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Publications tagged "Amplicons"

A rapid and cost-effective identification of invertebrate pests at the borders using MinION sequencing of DNA barcodes

The rapid and accurate identification of invertebrate pests detected at the border is a challenging task. Current diagnostic methods used at the borders are mainly based on time consuming visual and...

Monitoring SARS-CoV-2 variants alterations in Nice neighborhoods by wastewater nanopore sequencing

Background Wastewater surveillance has been proposed as an epidemiological tool to define the prevalence and evolution of the SARS-CoV-2 epidemics. However, most implemented SARS-CoV-2 wastewater su...

Accurate profiling of forensic autosomal STRs using the Oxford Nanopore Technologies MinION device

The high variability characteristic of short tandem repeat (STR) markers is harnessed for human identification in forensic genetic analyses. Despite the power and reliability of current typing techn...

In-field genetic stock identification of overwintering coho salmon in the Gulf of Alaska: Evaluation of Nanopore sequencing for remote real-time deployment

Genetic stock identification (GSI) by single nucleotide polymorphism (SNP) sequencing has become the gold standard for stock identification in Pacific salmon, which are found in mixed-stocks during ...

Nanopore sequencing provides rapid and reliable insight into microbial profiles of Intensive Care Units

Fast and accurate identification of pathogens is an essential task in healthcare settings. Next generation sequencing platforms such as Illumina have greatly expanded the capacity with which differe...

MinION nanopore sequencing and assembly of a complete human papillomavirus genome

Background The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to ch...

Intronic haplotypes in the GBA gene do not predict age at diagnosis of Parkinson's Disease

Background GBA mutations are a common risk factor for Parkinson's disease (PD). A recent study has suggested that GBA haplotypes, identified by intronic variants, can affect age at diagnosis of PD...

Single-molecule, full-length transcript isoform sequencing reveals disease mutation-associated RNA isoforms in cardiomyocytes

Alternative splicing generates differing RNA isoforms that govern phenotypic complexity of eukaryotes. Its malfunction underlies many diseases, including cancer and cardiovascular diseases. Comparat...

Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic

The origin and early spread of SARS-CoV-2 remains shrouded in mystery. Here I identify a data set containing SARS-CoV-2 sequences from early in the Wuhan epidemic that has been deleted from the NIH’...

Genetic diversity and evolution of SARS-CoV-2 in Belgium during the first wave outbreak

SARS-CoV-2, the causative agent of COVID-19 was first detected in Belgium on 3rd February 2020, albeit the first epidemiological wave started in March and ended in June 2020. One year after the firs...

Characterising foot-and-mouth disease virus in clinical samples using nanopore sequencing

The sequencing of viral genomes provides important data for the prevention and control of foot-and-mouth disease (FMD) outbreaks. Sequence data can be used for strain identification, outbreak tracin...

Extended-spectrum cephalosporin resistance in Escherichia coli from broiler chickens raised with or without antibiotics in Ontario, Canada

Extended-spectrum cephalosporin (ESC)-resistant Escherichia coli were isolated from fecal samples enriched in ESC-containing broth over two years from broiler chickens raised with and without therap...

New full-length sequences of blastocystis subtypes generated via Nanopore sequencing allow for comparisons between full-length and partial sequences of the rRNA gene

Blastocystis is a common food- and water-borne intestinal protist parasite of humans and many other animals. Blastocystis comprises multiple subtypes (STs) based on variability within the small subu...

Forensic nanopore sequencing of STRs and SNPs using Verogen's ForenSeq DNA Signature Prep Kit and MinION

The MinION nanopore sequencing device (Oxford Nanopore Technologies, Oxford, UK) is the smallest commercially available sequencer and can be used outside of conventional laboratories. The use of th...

Nanopore sequencing and its application to the study of microbial communities

Since its introduction, nanopore sequencing has enhanced our ability to study complex microbial samples through the possibility to sequence long reads in real time using inexpensive and portable tec...

Genomic and mobility data reveal mass population movement as a driver of SARS-CoV-2 dissemination and diversity in Bangladesh

Background New data streams are being used to track the pandemic of SARS-CoV-2, including genomic data which provides insights into patterns of importation and spatial spread of the virus, as well a...

Evaluating the lettuce metatranscriptome with MinION sequencing for future spaceflight food production applications

Healthy plants are vital for successful, long-duration missions in space, as they provide the crew with life support, food production, and psychological benefits. The microorganisms that associate w...

Inferring species compositions of complex fungal communities from long- and short-read sequence data

Background The kingdom fungi is crucial for life on earth and is highly diverse. Yet fungi are challenging to characterize. They can be difficult to culture and may be morphologically indistinct in ...

Limited within-host diversity and tight transmission bottlenecks limit SARS-CoV-2 evolution in acutely infected individuals

The recent emergence of divergent SARS-CoV-2 lineages has raised concerns about the role of selection within individual hosts in propagating novel variants. Of particular concern are variants associ...

Eicosanoid signaling as a therapeutic target in middle-aged mice with severe COVID-19

Coronavirus disease 2019 (COVID-19) is especially severe in aged populations. Resolution of the COVID-19 pandemic has been advanced by the recent development of SARS-CoV-2 vaccines, but vaccine effi...

Short report: Introduction of chikungunya virus ECSA genotype into the Brazilian Midwest and its dispersion through the Americas

Since introduction into Brazil in 2014, chikungunya virus (CHIKV) has presented sustained transmission, although much is unknown about its circulation in the midwestern states. Here, we analyze 24 n...

Field and classroom initiatives for portable sequence-based monitoring of dengue virus in Brazil

Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led fi...

Large-scale Integrative Taxonomy (LIT): resolving the data conundrum for dark taxa

New, rapid, accurate, scalable, and cost-effective species discovery and delimitation methods are needed for tackling “dark taxa”, that we here define as clades for which <10% of all species are ...

Heat treatment functionalizes hepatocyte-like cells derived from human embryonic stem cells

Hepatocyte-like cells derived from human pluripotent stem cells (hPSC-HLCs) offer an alternative to primary hepatocytes commonly used for drug screenings and toxicological tests. Although tremendous...

Rapid acquisition of high-quality SARS-CoV-2 genome via amplicon-Oxford Nanopore sequencing

Genome sequencing has shown strong capabilities in the initial stages of the COVID-19 pandemic such as pathogen identification and virus preliminary tracing. While the rapid acquisition of SARS-CoV-...

A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic

SARS-CoV-2 genomic surveillance in Uganda provides an opportunity to provide a focused description of the virus evolution in a small landlocked East African country. Here we show a recent shift in t...

Importation, circulation, and emergence of variants of SARS-CoV-2 in the South Indian State of Karnataka

As the pandemic of COVID-19 caused by the coronavirus SARS-CoV-2 continues, the selection of genomic variants which can influence how the pandemic progresses is of growing concern. Of particular con...

Metagenomic sequencing of municipal wastewater provides a near-complete SARS-CoV-2 genome sequence identified as the B.1.1.7 variant of concern

Laboratory-based wastewater surveillance for SARS-CoV-2, the causative agent of the ongoing COVID-19 pandemic, can be conducted using RT-qPCR-based screening of municipal wastewater samples. Althoug...

SARS-CoV-2 transmission in intercollegiate athletics not fully mitigated with daily antigen testing

Background High frequency, rapid turnaround SARS-CoV-2 testing continues to be proposed as a way of efficiently identifying and mitigating transmission in congregate settings. However, two SARS-CoV-...

Epidemiological and genomic analysis of a Sydney hospital COVID-19 outbreak

Australia’s early COVID-19 experience involved clusters in northern Sydney, including hospital and aged-care facility (ACF) outbreaks. We explore transmission dynamics, drivers and outcomes of a met...

A novel SARS-CoV-2 variant of concern, B.1.526, identified in New York

Recent months have seen surges of SARS-CoV-2 infection across the globe along with considerable viral evolution. Extensive mutations in the spike protein of variants B.1.1.7, B1.351, and P.1 have ra...

Phylodynamics reveals the role of human travel and contact tracing in controlling the first wave of COVID-19 in four island nations

Background New Zealand, Australia, Iceland, and Taiwan all saw success at controlling the first wave of the COVID-19 pandemic. As islands, they make excellent case studies for exploring the effects ...

