Robust neutralization of SARS-CoV-2 variants including JN.1 and BA.2.87.1 by trivalent XBB vaccine-induced antibodies

Dear Editor,The rapid and widespread transmission of SARS-CoV-2 has led to the emergence of multiple variants of concern(VOCs),most notably the Omicron variant,which continues to evolve and diversify into a range of sub-lineages.Our previous research has shown that these Omicron sub-lineages,spanning BA.1-BA.2.86,have been evolving to exhibit increased neutralization escape capabilities.

Genome-wide investigation to assess copy number variants in the Italian local chicken population

Background Copy number variants(CNV)hold significant functional and evolutionary importance.Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock.High-density chips have enabled the detection of CNV with increased resolution,leading to the identification of even small CNV.This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome.Results Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV.The majority of CNV in the investigated breeds were of types 0 and 1,and the minimum length of CNV was significantly larger than that reported in previous studies.Interestingly,a high proportion of the length of chromosome 16 was covered by copy number variation regions(CNVR),with the major histocompatibility complex being the likely cause.Among the genes identified within CNVR,only those present in at least five animals across breeds(n=95)were discussed to reduce the focus on redundant CNV.Some of these genes have been associated to functional traits in chickens.Notably,several CNVR on different chromosomes harbor genes related to muscle development,tissue-specific biological processes,heat stress resistance,and immune response.Quantitative trait loci(QTL)were also analyzed to investigate potential overlapping with the identified CNVR:54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size,carcass characteristics,egg production,egg components,fat deposition,and feed intake.Conclusions The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.

Genetic variants in C1GALT1 are associated with gastric cancer risk by influencing immune infiltration

Core 1 synthase glycoprotein-N-acetylgalactosamine 3-β-galactosyltransferase 1(C1GALT1)is known to play a critical role in the development of gastric cancer,but few studies have elucidated associations between genetic variants in C1GALT1 and gastric cancer risk.By using the genome-wide association study data from the database of Genotype and Phenotype(dbGAP),we evaluated such associations with a multivariable logistic regression model and identified that the rs35999583 G>C in C1GALT1 was associated with gastric cancer risk(odds ratio,0.83;95% confidence interval[CI],0.75-0.92;P=3.95×10^(-4)).C1GALT1 mRNA expression levels were significantly higher in gastric tumor tissues than in normal tissues,and gastric cancer patients with higher C1GALT1 mRNA levels had worse overall survival rates(hazards ratio,1.33;95%CI,1.05-1.68;P_(log-rank)=1.90×10^(-2)).Furthermore,we found that C1GALT1 copy number differed in various immune cells and that C1GALT1 mRNA expression levels were positively correlated with the infiltrating levels of CD4^(+)T cells and macrophages.These results suggest that genetic variants of C1GALT1 may play an important role in gastric cancer risk and provide a new insight for C1GALT1 into a promising predictor of gastric cancer susceptibility and immune status.

New recessive compound heterozygous variants of RP1L1 in RP1L1 maculopathy

AIM:To identify a maculopathy patient caused by new recessive compound heterozygous variants in RP1L1.METHODS:Comprehensive retinal morphological and functional examinations were evaluated for the patient with RP1L1 maculopathy.Targeted sequence capture array technique was used to screen potential pathologic variants.Polymerase chain reaction and Sanger sequencing were used to confirm the screening results.RESULTS:Fundus examination showed round macular lesions appeared in both eyes.Optical coherence tomography showed that the inner segment/outer segment continuity was disorganized and disruptive in the left eye,but it was uneven and slightly elevated in the right eye.Fundus autofluorescence showed patchy hyper-autofluorescence in the macula.Visual field examination indicates central defects in both eyes.Electroretinogram(ERG)and multifocal ERG showed no obvious abnormalities.Fundus fluorescein angiography in the macula showed obviously irregular hyper-fluorescence in the right eye and slightly hyper-fluorescence in the left eye.We found that the proband carried a missense variant(c.1972C>T)and a deletion variant(c.4717_4718del)of RP1L1,which were originated from the parents and formed compound heterozygous variants.Both variants are likely pathogenic according to the ACMG criteria.Multimodal imaging,ERG and detailed medical history are important diagnostic tools for differentiating between acquired and inherited retinal disorders.CONCLUSION:A maculopathy case with detailed retinal phenotype and new recessive compound heterozygous variants of RP1L1 is identified in a Chinese family,which expands the understanding of phenotype and genotype in RP1L1 maculopathy.

