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replication

The Esperanza Patient

2 December 2021 by Gertrud U. Rey

by Gertrud U. Rey

There is still no real cure for HIV infection. Only two people have been intentionally and successfully cleared of the virus thus far – the Berlin patient and the London patient. However, both subjects needed dangerous stem cell transplants to replenish their blood stem cells that had been destroyed during chemotherapy regimens needed to treat their HIV-induced blood cancers. In their transplants, doctors used bone marrow cells from a donor who was homozygous for a mutation in the gene encoding the HIV co-receptor CCR5 (CCR5 Δ32/Δ32), because this genotype confers resistance to HIV-1 infection. Such a transplant strategy cannot be realistically applied to most HIV patients.

Recently, a thirty-year-old female resident of Esperanza, Argentina, was declared to be cured of HIV-1 without receiving long-term treatment. The “Esperanza patient” is actually the second individual known to have cleared the infection naturally. The first person, known as the “San Francisco patient,” is a 67-year-old woman who appears to have cleared the virus in the absence of treatment after living with HIV for 28 years. Standard HIV treatment involves a combination of drugs known as antiretroviral therapy (ART), which is very effective at reducing the viral load in the blood of infected individuals and preventing transmission to others. However, ART does not eliminate all infected cells, allowing the persistence of a small pool of cells collectively known as the HIV reservoir. If ART is interrupted or terminated, the virus will begin replicating again within a couple of weeks because of this reservoir. The reservoir cells are capable of clonally expanding, and surprisingly, not all offspring of a clone exhibit identical levels of viral expression. Developing effective strategies to identify and eliminate such pools of cells is a prevailing challenge in the HIV field. Even the small group of HIV-infected individuals known as “elite controllers” who are able to maintain suppressed viral levels without ART retain a low frequency of intact integrated HIV DNA copies known as proviruses in their peripheral T helper cells.

The Esperanza patient was determined to be an elite controller because she had a very low viral load and no clinical or laboratory signs of HIV-1-associated disease for the entire eight years following her diagnosis, despite receiving no ART during that time. She only underwent ART when she became pregnant, but discontinued treatment after giving birth. To determine whether she had a persistent HIV-1 reservoir, the authors of a recent publication collected blood samples and placental tissue from the patient. They then isolated ~1.2 billion peripheral blood cells and ~0.5 million placental cells from the samples and subjected the cells to amplification and sequencing using primers and probes specific for HIV-1 in a technique that detects single, near full-length HIV-1 proviral genomes. The authors only detected seven proviral HIV-1 DNA species in the blood cells and none in the placenta. However, each of the seven HIV-1 DNA species was defective: one near-full-length sequence contained mutations that were lethal for the virus, and the other six sequences each contained large deletions. Three of these six sequences with deletions were completely identical to each other, suggesting that they were products of clonal expansion. These results distinguished the patient from other elite controllers, indicating that even though she had been infected with HIV-1 at some point and viral replication had occurred in the past, all viral DNA resulting from recent replication cycles was damaged.

The patient’s peripheral blood cells were also used to isolate 150 million T helper cells, which are the primary target of HIV-1. When the authors analyzed these T cells for the presence of replication-competent HIV-1 particles, they did not detect a single virion, a feature that further distinguished the Esperanza patient from other elite controllers, whose blood typically contains up to 50 replication-competent virions per milliliter.

The entry of HIV-1 into cells requires the presence of two cell surface proteins: the receptor CD4, and one of two co-receptors, either CXCR4 or CCR5. Individuals with a CCR5 Δ32/Δ32 genotype, which signifies a mutation in both copies of the gene encoding CCR5, are resistant to HIV-1 infection. Analysis of T helper cells isolated from the Esperanza patient revealed that they fully expressed both wild-type versions of CCR5 and CXCR4 co-receptors, and when tested in vitro, these cells were able to support HIV-1 infection and replication. This observation suggests that the patient was not resistant to infection. However, her serum did not contain the entire antibody profile usually found in HIV-1-positive patients, implying that even though she became infected and replicated virus, she never developed a full HIV-1-specific antibody response. 

