlighting the major role of biological collections in unveiling novel biodiversity data and the importance of continued sampling efforts to reduce knowledge gaps. Additionally, large-bodied and wide-ranged species, as well as terrestrial and aquatic amphibians and reptiles, are phylogenetically better known. Future efforts should prioritize phylogenetic research on organisms that are narrow-ranged, small-bodied and underrepresented in scientific collections, such as fossorial species. Addressing the Darwinian shortfall will be imperative for advancing our understanding of evolutionary drivers shaping biodiversity patterns and implementing comprehensive conservation strategies.


Assuntos
Biodiversidade , Evolução Biológica , Filogenia , Vertebrados , Animais , Vertebrados/genética , Vertebrados/classificação , Anfíbios/genética , Anfíbios/classificação , Répteis/classificação , Répteis/genética
8.
J Fungi (Basel) ; 10(6)2024 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-38921354

RESUMO

Cassava (Manihot esculenta Crantz) is a staple crop widely cultivated by small farmers in tropical countries. However, despite the low level of technology required for its management, it can be affected by several diseases, with anthracnose as the main threat. There is little information about the main species of Colletotrichum that infect cassava in Brazil. Thus, the objective of this work was to study the diversity, prevalence and virulence of Colletotrichum species that cause anthracnose in cassava leaves in northern Brazil. Twenty municipalities of the Pará and Tocantins states were selected, and leaves with symptoms were collected in those locations. Pure cultures were isolated in the laboratory. Species were identified using phylogenetic analyses of multiple loci, and their pathogenicity, aggressivity and virulence levels were assessed. Our results showed the greatest diversity of Colletotrichum associated with anthracnose in cassava plants of the "Formosa" cultivar in the Tocantins and Pará states. We determined the presence of Colletotrichum chrysophilum, C. truncatum, C. siamense, C. fructicola, C. plurivorum, C. musicola and C. karsti, with C. chrysophilum as the most aggressive and virulent. Our findings provide accurate identifications of species of Colletotrichum causing anthracnose in cassava crops, which are of great relevance for cassava breeding programs (e.g., the search for genotypes with polygenic resistance since the pathogen is so diverse) and for developing anthracnose management strategies that can work efficiently against species complexes of Colletotrichum.

9.
Vet World ; 17(5): 973-980, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38911095

RESUMO

Background and Aim: Leptospirosis is a re-emerging zoonosis that is under-reported in tropical countries, and canines can be a potential reservoir of the disease. The objective of this study was to diagnose Leptospira spp. that is actively infected and re-infected in stray dogs and cats from Bogota, D.C., Colombia. Materials and Methods: A sample of 200 animals, including dogs and cats from the animal protection programs of Bogota, Colombia, were used in this study. Blood was collected from these animals for serum and DNA analysis. Conventional polymerase chain reaction (PCR) was performed using the 16s rRNA primer set, and higher-quality amplification products were sequenced by Sanger. For serodiagnosis, a group of PCR-positive samples was tested using the microagglutination test (MAT). Results: The overall PCR positivity of stray dogs and cats was 56%, 52.9%, and 65.3% in dogs and cats, respectively. The MAT seropositivity was 77.3%, and only dogs showed titers higher than 1:400. Canicola, Icterohaemorrhagiae, Pomona, Hardjo Prajitno, and Canicola and Hardjo prajitno were the serogroups associated with dogs and cats, respectively. Phylogenetic analysis revealed that the strains belonging to Leptospira interrogans serovars related to isolated samples of American, European, and Asian bats (Myotis myotis), dogs, and bovines of American origin. Conclusion: These results showed that stray dogs and cats were previously exposed to different serovars of Leptospira spp. and re-infected with other serovars that actively participated in the transmission cycle. These findings highlight the importance of actively diagnosing infectious animals to design effective intervention strategies.