Sex Determination in Homo sapiens as a Multi-Step Process: Potential for Development of Variants and Sex Differences in Disease Risk

Reproduction via cis-binary mechanisms appears to have evolved fairly early in the evolution of complex organisms, and a system committed to prior to evolution of humans. While the evolution of a chromosomal-specific approach has been a successful strategy for survival of a large variety of species including humans, the fidelity of sex determination leading to 100% cis-binary outcomes is not achieved in many species, with evidence for homosexual or bisexual behaviour evident in more than 1500 species. Thus, such outcomes indicates that sex determination is a multi-step process and not a single event, and as such, could lead to the appearance of variants during the process which developed much earlier than humans. Variants could arise either due to intrinsic variation in the steps of determination, or also be influenced by environmental factors of a biological or psychological nature. In contrast to homosexual variants which do not require interventions such as hormone therapy or surgery, expression of gender dysphoria, is more based in psychology, but also has biological underpinnings and can be influenced by such hormonal interventions and surgery. While the numbers of those with gender dysphoria is small (~0.6% - 1.0% of population), the attention given to this issue raises the possibility of biological and psychological environmental factors impacting the emergence of some of those expressing gender dysphoria. Furthermore, transitioning from male-to-female or female-to-male can have consequences regarding disease risks latter in life, including the appearance of autoimmune diseases. This review will attempt to review some of the evidence regarding sex determination, discuss why the system has potentially not been improved upon during evolution, how a potential role for sex chromosome function on neurodevelopment may be central to variation in humans, and how commitment to the current strategy is likely integrated into other sex-related events such as puberty, pregnancy, and menopause to ensure species survival. It will also discuss how variants in sex determination could contribute to sex differences in disease risk and how epigenetic modifications could play a role in such risk. .

Lab results of COVID-19 patients:Omicron vs delta variants

BACKGROUND The coronavirus disease 2019(COVID-19)virus has been a world-known pan-demic since February 2020.Multiple variances had been established;the most common variants in Israel were omicron and delta.AIM To analyze and compare laboratory values in the"omicron"and"delta"variants of the coronavirus by conducting follow-up examinations and laboratory audits on COVID-19 patients admitted to our institution.METHODS A retrospective study,two groups,50 patients in each group.Patients examined positive for COVID-19 were divided into groups according to the common variant at the given time.We reviewed demographic data and laboratory results such as complete blood count and full chemistry,including electrolytes and coagulation parameters.RESULTS The mean age was 52%,66.53±21.7 were female.No significance was found comparing laboratory results in the following disciplines:Blood count,hemo-globin,and lymphocytes(P=0.41,P=0.87,P=0.97).Omicron and delta variants have higher neutrophil counts,though they are not significantly different(P=0.38).Coagulation tests:Activated paritial thromoplastin test and international normalized ratio(P=0.72,P=0.68).We found no significance of abnormality for all electrolytes.CONCLUSION The study compares laboratory results of blood tests between two variants of the COVID-19 virus–omicron and delta.We found no significance between the variants.Our results show the need for further research with larger data as well as the need to compare all COVID-19 variants.

