Care interruptions and mortality among adults in Europe and North America: a collaborative analysis of cohort studies.

OBJECTIVE: Interruptions in care of people with HIV (PWH) on antiretroviral therapy (ART) are associated with adverse outcomes, but most studies have relied on composite outcomes. We investigated whether mortality risk following care interruptions differed from mortality risk after first starting ART. DESIGN: Collaboration of 18 European and North American HIV observational cohort studies of adults with HIV starting ART between 2004-2019. METHODS: Care interruptions were defined as gaps in contact of ≥365 days, with a subsequent return to care (distinct from loss to follow-up), or ≥270 days and ≥545 days in sensitivity analyses. Follow-up time was allocated to no/pre-interruption or post-interruption follow-up groups. We used Cox regression to compare hazards of mortality between care interruption groups, adjusting for time-updated demographic and clinical characteristics and biomarkers upon ART initiation or re-initiation of care. RESULTS: Of 89197 PWH, 83.4% were male and median age at ART start was 39 years (interquartile range [IQR]: 31-48). 8654 PWH (9.7%) had ≥1 care interruption; 10913 episodes of follow-up following a care interruption were included. There were 6104 deaths in 536,334 person-years, a crude mortality rate of 11.4 (95%CI: 11.1-11.7) per 1000 person-years. The adjusted mortality hazard ratio (HR) for the post-interruption group was 1.72 (95%CI: 1.57-1.88) compared with the no/pre-interruption group. Results were robust to sensitivity analyses assuming ≥270-day (HR 1.49, 95%CI: 1.40-1.60) and ≥545-day (HR 1.67, 95%CI: 1.48-1.88) interruptions. CONCLUSIONS: Mortality was higher among PWH reinitiating care following an interruption, compared with when PWH initially start ART, indicating the importance of uninterrupted care.

Valorization of Cork Stoppers, Coffee-Grounds and Walnut Shells in the Development and Characterization of Pectin-Based Composite Films: Physical, Barrier, Antioxidant, Genotoxic, and Biodegradation Properties.

The development of sustainable materials from the valorization of waste is a good alternative to reducing the negative environmental impact of plastic packaging. The objectives of this study were to develop and characterize pectin-based composite films incorporated with cork or cork with either coffee grounds or walnut shells, as well as to test the films' genotoxicity, antioxidant properties, and biodegradation capacity in soil and seawater. The addition of cork, coffee grounds, or walnut shells modified the films' characteristics. The results showed that those films were thicker (0.487 ± 0.014 mm to 0.572 ± 0.014 mm), more opaque (around 100%), darker (L* = 25.30 ± 0.78 to 33.93 ± 0.84), and had a higher total phenolic content (3.17 ± 0.01 mg GA/g to 4.24 ± 0.02 mg GA/g). On the other hand, the films incorporated only with cork showed higher values of elongation at break (32.24 ± 1.88% to 36.30 ± 3.25%) but lower tensile strength (0.91 ± 0.19 MPa to 1.09 ± 0.08 MPa). All the films presented more heterogeneous and rougher microstructures than the pectin film. This study also revealed that the developed films do not contain DNA-reactive substances and that they are biodegradable in soil and seawater. These positive properties could subsequently make the developed films an interesting eco-friendly food packaging solution that contributes to the valorization of organic waste and by-products, thus promoting the circular economy and reducing the environmental impact of plastic materials.

Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites.

The vast amount of genome sequence data that is available, and that is predicted to drastically increase in the near future, can only be efficiently dealt with by building automated pipelines. Indeed, the Earth Biogenome Project will produce high-quality reference genome sequences for all 1.8 million named living eukaryote species, providing unprecedented insight into the evolution of genes and gene families, and thus on biological issues. Here, new modules for gene annotation, further BLAST search algorithms, further multiple sequence alignment methods, the adding of reference sequences, further tree rooting methods, the estimation of rates of synonymous and nonsynonymous substitutions, and the identification of positively selected amino acid sites, have been added to auto-phylo (version 2), a recently developed software to address biological problems using phylogenetic inferences. Additionally, we present auto-phylo-pipeliner, a graphical user interface application that further facilitates the creation and running of auto-phylo pipelines. Inferences on S-RNase specificity, are critical for both cross-based breeding and for the establishment of pollination requirements. Therefore, as a test case, we develop an auto-phylo pipeline to identify amino acid sites under positive selection, that are, in principle, those determining S-RNase specificity, starting from both non-annotated Prunus genomes and sequences available in public databases.

