GB Virus C Coinfections in West African Ebola Patients

Lauck, Michael; Bailey, Adam L.; Andersen, Kristian G.; Goldberg, Tony L.; Sabeti, Pardis C.; O’Connor, David H.

doi:10.1128/jvi.02752-14

Cited by 68 publications

(60 citation statements)

References 44 publications

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“…As positive [25] and detrimental [5] coinfections are common among EVD patients, expansion of multiplexing is necessary, but unlikely to exceed concomitant amplification capability need beyond five targets. Field data also indicate mucosal biofluids such as semen [26], ocular fluid [27] and breast milk [28] might be viral depots in convalescence.…”

Section: Future Directionsmentioning

confidence: 99%

Introducing EbolaCheck: potential for point-of-need infectious disease diagnosis

Moschos

2015

Expert Review of Molecular Diagnostics

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Section: Future Directionsmentioning

confidence: 99%

Introducing EbolaCheck: potential for point-of-need infectious disease diagnosis

Moschos

2015

Expert Review of Molecular Diagnostics

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“…While controversial, several groups have also reported that co-infection of HPgV and human immunodeficiency virus (HIV) can delay progression to AIDS, presumably by decreasing HIV replication or perturbing the host immune response [3][4][5]. More recently, co-infection with HPgV in patients with Ebola virus disease has been reported to be associated with improved survival [6].…”

Section: Introductionmentioning

confidence: 99%

Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection

Berg¹,

Lee²,

Coller³

et al. 2016

Journal of Hepatology

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Hepatitis C virus (HCV) and human pegivirus (HPgV), formerly GBV-C, are the only known human viruses in the Hepacivirus and Pegivirus genera, respectively, of the family Flaviviridae. We present the discovery of a second pegivirus, provisionally designated human pegivirus 2 (HPgV-2), by next-generation sequencing of plasma from an HCV-infected patient with multiple bloodborne exposures who died from sepsis of unknown etiology. HPgV-2 is highly divergent, situated on a deep phylogenetic branch in a clade that includes rodent and bat pegiviruses, with which it shares <32% amino acid identity. Molecular and serological tools were developed and validated for high-throughput screening of plasma samples, and a panel of 3 independent serological markers strongly correlated antibody responses with viral RNA positivity (99.9% negative predictive value). Discovery of 11 additional RNA-positive samples from a total of 2440 screened (0.45%) revealed 93-94% nucleotide identity between HPgV-2 strains. All 12 HPgV-2 RNA-positive cases were identified in individuals also testing positive for HCV RNA (12 of 983; 1.22%), including 2 samples co-infected with HIV, but HPgV-2 RNA was not detected in non-HCV-infected individuals (p<0.0001), including those singly infected by HIV (p = 0.0075) or HBV (p = 0.0077), nor in volunteer blood donors (p = 0.0082). Nine of the 12 (75%) HPgV-2 RNA positive samples were reactive for antibodies to viral serologic markers, whereas only 28 of 2,429 (1.15%) HPgV-2 RNA negative samples were seropositive. Longitudinal sampling in two individuals revealed that active HPgV-2 infection can persist in blood for at least 7 weeks, despite the presence of virus-specific antibodies. One individual harboring both HPgV-2 and HCV RNA was found to be seronegative for both viruses, suggesting a high likelihood of simultaneous acquisition of HCV and HPgV-2 infection from an acute co-transmission event. Taken together, our PLOS Pathogens |

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“…The genomic data were used to trace the disease and mutations in the Ebola genome and inform further public health and research efforts. Lauck et al (2015) reanalyzed one of the data sets (Gire et al 2014) in order to assess the prevalence and effect of GB virus C co-infection on the outcome of EVD.…”

Section: Application Of Centrifuge For Analyzing Samples With Ebola Vmentioning

confidence: 99%

Centrifuge: rapid and sensitive classification of metagenomic sequences

et al. 2016

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Centrifuge is a novel microbial classification engine that enables rapid, accurate, and sensitive labeling of reads and quantification of species on desktop computers. The system uses an indexing scheme based on the Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized specifically for the metagenomic classification problem. Centrifuge requires a relatively small index (4.2 GB for 4078 bacterial and 200 archaeal genomes) and classifies sequences at very high speed, allowing it to process the millions of reads from a typical high-throughput DNA sequencing run within a few minutes. Together, these advances enable timely and accurate analysis of large metagenomics data sets on conventional desktop computers. Because of its space-optimized indexing schemes, Centrifuge also makes it possible to index the entire NCBI nonredundant nucleotide sequence database (a total of 109 billion bases) with an index size of 69 GB, in contrast to k-mer-based indexing schemes, which require far more extensive space.

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GB Virus C Coinfections in West African Ebola Patients

Cited by 68 publications

References 44 publications

Introducing EbolaCheck: potential for point-of-need infectious disease diagnosis

Introducing EbolaCheck: potential for point-of-need infectious disease diagnosis

Discovery of a Novel Human Pegivirus in Blood Associated with Hepatitis C Virus Co-Infection

Centrifuge: rapid and sensitive classification of metagenomic sequences

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