Genetic Analysis of Two Novel GPI Variants Disrupting H Bonds and Localization Characteristics of 55 Gene Variants Associated with Glucose-6-phosphate Isomerase Deficiency

Objective:Glucose-6-phosphate isomerase(GPI)deficiency is a rare hereditary nonspherocytic hemolytic anemia caused by GPI gene variants.This disorder exhibits wide heterogeneity in its clinical manifestations and molecular characteristics,often posing challenges for precise diagnoses using conventional methods.To this end,this study aimed to identify the novel variants responsible for GPI deficiency in a Chinese family.Methods:The clinical manifestations of the patient were summarized and analyzed for GPI deficiency phenotype diagnosis.Novel compound heterozygous variants of the GPI gene,c.174C>A(p.Asn58Lys)and c.1538G>T(p.Trp513Leu),were identified using whole-exome and Sanger sequencing.The AlphaFold program and Chimera software were used to analyze the effects of compound heterozygous variants on GPI structure.Results:By characterizing 53 GPI missense/nonsense variants from previous literature and two novel missense variants identified in this study,we found that most variants were located in exons 3,4,12,and 18,with a few localized in exons 8,9,and 14.This study identified novel compound heterozygous variants associated with GPI deficiency.These pathogenic variants disrupt hydrogen bonds formed by highly conserved GPI amino acids.Conclusion:Early family-based sequencing analyses,especially for patients with congenital anemia,can help increase diagnostic accuracy for GPI deficiency,improve child healthcare,and enable genetic counseling.

Functional analysis of the novel mitochondrial tRNA^(Trp)and tRNA^(Ser(AGY))variants associated with type 2 diabetes mellitus

BACKGROUND Mutations in mitochondrial tRNA(mt-tRNA)genes that result in mitochondrial dysfunction play important roles in type 2 diabetes mellitus(T2DM).We previously reported a large Chinese pedigree with maternally inherited T2DM that harbors novel mt-tRNA^(Trp)A5514G and tRNA^(Ser(AGY))C12237T variants,however,the effects of these mt-tRNA variants on T2DM progression are largely unknown.AIM To assess the potential pathogenicity of T2DM-associated m.A5514G and m.C12237T variants at genetic,molecular,and biochemical levels.METHODS Cytoplasmic hybrid(cybrid)cells carrying both m.A5514G and m.C12237T variants,and healthy control cells without these mitochondrial DNA(mtDNA)variants were generated using trans-mitochondrial technology.Mitochondrial features,including mt-tRNA steady-state level,levels of adenosine triphosphate(ATP),mitochondrial membrane potential(MMP),reactive oxygen species(ROS),mtDNA copy number,nicotinamide adenine dinucleotide(NAD+)/NADH ratio,enzymatic activities of respiratory chain complexes(RCCs),8-hydroxy-deoxyguanine(8-OhdG),malondialdehyde(MDA),and superoxide dismutase(SOD)were examined in cell lines with and without these mt-tRNA variants.RESULTS Compared with control cells,the m.A5514G variant caused an approximately 35%reduction in the steady-state level of mt-tRNA^(Trp)(P<0.0001);however,the m.C12237T variant did not affect the mt-tRNA^(Ser(AGY))steady-state level(P=0.5849).Biochemical analysis revealed that cells with both m.A5514G and m.C12237T variants exhibited more severe mitochondrial dysfunctions and elevated oxidative stress than control cells:ATP,MMP,NAD+/NADH ratio,enzyme activities of RCCs and SOD levels were markedly decreased in mutant cells(P<0.05 for all measures).By contrast,the levels of ROS,8-OhdG and MDA were significantly increased(P<0.05 for all measures),but mtDNA copy number was not affected by m.A5514G and m.C12237T variants(P=0.5942).CONCLUSION The m.A5514G variant impaired mt-tRNA^(Trp)metabolism,which subsequently caused mitochondrial dysfunction.The m.C12237T variant did not alter the steady-state level of mt-tRNA^(Ser(AGY)),indicating that it may be a modifier of the m.A5514G variant.The m.A5514G variant may exacerbate the pathogenesis and progression of T2DM in this Chinese pedigree.