Incorporation of curcumin-loaded solid lipid nanoparticles into yogurt: Tribo-rheological properties and dynamic in vitro digestion.

The incorporation of nanostructures loaded with bioactive compounds into food matrices is a promising approach to develop new functional foods with improved nutritional, health profiles and good sensorial properties. The rheological and tribological properties of yogurt enriched with curcumin-loaded solid lipid nanoparticles (SLN) were evaluated. Also, the TCA solubility index, the bioaccessibility of curcumin and cell viability were assessed after dynamic in vitro digestion. The presence of SLN in yogurt did not affect its rheological properties; however, SLN addition increased the lubrication capability of yogurt. After in vitro digestion, yogurt with added SLN (yogurt_SLN) presented a lower TCA solubility index (22 %) than the plain yogurt (39 %). The bioaccessibility and stability of curcumin were statistically similar for yogurt_SLN (30 % and 42 %, respectively) and SLN alone (20 % and 39 %, respectively). Regarding cell viability results, the intestinal digesta filtrates of both controls (i.e., SLN alone and plain yogurt) did not affect significantly the cell viability, while the yogurt_SLN presented a possible cytotoxic effect at the concentrations tested. In general, the incorporation of SLN into yogurt seemed to promote the mouthfeel of the yogurt and did not adversely affect the bioaccessibility of curcumin. However, the interaction of SLN and yogurt matrix seemed to have a cytotoxic effect after in vitro digestion, which should be further investigated. Despite that, SLN has a high potential to be used as nanostructure in a functional food as a strategy to increase the bioactive compounds' bioaccessibility.

Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites.

SARS-CoV-2 amino acid variants that contribute to an increased transmissibility or to host immune system escape are likely to increase in frequency due to positive selection and may be identified using different methods, such as codeML, FEL, FUBAR, and MEME. Nevertheless, when using different methods, the results do not always agree. The sampling scheme used in different studies may partially explain the differences that are found, but there is also the possibility that some of the identified positively selected amino acid sites are false positives. This is especially important in the context of very large-scale projects where hundreds of analyses have been performed for the same protein-coding gene. To account for these issues, in this work, we have identified positively selected amino acid sites in SARS-CoV-2 and 15 other coronavirus species, using both codeML and FUBAR, and compared the location of such sites in the different species. Moreover, we also compared our results to those that are available in the COV2Var database and the frequency of the 10 most frequent variants and predicted protein location to identify those sites that are supported by multiple lines of evidence. Amino acid changes observed at these sites should always be of concern. The information reported for SARS-CoV-2 can also be used to identify variants of concern in other coronaviruses.

Quality indicators in prolonged hemodialysis with regional citrate anticoagulation with the genius system: retrospective cohort of critical patients with acute kidney injury.

BACKGROUND: Prolonged hemodialysis (HD) is performed from 6 to 12 h and can last up to 24 h. To prevent system clotting some studies suggest that Regional Citrate Anticoagulation (RCA) use reduces bleeding rates relative to systemic heparin. However, there may be difficulties in the patient's clinical management and completing the prescribed HD with Genius system using RCA. OBJECTIVE: To analyze safety Quality Indicators (IQs) and follow up on prolonged HD with 4% sodium citrate solution in a Genius® hybrid system. METHODS: This is a retrospective cohort conducted in an intensive care unit. RESULTS: 53 random sessions of prolonged HD with 4% sodium citrate solution of critically ill patients with AKI assessed. Evaluated safety indicators were dysnatremia and metabolic alkalosis, observed in 15% and 9.4% of the sessions, respectively. Indicators of effectiveness were system clotting which occurred in 17.3%, and the minimum completion of the prescribed HD time, which was 75.5%. CONCLUSION: The assessment of the indicators showed that the use of RCA with a 4% sodium citrate solution in prolonged HD with the Genius system in critically ill patients with AKI can be performed in a simple, safe, and effective way.