SARS-CoV-2 detection and genomic sequencing from hospital surface samples collected at UC Davis

Rationale There is little doubt that aerosols play a major role in the transmission of SARS-CoV-2. The significance of the presence and infectivity of this virus on environmental surfaces, especiall...

Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) plays critical roles in host cell entry. Non-synonymous substitutions affecting S are not uncommon and have become ...

Viral genetic sequencing identifies staff transmission of COVID-19 is important in a community hospital outbreak

Background We have successfully used whole-genome sequencing to provide additional information for transmission pathways in infectious spread. We report and interpret genomic sequencing results in c...

Characterization of SARS-CoV-2 genetic structure and infection clusters in a large German city based on integrated genomic surveillance, outbreak analysis, and contact tracing

Viral genome sequencing can address key questions about SARS-CoV-2 evolution and viral transmission. Here, we present an integrated system of genomic surveillance in the German city of Düsseldorf, c...

SARS-CoV-2 N501Y introductions and transmissions in Switzerland from beginning of October 2020 to February 2021 – implementation of Swiss-wide diagnostic screening and whole genome sequencing

The rapid spread of the SARS-CoV-2 lineages B.1.1.7 (N501Y.V1) throughout the UK, B.1.351 (N501Y.V2) in South Africa, and P.1 (B.1.1.28.1; N501Y.V3) in Brazil has led to the definition of variants o...

Genomic surveillance of SARS-CoV-2 in the Bronx enables clinical and epidemiological inference

The Bronx was an early epicenter of the COVID-19 pandemic in the USA. We conducted temporal genomic surveillance of SARS-CoV-2 genomes across the Bronx from March-October 2020. Although the local st...

Whole-genome sequencing of SARS-CoV-2 in the Republic of Ireland during waves 1 and 2 of the pandemic

Background Whole-genome sequencing (WGS) of SARS-CoV-2 laboratory-confirmed cases can provide insights into viral transmission and genetic diversity at a population level. However, less is known abo...

RAY: CRISPR diagnostic for rapid and accurate detection of SARS-CoV2 variants on a paper strip

The COVID-19 pandemic originating in the Wuhan province of China in late 2019 has impacted global health, causing increased mortality among elderly patients and individuals with comorbid conditions....

Multi-modality detection of SARS-CoV-2 in faecal donor samples for transplantation and in asymptomatic emergency surgical admissions

Introduction Faecal transplantation is an evidence based treatment for Clostridiodes difficile. Patients infected with SARS-CoV-2 have been shown to shed the virus in stool for up to 33 days, well b...

Molecular epidemiology of SARS-CoV-2 - a regional to global perspective

Background After a year of the global SARS-CoV-2 pandemic, a highly dynamic genetic diversity is surfacing. Among nearly 1000 reported virus lineages, dominant lineages such as B.1.1.7 or B.1.351 at...

Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: role of international travel and regional migration in spread

Zimbabwe reported its first case of SARS-Cov-2 infection in March 2020, and case numbers increased to more than 8,099 to 16th October 2020. An understanding of the SARS-Cov-2 outbreak in Zimbabwe wi...

Neutralising antibodies in spike mediated SARS-CoV-2 adaptation

SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed arou...

Simultaneous detection and mutation surveillance of SARS-CoV-2 and co-infections of multiple respiratory viruses by rapid field-deployable sequencing

Strategies for monitoring the COVID-19 infection are crucial for combating the pandemic. Here we describe a method for multiplex isothermal amplification-based sequencing and real-time analysis of m...

A novel, multiplexed RT-qPCR assay to distinguish lineage B.1.1.7 from the remaining SARS-CoV-2 lineages

The emergence of a novel SARS-CoV-2 variant called lineage B.1.1.7 sparked global alarm due to evidence of increased transmissibility, mortality, and uncertainty about vaccine efficacy, thus acceler...

Sequence analysis of 20,453 SARS-CoV-2 genomes from the Houston metropolitan area identifies the emergence of multiple isolates of all major variants of concern

Since the beginning of the SARS-CoV-2 pandemic, there has been international concern about the emergence of virus variants with mutations that increase transmissibility, enhance escape from the huma...

Viral sequencing reveals US healthcare personnel rarely become infected with SARS-CoV-2 through patient contact

Background Healthcare personnel (HCP) are at increased risk of infection with the severe acute respiratory coronavirus 2019 virus (SARS-CoV-2). Between 12 March 2020 and 10 January 2021, >1,170 H...

First and second SARS-CoV-2 waves in inner London: A comparison of admission characteristics and the impact of the B.1.1.7 variant

A second wave of SARS-CoV-2 infection spread across the UK in 2020 linked with emergence of the more transmissible B.1.1.7 variant. The emergence of new variants, particularly during relaxation of ...

Densely sampled viral trajectories suggest longer duration of acute infection with B.1.1.7 variant relative to non-B.1.1.7 SARS-CoV-2

To test whether acute infection with B.1.1.7 is associated with higher or more sustained nasopharyngeal viral concentrations, we assessed longitudinal PCR tests performed in a cohort of 65 individua...

Genomic epidemiology identifies emergence and rapid transmission of SARS-CoV-2 B.1.1.7 in the United States

As of January of 2021, the highly transmissible B.1.1.7 variant of SARS-CoV-2, which was first identified in the United Kingdom (U.K.), has gained a strong foothold across the world. Because of the ...

First detection and report of SARS-CoV-2 spike protein N501Y mutations in Oklahoma USA

We describe the detection of SARS-CoV-2 (VOC)B.1.1.7 lineage in Oklahoma, USA. Various mutations in the S gene and ORF8 with similarity to the genome of B.1.1.7 lineage were detected in 4 of the 6 g...

Genomic insights into early SARS-CoV-2 strains isolated in Reunion Island

The relative isolation of many island communities provides some protection from the COVID-19 pandemic, as imported cases can be limited and traced effectively. Until recently, this was true for the ...

The N501Y mutation in SARS-CoV-2 spike leads to morbidity in obese and aged mice and is neutralized by convalescent and post-vaccination human sera

The current COVID-19 (coronavirus disease 19) pandemic, caused by SARS-CoV-2, disproportionally affects the elderly and people with comorbidities like obesity and associated type 2 diabetes mellitus...

Recurrent dissemination of SARS-CoV-2 through the Uruguayan-Brazilian border

Background Uruguay is one of the few countries in the Americas that successfully contained the COVID-19 epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the ...

Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality

The ongoing evolution of SARS-CoV-2 into more easily transmissible and infectious variants has sparked concern over the continued effectiveness of existing therapeutic antibodies and vaccines. Hence...

Sequence analysis of SARS-CoV-2 in nasopharyngeal samples from patients with COVID-19 illustrates population variation

New variants of SARS-CoV-2 are continuing to emerge and dominate the regional and global sequence landscapes. Several variants have been labelled as Variants of Concern (VOCs) because of perceptions...

Rapid genotyping of tilapia lake virus (TiLV) using Nanopore sequencing

Infectious diseases represent one of the major challenges to sustainable aquaculture production. Rapid and accurate diagnosis of emerging pathogens during early-suspected disease cases is critical t...

A small number of early introductions seeded widespread transmission of SARS-CoV-2 in Québec, Canada

Using genomic epidemiology, we investigated the arrival of SARS-CoV-2 to Québec, the Canadian province most impacted by COVID-19, with >280,000 positive cases and >10,000 deaths in a populatio...

Case Study: Longitudinal immune profiling of a SARS-CoV-2 reinfection in a solid organ transplant recipient

Prior to the emergence of antigenically distinct SARS-CoV-2 variants, reinfections were reported infrequently - presumably due to the generation of durable and protective immune responses. However, ...

Genomic analysis of human noroviruses using hybrid Illumina-Nanopore data

Whole genome sequence (WGS) analysis of noroviruses is routinely performed by employing a metagenomic approach. While this methodology has several advantages, such as allowing for examination of co-...

