Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern.

Background: The advance of the COVID-19 pandemic and spread of SARS-CoV-2 around the world has generated the emergence of new genomic variants. Those variants with possible clinical and therapeutic implications have been classified as variants of concern (VOCs) and variants of interest (VOIs). Objective: This study aims to describe the COVID-19 pandemic and build the evolutionary and demographic dynamics of SARS-CoV-2 populations in Mexico, with emphasis on VOCs. Methods: 30,645 complete genomes of SARS-CoV-2 from Mexico were obtained from GISAID databases up to January 25, 2022. A lineage assignment and phylogenetic analysis was completed, and demographic history for Alpha, Gamma, Delta and Omicron VOCs, and the Mexican variant (B.1.1.519) was performed. Results: 148 variants were detected among the 30,645 genomes analyzed with the Delta variant being the most prevalent in the country, representing 49.7% of all genomes. Conclusion: The COVID-19 pandemic in Mexico was caused by several introductions of SARS-CoV-2, mainly from the United States of America and Europe, followed by local transmission. Regional molecular epidemiological surveillance must implement to detect emergence, introductions and spread of new variants with biologically important mutations.

Influence of Pleistocene climatic oscillations on the phylogeography and demographic history of endemic vulnerable trees (section Magnolia) of the Tropical Montane Cloud Forest in Mexico.

The Tropical Montane Cloud Forest (TMCF) is a highly dynamic ecosystem that has undergone frequent spatial changes in response to the interglacial-glacial cycles of the Pleistocene. These climatic fluctuations between cold and warm cycles have led to species range shifts and contractions-expansions, resulting in complex patterns of genetic structure and lineage divergence in forest tree species. In this study, we sequenced four regions of the chloroplast DNA (trnT-trnL, trnK5-matk, rpl32-trnL, trnS-trnG) for 20 populations and 96 individuals to evaluate the phylogeography, historical demography, and paleodistributions of vulnerable endemic TMCF trees in Mexico: Magnolia pedrazae (north-region), M. schiedeana (central-region), and M. schiedeana population Oaxaca (south-region). Our data recovered 49 haplotypes that showed a significant phylogeographic structure in three regions: north, central, and south. Bayesian Phylogeographic and Ecological Clustering (BPEC) analysis also supported the divergence in three lineages and highlighted the role of environmental factors (temperature and precipitation) in genetic differentiation. Our historical demography analyses revealed demographic expansions predating the Last Interglacial (LIG, ~125,000 years ago), while Approximate Bayesian Computation (ABC) simulations equally supported two contrasting demographic scenarios. The BPEC and haplotype network analyses suggested that ancestral haplotypes were geographically found in central Veracruz. Our paleodistributions modeling showed evidence of range shifts and expansions-contractions from the LIG to the present, which suggested the complex evolutionary dynamics associated to the climatic oscillations of the Pleistocene. Habitat management of remnant forest fragments where large and genetically diverse populations occur in the three TMCF regions analyzed would be key for the conservation of these magnolia populations.

Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging.

In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.

Exohidrolasas fructosílicas y su importancia en el metabolismo de fructanos en Agave tequilana Weber var. azul / Fructan exohydrolases y its importance in the metabolism of fructans in Agave tequilana Weber var. azul / Exoidrolases de frutanos e sua importância no metabolismo de frutanos em Agave tequilana Weber var. azul

Resumen Los fructanos son carbohidratos de estructura química diversa distribuidos en diferentes taxa. En las plantas, además de constituir una importante fuente de carbono, han sido asociados con la tolerancia a diferentes tipos de estrés. La biosíntesis de estos compuestos se lleva a cabo por la acción de las enzimas fructosiltransferasas, mientras que su degradación es mediada por las exohidrolasas fructosílicas, ambos tipos forman parte de la familia 32 de las enzimas hidrolasas glicosídicas. Las exohidrolasas fructosílicas son exoenzimas que liberan secuencialmente residuos de fructosa terminales de los fructanos para hacerlos disponibles como fuente de carbono en diferentes procesos celulares o bien moléculas de señalización. En esta revisión se hace una descripción de los fructanos y las exohidrolasas fructosílicas en algunas plantas importantes para el consumo humano y para el aprovechamiento industrial, con un enfoque particular en el género Agave, específicamente en A. tequilana. Concluimos, que el estudio de las exohidrolasas fructosílicas en agaves podría ser útil en varias aplicaciones biotecnológicas como en la hidrólisis de estructuras de fructanos no digeridos durante la etapa de cocción del agave en el proceso de producción de tequila. Sin embargo, el primer paso es conocer la funcionalidad de estas enzimas, lo que podría facilitar su incorporación en diferentes procesos biotecnológicos.

Abstract Fructans are carbohydrates of diverse chemical structure that are distributed in different taxa. In plants, in addition to be an important source of carbon, they have been associated with tolerance to different types of stress. The biosynthesis of these compounds is carried out by the action of enzymes called fructosyltransferases, while their degradation is mediated by fructan exohydrolases, both types are part of the 32 family of glycosidic hydrolase enzymes. Fructan exohydrolases are exo-enzymes that sequentially release terminal fructose residues from fructans to make them available as carbon sources for different cellular processes or as signaling molecules. In this review, a description is made of fructans, y of fructosyl exohydrolases in some plants important for human consumption or for industrial use, such as the Agave genus, specifically in A. tequilana. We conclude that the study of fructan exohydrolases in agaves could be useful in various biotechnological applications, for example, in the hydrolysis of undigested fructan structures during the agave cooking stage in the tequila production process. However, the first step is to determinate the enzymatic activity in which they are involved, for its posterior inclusion in biotechnology processes.

