Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status

The emergence and global dissemination of Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) variants of concern (VOCs) have been described as the main factor driving the Coronavirus Disease 2019 pandemic. In Brazil, the Gamma variant dominated the epidemiological scenario during the first period of 2021. Many Brazilian regions detected the Delta variant after its first description and documented its spread. To monitor the introduction and spread of VOC Delta, we performed Polymerase Chain Reaction (PCR) genotyping and genome sequencing in ten regional sentinel units from June to October 2021 in the State of Minas Gerais (MG). We documented the introduction and spread of Delta, comprising 70 per cent of the cases 8 weeks later. Comparing the viral loads of the Gamma and Delta dominance periods, we provide additional evidence that the latter is more transmissible. The spread and dominance of Delta did not culminate in the increase in cases and deaths, suggesting that the vaccination may have restrained the epidemic growth. Analysis of 224 novel Delta genomes revealed that Rio de Janeiro state was the primary source for disseminating this variant in the state of MG. We present the establishment of Delta, providing evidence of its enhanced transmissibility and showing that this variant shift did not aggravate the epidemiological scenario in a high immunity setting.

Origins, Admixture Dynamics, and Homogenization of the African Gene Pool in the Americas

The Transatlantic Slave Trade transported more than 9 million Africans to the Americas between the early 16th and the mid-19th centuries. We performed a genome-wide analysis using 6,267 individuals from 25 populations to infer how different African groups contributed to North-, South-American, and Caribbean populations, in the context of geographic and geopolitical factors, and compared genetic data with demographic history records of the Transatlantic Slave Trade. We observed that West-Central Africa and Western Africa-associated ancestry clusters are more prevalent in northern latitudes of the Americas, whereas the South/East Africa-associated ancestry cluster is more prevalent in southern latitudes of the Americas. This pattern results from geographic and geopolitical factors leading to population differentiation. However, there is a substantial decrease in the between-population differentiation of the African gene pool within the Americas, when compared with the regions of origin from Africa, underscoring the importance of historical factors favoring admixture between individuals with different African origins in the New World. This between-population homogenization in the Americas is consistent with the excess of West-Central Africa ancestry (the most prevalent in the Americas) in the United States and Southeast-Brazil, with respect to historical-demography expectations. We also inferred that in most of the Americas, intercontinental admixture intensification occurred between 1750 and 1850, which correlates strongly with the peak of arrivals from Africa. This study contributes with a population genetics perspective to the ongoing social, cultural, and political debate regarding ancestry, admixture, and the mestizaje process in the Americas.

Yeast communities associated with cacti in Brazil and the description of Kluyveromyces starmeri sp. nov. based on phylogenomic analyses

Yeast communities associated with cacti were studied in three ecosystems of Southeast, Central and North Brazil. A total of 473 yeast strains belonging to 72 species were isolated from 190 samples collected. Cactophilic yeast species were prevalent in necrotic tissues, flowers, fruits and insects of cacti collected in Southeast and North Brazil. Pichia cactophila, Candida sonorensis and species of the Sporopachydermia complex were the most prevalent cactophilic species in Southeast and Central regions. Kodamaea nitidulidarum, Candida restingae and Wickerhamiella cacticola were frequently associated with cactus flowers and fruits. The diversity of yeasts associated with the substrates studied was high. Twenty-one novel species were found. One is described here as Kluyveromyces starmeri sp. nov. based on 21 isolates obtained from necrotic tissues, flowers, fruits and associated insects of the columnar cacti Cereus saddianus, Micranthocereus dolichospermaticus and Pilosocereus arrabidae in two different ecosystems in Brazil. Phylogenetic analyses of sequences encoding the gene of the small subunit (SSU) rRNA gene, the internal transcribed spacer, the 5.8S rRNA gene and the D1/D2 domains of the large subunit (LSU) rRNA showed that the species is related to Kluyveromyces dobzhanskii, Kluyveromyces lactis and Kluyveromyces marxianus. Phylogenomic analyses based on 1264 conserved genes shared among the new species and 19 other members of the Saccharomycetaceae confirmed this phylogenetic relationship. The holotype is K. starmeri sp. nov. CBS 16103^T (=UFMG-CM-Y3682^T ). The Mycobank number is MB 836817.

