Deep Amplicon Sequencing Research Articles

NGS Techniques Reveal a High Diversity of RNA Viral Pathogens and Papillomaviruses in Fresh Produce and Irrigation Water.

Fresh fruits and vegetables are susceptible to microbial contamination at every stage of the food production chain, and as a potential source of pathogens, irrigation water quality is a critical factor. Next-generation sequencing (NGS) techniques have been flourishing and expanding to a wide variety of fields. However, their application in food safety remains insufficiently explored, and their sensitivity requires improvement. In this study, quantitative polymerase chain reaction (qPCR) assays showed low but frequent contamination of common circulating viral pathogens, which were found in 46.9% of samples of fresh produce: 6/12 lettuce samples, 4/12 strawberries samples, and 5/8 parsley samples. Furthermore, the application of two different NGS approaches, target enrichment sequencing (TES) for detecting viruses that infect vertebrates and amplicon deep sequencing (ADS), revealed a high diversity of viral pathogens, especially Norovirus (NoV) and Human Papillomavirus (HPV), in fresh produce and irrigation water. All NoV and HPV types found in fresh fruit and vegetable samples were also detected in irrigation water sources, indicating that these viruses are common circulating pathogens in the population and that irrigation water may be the most probable source of viral pathogens in food samples.

Whole genome sequencing of low input circulating cell-free DNA obtained from normal human subjects.

Cell‐free DNA circulates in plasma at low levels as a normal by‐product of cellular apoptosis. Multiple clinical pathologies, as well as environmental stressors can lead to increased circulating cell‐free DNA (ccfDNA) levels. Plasma DNA studies frequently employ targeted amplicon deep sequencing platforms due to limited concentrations (ng/ml) of ccfDNA in the blood. Here, we report whole genome sequencing (WGS) and read distribution across chromosomes of ccfDNA extracted from two human plasma samples from normal, healthy subjects, representative of limited clinical samples at <1 ml. Amplification was sufficiently robust with ~90% of the reference genome (GRCh38.p2) exhibiting 10X coverage. Chromosome read coverage was uniform and directly proportional to the number of reads for each chromosome across both samples. Almost 99% of the identified genomic sequence variants were known annotated dbSNP variants in the hg38 reference genome. A high prevalence of C>T and T>C mutations was present along with a strong concordance of variants shared between the germline genome databases; gnomAD (81.1%) and the 1000 Genome Project (93.6%). This study demonstrates isolation and amplification procedures from low input ccfDNA samples that can detect sequence variants across the whole genome from amplified human plasma ccfDNA that can translate to multiple clinical research disciplines.

CABE-RY: A PAM-flexible dual-mutation base editor for reliable modeling of multi-nucleotide variants

Multi-nucleotide variants (MNVs) represent an important type of genetic variation and have biological and clinical significance. To simulate MNVs, we designed four dual-mutation base editors combining hA3A(Y130F), TadA8e(V106W), and protospacer adjacent motif (PAM)-flexible SpRY and selected cytosine and adenine base editor-SpRY (CABE-RY), which had the best editing performance, for further study. Characterization and comparison showed that CABE-RY had a smaller DNA editing window and lower RNA off-target edits than the corresponding single base editors. Thus, we have established a versatile tool to efficiently simulate MNVs over the genome, which could be very useful for functional studies on MNVs in humans.

Deep Sequencing to Detect Diversity of Trypanosoma cruzi Infection in Patients Coinfected With Human Immunodeficiency Virus and Chagas Disease.

Chagas disease, caused by Trypanosoma cruzi, can reactivate and cause severe acute disease in immunocompromised patients such as those infected with human immunodeficiency virus (HIV). We conducted amplicon deep sequencing of a 327-bp fragment of the tcscd5 gene using an Ion Torrent PGM directly from clinical samples from HIV patients with high parasitemia. We describe the within-host diversity, both characterizing the discrete typing unit of the infections and confirming the presence of multistrain infections, directly from clinical samples. This method can rapidly provide information on the genetic diversity of T. cruzi infection, which can have direct impacts on clinical disease.

Functional Validation of cas9/guideRNA Constructs for Site-Directed Mutagenesis of Triticale ABA8'OH1 loci.

Cas endonuclease-mediated genome editing provides a long-awaited molecular biological approach to the modification of predefined genomic target sequences in living organisms. Although cas9/guide (g)RNA constructs are straightforward to assemble and can be customized to target virtually any site in the plant genome, the implementation of this technology can be cumbersome, especially in species like triticale that are difficult to transform, for which only limited genome information is available and/or which carry comparatively large genomes. To cope with these challenges, we have pre-validated cas9/gRNA constructs (1) by frameshift restitution of a reporter gene co-introduced by ballistic DNA transfer to barley epidermis cells, and (2) via transfection in triticale protoplasts followed by either a T7E1-based cleavage assay or by deep-sequencing of target-specific PCR amplicons. For exemplification, we addressed the triticale ABA 8′-HYDROXYLASE 1 gene, one of the putative determinants of pre-harvest sprouting of grains. We further show that in-del induction frequency in triticale can be increased by TREX2 nuclease activity, which holds true for both well- and poorly performing gRNAs. The presented results constitute a sound basis for the targeted induction of heritable modifications in triticale genes.