Incidence and Determinants of COVID-19 in Patients Seeking Treatment for Substance Use Disorder: A Patient-Based Linkage Study.

INTRODUCTION: People with substance use disorder (SUD) may be at increased risk of COVID-19 infection. However, there is little evidence regarding the incidence of and determinants associated with infection in this group. The aims of the study were to determine the cumulative incidence of COVID-19 among people who sought treatment for heroin, cocaine, cannabis, and alcohol use disorder in Catalonia; to identify sociodemographic, substance, and clinical determinants associated with COVID-19 infection among SUD patients; and to compare the cumulative incidence of COVID-19 infection in the population with SUD with that of the general population. METHODS: A patient-based retrospective observational study was conducted. The study population comprised people who sought treatment for heroin, cocaine, cannabis, or alcohol use disorder in Catalonia in 2018 and 2019. We analysed cumulative incidence of COVID-19 (confirmed by PCR test) from 25 February to 31 December 2020. Additionally, we used a log-link binomial generalized linear model for COVID-19 infection, using the substance as the exposition, adjusting for sociodemographic and clinical variables. RESULTS: Of the 23,092 individuals who sought treatment for SUD, 38.15% were considered suspected cases of COVID-19, and 2.60% (95% CI = 2.41-2.82) were confirmed positive for COVID-19 by PCR test during the study period. Those who sought treatment for alcohol use (cumulative incidence of COVID-19 of 3% [95% CI = 2.70-3.34]) had a higher risk ratio than, those who sought treatment for heroin use (cumulative incidence of 1.94% [95% CI = 1.47-2.56]). Being born outside of Spain, living in an institutionalized residence, having HIV, and being in a high morbidity group were associated with higher risk of COVID-19 infection. Meanwhile, the cumulative incidence of COVID-19 in the general population, according to public COVID-19 test data, was 3.86% (95% CI = 3.85-3.87). CONCLUSION: This study did not find higher cumulative incidence of COVID-19 infection among people with SUD in Catalonia in 2020, despite the clinical vulnerability of this population and their social disadvantage. However, differences were seen in the cumulative incidence of COVID-19 according to the substance for which treatment was sought. For example, those with alcohol dependence had a higher rate than those dependent on heroin. Further studies are needed to determine the factors contributing to these differences.

Syndemic conditions and quality of life in the PISCIS Cohort of people living with HIV in Catalonia and the Balearic Islands: a cross sectional study.

BACKGROUND: People living with HIV (PLWH) face structural and psychosocial factors that affect health-related quality of life (HRQoL). We aimed to evaluate how syndemic conditions affected HRQoL in PLWH. METHODS: A cross-sectional survey was conducted among 861 PLWH, to determine whether syndemic conditions (monthly income; sexual satisfaction; depressive symptoms; social role satisfaction; social isolation; cognitive function; nicotine dependence; perception of stigma) have an effect on HRQoL. A linear regression model and measures of Additive Interaction (AI) were used to determine the effects of syndemic conditions on HRQoL, controlling for other risk factors. RESULTS: Overall, the most frequently observed were stigma perception (56.9%), poor cognitive function (50.6%) and the perception of social isolation (51.6%). The presence of depressive symptoms was the risk factor most associated with worse Physical Health (PH) (B 3.93, 2.71-5.15) and Mental Health (MH) (B 5.08, 3.81-6.34) in linear regression model. Specifically, an interaction was observed between poor cognitive function and poor satisfaction with social role on worse PH and MH (AI 2.08, 0.14-4.02; AI 2.69, 0.15-5.22, respectively); and low income and perception of stigma (AI 2.98, 0.26-5.71), low income and perception of social isolation (AI 2.79, 0.27-5.32), and low income and poor satisfaction with social role (AI 3.45, 0.99-5.91) on MH. CONCLUSION: These findings provide evidence that syndemic factors impact HRQoL. HIV prevention programs should screen and address co-occurring health problems to improve patient-centered health care and outcomes.

