Virological characteristics of the SARS-CoV-2 Omicron EG.5.1 variant.

In middle to late 2023, a sublineage of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB, EG.5.1 (a progeny of XBB.1.9.2), is spreading rapidly around the world. We performed multiscale investigations, including phylogenetic analysis, epidemic dynamics modeling, infection experiments using pseudoviruses, clinical isolates, and recombinant viruses in cell cultures and experimental animals, and the use of human sera and antiviral compounds, to reveal the virological features of the newly emerging EG.5.1 variant. Our phylogenetic analysis and epidemic dynamics modeling suggested that two hallmark substitutions of EG.5.1, S:F456L and ORF9b:I5T are critical to its increased viral fitness. Experimental investigations on the growth kinetics, sensitivity to clinically available antivirals, fusogenicity, and pathogenicity of EG.5.1 suggested that the virological features of EG.5.1 are comparable to those of XBB.1.5. However, cryo-electron microscopy revealed structural differences between the spike proteins of EG.5.1 and XBB.1.5. We further assessed the impact of ORF9b:I5T on viral features, but it was almost negligible in our experimental setup. Our multiscale investigations provide knowledge for understanding the evolutionary traits of newly emerging pathogenic viruses, including EG.5.1, in the human population.

Concurrent D-loop cleavage by Mus81 and Yen1 yields half-crossover precursors.

Homologous recombination involves the formation of branched DNA molecules that may interfere with chromosome segregation. To resolve these persistent joint molecules, cells rely on the activation of structure-selective endonucleases (SSEs) during the late stages of the cell cycle. However, the premature activation of SSEs compromises genome integrity, due to untimely processing of replication and/or recombination intermediates. Here, we used a biochemical approach to show that the budding yeast SSEs Mus81 and Yen1 possess the ability to cleave the central recombination intermediate known as the displacement loop or D-loop. Moreover, we demonstrate that, consistently with previous genetic data, the simultaneous action of Mus81 and Yen1, followed by ligation, is sufficient to recreate the formation of a half-crossover precursor in vitro. Our results provide not only mechanistic explanation for the formation of a half-crossover, but also highlight the critical importance for precise regulation of these SSEs to prevent chromosomal rearrangements.

Effect of early vs. delayed extubation on functional outcome among patients with acute ischemic stroke treated with endovascular thrombectomy under general anesthesia: the prospective, randomized controlled EDESTROKE trial study protocol.

BACKGROUND: Recent meta-analyses and randomized studies have shown that among patients with acute ischemic stroke undergoing endovascular thrombectomy, general anesthesia with mechanical ventilation is associated with better functional status compared to local anesthesia and sedation, and they recommend its use. But once the procedure is completed, when is the optimal moment for extubation? Currently, there are no guidelines recommending the optimal moment for extubation. Prolonged mechanical ventilation time could potentially be linked to increased complications such as pneumonia or disturbances in cerebral blood flow due to the vasodilatation produced by most anesthetic drugs. However, premature extubation in a patient who has suffered a stroke could led to complications such as agitation, disorientation, abolished reflexes, sudden fluctuations in blood pressure, alterations in cerebral blood flow, respiratory distress, bronchial aspiration, and the need for reintubation. We therefore designed a randomized study hypothesizing that early compared with delayed extubation is associated with a better functional outcome 3 months after endovascular thrombectomy treatment under general anesthesia for acute ischemic stroke. METHODS: This investigator-initiated, single-center, prospective, parallel, evaluated blinded, superiority, randomized controlled trial will include 178 patients with a proximal occlusion of the anterior circulation treated with successful endovascular thrombectomy (TICI 2b-3) under general anesthesia. Patients will be randomly allocated to receive early (< 6 h) or delayed (6-12 h) extubation after the procedure. The primary outcome measure is functional independence (mRS of 0-2) at 90 days, measured with the modified Rankin Score (mRS), ranging from 0 (no symptoms) to 6 (death). DISCUSSION: This will be the first trial to compare the effect of mechanical ventilation duration (early vs delayed extubation) after satisfactory endovascular thrombectomy for acute ischemic stroke under general anesthesia. TRIAL REGISTRATION: The study protocol was approved April 11, 2023, by the by the Santiago-Lugo Research Ethics Committee (CEI-SL), number 2023/127, and was registered into the clinicaltrials.gov clinical trials registry with No. NCT05847309. Informed consent is required. Participant recruitment begins on April 18, 2023. The results will be submitted for publication in a peer-reviewed journal and presented at one or more scientific conferences.

