Illumina MiniSeq Research Articles

Novel <i>FLNC</i> Gene Variant Associated with Hypertrophic Cardiomyopathy

Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiomyopathy, affecting approximately 1 in 500 people. It is the most common genetic cardiomyopathy inherited as a Mendelian trait in approximately 50% of patients, mainly due to pathogenic variants in genes encoding sarcomeric proteins. Mutations in the sarcomeric protein filamin C (<em>FLNC</em>) gene, with a cytogenetic localization on 7q32.1, have been linked to hypertrophic cardiomyopathy, as they have been determined to increase the risk of ventricular arrhythmia and sudden death. We present the case of a patient with HCM recognized by magnetic resonance imaging and echocardiography with a family history of cardiopathies. The molecular study in this patient was performed by next-generation sequencing on the Illumina MiniSeq instrument, comparing the results with international databases. In genetic studies, a novel mutation in the protein <em>FLNC</em> was detected. It is heterozygous, missence type. It is a variant where Cytosine is changed by timina at position 6305 of the <em>FLNC</em> gene. This produces the change of the amino acid proline by leucine at position 2102 of the Filamin C protein. The rare variant is located in Ig-like domain 19 within the ROD2 domain. This variant report suggests that there may indeed be a direct relationship between <em>FLNC</em> variants, mainly the ROD2 domain, and HCM. We think this new result should be considered for future genetic counseling of families affected by this type of cardiomyopathy.

Exploring the gut microbiome composition and diversity of leopard cats (Prionailurus bengalensis) in captive population: a case study in Zoo Melaka, Malaysia

Abstract Gut microbiomes are crucial in determining wildlife’s health, especially in the captive population. The alternation of environment can lead to microbiome changes that could affect the host’s health. Therefore, the information regarding gut microbiomes is important in conducting effective husbandry management for captive animals especially in zoos. Thus, we conducted the gut microbiome study on captive leopard cat (Prionailurus bengalensis) using Illumina Miniseq platform. The 16S rRNA gene sequencing was performed on two samples from both male and female leopard cats. The sequencing analysis successfully unveiled the diversity of gut microbiomes within this species, identifying members from 12 phyla, 74 families, and 127 genera of bacteria. Proteobacteria and Firmicutes emerged as the dominant phyla, constituting 49% in females and 34.7% in males, respectively. Intriguingly, no significant differences in alpha diverisity indices were observed between the sexes of P. bengalensis. These findings contribute substantially to our comprehension of the gut microbiome diversity in leopard cats in Malaysia. Generally, the findings of this study provide the fundamental data for the captive management and health assessment of P. bengalensis, acting as a valuable resource for future conservation efforts. By establishing a baseline understanding of the gut microbiomes in captivity, this research supports the broader goal of preserving the biological integrity of leopard cat populations especially in Malaysia.

Impact of CYP2C19 Gene Variants on Long-Term Treatment with Atorvastatin in Patients with Acute Coronary Syndromes.

The effectiveness of lipid-lowering therapies may be insufficient in high-risk cardiovascular patients and depends on the genetic variability of drug-metabolizing enzymes. Customizing statin therapy, including treatment with atorvastatin, may improve clinical outcomes. Currently, there is a lack of guidelines allowing the prediction of the therapeutic efficacy of lipid-lowering statin therapy. This study aimed to determine the effects of clinically significant gene variants of CYP2C19 on atorvastatin therapy in patients with acute coronary syndromes. In total, 92 patients with a confirmed diagnosis of ST-elevation myocardial infarction (STEMI) or non-ST-elevation myocardial infarction (NSTEMI) were sequenced for target regions within the CYP2C19 gene on the Illumina Miniseq system. The CYP2C19 poor metabolizer phenotype (carriers of CYP2C19*2, CYP2C19*4, and CYP2C19*8 alleles) was detected in 29% of patients. These patients had significantly lower responses to treatment with atorvastatin than patients with the normal metabolizer phenotype. CYP2C19-metabolizing phenotype, patient age, and smoking increased the odds of undertreatment in patients (∆LDL-C (mmol/L) < 1). These results revealed that the CYP2C19 phenotype may significantly impact atorvastatin therapy personalization in patients requiring LDL lipid-lowering therapy.