The Josephin domain (JD) containing proteins are predicted to bind to the same interactors: Implications for spinocerebellar ataxia type 3 (SCA3) studies using Drosophila melanogaster mutants.

Spinocerebellar ataxia type 3, also known as Machado-Joseph disease (SCA3/ MJD), is the most frequent polyglutamine (polyQ) neurodegenerative disorder. It is caused by a pathogenic expansion of the polyQ tract, located at the C-terminal region of the protein encoded by the ATXN3 gene. This gene codes for a deubiquitinating enzyme (DUB) that belongs to a gene family, that in humans is composed by three more genes (ATXN3L, JOSD1, and JOSD2), that define two gene lineages (the ATXN3 and the Josephins). These proteins have in common the N-terminal catalytic domain (Josephin domain, JD), that in Josephins is the only domain present. In ATXN3 knock-out mouse and nematode models, the SCA3 neurodegeneration phenotype is not, however, reproduced, suggesting that in the genome of these species there are other genes that are able to compensate for the lack of ATXN3. Moreover, in mutant Drosophila melanogaster, where the only JD protein is coded by a Josephin-like gene, expression of the expanded human ATXN3 gene reproduces multiple aspects of the SCA3 phenotype, in contrast with the results of the expression of the wild type human form. In order to explain these findings, phylogenetic, as well as, protein-protein docking inferences are here performed. Here we show multiple losses of JD containing genes across the animal kingdom, suggesting partial functional redundancy of these genes. Accordingly, we predict that the JD is essential for binding with ataxin-3 and proteins of the Josephin lineages, and that D. melanogaster mutants are a good model of SCA3 despite the absence of a gene from the ATXN3 lineage. The molecular recognition regions of the ataxin-3 binding and those predicted for the Josephins are, however, different. We also report different binding regions between the two ataxin-3 forms (wild-type (wt) and expanded (exp)). The interactors that show an increase in the interaction strength with exp ataxin-3, are enriched in extrinsic components of mitochondrial outer membrane and endoplasmatic reticulum membrane. On the other hand, the group of interactors that show a decrease in the interaction strength with exp ataxin-3 is significantly enriched in extrinsic component of cytoplasm.

Chitosan Coating Functionalized with Flaxseed Oil and Green Tea Extract as a Bio-Based Solution for Beef Preservation.

Ecological and safe packaging solutions arise as pivotal points in the development of an integrated system for sustainable meat production. The aim of this study was to assess the effect of a combined chitosan (Ch) + green tea extract (GTE) + essential oil (thyme oil, TO; flaxseed oil, FO; or oregano oil, OO) coating on the safety and quality of vacuum-packaged beef during storage at 4 °C. An optimized bio-based coating formulation was selected (2% Ch + 2% GTE + 0.1% FO) to be applied to three fresh beef cuts (shoulder, Sh; knuckle, Kn; Striploin, St) based on its pH (5.8 ± 0.1), contact angle (22.3 ± 0.4°) and rheological parameters (viscosity = 0.05 Pa.s at shear rate > 20 s-1). Shelf-life analysis showed that the Ch-GTE-FO coating delayed lipid oxidation and reduced total viable counts (TVC) and Enterobacteriaceae growth compared with uncoated beef samples over five days. In addition, Ch-GTE-FO coating decreased total color changes of beef samples (e.g., ∆E* = 9.84 and 3.94, for non-coated and coated Kn samples, respectively) for up to five days. The original textural parameters (hardness, adhesiveness and springiness) of beef cuts were maintained during storage when Ch-GTE-FO coating was applied. Based on the physicochemical and microbial characterization results, the combination of the Ch-GTE-FO coating developed was effective in preserving the quality of fresh beef cuts during refrigerated storage along with vacuum packaging.

