SARS-CoV-2 susceptibility and COVID-19 disease severity are associated with genetic variants affecting gene expression in a variety of tissues

Variability in SARS-CoV-2 susceptibility and COVID-19 disease severity between individuals is partly due to genetic factors. Here, we identify 4 genomic loci with suggestive associations for SARS-CoV-2 susceptibility and 19 for COVID-19 disease severity. Four of these 23 loci likely have an ethnicity-specific component. Genome-wide association study (GWAS) signals in 11 loci colocalize with expression quantitative trait loci (eQTLs) associated with the expression of 20 genes in 62 tissues/cell types (range: 1:43 tissues/gene), including lung, brain, heart, muscle, and skin as well as the digestive system and immune system. We perform genetic fine mapping to compute 99% credible SNP sets, which identify 10 GWAS loci that have eight or fewer SNPs in the credible set, including three loci with one single likely causal SNP. Our study suggests that the diverse symptoms and disease severity of COVID-19 observed between individuals is associated with variants across the genome, affecting gene expression levels in a wide variety of tissue types

A first update on mapping the human genetic architecture of COVID-19

peer reviewe

Molecular Identification and Phylogenetic Analysis of Multidrug-resistant Bacteria using 16S rDNA Sequencing

In the present study, 30 multidrug-resistant bacterial samples were isolated from different hospitals in the Taif governorate in Saudi Arabia. Given its discriminating power as a universal phylogenetic marker, the 16S rDNA gene was sequenced in a comprehensive diversity study to determine the evolutionary and phylogenetic relationships among the bacterial isolates. The 16S rDNA genes of all isolates were successfully amplified using PCR, and comprehensive identification results were based on GenBank databases. Analysis revealed nucleotide identities ranging from 76% to 100% based on the consensus sequences of 21 species, namely, Bacillus cereus, Bacillus subtilis, Bacillus tequilensis, Caldimonas manganoxidans, Citrobacter freundii, Enterococcus faecium, Escherichia fergusonii, Klebsiella pneumoniae, Lactobacillus plantarum, Lactococcus garvieae, Leuconostoc mesenteroides, Myristica yunnanensis, Pantoea eucrina, Pseudomonas aeruginosa, Staphylococcus aureus, Staphylococcus capitis, Staphylococcus caprae, Staphylococcus epidermidis, Staphylococcus hominis, Staphylococcus petrasii, and Staphylococcus saccharolyticus. We observed high variability in terms of DNA length and GC content between and within species. Phylogenetic analysis clustered the isolates into three groups. The number of sites ranged from 827 (S. aureus) to 1,219 (L. mesenteroides). Estimation of nucleotide diversity (ð) showed that all analyzed sequences were diverse site-wise and also exhibited high nucleotide diversity, with ð values ranging from 0.17 to 0.94. All isolates showed significantly conserved regions (P>0.05). In conclusion, the observed variations in the sequences of the target bacterial strains can be attributed to resistance to antibiotics and gene transfer among bacterial strains in the hospital environment. Further sequence analyses of antibiotic resistance genes are warranted

Correlation Between Strain Distribution and Antibiotic Resistance Genes Pattern of Streptococcus agalactiae Group B from Patients in Taif, Saudi Arabia

The Group B Streptococcus (Streptococcus agalactiae) (GBS) is one of the natural flora bacteria in the female reproductive system. In the recent years, GBS has become the major bacterial infections throw the perinatal period causing many troubles. This study was undertaken to determine the prevalence and antibiotic genes of GBS colonization in pregnant women of obstetrics hospital in Taif, Saudi Arabia. Fourteen Streptococcus agalactiae isolates obtained after screening about 134 swabs samples from genitourinary tract specimens of women patients from obstetrics hospital in Taif governorate, Saudi Arabia. These isolates were studied for antibiotic resistance and virulence genes. All obtained isolates were identified as Streptococcus agalactiae by the 16S rDNA gene sequence. These strains were found by Disc diffusion method sensitive against Meropenem, Cefotaxime, Cefepime, Amoxicillin, Penicillin G, Daptomycin, Chloramphenicol, Linezolid and Levofloxacin. The highest resistance was for Tetracyclin (85.7%) whereas the lowest resistance was found for Vancomycin (21.4%). Resistance against Erythromycin and Clindamycin was 71.5%, and 28.5% respectively. PCR based detection revealed 50% of isolates were carrying the tetT genes, while 92.8% of isolates were carrying tetO and tetM genes associated with Tetracycline resistance. All isolates were harboring genes that associated with Erythromycin resistance like ErmB1, ErmB2, and Erm(A|TR) genes, but only 28.5% of isolates were carrying ErmTR gene. Molecular detection of virulence associated genes revealed that out of fourteen isolates of S. agalactiae, only one isolate was carrying the LinB gene, while all isolates were positive for MreA and VanA genes respectively. We can conclude that the GBS isolates were found sensitive to many antibiotic while most isolates were resistance to Tetracycline due to the existence of tetO and tetM genes. Resistance against Erythromycin and Clindamycin was 71.5%, and 28.5% respectively. The two erythromycin resistance genes (ErmB and ErmTR) were found in all isolates, while, the third erythromycin resistance gene Erm(A|TR) was found only in 25.8% of the isolates