Identification of Somatic Mutations in Expanded T Cell Clones of Patients with Chronic Graft-Versus-Host Disease (GVHD)

Background: GVHD is the main complication in allogeneic hematopoietic stem cell transplantation (allo-HSCT). Chronic GVHD (cGVHD) develops in 60-80 % of allo-HSCT survivors causing marked morbidity and mortality. Donor alloreactive T cells are the key drivers in the development of cGVHD, since they recognize and damage the host target tissues by cytokine release and direct cytolysis. Unbalanced reconstitution of T cell pool has been suggested to be a crucial factor in the development of cGVHD. In particular, disease-associated T cell receptor (TCR) clones have been detected and abnormally expanded within the blood and affected tissues in cGVHD patients. It is unclear why these T cell clones do not undergo physiologic FAS-mediated apoptosis. Here, we hypothesized that acquired somatic mutations in T cells may lead to skewed clonal expansions and contribute to the pathogenesis of cGVHD.Methods and Results: We collected blood samples from patients with cGVHD (n=39) and healthy controls (n=11). CD4+ and CD8+T cells were sorted with magnetic beads, and genomic DNA was extracted. TCR repertoire was analyzed by T cell receptor b-chain (TCRB CDR3) deep sequencing. Somatic mutations in CD4+ and CD8+ T cells were discovered using a custom NGS gene panel consisting of 2000 genes that are essential for innate and adaptive immunity.Interestingly, the index cGVHD patient had a marked clonal expansion within the CD4+T cell pool, and TCRB deep sequencing revealed one specific TCRVB clone (30-01, 50% of CD4+T cells). By performing the immune gene panel sequencing, we discovered 3 somatic mutations in mTOR, TLR2 , and NFkB2 genes in the expanded CD4+T cell clone. The mutations persisted during a 2-year follow-up and were not detected within the CD8+T cell compartment. To verify the sequencing results, targeted mTOR, TLR2, and NFkB2 sequencing was performed with an in-house developed deep (1,000x coverage) amplicon sequencing panel. Subsequently, 128 cGVHD patients were screened to assess whether the discovered mutations were recurrent. In total, the mTOR mutation was discovered in 3 patients, the TLR2 mutation in 19 patients, and the NFkB2 mutation only in the index case. Strikingly, the mTOR mutation was also identified in the sclerodermatic skin lesion from the index patient with a low variant allele frequency (VAF), and immunofluorescence staining confirmed CD4+T cell infiltration in the skin. In T cells of the index patient's sibling donor, no mTOR, TLR2, or NFkB2 mutations were detected. In a cohort of 29 additional healthy individuals, no mTOR or NFKB2 mutations were detected in sorted T-cell fractions, but small VAF TLR2 mutations were found in 7 controls implying them not to be GVHD related.To study the functional consequences of the identified mutations, we constructed expression vectors containing the mutations for transfection of HEK-293 cells. Alterations in transcriptional regulation were evaluated by analyzing mRNA expression levels of a subset of mTOR, TLR2 and NFkB2 downstream targets byqRT-PCR. The levels of MAPKAP1, RPS6, RHOA, NFKB1, NFKBIL1, NFRKB, ELK1, FOS, MAP3K1, MAP3K7 , and MAP4K4 were significantly increased in mutant cells compared to wild-type controls.Finally, the NFkB2 mutation was located in the c-terminal domain which is known to play an important role in the ubiquitination and partial proteolysis from NFkB2 (p100) to NFkB2 (p52). To analyze the molecular balance between p100 and p52, immunoblotting was pursued and revealed that the mutation induced overexpression of p52.Conclusions: We identified novel somatic mutations in T cells of patients with cGVHD. In our index patient, the mutations were discovered in the aberrantly expanded CD4+T cell clone. As the mutations were not observed in the T-cells of the sibling donor, we hypothesize that they were acquired during the immune activation and rapid expansion of T cells after the allo-HSCT. The discovered mTOR mutation was found to be recurrent in 3 patients based on a screening cohort of 128 cGVHD patients, but was not detected in healthy individuals. Functional analyses suggested the mutations to be gain-of-function of nature, and thus inducing marked activation of the mTOR and NFkB2 signaling pathways. As both pathways are crucial in T cell activation and function, our data may provide a novel explanation for the aberrant, persistent T cell activation in cGVHD and pave the way for novel targeted therapies. DisclosuresMustjoki:Novartis: Honoraria, Research Funding; Pfizer: Honoraria, Research Funding; Ariad: Research Funding; Celgene: Honoraria; BMS: Honoraria, Research Funding.