Genomic Epidemiology of African Swine Fever Virus Identified in Domestic Pig Farms in South Korea during 2019–2021

African swine fever (ASF), a contagious viral disease, poses a significant threat to the global swine industry. In South Korea, ASF outbreaks have occurred since 2019, highlighting the need for a comprehensive understanding of the epidemiology and genetic characterization of the circulating African swine fever viruses (ASFVs). We obtained 21 ASFV isolates from domestic pig farms and analyzed their whole-genome sequences using the Illumina MiniSeq. Phylogenetic analysis was conducted using the maximum likelihood and time-scaled approaches to determine the genetic relationships and evolutionary dynamics of the Korean ASFV isolates. Comparative analysis of the 21 ASFV genomes with the reference strain Georgia 2007/1 revealed that while Korean isolates shared 11 mutations, they also had 22 discrete mutations, including single nucleotide polymorphisms and insertion/deletion polymorphisms (Indels). Phylogenetic analysis indicated that all Korean isolates were within the Asian subgroup of ASFV genotype II but were further divided into at least three distinct subclusters. Spatiotemporal analysis indicated multiple introductions of ASFVs into South Korea, crossing the national border with North Korea. In addition, we observed putative self-recombination between MGF 505-9R and MGF 505-10R genes in the ASFV/Korea/Pig/Inje2/2021 strain. Our findings provide insights into the genetic variations and evolution of ASFVs on South Korean pig farms from 2019 to 2021, uncovering multiple introductions of ASFVs across the national border, and highlighting the need for enhanced disease control strategies.

Human leukocyte antigen association in systemic sclerosis patients: our experience at a tertiary care center in North India.

Systemic sclerosis (SSc) is a chronic multisystem autoimmune rheumatic disease of unknown etiology. Several studies have established that SSc is triggered by a dynamic interplay between genetic factors and environmental stimuli. In the present study, we aimed to study the association of human leukocyte antigen (HLA) with familial and non-familial SSc patients [limited cutaneous SSc (lcSSc) and diffuse cutaneous SSc (dcSSc)] from North India. The HLA-A, B, DRB1, and DQB1 genotyping of 150 (70 lcSSc and 80 dcSSc) adult-onset SSc patients and 150 age-gender-matched healthy controls were performed with sequence-specific oligonucleotide (SSO) typing kits using the luminex platform. HLA typing for HLA class I (A, B, and C) and II (DRB1, DQB1, and DPB1) in five North Indian families consisting of parent-child/sibling pairs affected with SSc or overlap syndrome was performed by Next Generation Sequencing (NGS) with Illumina MiniSeq. Among the non-familial SSc patients, HLA- DRB1*11 (P = 0.001, OR: 2.38, P c = 0.01) was identified as a risk allele, and DRB1*12 (P = .0001, OR: 0.00, P c = 0.001) as a protective allele. There was no statistical association found with HLA-DQB1*. Also, no significant association was observed between HLA antigens and different clinical subsets (lcSSc and dcSSc) of SSc. Two cases of familial SSc patients had the DRB1*11 allele. The DRB1*12 allele was absent in all the familial SSc patients. HLA DRB1*11 (risk allele) and DRB1*12 (protective allele) were found to be strongly associated with non-familial SSc patients and partially explain the disease's familial clustering, supporting the susceptible genetic background theory for SSc development. The study also indicates the HLA allele as a common genetic risk factor in distinct autoimmune diseases contributing to overlap syndrome or polyautoimmunity.

Epidemiological characteristics of mpox epidemic in Guangzhou

Objective: To understand the epidemiological characteristics of mpox epidemic in Guangzhou and provide scientific evidence for the prevention and control of the disease. Methods: Based on the mpox surveillance system in Guangzhou, suspected mpox cases with fever and rash were reported by local hospitals at all levels to centers for disease control and prevention in Guangzhou for sampling, investigation and diagnosis. Descriptive epidemiological analysis was conducted on the clinical characteristics and treatment of the mpox cases and positive detection rate reported in Guangzhou as of 24:00 on June 23. Whole genome sequencing of the virus isolates was performed using Illumina Miniseq high-throughput sequencing platform. Results: The first mpox case in Guangzhou was reported on June 10 in 2023. As of 24:00 on June 23, a total of 25 confirmed mpox cases were reported. All the mpox cases were men with a M(Q1,Q3) of 32 (26, 36) years, the majority of the cases were MSM (96.0%). The main clinical features were rash (100.0%, 25/25), lymphadenectasis (100.0%, 25/25) and fever (52.0%, 13/25). Rash usually occurred near the genitals (88.0%, 22/25). The close contacts, mainly family members (40.4%, 23/57), showed no similar symptoms, such as fever or rash. The positive rate of mpox virus in household environment samples was 30.5%. The analyses on 3 complete gene sequences of mpox virus indicated that the strains belonged to West African type Ⅱb clade, B.1.3 lineage. Conclusions: Hidden transmission of mpox virus had occurred in MSM in Guangzhou. However, the size of affected population is relatively limited, and the possibility of wide spread of the virus is low.

