Study of Genotypic and Phenotypic HIV-1 Dynamics of Integrase Mutations During Raltegravir Treatment: A Refined Analysis by Ultra-Deep 454 Pyrosequencing

Armenia, Daniele; Vandenbroucke, Ina; Fabeni, Lavinia; Marck, Herwig Van; Cento, Valeria; D’Arrigo, Roberta; Wesenbeeck, Liesbeth Van; Scopelliti, Fernanda; Micheli, Valeria; Bruzzone, Bianca; Caputo, Sergio Lo; Aerssens, Jeroen; Rizzardini, Giuliano; Tozzi, Valerio; Narciso, Pasquale; Antinori, Andrea; Stuyver, Lieven; Perno, Carlo Federico; Ceccherini‐Silberstein, Francesca

doi:10.1093/infdis/jir821

Cited by 47 publications

(33 citation statements)

References 44 publications

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“…Primary resistance mutations could be detected through use of a more sensitive method. Secondary and additional mutations are detected more frequently in baseline samples from therapy-naive and treatmentexperienced patients (12)(13)(14). The frequency of all detected mutations was < 1% of the viral population, but the frequency of variation was similar in patients that responded to raltegravir and patients that did not respond to raltegravir, suggesting that these lowfrequency resistance mutations do not significantly result in treatment failure.…”

Section: Discussionmentioning

confidence: 96%

Efficacy and safety of antiretroviral regimens including raltegravir to treat HIV-infected patients with hemophilia

Xiao

Xue

Shiming

et al. 2016

BST

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Section: Discussionmentioning

confidence: 96%

Efficacy and safety of antiretroviral regimens including raltegravir to treat HIV-infected patients with hemophilia

Xiao

Xue

Shiming

et al. 2016

BST

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“…In vivo studies of viral quasispecies evolving under selective pressure by antivirals have been completed in human subjects but typically only after antiviral failure. Most also focus on a few previously identified resistance mutations to virustargeting antivirals (23,(30)(31)(32).…”

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confidence: 99%

Dengue Virus Evolution under a Host-Targeted Antiviral

Plummer

Buck

et al. 2015

J Virol

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The host-targeted antiviral drug UV-4B reduces viral replication and promotes survival in a mouse model of experimental dengue virus (DENV) infection. UV-4B is an iminosugar that inhibits the ␣-glucosidase family of enzymes and subsequently the folding of glycosylated proteins, both viral and host. Here, we utilized next-generation sequencing to investigate evolution of a flavivirus under selective pressure by a host-targeted antiviral in vivo. In viral populations recovered from UV-4B-treated mice, there was a significant increase in the number of single-nucleotide polymorphisms (SNPs) and the ratio of nonsynonymous to synonymous SNPs compared to findings in viral populations from vehicle-treated mice. The strongest evidence of positive selection was in the glycosylated membrane protein, thereby providing in vivo validation of the mechanism of action of an iminosugar. In addition, mutations in glycosylated proteins were present only in drug-treated mice after a single passage. However, the bulk of the other mutations were present in both populations, indicating nonspecific selective pressure. Together with the continued control of viremia by UV-4B, these findings are consistent with the previously predicted high genetic barrier to escape mutations in host-targeted antivirals. IMPORTANCEAlthough hundreds of millions of people are infected with DENV every year, there is currently no approved vaccine or antiviral therapy. UV-4B has demonstrated antiviral activity against DENV and is expected to enter clinical trials soon. Therefore, it is important to understand the mechanisms of DENV resistance to UV-4B. Host-targeted antivirals are thought to have a higher genetic barrier to escape mutants than directly acting antivirals, yet there are very few published studies of viral evolution under host-targeted antivirals. No study to date has described flavivirus evolution in vivo under selective pressure by a host-based antiviral drug. We present the first in vivo study of the sequential progression of viral evolution under selective pressure by a hosttargeted antiviral compound. This study bolsters support for the clinical development of UV-4B as an antiviral drug against DENV, and it provides a framework to compare how treatment with other host-targeted antiflaviviral drugs in humans and different animal models influence viral genetic diversity. Dengue virus (DENV) is the most common mosquito-borne human pathogen. DENV can cause illnesses ranging from self-limited mild disease to severe and potentially life-threatening dengue hemorrhagic fever/dengue shock syndrome. Approximately 400 million people are infected each year with DENV (1), generally in tropical and subtropical areas, with 20,000 infections resulting in death (2). The current standard of care consists of fluid replacement and other supportive care. There is presently no vaccine to prevent or antiviral to treat DENV infection. Recent phase IIb and III trials of an attenuated, tetrameric vaccine showed limited efficacy, especially in naive individuals...