Recurrent STAT3 Mutations in the Lymphocytes of Pure Red Cell Aplasia without T-Cell Large Granular Lymphocytic Leukemia

▪Background: Activating somatic mutations of STAT3 are one of the most frequently recognized genetic alterations in T-cell lymphoma including T-cell large granular lymphocytic leukemia (T-LGLL). T-LGLL is associated with certain proportions of patients (pts) with acquired aplastic anemia (AA) and/or myelodysplastic syndromes (MDS). Pure red cell aplasia (PRCA), especially acquired PRCA, is a syndrome defined by an anemia with marked reduction or absence of erythroid production associated with immunological mechanisms. PRCA is classified into primary and secondary types including T-LGLL. Previous reports have described that T-LGLL with STAT3 mutations was closely associated with PRCA. However, it is yet to be clear whether STAT3-mutated T cells would be involved in the pathogenesis of other cytopenias, such as AA, MDS, primary PRCA or secondary PRCA without (w/o) T-LGLL. In this study, we analyzed the profiles of STAT3 gene mutations in bone marrow failure syndrome (BMFS)s including AA/MDS and PRCA.Methods: Peripheral blood samples were collected from 94 patients with BMFSs, including AA, MDS, AA/PNH, and PRCA with or w/o T-LGLL. When possible, T-cell receptor (TCR) Vβ repertoire of the patients was determined by flow cytometry. DNA was extracted from mononuclear cells (MNC), and STAT3 Y640F and D661Y, two hot spot mutations, were detected with sensitive allele specific-PCR (AsPCR) methods. Then we performed deep amplicon sequencing analysis of STAT3 in PRCA pts. CD8+ T cells were sorted if possible, and also subjected to the analyses.Results: The recruited pts included 38 AA, 20 MDS, 7 AA/PNH, 11 PRCA with T-LGLL, and 18 PRCA w/o T-LGLL. Among PRCA pts w/o apparent T-LGLL, 10 had primary PRCA and 8 had secondary PRCA including 2 with thymoma. The clinical characteristics of PRCA are shown in Table 1. TCR Vβ repertoire analysis were performed in 8 PRCA w/o T-LGLL and 5 PRCA with T-LGLL. All pts with PRCA associated with T-LGLL showed restricted Vβ repertoire. On the other hand, only 1pt showed monoclonal Vβ pattern in PRCA w/o TLGLL. AsPCR did not detect Y604F or D661Y mutations in any of 65 pts with AA, MDS, or AA/PNH. In contrast, 2 pts with PRCA and 4 pts with PRCA-T-LGLL were positive for either of the mutations, suggesting STAT3 mutations may be unique to PRCA pts. Further analysis with deep amplicon analysis in the 29 PRCA pts revealed STAT3 mutations in 11 pts (61%) of PRCA w/o T-LGLL, which included 6 pts with primary PRCA and 5 pts with secondary PRCA associated with autoimmune diseases (n=2), 2 thymoma (n=2) and thymic cancer (n=1). The median variant allele frequency of STAT3 mutations was 2.3% (0.2-48.9). N538Y and I653V were most frequent mutations in PRCA w/o T-LGLL. Eight pts (73%) with T-LGLL-associated PRCA were also positive for STAT3 mutation. Thirty-nine % and 70% of STAT3 mutation were found in SH2 domain in PRCA w/o T-LGLL and PRCA with T-LGL, respectively. There was no difference in clinical features between pts with and w/o STAT3 mutations.Discussion: The high frequency of STAT3 mutations in PRCA pts regardless of etiology and the absence of the mutation in pts with AA/MDS suggest that STAT3 mutations may serve as a molecular marker of PRCA. The discordant results with regard to AA/MDS pts from a previous report which detected STAT3 mutations in 4.9% of AA/MDS patients by AsPCR methods (Jerez et al. BLOOD 2013) may be due to the difference in ethnic backgrounds of the pts studied. Given very low frequencies of STAT3 mutations in AA and MDS that were revealed by several previous studies, JAK/STAT signaling systems in the axis of STAT3 mutations may have unique roles in the pathogenesis of PRCA.Conclusion: STAT3 mutations are frequently detected in pts with PRCA even in pts w/o T-LGLL and the JAK/STAT pathway may therefore be therapeutic targets of PRCA. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Quantitative Next-Generation Sequencing (NGS) Based Monitoring of Minimal Residual Disease (MRD) Predicts Imminent Relapse in Patients with Myeloid Malignancies after Allogeneic Hematopoietic Stem Cell Transplantation