Alternative translation initiation by ribosomal leaky scanning produces multiple isoforms of the Pif1 helicase.

In budding yeast, the integrity of both the nuclear and mitochondrial genomes relies on dual-targeted isoforms of the conserved Pif1 helicase, generated by alternative translation initiation (ATI) of PIF1 mRNA from two consecutive AUG codons flanking a mitochondrial targeting signal. Here, we demonstrate that ribosomal leaky scanning is the specific ATI mechanism that produces not only these, but also novel, previously uncharacterized Pif1 isoforms. Both in-frame, downstream AUGs as well as near-cognate start codons contribute to the generation of these alternative isoforms. This has crucial implications for the rational design of genuine separation-of-function alleles and provides an explanation for the suboptimal behaviour of the widely employed mitochondrial- (pif1-m1) and nuclear-deficient (pif1-m2) alleles, with mutations in the first or second AUG codon, respectively. We have taken advantage of this refined model to develop improved versions of these alleles, which will serve as valuable tools to elucidate novel functions of this helicase and to disambiguate previously described genetic interactions of PIF1 in the context of nuclear and mitochondrial genome stability.

The impact of Benevolent Childhood Experiences on adult Flourishing: the mediating role of Light Triad traits.

The literature has well documented the relationship between Adverse Childhood Experiences, personality traits, and well-being. However, less is known about how Benevolent Childhood Experiences (BCEs) relate to "light" personality traits and Flourishing. The study analyzed the effects of BCEs on Flourishing, considering the mediator role of Light Triad traits (Kantianism, Humanism, and Faith in Humanity). The study used a quantitative methodology with a non-experimental, cross-sectional design; 410 Honduran adults responded to the survey, including questions regarding Light Triad personality traits, Flourishing, and BCEs. On average, respondents reported 7.34 BCEs. The number of reported BCEs did not vary significantly between men and women. However, specific BCEs were categorically associated with subjects' sex. A higher proportion of men reported having at least one teacher who cared about the respondent, having opportunities to have a good time, and liking/feeling comfortable with oneself. Flourishing was significantly higher for participants who reported the presence of BCEs. The largest effect size was achieved for the difference in Flourishing scores between those who reported liking school as a child and those who disliked it. The number of Benevolent Childhood Experiences had a significant total and direct effect on Flourishing scores. Significant indirect effects were also identified. Faith in Humanity and Humanism, not Kantianism, mediated the relationship between BCEs and Flourishing. BCEs significantly explained all Light Triad traits. In conclusion, BCEs have significant direct and indirect effects on adult Flourishing; Faith in Humanity and Humanism mediate this relationship.

Exploring suicide ideation in university students: sleep quality, social media, self-esteem, and barriers to seeking psychological help.

The purpose of the current study is to analyze how variations in suicidal ideation scores can relate to sleep quality, social media consumption, self-esteem, and perceived barriers to seeking psychological help in a sample of university students in Honduras. A quantitative cross-sectional design was used. Self-reported data was collected from a non-random sample of 910 university students in Honduras; their average age was 24.03 years (SD=6.05). Most respondents were women (67%) with men accounting for 33% of the sample. Measurements included item 9 of the Patient Health Questionnaire-9, the Single-Item Sleep Quality Scale, Rosenberg's Self-Esteem Scale, Barriers to Seeking Psychological Help Scale for College Students, and a self-reported questionnaire on social media. In response to the query, "Over the past two weeks, how frequently have you experienced thoughts that you would be better off dead or of hurting yourself?" 54% (n=495) of participants indicated "not at all" 18% (n=168) reported "several days" 14% (n=129) responded "more than half of the days" and 13% (n=118) stated "nearly every day". The results from the ordinal logistic regression model indicate that sleep quality and self-esteem serve as protective factors associated with decreased suicide ideation. At the same time, a higher number of social media platforms used per week and perceived barriers to seeking psychological help increase suicide ideation. Altogether, these variables explained 19% of the variance in suicidal ideation scores. Suicidal ideation is highly prevalent among the sampled university students.