Clinicopathological features and medium-term outcomes of histologic variants of primary focal segmental glomerulosclerosis in adults:A retrospective study

BACKGROUND The Columbia classification identified five histological variants of focal segmental glomerulosclerosis(FSGS).The prognostic significance of these variants remains controversial.AIM To evaluate the relative frequency,clinicopathologic characteristics,and medium-term outcomes of FSGS variants at a single center in Pakistan.METHODS This retrospective study was conducted at the Department of Nephrology,Sindh Institute of Urology and Transplantation,Karachi,Pakistan on all consecutive adults(≥16 years)with biopsy-proven primary FSGS from January 1995 to December 2017.Studied subjects were treated with steroids as a first-line therapy.The response rates,doubling of serum creatinine,and kidney failure(KF)with replacement therapy were compared between histological variants using ANOVA or Kruskal Wallis,and Chi-square tests as appropriate.Data were analyzed by SPSS version 22.0.P-value≤0.05 was considered significant.RESULTS A total of 401 patients were diagnosed with primary FSGS during the study period.Among these,352(87.7%)had a designated histological variant.The not otherwise specified(NOS)variant was the commonest,being found in 185(53.9%)patients,followed by the tip variant in 100(29.1%)patients.Collapsing(COL),cellular(CEL),and perihilar(PHI)variants were seen in 58(16.9%),6(1.5%),and 3(0.7%)patients,respectively.CEL and PHI variants were excluded from further analysis due to small patient numbers.The mean follow-up period was 36.5±29.2 months.Regarding response rates of variants,patients with TIP lesions achieved remission more frequently(59.5%)than patients with NOS(41.8%)and COL(24.52%)variants(P<0.001).The hazard ratio of complete response among patients with the COL variant was 0.163[95%confidence interval(CI):0.039-0.67]as compared to patients with NOS.The TIP variant showed a hazard ratio of 2.5(95%CI:1.61-3.89)for complete remission compared to the NOS variant.Overall,progressive KF was observed more frequently in patients with the COL variant,43.4%(P<0.001).Among these,24.53%of patients required kidney replacement therapy(P<0.001).The hazard ratio of doubling of serum creatinine among patients with the COL variant was 14.57(95%CI:1.87-113.49)as compared to patients with the TIP variant.CONCLUSION In conclusion,histological variants of FSGS are predictive of response to treatment with immunosuppressants and progressive KF in adults in our setup.

Development of Oligo-GISH kits for efficient detection of chromosomal variants in peanut

Oligo probe staining is a low-cost and efficient chromosome identification technique.In this study,oligo genomic in situ hybridization(Oligo-GISH)technology was established in peanut.Peanut A and B subgenome-specific interspersed repeat(IR)oligo probe sets were developed based on clustering and electronic localization of tandem repeat sequences in the reference genome of Tifrunner.The OligoGISH kit was then used to perform staining of 15 Arachis species.The A-subgenome probe set stained the chromosomes of A-and E-genome Arachis species,the B-subgenome probe set stained those of B-,F-,K-,and E-genome species,and neither set stained those of H-genome species.These results indicate the relationships among the genomes of these Arachis species.The Oligo-GISH kit was also used for batch staining of the chromosomes of 389 seedlings from the irradiated M1generation,allowing 67 translocation and deletion lines to be identified.Subsequent Oligo-FISH karyotyping,FISH using single-copy probe libraries,and trait investigation identified seven homozygous chromosomal variants from the M3generation and suggested that there may be genes on chromosome 4B controlling seed number per pod.These findings demonstrate that the IR probe sets and method developed in this study can facilitate research on distant hybridization and genetic improvement in peanut.