Rapid genomic surveillance of SARS-CoV-2 in a dense urban community using environmental (sewage) samples

Understanding disease burden and transmission dynamics in resource-limited, developing countries like Nepal is often challenging due to a lack of adequate surveillance systems. These issues are exac...

Targeted RNA-Based Oxford Nanopore Sequencing for Typing 12 Classical HLA Genes

Identification of human leukocyte antigen (HLA) alleles from next-generation sequencing (NGS) data is challenging because of the high polymorphism and mosaic nature of HLA genes. Owing to the comple...

Genomic surveillance and phylodynamic analyses reveal emergence of novel mutation and co-mutation patterns within SARS-CoV2 variants prevalent in India

Emergence of distinct viral clades has been observed in SARS-CoV2 variants across the world and India. Identification of the genomic diversity and the phylodynamic profiles of the prevalent strains ...

Developmental validation of Oxford Nanopore Technology MinION sequence data and the NGSpeciesID bioinformatic pipeline for forensic genetic species identification

Species identification of non-human biological evidence through DNA nucleotide sequencing is routinely used for forensic genetic analysis to support law enforcement. The gold standard for forensic g...

Sequence features around cleavage sites are highly conserved among different species and a critical determinant for RNA cleavage position across eukaryotes

RNA degradation is critical for control of gene expression, and endonucleolytic cleavage– dependent RNA degradation is conserved among eukaryotes. Some cleavage sites are secondarily capped in the c...

The MinION as a cost-effective technology for diagnostic screening of the SCN1A gene in epilepsy patients

The MinION is a portable DNA sequencer that allows real time sequencing at low capital cost investment. We assessed accuracy and cost-effectivess of the MinION for genetic diagnostic testing of know...

Bacterial filamentation drives colony chirality

Chirality is ubiquitous in nature, with consequences at the cellular and tissue scales. As Escherichia coli colonies expand radially, an orthogonal component of growth creates a pinwheel-like patter...

MinION barcodes: biodiversity discovery and identification by everyone, for everyone

DNA barcodes are a useful tool for discovering, understanding, and monitoring biodiversity. This is critical at a time when biodiversity loss is a major problem for many countries. However, widespre...

An integrated sequencing approach for updating the pseudorabies virus transcriptome

In the last couple of years, the implementation of long-read sequencing (LRS) technologies for transcriptome profiling has uncovered an extreme complexity of viral gene expression. In this study, we...

Adaptation of Oxford Nanopore technology for hepatitis C whole genome sequencing and identification of within-host viral variants

Background Hepatitis C (HCV) and many other RNA viruses exist as rapidly mutating quasi-species populations in a single infected host. High throughput characterization of full genome, within-host v...

Altered subgenomic RNA expression in SARS-CoV-2 B.1.1.7 infections

SARS-CoV-2 lineage B.1.1.7 viruses are more transmissible, may lead to greater clinical severity, and result in modest reductions in antibody neutralization. subgenomic RNA (sgRNA) is produced by di...

Identification and quantification of SARS-CoV-2 leader subgenomic mRNA gene junctions

Introduction: SARS-CoV-2 has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgRNAs has a unique 5 sequenc...

Epstein-Barr virus long non-coding RNA RPMS1 full-length spliceome in transformed epithelial tissue

Epstein-Barr virus is associated with two types of epithelial neoplasms, nasopharyngeal carcinoma and gastric adenocarcinoma. The viral long non-coding RNA RPMS1 is the most abundantly expressed pol...

A streamlined clinical metagenomic sequencing protocol for rapid pathogen identification

Metagenomic next-generation sequencing (mNGS) holds promise as a diagnostic tool for unbiased pathogen identification and precision medicine. However, its medical utility depends largely on assay si...

NGSpeciesID: DNA barcode and amplicon consensus generation from long‐read sequencing data

Third‐generation sequencing technologies, such as Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), have gained popularity over the last years. These platforms can generate millio...

Evaluation of full-length nanopore 16S sequencing for detection of pathogens in microbial keratitis

Background Microbial keratitis is a leading cause of preventable blindness worldwide. Conventional sampling and culture techniques are time-consuming, with over 40% of cases being culture-negative...

High-resolution HLA typing by long reads from the R10.3 Oxford nanopore flow cells

Nanopore sequencing has been investigated as a rapid and cost-efficient option for HLA typing in recent years. Despite the lower raw read accuracy, encouraging typing accuracy has been reported, and...

Promoting axon regeneration by enhancing the non-coding function of the injury-responsive coding gene Gpr151

Gene expression profiling in response to nerve injury has been mainly focused on protein functions of coding genes to understand mechanisms of axon regeneration and to identify targets of potential ...

Potential early rabies infection detected in two raccoon cases by LN34 pan-lyssavirus real-time RT-PCR assay in Pennsylvania

During 2017 – 2019, the Pennsylvania Department of Health Bureau of Laboratories (PABOL) tested 6,855 animal samples for rabies using both the gold standard direct fluorescent antibody (DFA) test an...

The genomes of precision edited cloned calves show no evidence for off-target events or increased de novo mutagenesis

Animal health and welfare are at the forefront of public concern and the agricultural sector is responding by prioritising the selection of welfare-relevant traits in their breeding schemes. In some...

Genome sequences of 10 SARS-CoV-2 viral strains obtained by nanopore sequencing of nasopharyngeal swabs in Malta

The genome sequences of 10 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains from Sliema, Malta, were obtained by Nanopore sequencing using the amplicon sequencing approach develo...

Application of targeted next-generation sequencing assay on a portable sequencing Platform for culture-free detection of drug-resistant tuberculosis from clinical samples

Targeted next-generation sequencing (tNGS) has emerged as a comprehensive alternative to existing methods for drug susceptibility testing (DST) of Mycobacterium tuberculosis from patient sputum samp...

Evaluation of PCR conditions for characterizing bacterial communities with full-length 16S rRNA genes using a portable nanopore sequencer

MinION (Oxford Nanopore Technologies), a portable nanopore sequencer, was introduced in 2014 as a new DNA sequencing technology. MinION is now widely used because of its low initial start-up costs r...

Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy

Background Analysis of vector integration sites in gene-modified cells can provide critical information on clonality and potential biological impact on nearby genes. Current short-read next-generati...

A new long-read dog assembly uncovers thousands of exons and functional elements missing in the previous reference

Here we present a new high-quality canine reference genome with gap number reduced 41-fold, from 23,836 to 585. Analysis of existing and novel data, RNA-seq, miRNA-seq and ATAC-seq, revealed a large...

Characterization of the genomic sequence data around common cutworm resistance genes in soybean (Glycine max) using short- and long-read sequencing methods

The common cutworm (CCW, Spodopteraab litura Fabricius) is one of the pests that most severely infect soybean (Glycine max L. Merr.). In a previous report, quantitative trait loci (QTL) analysis of ...

Real-time, MinION-based, amplicon sequencing for lineage typing of infectious bronchitis virus from upper respiratory samples

Infectious bronchitis (IB) causes significant economic losses in the global poultry industry. Control of IB is hindered by the genetic diversity of the causative agent, infectious bronchitis virus (...

Fluorescent in vivo editing reporter (FIVER): A novel multispectral reporter of in vivo genome editing

Advances in genome editing technologies have created opportunities to treat rare genetic diseases, which are often overlooked in terms of therapeutic development. Nonetheless, substantial challenges...

Evaluation of the microbial community structure of potable water samples from occupied and unoccupied buildings using16S rRNA amplicon sequencing

We conducted a two studies of water samples from buildings with normal occupancy and water usage compared to water from buildings that were unoccupied with little or no water usage due to the COVID-...

A survey of rare epigenetic variation in 23,116 human genomes identifies disease-relevant epivariations and novel CGG expansions

There is growing recognition that epivariations, most often recognized as promoter hypermethylation events that lead to gene silencing, are associated with a number of human diseases. However, littl...

Analyzing the dietary diary of bumble bee

Bumble bees are important crop pollinators and provide important pollination services to their respective ecosystems. Their pollen diet and thus food preferences can be characterized through nucleic...

Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome

Background The number of studies using third-generation sequencing utilising Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) is rapidly increasing in many different research are...

