Mapping where HIV hides suggests cure strategy

Science ◽  
2022 ◽  
Vol 375 (6577) ◽  
pp. 130-131
Author(s):  
Jon Cohen
Keyword(s):  
Viral Genomes

Long-term antiretrovirals may corner viral genomes in inactive regions of DNA

scholarly journals Latently KSHV-Infected Cells Promote Further Establishment of Latency upon Superinfection with KSHV

2021 ◽  
Vol 22 (21) ◽  
pp. 11994
Author(s):  
Chen Gam ze Letova ◽  
Inna Kalt ◽  
Meir Shamay ◽  
Ronit Sarid
Keyword(s):  
Latent Infection ◽  
Fluorescent Proteins ◽  
Cell Types ◽  
Lytic Cycle ◽  
Viral Reservoir ◽  
Virus Spread ◽  
Viral Genomes ◽  
Latently Infected ◽  
Infected Cells

Kaposi’s sarcoma-associated herpesvirus (KSHV) is a cancer-related virus which engages in two forms of infection: latent and lytic. Latent infection allows the virus to establish long-term persistent infection, whereas the lytic cycle is needed for the maintenance of the viral reservoir and for virus spread. By using recombinant KSHV viruses encoding mNeonGreen and mCherry fluorescent proteins, we show that various cell types that are latently-infected with KSHV can be superinfected, and that the new incoming viruses establish latent infection. Moreover, we show that latency establishment is enhanced in superinfected cells compared to primary infected ones. Further analysis revealed that cells that ectopically express the major latency protein of KSHV, LANA-1, prior to and during infection exhibit enhanced establishment of latency, but not cells expressing LANA-1 fragments. This observation supports the notion that the expression level of LANA-1 following infection determines the efficiency of latency establishment and avoids loss of viral genomes. These findings imply that a host can be infected with more than a single viral genome and that superinfection may support the maintenance of long-term latency.

scholarly journals Persistence of an Oncogenic Papillomavirus Genome RequirescisElements from the Viral Transcriptional Enhancer

mBio ◽  
2017 ◽  
Vol 8 (6) ◽  
Author(s):  
Koenraad Van Doorslaer ◽  
Dan Chen ◽  
Sandra Chapman ◽  
Jameela Khan ◽  
Alison A. McBride
Keyword(s):  
Persistent Infection ◽  
Viral Genome ◽  
Replication Origin ◽  
Human Papillomaviruses ◽  
Wild Type ◽  
Transcriptional Enhancer ◽  
Complementation Assay ◽  
Viral Genomes ◽  
Stable Maintenance

ABSTRACTHuman papillomavirus (HPV) genomes are replicated and maintained as extrachromosomal plasmids during persistent infection. The viral E2 proteins are thought to promote stable maintenance replication by tethering the viral DNA to host chromatin. However, this has been very difficult to prove genetically, as the E2 protein is involved in transcriptional regulation and initiation of replication, as well as its assumed role in genome maintenance. This makes mutational analysis of viraltransfactors andciselements in the background of the viral genome problematic and difficult to interpret. To circumvent this problem, we have developed a complementation assay in which the complete wild-type HPV18 genome is transfected into primary human keratinocytes along with subgenomic or mutated replicons that contain the minimal replication origin. The wild-type genome provides the E1 and E2 proteins intrans, allowing us to determine additionalciselements that are required for long-term replication and partitioning of the replicon. We found that, in addition to the core replication origin (and the three E2 binding sites located therein), additional sequences from the transcriptional enhancer portion of the URR (upstream regulatory region) are required incisfor long-term genome replication.IMPORTANCEHuman papillomaviruses infect cutaneous and mucosal epithelial cells of the host, and this results in very-long-lived, persistent infection. The viral genomes are small, circular, double-stranded DNA molecules that replicate extrachromosomally in concert with cellular DNA. This replication strategy requires that the virus has a robust mechanism to partition and retain the viral genomes in dividing cells. This has been difficult to study, because viral transcription, replication, and partitioning are regulated by the same viral proteins and involve overlapping elements in the viral genome. We developed a complementation assay that allows us to separate these functions and define the elements required for long-term replication and stable maintenance replication of the HPV genome. This has important implications, as disruption of viral maintenance replication can eliminate viral genomes from infected cells, thus curing persistent HPV infection.

scholarly journals Spatiotemporal dissemination pattern of SARS-CoV-2 B1.1.28-derived lineages introduced into Uruguay across its southeastern border with Brazil.

