Sub-lineage B.1.6 of hMPXV in a global context: Phylogeny and epidemiology.

During the 2022 COVID-19 pandemic, monkeypox emerged as a significant threat to global health. The virus responsible for the disease, the human monkeypox virus (hMPXV), underwent various genetic changes, resulting in the emergence of over a dozen distinct lineages, which could be identified by only a small number of unique mutations. As of January 25, 2023, genomic information of hMPXV generated had reached 4632 accessions in the GISAID database. In this study, we aimed to investigate the epidemiological and phylogenetic characteristics of the B.1.6 sub-lineage of hMPXV in Peru, compared with other circulating sub-lineages during the global outbreak. The B.1.6 sub-lineage, characterized by the 111029G>A mutation, was estimated to have emerged in June 2022 and was found mainly in Peru. Most cases (95.8%) were men with an average age of 33 years, and nearly half of the patients had HIV, of whom only 77.35% received antiretroviral therapy. Our findings revealed that the B.1.6, B.1.4, and B.1.2 sub-lineages were well represented and had a higher number of mutations despite having the lowest media substitution rates per site per year. Moreover, it was estimated that B.1.2 and B.1.4 appeared in February 2022 and were the first two sub-lineages to emerge. A mutation profile was also obtained for each sub-lineage, reflecting that several mutations had a pattern similar to the characteristic mutation. This study provides the first estimation of the substitution rate and ancestry of each monkeypox sub-lineage belonging to the 2022 outbreak. Based on our findings, continued genomic surveillance of monkeypox is necessary to understand better and track the evolution of the virus.

Genomic surveillance of the Lambda SARS-CoV-2 variant in a global phylogenetic context.

The massive sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and global genomic surveillance strategies allowed the detection of many variants of concern and interest. The variant of interest Lambda (C.37), which originated in South America, has been the most prevalent in Peru and Chile, but its dispersion in other continents still remains unknown. The current study aims to determine the phylogenetic relationship among C.37 isolates worldwide, focusing on spike mutations to understand the spread of Lambda in pandemics. A total of 7441 sequences identified as C.37 were downloaded from the GISAID database; local analysis was carried out to identify spike mutations and phylogenetic analysis was carried out to determine the rate of spread of the virus. Our results showed some spike mutations of Lambda that allowed us to detect small local outbreaks in different countries that occurred in the past and identify several clades that have not yet been designated. Although the lineage C.37 is not epidemiologically relevant in Europe or North America, the endemic behavior of this variant in Peru had a major impact on the second SARS-CoV-2 wave.

Genomic analysis reveals a rapid spread and predominance of lambda (C.37) SARS-COV-2 lineage in Peru despite circulation of variants of concern.

The pandemic generated by SARS-Cov-2 has caused a large number of cases and deaths in the world, but South America has been one of the continents that were most hard hit. The appearance of new variants causes concern because of the possibility that they may evade the protection generated by vaccination campaigns, their greater capacity to be transmitted, or their higher virulence. We analyzed the circulating variants in Peru after improving our Genomic Surveillance program. The results indicate a steep increase of the lambda lineage (C.37) until becoming predominant between January and April 2021, despite the cocirculation of other variants of concern or interest. Lambda lineage deserves close monitoring and could probably become a variant of concern in the near future.

Disseminated lomentosporiosis in a heart transplant recipient: Case report and review of the literature.