A rapid and affordable amplicon-based method for next-generation genome sequencing of the infectious bursal disease virus

The infectious bursal disease virus (IBDV) causes a severe immunosuppressive disorder in young chickens. IBDV evolution resulted in the emergence of strains with divergent genetic, antigenic, and pathogenic characteristics. Genetic classification is typically performed by sequencing the coding region of the most immunogenic region of the viral protein 2 (VP2). Sequencing both double-stranded RNA genome segments is essential to achieve a more comprehensive IBDV classification that can detect recombinants and reassortments. Here, we report the development and standardization of a tiled PCR amplicon protocol for the direct and cost-effective genome sequencing of global IBDV strains using next-generation technology. Primers for tiled PCR were designed with adapters to bypass expensive and time-consuming library preparation steps. Sequencing was performed on Illumina MiniSeq equipment, and fourteen complete genomes of field strains were assembled using reference sequences. The PCR-enrichment step was used to obtain genomes from low-titer biological samples that were difficult to amplify using traditional sequencing. Phylogenetic analyses of the obtained genomes confirmed previous strain classification. By combining the enrichment methodology with massive sequencing, it is possible to obtain IBDV genomic sequences in a fast and affordable manner. This procedure can be a valuable tool to better understand virus epidemiology.

Unraveling the Mystery: Next Generation Sequencing Sheds Light on Neuroblastoma Pathogenesis and Targeted Therapies.

There is considerable interest in the molecular evaluation of solid tumors in pediatric cases. Although clinical trials are in progress for targeted therapies against neuroblastoma (NB), novel therapeutic strategies are needed for high-risk cases that are resistant to therapy. The aim of the present study was to document the specific gene mutations related to targeted therapy in relapsed or refractory NB patients by using next generation sequencing (NGS). The study included 57 NB patients from amongst 1965 neuroblastic cases in Turkey who experienced a recurrence after multi-model therapy. The cases were diagnosed, risk-stratified, and treated according to the classification system from the International Neuroblastoma Risk Group. Single nucleotide variations in 60 genes were investigated using the Pillar Onco/Reveal Multicancer v4 panel and Pillar RNA fusion panel on the Illumina Miniseq platform. ERBB2 I655V was the most frequent mutation and was found in 39.65% of cases. Anaplastic Lymphoma Kinase (ALK) mutations (F1174L, R1275Q, and rare mutations in the tyrosine kinase domain) were detected in 29.3% of cases. Fusion mutations in NTRK1, NTRK3, ROS1, RET, FGFR3, ALK and BRAF were observed in 19.6% of cases. This study presents valuable mutation data for relapsed and refractory NB patients. The high frequency of the ERBB2 I655V mutation may allow further exploration of this mutation as a potential therapeutic target. Rare BRAF mutations may also provide opportunities for targeted therapy. The role of ABL1 mutations in NB should also be explored further.

Salmonella Typhi whole genome sequencing in Rwanda shows a diverse historical population with recent introduction of haplotype H58.

Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, presenting high rates of morbidity and mortality in low- and middle-income countries. The H58 haplotype shows high levels of antimicrobial resistance (AMR) and is the dominant S. Typhi haplotype in endemic areas of Asia and East sub-Saharan Africa. The situation in Rwanda is currently unknown and therefore to reveal the genetic diversity and AMR of S. Typhi in Rwanda, 25 historical (1984-1985) and 26 recent (2010-2018) isolates from Rwanda were analysed using whole genome sequencing (WGS). WGS was locally implemented using Illumina MiniSeq and web-based analysis tools, thereafter complemented with bioinformatic approaches for more in-depth analyses. Whereas historical S. Typhi isolates were found to be fully susceptible to antimicrobials and show a diversity of genotypes, i.e 2.2.2, 2.5, 3.3.1 and 4.1; the recent isolates showed high AMR rates and were predominantly associated with genotype 4.3.1.2 (H58, 22/26; 84,6%), possibly resulting from a single introduction in Rwanda from South Asia before 2010. We identified practical challenges for the use of WGS in endemic regions, including a high cost for shipment of molecular reagents and lack of high-end computational infrastructure for the analyses, but also identified WGS to be feasible in the studied setting and giving opportunity for synergy with other programs.