The complete elimination of all virus-carrying cells in the context of HIV infection is termed a “sterilizing cure,” and the mechanism responsible for this exceedingly rare phenomenon is unclear. The human immune proteins APOBEC3G and APOBEC3F are known to induce destructive nucleotide changes in the HIV genome, and the authors hypothesize that the lethal mutations found in the near full-length HIV-1 proviral sequence were likely induced by these immune proteins. However, it is unclear why the overall number of proviral species was so low.

Whether or not the Esperanza patient will remain permanently free of HIV is currently unclear. The authors are careful to note that “absence of evidence for intact HIV-1 proviruses in large numbers of cells is not evidence of absence of intact HIV-1 proviruses.” Nevertheless, this study suggests that a sterilizing cure of HIV-1 infection is possible, even if it is rare. The authors hope that additional data collected from the San Francisco and Esperanza patients will provide further insight into the mechanism responsible for a sterilizing cure, which might lead to treatments that cause the immune system to mimic the responses observed in these two patients.

[This article was written in honor of World AIDS Day, which occurs annually on December 1.]

Filed Under: Basic virology, Gertrud Rey Tagged With: AIDS, AIDS cure, Antiretroviral therapy, APOBEC3F, APOBEC3G, Berlin patient, ccr5 receptor, CD4, elite controller, HIV, hiv reservoir, HIV-1, infection, London patient, provirus, replication, sterilizing cure, T helper cells

Early Immune Responses to Herpes Simplex Virus Type I Infection

6 May 2021 by Gertrud U. Rey

by Gertrud U. Rey

Herpes simplex viruses infect cells of the skin and mucous membranes, where they establish a lifelong persistent infection in sensory neurons. Sporadic reactivation and viral shedding may lead to painful oral and genital disease and a three to five-fold increased risk of HIV transmission. There is currently no vaccine to prevent infection with herpes simplex virus type 1 or type 2 (HSV-1 or HSV-2).

Until recently it was thought that initial interactions of HSV-1 with the immune system only involve Langerhans cells. Langerhans cells are skin-resident sentinel macrophages that detect microbial antigens, and they engulf, process, and present these antigens to T cells for downstream immune functions. However, a recent study suggests that early during infection, HSV-1 also interacts with a newly identified immune cell known as an epidermal conventional dendritic cell type 2 (Epi-cDC2). Like Langerhans cells, dendritic cells can swallow microbe-infected cells and present the microbial antigens to T helper cells, ultimately triggering the actions of cytotoxic T cells, which directly kill infected cells.

The study aimed to better define the role of Epi-cDC2s in early HSV-1 infection using ex vivo explants as a model system. The explants consisted of pieces of human inner foreskin that were mounted on specialized gelatin scaffolds to mimic the in vivo environment encountered by HSV-1 during infection. The authors exposed the explants to an HSV-1 virus in which a viral membrane protein was fused to a green fluorescent protein (GFP), allowing them to visually track a resulting infection using a fluorescence microscope. This method revealed that at 24 hours after exposure to the GFP-tagged HSV-1, both Langerhans cells and Epi-cDC2s contained the virus in their cytoplasm, suggesting that these cells either engulfed HSV-1-infected skin cells and/or were themselves infected by HSV-1.

To determine whether the presence of HSV-1 in the cytoplasm of Epi-cDC2s resulted from infection and replication and not just from engulfing infected skin cells, the authors first did the following. They exposed cell cultures of Epi-cDC2s to HSV-1. After six hours of this exposure, Epi-cDC2s contained about as much virus as did control Langerhans cells, which are known to be infected by HSV-1. However, at 18 hours, Epi-cDC2s contained significantly higher HSV-1 levels than Langerhans cells, suggesting increased entry/uptake of virus into Epi-cDC2s compared to Langerhans cells. Next, to assess whether HSV-1 was also replicating in the Epi-cDC2 cells, not just entering them, the authors treated the cells with a fluorescent antibody that binds ICP27, a viral protein needed for replication. A significantly greater portion of Epi-cDC2s than Langerhans cells expressed ICP27, suggesting that HSV-1 was replicating, and doing so more efficiently in Epi-cDC2s.