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“…The techniques that have been applied for the direct detection of MRMP include PCR followed by Sanger sequencing (11,14,16), pyrosequencing (17,18), high-resolution melting curve analysis (19)(20)(21), allele-specific PCR (22), and PCRrestriction fragment length polymorphism (23). In the context of viral infections, natural occurrences of mixed drug-sensitive and -resistant subpopulations are well documented (24)(25)(26)(27)(28). The enrichment of minor resistant subpopulations has further been demonstrated to be associated with antiviral treatment failure (25,26).…”

mentioning

confidence: 99%

“…In the context of viral infections, natural occurrences of mixed drug-sensitive and -resistant subpopulations are well documented (24)(25)(26)(27)(28). The enrichment of minor resistant subpopulations has further been demonstrated to be associated with antiviral treatment failure (25,26). This has led to the term "quasispecies," which has been used widely to describe sequence variants in heterogeneous virus populations (25,26).…”

mentioning

confidence: 99%

“…The enrichment of minor resistant subpopulations has further been demonstrated to be associated with antiviral treatment failure (25,26). This has led to the term "quasispecies," which has been used widely to describe sequence variants in heterogeneous virus populations (25,26). Recent studies involving Sanger sequencing suggested that mycoplasma infections might also comprise mixed populations of drug-sensitive and drug-resistant molecular mutants (i.e., quasispecies at the 23S rRNA macrolide resistance motif) (29).…”

mentioning

confidence: 99%

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Comparison of Pyrosequencing, Sanger Sequencing, and Melting Curve Analysis for Detection of Low-Frequency Macrolide-Resistant Mycoplasma pneumoniae Quasispecies in Respiratory Specimens

Chan

et al. 2013

J Clin Microbiol

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Macrolide-resistant Mycoplasma pneumoniae (MRMP) is emerging worldwide and has been associated with treatment failure. In this study, we used pyrosequencing to detect low-frequency MRMP quasispecies in respiratory specimens, and we compared the findings with those obtained by Sanger sequencing and SimpleProbe PCR coupled with a melting curve analysis (SimpleProbe PCR). Sanger sequencing, SimpleProbe PCR, and pyrosequencing were successfully performed for 96.7% (88/91), 96.7% (88/91), and 93.4% (85/91) of the M. pneumoniae-positive specimens, respectively. The A-to-G transition at position 2063 was the only mutation identified. Pyrosequencing identified A2063G MRMP quasispecies populations in 78.8% (67/88) of the specimens. Only 38.8% (26/67) of these specimens with the A2063G quasispecies detected by pyrosequencing were found to be A2063G quasispecies by Sanger sequencing or SimpleProbe PCR. The specimens that could be detected by SimpleProbe PCR and Sanger sequencing had higher frequencies of MRMP quasispecies (51% to 100%) than those that could not be detected by those two methods (1% to 44%). SimpleProbe PCR correctly categorized all specimens that were identified as wild type or mutant by Sanger sequencing. The clinical characteristics of the patients were not significantly different when they were grouped by the presence or absence of MRMP quasispecies, while patients with MRMP identified by Sanger sequencing more often required a switch from macrolides to an alternative M. pneumoniae-targeted therapy. The clinical significance of mutant quasispecies should be investigated further with larger patient populations and with specimens obtained before and after macrolide therapy.

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Study of Genotypic and Phenotypic HIV-1 Dynamics of Integrase Mutations During Raltegravir Treatment: A Refined Analysis by Ultra-Deep 454 Pyrosequencing

Cited by 47 publications

References 44 publications

Efficacy and safety of antiretroviral regimens including raltegravir to treat HIV-infected patients with hemophilia

Efficacy and safety of antiretroviral regimens including raltegravir to treat HIV-infected patients with hemophilia

Dengue Virus Evolution under a Host-Targeted Antiviral

Comparison of Pyrosequencing, Sanger Sequencing, and Melting Curve Analysis for Detection of Low-Frequency Macrolide-Resistant Mycoplasma pneumoniae Quasispecies in Respiratory Specimens

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