Microbial and epidemiological factors in early detection of esophageal squamous cell carcinoma and precancerous lesions.

Microbial and epidemiological factors in early detection of esophageal squamous cell carcinoma and precancerous lesions.

Long QTc in hypertrophic cardiomyopathy: A consequence of structural myocardial damage or a distinct genetic disease?

Hypertrophic cardiomyopathy (HCM) is an autosomal dominant disease, characterized by the presence of unexplained left ventricular hypertrophy. This condition is often associated with electrocardiographic abnormalities including QTc prolongation occurring in 13% of patients. The main explanation for prolonged QTc in HCM is myocardial hypertrophy and the related structural damage. However, other mechanisms, including long QT syndrome (LQTS) genes mutations, may be involved. In the present study we explored the hypothesis of a distinct genetic basis underlying QTc prolongation in HCM by investigating the potential co-inheritance of pathogenic gene variants associated with LQTS and HCM. For this purpose, starting from a cohort of 150 HCM patients carrying pathogenic variants in sarcomere genes, we selected 25 patients carrying a QTc prolongation unexplained by any other cause. The QTc was considered prolonged if greater than 450 ms in males and greater than 470 ms in females. The NGS analysis was performed with Illumina TrueSight Cardio panel genes on Illumina MiniSeq platform. We identified pathogenic/likely pathogenic variants in the KCNQ1 in two patients (c.1781G > A, p. Arg594Gln; c.532G > A, p. Ala178Thr) (8%). Variants of uncertain significance were identified in SCN5A, KCNJ5, AKAP9 and ANK2 in four patients (16%). Although the results are limited by the small number of patients included in the study, they highlight a minor contribution of LQTS genes for QTc prolongation in HCM patients. The screening for ion channel genes mutations may be considered in HCM patients with prolonged QTc unexplained by any other cause. This in-depth molecular diagnosis may contribute to improve risk stratification and treatment planning.

Optimization of the Illumina COVIDSeq™ protocol for decentralized, cost-effective genomic surveillance

A decentralized surveillance system to identify local outbreaks and monitor SARS-CoV-2 Variants of Concern is one of the primary strategies for the pandemic's containment. Although next-generation sequencing (NGS) is a gold standard for genomic surveillance and variant discovery, the technology is still cost-prohibitive for decentralized sequencing, particularly in small independent labs with limited resources. We have optimized the Illumina COVIDSeq™ protocol for the Illumina MiniSeq instrument to reduce cost without compromising accuracy. We slashed the library preparation cost by half by using 50% of recommended reagents at each step and normalizing the libraries before pooling to achieve uniform coverage. Reagent-only cost (∼$43.27/sample) for SARS-CoV-2 variant analysis with this normalized input protocol on MiniSeq instruments is comparable to what is achieved on high throughput instruments such as NextSeq and NovaSeq. Using this modified protocol, we tested 153 clinical samples, and 90% of genomic coverage was achieved for 142/153 samples analyzed in this study. The lineage was correctly assigned to all samples (152/153) except for one. This modified protocol can help laboratories with constrained resources to contribute in decentralized COVID-19 surveillance in the post-vaccination era.

2048. Molecular Characterization and Resistance Factors of Circulating Acinetobacter baumannii isolates in South-East Michigan