The impact of adverse childhood experiences on mental health, sexual risk behaviors, and alcohol consumption in adulthood.

The purpose of the study was to determine how Adverse Childhood Experiences (ACE) relate to adulthood flourishing, symptoms of depression, anxiety, somatization, self-reported health, sexual risk behaviors, and alcohol consumption. A quantitative cross-sectional methodology was used. A total of 452 adults completed the survey. The most prevalent ACE include physical abuse (44.69%), separation/divorce of parents (41.81%), living with someone with alcohol problems (39.38%), and being sworn, insulted, or humiliated by adults at home (35.62%). Almost one out of every four respondents (24.34%) reported being touched by an adult, 17.92% reported that an adult tried to manipulate the respondent into touching them, and 8.19% were forced to have sexual intercourse. Results indicate that women reported a higher number of ACE than men. The number of ACE is inversely related to flourishing and self-reported health; while being positively associated with participant's scores in depression, anxiety, somatization, sexual risk behaviors, and alcohol use. The regression model, including the eleven ACE and respondents' sex and age, achieved medium effect sizes for somatization, depression, and anxiety symptoms and small effect sizes for flourishing, self-reported health, sexual risk behaviors, and alcohol consumption. Specific ACE have a particularly significant negative impact on mental health outcomes: forced intercourse, witnessing familial violence, verbal humiliation, and living with individuals struggling with mental health issues and drug consumption or who were incarcerated. In conclusion, the study highlights the alarming prevalence of ACE among the Honduran population and their significant negative impact on mental health outcomes during adulthood.

Neddylation orchestrates the complex transcriptional and posttranscriptional program that drives Schwann cell myelination.

Myelination is essential for neuronal function and health. In peripheral nerves, >100 causative mutations have been identified that cause Charcot-Marie-Tooth disease, a disorder that can affect myelin sheaths. Among these, a number of mutations are related to essential targets of the posttranslational modification neddylation, although how these lead to myelin defects is unclear. Here, we demonstrate that inhibiting neddylation leads to a notable absence of peripheral myelin and axonal loss both in developing and regenerating mouse nerves. Our data indicate that neddylation exerts a global influence on the complex transcriptional and posttranscriptional program by simultaneously regulating the expression and function of multiple essential myelination signals, including the master transcription factor EGR2 and the negative regulators c-Jun and Sox2, and inducing global secondary changes in downstream pathways, including the mTOR and YAP/TAZ signaling pathways. This places neddylation as a critical regulator of myelination and delineates the potential pathogenic mechanisms involved in CMT mutations related to neddylation.

Social media addiction relationship with academic engagement in university students: The mediator role of self-esteem, depression, and anxiety.

This research analyzed how addiction to social media relates to academic engagement in university students, considering the mediating role of self-esteem, symptoms of depression, and anxiety. A quantitative methodology was used with a non-experimental-relational design. A set of questionnaires was applied to a non-probabilistic sample of 412 students enrolled at the National Autonomous University of Honduras. On average, participants use 4.83 different social media platforms at least once a week. Instagram and TikTok users report significantly higher levels of social media addiction, symptoms of depression, and anxiety compared to non-users. Directly, social media addiction does not significantly influence academic engagement scores. However, there are significant indirect inverse effects on academic engagement. Symptoms of depression and self-esteem mediate these effects. Social media addiction increases symptoms of depression, which in turn decreases academic engagement scores. Social media addiction decreases self-esteem, which serves as a variable that significantly increases academic engagement. Overall, findings suggest that social media addiction has a total inverse effect on academic engagement; symptoms of depression and self-esteem mediate this relationship. The implications of these findings are discussed.