BACKGROUND: Lomentospora prolificans (formerly S prolificans) is a saprophyte fungi that causes opportunistic infections in solid organ transplant (SOT) recipients. Resulting disseminated infections are difficult to treat and have a high mortality. Indications for antifungal prophylaxis after heart transplantation (HT) include CMV disease, reoperation, renal replacement therapy, extracorporeal membrane oxygenation (ECMO), and high environmental exposure to Aspergillus spores. However, the risk of breakthrough infections, such as Lomentosporiosis, remains a cause of concern. METHODS: We report the clinical findings, microbiology, treatment and outcome of a disseminated Lomentosporiosis in a heart transplant recipient with ECMO and antifungal prophylaxis. RESULTS: A 25-year-old male with complex grown-up congenital heart disease (GUCHD) was admitted for HT. He presented severe post-surgical complications including acute kidney injury and right heart and respiratory failure requiring venoarterial-ECMO, continuous renal replacement therapy (CCRT) and later on (+14) a ventricular assist device (VAD). Ganciclovir, cotrimoxazole, and antifungal prophylaxis with anidulafungin at standard doses had been started on day + 3 post HT. The patient presented seizures (+4), pancytopenia with mild neutropenia (days + 6 to + 11), influenza B (+7), and bacteremic Pseudomonas aeruginosa ventilator associated pneumonia (VAP) (+10). On days + 14 to + 16 Lomentospora prolificans was recovered from blood cultures, broncho aspirate, catheter tip, and skin biopsy. Despite treatment with L-AMB, voriconazole and terbinafine the patients died on day 17 after HT. Necropsy revealed disseminated infection with fungal invasion in central nervous system, heart, lung, cutaneous, and subcutaneous tissue. Broth microdilution tests demonstrated resistance to all antifungals. CONCLUSIONS: Lomentosporiosis is a rare complication that may emerge as a breakthrough invasive fungal infection in heart transplant recipients on ECMO despite antifungal prophylaxis.

Phase Stability and Miscibility in Ethanol/AOT/n-Heptane Systems: Evidence of Multilayered Cylindrical and Spherical Microemulsion Morphologies.

We describe the effects of ethanol on the phase behavior of sodium bis(2-ethylhexyl) sulfosuccinate (AOT) in n-heptane. Using dynamic light scattering (DLS), molecular dynamics (MD) simulations, and nuclear magnetic resonance (1H NMR) spectroscopy, we investigate the aggregation behavior of AOT across a wide range of ethanol/AOT/n-heptane compositions. We conclude that reverse micelles do not form at any of the investigated concentrations. Instead, we observe the formation of other surfactant aggregate morphologies unique to this system, namely, multilayered cylindrical structures and spherical AOT-in-ethanol structures, which vary significantly with changes in ethanol concentration. We also identify mixed-solvent polarity as a driving factor for the surfactant behavior in the system. When the concentration of ethanol is 20 wt % or below, the system is inhomogeneous with varying sizes of AOT, ethanol, and AOT + ethanol aggregates, with the ethanol primarily exhibiting a cosurfactant behavior, almost exclusively binding at the surface of AOT aggregates. With increased ethanol concentration, the ethanol in the system also exhibits solvent-like behaviors in addition to the cosurfactant behaviors. Most significantly, when the ethanol concentration is raised above 35 wt %, the transition to solvent-like behavior allows AOT Na+ counterions to dissociate from the headgroups and they are dissolved in the ethanol. We use these results to construct a preliminary phase diagram for the ethanol/AOT/n-heptane system.

Toxicity and Alkaloid Profiling of the Skin of the Golfo Dulcean Poison Frog Phyllobates vittatus (Dendrobatidae).

Frogs in the genus Phyllobates are known for the presence of batrachotoxin, a highly toxic alkaloid, in their skin. Nevertheless, Phyllobates frogs from Costa Rica and Panama (P. lugubris and P. vittatus) are considered non-toxic, as they have been reported to harbor low concentrations of this alkaloid. However, the potential toxicity of Central American Phyllobates has not been assessed experimentally. Our goal was to determine the toxicity of the whole skin of P. vittatus, an endemic species from the Southeastern Pacific region of Costa Rica. We performed median lethal dose (LD50) tests in mice to determine general toxicity, and an irritant assay based on the behavioral responses of mice to subcutaneous injection, to determine differences in irritability, as a measure of toxicity, among three study localities. Using UPLC-ESI-QTOF, we obtained chemical profiles of the methanolic extract of frog skins. Due to the absence of mortality at the studied doses, we were unable to estimate LD50. However, we recorded a list of toxicity symptoms in mice that are consistent with cardiotoxic effects, and found that mice presented more symptoms at higher concentrations of skin extracts during the first hour of the LD50 assays, recovering completely at all doses by the end of the assay. On the other hand, we did not detect differences in irritability among studied localities. Additionally, we putatively identified three toxic alkaloids (Batrachotoxinin A, DHQ 251A and Lehm 275A). This study provides the first experimental data on the toxicity and associated symptoms in mice, as well as the chemical profile of the skin of P. vittatus. We suggest that the skin alkaloids of P. vitattus may confer a chemical defense towards predators.