Speeding up the detection of invasive aquatic species using environmental DNA and nanopore sequencing

Traditional detection of aquatic invasive species, via morphological identification is often time-consuming and can require a high level of taxonomic expertise, leading to delayed mitigation respons...

Verification of CRISPR editing by Xdrop™ Indirect Sequence Capture followed by short- and long- read sequencing

Validation of CRISPR-Cas9 editing typically explore the immediate vicinity of the target site and distal off-target sequences, which have led to the conclusion that CRISPR-Cas9 editing is very speci...

Efficiently processing amplicon sequencing data for microbial ecology with dadasnake, a DADA2 implementation in Snakemake

Background Amplicon sequencing of phylogenetic marker genes, e.g. 16S, 18S or ITS rRNA sequences, is still the most commonly used method to estimate the structure of microbial communities. Microbial...

Rbfox2 is critical for maintaining alternative polyadenylation and mitochondrial health in myoblasts

The RNA binding protein RBFOX2 is linked to heart and skeletal muscle diseases; yet, RBFOX2-regulated RNA networks have not been systematically identified. Although RBFOX2 has a well-known function ...

The application of Nanopore sequencing technology to the study of dinoflagellates: a proof of concept study for rapid sequence-based discrimination of potentially harmful algae

Harmful algal blooms (HABs) are a naturally occurring global phenomena that have the potential to impact fisheries, leisure and ecosystems, as well as posing a significant hazard to animal and human...

Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution

Species-level genetic characterization of complex bacterial communities has important clinical applications. In the present study, we assessed the performance of full-length 16S rRNA gene analysis o...

DNA barcoding of nematodes using the MinION

Many nematode species are parasitic and threaten the health of plants and animals, including humans, on a global scale. Advances in DNA sequencing techniques have allowed for the rapid and accurate ...

Microbial retention and resistances in stormwater quality improvement devices treating road runoff

Current knowledge about the microbial communities inhabiting the stormwater quality improvement devices (SQIDs) for road runoff is scarce. However, as a bioactive compound of these systems, microbes...

Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens

Caligus rogercresseyi is a copepod ectoparasite with a high prevalence in salmon farms in Chile, causing severe welfare and economic concerns to the sector. Information on the parasite’s underpinnin...

High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abunda...

Capturing in situ virus-host range and interaction dynamics through gene fusion with epicPCR

Viruses impact microbial diversity, phenotype, and gene flow through virus-host interactions that in turn alter ecology and biogeochemistry. Though metagenomics surveys are rapidly cataloging viral ...

An ERF transcription factor from Brassica oleracea: a new member of the emerging pathogenicity hub in plant-Xanthomonas interactions

TAL effectors (TALEs), which induce the expression of specific plant genes to promote infection, are the main pathogenic determinants of different Xanthomonas bacteria. However, investigation of TAL...

Tissue-specific transcription footprinting using RNA PoI DamID (RAPID) in C. elegans

Differential gene expression across cell types underlies the development and cell physiology in multicellular organisms. C. elegans is a powerful, extensively used model to address these biological ...

Amyloid-β1–43 cerebrospinal fluid levels and the interpretation of APP, PSEN1 and PSEN2 mutations

Background Alzheimer’s disease (AD) mutations in amyloid precursor protein (APP) and presenilins (PSENs) could potentially lead to the production of longer amyloidogenic Aβ peptides. Amongst these,...

Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets

The direct use of medical zinc oxide (ZnO) in feed will be abandoned after 2022 in Europe, leaving an urgent need for substitutes to prevent post-weaning disorders. This study assessed whether rapes...

Amplicon and metagenomic analysis of MERS-CoV and the microbiome in patients with severe Middle East respiratory syndrome (MERS)

Middle East Respiratory Syndrome coronavirus (MERS-CoV) is a zoonotic infection that emerged in the Middle East in 2012. Symptoms range from mild to severe and include both respiratory and gastroint...

Allelic diversity of the PRDM9 coding minisatellite in minke whales

The PRDM9 protein controls the reshuffling of parental genomes in most metazoans. During meiosis the PRDM9 protein recognizes and binds specific target motifs via its zinc-finger array, which is enc...

DAJIN-assisted multiplex genotyping to validate the outcomes of CRISPR-Cas-based genome editing

Genome editing induces various on-target mutations. Accurate identification of mutations in founder mice and cell clones is essential to perform reliable genome editing experiments. However, no geno...

Characterization of fecal microbiota with clinical specimen using long-read and short-read sequencing platform

Accurate and rapid identification of microbiotic communities using 16S ribosomal (r)RNA sequencing is a critical task for expanding medical and clinical applications. Next-generation sequencing (NGS...

Gross chromosomal rearrangements in Kluyveromyces marxianus revealed by Illumina and Oxford Nanopore Sequencing

Kluyveromyces marxianus (K. marxianus) is an increasingly popular industrially relevant yeast. It is known to possess a highly efficient non-homologous end joining (NHEJ) pathway that promotes rando...

A framework for in situ molecular characterization of coral holobionts using nanopore sequencing

Molecular characterization of the coral host and the microbial assemblages associated with it (referred to as the coral holobiont) is currently undertaken via marker gene sequencing. This requires b...

Amplicon-based, next-generation sequencing approaches to characterize single nucleotide polymorphisms of orthohantavirus species

Whole-genome sequencing (WGS) of viruses from patient or environmental samples can provide tremendous insight into the epidemiology, drug resistance or evolution of a virus. However, we face two com...

Long rDNA amplicon sequencing of insect-infecting nephridiophagids reveals their affiliation to the Chytridiomycota (Fungi) and a potential to switch between hosts

Nephridiophagids are unicellular eukaryotes that parasitize the Malpighian tubules of numerous insects. Their life cycle comprises multinucleate vegetative plasmodia that divide into oligonucleate a...

Single molecule, near full-length genome sequencing of dengue virus

Current methods for dengue virus (DENV) genome amplification, amplify parts of the genome in at least 5 overlapping segments and then combine the output to characterize a full genome. This process i...

Integrating indigenous knowledge, ontology, and molecular barcoding to characterize spider monkey (Ateles paniscus) filariasis

Zoonotic disease risk is greatly influenced by cultural practices and belief systems. Yet, few studies have integrated traditional ecological knowledge and ontology with western ways of knowing to b...

Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes

Abstract Background Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose...

Classification of changes in the fecal microbiota associated with colonic adenomatous polyps using a long-read sequencing platform

The microbiota is the community of microorganisms that colonizes the oral cavity, respiratory tract, and gut of multicellular organisms. The microbiota exerts manifold physiological and pathological...

Use of Oxford Nanopore MinION to generate full-length sequences of the Blastocystis small subunit (SSU) rRNA gene

Background Blastocystis sp. is one of the most common enteric parasites of humans and animals worldwide. It is well recognized that this ubiquitous protist displays a remarkable degree of genetic d...

A long-read sequencing approach for direct haplotype phasing in clinical settings

The reconstruction of individual haplotypes can facilitate the interpretation of disease risks; however, high costs and technical challenges still hinder their assessment in clinical settings. Seco...

Nanopore amplicon sequencing reveals molecular convergence and local adaptation of rhodopsin in Great Lakes Salmonids

Local adaptation can drive diversification of closely related species across environmental gradients and promote convergence of distantly related taxa that experience similar conditions. We examined...

EcDNA hubs drive cooperative intermolecular oncogene expression

Extrachromosomal DNAs (ecDNAs) are prevalent in human cancers and mediate high oncogene expression through elevated copy number and altered gene regulation. Gene expression typically involves distal...

Virus-derived variation in diverse human genomes

Acquisition of genetic material from viruses by their hosts can generate inter-host structural genome variation. We developed computational tools enabling us to study virus-derived structural varian...

The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity

SARS-CoV-2 can mutate to evade immunity, with consequences for the efficacy of emerging vaccines and antibody therapeutics. Herein we demonstrate that the immunodominant SARS-CoV-2 spike (S) recep...

SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility

During the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic. However, whether ...

The wastewater microbiome: A novel insight for COVID-19 surveillance

Wastewater-Based Epidemiology is a tool to face and mitigate COVID-19 outbreaks by evaluating conditions in a specific community. This study aimed to analyze the microbiome profiles using nanopore ...