Abstract Background Carbapenem-resistant Acinetobacter baumannii (CRAb) is increasing due to widespread use of antibiotics. Multidrug resistant (MDR) CRAb is a major threat to public health as treatment options are limited. The objective of this study is to elucidate the molecular epidemiology of circulating antibiotic resistance genes causing MDR CRAb infections by using a combination of whole-genome Multi-Locus Sequence Typing (wgMLST) and antibiotic susceptibility phenotyping. Table 1.Molecular characterization of MDR CRAb isolates*The numbers indicate % of sequence identity match for each Beta-lactamase gene. Methods Bacterial isolates were derived from cultures taken from subjects 48 hours following admission as part of routine clinical care for patients between 2017-2020. Isolates were obtained from 16 hospital units (both ICU and non-ICU) across two hospitals in the Detroit area. Whole Genome Sequencing (WGS) was performed using Illumina MiniSeq or Nextseq. WgMLST analysis was performed using BioNumerics software v7.6. ResFinder software was used for analysis of antibiotic resistance genes. Isolates underwent antibiotic susceptibility testing using a broth microdilution method (VITEK2) and Clinical &amp; Laboratory Standards Institute (CLSI) minimum inhibitory concentration (MIC) cut offs. Results Out of the 95 total isolates, 51(54%) were CRAb isolates and of the CRAb isolates, 21(41%) were MDR CRAb. WgMLST identified that majority of the circulating MDR CRAb isolates belonged to ST2Pas (ST195Ox and ST208Ox) based on CDC definitions (Table 1). MDR CRAb isolates were resistant to 3 different classes of antibiotics including aminoglycosides, fluroquinolones and β-lactams. β-lactamase genes present include (blaADC-25, blaOXA-23, blaOXA-66 and blaTEM1D) for both ST195Ox and ST208Ox and (blaADC-25, blaOXA-23 and blaOXA-223) for ST406Pas (ST310Ox). Among the patients with MDR CRAb infections, most were males with respiratory infections in a non-ICU setting. Conclusion The study demonstrated a high proportion of isolates belonged to ST2 Pas carrying multiple beta-lactamase genes including blaOXA-23 gene. ST406Pas might be an emerging lineage carrying the blaOXA-23 gene. In addition to stringent infection control measures, continuous surveillance is recommended in limiting the spread of MDR CRAb isolates in the healthcare settings. Disclosures Chetan Jinadatha, MD, MPH, AHRQ R01 Grant-5R01HS025598: Grant/Research Support|EOS Surfaces: Copper Coupons and materials for testing Keith S. Kaye, MD, MPH, Allecra: Advisor/Consultant|GlaxoSmithKline plc.: Receiving symposia honoraria|GlaxoSmithKline plc.: GlaxoSmithKline plc.-sponsored study 212502|Merck: Advisor/Consultant|qpex: Advisor/Consultant|Shionogi: Grant/Research Support|Spero: Advisor/Consultant Piyali Chatterjee, PhD, AHRQ Grant # 1R03HS027667-01: Grant/Research Support|AHRQ Grant # 1R03HS027667-01: Central Texas Veterans Health Care System.

1064 LONG QTC IN HCM: A CONSEQUENCE OF MYOCARDIAL HYPERTROPHY OR A DISTINCT GENETIC DISEASE?

Abstract Hypertrophic cardiomyopathy (HCM) is an autosomal dominant condition, characterized by the presence of unexplained left ventricular hypertrophy. This condition is usually associated with electrocardiographic abnormalities including QTc prolongation reported in the 13% of HCM patients. The main explanation for QTc prolongation in HCM is myocardial hypertrophy and the related structural damage. However, mechanisms other than myocardial hypertrophy, including long QT syndrome (LQTS) gene mutations, may also be involved. The addictive effect of 2 disease-causing mutations has been already reported in other pathological conditions. In the present study we investigated the possible co-inheritance of pathogenic variants associated with both LQTS and HCM, exploring the hypothesis of a distinct genetic basis underlying QTc prolongation in HCM. For this purpose, we considered a cohort of 150 HCM patients carrying pathogenic variants in sarcomeric genes. Out of them we selected 25 patients carrying a QTc prolongation not explained by any other cause (drugs, etc). The QTc was considered prolonged if greater than 450 ms in males and greater than 470 ms in females. NGS analysis was performed with Illumina TrueSight Cardio panel genes on Illumina MiniSeq platform to evaluate the presence of pathogenetic variants in LQTS related genes. We identified pathogenic/likely pathogenic variants in LQTS related gene KCNQ1 (c.1781G&amp;gt;A, p. Arg594Gln; c.532G&amp;gt;A, p. Ala178Thr) in two patients (8%) and uncertain significant variants in SCN5A, KCNJ5, AKAP9 and ANK2 in four patients (16%). Although the results of our study are limited by the small number of patients included in the analysis, they highlight a minor contribution of LQTS genes in HCM patients with a QTc prolongation. The screening for ion channel gene mutations should be considered in HCM patients with QTc prolongation, not explained by any other cause. This strategy may be important for risk stratification and treatment planning.