2021 ◽  
Author(s):  
Natalia Rego ◽  
Tamara Fernandez-Calero ◽  
Ighor Arantes ◽  
Veronica Noya ◽  
daiana mir ◽  
...  
Keyword(s):  
Spike Protein ◽  
Partial Replacement ◽  
Viral Dynamics ◽  
Rio Grande Do Sul ◽  
Viral Genomes ◽  
Replacement Process ◽  
Functional Relevance ◽  
The Impact ◽  
Epidemic Wave

During the first nine months of the SARS-CoV-2 pandemic, Uruguay successfully kept it under control, even when our previous studies support a recurrent viral flux across the Uruguayan-Brazilian border that sourced several local outbreaks in Uruguay. However, towards the end of 2020, a remarkable exponential growth was observed and the TETRIS strategy was lost. Here, we aimed to understand the factors that fueled SARS-CoV-2 viral dynamics during the first epidemic wave in the country. We recovered 84 whole viral genomes from patients diagnosed between November, 2020 and February, 2021 in Rocha, a sentinel eastern Uruguayan department bordering Brazil. The lineage B.1.1.28 was the most prevalent in Rocha during November-December 2020, P.2 became the dominant one during January-February 2021, while the first P.1 sequences corresponds to February, 2021. The lineage replacement process agrees with that observed in several Brazilian states, including Rio Grande do Sul (RS). We observed a one to three month delay between the appearance of P.2 and P.1 in RS and their subsequent detection in Rocha. The phylogenetic analysis detected two B.1.1.28 and one P.2 main Uruguayan SARS-CoV-2 clades, introduced from the southern and southeastern Brazilian regions into Rocha between early November and mid December, 2020. One synonymous mutation distinguishes the sequences of the main B.1.1.28 clade in Rocha from those widely distributed in RS. The minor B.1.1.28 cluster, distinguished by several mutations, harbours non-synonymous changes in the Spike protein: Q675H and Q677H, so far not concurrently reported. The convergent appearance of S:Q677H in different viral lineages and its proximity to the S1/S2 cleavage site raise concerns about its functional relevance. The observed S:E484K-VOI P.2 partial replacement of previously circulating lineages in Rocha might have increased transmissibility as suggested by the significant decrease in Ct values. Our study emphasizes the impact of Brazilian SARS-CoV-2 epidemics in Uruguay and the need of reinforcing real-time genomic surveillance on specific Uruguayan border locations, as one of the key elements for achieving long-term COVID-19 epidemic control.

scholarly journals Diel cycling and long-term persistence of viruses in the ocean’s euphotic zone

2017 ◽  
Vol 114 (43) ◽  
pp. 11446-11451 ◽  
Author(s):  
Frank O. Aylward ◽  
Dominique Boeuf ◽  
Daniel R. Mende ◽  
Elisha M. Wood-Charlson ◽  
Alice Vislova ◽  
...  
Keyword(s):  
Euphotic Zone ◽  
Ecosystem Dynamics ◽  
Viral Gene ◽  
Viral Genomes ◽  
Diel Cycles ◽  
Cellular Replication ◽  
Natural Settings ◽  
Marine Microbial Communities ◽  
Dsdna Viruses

Viruses are fundamental components of marine microbial communities that significantly influence oceanic productivity, biogeochemistry, and ecosystem processes. Despite their importance, the temporal activities and dynamics of viral assemblages in natural settings remain largely unexplored. Here we report the transcriptional activities and variability of dominant dsDNA viruses in the open ocean’s euphotic zone over daily and seasonal timescales. While dsDNA viruses exhibited some fluctuation in abundance in both cellular and viral size fractions, the viral assemblage was remarkably stable, with the most abundant viral types persisting over many days. More extended time series indicated that long-term persistence (>1 y) was the rule for most dsDNA viruses observed, suggesting that both core viral genomes as well as viral community structure were conserved over interannual periods. Viral gene transcription in host cell assemblages revealed diel cycling among many different viral types. Most notably, an afternoon peak in cyanophage transcriptional activity coincided with a peak inProchlorococcusDNA replication, indicating coordinated diurnal coupling of virus and host reproduction. In aggregate, our analyses suggested a tightly synchronized diel coupling of viral and cellular replication cycles in both photoautotrophic and heterotrophic bacterial hosts. A surprising consequence of these findings is that diel cycles in the ocean’s photic zone appear to be universal organizing principles that shape ecosystem dynamics, ecological interactions, and biogeochemical cycling of both cellular and acellular community components.

Regulation of HPV18 Genome Replication, Establishment and Persistence by Sequences in the Viral Upstream Regulatory Region

2021 ◽  
Author(s):  
Tami L. Coursey ◽  
Koenraad Van Doorslaer ◽  
Alison A. McBride
Keyword(s):  
Replication Origin ◽  
Regulatory Region ◽  
Unique Element ◽  
Genome Replication ◽  
Transcriptional Enhancer ◽  
Viral Genomes ◽  
Daughter Cells ◽  
Papillomavirus Infection ◽  
Stable Dna Replication

During persistent human papillomavirus infection, the viral genome replicates as an extrachromosomal plasmid that is efficiently partitioned to daughter cells during cell division. We have previously shown that an element which overlaps the HPV18 transcriptional enhancer promotes stable DNA replication of replicons containing the viral replication origin. Here we perform comprehensive analyses to elucidate the function of this maintenance element. We conclude that no unique element or binding site in this region is absolutely required for persistent replication and partitioning, and instead propose that the overall chromatin architecture of this region is important to promote efficient use of the replication origin. These results have important implications on the genome partitioning mechanism of papillomaviruses. Importance Persistent infection with oncogenic HPVs is responsible for ∼5% human cancers. The viral DNA replicates as an extrachromosomal plasmid and is partitioned to daughter cells in dividing keratinocytes. Using a complementation assay that allows us to separate viral transcription and replication, we provide insight into viral sequences that are required for long term replication and persistence in keratinocytes. Understanding how viral genomes replicate persistently for such long periods of time will guide the development of anti-viral therapies.

