Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection

Abbate, Isabella; Vlassi, Chrysoula; Rozera, Gabriella; Bruselles, Alessandro; Bartolini, Barbara; Giombini, Emanuela; Corpolongo, Angela; D’Offizi, Gianpiero; Narciso, Pasquale; Desideri, Alessandro; Ippolito, Giuseppe; Capobianchi, Maria Rosaria

doi:10.1097/qad.0b013e328343489e

Cited by 40 publications

(33 citation statements)

References 28 publications

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“…Early in the course of infection, most HIV isolates utilize CCR5 (56,74,86); however, several recent reports have demonstrated that CXCR4-utilizing viral subpopulations are found in as many as 10 to 50% of recently infected individuals (1,14). In addition, CXCR4-utilizing viruses emerge in many patients later in the course of infection (55,66).…”

Section: Cd45romentioning

confidence: 99%

Latent HIV-1 Infection Occurs in Multiple Subsets of Hematopoietic Progenitor Cells and Is Reversed by NF-κB Activation

McNamara

Ganesh

Collins

2012

J Virol

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The ability of HIV-1 to establish a latent infection presents a barrier to curing HIV. The best-studied reservoir of latent virus in vivo is resting memory CD4 + T cells, but it has recently been shown that CD34 + hematopoietic progenitor cells (HPCs) can also become latently infected by HIV-1 in vitro and in vivo . CD34 + cells are not homogenous, however, and it is not yet known which types of CD34 + cells support a latent infection. Furthermore, the mechanisms through which latency is established in this cell type are not yet known. Here we report the development of a primary cell model for latent HIV-1 infection in HPCs. We demonstrate that in this model, latent infection can be established in all subsets of HPCs examined, including HPCs with cell surface markers consistent with immature hematopoietic stem and progenitor cells. We further show that the establishment of latent infection in these cells can be reversed by tumor necrosis factor alpha (TNF-α) through an NF-κB-dependent mechanism. In contrast, we do not find evidence for a role of positive transcription elongation factor b (P-TEFb) in the establishment of latent infection in HPCs. Finally, we demonstrate that prostratin and suberoylanilide hydroxamic acid (SAHA), but not hexamethylene bisacetamide (HMBA) or 5-aza-2′-deoxycytidine (Aza-CdR), reactivate latent HIV-1 in HPCs. These findings illuminate the mechanisms through which latent infection can be established in HPCs and suggest common pathways through which latent virus could be reactivated in both HPCs and resting memory T cells to eliminate latent reservoirs of HIV-1.

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Section: Cd45romentioning

confidence: 99%

Latent HIV-1 Infection Occurs in Multiple Subsets of Hematopoietic Progenitor Cells and Is Reversed by NF-κB Activation

McNamara

Ganesh

Collins

2012

J Virol

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“…However, there is no detailed analysis of NDV quasispecies yet, and the relationship between emergent virulent strains and NDV quasispecies has not been clarified. Ultradeep pyrosequencing (UDPS) has emerged as an important tool with which to investigate viral diversity and to detect mutants in a group of quasispecies (24)(25)(26)(27)(28)(29).…”

mentioning

confidence: 99%

Evolution of Newcastle Disease Virus Quasispecies Diversity and Enhanced Virulence after Passage through Chicken Air Sacs

Chen

Qiu

et al. 2016

J Virol

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It has been reported that lentogenic Newcastle disease virus (NDV) isolates have the potential to become velogenic after their transmission and circulation in chickens, but the underlying mechanism is unclear. In this study, a highly velogenic NDV variant, JS10-A10, was generated from the duck-origin lentogenic isolate JS10 through 10 consecutive passages in chicken air sacs. The velogenic properties of this selected variant were determined using mean death time (MDT) assays, intracerebral pathogenicity index (ICPI), the intravenous pathogenicity index (IVPI), histopathology, and the analysis of host tissue tropism. In contrast, JS10 remained lentogenic after 20 serial passages in chicken eggs (JS10-E20). The JS10, JS10-A10, and JS10-E20 genomes were sequenced and found to be nearly identical, suggesting that both JS10-A10 and JS10-E20 were directly generated from JS10. To investigate the mechanism for virulence enhancement, the partial genome covering the F0 cleavage site of JS10 and its variants were analyzed using ultradeep pyrosequencing (UDPS) and the proportions of virulence-related genomes in the quasispecies were calculated. Velogenic NDV genomes accumulated as a function of JS10 passaging through chicken air sacs. Our data suggest that lentogenic NDV strains circulating among poultry might be a risk factor to future potential velogenic NDV outbreaks in chickens. IMPORTANCEAn avirulent isolate, JS10, was passaged through chicken air sacs and embryos, and the pathogenicity of the variants was assessed. A virulent variant, JS10-A10, was generated from consecutive passage in air sacs. We developed a deep-sequencing approach to detect low-frequency viral variants across the NDV genome. We observed that virulence enhancement of JS10 was due to the selective accumulation of velogenic quasispecies and the concomitant disappearance of lentogenic quasispecies. Our results suggest that because it is difficult to avoid contact between natural waterfowl reservoirs and sensitive poultry operations, circulating lentogenic NDV strains may represent a potential reservoir for emergent velogenic NDV strains that could cause outbreaks in chickens.

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“…In the past, efforts have been made to use NGS-based approaches, in particular pyrosequencing, for obtaining genetic data from different viral pathogens, such as HIV; avian leukosis virus; lyssaviruses; enteric viruses, and few arboviruses, including DENV-1 and phleboviruses (Victoria et al, 2009;Bimber et al, 2010;Bishop-Lilly et al, 2010;Day et al, 2010;Hedskog et al, 2010;De Wolf et al, 2011;Schinazi et al, 2011;Abbate et al, 2011;De Benedictis et al, 2011;Palacios et al, 2011).…”

Section: Discussionmentioning

confidence: 99%

Optimization of dengue virus genome assembling using GSFLX 454 pyrosequencing data: evaluation of assembling strategies

Casseb¹,

Cardoso²,

Ramos³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Currently assembling genomes without reference is one of the most important challenges for bioinformaticists all over the world in an attempt to characterize new organisms. The current study has used two dengue virus type 4 (DENV-4) strains recently isolated in Brazil, which have its genomes sequenced using the GSFLX 454 sequencer (Roche, Life Science) by the pyrosequencing method. The GSFLX 454 data were used for testing different genome assembling strategies. We described a pipeline that was able to recover more than 96% of the sequenced genome in a single run and could be helpful for further assembly attempts of other DENV genomes, as well as other RNA virus-like genomes.

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Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection

Cited by 40 publications

References 28 publications

Latent HIV-1 Infection Occurs in Multiple Subsets of Hematopoietic Progenitor Cells and Is Reversed by NF-κB Activation

Latent HIV-1 Infection Occurs in Multiple Subsets of Hematopoietic Progenitor Cells and Is Reversed by NF-κB Activation

Evolution of Newcastle Disease Virus Quasispecies Diversity and Enhanced Virulence after Passage through Chicken Air Sacs

Optimization of dengue virus genome assembling using GSFLX 454 pyrosequencing data: evaluation of assembling strategies

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