Analysis the molecular similarity of least common amino acid sites in ACE2 receptor to predict the potential susceptible species for SARS-CoV-2 (preprint)

This research offers a bioinformatics approach to forecasting both domestic and wild animals' likelihood of being susceptible to SARS-CoV-2 infection. Genomic sequencing can resolve phylogenetic relationships between the virus and the susceptible host. The genome sequence of SARS-CoV-2 is highly interactive with the specific sequence region of the ACE2 receptor of the host species. We further evaluate this concept to identify the most important SARS-CoV-2 binding amino acid sites in the ACE2 receptor sequence through the common similarity of the last common amino acid sites (LCAS) in known susceptible host species. Therefore, the SARS-CoV-2 viral genomic interacting key amino acid region in the ACE2 receptor sequence of known susceptible human host was summarized and compared with other reported known SARS-CoV-2 susceptible host species. We identified the 10 most significant amino acid sites for interaction with SARS-CoV-2 infection from the ACE2 receptor sequence region based on the LCAS similarity pattern in known sensitive SARS-CoV-2 hosts. The most significant 10 LCAS were further compared with ACE2 receptor sequences of unknown species to evaluate the similarity of the last common amino acid pattern (LCAP). We predicted the probability of SARS-CoV-2 infection risk in unknown species through the LCAS similarity pattern. This method can be used as a screening tool to assess the risk of SARS-CoV-2 infection in domestic and wild animals to prevent outbreaks of infection.

A Deadly Case of Dehydration: Organic Acidemias in the Emergency Department.

BACKGROUND: Organic acidemias are rare genetic mutations, most commonly identified in the newborn period. Late-onset presentations present a diagnostic conundrum. Early identification and appropriate management can be lifesaving. CASE REPORT: We describe the case of a 3-year-old boy who presented to urgent care with 2 days of nausea, vomiting, and diarrhea followed by respiratory distress, shock, and encephalopathy. Brisk recognition of his shock state led to an urgent transfer to a tertiary care pediatric emergency department by air where his shock was treated and hyperammonemia was uncovered, leading to the diagnosis of late-onset propionic acidemia, which was subsequently managed with a good outcome. WHY SHOULD AN EMERGENCY PHYSICIAN BE AWARE OF THIS?: Late-onset presentations of inborn errors of metabolism, including organic acidemias, represent one of the most challenging pediatric cases an emergency physician can encounter. This case reviews the management and diagnosis of a late-onset inborn error of metabolism and emphasizes how prompt diagnosis and treatment can lead to a favorable outcome.

Inborn errors of metabolism and coronavirus disease 2019: Evaluation of the metabolic outcome.

BACKGROUND: Infectious diseases can result in a catabolic state and possibly trigger an acute metabolic decompensation in inborn errors of metabolism (IEM), which could be life threatening. Studies regarding the course of severe acute respiratory syndrome coronavirus 2 infections in patients with IEM are generally limited to case reports. Here, we aimed to evaluate the clinical findings of coronavirus disease 2019 (COVID-19) and describe the impact of severe acute respiratory syndrome coronavirus 2 infections on metabolic outcomes in IEM patients. METHODS: Patients who were diagnosed with different types of IEM and developed microbiologically confirmed COVID-19 infection were included. Clinical findings and laboratory results were recorded retrospectively in terms of both IEM and COVID-19. RESULTS: Eleven patients with diagnosis of intoxication type metabolic disorders, five patients with energy metabolism disorders, and six patients with complex molecular disorders were enrolled. The most frequent clinical finding was fever (52.1%) followed by fatigue/myalgia (47.8%). None of the patients was younger than 1 year. None of the patients presented severe or critical disease. In terms of metabolic decompensation, two patients diagnosed with propionic acidemia, one patient with methylmalonic acidemia and one patient with 3-hydroxy-3-methylglutaryl-CoA lyase deficiency presented clinical and biochemical findings of an acute metabolic attack. CONCLUSIONS: Based on our results, IEM are not found to be an additional risk factor for severe COVID-19 infection. However, patients with intoxication type and energy metabolism disorders should be considered as a vulnerable population for COVID-19 and have a major risk of developing acute metabolic decompensation that can lead to life-threatening complications.

