MinION nanopore sequencing and assembly of a complete human papillomavirus genome

Brancaccio, Rosario Nicola; Robitaille, Alexis; Dutta, Sankhadeep; Rollison, Dana E.; Tommasino, Massimo; Gheit, Tarik

doi:10.1016/j.jviromet.2021.114180

Cited by 8 publications

(8 citation statements)

References 65 publications

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“…In contrast to short-read sequencing, ONT's portable MinION sequencer yields sequences up to hundreds of kilobases (kb) in length [19][20][21][22]. Furthermore, while Illumina sequencing requires extensive human and capital resources and is typically performed in established laboratories [23], the MinION sequencer is small, cost-effective, and can be run on a standard desktop or laptop, making it an ideal option for real-time sequencing in the field, especially in resource-depleted areas [24,25]. While ONT sequencing has significant limitations including its relatively high error rate of up to 10% [26], recent studies have used ONT sequencing to reconstruct repetitive sequences and discover structural variation not previously detected with Illumina sequencing [27].…”

Section: Introductionmentioning

confidence: 99%

Interchromosomal segmental duplication drives translocation and loss ofP. falciparumhistidine-rich protein 3

Hathaway

Kim

Young

et al. 2022

Preprint

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Background: Significant progress has been made in the fight against P. falciparum malaria due in part to the widespread adoption of rapid diagnostic tests (RDTs) that detect histidine-rich protein 2 (PfHRP2) and its paralog PfHRP3 encoded by the pfhrp2 and pfhrp3 genes, respectively. Parasites without pfhrp2 and pfhrp3 genes are not detected by these RDTs. Pfhrp3 loss appears to be more common in some geographical regions and has been observed in vitro. We sought to gain insight into geographic patterns of pfhrp3 deletion and define the mechanism of gene loss. Methods: Over 9,830 publicly available, whole-genome sequenced (WGS) P. falciparum field samples were analyzed for genotypes and coverage using PathWeaver for local assembly . DNA from two cultured isolates with pfhrp3 deletion, HB3 and SD01, were sequenced with Oxford Nanopore Technologies (ONT) long-read sequencing, assembled with Canu and Flye, and genes annotated with Companion. Results: Two distinct pfhrp3 deletion patterns were detected: 1) segmental deletion of chromosome 13 just centromeric to pfhrp3 extending to the end of the chromosome, with co-occurring segmental duplication of the chromosome 11 subtelomeric region, and 2) segmental deletion of chromosome 13 starting at various locations centromeric to pfhrp3 without chromosome 11 duplication. Pattern 1 was almost exclusively found in samples from Africa and South America, while pattern 2 was observed predominantly in Southeast Asia. The pattern 1 boundary fell within a 15kb nearly identical duplication on both chromosomes containing ribosomal genes. ONT assembly of HB3 and SD01 parasite lines revealed hybrid chromosomes and long-reads spanning the ribosomal duplication, consistent with recombination between non-homologous chromosomes. Conclusion: Our findings demonstrate duplication-mediated non-homologous recombination creating a hybrid 13-11 chromosome that replaces pfhrp3 and telomeric chromosome 13 with a translocated telomeric chromosome 11 sequence--essentially yielding a deletion of chromosome 13 sequence and interchromosomal duplication of chromosome 11 sequence. Given that existing ribosomal duplications likely predispose to the frequent occurrence of this translocation during meiosis, it suggests that subsequent selective forces are driving its presence or absence in different geographical regions. This mechanism appears to explain pfhrp3 deletion in South America and Africa and may explain why pfhrp3 deletions are more prevalent than pfhrp2 deletions in many localities. However, the forces driving emergence of pfhrp3- parasites may be complex and encompass other genes affected by the recombination event. Further studies of the origins of pfhrp2- and pfhrp3-deleted strains and the selective pressures suppressing their occurrence or driving their expansion are needed.