10.
Appl Plant Sci ; 12(3): e11587, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38912125

RESUMO

Premise: Conservation policies typically focus on biodiversity hotspots. An alternative approach involves analyzing the evolutionary history of lineages in geographic areas along with their threat levels to guide conservation efforts. Mountains exhibit high levels of plant species richness and micro-endemism, and biogeographic studies commonly point to recent and rapid evolutionary radiations in these areas. Using a nearly endemic clade of legumes, our study evaluates conservation prioritization approaches in the campo rupestre, a Neotropical ecosystem associated with mountaintops that is located between two biodiversity hotspots. Methods: We compared the EDGE and EDGE2 metrics, which combine the evolutionary distinctiveness and the extinction risk of a species in a single value. These metrics are compared with traditional metrics used to assess conservation priority, such as phylogenetic diversity. Results: The EDGE values reported are lower than those of other studies using this metric, mostly due to the prevalence of threatened species with short phylogenetic branch lengths (low values of evolutionary distinctiveness). Certain areas of campo rupestre with relatively high phylogenetic diversity and EDGE values do not correspond to areas with high species richness, agreeing with previous studies on biodiversity hotspots. Discussion: Our study highlights the necessity of conservation of the campo rupestres as well as advantages and disadvantages of using EDGE, EDGE2, and phylogenetic diversity for appropriate selection of conservation areas with rapid evolutionary radiations. The selection of the metrics will depend primarily on the life history of the focus group and the data availability, as well as the conservation approach.

11.
Microbiol Resour Announc ; 13(7): e0015824, 2024 Jul 18.
Artigo em Inglês | MEDLINE | ID: mdl-38860813

RESUMO

The whole genome sequence of a low pathogenicity avian influenza virus (H6N2) was sequenced from a Brazilian teal (Amazonetta brasiliensis) in Brazil, 2023. Phylogenetic analysis of the whole genome revealed a distinct genome pertaining to South American LPAIV from 2014 to 2016, indicating extensive circulation among South American wild birds.

12.
Integr Zool ; 2024 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-38880782

RESUMO

Adaptation or acclimation of thermal requirements to environmental conditions can reduce thermoregulation costs and increase fitness, especially in ectotherms, which rely heavily on environmental temperatures for thermoregulation. Insight into how thermal niches have shaped thermal requirements across evolutionary history may help predict the survival of species during climate change. The lizard genus Sceloporus has a widespread distribution and inhabits an ample variety of habitats. We evaluated the effects of geographical gradients (i.e. elevation and latitude) and local environmental temperatures on thermal requirements (i.e. preferred body temperature, active body temperature in the field, and critical thermal limits) of Sceloporus species using published and field-collected data and performing phylogenetic comparative analyses. To contrast macro- and micro-evolutional patterns, we also performed intra-specific analyses when sufficient reports existed for a species. We found that preferred body temperature increased with elevation, whereas body temperature in the field decreased with elevation and increased with local environmental temperatures. Critical thermal limits were not related to the geographic gradient or environmental temperatures. The apparent lack of relation of thermal requirements to geographic gradient may increase vulnerability to extinction due to climate change. However, local and temporal variations in thermal landscape determine thermoregulation opportunities and may not be well represented by geographic gradient and mean environmental temperatures. Results showed that Sceloporus lizards are excellent thermoregulators, have wide thermal tolerance ranges, and the preferred temperature was labile. Our results suggest that Sceloporus lizards can adjust to different thermal landscapes, highlighting opportunities for continuous survival in changing thermal environments.

13.
Braz J Microbiol ; 55(3): 2937-2942, 2024 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38833117

RESUMO

This study aimed to investigate the presence of Mycoplasma spp. and identify the species of mycoplasma isolates obtained from seabirds found on Brazilian coastal beaches. Tracheal and cloacal swab samples were collected from 50 seabirds rescued by three conservation and marine animal rehabilitation centers located in Brazil. The tracheal and cloacal samples were subjected to mycoplasma culture and the isolates were identified through PCR. A "Mollicutes-specific" 16S rRNA PCR reaction was employed for triage. Four species-specific PCR reactions were used to detect Mycoplasma gallisepticum, Mycoplasma synoviae, Mycoplasma meleagridis, or M. gallinarum. The Mollicutes positive and species negative samples were submitted do 16S rRNA sequencing. Eighteen (36%) of 50 seabirds tested positive for mycoplasma by culture. In the PCR for the genus, 28 (56%) of 50 seabirds were positive for Mycoplasma spp., with 13 (26%) detected in the trachea, one (2%) in the cloaca, and 14 (28%) in both sites. In the species-specific PCR, M. gallisepticum was detected in 17.8%, and M. meleagridis in 17.8%. Both species were detected in 14.3%. Of the isolates not characterized at species level, we obtained ten sequences and they were divided into three clusters. The first cluster was closely related to M. meleagridis, the second to M. synoviae, and the third grouped M. tully, M. gallisepticum, and M. imitans. Four and five of nine species of seabirds studied had mycoplasma detected by culture or PCR, respectively. Mycoplasmas were found in the majority of the animals studied, with the highest prevalence proportionally found in Sula leucogaster, and the lowest in Fregata magnificens. The phylogenetic analysis identified Mycoplasma spp. adapted to aquatic birds.