Infections in patients after Berlin Heart® EXCOR assist device implantation.

OBJECTIVES: Berlin Heart® EXCOR devices (BHED) are ventricular assist devices (VAD) used mainly as a bridge to heart transplantation (HT) in pediatric population. The aim of our study is to report the infections diagnosed in adult patients undergoing a BHED implantation. METHODS: Adult patients receiving a BHED between Jul 2009 and Oct 2017 at our institution were included. Infections were classified according to the International Society of Heart and Lung Transplantation definitions in VAD-Specific (VAD-S), VAD-Related (VAD-R) and non-VAD (N-VAD). RESULTS: Fifteen patients underwent BHED implantation, which was maintained for a mean of 92 (19-195) days. Infection occurred in 13 patients who developed 36 infectious episodes: 5 VAD-S (5 cannula infections); 8 VAD-R (5 bloodstream infections and 3 mediastinitis) and 24 N-VAD (7 urinary tract infections, 6 Cytomegalovirus diseases and others). Overall, 27 (75%) were bacterial, 7 (19.4%) were viral and there was one (2.7%) fungal infection. Eleven patients underwent HT and all of them developed at least one infection after it. In 3 cases, all VAD-R or VAD-S infections were caused by the same etiology as before HT. Their median time of appearance was on day +6 (3-11) after BHED removal and HT. Overall mortality was 6/15 (40%). None of the deaths were related to VAD Infection. CONCLUSIONS: Infection complicated BHED implantation in 86.7% of the patients. Overall, 13.9% were specific of BHED and 22.2% were related. However, infections did not preclude HT in any case and carried no attributable mortality.

A generalized method for the inversion of cohesive energy curves from isotropic and anisotropic lattice expansions.

Cohesive energy curves contain important information about energetics of atomic interactions in crystalline materials, and these are more often obtained using ab initio methods such as density functional theory. Decomposing these curves into the different interatomic contributions is of great value to evaluate and characterize the energetics of specific types of atom-atom interactions. In this work, we present and discuss a generalized method for the inversion of cohesive energy curves of crystalline materials for pairwise interatomic potentials extraction using detailed geometrical descriptions of the atomic interactions to construct a list of atomic displacements and degeneracies, which is modified using a Gaussian elimination process to isolate the pairwise interactions. The proposed method provides a more general framework for cohesive energy inversions that is robust and accurate for systems well-described by pairwise potential interactions. Results show very good reproduction of cohesive energies with the same or better accuracy than current approaches with the advantage that the method has broader applications.

Dispersion of SARS-CoV-2 lineage BA.5.1.25 and its descendants in Peru during two COVID-19 waves in 2022.

During the third year of the pandemic in Peru, the persistent transmission of SARS-CoV-2 led to the appearance of more transmissible and immune-evasive Omicron sublineages; in that context, the National Genomic Surveillance of SARS-CoV-2 performed by the Peruvian National Institute of Health detected spike mutations in the circulating Omicron BA.5.1.25 sublineage which was later designated as DJ.1 and increased during the fourth COVID-19 wave, this eventually branched into new sublineages. The introduction, emergence, and timing of the most recent common ancestor (tMRCA) of BA.5.1.25 and its descendants (DJ.1, DJ.1.1, DJ.1.2, and DJ.1.3) were investigated in this paper as well as the time lags between their emergence and identification by the Peruvian National Institute of Health. Our findings show that ongoing genomic surveillance of SARS-CoV-2 is critical for understanding its phylogenetic evolution and the emergence of novel variations.

Molecular characterization of the meq oncogene of Marek's disease virus in vaccinated Brazilian poultry farms reveals selective pressure on prevalent strains.