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Section: Introductionmentioning

confidence: 99%

Interchromosomal segmental duplication drives translocation and loss ofP. falciparumhistidine-rich protein 3

Hathaway

Kim

Young

et al. 2022

Preprint

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“…Assembly was performed following the bioinformatics pipeline introduced by Brancaccio et al for human papillomavirus [30]. After base calling the raw data on a "high" setting with Guppy [31], the results were filtered for reads between 500 and 2300 nucleotides long using Filtlong v.0.2.1 [32].…”

Section: Nanopore Sequencing and Assemblymentioning

confidence: 99%

“…RBDV RNA2 was characterized in this study because the corresponding sequences from many isolates are available in GenBank [30], providing a better scaffolding for an informative phylogenetic tree to analyse relationships between RBDV isolates from different locations.…”

Section: Occurrence Of Rbdv In Kazakhstanmentioning

confidence: 99%

Genetic Characterization of Raspberry Bushy Dwarf Virus Isolated from Red Raspberry in Kazakhstan

Kolchenko

Kapytina

Kerimbek

et al. 2023

Viruses

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Raspberry bushy dwarf virus (RBDV) is an economically significant pathogen of raspberry and grapevine, and it has also been found in cherry. Most of the currently available RBDV sequences are from European raspberry isolates. This study aimed to sequence genomic RNA2 of both cultivated and wild raspberry in Kazakhstan and compare them to investigate their genetic diversity and phylogenetic relationships, as well as to predict their protein structure. Phylogenetic and population diversity analyses were performed on all available RBDV RNA2, MP and CP sequences. Nine of the isolates investigated in this study formed a new, well-supported clade, while the wild isolates clustered with the European isolates. Predicted protein structure analysis revealed two regions that differed between α- and β-structures among the isolates. For the first time, the genetic composition of Kazakhstani raspberry viruses has been characterized.

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“…It also can be used to detect the complex mutation of HBV genome ( Zhuo et al, 2021 ; Li et al, 2022 ). Researchers utilize long reads obtained through nanopore sequencing to assemble the HPV genome in a single sample, leveraging the long-reads for a comprehensive analysis of virus integration characteristics ( Brancaccio et al, 2021 ; Yang et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Multiple HPV integration mode in the cell lines based on long-reads sequencing

Cui,

Li,

Zhang

et al. 2023

Front. Microbiol.

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BackgroundThe integration of human papillomavirus (HPV) is closely related to the occurrence of cervical cancer. However, little is known about the complete state of HPV integration into the host genome.MethodsIn this study, three HPV-positive cell lines, HeLa, SiHa, and CaSki, were subjected to NANOPORE long-read sequencing to detect HPV integration. Analysis of viral integration patterns using independently developed software (HPV-TSD) yielded multiple complete integration patterns for the three HPV cell lines.ResultsWe found distinct differences between the integration patterns of HPV18 and HPV16. Furthermore, the integration characteristics of the viruses were significantly different, even though they all belonged to HPV16 integration. The HPV integration in the CaSki cells was relatively complex. The HPV18 integration status in HeLa cells was the dominant, whereas the percentage of integrated HPV 16 in SiHa and CaSki cells was significantly lower. In addition, the virus sequences in the HeLa cells were incomplete and existed in an integrated state. We also identified a large number of tandem repeats in HPV16 and HPV18 integration. Our study not only clarified the feasibility of high-throughput long-read sequencing in the study of HPV integration, but also explored a variety of HPV integration models, and confirmed that viral integration is an important form of HPV in cell lines.ConclusionElucidating HPV integration patterns will provide critical guidance for developing a detection algorithm for HPV integration, as well as the application of virus integration in clinical practice and drug research and development.

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MinION nanopore sequencing and assembly of a complete human papillomavirus genome

Abstract: Highlights The MinION sequencer allows whole HPV genome sequencing. The proposed bioinformatics pipeline enables the reconstruction of whole HPV genome. Rapid whole-genome characterization of HPV genomes with a minimal error rate.

Cited by 8 publications

References 65 publications

Interchromosomal segmental duplication drives translocation and loss ofP. falciparumhistidine-rich protein 3

Interchromosomal segmental duplication drives translocation and loss ofP. falciparumhistidine-rich protein 3

Genetic Characterization of Raspberry Bushy Dwarf Virus Isolated from Red Raspberry in Kazakhstan

Multiple HPV integration mode in the cell lines based on long-reads sequencing

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