Assuntos
Doenças das Aves , Cloaca , Infecções por Mycoplasma , Mycoplasma , Filogenia , RNA Ribossômico 16S , Animais , Mycoplasma/isolamento & purificação , Mycoplasma/genética , Mycoplasma/classificação , Infecções por Mycoplasma/veterinária , Infecções por Mycoplasma/microbiologia , Brasil , RNA Ribossômico 16S/genética , Cloaca/microbiologia , Doenças das Aves/microbiologia , Traqueia/microbiologia , DNA Bacteriano/genética , Reação em Cadeia da Polimerase , Aves/microbiologia
14.
BMC Plant Biol ; 24(1): 476, 2024 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-38816799

RESUMO

BACKGROUND: Interest in the evolution of climatic niches, particularly in understanding the potential adaptive responses of species under climate change, has increased both theoretically and within macroecological studies. These studies have provided valuable insights into how climatic traits of species influence their niche evolution. In this study, we aim to investigate whether niche conservatism plays a role in the species diversification of Nymphaea, a group of aquatic plants with a cosmopolitan distribution that is facing severe habitat loss. We will use climatic models and phylogenetic data for 23 species to reconstruct Nymphaea's niche evolution, measure niche overlap, and assess disparity through time while testing for evolutionary models. RESULTS: There was a lot of overlap in niches both within and between groups, especially for species that can be found in many places. The breadth and peaks of the niche profile varied depending on the bioclimatic variables, which suggested that the species evolved differently to cope with changes in climate. The analysis also showed that evolutionary changes happened across the phylogeny, with weak to moderate signals. The morphological disparity index (MDI) values indicated that there were disparities within subclades over time but not between or among them. Niche reconstruction and evolution analysis revealed both convergent and divergent evolution among various variables. For example, N. immutabilis, N. atrans, N. violancea, and N. nouchali evolved towards intermediate temperatures for bio2 and bio3 (isothermity) while moving towards extreme temperatures for bio8 and bio9 (wettest and driest average quarterly temperatures). CONCLUSION: Our study will improve our understanding of how changes in climatic niches are potentially driving the evolution of Nymphaea. It has significant scientific implications for the limits, assemblages, evolution, and diversification of species. This information is crucial for the ongoing efforts of conservation and management, particularly considering the inevitable effects of climate change.


Assuntos
Evolução Biológica , Clima , Ecossistema , Filogenia , América do Sul , Austrália , África , Mudança Climática
15.
Methods Mol Biol ; 2802: 107-134, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38819558

RESUMO

Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences. The workflow uses state-of-the-art, open-source tools. The workflow is presented by means of a comparative analysis of Salmonella enterica serovar Typhimurium genomes. The workflow is based on Linux commands and scripts, and result visualization relies on the R environment. The chapter provides a step-by-step protocol that researchers with basic expertise in bioinformatics can easily follow to conduct investigations on their own genome datasets.


Assuntos
Biologia Computacional , Genoma Bacteriano , Genômica , Filogenia , Software , Genômica/métodos , Biologia Computacional/métodos , Fluxo de Trabalho , Bases de Dados Genéticas , Anotação de Sequência Molecular , Salmonella typhimurium/genética
16.
Methods Mol Biol ; 2802: 267-345, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38819564

RESUMO

Phylogenomics aims at reconstructing the evolutionary histories of organisms taking into account whole genomes or large fractions of genomes. Phylogenomics has significant applications in fields such as evolutionary biology, systematics, comparative genomics, and conservation genetics, providing valuable insights into the origins and relationships of species and contributing to our understanding of biological diversity and evolution. This chapter surveys phylogenetic concepts and methods aimed at both gene tree and species tree reconstruction while also addressing common pitfalls, providing references to relevant computer programs. A practical phylogenomic analysis example including bacterial genomes is presented at the end of the chapter.