▪IntroductionThe introduction of novel techniques such as next-generation sequencing (NGS) enabled the discovery of several gene mutations in myeloid malignancies during the last years. This has not only improved our understanding of the pathogenesis but also allows refinement of current risk stratification systems including those predicting outcome after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Still, in patients (pts) with myeloid malignancies relapse represents the main cause of treatment failure after allo-HSCT. The success of therapeutic interventions for relapse after allo-HSCT strongly depends on disease burden implicating that early and sensitive relapse detection is essential. NGS generally allows the identification of candidate mutations prior to transplant which can be used to monitor minimal residual disease (MRD) after transplant. So far, NGS is not broadly employed to monitor MRD in pts with myeloid malignancies after allo-HSCT and evidence from literature is restricted to a few reports (Fu et al., 2013). Here we report our real-life experience regarding the use of NGS to quantitatively monitor MRD after allo-HSCT.Patients and MethodsFor this purpose, pts with myeloid malignancies undergoing allo-HSCT at our center between 2012 and 2016 were screened for mutations in the following genes: ASXL1, CBL, CEBPA, DNMT3A, ETV6, EZH2, IDH1, IDH2, SF3B1, SRSF2, KRAS, MPL, NRAS, RUNX1, TET2 and TP53. For this screening prior to transplantation amplicon deep-sequencing was applied to detect mutations. Patients with at least one mutation identified prior to transplant were quantitatively monitored after allo-HSCT for the individual mutations using the Nextera® XT DNA Kit (Illumina, San Diego, USA). This quantitative NGS assay has a sensitivity of <1%. Results of this NGS-based monitoring were correlated with the clinical courses of the individual pts and compared with the results obtained by other methods such as STR-based chimerism analyses, cytogenetics, XY-FISH and WT1 mRNA expression.ResultsA total of 26 pts (11 female, 15 male, median age 58 years) who received an allo-HSCT from a related (n = 3) or unrelated donor (n = 23) for the treatment of AML (n = 4), MDS (n = 18) or CMML (n = 4) exhibited at least one mutation detectable by NGS pre-transplant and were therefore included into this retrospective analysis. Among those, in 21 pts (81%) one, in 4 pts (15%) two and in one patient (4%) even three mutations were detectable in the investigated genes. The most frequently mutated genes were ASXL1 in 11 pts (42%), followed by EZH2 in 5 (19%) and TP53, TET2 and RUNX1 in 4 pts (15%), respectively. IDH2 and DNMT3A were mutated in two pts (8%) and SRSF2, SF3B1 and CEBPA in one patient (4%) each. The variant allele frequency (VAF) prior to transplant ranged from 6% to 53%. Eleven pts (42%) suffered from a hematological (73%) or molecular (27%) relapse in a median of 85 days (range, 28 - 383) after allo-HSCT. During a median post-transplant follow-up of 28 months (range, 9 - 70) a total of 86 samples were analyzed by NGS corresponding to a median of 3 samples per patient (range, 1 - 7). MRD positivity was defined as presence of the known mutation in at least 1% of reads. According to this definition, in 12 pts (46%) at least one molecular alteration became detectable again after a median of 3 months after allo-HSCT (range, 1 - 13,7) and was associated with a higher relapse incidence compared to pts without evidence of known molecular alterations (83% vs. 7%, p = 0.0002).ConclusionIn conclusion, this study shows that molecular monitoring by NGS pre-and post-transplantation can identify biomarkers which may help to predict imminent relapse and may be used to guide therapeutic interventions after transplantation. Taking into account the methodical restrictions of this retrospective analysis, this requires confirmation by a well-designed prospective trial. DisclosuresRautenberg:Celgene: Other: travel support. Nachtkamp:Celgene: Other: Travel Support. Gattermann:Novartis: Honoraria, Other: Travel support; Celgene: Honoraria; Takeda Pharmaceutical International Co.: Research Funding. Kobbe:Celgene: Other: Advisory Board, Research Funding. Schroeder:Celgene: Consultancy, Honoraria, Other: travel support.

Sources of persistent malaria transmission in a setting with effective malaria control in eastern Uganda: a longitudinal, observational cohort study