Community structure and temporal dynamics of SARS-CoV-2 epistatic network allows for early detection of emerging variants with altered phenotypes (preprint)

The rise of viral variants with altered phenotypes presents a significant public health challenge. In particular, the successive waves of COVID-19 have been driven by emerging variants of interest (VOIs) and variants of concern (VOCs), which are linked to modifications in phenotypic traits such as transmissibility, antibody resistance, and immune escape. Consequently, devising effective strategies to forecast emerging viral variants is critical for managing present and future epidemics. Although current evolutionary prediction tools mainly concentrate on single amino acid variants (SAVs) or isolated genomic changes, the observed history of VOCs and the extensive epistatic interactions within the SARS-CoV-2 genome suggest that predicting viral haplotypes, rather than individual mutations, is vital for efficient genomic surveillance. However, haplotype prediction is significantly more challenging problem, which precludes the use of traditional AI and Machine Learning approaches utilized in most mutation-based studies. This study demonstrates that by examining the community structure of SARS-CoV-2 spike protein epistatic networks, it is feasible to efficiently detect or predict emerging haplotypes with altered transmissibility. These haplotypes can be linked to dense network communities, which become discernible significantly earlier than their associated viral variants reach noticeable prevalence levels. From these insights, we developed HELEN (Heralding Emerging Lineages in Epistatic Networks), a computational framework that identifies densely epistatically connected communities of SAV alleles and merges them into haplotypes using a combination of statistical inference, population genetics, and discrete optimization techniques. HELEN was validated by accurately identifying known SARS-CoV-2 VOCs and VOIs up to 10-12 months before they reached perceptible prevalence and were designated by the WHO. For example, our approach suggests that the spread of the Omicron haplotype or a closely related genomic variant could have been foreseen as early as the start of 2021, almost a year before its WHO designation. Moreover, HELEN offers greater scalability than phylogenetic lineage tracing methods, allowing for the analysis of millions of available SARS-CoV-2 genomes. Besides SARS-CoV-2, our methodology can be employed to detect emerging and circulating strains of any highly mutable pathogen with adequate genomic surveillance data.

The novel P330L pathogenic variant of aromatic amino acid decarboxylase maps on the catalytic flexible loop underlying its crucial role.

Aromatic amino acid decarboxylase (AADC) deficiency is a rare monogenic disease, often fatal in the first decade, causing severe intellectual disability, movement disorders and autonomic dysfunction. It is due to mutations in the gene coding for the AADC enzyme responsible for the synthesis of dopamine and serotonin. Using whole exome sequencing, we have identified a novel homozygous c.989C > T (p.Pro330Leu) variant of AADC causing AADC deficiency. Pro330 is part of an essential structural and functional element: the flexible catalytic loop suggested to cover the active site as a lid and properly position the catalytic residues. Our investigations provide evidence that Pro330 concurs in the achievement of an optimal catalytic competence. Through a combination of bioinformatic approaches, dynamic light scattering measurements, limited proteolysis experiments, spectroscopic and in solution analyses, we demonstrate that the substitution of Pro330 with Leu, although not determining gross conformational changes, results in an enzymatic species that is highly affected in catalysis with a decarboxylase catalytic efficiency decreased by 674- and 194-fold for the two aromatic substrates. This defect does not lead to active site structural disassembling, nor to the inability to bind the pyridoxal 5'-phosphate (PLP) cofactor. The molecular basis for the pathogenic effect of this variant is rather due to a mispositioning of the catalytically competent external aldimine intermediate, as corroborated by spectroscopic analyses and pH dependence of the kinetic parameters. Altogether, we determined the structural basis for the severity of the manifestation of AADC deficiency in this patient and discussed the rationale for a precision therapy.

Amino Acid Sensor GCN2 Promotes SARS-CoV-2 Receptor ACE2 Expression in Response to Amino Acid Deprivation (preprint)

Angiotensin-converting enzyme 2 (ACE2) has been identified as a primary receptor for severe acute respiratory syndrome coronaviruses 2 (SARS-CoV-2). Here, we investigated the expression regulation of ACE2 in enterocytes under amino acid deprivation conditions. In this study, we confirmed that ACE2 protein was highly expressed in intestinal epithelial cells in mice and found that ACE2 expression was upregulated upon all or only an essential amino acid deprivation in human colonic epithelial CCD841 cells. Furthermore, we found that knockdown of general control nonderepressible 2 ( GCN2 ) reduced intestinal ACE2 mRNA and protein levels in vitro and in vivo . Consistently, we revealed two GCN2 inhibitors, GCN2iB and GCN2-IN-1, downregulated ACE2 protein expression in CCD841 cells in a dose-dependent manner. Moreover, we found that increased ACE2 expression in response to leucine deprivation was GCN2 dependent. Through RNA-seq analysis, we identified that two novel transcription factors, MAFB and MAFF, positively regulated ACE2 expression under leucine deprivation in CCD841 cells. These findings demonstrate that amino acid deficiency increases ACE2 expression and thereby likely aggravates intestinal SARS-CoV-2 infection.

COVID-19 triggered encephalopathic crisis in a patient with glutaric aciduria type 1.