Mitigation of the Onset of Hosing in the Linear Regime through Plasma Frequency Detuning.

The hosing instability poses a feasibility risk for plasma-based accelerator concepts. We show that the growth rate for beam hosing in the linear regime (which is relevant for concepts that use a long driver) is a function of the centroid perturbation wavelength. We demonstrate how this property can be used to damp centroid oscillations by detuning the plasma response sufficiently early in the development of the instability. We also develop a new theoretical model for the early evolution of hosing. These findings have implications for the general control of an instability's growth rate.

Who is lost to follow-up in HIV care? Assessment of care retention over time and the impact of COVID-19. Longitudinal analysis of the PISCIS cohort.

INTRODUCTION: People living with HIV who are lost to follow-up have a greater risk of health deterioration, mortality, and community transmission. OBJECTIVE: Our aim was to analyse both how rates of loss to follow-up (LTFU) changed between 2006 and 2020 and how the COVID-19 pandemic affected these rates in the PISCIS cohort study of Catalonia and the Balearic Islands. METHODS: We analysed socio-demographic and clinical characteristics of LTFU yearly and with adjusted odds ratios to assess the impact of these determinants on LTFU in 2020 (the year of COVID-19). We used latent class analysis to categorize classes of LTFU based on their socio-demographic and clinical characteristics at each year. RESULTS: In total, 16.7% of the cohort were lost to follow-up at any time in the 15 years (n = 19 417). Of people living with HIV who were receiving follow-up, 81.5% were male and 19.5% were female; of those who were lost to follow-up, 79.6% and 20.4% were male and female, respectively (p < 0.001). Although rates of LTFU increased during COVID-19 (1.11% vs. 0.86%, p = 0.024), socio-demographic and clinical factors were similar. Eight classes of people living with HIV who were lost to follow-up were identified: six for men and two for women. Classes of men (n = 3) differed in terms of their country of birth, viral load (VL), and antiretroviral therapy (ART); classes of people who inject drugs (n = 2) differed in terms of VL, AIDS diagnosis, and ART. Changes in rates of LTFU included higher CD4 cell count and undetectable VL. CONCLUSIONS: The socio-demographic and clinical characteristics of people living with HIV changed over time. Although the circumstances of the COVID-19 pandemic increased the rates of LTFU, the characteristics of these people were similar. Epidemiological trends among people who were lost to follow-up can be used to prevent new losses of care and to reduce barriers to achieve Joint United Nations Programme on HIV/AIDS 95-95-95 targets.

On the identification of potential novel therapeutic targets for spinocerebellar ataxia type 1 (SCA1) neurodegenerative disease using EvoPPI3.

EvoPPI (http://evoppi.i3s.up.pt), a meta-database for protein-protein interactions (PPI), has been upgraded (EvoPPI3) to accept new types of data, namely, PPI from patients, cell lines, and animal models, as well as data from gene modifier experiments, for nine neurodegenerative polyglutamine (polyQ) diseases caused by an abnormal expansion of the polyQ tract. The integration of the different types of data allows users to easily compare them, as here shown for Ataxin-1, the polyQ protein involved in spinocerebellar ataxia type 1 (SCA1) disease. Using all available datasets and the data here obtained for Drosophila melanogaster wt and exp Ataxin-1 mutants (also available at EvoPPI3), we show that, in humans, the Ataxin-1 network is much larger than previously thought (380 interactors), with at least 909 interactors. The functional profiling of the newly identified interactors is similar to the ones already reported in the main PPI databases. 16 out of 909 interactors are putative novel SCA1 therapeutic targets, and all but one are already being studied in the context of this disease. The 16 proteins are mainly involved in binding and catalytic activity (mainly kinase activity), functional features already thought to be important in the SCA1 disease.

Community pharmacists' roles, attitudes and knowledge regarding provision of screening and brief intervention activities for alcohol use in Catalonia.