Assuntos
Genômica , Filogenia , Genômica/métodos , Software , Evolução Molecular , Genoma Bacteriano , Biologia Computacional/métodos , Bactérias/genética , Bactérias/classificação
17.
Viruses ; 16(5)2024 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-38793690

RESUMO

The Mayaro virus (MAYV) is an arbovirus with emerging potential, though with a limited understanding of its epidemiology and evolution due to the lack of studies and surveillance. Here, we investigated 71 MAYV genome sequences from the Americas available at GenBank and characterized the phylogenetic relationship among virus strains. A phylogenetic analysis showed that sequences were grouped according to the genotypes L, D, and N. Genotype D sequences were closely related to sequences collected in adjacent years and from their respective countries, suggesting that isolates may have originated from circulating lineages. The coalescent analysis demonstrated similar results, indicating the continuous circulation of the virus between countries as well. An unidentified sequence from the USA was grouped with genotype D, suggesting the insertion of this genotype in the country. Furthermore, the recombination analysis detected homologous and three heterologous hybrids which presented an insertion into the nsP3 protein. Amino acid substitutions among sequences indicated selective pressure sites, suggesting viral adaptability. This also impacted the binding affinity between the E1-E2 protein complex and the Mxra8 receptor, associated with MAYV entry into human cells. These results provide information for a better understanding of genotypes circulating in the Americas.


Assuntos
Evolução Molecular , Variação Genética , Genoma Viral , Genótipo , Filogenia , América/epidemiologia , Humanos , Alphavirus/genética , Alphavirus/classificação , Alphavirus/isolamento & purificação , Animais , Recombinação Genética , Infecções por Alphavirus/virologia , Infecções por Alphavirus/epidemiologia
18.
Biomedica ; 44(1): 54-66, 2024 03 31.
Artigo em Inglês, Espanhol | MEDLINE | ID: mdl-38648352

RESUMO

Introduction. During the development of the SARS-CoV-2 pandemic in Antioquia, we experienced epidemiological peaks related to the α, É£, ß, ƛ, and δ variants. δ had the highest incidence and prevalence. This lineage is of concern due to its clinical manifestations and epidemiological characteristics. A total of 253 δ sublineages have been reported in the PANGOLIN database. The sublineage identification through genomic analysis has made it possible to trace their evolution and propagation. Objective. To characterize the genetic diversity of the different SARS-CoV-2 δ sublineages in Antioquia and to describe its prevalence. Materials and methods. We collected sociodemographic information from 2,675 samples, and obtained 1,115 genomes from the GISAID database between July 12th, 2021, and January 18th, 2022. From the analyzed genomes, 515 were selected because of their high coverage values (>90%) to perform phylogenetic analysis and to infer allele frequencies of mutations of interest. Results. We characterized 24 sublineages. The most prevalent was AY.25. Mutations of interest as L452R, P681R, and P681H were identified in this sublineage, comprising a frequency close to 0.99. Conclusions. This study identified that the AY.25 sublineage has a transmission advantage compared to the other δ sublineages. This attribute may be related to the presence of the L452R and P681R mutations associated in other studies with higher evasion of the immune system and less efficacy of drugs against SARS-CoV-2.