Gonadal remodeling and hormonal regulation during sex change of juvenile dusky grouper Epinephelus marginatus (Teleostei, Serranidae), an endangered protogynous hermaphrodite fish

Sex change was induced in Epinephelus marginatus juveniles using a nonsteroidal aromatase inhibitor (AI), a synthetic androgen (17α-methyltestosterone; MT), and a combination of both (MT + AI) in a 90-day experiment. A detailed remodeling of the gonads, the plasma level of gonadal steroids, and immunostaining of pituitary follicle-stimulating hormone (FSH), luteinizing hormone (LH), and somatolactin (SL) cells were analyzed. Sex inversion reached the final spermatogenesis stages using MT, while AI triggered spermatogenesis, but reaching only the spermatid stage. Estradiol (E₂) levels did not change in fish treated with AI but decreased throughout the experimental period in animals treated with MT and MT + AI. Testosterone (T) levels increased in animals treated with MT during the first 60 days (and combined with AI in the first 30 days), decreasing in all experimental groups at 90 days, while AI-treated animals had increased plasma 11-ketotestosterone (11-KT) levels after 90 days. In control fish, FSH- and SL-producing cells (ir-FSH and ir-SL) were restricted to pars intermedia (PI) of the adenohypophysis. Pituitary ir-FSH cells were decreased at the end of the experimental period in all treatments compared with the CT animals. LH-producing cells (ir-LH) were present in proximal pars distalis (PPD) and pars intermedia (PI) of adenohypophysis and did not change after the experimental period. The decreased number of ir-FSH cells at the end of the experiment in all treatments could be related to the negative feedback loop triggered by the increase in natural and/or synthetic androgens.

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Brazil currently has one of the fastest-growing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemics in the world. Because of limited available data, assessments of the impact of nonpharmaceutical interventions (NPIs) on this virus spread remain challenging. Using a mobility-driven transmission model, we show that NPIs reduced the reproduction number from >3 to 1 to 1.6 in São Paulo and Rio de Janeiro. Sequencing of 427 new genomes and analysis of a geographically representative genomic dataset identified >100 international virus introductions in Brazil. We estimate that most (76%) of the Brazilian strains fell in three clades that were introduced from Europe between 22 February and 11 March 2020. During the early epidemic phase, we found that SARS-CoV-2 spread mostly locally and within state borders. After this period, despite sharp decreases in air travel, we estimated multiple exportations from large urban centers that coincided with a 25% increase in average traveled distances in national flights. This study sheds new light on the epidemic transmission and evolutionary trajectories of SARS-CoV-2 lineages in Brazil and provides evidence that current interventions remain insufficient to keep virus transmission under control in this country.

Influence of tropical reservoirs eutrophication on the polyunsaturated fatty acid profile in Astyanax altiparanae (Pisces: Characidae)