Genetic Analysis of Variants of the MYH6 Gene Promoter in Congenital Atrial Septal Defects

Background:Atrial septal defect(ASD)is one of the common congenital heart diseases.The MYH6 gene has a critical role in cardiac development but the role of MYH6 promoter variants in patients with ASD has not been explored.Methods:In 613 subjects including 320 ASD patients,we investigated the MYH6 gene promoter variants and verified the effect on gene expression by using cellular functional experiments and bioinformatics analysis.Results:Eleven variants were identified in the MYH6 gene promoter,of which four variants were found only in ASD patients,and two variants(g.3434G>C and g.4524C>T)were identified for the first time.Cellular functional experiments indicated that all four variants reduced the transcriptional activity of the MYH6 gene promoter(p<0.05).Subsequent analysis through the JASPAR(A database of transcription factor binding profiles)suggests that these variants may alter transcription factor binding sites,which may in turn lead to changes in myocardin subunit expression and ASD formation.Conclusions:Our study for the first time focuses on variants in the promoter region of the MYH6 gene in Chinese patients with ASD and the discovered variants have functional significance.The study provides new insights in the role of the MYH6 gene promoter region to better understand the genetic basis of ASD formation and facilitates clinical diagnosis.

Chest computed tomography findings of the Omicron variants of SARS-CoV-2 with different cycle threshold values

BACKGROUND The Omicron variant of severe acute respiratory syndrome coronavirus 2(SARSCoV-2)mainly infects the upper respiratory tract.This study aimed to determine whether the probability of pulmonary infection and the cycle threshold(Ct)measured using the fluorescent polymerase chain reaction(PCR)method were related to pulmonary infections diagnosed via computed tomography(CT).AIM To analyze the chest CT signs of SARS-CoV-2 Omicron variant infections with different Ct values,as determined via PCR.METHODS The chest CT images and PCR Ct values of 331 patients with SARS-CoV-2Omicron variant infections were retrospectively collected and categorized into low(<25),medium(25.00-34.99),and high(≥35)Ct groups.The characteristics of chest CT images in each group were statistically analyzed.RESULTS The PCR Ct values ranged from 13.36 to 39.81,with 99 patients in the low,155 in the medium,and 77 in the high Ct groups.Six abnormal chest CT signs were detected,namely,focal infection,patchy consolidation shadows,patchy groundglass shadows,mixed consolidation ground-glass shadows,subpleural interstitial changes,and pleural changes.Focal infections were less frequent in the low Ct group than in the medium and high Ct groups;these infections were the most common sign in the medium and high Ct groups.Patchy consolidation shadows and pleural changes were more frequent in the low Ct group than in the other two groups.The number of patients with two or more signs was greater in the low Ct group than in the medium and high Ct groups.CONCLUSION The chest CT signs of patients with pulmonary infection caused by the Omicron variants of SARSCoV-2 varied depending on the Ct values.Identification of the characteristics of Omicron variant infection can help subsequent planning of clinical treatment.

A computational framework for improving genetic variants identification from 5,061 sheep sequencing data

Background Pan-genomics is a recently emerging strategy that can be utilized to provide a more comprehensive characterization of genetic variation.Joint calling is routinely used to combine identified variants across multiple related samples.However,the improvement of variants identification using the mutual support information from mul-tiple samples remains quite limited for population-scale genotyping.Results In this study,we developed a computational framework for joint calling genetic variants from 5,061 sheep by incorporating the sequencing error and optimizing mutual support information from multiple samples’data.The variants were accurately identified from multiple samples by using four steps:(1)Probabilities of variants from two widely used algorithms,GATK and Freebayes,were calculated by Poisson model incorporating base sequencing error potential;(2)The variants with high mapping quality or consistently identified from at least two samples by GATK and Freebayes were used to construct the raw high-confidence identification(rHID)variants database;(3)The high confidence variants identified in single sample were ordered by probability value and controlled by false discovery rate(FDR)using rHID database;(4)To avoid the elimination of potentially true variants from rHID database,the vari-ants that failed FDR were reexamined to rescued potential true variants and ensured high accurate identification variants.The results indicated that the percent of concordant SNPs and Indels from Freebayes and GATK after our new method were significantly improved 12%-32%compared with raw variants and advantageously found low frequency variants of individual sheep involved several traits including nipples number(GPC5),scrapie pathology(PAPSS2),sea-sonal reproduction and litter size(GRM1),coat color(RAB27A),and lentivirus susceptibility(TMEM154).Conclusion The new method used the computational strategy to reduce the number of false positives,and simulta-neously improve the identification of genetic variants.This strategy did not incur any extra cost by using any addi-tional samples or sequencing data information and advantageously identified rare variants which can be important for practical applications of animal breeding.