Electronic DNA analysis of CSF cell-free tumor DNA to quantify multi-gene molecular response in pediatric high-grade glioma

Purpose Pediatric high-grade glioma (pHGG) diagnosis portends poor prognosis and therapeutic monitoring remains difficult. Tumors release cell-free tumor DNA (cf-tDNA) into cerebrospinal fluid (CSF)...

COVID-19 CG: Tracking SARS-CoV-2 mutations by locations and dates of interest

COVID-19 CG is an open resource for tracking SARS-CoV-2 single-nucleotide variations (SNVs) and lineages while filtering by location, date, gene, and mutation of interest. COVID-19 CG provides sign...

Assessing the utility of long-read nanopore sequencing for rapid and efficient characterisation of mobile element insertions

Short-read next generation sequencing (NGS) has become the predominant first-line technique used to diagnose patients with rare genetic conditions. Inherent limitations of short-read technology, no...

Substitutions in spike and nucleocapsid proteins of SARS-CoV-2 circulating in South America

SARS-CoV-2 is a new member of the genus Betacoronavirus, responsible for the COVID-19 pandemic. The virus crossed the species barrier and established in the human population taking advantage of the ...

Strand-wise and bait-assisted assembly of nearly-full rrn operons applied to assess species engraftment after faecal microbiota transplantation

Background Effective methodologies to accurately identify members of the gut microbiota at the species and strain levels are necessary to unveiling more specific and detailed host-microbe interacti...

Targeted MinION sequencing of transgenes

The presence of genetically modified organisms (GMO) is commonly assessed using real-time PCR methods targeting the most common transgenic elements found in GMOs. Once the presence of GM material h...

Rapid multiplex MinION nanopore sequencing workflow for Influenza A viruses

Background Due to the frequent reassortment and zoonotic potential of influenza A viruses, rapid gain of sequence information is crucial. Alongside established next-generation sequencing protocols, ...

Improvements to the ARTIC multiplex PCR method for SARS-CoV-2 genome sequencing using nanopore

Genome sequencing has been widely deployed to study the evolution of SARS-CoV-2 with more than 90,000 genome sequences uploaded to the GISAID database. We published a method for SARS-CoV-2 genome se...

Mutational landscape and dominant lineages in the SARS-CoV-2 infections in the state of Telangana, India

The novel Severe Acute Respiratory Syndrome CoronaVirus 2 (SARS-CoV-2) causing COVID-19 has rapidly turned into a pandemic, infecting millions and causing ~7 million deaths across the globe. In addi...

Unique mutational changes in SARS-CoV2 genome of different state of India

COVID-19 leads to a global emergency that causes more than 7 million causalities until mid-August throughout the world. In India alone, 2 million confirmed cases were reported that increased abruptl...

Genomic diversity of SARS-CoV-2 during early introduction into the United States national capital region

Background: The early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first de...

Genomic epidemiology reveals transmission patterns and dynamics of SARS-CoV-2 in Aotearoa New Zealand

New Zealand, a geographically remote Pacific island with easily sealable borders, implemented a nation-wide lockdown of all non-essential services to curb the spread of COVID-19. New Zealand experie...

Genomic epidemiology of SARS-CoV-2 in Colombia

Coronavirus disease 2019 (COVID-19) was first diagnosed in Colombia from a traveler arriving from Italy on February 26, 2020. To date, available data on the origins and number or introductions of SA...

Nanopore targeted sequencing for the accurate and comprehensive detection of SARS‐CoV‐2 and other respiratory viruses

The ongoing global novel coronavirus pneumonia COVID‐19 outbreak has engendered numerous cases of infection and death. COVID‐19 diagnosis relies upon nucleic acid detection; however, currently reco...

Genome sequences of six SARS-CoV-2 strains isolated in Morocco, obtained using Oxford Nanopore MinION technology

Here, we report the draft genome sequences of six severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains. SARS-CoV-2 is responsible for the COVID-19 pandemic, which started at the end ...

Clinical, immunological and virological characterization of COVID-19 patients that test re-positive for SARS-CoV-2 by RT-PCR

Background COVID-19 pandemic is underway. Some COVID-19 cases re-tested positive for SARS-CoV-2 RNA after discharge raising the public concern on their infectivity. Characterization of re-positive c...

Accurate detection of circulating tumor DNA using nanopore consensus sequencing

Levels of circulating tumor DNA (ctDNA) in liquid biopsies may serve as a sensitive biomarker for real-time, minimally-invasive tumor diagnostics and monitoring. However, detecting ctDNA is challeng...

Evolution and epidemic spread of SARS-CoV-2 in Brazil

Brazil currently has one of the fastest growing SARS-CoV-2 epidemics in the world. Owing to limited available data, assessments of the impact of non-pharmaceutical interventions (NPIs) on virus spre...

Utilizing nanopore sequencing technology for the rapid and comprehensive characterization of eleven HLA loci; addressing the need for deceased donor expedited HLA typing

The comprehensive characterization of human leukocyte antigen (HLA) genomic sequences remains a challenging problem. Despite the significant advantages of next-generation sequencing (NGS) in the fie...

CoronaHiT: large scale multiplexing of SARS-CoV-2 genomes using nanopore sequencing

The COVID-19 pandemic has spread to almost every country in the world since it started in China in late 2019. Controlling the pandemic requires a multifaceted approach including whole genome sequenc...

SARS-CoV-2 growth, furin-cleavage-site adaptation and neutralization using serum from acutely infected, hospitalized COVID-19 patients

SARS-CoV-2, the causative agent of COVID-19, emerged at the end of 2019 and by mid-June 2020, the virus has spread to at least 215 countries, caused more than 8,000,000 confirmed infections and over...

Genomic surveillance of SARS-CoV-2 reveals community transmission of a major lineage during the early pandemic phase in Brazil

Despite all efforts to control the COVID-19 spread, the SARS-CoV-2 reached South America within three months after its first detection in China, and Brazil became one of the hotspots of COVID-19 in ...

Relationship between anti-spike protein antibody titers and SARS-CoV-2 in vitro virus neutralization in convalescent plasma

Newly emerged pathogens such as SARS-CoV-2 highlight the urgent need for assays that detect levels of neutralizing antibodies that may be protective. We studied the relationship between anti-spike ...

Integrated genomic view of SARS-CoV-2 in India

Background India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest o...

Rapid and inexpensive whole-genome sequencing of SARS-CoV2 using 1200 bp tiled amplicons and Oxford Nanopore rapid barcoding

Rapid and cost-efficient whole-genome sequencing of SARS-CoV-2, the virus that causes COVID-19, is critical for understanding viral transmission dynamics. Here we show that using a new multiplexed s...

Rapid, highly accurate and cost‐effective open‐source simultaneous complete HLA typing & phasing of Class I & II alleles using nanopore sequencing

Introduction Accurate rapid genotyping of the genes within the HLA region presents many difficulties due to the complexity of this region. Here we present the results of our proof of concept Nanop...

An economical nanopore sequencing assay for human papillomavirus (HPV) genotyping

Background Human papillomavirus (HPV) testing has been employed by several European countries to augment cytology-based cervical screening programs. A number of research groups have demonstrated pot...

Multiple SARS-CoV-2 introductions shaped the early outbreak in Central Eastern Europe: comparing Hungarian data to a worldwide sequence data-matrix

Severe Acute Respiratory Syndrome Coronavirus 2 is the third highly pathogenic human coronavirus in history. Since the emergence in Hubei province, China, during late 2019 the situation evolved to p...

COVID-19 in healthcare workers in three hospitals in the South of the Netherlands, March 2020

Background Ten days after the first reported case of SARS-CoV-2 infection in the Netherlands, 3.9% of healthcare workers (HCWs) in nine hospitals located in the South of the Netherlands tested posit...

Molecular architecture of early dissemination and evolution of the SARS-CoV-2 Virus in metropolitan Houston, Texas

We sequenced the genomes of 320 SARS-CoV-2 strains from COVID-19 patients in metropolitan Houston, Texas, an ethnically diverse region with seven million residents. These genomes were from the virus...