Virological characteristics of the SARS-CoV-2 BA.2.86 variant.

In late 2023, several SARS-CoV-2 XBB descendants, notably EG.5.1, were predominant worldwide. However, a distinct SARS-CoV-2 lineage, the BA.2.86 variant, also emerged. BA.2.86 is phylogenetically distinct from other Omicron sublineages, accumulating over 30 amino acid mutations in its spike protein. Here, we examined the virological characteristics of the BA.2.86 variant. Our epidemic dynamics modeling suggested that the relative reproduction number of BA.2.86 is significantly higher than that of EG.5.1. Additionally, four clinically available antivirals were effective against BA.2.86. Although the fusogenicity of BA.2.86 spike is similar to that of the parental BA.2 spike, the intrinsic pathogenicity of BA.2.86 in hamsters was significantly lower than that of BA.2. Since the growth kinetics of BA.2.86 are significantly lower than those of BA.2 both in vitro and in vivo, the attenuated pathogenicity of BA.2.86 is likely due to its decreased replication capacity. These findings uncover the features of BA.2.86, providing insights for control and treatment.

SUMOylation modulates eIF5A activities in both yeast and pancreatic ductal adenocarcinoma cells.

BACKGROUND: The eukaryotic translation initiation protein eIF5A is a highly conserved and essential factor that plays a critical role in different physiological and pathological processes including stress response and cancer. Different proteomic studies suggest that eIF5A may be a small ubiquitin-like modifier (SUMO) substrate, but whether eIF5A is indeed SUMOylated and how relevant is this modification for eIF5A activities are still unknown. METHODS: SUMOylation was evaluated using in vitro SUMOylation assays, Histidine-tagged proteins purification from His6-SUMO2 transfected cells, and isolation of endogenously SUMOylated proteins using SUMO-binding entities (SUBES). Mutants were engineered by site-directed mutagenesis. Protein stability was measured by a cycloheximide chase assay. Protein localization was determined using immunofluorescence and cellular fractionation assays. The ability of eIF5A1 constructs to complement the growth of Saccharomyces cerevisiae strains harboring thermosensitive mutants of a yeast EIF5A homolog gene (HYP2) was analyzed. The polysome profile and the formation of stress granules in cells expressing Pab1-GFP (a stress granule marker) by immunofluorescence were determined in yeast cells subjected to heat shock. Cell growth and migration of pancreatic ductal adenocarcinoma PANC-1 cells overexpressing different eIF5A1 constructs were evaluated using crystal violet staining and transwell inserts, respectively. Statistical analysis was performed with GraphPad Software, using unpaired Student's t-test, or one-way or two-way analysis of variance (ANOVA). RESULTS: We found that eIF5A is modified by SUMO2 in vitro, in transfected cells and under endogenous conditions, revealing its physiological relevance. We identified several SUMO sites in eIF5A and found that SUMOylation modulates both the stability and the localization of eIF5A in mammalian cells. Interestingly, the SUMOylation of eIF5A responds to specific stresses, indicating that it is a regulated process. SUMOylation of eIF5A is conserved in yeast, the eIF5A SUMOylation mutants are unable to completely suppress the defects of HYP2 mutants, and SUMOylation of eIF5A is important for both stress granules formation and disassembly of polysomes induced by heat-shock. Moreover, mutation of the SUMOylation sites in eIF5A abolishes its promigratory and proproliferative activities in PANC-1 cells. CONCLUSIONS: SUMO2 conjugation to eIF5A is a stress-induced response implicated in the adaptation of yeast cells to heat-shock stress and required to promote the growth and migration of pancreatic ductal adenocarcinoma cells.

The experiences of family members of persons with intellectual disabilities who used residential care homes during the COVID-19 pandemic.