Alternative polyadenylation-related genetic variants contribute to bladder cancer risk

Aberrant alternative polyadenylation(APA)events play an important role in cancers,but little is known about whether APA-related genetic variants contribute to the susceptibility to bladder cancer.Previous genome-wide association study performed APA quantitative trait loci(apaQTL)analyses in bladder cancer,and identified 17955 single nucleotide polymorphisms(SNPs).We found that gene symbols of APA affected by apaQTL-associated SNPs were closely correlated with cancer signaling pathways,high mutational burden,and immune infiltration.Association analysis showed that apaQTL-associated SNPs rs34402449 C>A,rs2683524 C>T,and rs11540872 C>G were significantly associated with susceptibility to bladder cancer(rs34402449:OR=1.355,95%confidence interval[CI]:1.159-1.583,P=1.33×10^(−4);rs2683524:OR=1.378,95%CI:1.164-1.632,P=2.03×10^(−4);rs11540872:OR=1.472,95%CI:1.193-1.815,P=3.06×10^(−4)).Cumulative effect analysis showed that the number of risk genotypes and smoking status were significantly associated with an increased risk of bladder cancer(P_(trend)=2.87×10^(−12)).We found that PRR13,being demonstrated the most significant effect on cell proliferation in bladder cancer cell lines,was more highly expressed in bladder cancer tissues than in adjacent normal tissues.Moreover,the rs2683524 T allele was correlated with shorter 3′untranslated regions of PRR13 and increased PRR13 expression levels.Collectively,our findings have provided informative apaQTL resources and insights into the regulatory mechanisms linking apaQTL-associated variants to bladder cancer risk.

Radio-Anatomical Study of Anterior Variants of the Polygon of Willis

The anterior system of the polygon of Willis plays an anastomotic role between the carotid territories and communicates with the posterior system. It ensures adequate cerebral blood flow in the event of internal occlusion. Its ability to redistribute blood flow depends on its morphology, the presence and size of the vessels that constitute it and their variants, knowledge of which is essential. The morphology of the carotid system is not constant and a number of variants are well recognized with greater hemodynamic importance. In this context, we undertook this work which aims to seek the anatomical variants of the anterior part of the PW;to determine the diameters of the vessels of the latter and to correlate these results with epidemiological data. We carried out a retrospective, descriptive and analytical study over a period of 4 months at Fann University Hospital, targeting patients who had undergone brain MRI with a 3D TOF sequence whatever the indication. Patients with lesions of cerebrovascular pathologies such as ischemia, hemorrhage, aneurysm, arteriovenous malformations or presenting a limited analysis examination due to the presence of kinetic or other artifact, were not included. Demographic data and anatomical variants were studied as well as the measurements of any continuous arterial segment greater than 0.8 mm in diameter. Those less than 0.8 mm in diameter were considered hypoplastic. The C3 segment of the internal carotid arteries, the A1 segment of the anterior cerebral arteries, the anterior communicating artery, constituted our main measurement sites. The sex ratio was 1.06, the mean age of the patients was 43 years ± 17.9 with extremes of 11 and 85 years. The anterior configuration of the polygon was complete in 57.5% representing 50% of men and 65.5% of women, in 56% of subjects under 40 years old and 58% in subjects over 40 years old. We noted a predominance of type a in 47% of patients followed by type g found in 35% of patients. The morphology of the anterior system of the Willis polygon is a function of its variants, some of which have greater hemodynamic importance than others. Its knowledge is essential for the management of cerebrovascular diseases.