OBJECTIVES: The impact of coronavirus disease-19 (COVID-19) on metabolic outcome in patients with inborn errors of metabolism has rarely been discussed. Herein, we report a case with an acute encephalopathic crisis at the course of COVID-19 disease as the first sign of glutaric aciduria type 1 (GA-1). CASE PRESENTATION: A 9-month-old patient was admitted with encephalopathy and acute loss of acquired motor skills during the course of COVID-19 disease. She had lethargy, hypotonia, and choreoathetoid movements. In terms of COVID-19 encephalopathy, the reverse transcription-polymerase chain reaction assay test for COVID-19 was negative in cerebral spinal fluid. Brain imaging showed frontotemporal atrophy, bilateral subcortical and periventricular white matter, basal ganglia, and thalamic involvement. Elevated glutarylcarnitine in plasma and urinary excretion of glutaric and 3-OH-glutaric acids was noted. A homozygote mutation in the glutaryl-CoA dehydrogenase gene led to the diagnosis of GA-1. CONCLUSIONS: With this report, neurological damage associated with COVID-19 has been reported in GA-1 patients for the first time in literature.

Management of COVID-19 infection in organic acidemias.

The COVID-19 pandemic has affected the health and healthcare of individuals of all ages worldwide. There have been multiple reports and reviews documenting a milder effect and decreased morbidity and mortality in the pediatric population, but there have only been a small number of reports discussing the SARS-CoV-2 infection in the setting of an inborn error of metabolism (IEM). Here, we report two patients with underlying metabolic disorders, propionic acidemia and glutaric aciduria type 1, and discuss their clinical presentation, as well as their infectious and metabolic management. Our report demonstrates that individuals with an underlying IEM are at risk of metabolic decompensation in the setting of a COVID-19 infection. The SARS-CoV-2 virus does not appear to cause a more severe metabolic deterioration than is typical.

Successful Remote Monitoring During COVID-19 Pandemic of Patients with Inborn Errors of the Amino acid Metabolism not including PKU from a Single Reference center using Filter Paper Samples (preprint)

Background. Patients with inborn errors of metabolism (IEM) pose specific management challenges, considering their multisystem involvement. Among them, children and adults with organic acidemias (OA) and other disorders of the amino acid metabolism have a high risk for severe metabolic events that need to be recognized and promptly treated, and therefore require frequent clinical and biochemical evaluations. The novel highly pathogenic SARS-CoV2 virus appeared in Europe in the first trimester of 2020. This pandemic has a huge impact on the health care systems all over the world, interrupting the follow-up of many chronic diseases. For metabolic patients, travel to reference units may be reduced due to mobility restrictions but more importantly, attendance to medical facilities can be a risk of infection that can be a danger in itself but also trigger a metabolic decompensation.Methods. During the first coronavirus disease (COVID-19) outbreak in Spain from March to June 2020, we designed a model of remote monitoring of our patients with amino acid disorders using telephone and/or online clinical assessments and using filter paper samples to continue the biochemical control. Results. Fourteen patients with inborn errors of amino acid metabolism other than PKU received filter papers and instructions to collect blood and urine samples home and send them to our reference laboratory. Conclusions. Considering the COVID19 pandemic evolution, new strategies to ensure IEM patients have an evaluation continuity need to be implemented. We believe that blood and urine filter paper biochemical follow-up, together with online or telephone clinical assessments, can help minimize the need for in-hospital visits. 

Single Amino Acid Variant (SAV) Percentage and Monomer Modeling of Spike Protein of SARS-CoV-2 in Jordan (preprint)

Spike protein is the surface glycoprotein of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) necessary for the entry of the virus via the transmembrane receptors of the human endothelial cells of the respiratoty system for the virus to be engulfed causing COVID-19 disease after priming by type II transmembrane protease TMPRSS2 and then binding with the angiotensin-converting enzyme 2 (ACE2). Therefore, mutations and amino acid variants analysis are essential in understanding the mechanism of binding of spike protein with its receptor to have an insights on possibilities to design a peptide or nucleotide-based vaccine for COVID-19. Here, we employed Iterative Threading Assembly Refinement (I-TASSER) and Multiple Alignment using Fast Fourier Transform (MAFFT) to predict the three-dimensional monomer structure of spike protein of SARS-CoV-2 and to analyze the amino acid variants for protein sequences from GISAID database for samples collected from Jordan in a try to find an explanation for the low confirmed number of COVID-19 in Jordan. Our Protein Homology/analogY Recognition Engine V 2.0 (Phyre2) findings showed four single amino acid variants (SAV) found in 20 samples of SARS-CoV-2. What is equal to 5% of samples showed tyrosine deletion at Y144 located in the SARS-CoV-like_Spike_S1_NTD (N terminal domain), 62% showed aspartate substitution to glycine at D614G located in the SARS-CoV-2_Spike_S1_RBD (spike recognition binding site), 5% showed aspartate substitution to tyrosine at D1139Y and 5% showed glycine substitution to serine at G1167S both located in the Corona_S2 domain. The findings have shown lower mutational sensitivity in all variants that might not affect the function of spike glycoprotein except for D614G, which has the highest mutational sensitivity score (5 out of 9) indicating a higher likelihood to affect the function of the spike protein. This might suggest, in general, a reduced transmitability of SARS-CoV-2 in Jordan.