BACKGROUND: The global COVID-19 pandemic has shown the vulnerability of some population groups, including persons with intellectual and developmental disabilities (IDD). AIM: The present paper will provide more clarity and understanding of the experiences of family members of persons with IDD housed in residential facilities in Catalonia within the period of maximum restrictions during the COVID-19 pandemic. METHODS AND PROCEDURES: Semi-structured interviews were conducted using an interpretive phenomenological qualitative approach. Study participants consisted of 14 relatives of IDD individuals who were institutionalized in residence facilities or homes. The guiding questions emerged from group discussions with relatives of those with IDD who did not participate in the subsequent interviews. Drawing from this group, the factors that were identified to have had the greatest impact on their lives were later used to guide the interviews. Data collection was carried out in face-to-face individual interviews that were recorded together with the observations of two researchers between February and October 2022. RESULTS: Our analysis identified 4 main themes that developed into additional factors: the decision to stay at home or in the residence, fear, illness, and protocol. Individuals with IDD lost their daily routines, suffered from social isolation, and did not understand the situation. CONCLUSION: The results of this study allow for a better understanding of the experiences of families of persons with IDD in residential centres during the lockdown by identifying their needs and how to better support them in the future. OUTCOMES AND RESULTS: Knowledge and understanding of these events should allow for better management of similar situations in the future.

This study contributes to a growing body of research that examines the experiences of IDD individuals and their families during the early months of the COVID-19 pandemic. A qualitative phenomenological interpretative approach was used following the recommendations of qualitative research practices in health care. Our findings reveal that relatives of persons with IDD who lived in residential care homes felt that the residents were not adequately cared for by the staff, who applied measures for containment and contagion prevention that were disproportionate, resulting in their needs not being considered; these recommended measures had been developed for elderly care homes. Individuals with IDD lost their daily routines, suffered from social isolation, and did not understand the situation. The present findings show that residential care homes for persons with IDD require specific action protocols in crisis situations that are adapted to the needs and characteristics of each centre,thus adopting a model of care based on human rights.

Age and treatment on the day of embryo transfer in recipient mares affect likelihood of pregnancy.

OBJECTIVE: This retrospective evaluation of data from a large commercial embryo transfer facility aimed to determine the extent to which age and treatment on the day of embryo transfer in recipient mares influence the likelihood of pregnancy. MATERIAL AND METHODS: Embryo recovery was carried out on days 8-10 post-ovulation using transcervical uterine flushing. Recipient mares grouped according to their age were treated once on the day of embryo transfer (Day 3-8 post ovulation) and were assigned randomly to 1 of 3 groups: Mares in Group A (n=101) received antispasmodic, antimicrobial, and anti-inflammatory drugs. Mares in Group B (n=100) received gentamicin and flunixin meglumine. Group C (control) (n=103) did not receive any treatment. Detomidine (0.008 mg/kg bwt i.v.) was administered to all recipients before transfer of the embryo. The influence of treatment and recipient´s age was calculated using binary logistic regression. RESULTS: Day 16 post-transfer pregnancy rates were highest in Group A (74/101, 73.3a%), when compared to Group B (60/100, 60%), and Group C (57/103, 55.3b%) (a vs b, p<0.05). Pregnancy loss rates at D45 were not different between groups, A (8/74, 10.8%), B (5/60, 8.3%), and C (6/57, 10.5%), respectively (p>0.05). Pregnancy losses were increased in recipient mares 17-22 years (33.3a%) compared to younger recipient mares (2-6 years 7b%, 7-11 years 10%, 12-16 years 8b%) (a:b p<0.05). The regression model showed that the predicted probability for pregnancy after embryo transfer decreased as the age of the recipient mare increased for treated recipients in Group A (p=0.012), there was no effect of treatment and recipient´s age in Group B, and a decreased likelihood of pregnancy in recipients of advanced age (≥12 years of age) in untreated recipients (group C). CONCLUSIONS AND CLINICAL RELEVANCE: Likelihood of pregnancy increased following single administration of antispasmodic, antimicrobial, and anti-inflammatory drugs at the time of embryo transfer in recipients 2-12 years of age. Likelihood of pregnancy in recipients decreased in recipients≥12 years of age. These results, obtained under the conditions of a large commercial embryo transfer program, offer an opportunity to improve pregnancy rates in recipient mares≤12 years of age.