INTRODUCTION: Community pharmacists (CP) are among the health professionals with closest contact to the general population. They play a key role in delivering public health programs. The aim of this study was to analyse the attitudes, knowledge, preparedness and ability to screen and advise on alcohol of CP in Catalonia and their perceptions about the provision of alcohol screening and brief interventions (SBI) in community pharmacies. METHODS: This is an observational, cross-sectional study. An online survey on attitudes, knowledge and behaviours was sent to all registered CP in Catalonia, and bivariate and multivariate statistical analyses were conducted. RESULTS: The response rate was 7.96% (639/8027), more than two-thirds of respondents were 41 years of age or older and 79.9% were female. Results showed that CP readiness to offer advice on alcohol problems was higher than their preparedness to screen (37.5% vs. 31.8%, respectively). They also showed that having received 1 h or more of training on alcohol and drug-related health promotion and prevention during the last 5 years increased CP perception of role security and therapeutic commitment related to alcohol. DISCUSSION AND CONCLUSION: This study showed that involving CP in the provision of alcohol SBIs may be feasible in Catalonia. Furthermore, this and previous research show an association between CP training in alcohol or drugs and preparedness to screen and advise on alcohol use. Consequently, promoting alcohol-related training programs to enhance CP skills is recommended to support successful implementation of alcohol SBI in community pharmacy settings.

Determinants of Depressive Symptoms in People Living with HIV: Findings from a Population-Based Study with a Gender Perspective.

Depressive symptoms are common among people living with HIV (PLWH). The aim of this study was to identify the determinants of depressive symptoms in PLWH in Spain. A total of 1060 PLWH participated in this cross-sectional study and completed the Patient Health Questionnaire-9. The odds ratios for the presence of depressive symptoms were analyzed in a multivariable logistic regression model, including sociodemographic data, comorbidities, health-related behaviors, and social-environment-related variables. We found an overall prevalence of depressive symptoms of 21.42%; by subgroup, namely men, women, and transgender persons, prevalence was 18.13%, 32.81%, and 37.14%, respectively. Moreover, social isolation (OR = 1.05 [CI, 1.02-1.08]) and poor physical and mental quality of life (OR = 1.06 [CI, 1.02-1.09] and OR = 1.13 [CI, 1.09-1.17], respectively) were associated with depressive symptoms. As protective factors, we identified serodisclosure to more people (vs. none; OR = 0.39 [CI, 0.17-0.87]), satisfaction with social roles (OR = 0.86 [CI, 0.79-0.94]), better cognitive function (OR = 0.92 [CI, 0.89-0.95]), and sexualized drug use once in a lifetime (OR = 0.52 [CI, 0.29-0.93]). This study showed a high prevalence of depressive symptoms in PLWH, especially among women and transgender people. The association between psychosocial variables and depressive symptoms highlights the multidimensionality of the problem and identifies areas for intervention. This study found that the management of mental health issues is an area that needs to be improved and tailored to specific groups, with the aim of enhancing the well-being of PLWH.

Postharvest Quality Improvement of Tomato (Solanum lycopersicum L.) Fruit Using a Nanomultilayer Coating Containing Aloe vera.

The effectiveness of an alginate/chitosan nanomultilayer coating without (NM) and with Aloe vera liquid fraction (NM+Av) was evaluated on the postharvest quality of tomato fruit at 20 °C and 85% relative humidity (RH) to simulate direct consumption. Both nanomultilayer coatings had comparable effects on firmness and pH values. However, the NM+Av coating significantly reduced weight loss (4.5 ± 0.2%) and molds and yeasts (3.5-4.0 log CFU g-1) compared to uncoated fruit (16.2 ± 1.2% and 8.0 ± 0.0 log CFU g-1, respectively). It notably lowered O2 consumption by 70% and a 52% decrease in CO2 production, inhibiting ethylene synthesis. Visual evaluation confirmed NM+Av's efficacy in preserving the postharvest quality of tomato. The preservation of color, indicated by the Minolta color (a*/b*) values, demonstrated NM+Av's ability to keep the light red stage compared to uncoated fruit. The favorable effects of NM+Av coating on enhancing postharvest quality indicates it as a potential alternative for large-scale tomato fruit preservation.