Training and Validation Cohorts for Predicting the Impact of High Molecular Risk Mutations after Allogeneic Stem Cell Transplantation in Myelofibrosis

Introduction Myelofibrosis (MF) is the most aggressive form of Philadelphia negative myeloproliferative neoplasm and allogeneic hematopoietic stem cell transplantation (HSTC) is the only curative approach, but non relapse mortality limits the indication for HSTC to high-risk patients. The prognostic evaluation of MF patients is evolving during time together with a better understanding of the mutational landscape of this disease. The presence of high molecular risk (HMR) mutations, specifically ASXL1, SRSF2, EZH2, IDH1, IDH2 and U2AF1Q157, harbors a detrimental effect on survival and leukemic transformation and has been incorporated in different prognostic scoring systems. In this multicenter study we aimed to determine the impact of HMR mutations on transplant outcome. Methods We studied two independent cohorts of patients: 44 patients (training, retrospective cohort) were part of a multicenter, randomized GITMO (Gruppo Italiano Trapianti di Midollo Osseo) clinical trial (Patriarca F, BBMT 2019) and 29 patients (validation, prospective cohort) were subsequently recruited at the Bergamo Bone Marrow Transplant Unit. Patients from the training cohort (median age 56, range 36-66) were conditioned with busulfan-fludarabine or thiotepa-fludarabin while patients in the validation cohort (median age 61, range 36-67) were conditioned with a reduced intensity thiotepa-busulfan-fludarabin regimen. The mutational profile obtained on the pre-transplant DNA was performed by sequencing 30 myeloid related genes by applying SOPHia GENETICS Myeloid Solution on Illumina MiniSeq platform. Results In the training retrospective cohort, driver mutations were detected in 40 (29 JAK2/8 CALR/3 MPL) patients, with 4 patients having a triple negative MF. At least one HMR mutation was detected in 43% of patients and an unfavorable karyotype was present in 18% of patients. According to the Mutation-Enhanced International Prognostic Scoring System 70 plus (MIPPS70+) scoring system, 77% of patients were allocated in the high/very high groups. With a median follow up of 4.2 years (range 0.02-9), the 5-years Overall Survival (OS) and Progression Free Survival (PFS) were 61% and 45% respectively. The 5-years Non-Relapse Mortality (NRM) and Cumulative Incidence of Relapse (CIR) were 25% and 30%. In the prospective validation cohort, a driver mutation was detected in all patients (15 JAK2/7 CALR/7MPL). At least one HMR mutation was detected in 48% of patients and an unfavorable karyotype was present in 24% of patients. Patients allocated to the MIPPS70+ high/very group were 52%. After a median follow up of 10.7 months (range 0-44), the 2-years OS and PFS were 61% and 49% respectively. The 2-years NRM and CIR were 33% and 18%. In the training cohort, a higher risk of death and progression was observed in patients with high/very high risk MIPPS70+ prognostic index [HR for OS 4.3 (95% CI 0.6-33.1), HR for PFS 4.1 (95% CI 0.9-16.9)]. Conversely, the presence of HMR mutations did not significantly affect OS, PFS (Figure 1), NRM or CIR. The prognostic significance of MIPSS70+ risk classification was confirmed in the validation cohort, with a higher risk of death and progression for high/very high MIPSS70+ group [OS HR 3.2 (95% CI 0.4-27.1), PFS HR 3.8 (95% CI 0.5-31.4)]. Similarly, in the validation cohort the presence of HMR mutations did not affect transplant outcome, with no impact on OS, PFS (Figure 2), NRM or CIR. In the whole group of 73 patients, the presence of JAK2V617F mutation showed an adverse prognostic impact on CIR [HR 3.4 (95% CI 1-11.8)], while MIPPS70+ confirmed its role on PFS. Conclusions In this study we prospectively confirmed that the presence of HMR mutations did not impact on transplant outcome. Allogeneic stem cell transplantation can lead to a significant cure rate of MF patients, regardless the presence of HMR mutations. Patients in the high/very high MIPSS70+ risk group had a higher risk of death and progression after transplant. Appropriate timing and selection of patients is crucial for transplant outcome in MF. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

A Preliminary Genomic Analysis of the Omicron Variants of SARS-CoV-2 in Central India During the third wave of the COVID-19 Pandemic

