Performance of a clonal-based HIV-1 tropism phenotypic assay

Asin-Milan, Odalis; Wei, Yangyang; Sylla, Mohamed; Vaisheva, Farida; Chamberland, Annie; Tremblay, Cécile

doi:10.1016/j.jviromet.2014.04.004

Cited by 5 publications

(3 citation statements)

References 53 publications

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“…Total nucleic acids were extracted from 100 μl of serum using an automated BioRobot MDx extraction platform using the QIAamp ® Virus BioRobot ® MDx Kit (QIAGEN, Valencia, CA, USA). HIV-1 RNA was amplified using the Superscript III One-Step RT-PCR system with Platinium ® Taq DNA polymerase (Invitrogen, Thermo Fisher Scientific, Carlsbad, CA, USA) and the primers env-up forward [ 57 ]. The amplification conditions were as follows: 53°C for 30 minutes (for reverse transcription) and 94°C for 2 minutes for Taq DNA polymerase activation, followed by 40 cycles at 94°C for 15 s, 55°C for 30 s, and 68°C for 4 min.…”

Section: Methodsmentioning

confidence: 99%

HIV-1 envelope sequence-based diversity measures for identifying recent infections

et al. 2017

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Identifying recent HIV-1 infections is crucial for monitoring HIV-1 incidence and optimizing public health prevention efforts. To identify recent HIV-1 infections, we evaluated and compared the performance of 4 sequence-based diversity measures including percent diversity, percent complexity, Shannon entropy and number of haplotypes targeting 13 genetic segments within the env gene of HIV-1. A total of 597 diagnostic samples obtained in 2013 and 2015 from recently and chronically HIV-1 infected individuals were selected. From the selected samples, 249 (134 from recent versus 115 from chronic infections) env coding regions, including V1-C5 of gp120 and the gp41 ectodomain of HIV-1, were successfully amplified and sequenced by next generation sequencing (NGS) using the Illumina MiSeq platform. The ability of the four sequence-based diversity measures to correctly identify recent HIV infections was evaluated using the frequency distribution curves, median and interquartile range and area under the curve (AUC) of the receiver operating characteristic (ROC). Comparing the median and interquartile range and evaluating the frequency distribution curves associated with the 4 sequence-based diversity measures, we observed that the percent diversity, number of haplotypes and Shannon entropy demonstrated significant potential to discriminate recent from chronic infections (p<0.0001). Using the AUC of ROC analysis, only the Shannon entropy measure within three HIV-1 env segments could accurately identify recent infections at a satisfactory level. The env segments were gp120 C2_1 (AUC = 0.806), gp120 C2_3 (AUC = 0.805) and gp120 V3 (AUC = 0.812). Our results clearly indicate that the Shannon entropy measure represents a useful tool for predicting HIV-1 infection recency.

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Section: Methodsmentioning

confidence: 99%

HIV-1 envelope sequence-based diversity measures for identifying recent infections

et al. 2017

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“…Thus, ZIKV envelope-pseudotypes using the HIV-1 lentiviral packaging system, as described in our study, are new and not described in the literature up to now. In a first experiment, we used the HIV-1 viral packaging vector pNL4-3-R − E − , which works very effectively for env-pseudotypes of HIV [50], Ebola [51], SARS-CoV [52], MERS-CoV [53], and influenza [54,55]. Unfortunately, this vector was highly insufficient in prME-pseudotype production.…”

Section: Discussionmentioning

confidence: 99%

Zikavirus prME Envelope Pseudotyped Human Immunodeficiency Virus Type-1 as a Novel Tool for Glioblastoma-Directed Virotherapy