Resumo Os frutanos são carboidratos de estrutura química diversificada distribuídos em diferentes táxons. Nas plantas, além de serem uma importante fonte de carbono, eles têm sido associados à tolerância a diferentes tipos de estresse. A biossíntese desses compostos é realizada pela ação das enzimas fructosiltransferases, enquanto sua degradação é mediada por frutossil exohidrolases, ambos os tipos fazem parte da família 32 de enzimas glicosídicas da hidrolase. As exo-hidrolases de frutossil são exo-enzimas que liberam seqüencialmente resíduos terminais de frutose dos frutanos para torná-los disponíveis como fonte de carbono em diferentes processos celulares, ou como sinalizadores. Nesta revisão, é feita uma descrição dos frutanos e das frutossil exohidrolases em algumas plantas importantes para o consumo humano ou para uso industrial, como o gênero Agave, especificamente no A. tequilana. Concluímos que o estudo de frutossil exo-hidrolases em agaves pode ser útil em várias aplicações biotecnológicas, por exemplo, na hidrólise de estruturas de frutano não digeridas durante a fase de cozimento da agave no processo de produção de tequila. Para isso, o primeiro passo é conhecer o tipo de atividade enzimática que eles desempenham, para sua posterior inclusão no campo da biotecnologia.

Influence of Pleistocene glacial/interglacial cycles on the genetic structure of the mistletoe cactus Rhipsalis baccifera (Cactaceae) in Mesoamerica.

Phylogeographical work on cloud forest-adapted species provides inconsistent evidence on cloud forest dynamics during glacial cycles. A study of Rhipsalis baccifera (Cactaceae), a bird-dispersed epiphytic mistletoe cactus, was conducted to investigate genetic variation at sequence data from nuclear [internal transcribed spacer (ITS), 677 bp] and chloroplast (rpl32-trnL, 1092bp) DNA for 154 individuals across the species range in Mesoamerica to determine if such patterns are consistent with the expansion/contraction model of cloud forest during glacial cycles. We conducted population and spatial genetic analyses as well as gene flow and divergence time estimates between 24 populations comprising the distribution of R. baccifera in Mexico and Guatemala to gain insight of the evolutionary history of these populations, and a complementary species distribution modeling approach to frame information derived from the genetic analyses into an explicit paleoecological context. The results revealed a phylogeographical break at the Isthmus of Tehuantepec, and high levels of genetic diversity among populations and cloud forest areas. Despite the genetic differentiation of some R. baccifera populations, the widespread ITS ribotypes suggest effective nuclear gene flow via pollen and population differentiation shown by the rpl32-trnL suggests more restricted seed flow. Predictions of species distribution models under past last glacial maximum (LGM) climatic conditions and a significant signal of demographic expansion suggest that R. baccifera populations experienced a range expansion tracking the conditions of the cloud forest distribution and shifted to the lowlands with population connectivity during the LGM.

Chloroplast DNA phylogeography of a distylous shrub (Palicourea padifolia, Rubiaceae) reveals past fragmentation and demographic expansion in Mexican cloud forests.

Several phylogeographic studies in northern Mesoamerica have examined the influence of Pleistocene glaciations on the genetic structure of temperate tree species with their southern limit by the contact zone between species otherwise characteristic of North or South America, but few have featured plant species that presumably colonized northern Mesoamerica from South America. A phylogeographical study of Palicourea padifolia, a fleshy-fruited, bird dispersed distylous shrub, was conducted to investigate genetic variation at two chloroplast regions (trnS-trnG and rpl32-trnL) across cloud forest areas to determine if such patterns are consistent with the presence of Pleistocene refugia and/or with the historical fragmentation of the Mexican cloud forests. We conducted population and spatial genetic analyses as well as phylogenetic and isolation with migration analyses on 122 individuals from 22 populations comprising the distribution of P. padifolia in Mexico to gain insight of the evolutionary history of these populations. Twenty-six haplotypes were identified after sequencing 1389 bp of chloroplast DNA. These haplotypes showed phylogeographic structure (N(ST) = 0.508, G(ST) = 0.337, N(ST) > G(ST), P < 0.05), including a phylogeographic break at the Isthmus of Tehuantepec, with private haplotypes at either side of the isthmus, and a divergence time of the split in the absence of gene flow dating back c. 309,000-103,000 years ago. The patterns of geographic structure found in this study are consistent with past fragmentation and demographic range expansion, supporting the role of the Isthmus of Tehuantepec as a biogeographical barrier in the dispersal of P. padifolia. Our data suggest that P. padifolia populations were isolated throughout glacial cycles by the Isthmus of Tehuantepec, accumulating genetic differences due to the lack of migration across the isthmus in either direction, but the results of our study are not consistent with the existence of the previously proposed Pleistocene refugia for rain forest plant species in the region.