BackgroundOmicron was detected in South Africa for the first time at the month of November 2021, from then it expanded swiftly over the world, outcompeting other SARS-CoV-2 variants such as Delta. The toxicity, resistance to antiviral medicines, transmissibility, and vaccine-induced immunity of newly developed SARS-CoV-2 variants are major worldwide health concerns.Aim of studyThis study investigates the comprehensive explanation of all mutations and their evolutionary linkages between the Omicron variant and recently discovered SARS‐CoV‐2 variants.MethodOn Illumina MiniSeq Machine, 31 RNA isolates from clinical specimens were sequenced utilizing next-generation sequencing technique. Different bioinformatics tools have been used to analyze the mutations in omicron variant. A phylogenetic tree was constructed to determine Omicron's evolutionary relationships with other variants.ResultsIn our investigation, we discovered 79 distinct types of mutations in 31 fully vaccinated COVID-19 positive samples. Mostly mutations were found in non-spike region. According to the NJ approach of phylogenetic tree revels, the nearest variants were in the order listed, based on sequence identity: Omicron, Gamma, Alpha, Delta, Mu and Beta. On the other hand as per UPGMA approach, the Omicron variation creates a novel monophyletic clade that is distinct from previous SARS-CoV-2 variants.ConclusionDespite the fact that some of the mutations are prevalent in Omicron and other VOCs, there are several unique mutations that have been connected to the virus's transmissibility and immune evasion, indicating a substantial shift in SARS-CoV-2 evolution.

First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador

BackgroundCOVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. MethodologyA genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. ResultsThe raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. ConclusionsWe concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.

Genome Sequencing of Omicron Variants of SARS-CoV-2 Circulating in Bangladesh during the Third Wave of the COVID-19 Pandemic.

ABSTRACTThe coding-complete genome sequence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was obtained from 39 nasopharyngeal swab samples collected in January 2022 from Dhaka, Bangladesh, during the 3rd wave of the COVID-19 pandemic, using Illumina MiniSeq sequencing technology. Sequence analysis showed that all of them belonged to the WHO-designated variant of concern (VOC) Omicron. The presence of different sublineages of Omicron was noted, among which sublineage BA.2 (Nextstrain clade 21L) was the most prevalent one.

Complete Genome Sequences of Five Gram-Negative Bacterial Strains Comprising Synthetic Bacterial Consortium "The Great Five" with Antagonistic Activity Against Plant-Pathogenic Pectobacterium spp. and Dickeya spp.

Complete Genome Sequences of Five Gram-Negative Bacterial Strains Comprising Synthetic Bacterial Consortium "The Great Five" with Antagonistic Activity Against Plant-Pathogenic Pectobacterium spp. and Dickeya spp.

Gut bacterial profile associated with healthy and diseased (AHPND) shrimp Penaeus vannamei

The effect of Vibrio parahaemolyticus IPNGS16 on the bacterial profile of the gut of Penaeus vannamei was assessed by 16S metagenomic analysis. The V3 hypervariable region of the bacterial 16S rDNA was amplified by PCR. Sequencing reads were generated using the 2×150 (300 cycles) for the base-read length chemistry of the Illumina MiniSeq platform. The web-based Shaman and MicrobiomeAnalyst platforms were used to analyze the sequences. The phyla Proteobacteria, Bacteroidetes, and the genera Vibrio, Ruegeria, Nautella, and Pseudoalteromonas were found among the most abundant taxonomic ranks in control, diseased, and healthy shrimp. Alpha and beta indices showed significant differences between shrimp survival in the control condition and dying shrimp (lower diversity). Metabolism (carbohydrate and amino acid metabolism-related genes and, to a lesser extent, energy, lipid, and cofactors and vitamin metabolism-related genes) of dying and surviving shrimp was affected by Vibrio infection. The top metabolic functions (cell cycle, glycine, serine, threonine, cysteine, methionine, purine, pyrimidine, pyruvate, and quorum sensing) in dying and surviving shrimp were affected by Vibrio, especially quorum sensing. The interaction network analysis showed fewer interactions in dying shrimp than control and surviving shrimp. Proteobacteria, Bacteroidetes, Vibrio, and Ruegeria predominated in all samples, and Vibrio changed bacterial diversity and metabolism in the intestine of P. vannamei. Ruegeria and Pseudoalteromonas showed negative interactions with Vibrio, suggesting their use as probiotics. This study sheds light on the Vibrio infection in the gut microbiota of shrimp.