Advances in Novel Animal Vitamin C Biosynthesis Pathways and the Role of Prokaryote-Based Inferences to Understand Their Origin.

Vitamin C (VC) is an essential nutrient required for the optimal function and development of many organisms. VC has been studied for many decades, and still today, the characterization of its functions is a dynamic scientific field, mainly because of its commercial and therapeutic applications. In this review, we discuss, in a comparative way, the increasing evidence for alternative VC synthesis pathways in insects and nematodes, and the potential of myo-inositol as a possible substrate for this metabolic process in metazoans. Methodological approaches that may be useful for the future characterization of the VC synthesis pathways of Caenorhabditis elegans and Drosophila melanogaster are here discussed. We also summarize the current distribution of the eukaryote aldonolactone oxidoreductases gene lineages, while highlighting the added value of studies on prokaryote species that are likely able to synthesize VC for both the characterization of novel VC synthesis pathways and inferences on the complex evolutionary history of such pathways. Such work may help improve the industrial production of VC.

Predictive Models of within- and between-Species SARS-CoV-2 Transmissibility.

Viruses from the Coronaviridae family have been reported to infect a large range of hosts, including humans. The latest human-infecting coronavirus, SARS-CoV-2, turned into a pandemic and subtypes with different transmissibility have appeared since then. The SARS-CoV-2 Spike (S) protein interacts with the angiotensin-converting enzyme 2 (ACE2) host receptor, and thus, in silico models, based on the structural features of the SARS-CoV-2 S protein-ACE2 receptor complex, as well as ACE2 amino acid patterns, may be used to predict the within- and between-species transmissibility of SARS-CoV-2 subtypes. Here, it is shown that at the beginning of the pandemic, the SARS-CoV-2 S protein was, as expected for a virus that just jumped the species barrier, ill-adapted to the human ACE2 receptor, and that the replacement of one SARS-CoV-2 variant by another is partially due to a better fitting of the S protein-human ACE2 complex. Moreover, it is shown that mutations that are predicted to lead to a better fit have increased in the population due to positive selection. It is also shown that the number of ACE2-interfacing residues is positively correlated with the transmissibility rate of SARS-CoV-2 variants. Finally, it is shown that the number of species that are susceptible to infection by SARS-CoV-2, and that could be a reservoir for this virus, is likely higher than previously thought.

The evolution of vitamin C biosynthesis and transport in animals.

BACKGROUND: Vitamin C (VC) is an indispensable antioxidant and co-factor for optimal function and development of eukaryotic cells. In animals, VC can be synthesized by the organism, acquired through the diet, or both. In the single VC synthesis pathway described in animals, the penultimate step is catalysed by Regucalcin, and the last step by L-gulonolactone oxidase (GULO). The GULO gene has been implicated in VC synthesis only, while Regucalcin has been shown to have multiple functions in mammals. RESULTS: Both GULO and Regucalcin can be found in non-bilaterian, protostome and deuterostome species. Regucalcin, as here shown, is involved in multiple functions such as VC synthesis, calcium homeostasis, and the oxidative stress response in both Deuterostomes and Protostomes, and in insects in receptor-mediated uptake of hexamerin storage proteins from haemolymph. In Insecta and Nematoda, however, there is no GULO gene, and in the latter no Regucalcin gene, but species from these lineages are still able to synthesize VC, implying at least one novel synthesis pathway. In vertebrates, SVCT1, a gene that belongs to a family with up to five members, as here shown, is the only gene involved in the uptake of VC in the gut. This specificity is likely the result of a subfunctionalization event that happened at the base of the Craniata subphylum. SVCT-like genes present in non-Vertebrate animals are likely involved in both VC and nucleobase transport. It is also shown that in lineages where GULO has been lost, SVCT1 is now an essential gene, while in lineages where SVCT1 gene has been lost, GULO is now an essential gene. CONCLUSIONS: The simultaneous study, for the first time, of GULO, Regucalcin and SVCTs evolution provides a clear picture of VC synthesis/acquisition and reveals very different selective pressures in different animal taxonomic groups.