The eutrophication increases the quantity of algae that are deficient in highly unsaturated fatty acids (HUFA) n3, as EPA (eicosapentaenoic acid) and DHA (docosahexaenoic acid), altering the bottom-up transfer of the entire food chain. Due to the importance of the fatty acids (FA) in physiological processes related to the main role of the membrane phospholipids (PL) and precursors of eicosanoids, and also the little knowledge about the influence of eutrophication in tropical ecosystems, it is important to understand how anthropogenic changes in the aquatic ecosystem affect the lipid quality, specifically n3 HUFAs. This study aimed to investigate the influence of eutrophication on the FA profile of the hepatic PL, as well as prostaglandin (PG) levels in Astyanax altiparanae females. Fish were collected in reservoirs with different eutrophication degrees: Jundiaí (Ju) reservoir and Embu-Guaçu (EG) branch, considered as mesotrophic points, and Barragem (Ba) and Aracati (Ar), branches from Guarapiranga reservoir, considered as supereutrophic and hypereutrophic points, respectively. The FA profile of the liver PL was analyzed by gas chromatography, and the concentration of liver PGE2 was analyzed using ELISA immunoassay kits. The degree of eutrophication did not alter the PG concentration and produced few modifications in the FA profile of hepatic PL. Fish collected at Ba and EG presented similar FA profiles, both with high percentages of n3 HUFA, especially DHA, in comparison to fish from Ju. However, no change was observed in the n3 HUFA profile of the fish from Ar. These data demonstrated that the FA profile in A. altiparanae seems to be more related to different physiological requirements of n3 HUFA of the species than eutrophication. So, this study contributed to findings on the trophic transfer dynamics in tropical freshwater reservoirs, where a direct effect of eutrophication on the availability of HUFA n3 to animals is not suggested.

Thermal manipulation and GnRHa therapy applied to the reproduction of lambari-do-rabo-amarelo, Astyanax altiparanae females (Characiformes: Characidae) during the non-breeding season

Lambari-do-rabo-amarelo Astyanax altiparanae in the wild reproduce during spring and summer, but females undergo vitellogenesis throughout the year, including the non-spawning winter period when water temperatures are low. The present study investigated the physiological role of temperature modulation on the hypothalamus-pituitary-gonads axis of lambari during winter, as well as the effects of gonadotropin releasing hormone agonist (GnRHa) therapy. Captive females were exposed to two different temperatures (20 °C and 27 °C) and were injected weekly with GnRHa for 21 days during winter (Control, CTR; Low dose; LD and high dose of GnRHa, HD). At the end of the 21-days period gonadosomatic index (GSI), oocyte stage of development and theoretical fecundity were evaluated, together with plasma levels of 17β-estradiol (E₂). Gene expression of the two pituitary gonadotropins follicle-stimulating hormone (fshβ) and luteinizing hormone (lhβ), as well as hepatic vitellogenin-A (vtgA) expression were also analyzed. At the end of the experimental period, females from the six different experimental conditions were induced to spawn using human chorionic gonadotropin (hCG). Spawning performance parameters and plasma levels of the maturation inducing steroid (MIS) were analyzed. Gene expression of fshβ did not change with temperature manipulation, but females exposed to 27 °C and supplemented with a HD of GnRHa exhibited an increased fshβ gene expression, associated with higher E₂ levels. The higher water temperature alone was able to increase E₂ levels. At both water temperatures GnRHa injections induced a decrease in E₂ levels. GnRHa injected females had a lower vtgA gene expression levels at 20 °C. Even with differences in the gene expression of gonadotropins among the various temperature/GnRHa treatments, GSI and oocyte diameter did not change, but GnRHa enhanced the number of vitellogenic oocytes at 20 °C. The reproductive performance of lambari induced to spawn with hCG was better after the combined treatment with GnRHa and summer temperature.

Exposure to aluminum, aluminum + manganese and acid pH triggers different antioxidant responses in gills and liver of Astyanax altiparanae (Teleostei: Characiformes: Characidae) males