SARS-CoV-2 genomes recovered by long amplicon tiling multiplex approach using nanopore sequencing and applicable to other sequencing platforms

Genomic surveillance has become a useful tool for better understanding virus pathogenicity, origin and spread. Obtaining accurately assembled, complete viral genomes directly from clinical samples i...

Zika virus amplification using strand displacement isothermal method and sequencing using nanopore technology

Development of novel point of care diagnostic methods in order to help in implementing disease control program and identifying the causative agent of an outbreak is crucial. Classical diagnostic te...

First genomic characterization of a Belgian Enterovirus C104 using sequence-independent Nanopore sequencing

Because of the enormous variation in their genome sequence, genotyping enteroviruses by standard methods can prove to be quite challenging. Nanopore sequencing offers the potential to overcome the l...

Nanopore sequencing reveals novel targets for the diagnosis and surveillance of human and avian influenza A virus

Accurate detection of influenza A virus (IAV) is crucial for patient management, infection control, and epidemiological surveillance. The World Health Organization and the Centers for Disease Contro...

Origin of imported SARS-CoV-2 strains in The Gambia identified from whole genome sequences

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a positive-sense single stranded RNA virus with high human transmissibility. This study generated Whole Genome data to determine the ...

Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands

SARS-CoV-2 is a novel coronavirus that has rapidly spread across the globe. In the Netherlands, the first case of SARS-CoV-2 has been notified on the 27th of February. Here, we describe the first t...

Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing

Global poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR and sequencing of the VP1 region to distinguish vaccine (Sabin), va...

Rapid, sensitive, full genome sequencing of Severe Acute Respiratory Syndrome Virus Coronavirus 2 (SARS-CoV-2)

SARS-CoV-2 recently emerged, resulting a global pandemic. Rapid genomic information is critical to understanding transmission and pathogenesis. Here, we describe validated protocols for generating ...

Rapid high resolution HLA genotyping by MinION Oxford Nanopore sequencing for deceased donor organ allocation

Recently, HLA epitopes on donor HLA molecules have been shown to be important in the success of solid organ transplantation. However, these epitopes can only be defined using high resolution typing ...

Limited SARS-CoV-2 diversity within hosts and following passage in cell culture

Since the first reports of pneumonia associated with a novel coronavirus (COVID-19) emerged in Wuhan, Hubei province, China, there have been considerable efforts to sequence the causative virus, SAR...

Coast-to-coast spread of SARS-CoV-2 during the early epidemic in the United States

The novel coronavirus SARS-CoV-2 was first detected in the Pacific Northwest region of the United States in January, 2020, with subsequent COVID-19 outbreaks detected in all 50 states by early March...

Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China

COVID-19 is caused by SARS-CoV-2 infection and was first reported in central China in December 2019. Extensive molecular surveillance in Guangdong, China’s most populous province, during early 2020 ...

CovProfile: profiling the viral genome and gene expressions of SARS-COV2

SARS-COV2 is infecting more than one million people. Knowing its genome and gene expressions is essential to understand the virus. Here, we propose a computational tool to detect viral genomic vari...

Identification of a common deletion in the spike protein of SARS-CoV-2

Two notable features have been identified in the SARS-CoV-2 genome: (1) the receptor binding domain of SARS-CoV-2; (2) a unique insertion of twelve nucleotide or four amino acids (PRRA) at the S1 an...

MinION-in-ARMS: Nanopore sequencing to expedite barcoding of specimen-rich macrofaunal samples from Autonomous Reef Monitoring Structures

Autonomous Reef Monitoring Structure (ARMS) are standardised devices for sampling biodiversity in complex marine benthic habitats such as coral reefs. When coupled with DNA sequencing, these devices...

Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2: an observational cohort study

Coronavirus disease 2019 (COVID-19) causes severe community and nosocomial outbreaks. Comprehensive data for serial respiratory viral load and serum antibody responses from patients infected with se...

Accurate detection of single nucleotide polymorphisms using nanopore sequencing

Nanopore sequencing is a powerful single molecule DNA sequencing technology which provides a high throughput and long sequence reads. Nevertheless, its relatively high native error rate limits the d...

Long-read sequencing to interrogate strain-level variation among adherent-invasive Escherichia coli isolated from human intestinal tissue

Adherent-invasive Escherichia coli (AIEC) are a pathovar linked to inflammatory bowel diseases (IBD), especially Crohn’s disease, and colorectal cancer. AIEC have no known molecular or genomic marke...

Amplicon-based detection and sequencing of SARS-CoV-2 in nasopharyngeal swabs from patients with COVID-19 and identification of deletions in the viral genome

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). Sequencing the viral genome as the outbreak progresses is important, parti...

Metagenomic sequencing with spiked primer enrichment for viral diagnostics and genomic surveillance

Metagenomic next-generation sequencing (mNGS), the shotgun sequencing of RNA and DNA from clinical samples, has proved useful for broad-spectrum pathogen detection and the genomic surveillance of vi...

nanoMLST: accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples

Multilocus sequence typing (MLST) is one of the most commonly used methods for studying microbial lineage worldwide. However, the traditional MLST process using Sanger sequencing is time-consuming a...

Comparison of the performance of an amplicon sequencing assay based on Oxford Nanopore technology to real-time PCR assays for detecting bacterial biodefense pathogens

Background The state-of-the-art in nucleic acid based biodetection continues to be polymerase chain reaction (PCR), and many real-time PCR assays targeting biodefense pathogens for biosurveillance a...

Rapid in-country sequencing of whole virus genomes to inform rabies elimination programmes

Genomic surveillance is an important aspect of contemporary disease management but has yet to be used routinely to monitor endemic disease transmission and control in low- and middle-income countrie...

MinION-based DNA barcoding of preserved and non-invasively collected wildlife samples

The ability to sequence a variety of wildlife samples with portable, field-friendly equipment will have significant impacts on wildlife conservation and health applications. However, the only curren...

Real-time detection of BRAF V600E mutation from archival hairy cell leukemia FFPE tissue by nanopore sequencing

The MinION is a miniaturized high-throughput next generation sequencing platform of novel conception. The use of nucleic acids derived from formalin-fixed paraffin-embedded samples is highly desirab...

Applying Nanopore sequencing to a One-Health scenario for colistin resistance transmission among pigs, cows and the farmer

One-Health studies applying massive-parallel and single-molecule sequencing are a suitable approximation to try to understand how antibiotic resistances flow between the human-animal-environment sce...

A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants

Background Mitochondrial DNA is remarkably polymorphic. This is why animal geneticists survey mitochondrial genomes variations for fundamental and applied purposes. We present here an approach to s...

Simultaneous detection and comprehensive analysis of HPV and microbiome status of a cervical liquid-based cytology sample using Nanopore MinION sequencing

Human papillomavirus (HPV) is a major pathogen that causes cervical cancer and many other related diseases. The HPV infection-related cervical microbiome could be an inducing factor of cervical canc...

A rapid approach to profiling diverse fungal communities using the MinION™ nanopore sequencer

The Oxford Nanopore Technologies MinION™ sequencer holds the capability to generate long amplicon reads; however, only a small amount of information is available regarding methodological approaches ...

Nanopore targeted sequencing for rapid gene mutations detection in acute myeloid leukemia

Acute myeloid leukemia (AML) clinical settings cannot do without molecular testing to confirm or rule out predictive biomarkers for prognostic stratification, in order to initiate or withhold target...

Rapid, large-scale species discovery in hyperdiverse taxa using 1D MinION sequencing

Background More than 80% of all animal species remain unknown to science. Most of these species live in the tropics and belong to animal taxa that combine small body size with high specimen abundan...

A novel field-deployable method for sequencing and analyses of Henipavirus genomes from complex samples on the MinION platform

Viruses in the genus Henipavirus encompass 2 highly pathogenic emerging zoonotic pathogens, Hendra virus (HeV) and Nipah virus (NiV). Despite the impact on human health, there is currently limited f...

Direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on Nanopore MinION – promising strategies for multiplex identification of viable pathogens in food

Viable pathogenic bacteria are major biohazards that pose a significant threat to food safety. Despite the recent developments in detection platforms, multiplex identification of viable pathogens in...