The Antimicrobial Resistance and Prevalence of Enterococcus Species in Saudi Arabia

Monitoring the distribution and resistance of antibiotics to enterococcal species is critical aspect to controlling and preventing enterococcal infection. The aim of the present study is to screen the antimicrobial resistance genes within Enterococcus species isolates that collected from Taif governorate, Saudi Arabia. Out of 134 clinical samples, nineteen enterococcal isolates were identified using 16S rRNA sequence gene. Phylogenetic tree analysis using 16S rRNA gene sequence of the 19 strains divided them into 15 strains as E. faecalis and 4 strains as E. faecium. In addition, these the species of these isolates were recognized using VITEK-2 COMPACT system. The PCR technique was used to screen the multi-drug resistant genes within enterococcal isolates. The KpsII, tetL, aac(6)-Ie-aph(2)-Ia, vanA and Erm(B) genes were found in all strains. The distribute of resistance against antibiotic drugs were differs greatly between the two species, a considerably higher prevalence of resistance to penicillin, gentamicin, cefoxitin, cefotaxime, clindamycin, erthromycin and fusidic acid was identified in E. faecalis than in E. faecium, while greater spread was detected to resist to Trim/Sulf and tetracycline in E. faecalis. Finally, rep-PCR markers investigated genomic diversity of Enterococcus strains. Results of rep-PCR markers generated 142 distinct loci; 96 were polymorphic (67.6%) and 46 were monomorphic (32.4%). Number of loci for individual rep-PCR primers ranged from 9 for rep-08 to 18 for rep-02

Generating homogenous cortical preplate and deep-layer neurons using a combination of 2D and 3D differentiation cultures

AbstractEmbryonic stem cells (ESCs) can be used to derive different neural subtypes. Current differentiation protocols generate heterogeneous neural subtypes rather than a specific neuronal population. Here, we present a protocol to derive separate two-deep layer cortical neurons from mouse ESCs (mESCs). mESCs were differentiated into mature Tbr1 or Ctip2-positive neurons using a monolayer-based culture for neural induction and neurosphere-based culture for neural proliferation and expansion. The differentiation protocol relies on SMAD inhibition for neural induction and the use of FGF2 and EGF for proliferation and it is relatively short as mature neurons are generated between differentiation days 12–16. Compared with the monolayer-based differentiation method, mESCs can be directed to generate specific deep-layer cortical neurons rather than heterogeneous cortical neurons that are generated using the monolayer differentiation culture. The early analysis of progenitors using flow cytometry, immunocytochemistry, and qRT-PCR showed high neuralization efficiency. The immunocytochemistry and flow cytometry analyses on differentiation days 12 and 16 showed cultures enriched in Tbr1- and Ctip2-positive neurons, respectively. Conversely, the monolayer differentiation culture derived a mixture of Tbr1 and Ctip2 mature neurons. Our findings suggested that implementing a neurosphere-based culture enabled directing neural progenitors to adopt a specific cortical identity. The generated progenitors and neurons can be used for neural-development investigation, drug testing, disease modelling, and examining novel cellular replacement therapy strategies.</jats:p

Whole-genome sequencing reveals host factors underlying critical COVID-19

Altres ajuts: Department of Health and Social Care (DHSC); Illumina; LifeArc; Medical Research Council (MRC); UKRI; Sepsis Research (the Fiona Elizabeth Agnew Trust); the Intensive Care Society, Wellcome Trust Senior Research Fellowship (223164/Z/21/Z); BBSRC Institute Program Support Grant to the Roslin Institute (BBS/E/D/20002172, BBS/E/D/10002070, BBS/E/D/30002275); UKRI grants (MC_PC_20004, MC_PC_19025, MC_PC_1905, MRNO2995X/1); UK Research and Innovation (MC_PC_20029); the Wellcome PhD training fellowship for clinicians (204979/Z/16/Z); the Edinburgh Clinical Academic Track (ECAT) programme; the National Institute for Health Research, the Wellcome Trust; the MRC; Cancer Research UK; the DHSC; NHS England; the Smilow family; the National Center for Advancing Translational Sciences of the National Institutes of Health (CTSA award number UL1TR001878); the Perelman School of Medicine at the University of Pennsylvania; National Institute on Aging (NIA U01AG009740); the National Institute on Aging (RC2 AG036495, RC4 AG039029); the Common Fund of the Office of the Director of the National Institutes of Health; NCI; NHGRI; NHLBI; NIDA; NIMH; NINDS.Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care or hospitalization after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes-including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)-in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease