scholarly journals Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

2012 ◽  
Vol 8 (3) ◽  
pp. e1002529 ◽  
Author(s):  
Matthew R. Henn ◽  
Christian L. Boutwell ◽  
Patrick Charlebois ◽  
Niall J. Lennon ◽  
Karen A. Power ◽  
...  
Retrovirology ◽  
2009 ◽  
Vol 6 (S3) ◽  
Author(s):  
W Fischer ◽  
B Keele ◽  
T Bhattacharya ◽  
C Lo ◽  
E Giorgi ◽  
...  

2017 ◽  
Vol 239 ◽  
pp. 106-114 ◽  
Author(s):  
Fabio Zanini ◽  
Johanna Brodin ◽  
Jan Albert ◽  
Richard A. Neher

2016 ◽  
Vol 213 (10) ◽  
pp. 2049-2063 ◽  
Author(s):  
Daniela C. Mónaco ◽  
Dario A. Dilernia ◽  
Andrew Fiore-Gartland ◽  
Tianwei Yu ◽  
Jessica L. Prince ◽  
...  

HIV-1 adapts to a new host through mutations that facilitate immune escape. Here, we evaluate the impact on viral control and disease progression of transmitted polymorphisms that were either preadapted to or nonassociated with the new host’s HLA. In a cohort of 169 Zambian heterosexual transmission pairs, we found that almost one-third of possible HLA-linked target sites in the transmitted virus Gag protein are already adapted, and that this transmitted preadaptation significantly reduced early immune recognition of epitopes. Transmitted preadapted and nonassociated polymorphisms showed opposing effects on set-point VL and the balance between the two was significantly associated with higher set-point VLs in a multivariable model including other risk factors. Transmitted preadaptation was also significantly associated with faster CD4 decline (<350 cells/µl) and this association was stronger after accounting for nonassociated polymorphisms, which were linked with slower CD4 decline. Overall, the relative ratio of the two classes of polymorphisms was found to be the major determinant of CD4 decline in a multivariable model including other risk factors. This study reveals that, even before an immune response is mounted in the new host, the balance of these opposing factors can significantly influence the outcome of HIV-1 infection.


2016 ◽  
Vol 90 (19) ◽  
pp. 8552-8562 ◽  
Author(s):  
Esther Jimenez-Moyano ◽  
Alba Ruiz ◽  
Henrik N. Kløverpris ◽  
Maria T. Rodriguez-Plata ◽  
Ruth Peña ◽  
...  

ABSTRACTTripartite motif-containing protein 5 (TRIM5) restricts human immunodeficiency virus type 1 (HIV-1) in a species-specific manner by uncoating viral particles while activating early innate responses. Although the contribution of TRIM5 proteins to cellular immunity has not yet been studied, their interactions with the incoming viral capsid and the cellular proteasome led us to hypothesize a role for them. Here, we investigate whether the expression of two nonhuman TRIM5 orthologs, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), both of which are potent restrictors of HIV-1, could enhance immune recognition of infected cells by CD8+T cells. We illustrate how TRIM5 restriction improves CD8+T-cell-mediated HIV-1 inhibition. Moreover, when TRIM5 activity was blocked by the nonimmunosuppressive analog of cyclosporine (CsA), sarcosine-3(4-methylbenzoate)–CsA (SmBz-CsA), we found a significant reduction in CD107a/MIP-1β expression in HIV-1-specific CD8+T cells. This finding underscores the direct link between TRIM5 restriction and activation of CD8+T-cell responses. Interestingly, cells expressing RhT5 induced stronger CD8+T-cell responses through the specific recognition of the HIV-1 capsid by the immune system. The underlying mechanism of this process may involve TRIM5-specific capsid recruitment to cellular proteasomes and increase peptide availability for loading and presentation of HLA class I antigens. In summary, we identified a novel function for nonhuman TRIM5 variants in cellular immunity. We hypothesize that TRIM5 can couple innate viral sensing and CD8+T-cell activation to increase species barriers against retrovirus infection.IMPORTANCENew therapeutics to tackle HIV-1 infection should aim to combine rapid innate viral sensing and cellular immune recognition. Such strategies could prevent seeding of the viral reservoir and the immune damage that occurs during acute infection. The nonhuman TRIM5 variants, rhesus TRIM5α (RhT5) and TRIM-cyclophilin A (TCyp), are attractive candidates owing to their potency in sensing HIV-1 and blocking its activity. Here, we show that expression of RhT5 and TCyp in HIV-1-infected cells improves CD8+T-cell-mediated inhibition through the direct activation of HIV-1-specific CD8+T-cell responses. We found that the potency in CD8+activation was stronger for RhT5 variants and capsid-specific CD8+T cells in a mechanism that relies on TRIM5-dependent particle recruitment to cellular proteasomes. This novel mechanism couples innate viral sensing with cellular immunity in a single protein and could be exploited to develop innovative therapeutics for control of HIV-1 infection.


Retrovirology ◽  
2009 ◽  
Vol 6 (Suppl 3) ◽  
pp. P400 ◽  
Author(s):  
MR Henn ◽  
C Boutwell ◽  
N Lennon ◽  
K Power ◽  
C Malboeuf ◽  
...  