Can we use it? On the utility of de novo and reference-based assembly of Nanopore data for plant plastome sequencing

The chloroplast genome harbors plenty of valuable information for phylogenetic research. Illumina short-read data is generally used for de novo assembly of whole plastomes. PacBio or Oxford Nanopore...

Application of long-read sequencing for robust identification of correct alleles in genome edited animals

Recent developments in CRISPR/Cas9 genome editing tools have facilitated the introduction of more complex alleles, often spanning genetic intervals of several kilobases, directly into the embryo. Th...

Rapid identification of genomic structural variations with nanopore sequencing enables blood-based cancer monitoring

Somatic genomic structural variations (SVs) are promising personalized biomarkers for sensitive and specific detection of circulating tumor DNA (ctDNA) in liquid biopsies. However, affordable and fa...

Analysis of polyclonal vector integration sites using Nanopore sequencing as a scalable, cost-effective platform

Vector integration site analysis can be important in the follow-up of patients who received gene-modified cells, but current platforms based on next-generation sequencing are expensive and relativel...

Uncovering the microbiome of invasive sympatric European brown hares and European rabbits in Australia

European brown hares (Lepus europaeus) and European rabbits (Oryctolagus cuniculus) are invasive pest species in Australia, with rabbits having a substantially larger environmental impact than hares...

A comparative assessment of conventional and molecular methods, including MinION nanopore sequencing, for surveying water quality

Nucleic acid based techniques, such as quantitative PCR (qPCR) and next generation sequencing (NGS), provide new insights into microbial water quality, but considerable uncertainty remains around th...

MinION sequencing of seafood in Singapore reveals creatively labelled flatfishes, confused roe, pig DNA in squid balls, and phantom crustaceans

Food mislabelling is a growing world-wide problem that can be addressed through the authentication of ingredients via techniques like mass spectrometry or DNA sequencing. However, unfortunately trad...

Highly multiplexed, fast and accurate nanopore sequencing for verification of synthetic DNA constructs and sequence libraries

Synthetic biology utilises the Design-Build-Test-Learn pipeline for the engineering of biological systems. Typically, this requires the construction of specifically designed, large and complex DNA a...

Long-read sequencing reveals the complex splicing profile of the psychiatric risk gene CACNA1C in human brain

RNA splicing is a key mechanism linking genetic variation with psychiatric disorders. Splicing profiles are particularly diverse in brain and difficult to accurately identify and quantify. We develo...

Human short tandem repeat identification using a nanopore-based DNA sequencer: a pilot study

Short tandem repeats (STRs) are repetitive DNA sequences that are highly polymorphic and widely used for personal identification in the field of forensic medicine. The standard method for determinin...

Nanopore sequencing for the detection and the identification of Xylella fastidiosa subspecies and sequence types from naturally infected plant material

Xylella fastidiosa (Xf) is a polyphagous gram-negative bacterial plant pathogen that can infect more than 300 plant species. It is endemic in America while, in 2013, Xf subsp. pauca was for the firs...

DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq

Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the probl...

LAMBDR: Long-range amplification and Nanopore sequencing of Mycobacterium bovis direct-repeat region. A novel method for in-silico spoligotyping of M. bovis directly from badger faeces.

The environment is an overlooked source of Mycobacterium bovis, the causative agent of bovine TB. Long read, end to end sequencing of variable repeat regions across the M. bovis genome was evaluated...

Targeted sequencing workflows for comprehensive drug resistance profiling of Mycobacterium tuberculosis cultures using Illumina MiSeq and Nanopore MinION: comparison of analytical and diagnostic performance, turnaround time and cost

The emergence of Mycobacterium tuberculosis strains with complex drug resistance profiles necessitates a rapid and extensive drug susceptibility test for comprehensive guidance of patient treatment....

Rapid diagnosis of bacterial meningitis by nanopore 16S amplicon sequencing: A pilot study

Early administration of antibiotics is crucial in the management of bacterial meningitis. Rapid pathogen identification helps to make a definite diagnosis of bacterial meningitis and enables tailore...

A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing

Amplicon sequencing of 16S rRNA gene is commonly used for the identification of bacterial isolates in diagnostic laboratories, and mostly relies on the Sanger sequencing method. The latter, however,...

Rapid and cost-efficient Enterovirus genotyping from clinical samples using Flongle Flow Cells

Enteroviruses affect millions of people worldwide and are of significant clinical importance. The standard method for enterovirus identification and genotyping still relies on Sanger sequencing of s...

Nanopore sequencing of the glucocerebrosidase (GBA) gene in a New Zealand Parkinsons disease cohort

Mutations in the gene for glucocerebrosidase (GBA) cause Gaucher disease, an autosomal recessive lysosomal storage disorder. GBA mutation carriers have an elevated risk of Parkinson's disease (PD) c...

Resistance to piperacillin/tazobactam in Escherichia coli resulting from extensive IS26-associated gene amplification of blaTEM-1

Background blaTEM-1 encodes a narrow-spectrum β-lactamase that is inhibited by β-lactamase inhibitors and commonly present in Escherichia coli. Hyperproduction of blaTEM-1 may cause resistance to p...

A multiplex pharmacogenetics assay using the MinION nanopore sequencing device

Aim The MinION nanopore sequencing device opens the opportunity to cost-effective and point-of-care DNA sequencing. We developed a multiplex assay targeting pharmacogenetic variants related to clop...

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

High-throughput amplicon sequencing of large genomic regions remains challenging for short-read technologies. Here, we report a high-throughput amplicon sequencing approach combining unique molecula...

Resolving MiSeq-generated ambiguities in HLA-DPB1 typing by using the Oxford Nanopore technology

The technical limitations of current next-generation sequencing technologies, combined with an ever-increasing number of human leukocyte antigen (HLA) alleles, forms the basis for the additional amb...

MinION Sequencing of colorectal cancer tumour microbiomes – a comparison with amplicon-based and RNA-Sequencing

Recent evidence suggests a role for the gut microbiome in the development and progression of colorectal cancer. In this study we compare MinION sequencing with meta-transcriptomics and amplicon-base...

MinION sequencing technology to characterize unauthorized GM petunia plants circulating on the European Union market

In order to characterize unauthorized genetically modified petunia, an integrated strategy has been applied here on several suspected petunia samples from the European market. More precisely, DNA fr...

Towards high quality real-time whole genome sequencing during outbreaks using Usutu virus as example

Recently, protocols for amplicon based whole genome sequencing using Nanopore technology have been described for Ebola virus, Zika virus, yellow fever virus and West Nile virus. However, there is so...

Severe haemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing

Background No F8 genetic abnormality is detected in about 2% of severe haemophilia A patients using conventional genetic approaches. In these patients, deep intronic variation or F8 disrupting geno...

Distinguishing between carrier and noncarrier embryos with the use of long-read sequencing in preimplantation genetic testing for reciprocal translocations

Balanced reciprocal translocation carriers are usually phenotypically normal but are at an increased risk of infertility, recurrent miscarriage or having affected children. Preimplantation genetic t...

Rapid profiling of tropical marine cyanobacterial communities

Cyanobacteria are important organisms in the marine ecosystem as they play vital roles in nutrient cycling and oxygen production. In this study, tropical marine cyanobacterial communities from vario...

Characterization of the stability and dynamics of Tn6330 in an Escherichia coli strain by nanopore long reads

Background The mcr-1 gene has been widely reported in both bacterial chromosomes and plasmids, while its stability in these genetic materials is not well understood. Objectives Our aim was to ch...

Influenza A virus field surveillance at a swine-human interface

While working overnight at a swine exhibition, we identified an influenza A virus (IAV) outbreak in swine, Nanopore sequenced 13 IAV genomes from samples we collected, and predicted in real time tha...

Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinION nanopore sequencer

Rapid identification of bacterial pathogens is crucial for appropriate and adequate antibiotic treatment, which significantly improves patient outcomes. 16S ribosomal RNA (rRNA) gene amplicon sequen...

Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications

CYP2D6 is one of the most important and widely studied genes in pharmacogenetics but it is highly polymorphic, can be affected by different forms of structural variation, and has a nearby pseudogene...