Psychometric properties of the Spanish version of the Flourishing Scale in the Honduran population.

Studying Flourishing is important to understand wellbeing. The current study aimed to determine the psychometric properties of the Spanish version of the Flourishing Scale (FS) in the Honduran population. The primary sample consisted of 422 residents of the Central District of Honduras; this included 275 (65.17%) women and 147 men (34.83%). Their average age was 28.18 years (SD = 10.58). Findings from the Exploratory Factor Analysis and Confirmatory Factor Analysis support a unidimensional factor structure. The FS achieved a high internal consistency with McDonald's ω = 0.89, 95% CI [0.86, 0.91]. The average inter-item correlation was 0.48, 95% CI [0.43, 0.53]. Using Student's t-test for paired samples, results indicate that none of the FS items varied significantly between baseline and post-test. Additionally, Spearman's rho was used to correlate test-retest scores; this yielded a statistically significant correlation coefficient of 0.66. The Flourishing Scale had adequate convergent validity with the Subjective Happiness Scale (r = 0.70) and the PANAS-Positive Affect Subscale (r = 0.70) (p < 0.001). In contrast, it correlates inversely with the PANAS-Negative Affect Subscale (r = -0.34) and the PHQ-9 (r = -0.51). Strict measurement invariance for sex was supported. The results indicate that the Flourishing Scale has robust psychometric properties for the Honduran population. Practical implications for public policy are discussed.

Análisis de las complicaciones del acceso vascular en hemodiálisis. Una revisión sistemática / Analysis of complications of vascular access in hemodialysis: A systematic review

Introducción:El acceso vascular sigue siendo uno de los retos más importantes en todas las unidades de diálisis, por todas las complicaciones derivadas de su uso y el gran impacto en la mor-bimortalidad del enfermo renal. Los tres tipos de acceso vascu-lar más utilizados son la fístula arteriovenosa nativa, el injerto o fístula arteriovenosa protésica y el catéter venoso central. Objetivo: Analizar y evaluar la situación actual y la incidencia de las complicaciones relacionadas con los diferentes accesos vasculares en hemodiálisis. Metodología: Se realizó una revisión sistemática en las bases de datos PubMed, CINAHL, SCOPUS y SciELO. Se incluyeron todos los artículos originales de menos de 5 años de antigüe-dad en los que uno de sus objetivos fuera analizar la preva-lencia o incidencia de las complicaciones de cualquier acceso vascular en hemodiálisis en población adulta. Resultados: El número de artículos para el análisis fueron 15. De ellos, 14 fueron estudios observacionales y uno, un ensa-yo clínico multicéntrico. Se analizaron datos demográficos de los pacientes, la prevalencia de complicaciones entre todos los accesos vasculares y la incidencia de complicaciones se-gún fístula nativa/protésica/catéter venoso central.Conclusiones: La fístula arteriovenosa nativa es el acceso vas-cular de elección ya que tiene tasas de complicaciones muy bajas. De entre ellas, la trombosis, es la complicación con más incidencia. El uso de catéter venoso central todavía es muy habitual, pese a ser el acceso vascular que presenta mayores tasas de complicaciones como las infecciones y la bacteriemia, produciéndose en un 10%-17% de los pacientes portadores.(AU)