SummaryBackgroundSymptomatic malaria cases reflect only a small proportion of all Plasmodium spp infections. Many infected individuals are asymptomatic, and persistent asymptomatic Plasmodium falciparum infections are common in endemic settings. We aimed to quantify the contribution of symptomatic and asymptomatic infections to P falciparum transmission in Tororo, Uganda.MethodsWe did a longitudinal, observational cohort study in Tororo district, Uganda. We recruited participants of all ages from randomly selected households within this district. Participants were eligible if the selected household had no more than nine permanent residents and at least two members younger than 10 years, and the household was their primary residence, and they agreed to come to the study clinic for any fever episode and avoid antimalarial medications outside the study. Participants were followed-up by continuous passive surveillance for the incidence of symptomatic infections; routine assessments (ie, standardised clinical evaluation and blood samples) were done at baseline and at routine visits every 4 weeks for 2 years. P falciparum parasite density, gametocyte density, and genetic composition were determined molecularly using quantitative PCR (qPCR), quantitative reverse transcriptase PCR (qRT-PCR), and amplicon deep sequencing, respectively. Membrane feeding assays were also done to assess infectivity to mosquitoes. The contribution of different populations to the infectious reservoir was estimated for symptomatic infections, asymptomatic but microscopically detected infections, and asymptomatic but qPCR-detected infections; and for age groups younger than 5 years, 5–15 years, and 16 years or older.FindingsBetween Oct 4, 2017, and Oct 31, 2019, 531 individuals were enrolled from 80 randomly selected households and were followed-up for 2 years. At baseline, P falciparum was detected in 28 (5·3%) of 531 participants by microscopy and an additional 64 (12·1%) by qPCR and declined thereafter. In 538 mosquito feeding experiments on 107 individuals, 446 (1·2%) of 37 404 mosquitoes became infected, with mosquito infection rates being strongly associated with gametocyte densities (β=2·11, 95% CI 1·62–2·67; p<0·0001). Considering both transmissibility of infections and their relative frequency, the estimated human infectious reservoir consisted primarily of asymptomatic microscopy-detected infections (83·8%), followed by asymptomatic submicroscopic infections (15·6%), and symptomatic infections (0·6%). Children aged 5–15 years accounted for more than half of the infectious reservoir (58·7%); individuals younger than 5 years (25·8%) and those 16 years or older (15·6%) contributed less. Samples from four children contribued to 279 (62·6%) of 446 infected mosquitoes after multiple mosquito-feeding assays.InterpretationIndividuals with asymptomatic infections were important drivers of malaria transmission. School-aged children contributed to more than half of all mosquito infections, with a small minority of asymptomatic children being highly infectious. Demographically targeted interventions, aimed at school-aged children, could further reduce transmission in areas under effective vector control.FundingUS National Institutes of Health, Bill & Melinda Gates Foundation, and the European Research Council.

CRISPR/Cas9-mediated mutagenesis of sweet basil candidate susceptibility gene ObDMR6 enhances downy mildew resistance.

Sweet basil (Ocimum basilicum) is an economically important allotetraploid (2n = 4x = 48) herb whose global production is threatened by downy mildew disease caused by the obligate biotrophic oomycete, Peronospora belbahrii. Generation of disease resistant cultivars by mutagenesis of susceptibility (S) genes via CRISPR/Cas9 is currently one of the most promising strategies to maintain favored traits while improving disease resistance. Previous studies have identified Arabidopsis DMR6 (Downy Mildew Resistance 6) as an S gene required for pathogenesis of the downy mildew-causing oomycete pathogen Hyaloperonospora arabidopsidis. In this study, a sweet basil homolog of DMR6, designated ObDMR6, was identified in the popular sweet basil cultivar Genoveser and found to exist with a high copy number in the genome with polymorphisms among the variants. Two CRISPR/Cas9 constructs expressing one or two single guide RNAs (sgRNAs) targeting the conserved regions of ObDMR6 variants were generated and used to transform Genoveser via Agrobacterium-mediated transformation. 56 T0 lines were generated, and mutations of ObDMR6 were detected by analyzing the Sanger sequencing chromatograms of an ObDMR6 fragment using the Interference of CRISPR Edits (ICE) software. Among 54 lines containing mutations in the targeted sites, 13 had an indel percentage greater than 96% suggesting a near-complete knockout (KO) of ObDMR6. Three representative transgene-free lines with near-complete KO of ObDMR6 determined by ICE were identified in the T1 segregating populations derived from three independent T0 lines. The mutations were further confirmed using amplicon deep sequencing. Disease assays conducted on T2 seedlings of the above T1 lines showed a reduction in production of sporangia by 61–68% compared to the wild-type plants and 69–93% reduction in relative pathogen biomass determined by quantitative PCR (qPCR). This study not only has generated transgene-free sweet basil varieties with improved downy mildew resistance, but also contributed to our understanding of the molecular interactions of sweet basil-P. belbahrii.

Deep amplicon sequencing highlights low intra-host genetic variability of Echinococcus multilocularis and high prevalence of the European-type haplotypes in coyotes and red foxes in Alberta, Canada.