Exposure to aluminum (Al) and aluminum + manganese (Mn) can trigger an increase in reactive oxygen species (ROS) and modify the activity of oxidative defense enzymes. This study investigated whether exposure to Al and Al + Mn at acid pH for 24 and 96 h causes oxidative stress evidenced by antioxidants and oxidative damage in the gills and liver of sexually mature Astyanax altiparanae males. The fish were subsequently immersed in metal-free water for 24 and 96 h to see whether they recovered from the effects of these metals. Exposure to an acid pH boosted the activity of gill superoxide dismutase (SOD) at 96 h and the fish did not recover when immersed for the same period in water at neutral pH. Exposure to Al increased glutathione (GSH) levels (24 h) in the gills, returning to control levels during the recovery period, showing the efficiency of the antioxidant system in preventing lipid peroxidation of the gills and liver. Mn did not modify the activity of the enzymes studied, but did trigger late hepatic lipid peroxidation during the recovery period. The group exposed to Al + Mn exhibited several alterations, including increased concentration of GSH, as well as higher GPx and GR activity in the gills. Despite the defensive responses triggered by acute exposure, during the recovery period there were alterations in catalase (96 h) and an increase in hepatic metallothionein (24 h), but this did not prevent hepatic lipid peroxidation. Al and Al + Mn produced different effects, and the timing of enzymatic and non-enzymatic antioxidant defenses also differed.

Scheffersomyces stambukii f.a., sp. nov., a d-xylose-fermenting species isolated from rotting wood

Two isolates representing a new species of Scheffersomyces were isolated from rotting wood samples collected in an Amazonian forest ecosystem in Brazil. Analysis of the sequences of the D1/D2 domains showed that this new species is phylogenetically related to Scheffersomyces NYMU 15730, a species without a formal description, and the two are in an early emerging position with respect to the xylose-fermenting subclade containing Scheffersomyces titanus and Scheffersomyces stipitis. Phylogenomic analyses using 474 orthologous genes placed the new species in an intermediary position between Scheffersomyces species and the larger genus Spathaspora and the Candida albicans/Lodderomyces clade. The novel species, Scheffersomyces stambukii f.a., sp. nov., is proposed to accommodate these isolates. The type strain of Scheffersomyces stambukii sp. nov. is UFMG-CM-Y427^T (=CBS 14217^T). The MycoBank number is MB 824093. In addition, we studied the xylose metabolism of this new species.

Embryonic and larval development and fatty-acid profile of Epinephelus marginatus spawned in captivity: tools applied to captive rearing

Development, ontogeny of the digestive system and the fatty-acid (FA) profile, were analysed during development of Epinephelus marginatus. Larvae were analysed 7 and 17 days post fertilization (dpf) to evaluate fatty-acid profile and morphological variables, respectively. Epinephelus marginatus larvae have relatively slow development of digestive structures, but were able to capture, ingest and digest prey by 5 dpf. Eggs were composed of high percentages of polyunsaturated fatty acids (PUFA) in phospholipids. The percentage of n3 PUFAs was higher than n6, especially docosahexaenoic acid (DHA), which exhibited higher levels compared with other marine species during the first 3 days of development, both in terms of phospholipids and triglycerides. The larvae present a high content of docosahexaenoic acid-eicosapentaenoic acid (DHA-EPA) and, during this phase, live food of small size was required (copepods or SS-strain Brachionus rotundiformes), enriched with DHA-EPA. These results may guide future studies on the contribution of FAs required during this stage of the life cycle of E. marginatus, to advance knowledge of the use of these FAs throughout ontogeny and contribute to the culture of this species commercial production or restocking.

Draft genome sequence of Sugiyamaella xylanicola UFMG-CM-Y1884T, a xylan-degrading yeast species isolated from rotting wood samples in Brazil

We present the draft genome sequence of the type strain of the yeast Sugiyamaella xylanicola UFMG-CM-Y1884^T (= UFMG-CA-32.1^T = CBS 12683^T), a xylan-degrading species capable of fermenting d-xylose to ethanol. The assembled genome has a size of ~ 13.7 Mb and a GC content of 33.8% and contains 5971 protein-coding genes. We identified 15 genes with significant similarity to the d-xylose reductase gene from several other fungal species. The draft genome assembled from whole-genome shotgun sequencing of the yeast Sugiyamaella xylanicola UFMG-CM-Y1884^T (= UFMG-CA-32.1^T = CBS 12683^T) has been deposited at DDBJ/ENA/GenBank under the accession number MQSX00000000 under version MQSX01000000.