Marek's disease virus (MDV) has become an increasingly virulent pathogen in the poultry industry despite vaccination efforts to control it. Brazil has experienced a significant rise of Marek's disease (MD) outbreaks in recent years. Our study aimed to analyze the complete meq gene sequences to understand the molecular epidemiological basis of MD outbreaks in Brazilian vaccinated layer farms. We detected a high incidence rate of visceral MD (67.74%) and multiple circulating MDV strains. The most prevalent and geographically widespread genotype presented several clinical and molecular characteristics of a highly virulent strain and evolving under positive selective pressure. Phylogenetic and phylogeographic analysis revealed a closer relationship with strains from the USA and Japan. This study sheds light on the circulation of MDV strains capable of infecting vaccinated birds. We emphasize the urgency of adopting preventive measures to manage MDV outbreaks threatening the poultry farming industry.

Isolation of major components from the roots of Godmania aesculifolia and determination of their antifungal activities.

From the methanol root extract of Godmania aesculifolia, a species selected in a multinational OAS program aimed at discovering antifungal compounds from Latin American plants, a new chavicol diglycoside (1), the known 3,4-dihydroxy-2-(3-methylbut-2-en-1-yl)-3,4-dihydronaphthalen-1(2H)-one (2), and lapachol (3) were isolated and characterized by 1D and 2D NMR and MS techniques. Only 3 exhibited fairly good activity against a panel of clinical isolates of Cryptococcus neoformans (MIC50 between 7.8 and 31.2 µg/mL) and moderate activities against Candida spp. and non-albicans Candida spp.

In-silico identification of linear B-cell epitopes in specific proteins of Bartonella bacilliformis for the serological diagnosis of Carrion's disease.

Carrion´s disease is caused by Bartonella bacilliformis, it is a Gram-negative pleomorphic bacterium. B. bacilliformis is transmitted by Lutzomyia verrucarum in endemic areas of the Peruvian Inter-Andean valleys. Additionally, the pathogenicity of B. bacilliformis involves an initial infection of erythrocytes and the further infection of endothelial cells, which mainly affects children and expectant women from extreme poverty rural areas. Therefore, the implementation of serological diagnostic methods and the development of candidate vaccines for the control of CD could be facilitated by the prediction of linear b-cell epitopes in specific proteins of B. bacilliformis by bioinformatics analysis. In this study, We used an in-silico analysis employing six web servers for the identification of epitopes in proteins of B. bacilliformis. The selection of B. bacilliformis-specific proteins and their analysis to identify epitopes allowed the selection of seven protein candidates that are expected to have high antigenic activity.

Single-nucleotide polymorphisms in ialB, gltA and rpoB genes of Bartonella bacilliformis isolated from patients in endemic Peruvian regions.

Bartonella bacilliformis is a Gram-negative, aerobic bacterium and the known causal agent of Carrion's disease, still considered a neglected disease. There is limited information about the nucleotide sequences of this bacterium in international databases, and few studies have addressed the genetic diversity of B. bacilliformis. We analyzed a total of 20 isolates of B. bacilliformis from the Peruvian regions of Ancash and Cajamarca. Three genes (ialB, gltA, and rpoB) were sequenced in each isolate and nucleotide sequences retrieved from GenBank (16 B. bacilliformis genomes) were also included in the study. All this information was merged in order to obtain clearer evidence of the phylogenetic relationships of B. bacilliformis. In the phylogenetic analysis conducted with the concatenated markers, four isolates (B.b-1, B. b-3, B. b- 7, B.b-8) from the Ancash region were observed to form a subgroup different from B. bacilliformis type strain KC583, showing dissimilarity levels of 5.96% (ialB), 3.69% (gltA) and 3.04% (rpoB). Our results suggest that B. bacilliformis consists of two different subgroups. Future investigations are needed to establish the taxonomic status of these subgroups.

Ionic concentration effects on reverse micelle size and stability: implications for the synthesis of nanoparticles.