Echinococcus multilocularis (Em) is a zoonotic parasite considered a global emergent pathogen. Recent findings indicate that the parasite is expanding its range in North America and that European-type haplotypes are circulating in western Canada. However, genetic analyses are usually conducted only on a few parasites out of thousands of individuals within each definitive host, likely underestimating the prevalence of less common haplotypes. Moreover, mixed infections with several mtDNA haplotypes in the same host have been reported, but their relative abundance within the host was never estimated. We aimed to 1) estimate the frequency of co-infections of different Em haplotypes in coyotes (Canis latrans) and red foxes (Vulpes vulpes) from western Canada and their relative abundance within the definitive hosts, 2) detect less prevalent haplotypes by sampling a larger proportion of the parasite subpopulation per host, and 3) investigate differences in the distribution of Em haplotypes in these main definitive hosts; foxes and coyotes. We extracted DNA from ~10% of the worm subpopulation per host (20 foxes and 47 coyotes) and used deep amplicon sequencing (NGS technology) on four loci, targeting the most polymorphic regions from the mitochondrial genes cox1 (814 bp), nad1 (344 bp), and cob (387 bp). We detected the presence of mixed infections with multiple Em haplotypes and with different Echinococcus species including Em and E. granulosus s.l. genotypes G8/G10, low intraspecific diversity of Em, and a higher abundance of the European-type haplotypes in both hosts. Our results suggest a population expansion of the European over the North American strain in Alberta and a limited distribution of some European-type haplotypes. Our findings indicate that deep amplicon sequencing represents a valuable tool to characterize Em in multiple hosts, to assess the current distribution and possible origins of the European strain in North America. The potential use of next-generation sequencing technologies is particularly important to understand the patterns of geographic expansion of this parasite.

Confirming the contribution and genetic spectrum of de novo mutation in infantile spasms: Evidence from a Chinese cohort.

ObjectiveWe determined the yield, genetic spectrum, and actual origin of de novo mutations (DNMs) for infantile spasms (ISs) in a Chinese cohort. The efficacy of levetiracetam (LEV) for STXBP1‐related ISs was explored also.MethodsTargeted sequencing of 153 epilepsy‐related candidate genes was applied to 289 Chinese patients with undiagnosed ISs. Trio‐based amplicon deep sequencing was used for all DNMs to distinguish somatic/mosaic mutations from germline ones.ResultsTotal of 26 DNMs were identified from 289 recruited Chinese patients with undiagnosed ISs. Among them, 24 DNMs were interpreted as pathogenic mutations based on American College of Medical Genetics and Genomics guidelines, contributing to 8.3% (24/289) of diagnosis yield in the Chinese IS cohort. CDKL5 and STXBP1 are the top genes with recurrent DNMs, accounting for 3.1% (9/289) of yield. Further deep resequencing for the trio members showed that 22.7% (5/22) of DNMs are actually somatic in the proband or a parent. These somatic carriers presented milder seizure attacks than those with true germline DNMs. After treatment with LEV for half a year, three patients with DNM in STXBP1 showed improved clinical symptoms, including seizure‐free and normal electroencephalogram, except for a patient with a second DNM in DIAPH3.SignificanceOur study confirmed the contribution and genetic spectrum of DNMs in Chinese IS patients. Somatic mutation account for a quarter of DNMs in IS cases. Treatment with LEV improved the prognosis of STXBP1‐related ISs.

Targeted deep amplicon sequencing of antimalarial resistance markers in Plasmodium falciparum isolates from Cameroon

BackgroundRecent studies showed the first emergence of the R561H artemisinin-associated resistance marker in Africa, which highlights the importance of continued molecular surveillance to assess the selection and spread of this and other drug resistance markers in the region. MethodIn this study, we used targeted amplicon deep sequencing of 116 isolates collected in two areas of Cameroon to genotype the major drug resistance genes, k13, crt, mdr1, dhfr, and dhps, and the cytochrome b gene (cytb) in Plasmodium falciparum. ResultsNo confirmed or associated artemisinin resistance markers were observed in Pfk13. In comparison, both major and minor alleles associated with drug resistance were found in Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps. Notably, a high frequency of other nonsynonymous mutations was observed across all the genes, except for Pfcytb, suggesting continued selection pressure. ConclusionsThe results from this study supported the continued use of artemisinin-based combination therapy and administration of sulfadoxine-pyrimethamine for intermittent preventive therapy in pregnant women, and for seasonal chemoprevention in these study sites in Cameroon.

Exposure to Diverse Plasmodium falciparum Genotypes Shapes the Risk of Symptomatic Malaria in Incident and Persistent Infections: A Longitudinal Molecular Epidemiologic Study in Kenya.

Repeated exposure to malaria infections could protect against symptomatic progression as people develop adaptive immunity to infections acquired over time. We investigated how new, recurrent, and persistent Plasmodium falciparum infections were associated with the odds of developing symptomatic compared with asymptomatic malaria. Using a 14-month longitudinal cohort in Western Kenya, we used amplicon deep sequencing of 2 polymorphic genes (pfama1 and pfcsp) to assess overlap of parasite genotypes (represented by haplotypes) acquired within an individual's successive infections. We hypothesized infections with novel haplotypes would increase the odds of symptomatic malaria. After excluding initial infections, we observed 534 asymptomatic and 88 symptomatic infections across 186 people. We detected 109 pfcsp haplotypes, and each infection was classified as harboring novel, recurrent, or persistent haplotypes. Incident infections with only new haplotypes had higher odds of symptomatic malaria when compared with infections with only recurrent haplotypes [odds ratio (OR): 3.24; 95% confidence interval (CI), 1.20-8.78], but infections with both new and recurrent haplotypes (OR: 0.64; 95% CI: 0.15-2.65) did not. Assessing persistent infections, those with mixed (persistent with new or recurrent) haplotypes (OR: 0.77; 95% CI: 0.21-2.75) had no association with symptomatic malaria compared with infections with only persistent haplotypes. Results were similar for pfama1. These results confirm that incident infections with only novel haplotypes were associated with increased odds of symptomatic malaria compared with infections with only recurrent haplotypes but this relationship was not seen when haplotypes persisted over time in consecutive infections.