Aluminum as an endocrine disruptor in female Nile tilapia (Oreochromis niloticus)

The effects of aluminum on plasma ion, lipid, protein and steroid hormone concentration were evaluated in Oreochromis niloticus broodstock females. Lipid and protein concentrations from the gonads and liver were also measured. Experiments were performed at neutral and acidic water pH. Four groups of fish were tested for 96h: 1) control conditions at neutral water pH; 2) control conditions at acidic water pH (CTR-Ac); 3) aluminum at neutral water pH (Al-N); and 4) aluminum at acidic water pH (Al-Ac). Aluminum and acidic water pH exposure caused no ionoregulatory disturbances. Total lipid concentration increased in the mature gonads and decreased in the liver, suggesting an acceleration of lipid mobilization to the ovaries in animals exposed to aluminum. However, a decreased protein concentration in ovaries was also observed. Exposure of control fish to acidic water pH caused an increased concentration of plasma 17alpha-hydroxyprogesterone. However, females exposed to aluminum at acidic water pH showed a decreased of plasma 17alpha-hydroxyprogesterone and cortisol. No differences in plasma 17beta-estradiol were observed. The physiological mechanisms underlying the disturbances observed are discussed focusing on reproduction. We suggest that aluminum can be considered an endocrine disrupting compound in mature O. niloticus females.

Patterns of oocyte development in natural habitat and captive Salminus hilarii Valenciennes, 1850 (Teleostei: Characidae)

Fecundity and oocyte development in Salminus hilarii female brood stock were analyzed with the aim of investigating the impact of migration impediment on oogenesis. Histological analyses of the ovaries were performed in adult females caught in two different environments--the Tietê River (natural) and captivity--and the gonadossomatic index, oocyte diameter and fecundity determined. Five germ cell development stages (oogonium, perinucleolar, cortical alveoli, vitellogenic, ripe) and two other structures (postovulatory follicles and atretic oocytes) were observed in females caught in the river. Captive animals lacked the ripe oocytes and postovulatory follicles and had a relatively higher number of atretic oocytes. Females in captivity are known to produce larger oocytes, and they release fewer eggs in each spawn (absolute fecundity) when compared with animals that are able to migrate. Our results suggest that the Tietê River is undergoing alterations which are being reflected in the reproductive performance of S. hilarii, mainly due to the presence of atretic oocytes in females caught in the river. The lack of postovulatory follicles and ripe oocytes in captive animals reveals that migratory impediment negatively impacts final oocyte maturation. However, the stage of maturation reached is adequate for ovulation induction with hormone manipulation.

Application of high hydrostatic pressure to eliminate Listeria monocytogenes from fresh pork sausage

Ground pork patties were inoculated separately with 10(9) CFU/g each of three strains of Listeria monocytogenes obtained from the National Animal Disease Center (NADC). Inoculated patties were packaged under vacuum and treated at 414 megapascals (60,000 lb/in2) for up to 60 min by high hydrostatic pressure (HHP). Survivors were determined by surface plating onto modified Oxford agar and trypticase soy agar with yeast extract, as well as by the most probable number method using Listeria enrichment broth. Average D values ranged from 1.89 to 4.17 min, depending on the strain, with the most virulent strain (reported by the NADC) having the highest D value. We tested the usefulness of applying a mild heat treatment at 50 degrees C, simultaneously with HHP, to lower these values. Average D values ranged from 0.37 to 0.63 min, depending on the strain. Thus, a 10-log10 reduction could be achieved even in the most pressure-resistant strain of L. monocytogenes by a 6-min application of heat and HHP. Shelf life studies were also conducted, with spoilage levels reached after 5 days of storage at 4 degrees C for controls versus 28 days for treated samples. Sensory evaluation of uninoculated grilled patties showed that panelists could not distinguish between those treated by heat and HHP and untreated controls (P<0.05). Thus, treatment by HHP in combination with mild heating can be used successfully to produce safer, longer-lasting fresh pork without affecting quality.