We present a systematic investigation and analysis of the structure and stability of reverse micelle systems with the addition of NH(4)OH, ZrOCl(2), and Al(NO(3))(3) salts. We demonstrate that the reverse micelle size decreases with increasing salt additions until one reaches a critical concentration, which characterizes the onset of system destabilization. The concept of an electrical double layer, as it applies to reverse micelles, is considered for explaining features of destabilization, including the initial decrease in reverse micelle size, the destabilization concentration, and the effect of cation valence. We propose that the reduction in size prior to instability is caused by compression of the reverse micelle electrical double layers, as higher concentrations of salts are present. The reduced thickness of the electrical double layers allows the decaying potentials to move into closer proximity to each other before generating enough repulsion to balance the forces for reverse micelle formation and form a new equilibrium average reverse micelle size. The point of reverse micelle instability has been related to the formation of a two-phase system as a result of the inability to further compress the salt co-ions in the core of the reverse micelles, which would cause an excessive repulsive force between the overlapping potentials. We have extracted a critical potential of -89 nV between the two overlapping potentials for the AOT/water/isooctane (ω(0) = 10) systems studied. All these effects have important implications for the preparation of nanopowders by reverse micelle synthesis. If the reverse micelles are unstable before the precipitates are formed, then the advantage of reverse micelle synthesis is immediately lost.

Sekikaic acid and lobaric acid target a dynamic interface of the coactivator CBP/p300.

Capturing a coactivator, naturally: the natural products sekikaic acid and lobaric acid, isolated after a high-throughput screen of a structurally diverse extract collection, effectively target the dynamic binding interfaces of the GACKIX domain of the coactivator CBP/p300. These molecules are the most effective inhibitors of the GACKIX domain yet described and are uniquely selective for this domain.

Confirmed Severe Acute Respiratory Syndrome Coronavirus 2 Reinfections After a Second Wave With Predominance of Lambda in Lima and Callao, Peru.

Background: Coronavirus disease 2019 (COVID-19) infection is a major public health problem in the world and reinfections are becoming more frequent. Our main objective was to describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the capital of Lima and Callao, Peru. Methods: We searched in the Peruvian laboratory information system from April 2020 up to May 2021, looking for cases having 2 positive molecular tests for SARS-CoV-2 with more than 90 days between them. We performed genomic sequencing to the available pairs of samples and described the clinical characteristics, epidemiological impact, and genomic analysis of the confirmed reinfections. Results: There were 1 694 164 people with a positive diagnostic test for SARS-CoV-2 in Lima/Callao during the study period. Of these, 1695 had 2 positive molecular tests with more than 90 days between them. Two hundred eleven had both samples available for genomic analysis according to our selection criteria, and these were retrieved and submitted to sequencing. Thirty cases were confirmed to be SARS-CoV-2 reinfections with 2 different lineages in the 2 episodes. The variant Lambda (C.37) was the most common during the second infection and accounted for 19 (63.3%) of the 30 cases. Conclusions: We report 30 cases of confirmed SARS-CoV-2 reinfections. The Lambda variant was the most common cause of the second infections, in concordance with its predominant circulation during Peru's second wave. This report describes the largest series of confirmed reinfections by SARS-CoV-2 in Latin America.We describe the epidemiological, clinical, and genomic characteristics of the confirmed cases of reinfection by severe acute respiratory syndrome coronavirus 2 in Lima and Callao, durante la segunda ola en Peru. The Lambda variant (C.37) was the most common cause of the second infections.

Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review.

Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.

Predicting the size of salt-containing aqueous Na-AOT reverse micellar water-in-oil microemulsions with consideration for specific ion effects.