The transcriptome analysis of cleft lip/palate-related PTCH1 variants in GMSM-K cells show carcinogenic potential

Cancer progression involves the sonic hedgehog(SHH)pathway,in which the receptor PTCH1 actives the downstream pathways.Dysfunction of PTCH1 can lead to nevoid basal cell carcinoma Syndrome(NBCCs)including neoplastic disease and congenital disorder.To evaluate the relationship between PTCH1 and cancer,we applied the CRISPR/Cas9 system to knock out PTCH1 in oral nontumorous epithelial cells(GMSM-K).Then we screened six PTCH1 variants associated with cleft lip/palate(CL/P),one of the congenital disorders in NBCCs,and generated PTCH1 variant and wild-type recombinant PTCH1^(−/−)GMSM-K cell lines.Transcriptome sequencing was conducted in these cell lines.The results revealed that differentially expressed genes(DEGs)in PTCH1^(−/−)GMSM-K were enriched in extracellular compartments,contributing epithelial diseases by pathway enrichment analysis.RT-PCR confirmed that KRT34,KRT81,KRT86,PDGFB,and WNT10B genes,associated with extracellular compartments were highly expressed in PTCH1^(−/−).The Kyoto Encyclopedia of Genes and Genomes analysis also suggested that DEGs are closely related to focal adhesion,transcriptional misregulation,and proteoglycans in breast and gastric cancers.Comparative analysis of samples revealed that the CL/P-associated PTCH1 variants A443G and V908G are potentially carcinogenic.These findings provide new insights into the carcinogenic potential of PTCH1 dysfunction.

Surveillance of emerging SARS-CoV-2 variants by nanopore technology-based genome sequencing

Objective:To surveill emerging variants by nanopore technology-based genome sequencing in different COVID-19 waves in Sri Lanka and to examine the association with the sample characteristics,and vaccination status.Methods:The study analyzed 207 RNA positive swab samples received to sequence laboratory during different waves.The N gene cut-off threshold of less than 30 was considered as the major inclusion criteria.Viral RNA was extracted,and elutes were subjected to nanopore sequencing.All the sequencing data were uploaded in the publicly accessible database,GISAID.Results:The Omicron,Delta and Alpha variants accounted for 58%,22%and 4%of the variants throughout the period.Less than 1%were Kappa variant and 16%of the study samples remained unassigned.Omicron variant was circulated among all age groups and in all the provinces.Ct value and variants assigned percentage was 100%in Ct values of 10-15 while only 45%assigned Ct value over 25.Conclusions:The present study examined the emergence,prevalence,and distribution of SARS-CoV-2 variants locally and has shown that nanopore technology-based genome sequencing enables whole genome sequencing in a low resource setting country.

PCR-HRM for Genomic Surveillance of SARS-CoV-2: A Variant Detection Tool in Côte d’Ivoire, West Africa

