Deep sequencing increases hepatitis C virus phylogenetic cluster detection compared to Sanger sequencing

Montoya, Vincent; Olmstead, Andrea D.; Tang, Patrick; Cook, Darrel; Janjua, Naveed Z.; Grebely, Jason; Jacka, Brendan; Poon, Art F. Y.; Krajden, Mel

doi:10.1016/j.meegid.2016.06.015

Cited by 15 publications

(15 citation statements)

References 47 publications

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“…Hence, the GHOST-based analysis of the Illumina data using the established threshold provides a more reliable estimate of transmission clusters than analysis of sequences generated using EPLD and 454 technologies. Recently, new methods have been developed that make use of sample-specific differences [ 22 , 32 ]. Application of advanced clustering techniques and probabilistic evolutionary models in conjunction with the implemented GHOST workflows should further improve reliability of transmission detection.…”

Section: Discussionmentioning

confidence: 99%

“…HCV exists as a population of numerous variants in each infected individual [ 19 ]. It has been observed that minority variants in the source are often those responsible for transmission [ 20 , 21 ], a situation that precludes the use of a single sequence per individual because many such transmissions would be missed [ 22 ]. Computational analysis of the NGS data for the detection of HCV transmission is a very complex process and requires significant expertise in application of phylogenetic methods and interpretation of phylogenetic data within an epidemiological context.…”

Section: Introductionmentioning

confidence: 99%

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GHOST: global hepatitis outbreak and surveillance technology

et al. 2017

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Background: Hepatitis C is a major public health problem in the United States and worldwide. Outbreaks of hepatitis C virus (HCV) infections associated with unsafe injection practices, drug diversion, and other exposures to blood are difficult to detect and investigate. Effective HCV outbreak investigation requires comprehensive surveillance and robust case investigation. We previously developed and validated a methodology for the rapid and cost-effective identification of HCV transmission clusters. Global Hepatitis Outbreak and Surveillance Technology (GHOST) is a cloud-based system enabling users, regardless of computational expertise, to analyze and visualize transmission clusters in an independent, accurate and reproducible way.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

GHOST: global hepatitis outbreak and surveillance technology

et al. 2017

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“…Sanger sequencing is, until now, considered to be the reference technology in terms of sequencing quality (e.g. Montoya et al 2016;Khalifa et al 2016). Such problems were particularly common in the case of Epithemia hirudiniformis, where many sequences showed deletions, and were therefore not included in the reference database.…”

Section: What Are the Advantages/disadvantages Associated With Use Ofmentioning

confidence: 99%

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

Rimet¹,

Abarca²,

Bouchez³

et al. 2018

Fottea

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Diatoms are used routinely to assess pollution level in rivers and lakes. Current methods are based on identification by light microscopy, which is laborious. An alternative is to identify species based on short DNA fragments and High-Throughput Sequencing (HTS). However a potential limitation is the incomplete coverage of species in reference barcode libraries. Usually these libraries are compiled by isolating cells, before culturing and sequencing them, which is tedious and often unsuccessful. Here we propose the use of rbcL sequences from environmental samples analysed by HTS. We set several criteria to ensure good sequence quality and correspondence with the target species observed in microscopy: the sequence needed to be abundant in the sample, and with no insertions nor deletions or stop codon, phylogenetic neighbour taxa had to correspond to neighbour taxonomic taxa expected from morphological observations. Four species from tropical rivers are given as examples, including one that is new to science.

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“…The study was aimed at evaluating the dynamics of HIV transmission in the Lazio region during the years 2013 to early 2020, by identifying HIV TC, and factors associated with probability of patients to be included in TC. In addition, as UDS has proven to be useful for the analysis of HIV quasispecies [16][17][18][19] and has been used for the analysis of TC of HIV and of other infections [5,[20][21][22], we performed a detailed analysis of env quasispecies harbored by individuals included in the largest TC involving B subtype.…”

Section: Introductionmentioning

confidence: 99%

Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013–2020

Fabeni

Rozera

Berno

et al. 2021

Viruses

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Molecular investigation of primary HIV infections (PHI) is crucial to describe current dynamics of HIV transmission. Aim of the study was to investigate HIV transmission clusters (TC) in PHI referred during the years 2013–2020 to the National Institute for Infectious Diseases in Rome (INMI), that is the Lazio regional AIDS reference centre, and factors possibly associated with inclusion in TC. These were identified by phylogenetic analysis, based on population sequencing of pol; a more in depth analysis was performed on TC of B subtype, using ultra-deep sequencing (UDS) of env. Of 270 patients diagnosed with PHI during the study period, 229 were enrolled (median follow-up 168 (IQR 96–232) weeks). Median age: 39 (IQR 32–48) years; 94.8% males, 86.5% Italians, 83.4% MSM, 56.8% carrying HIV-1 subtype B. Of them, 92.6% started early treatment within a median of 4 (IQR 2–7) days after diagnosis; median time to sustained suppression was 20 (IQR 8–32) weeks. Twenty TC (median size 3, range 2–9 individuals), including 68 patients, were identified. A diagnosis prior to 2015 was the unique factor associated with inclusion in a TC. Added value of UDS was the identification of shared quasispecies components in transmission pairs within TC.

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Deep sequencing increases hepatitis C virus phylogenetic cluster detection compared to Sanger sequencing

Cited by 15 publications

References 47 publications

GHOST: global hepatitis outbreak and surveillance technology

GHOST: global hepatitis outbreak and surveillance technology

The potential of High-Throughput Sequencing (HTS) of natural samples as a source of primary taxonomic information for reference libraries of diatom barcodes

Molecular Transmission Dynamics of Primary HIV Infections in Lazio Region, Years 2013–2020

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