Clinical spectrum and genetic variations of LMNA-related muscular dystrophies in a large cohort of Chinese patients

BackgroundLMNA-related muscular dystrophy is caused by mutations in LMNA gene. We aimed to identify genetic variations and clinical features in a large cohort of Chinese patients with LMNA mutations in...

A new subspecies of Trypanosoma cyclops found in the Australian terrestrial leech Chtonobdella bilineata.

Previously, it was suggested that haemadipsid leeches represent an important vector of trypanosomes amongst native animals in Australia. Consequently, Chtonobdella bilineata leeches were investigated for the presence of trypanosome species by polymerase chain reaction (PCR), DNA sequencing and in vitro isolation. Phylogenetic analysis ensued to further define the populations present. PCR targeting the 28S rDNA demonstrated that over 95% of C. bilineata contained trypanosomes; diversity profiling by deep amplicon sequencing of 18S rDNA indicated the presence of four different clusters related to the Trypanosoma (Megatrypanum) theileri. Novy–MacNeal–Nicolle slopes with liquid overlay were used to isolate trypanosomes into culture that proved similar in morphology to Trypanosoma cyclops in that they contained a large numbers of acidocalcisomes. Phylogeny of 18S rDNA/GAPDH/ND5 DNA sequences from primary cultures and subclones showed the trypanosomes were monophyletic, with T. cyclops as a sister group. Blood-meal analysis of leeches showed that leeches primarily contained blood from swamp wallaby (Wallabia bicolour), human (Homo sapiens) or horse (Equus sp.). The leech C. bilineata is a host for at least five lineages of Trypanosoma sp. and these are monophyletic with T. cyclops; we propose Trypanosoma cyclops australiensis as a subspecies of T. cyclops based on genetic similarity and biogeography considerations.

Population Density Affects the Outcome of Competition in Co-cultures of Gardnerella Species Isolated from the Human Vaginal Microbiome.

Negative frequency-dependent selection is one possible mechanism for maintenance of rare species in communities, but the selective advantage of rare species may be checked at lower overall population densities where resources are abundant. Gardnerella spp. belonging to cpn60 subgroup D, are detected at low levels in vaginal microbiomes and are nutritional generalists relative to other more abundant Gardnerella spp., making them good candidates for negative frequency-dependent selection. The vaginal microbiome is a dynamic environment, and the resulting changes in density of the microbiota may explain why subgroup D never gains dominance. To test this, we co-cultured subgroup D isolates with isolates from the more common and abundant subgroup C. Deep amplicon sequencing of rpoB was used to determine proportional abundance of each isolate at 0 h and 72 h in 152 co-cultures and to calculate change in proportion. D isolates had a positive change in proportional abundance in most co-cultures regardless of initial proportion. Initial density affected the change in proportion of subgroup D isolates either positively or negatively depending on the particular isolates combined, suggesting that growth rate, population density and other intrinsic features of the isolates influenced the outcome. Our results demonstrate that population density is an important factor influencing the outcome of competition between Gardnerella spp. isolated from the human vaginal microbiome.Supplementary InformationThe online version contains supplementary material available at 10.1007/s00248-021-01745-4.

Human Enterovirus Diversity by Next-Generation Sequencing Analysis in Urban Sewage Samples From Buenos Aires Metropolitan Area, Argentina: A Retrospective Study.

Human Enteroviruses (hEVs) are responsible for a wide variety of human diseases. During hEVs infection, virions are excreted in human feces and the fecal-oral route is the primary pathway for person-to-person transmission. Sewage surveillance could help in monitoring hEVs circulation and describing their diversity in a specific population. In this study, sewage samples collected in Buenos Aires Metropolitan Area (Argentina) were retrospectively studied through an amplicon-deep sequencing approach and phylogenetic analyses to characterize hEVs spread. We identified 17 different hEVs types belonging to A, B, and C species. To the best of our knowledge, this is the first report in Buenos Aires for 7 identified hEV-C types. Phylogenetic analyses suggest several introductions of coxsackievirus B4, echovirus 1, and echovirus 9 in the country, along with the national spread reached by some variants. Besides, well-supported monophyletic groups of Argentine, Uruguayan, and Brazilian strains unveiled regional circulation patterns for some variants. These results extend our knowledge about hEVs circulation in Buenos Aires and might exhort authorities to implement more active sewage surveillance in the region.