The rise of new viruses, like SARS-CoV-2 causing the COVID-19 outbreak, along with the return of antibiotic resistance in harmful bacteria, demands a swift and efficient reaction to safeguard the health and welfare of the global population. It is crucial to have effective measures for prevention, intervention, and monitoring in place to address these evolving and recurring risks, ensuring public health and international security. In countries with limited resources, utilizing recombinant mutation plasmid technology in conjunction with PCR-HRM could help differentiate the existence of novel variants. cDNA synthesis was carried out on 8 nasopharyngeal samples following viral RNA extraction. The P1 segment of the SARS-CoV-2 Spike S protein was amplified via conventional PCR. Subsequently, PCR products were ligated with the pGEM-T Easy vector to generate eight recombinant SARS-CoV-2 plasmids. Clones containing mutations were sequenced using Sanger sequencing and analyzed through PCR-HRM. The P1 segment of the S gene from SARS-CoV-2 was successfully amplified, resulting in 8 recombinant plasmids generated from the 231 bp fragment. PCR-HRM analysis of these recombinant plasmids differentiated three variations within the SARS-CoV-2 plasmid population, each displaying distinct melting temperatures. Sanger sequencing identified mutations A112C, G113T, A114G, G214T, and G216C on the P1 segment, validating the PCR-HRM findings of the variations. These mutations led to the detection of L452R or L452M and F486V protein mutations within the protein sequence of the Omicron variant of SARS-CoV-2. In summary, PCR-HRM is a vital and affordable tool for distinguishing SARS-CoV-2 variants utilizing recombinant plasmids as controls.

Genetic variant in a BaP-activated super-enhancer increases prostate cancer risk by promoting AhR-mediated FAM227A expression

Genetic variants in super-enhancers(SEs)are increasingly implicated as a disease risk-driving mechanism.Previous studies have reported an associations between benzo[a]pyrene(BaP)exposure and some malignant tumor risk.Currently,it is unclear whether BaP is involved in the effect of genetic variants in SEs on prostate cancer risk,nor the associated intrinsic molecular mechanisms.In the current study,by using logistic regression analysis,we found that rs5750581T>C in 22q-SE was significantly associated with prostate cancer risk(odds ratio=1.26,P=7.61×10^(-5)).We also have found that the rs6001092T>G,in a high linkage disequilibrium with rs5750581T>C(r^(2)=0.98),is located in a regulatory aryl hydrocarbon receptor(AhR)motif and may interact with the FAM227A promoter in further bioinformatics analysis.We then performed a series of functional and BaP acute exposure experiments to assess biological function of the genetic variant and the target gene.Biologically,the rs6001092-G allele strengthened the transcription factor binding affinity to AhR,thereby upregulating FAM227A,especially upon exposure to BaP,which induced the malignant phenotypes of prostate cancer.The current study highlights that AhR acts as an environmental sensor of BaP and is involved in the SE-mediated prostate cancer risk,which may provide new insights into the etiology of prostate cancer associated with the inherited SE variants under environmental carcinogen stressors.

YOLO-O2E:A Variant YOLO Model for Anomalous Rail Fastening Detection

Rail fasteners are a crucial component of the railway transportation safety system.These fasteners,distinguished by their high length-to-width ratio,frequently encounter elevated failure rates,necessitating manual inspection and maintenance.Manual inspection not only consumes time but also poses the risk of potential oversights.With the advancement of deep learning technology in rail fasteners,challenges such as the complex background of rail fasteners and the similarity in their states are addressed.We have proposed an efficient and high-precision rail fastener detection algorithm,named YOLO-O2E(you only look once-O2E).Firstly,we propose the EFOV(Enhanced Field of View)structure,aiming to adjust the effective receptive field size of convolutional kernels to enhance insensitivity to small spatial variations.Additionally,The OD_MP(ODConv and MP_2)and EMA(EfficientMulti-Scale Attention)modules mentioned in the algorithm can acquire a wider spectrum of contextual information,enhancing the model’s ability to recognize and locate objectives.Additionally,we collected and prepared the GKA dataset,sourced from real train tracks.Through testing on the GKA dataset and the publicly available NUE-DET dataset,our method outperforms general-purpose object detection algorithms.On the GKA dataset,our model achieved a mAP 0.5 value of 97.6%and a mAP 0.5:0.95 value of 83.9%,demonstrating excellent inference speed.YOLO-O2E is an algorithm for detecting anomalies in railway fasteners that is applicable in practical industrial settings,addressing the industry gap in rail fastener detection.