Abstract 2882: Directed Evolution of Cardiac Specific Adeno-Associated Vector Variants

Circulation ◽  
2008 ◽  
Vol 118 (suppl_18) ◽  
Author(s):  
Roger J Hajjar ◽  
Jiqiu Chen ◽  
Yoshiaki Kawase ◽  
Scott McPhee ◽  
Jade Samulski ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Neutralizing Antibodies ◽  
Cardiac Tissue ◽  
Marker Gene ◽  
Green Fluorescence ◽  
Viral Genomes ◽  
Large Animals ◽  
Time Point

Adeno-associated vectors (AAV) have gained popularity in cardiovascular gene transfer because of their distinct characteristics: long-term expression, minimal immune response and strong tropism to cardiac tissue for specific serotypes (such as AAV9). However AAVs have certain limitations: Neutralizing antibodies in 40% of humans for each AAV serotype and non-specificity of the AAV serotypes to various organs. Chimeric viruses composed of capsid proteins of different serotypes, show distinct transduction profiles. To identify hybrid viruses that can selectively transduce cardiomyocytes in vivo, we generated a library of diverse AAV variants, obtained by DNA shuffling, with an enrichment of cardiotropic AAV variants, called biological nanoparticles (BNPs). We selected five BNPs from these experiments: BNP 108, 109, 111, 689, and 693. We then injected these different BNPs using GFP as a marker gene under the control of CMV along with AAV9 into rats (3 in each group and each time point) through their tail vein at a concentration of 1011 vg (viral genomes). We sacrificed the animals at one and four weeks and examined expression in the heart, liver, lung, kidneys, and aorta. We found that at 1 week, BNP 108 and 109 had the best expression in the heart (61±12% of the myocytes with green fluorescence) while BNP 111 and AAV9 had strong cardiac expression at 4 weeks (93±11% and 79±12% of the myocytes with green fluorescence). None of the BNPs showed expression in the liver, lung, kidneys, and aorta, while AAV9 demonstrated widespread expression in all these tissues. Transcoronary injection of BNP111 at a concentration of 1012 vg demonstrated the efficiency of BNP in transducing myocardium of large animals. We also found that all the BNPs are resistant to preexisting neutralizing antibodies against parent serotypes. These results show that directed evolution of AAV variants can yield BNPs that are highly cardiotropic and highly efficient of transducing cardiac tissue without infecting other organs and having resistance to preexisting neutralizing antibodies against parent serotypes. These BNPs may become very useful for clinical applications.

scholarly journals Adeno-Associated Virus Vector Genomes Persist as Episomal Chromatin in Primate Muscle

2008 ◽  
Vol 82 (16) ◽  
pp. 7875-7885 ◽  
Author(s):  
Magalie Penaud-Budloo ◽  
Caroline Le Guiner ◽  
Ali Nowrouzi ◽  
Alice Toromanoff ◽  
Yan Chérel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transgene Expression ◽  
Adeno Associated Virus ◽  
Viral Genomes ◽  
Bona Fide ◽  
Episomal Maintenance ◽  
Insight Into ◽  
Intramuscular Delivery

ABSTRACT Recombinant adeno-associated virus (rAAV) vectors are capable of mediating long-term gene expression following administration to skeletal muscle. In rodent muscle, the vector genomes persist in the nucleus in concatemeric episomal forms. Here, we demonstrate with nonhuman primates that rAAV vectors integrate inefficiently into the chromosomes of myocytes and reside predominantly as episomal monomeric and concatemeric circles. The episomal rAAV genomes assimilate into chromatin with a typical nucleosomal pattern. The persistence of the vector genomes and gene expression for years in quiescent tissues suggests that a bona fide chromatin structure is important for episomal maintenance and transgene expression. These findings were obtained from primate muscles transduced with rAAV1 and rAAV8 vectors for up to 22 months after intramuscular delivery of 5 × 1012 viral genomes/kg. Because of this unique context, our data, which provide important insight into in situ vector biology, are highly relevant from a clinical standpoint.

Therapy and prevention for mental health: What if mental diseases are mostly not brain disorders?

2019 ◽  
Vol 42 ◽  
Author(s):  
John P. A. Ioannidis
Keyword(s):  
Mental Health ◽  
Mental Disease ◽  
Brain Disorders ◽  
Social Stressors ◽  
Labor Education ◽  
Mental Diseases ◽  
Long Term Follow Up ◽  
Political Decisions

AbstractNeurobiology-based interventions for mental diseases and searches for useful biomarkers of treatment response have largely failed. Clinical trials should assess interventions related to environmental and social stressors, with long-term follow-up; social rather than biological endpoints; personalized outcomes; and suitable cluster, adaptive, and n-of-1 designs. Labor, education, financial, and other social/political decisions should be evaluated for their impacts on mental disease.

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