HYPOTHESIS: Reverse micellar solutions are thermodynamically stable systems in which surfactant molecules surround water droplets within a continuous organic phase. Among their many applications, they can be used for the synthesis of nanoparticles of controlled agglomeration. Here, we consider the role specific ion effects play in reverse micelle size reduction. EXPERIMENTS: Dynamic light scattering measurements and the Gouy-Chapman electrical double layer model were combined to study water/AOT/isooctane reverse micellar systems (wo = 10). Linear relationships between the solvodynamic diameter (D) of reverse micelles containing various concentrations of FeSO4, Mg(NO3)2, CuCl2, Al(NO3)3, Fe(NO3)3, Y(NO3)3, NaBH4, ZrOCl2, and NH4OH, and their calculated Debye screening lengths, κ-1, were observed with decreasing D and increasing salt concentration (c). FINDINGS: By comparing the linear fits for reverse micelle size as a function of c-1/2, we determined the size can be described as a function of the Debye screening length, cation valency (z), and specific anion hydrated radius (ran), where D = 3.1z κ-1 + bi, and bi is linearly related to ran. Our model accurately predicts reverse micelle sizes with the addition of monovalent, divalent, and trivalent salts for which the primary hydrolyzed cation species has a charge that is equal to the cation valency.

Interaction of Hydrogen with MB6 (M = Ba, Ca, La, and Sr) Surfaces from First Principles.

We show results of basic energetics and interacting behavior of hydrogen with metal hexaboride surfaces using a combination of self-consistent density functional calculations and dynamics based on the Car-Parrinello method. Our results show that hydrogen is strongly attracted to localized exposed boron atoms and interactions with the terminal cations are strictly repulsive. From these, preliminary local adsorption energy calculations suggest that a single hydrogen molecule per surface unit-cell is possible (one ML). Strongest bonds are found when hydrogen is above the terminal boron atoms affected by reduced coordination and dangling bonds. This location serves to restore the hexaboride unit to a more stable structure by providing electronic density to the deficient surface octahedra. Additionally, trajectories from dynamic simulations provide insight into how hydrogen recombination reactions occur on the surface through dissociative adsorption and the method of travel prior to recombination to be along the octahedral face and bridging sites connecting separate unit cells on the surface. Upon adsorption, a single hydrogen atom becomes localized at the dangling bond site while the second interacts with the surface along a weaker potential energy path. Desorption at lower temperatures occurs when migrating atoms from separate adsorption sites intersect to form a new pair.

Dengue, chikungunya, and Zika virus infections imported to Paris between 2009 and 2016: Characteristics and correlation with outbreaks in the French overseas territories of Guadeloupe and Martinique.

BACKGROUND: Dengue virus (DENV), chikungunya virus (CHIKV), and Zika virus (ZIKV) infections are rapidly expanding across countries and are being diagnosed in returned travellers who represent epidemiological sentinels. The French Territories of America (FTA) such as Guadeloupe and Martinique see high levels of tourism and have experienced three consecutive outbreaks by these viruses in the last decade. OBJECTIVE: This study was performed to evaluate how ill returned travellers could have represented epidemiological sentinels for these three expanding arboviral diseases over eight consecutive years. The degree of correlation between the cases of ill returned travellers arriving at a French tertiary hospital in Paris and the three outbreaks that occurred in the FTA during the study period was estimated. METHODS: All consecutive ill returned travellers diagnosed at the hospital in Paris with imported DENV, CHIKV, or ZIKV infections from January 2009 to December 2016 were included. Epidemiological and clinical variables were evaluated. Data concerning the incidence of arboviruses in the FTA, as well as the temporal relationship between the occurrence of imported cases and outbreaks in the FTA, were analyzed. RESULTS: Overall, 320 cases of arboviral infection were reported: 216 DENV, 68 CHIKV, and 36 ZIKV. Most of the patients presented with fever and exanthema. One hundred and fifteen patients were exposed in Guadeloupe or Martinique, which were the at-risk destinations in 25% of patients with DENV, 59% of patients with CHIKV, and 58% of patients with ZIKV. The occurrence of cases diagnosed in returning travellers followed the same time pattern as the outbreaks in these areas. CONCLUSIONS: A temporal correlation was found between newly diagnosed imported cases of arboviruses and the three corresponding outbreaks that occurred in Martinique and Guadeloupe during 8 consecutive years. Thus, ill returned travellers act as epidemiological sentinels from the beginning up to the end of outbreaks occurring in touristic locations.