Introduction: Vascular access remains one of the most important challenges in all dialysis units due to the complications associated with its use and its significant impact on the morbidity and mortality of renal patients. The three most used types of vascular access are native arteriovenous fistula, graft or prosthetic arteriovenous fistula, and central venous catheter. Objective: To analyze and evaluate the current situation and incidence of complications related to different vascular accesses in hemodialysis. Methodology : A systematic review was conducted using the PubMed, CINAHL, SCOPUS, and SciELO databases. All original articles published within the last 5 years that aimed to analyze the prevalence or incidence of complications related to any vascular access in hemodialysis in the adult population were included. Results: A total of 15 articles were included for analysis. Among them, 14 were observational studies, and one was a multicenter clinical trial. Demographic data of the patients, the prevalence of complications across all vascular accesses, and the incidence of complications for native fistula/prosthetic fistula/central venous catheter were analyzed. Conclusions: Native arteriovenous fistula is the preferred vascular access due to its very low complication rates. Among the complications, thrombosis has the highest incidence. The use of central venous catheters is still common, despite having higher rates of complications such as infections and bacteremia, occurring in 10%-17% of the patients.(AU)

A SARS-CoV-2 full genome sequence of the B.1.1 lineage sheds light on viral evolution in Sicily in late 2020.

To investigate the influence of geographic constrains to mobility on SARS-CoV-2 circulation before the advent of vaccination, we recently characterized the occurrence in Sicily of viral lineages in the second pandemic wave (September to December 2020). Our data revealed wide prevalence of the then widespread through Europe B.1.177 variant, although some viral samples could not be classified with the limited Sanger sequencing tools used. A particularly interesting sample could not be fitted to a major variant then circulating in Europe and has been subjected here to full genome sequencing in an attempt to clarify its origin, lineage and relations with the seven full genome sequences deposited for that period in Sicily, hoping to provide clues on viral evolution. The obtained genome is unique (not present in databases). It hosts 20 single-base substitutions relative to the original Wuhan-Hu-1 sequence, 8 of them synonymous and the other 12 encoding 11 amino acid substitutions, all of them already reported one by one. They include four highly prevalent substitutions, NSP12:P323L, S:D614G, and N:R203K/G204R; the much less prevalent S:G181V, ORF3a:G49V and N:R209I changes; and the very rare mutations NSP3:L761I, NSP6:S106F, NSP8:S41F and NSP14:Y447H. GISAID labeled this genome as B.1.1 lineage, a lineage that appeared early on in the pandemic. Phylogenetic analysis also confirmed this lineage diagnosis. Comparison with the seven genome sequences deposited in late 2020 from Sicily revealed branching leading to B.1.177 in one branch and to Alpha in the other branch, and suggested a local origin for the S:G118V mutation.

Detection of SARS-CoV-2 in a dog with hemorrhagic diarrhea.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, has infected several animal species, including dogs, presumably via human-to-animal transmission. Most infected dogs reported were asymptomatic, with low viral loads. However, in this case we detected SARS-CoV-2 in a dog from the North African coastal Spanish city of Ceuta presenting hemorrhagic diarrhea, a disease also reported earlier on in an infected dog from the USA. CASE PRESENTATION: In early January 2021, a West Highland Terrier pet dog from Ceuta (Spain) presented hemorrhagic diarrhea with negative tests for candidate microbial pathogens. Since the animal was in a household whose members suffered SARS-CoV-2 in December 2020, dog feces were analyzed for SARS-CoV-2, proving positive in a two-tube RT-PCR test, with confirmation by sequencing a 399-nucleotide region of the spike (S) gene. Furthermore, next-generation sequencing (NGS) covered > 90% SARS-CoV-2 genome sequence, allowing to classify it as variant B.1.177. Remarkably, the sequence revealed the Ile402Val substitution in the spike protein (S), of potential concern because it mapped in the receptor binding domain (RBD) that mediates virus interaction with the cell. NGS reads mapping to bacterial genomes showed that the dog fecal microbiome fitted best the characteristic microbiome of dog's acute hemorrhagic diarrhea. CONCLUSION: Our findings exemplify dog infection stemming from the human SARS-CoV-2 pandemic, providing nearly complete-genome sequencing of the virus, which is recognized as belonging to the B.1.177 variant, adding knowledge on variant circulation in a geographic region and period for which there was little viral variant characterization. A single amino acid substitution found in the S protein that could have been of concern is excluded to belong to this category given its rarity and intrinsic nature. The dog's pathology suggests that SARS-CoV-2 could affect the gastrointestinal tract of the dog.