From microbes to mammals: agriculture homogenizes pond biodiversity across different land-use types

The diversity and composition of biological communities in ecosystems is typically linked to land use. Consequently, intensive agriculture has a strong influence on these patterns, including a reduction and homogenization of species diversity. Kettle holes (KH; also known as potholes) are small water bodies (&amp;lt;1 ha) typical to formerly glaciated land on the northern hemisphere, reaching densities up to several dozen per km2. They often function as drainage centers, linking various landscape elements in their surroundings and are hotspots of aquatic biodiversity in terrestrial landscapes. In the 1950s, the land use surrounding KH in Europe (e.g., Germany, Poland, The Netherlands) and North America (USA and Canada) shifted towards intensive agriculture, likely affecting the local and regional biodiversity of the KH. Reports on the biodiversity of ponds in agricultural landscapes are scarce, and mostly focus on single taxa. We used deep eDNA amplicon sequencing of eukaryotic, bacterial, and archaeal SSU rRNA genes to assess effects of land use on the overall species biodiversity of 67 KH in either arable fields, grasslands, or forests, all embedded in a landscape subjected to intensive agriculture for decades. These were later contrasted with Berlin city ponds. Metatranscriptomic analyses were conducted in parallel to investigate the taxonomic diversity and functionality of the active communities. The amplicon data, &amp;gt;300 million reads, were analyzed with phyloFlash and Kraken2 using the SILVA_SSU_Ref database. Subsequently, the sequences were grouped based on taxonomy. The use of different annotation pipelines resulted in similar patterns. A subset of the data was analyzed using DADA2, generating amplicon sequence variants. Clustering the sequences as variants or according to taxonomy resulted in identical patterns, suggesting that broad taxonomical groupings provide sufficient resolution for general overviews. Annotation of the eukaryotic community was challenging, as none of the currently available databases contains sufficient high-quality sequences to cover the entire phylogenetic breadth. To overcome this limitation, we used the SILVA_SSU_Parc database, which also contains short sequences excluded from SILVA_SSU_Ref, thus extending the taxonomic base of the analysis. The curated, high-quality PR2 eukaryotic database did not provide better results than the SILVA_SSU_Ref database. An incompatibility between the SILVA and classical taxonomic nomenclature resulted in a ‘language barrier,’ which could be partly resolved by using the parallel EMBL taxonomy provided in the SILVA databases. Nevertheless, we propose that short-read SSU-based eukaryotic taxonomic annotations should be validated by other means. Despite such methodological limitations, our study demonstrates that deep amplicon sequencing of eDNA return a reliable picture of the biodiversity in complex ecosystems. Such information is sufficient to identify biodiversity patterns across the three domains of life and can serve to pinpoint taxonomic groups which should be investigated by a more detailed approach. Our study concluded that long-term exposure to intensive agriculture results in biodiversity homogenization across diverse taxonomic groups, removing most differences in biodiversity patterns among land-use types. This outcome contrasts with biodiversity patterns associated with sediments of the KH, where temporal coverage by the eDNA analyses extends back to at least the onset of intensive agriculture. However, metatranscriptomic analyses, reflecting the distribution of activities rather than relative abundance, revealed temporal differences in the structure of the active community in KH of the investigated land-use types, matching times of field fertilization. Thus, even in a landscape where biodiversity has been homogenized, inputs from the surroundings result in short-term activity changes of different organisms. This needs to be considered when developing new management schemes needed to counteract the current biodiversity loss.

Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater

In this study, nitrification before and after abrupt cross-transfer in salinity was investigated in two moving bed biofilm reactors inoculated with nitrifying cultures that had adaptation to freshwater (FR) and seawater salinities (SR). FR and SR MBRRs were exposed to short and long term cross-transfer in salinity, and the functional capacity of nitrifying microbial communities was quantified by the estimation of ammonia and nitrite oxidation rates. Salinity induced successions were evaluated before and after salinity change by deep sequencing of 16S rRNA gene amplicons and statistical analysis. The bacterial community structure was characterized and Venn diagrams were included. The results indicated that after salinity cross-transfer, the FR was not significantly recovered at seawater salinity whereas SR showed high resistance to stress caused by low-salt. Succession and physiological plasticity were the main mechanisms of the long-term adaption of the nitrifying communities exposed to abrupt salinity changes. Independently of salinity, some nitrifiers presented high physiological plasticity towards salinity and were very successful at both zero and full seawater salinity. SR culture is robust and suitable inoculum for ammonium removal from recirculating aquaculture systems and industrial wastewaters with variable and fast salinity changes. Our findings contradict the current perspective of the significance of salinity on the structure of nitrifying communities.