Introducción. Durante el desarrollo de la pandemia por SARS-CoV-2 en Antioquia se presentaron picos epidemiológicos relacionados con las variantes α, É£, ß, ƛ y δ, donde δ tuvo la mayor incidencia y prevalencia. Este linaje se considera una variante de preocupación dadas las manifestaciones clínicas que desencadena y sus características epidemiológicas. Se han informado 253 sublinajes δ en la base de datos PANGOLIN. La identificación de estos sublinajes mediante análisis genómico ha permitido rastrear su evolución y propagación. Objetivo. Caracterizar la diversidad genética de los diferentes sublinajes δ de SARSCoV-2 en Antioquia y determinar su prevalencia. Materiales y métodos. Se recopiló información sociodemográfica de 2.675 muestras y de 1.115 genomas del repositorio GISAID entre el 12 de julio de 2021 y el 18 de enero de 2022. Se seleccionaron 501 por su alto porcentaje de cobertura (>90 %) para realizar análisis filogenéticos e inferencia de frecuencias alélicas de mutaciones de interés. Resultados. Se caracterizaron 24 sublinajes donde el más prevalente fue AY.25. En este sublinaje se identificaron mutaciones de interés como L452R, P681R y P681H, que comprendían una frecuencia cercana a 0,99. Conclusiones. Este estudio permitió identificar que el sublinaje AY.25 tiene una ventaja de transmisión en comparación con los otros sublinajes δ. Esto puede estar relacionado con la presencia de las mutaciones L452R y P681R que en otros estudios se han visto asociadas con una mayor transmisibilidad, evasión del sistema inmunitario y menor eficacia de los medicamentos contra SARS-CoV-2.


Assuntos
COVID-19 , Genoma Viral , Filogenia , SARS-CoV-2 , Colômbia/epidemiologia , COVID-19/epidemiologia , Humanos , SARS-CoV-2/genética , Masculino , Feminino , Mutação , Adulto , Pessoa de Meia-Idade , Pandemias , Adulto Jovem , Idoso , Adolescente , Frequência do Gene , Variação Genética
19.
Mitochondrial DNA B Resour ; 9(4): 536-540, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38655148

RESUMO

Agave durangensis commonly known as agave cenizo, is an endemic Agave species in Mexico used for mescal production, yet its taxonomic delimitation is still controversial. This study aimed to enhance taxonomic clarity by characterizing its chloroplast genome. Chloroplast DNA was isolated from 2-year-old A. durangensis leaves. The complete chloroplast genome size was 156,441 bp, comprising a large single-copy region (LSC), a pair of inverted repeat regions (IR), and a small single-copy region (SSC). Annotation revealed 87 protein-coding genes, 38 tRNAs, and 8 rRNAs, with notable gene inversions. Phylogenetic analysis suggests, A. durangensis forms a separate lineage within the Agave genus.

20.
Ann Bot ; 2024 Apr 27.
Artigo em Inglês | MEDLINE | ID: mdl-38676472

RESUMO

BACKGROUND AND AIMS: The size and shape of reproductive structures is especially relevant in evolution because these characters are directly related to the capacity of pollination and seed dispersal, a process that plays a basic role in evolutionary patterns. The evolutionary trajectories of reproductive phenotypes in gymnosperms have received special attention in terms of pollination and innovations related to the emergence of the Spermatophytes. However, variability of reproductive structures, evolutionary trends and the role of environment in the evolution of cycad species have not been well documented and explored. This study considered this topic under an explicitly phylogenetic and evolutionary approach that included a broad sampling of reproductive structures in the genus Ceratozamia. METHODS: We sampled 1400 individuals of 36 Ceratozamia species to explore evolutionary pattern and identify and evaluate factors that potentially drove their evolution. We analyzed characters for both pollen and ovulate strobili within a phylogenetic framework using different methods and characters (i. e., molecular and both quantitative and qualitative morphological) to infer phylogenetic relationships. Using this phylogenetic framework, evolutionary models of trait evolution for strobilar size were evaluated. In addition, quantitative morphological variation and its relation to environmental variables across species were analyzed. KEY RESULTS: We found contrasting phylogenetic signals between characters of pollen and ovulate strobili. These structures exhibited high morphological disparity in several characters related to size. Results of analyses of evolutionary trajectories suggested a stabilizing selection model. In regards to phenotype-environment, the analysis produced mixed results and differences for groups in the vegetation type where the species occur; however, a positive relationship with climatic variables was found. CONCLUSIONS: The integrated approach synthesized reproductive phenotypic variation with current phylogenetic hypotheses and provided explicit statements of character evolution. The characters of volume for ovulate strobili were the most informative, which could provide a reference for further study of the evolutionary complexity in Ceratozamia. Finally, heterogeneous environments, which are under changing weather conditions, promote variability of reproductive structures.

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