2020 ◽  
Vol 94 (12) ◽  
Author(s):  
Olivia D. Council ◽  
Shuntai Zhou ◽  
Chase D. McCann ◽  
Irving Hoffman ◽  
Gerald Tegha ◽  
...  

ABSTRACT Concurrent sexually transmitted infections (STI) can increase the probability of HIV-1 transmission primarily by increasing the viral load present in semen. In this study, we explored the relationship of HIV-1 in blood and seminal plasma in the presence and absence of urethritis and after treatment of the concurrent STI. Primer ID deep sequencing of the V1/V3 region of the HIV-1 env gene was done for paired blood and semen samples from antiretroviral therapy (ART)-naive men living in Malawi with (n = 19) and without (n = 5) STI-associated urethritis; for a subset of samples, full-length env genes were generated for sequence analysis and to test entry phenotype. Cytokine concentrations in the blood and semen were also measured, and a reduction in the levels of proinflammatory cytokines was observed following STI treatment. We observed no difference in the prevalence of diverse compartmentalized semen-derived lineages in men with or without STI-associated urethritis, and these viral populations were largely stable during STI treatment. Clonal amplification of one or a few viral sequences accounted for nearly 50% of the viral population, indicating a recent bottleneck followed by limited viral replication. We conclude that the male genital tract is a site where virus can be brought in from the blood, where localized sustained replication can occur, and where specific genotypes can be amplified, perhaps initially by cellular proliferation but further by limited viral replication. IMPORTANCE HIV-1 infection is a sexually transmitted infection that coexists with other STI. Here, we examined the impact of a concurrent STI resulting in urethritis on the HIV-1 population within the male genital tract. We found that viral populations remain largely stable even with treatment of the STI. These results show that viral populations within the male genital tract are defined by factors beyond transient inflammation associated with a concurrent STI.


2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Yuping Fu ◽  
Yan Liu ◽  
Zhiying Liu ◽  
Lifeng Liu ◽  
Lin Yuan ◽  
...  

microRNAs (miRNAs) are small noncoding RNAs involved in a large range of cellular activities and can be used as biomarkers and indicators for diagnosis. We investigated the alterations in miRNA profiles in immune reconstituted vs. nonimmune reconstituted HIV-1-infected individuals to assess the association between miRNAs and the occurrence of immunological nonresponses, with the aim of searching for miRNA-based biomarkers for these HIV-1-infected individuals. Thirteen immunological responders (IRs) and 12 immunological nonresponders (INRs) were recruited, and RNA was collected from the plasma samples of the 25 HIV-1-infected individuals at both baseline and after 24 months of maintaining virological suppression (VS). Next-generation sequencing was used to detect miRNAs and evaluate the expression differences in miRNAs between IR and INR patients and between baseline and after 24 months of maintaining VS. Samples from 13 IRs and 11 INRs were successfully sequenced. The horizontal comparison of differentially expressed miRNAs between the groups and the longitudinal comparison of differentially expressed miRNAs between baseline and after 24 months of maintaining VS showed that a large proportion of miRNAs in INRs are downregulated compared to the levels in IRs. We also found that the miRNA let-7d-5p was downregulated in 9 INRs but only in 2 IRs by more than 2-fold. The difference was significant. In summary, these results demonstrate for the first time that a large proportion of miRNAs are downregulated in INRs compared with IRs, and the miRNA let-7d-5p is a potential biomarker for INRs.


2020 ◽  
Author(s):  
Olivia D. Council ◽  
Shuntai Zhou ◽  
Chase D. McCann ◽  
Irving Hoffman ◽  
Gerald Tegha ◽  
...  

AbstractConcurrent sexually transmitted infections (STI) can increase the probability of HIV-1 transmission primarily by increasing the viral load present in semen. In this study, we explored the relationship of HIV-1 in blood and seminal plasma in the presence and absence of urethritis and after treatment of the concurrent STI. Primer ID deep sequencing of the V1/V3 region of the HIV-1 env gene was done for paired blood and semen samples from ART-naïve men living in Malawi with (n = 19) and without (n = 5) STI-associated urethritis; for a subset of samples full length env genes were generated for sequence analysis and to test entry phenotype. Cytokine concentrations in the blood and semen were also measured, and a reduction in the levels of pro-inflammatory cytokines was observed following STI treatment. We observed no difference in the prevalence of diverse compartmentalized semen-derived lineages in men with or without STI-associated urethritis, and these viral populations were largely stable during STI treatment. Clonal amplification of one or a few viral sequences accounted for nearly 50% of the viral population indicating a recent bottleneck followed by limited viral replication. We documented a case of superinfection where the new strain was restricted to the genital tract. We conclude that the male genital tract is a site where virus can be brought in from the blood, where localized sustained replication can occur, where a superinfecting strain can persist, and where specific genotypes can be amplified perhaps initially by cellular proliferation but further by limited viral replication.ImportanceHIV-1 is a sexually transmitted infection that co-exists with other STIs. Here we examine the impact of a concurrent STI resulting in urethritis on the HIV-1 population within the male genital tract. We found that viral populations remain largely stable even with treatment of the STI. These results show that viral populations within the male genital tract are defined by factors beyond transient inflammation associated with a concurrent STI.


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