Pooled CRISPR Inverse PCR sequencing (PCIP-seq): simultaneous sequencing of retroviral insertion points and the associated provirus in thousands of cells with long reads

Retroviral infections create a large population of cells, each defined by a unique proviral insertion site. Methods based on short-read high throughput sequencing can identify thousands of insertion...

MinION sequencing to genotype US strains of infectious laryngotracheitis virus

Over the last decade the US broiler industry has fought long-lasting outbreaks of infectious laryngotracheitis (ILTV). Previous nine genotypes (I-IX) of ILTVs have been recognized using the polymera...

A Nanopore-based method for generating complete coding region sequences of dengue virus in resource-limited settings

Dengue virus (DENV) sequencing is a vital tool for surveillance and epidemiology studies. However, the current methods employed for sequencing DENV are expensive, laborious and technically demanding...

Nanopore sequencing: An enrichment‐free alternative to mitochondrial DNA sequencing

Mitochondrial DNA sequence data is often utilized in disease studies, conservation genetics and forensic identification. The current approaches for sequencing the full mtGenome typically require sev...

NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform

Background Amplicon sequencing on Illumina sequencing platforms leverages their deep sequencing and multiplexing capacity, but is limited in genetic resolution due to short read lengths. While Oxfor...

Nanopore sequencing for rapid diagnostics of salmonid RNA viruses

Analysis of pathogen genome variation is essential for informing disease management and control measures in farmed animals. For farmed fish, the standard approach is to use PCR and Sanger sequencing...

Forensic STR profiling using Oxford Nanopore Technologies' MinION

Forensic STR profiling using massively parallel sequencing (MPS) has gained much attention as an alternative for the traditional capillary electrophoresis (CE) methods. Oxford Nanopore Technologies ...

Human-Specific Abnormal Alternative Splicing of Wild-Type PKD1 Induces Premature Termination of Polycystin-1

Background The major form of autosomal dominant polycystic kidney disease is caused by heterozygous mutations in PKD1, the gene that encodes polycystin-1 (PC1). Unlike PKD1 genes in the mouse and mo...

Rapid and sensitive virulence prediction and identification of Newcastle disease virus genotypes using third-generation sequencing

Newcastle disease (ND) outbreaks are global challenges to the poultry industry. Effective management requires rapid identification and virulence prediction of the circulating Newcastle disease virus...

Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale

Background In light of the current biodiversity crisis, DNA barcoding is developing into an essential tool to quantify state shifts in global ecosystems. Current barcoding protocols often rely on s...

A new hybrid approach for MHC genotyping: high-throughput NGS and long read MinION nanopore sequencing, with application to the non-model vertebrate Alpine chamois (Rupicapra rupicapra)

The major histocompatibility complex (MHC) acts as an interface between the immune system and infectious diseases. Accurate characterization and genotyping of the extremely variable MHC loci are cha...

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

Background Mutations in GBA cause Gaucher disease when biallelic and are strong risk factors for Parkinson's disease when heterozygous. GBA analysis is complicated by the nearby pseudogene. We aime...

Rapid and Accurate Sequencing of Enterovirus Genomes Using MinION Nanopore Sequencer*

Objective Knowledge of an enterovirus genome sequence is very important in epidemiological investigation to identify transmission patterns and ascertain the extent of an outbreak. The MinION sequenc...

Detection of subclonal L1 transductions in colorectal cancer by long-distance inverse-PCR and Nanopore sequencing

Long interspersed nuclear elements-1 (L1s) are a large family of retrotransposons. Retrotransposons are repetitive sequences that are capable of autonomous mobility via a copy-and-paste mechanism. I...

Profiling bacterial communities by MinION sequencing of ribosomal operons

Note: the chemistry used in this paper has since been superseded. Background An approach utilizing the long-read capability of the Oxford Nanopore MinION to rapidly sequence bacterial ribosomal op...

Real-time DNA barcoding in a remote rainforest using nanopore sequencing

Advancements in portable scientific instruments provide promising avenues to expedite field work in order to understand the diverse array of organisms that inhabit our planet. Here we tested the fea...

Accurate typing of class I human leukocyte antigen by Oxford nanopore sequencing

Oxford Nanopore Technologies' MinION has expanded the current DNA sequencing toolkit by delivering long read lengths and extreme portability. The MinION has the potential to enable expedited point-o...

The potential impact of nanopore sequencing on human genetics.

Nanopore sequencing has been available to customers for a little over three years. Recently the milestone of sequencing and assembling a human genome on this platform was achieved for the first time...

Multiplexed Nanopore Sequencing of HLA-B Locus in Māori and Pacific Island Samples

The human leukocyte antigen (HLA) system encodes the human major histocompatibility complex (MHC). HLA-B is the most polymorphic gene in the MHC class I region and many HLA-B alleles have been assoc...

Sequencing and phasing cancer mutations in lung cancers using a long-read portable sequencer

Here, we employed cDNA amplicon sequencing using a long-read portable sequencer, MinION, to characterize various types of mutations in cancer-related genes, namely, EGFR, KRAS, NRAS and NF1. For hom...

Multi-locus and long amplicon sequencing approach to study microbial diversity at species level using the MinION™ portable nanopore sequencer

Background: The miniaturised and portable DNA sequencer MinIONTM has demonstrated great potential in different analyses such as genome-wide sequencing, pathogen outbreak detection and surveillance, ...

Non-invasive diagnosis of cutaneous leishmaniasis by the direct boil loop-mediated isothermal amplification method and MinION™ nanopore sequencing

Cutaneous leishmaniasis (CL) is gaining attention as a public health problem. We present two cases of CL imported from Syria and Venezuela in Japan. We diagnosed them as CL non-invasively by the dir...

A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer

We developed a portable system for 16S rDNA analyses consisting of a nanopore technology-based sequencer, the MinION, and laptop computers, and assessed its potential ability to determine bacterial ...

Evaluation of Oxford Nanopore MinION Sequencing for 16S rRNA Microbiome Characterization

In this manuscript we evaluate the potential for microbiome characterization by sequencing of near-full length 16S rRNA gene region fragments using the Oxford Nanopore MinION (hereafter Nanopore) se...

TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

Background The assessment of TP53 mutational status is becoming a routine clinical practice for chronic lymphocytic leukemia patients (CLL). A broad spectrum of molecular techniques has been employ...

In-field metagenome and 16S rRNA gene amplicon nanopore sequencing robustly characterize glacier microbiota

In the field of observation, chance favours only the prepared mind (Pasteur). Impressive developments in genomics have led microbiology to its third Golden Age. However, conventional metagenomics st...

Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing

Demands for faster and more accurate methods to analyze microbial communities from natural and clinical samples have been increasing in the medical and healthcare industry. Recent advances in next-...

Real time selective sequencing using nanopore technology

The Oxford Nanopore Technologies MinION sequencer enables the selection of specific DNA molecules for sequencing by reversing the driving voltage across individual nanopores. To directly select mole...

Species level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

Background: The miniaturised and portable DNA sequencer MinION has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide ...

INC-Seq: Accurate single molecule reads using nanopore sequencing

Background Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionize genomics. However, several applications are limited by relative...

Complete nitrification by Nitrospira bacteria

Nitrification, the oxidation of ammonia via nitrite to nitrate, has always been considered to be a two-step process catalysed by chemolithoautotrophic microorganisms oxidising either ammonia or nitr...

MinION nanopore sequencing of an influenza genome

Influenza epidemics and pandemics have significant impacts on economies, morbidity and mortality worldwide. The ability to rapidly, and accurately, sequence influenza viruses is instrumental in the ...

Nanopore sequencing for genotyping pathogens of tropical diseases

Nanopore sequencer, MinION, has enabled sequencing analysis without pre-installation of expensive conventional sequencers or pre-requisite of specific skills in biological experiments. Even electric...

Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

The MinION™ nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications. Recent reports have tested the ability of the MinION™ ...

Long read nanopore sequencing for detection of HLA and CYP2D6 variants and haplotypes

Haplotypes are often critical for the interpretation of genetic laboratory observations into medically actionable findings. Current massively parallel DNA sequencing technologies produce short seque...