Evaluation of haplotype callers for next-generation sequencing of viruses

Eliseev, Anton; Gibson, Keylie M.; Avdeyev, Pavel; Novik, Dmitry; Bendall, Matthew L.; Pérez‐Losada, Marcos; Alexeev, Nikita; Crandall, Keith A.

doi:10.1016/j.meegid.2020.104277

Cited by 36 publications

(34 citation statements)

References 70 publications

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“…It can be impacted by the quality of the HTS sequences produced, by read length, but also by the algorithms used for quality control, contig assembly, and SNP identification. The statistical approach selected for the haplotyping analysis is another key factor to consider; its performance is determined by mutation rate and was demonstrated to decrease with genetic diversity of the sample (see McCrone and Lauring, 2016;Posada-Cespedes and Seifert, 2017;Eliseev et al, 2020).…”

Section: Single-nucleotide Polymorphisms (Snps) and Virus Populationsmentioning

confidence: 99%

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

et al. 2020

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The ecology of plant viruses began to be explored at the end of the 19th century. Since then, major advances have revealed mechanisms of virus-host-vector interactions in various environments. These advances have been accelerated by new technlogies for virus detection and characterization, most recently including high throughput sequencing (HTS). HTS allows investigators, for the first time, to characterize all or nearly all viruses in a sample without a priori information about which viruses might be present. This powerful approach has spurred new investigation of the viral metagenome (virome). The rich virome datasets accumulated illuminate important ecological phenomena such as virus spread among host reservoirs (wild and domestic), effects of ecosystem simplification caused by human activities (and agriculture) on the biodiversity and the emergence of new viruses in crops. To be effective, however, HTS-based virome studies must successfully navigate challenges and pitfalls at each procedural step, from plant sampling to library preparation and bioinformatic analyses. This review summarizes major advances in plant virus ecology associated with technological developments, and then presents important considerations and best practices for HTS use in virome studies.

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Section: Single-nucleotide Polymorphisms (Snps) and Virus Populationsmentioning

confidence: 99%

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

et al. 2020

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“…Like HAPHPIPE, but unlike viral-ngs and MiCall, V-pipe calls haplotypes. Rather than using PredictHaplo, V-pipe implements HaploClique and Savage for global haplotype reconstruction and ShoRAH for local reconstruction, all of which performed poorly relative to PredictHaplo in a recent comparison of haplotype reconstruction tools [ 65 ].…”

Section: Discussionmentioning

confidence: 99%

“…For the purposes of this study, we focus on the composition of the consensus sequences, but additionally report haplotype data for the HIV and HCV empirical datasets as validation of HAPHPIPE’s intra-host analytical capabilities. See Eliseev et al [ 65 ] for an evaluation of haplotype reconstruction tools.…”

Section: Introductionmentioning

confidence: 99%

Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses

Gibson

Steiner

Rentia

et al. 2020

Viruses

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Next-generation sequencing (NGS) offers a powerful opportunity to identify low-abundance, intra-host viral sequence variants, yet the focus of many bioinformatic tools on consensus sequence construction has precluded a thorough analysis of intra-host diversity. To take full advantage of the resolution of NGS data, we developed HAplotype PHylodynamics PIPEline (HAPHPIPE), an open-source tool for the de novo and reference-based assembly of viral NGS data, with both consensus sequence assembly and a focus on the quantification of intra-host variation through haplotype reconstruction. We validate and compare the consensus sequence assembly methods of HAPHPIPE to those of two alternative software packages, HyDRA and Geneious, using simulated HIV and empirical HIV, HCV, and SARS-CoV-2 datasets. Our validation methods included read mapping, genetic distance, and genetic diversity metrics. In simulated NGS data, HAPHPIPE generated pol consensus sequences significantly closer to the true consensus sequence than those produced by HyDRA and Geneious and performed comparably to Geneious for HIV gp120 sequences. Furthermore, using empirical data from multiple viruses, we demonstrate that HAPHPIPE can analyze larger sequence datasets due to its greater computational speed. Therefore, we contend that HAPHPIPE provides a more user-friendly platform for users with and without bioinformatics experience to implement current best practices for viral NGS assembly than other currently available options.

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“…While the length of individual sequences has little effect on the identification of HIV DRMs, short NGS read lengths and high genetic diversity makes it difficult to analyze HIV quasispecies at the haplotype or variant level using existing haplotype callers [ 56 ].…”

Section: Figurementioning

confidence: 99%

“…While HIV pol gene sequencing largely serves the needs for HIVDR genotyping, such sequencing data is often also applied in molecular epidemiology, such as cluster analysis. Thus far, NGS-based cluster analyses are largely based upon (1) NGS consensus sequences that simply mimic SS sequences; (2) reconstructed viral variants using quasispecies reconstruction tools that often perform poorly on HIV NGS data [ 56 , 57 ].…”

Section: Figurementioning

confidence: 99%

Are We Ready for NGS HIV Drug Resistance Testing? The Second “Winnipeg Consensus” Symposium

Sandstrom

Paredes

et al. 2020

Viruses

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HIV drug resistance is a major global challenge to successful and sustainable antiretroviral therapy. Next-generation sequencing (NGS)-based HIV drug resistance (HIVDR) assays enable more sensitive and quantitative detection of drug-resistance-associated mutations (DRMs) and outperform Sanger sequencing approaches in detecting lower abundance resistance mutations. While NGS is likely to become the new standard for routine HIVDR testing, many technical and knowledge gaps remain to be resolved before its generalized adoption in regular clinical care, public health, and research. Recognizing this, we conceived and launched an international symposium series on NGS HIVDR, to bring together leading experts in the field to address these issues through in-depth discussions and brainstorming. Following the first symposium in 2018 (Winnipeg, MB Canada, 21–22 February, 2018), a second “Winnipeg Consensus” symposium was held in September 2019 in Winnipeg, Canada, and was focused on external quality assurance strategies for NGS HIVDR assays. In this paper, we summarize this second symposium’s goals and highlights.

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Evaluation of haplotype callers for next-generation sequencing of viruses

Cited by 36 publications

References 70 publications

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

Illuminating an Ecological Blackbox: Using High Throughput Sequencing to Characterize the Plant Virome Across Scales

Validation of Variant Assembly Using HAPHPIPE with Next-Generation Sequence Data from Viruses

Are We Ready for NGS HIV Drug Resistance Testing? The Second “Winnipeg Consensus” Symposium

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