Kretschmer

Kadlubowska

Hoffmann

et al. 2020

Cancers

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Glioblastoma multiforme is the most lethal type of brain tumor that is not yet curable owing to its frequent resurgence after surgery. Resistance is mainly caused by the presence of a subpopulation of tumor cells, the glioma stem cells (GSCs), which are highly resistant to radiation and chemotherapy. In 2015, Zikavirus (ZIKV)-induced microcephaly emerged in newborns, indicating that ZIKV has a specific neurotropism. Accordingly, an oncolytic tropism for infecting GSCs was demonstrated in a murine tumor model. Like other flaviviruses, ZIKV is enveloped by two proteins, prM and E. The pME expression plasmid along with the HIV-1 vector pNL Luc AM generated prME pseudotyped viral particles. Four different prME envelopes, Z1 to Z4, were cloned, and the corresponding pseudotypes, Z1-to Z4-HIVluc, produced by this two-plasmid system, were tested for entry efficiency using Vero-B4 cells. The most efficient pseudotype, Z1-HIVluc, also infected glioma-derived cell lines U87 and 86HG39. The pseudotype system was then extended by using a three-plasmid system including pME-Z1, the HIV-1 packaging plasmid psPAX2, and the lentiviral vector pLenti-luciferase-P2A-Neo. The corresponding pseudotype, designated Z1-LENTIluc, also infected U87 and 86HG39 cells. Altogether, a pseudotyped virus especially targeting glioma-derived cells might be a promising candidate for a prospective glioblastoma-directed virotherapy. Cancers 2020, 12, 1000 2 of 18 biology, leading to the generation of recombinant, genetically modified virus candidates. Clinical trials have been completed using modified versions of herpes simplex virus [7-12], adenovirus [13,14], Newcastle disease virus [15], reovirus [16,17], parvovirus [18], and poliovirus [19]. Some of these studies demonstrated that a small subset of patients had a benefit from such virotherapy applications, but the statistical significance of these findings must be demonstrated in larger control trials [20].A new discovery, with a high impact on the future aspects of glioma virotherapy, was that Zikavirus (ZIKV) showed a specific neurotropism for glial cells [21]. ZIKV is a new emerging mosquito-borne virus belonging to the Flaviviridae family [22]. In the Flaviviridae family, all members are enveloped viruses with two external, membranous proteins, the envelope E and the precursor of the membrane protein prM [23], both relevant for viral entry. In early 2015, abnormal rates of ZIKV infections were seen in Brazil, and in late 2015, an unexpected high number of newborns showed microcephaly, a disease where a baby's head is much smaller than expected. Altogether, the new emerging ZIKV was shown to be the cause of Guillain-Barré syndrome (GBS), microcephaly, and other congenital brain abnormalities, proving its neurotropic phenotype [24]. An interesting finding was the oncolytic activity of ZIKV against GSCs [25]. A selective effect of ZIKV was observed for GSCs, causing loss of self-renewal and proliferation in glioblastoma organoids. In mice, ZIKV infection prolonged survival by slowing down tumor g...

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“…HIV-1 RNA was amplified using the Superscript III One-Step RT-PCR system with Platinum Ò Taq DNA polymerase (Invitrogen, Thermo Fisher Scientific, and Carlsbad, CA) with primers env-up forward (5¢-GTTTCTTTTAGGCATCTCCTATGGCAGGA AGAAG-3¢, HXB2 positions 5957-5983) and env-lo reverse (5¢-GTTTCTTCCAGTCCCCCCTTTTCTTTTAAAAAG-3¢, HXB2 positions 9063-9088). 31 Nested amplification was performed using the ExpandÔ High Fidelity PCR System Kit (Roche Diagnostics, Indianapolis). Primers E60F forward (5¢-TAATCAGTTTATGGGATCAAAGC-3¢, HXB2 positions 6547-6569) 32 and E55R reverse (5¢-GCCCCAGAC TGTGAGTTGCAACAGATG-3¢, HXB2 positions 7940-7914), 33 were used, generating PCR products covering &1,400 bp of the env gene.…”

Section: Amplification and Sequencing Of Partial Envelope Fragmentmentioning

confidence: 99%

A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses

Kafando

Serhir

Doualla-Bell

et al. 2019

AIDS Research and Human Retroviruses

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The identification of transmission clusters (TCs) of HIV-1 using phylogenetic analyses can provide insights into viral transmission network and help improve prevention strategies. We compared the use of partial HIV-1 envelope fragment of 1,070 bp with its loop 3 (108 bp) to determine its utility in inferring HIV-1 transmission clustering. Serum samples of recently (n = 106) and chronically (n = 156) HIV-1-infected patients with status confirmed were sequenced. HIV-1 envelope nucleotide-based phylogenetic analyses were used to infer HIV-1 TCs. Those were constructed using ClusterPickerGUI_1.2.3 considering a pairwise genetic distance of ≤10% threshold. Logistic regression analyses were used to examine the relationship between the demographic factors that were likely associated with HIV-1 clustering. Ninety-eight distinct consensus envelope sequences were subjected to phylogenetic analyses. Using a partial envelope fragment sequence, 42 sequences were grouped into 15 distinct small TCs while the V3 loop reproduces 10 clusters. The agreement between the partial envelope and the V3 loop fragments was significantly moderate with a Cohen's kappa (κ) coefficient of 0.59, p < .00001. The mean age (<38.8 years) and HIV-1 B subtype are two factors identified that were significantly associated with HIV-1 transmission clustering in the cohort, odds ratio (OR) = 0.25, 95% confidence interval (CI, 0.04–0.66), p = .002 and OR: 0.17, 95% CI (0.10–0.61), p = .011, respectively. The present study confirms that a partial fragment of the HIV-1 envelope sequence is a better predictor of transmission clustering. However, the loop 3 segment may be useful in screening purposes and may be more amenable to integration in surveillance programs.

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Performance of a clonal-based HIV-1 tropism phenotypic assay

Cited by 5 publications

References 53 publications

HIV-1 envelope sequence-based diversity measures for identifying recent infections

HIV-1 envelope sequence-based diversity measures for identifying recent infections

Zikavirus prME Envelope Pseudotyped Human Immunodeficiency Virus Type-1 as a Novel Tool for Glioblastoma-Directed Virotherapy

A Short-Term Assessment of Nascent HIV-1 Transmission Clusters Among Newly Diagnosed Individuals Using Envelope Sequence-Based Phylogenetic Analyses

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