Viruses may enter a host cell by a variety of mechanisms. One common mechanism, called receptor-mediated endocytosis, involves the formation of cell membrane-derived vesicles. In one version of this process, which requires a low pH, viral binding to a cell surface receptor triggers the cellular membrane to fold inward and form a slightly acidic “endosome” around the virus. Another version of receptor-mediated endocytosis is not dependent on a low pH, but requires cholesterol molecules and the motor protein actin to form cell surface protrusions called “ruffles.” When the ruffles become large enough, they collapse back onto the membrane and form large fluid-filled vesicles encasing the virus. In both of these versions of receptor-mediated endocytosis, the resulting vesicles enter the cytoplasm, where they eventually release their contents. In yet another mechanism of entry, also independent of acidic pH, viruses may simply fuse with the plasma membrane and deliver their contents into the cytoplasm.

Although HSV-1 can enter cells by any of these pathways, its entry mechanism differs in different types of cells. To determine which pathway HSV-1 uses to enter Langerhans cells and Epi-cDC2s, the authors treated both types of cells with a drug that prevents acidification of endosomes. They then infected the cells with the GFP-tagged HSV-1 and measured infection by quantitating GFP with a fluorescence microscope. Increasing doses of the drug led to increased inhibition of infection of Langerhans cells, suggesting that these cells are infected with HSV-1 via a pH-dependent mechanism. In contrast, the drug did not affect infection of Epi-cDC2s, suggesting that HSV-1 does not require an acidic pH for entering Epi-cDC2s.

To determine whether HSV-1 entry into Epi-cDC2s occurred via actin and cholesterol-dependent endocytosis, the authors treated Epi-cDC2s with inhibitors of actin or cholesterol prior to infection. Both treatments led to significant reduction in GFP fluorescence inside the cells, suggesting that cholesterol and actin are both important mediators of HSV-1 entry into Epi-cDC2s.

Langerhans cells express a cell surface receptor called langerin, which mediates entry of HIV and influenza A. To see whether this receptor is also required for entry of HSV-1, the authors infected Langerhans cells with HSV-1 in the presence of an antibody that neutralizes langerin. This inhibition of langerin expression led to diminished infection of Langerhans cells, suggesting that langerin is required for HSV-1 entry into them. In contrast, inhibition of langerin on Epi-cDC2s had no effect on HSV-1 infection efficiency, suggesting that, even though Epi-cDC2s do express some langerin, this receptor is not required for HSV-1 entry of these cells.

HSV-1 and HSV-2 are of high public health concern, and a vaccine to prevent infection with these viruses is urgently needed. Immune control of HSV-1/-2 infection and resolution of genital herpes lesions requires the collective action of various types of T cells, which are likely primed by different dendritic cell subsets. Understanding the dynamics of the initial interactions of HSV-1 and HSV-2 with cells of the immune system may result in better strategies for HSV-1/-2 vaccines. The pathways described here have important implications in vaccine design and prevention of persistent infection of neuronal cells.

Filed Under: Basic virology, Gertrud Rey Tagged With: actin, cholesterol, dendritic cell, herpes, herpes simplex virus, herpes simplex virus 1, HSV-1, infection, Langerhans cell, macrophage, receptor-mediated endocytosis, replication

Viral reproduction and replication

27 July 2019 by Vincent Racaniello

Most contemporary virologists use the term replication to indicate either the production of new virus particles or viral genomes. Because these are very different processes, during the preparation of the fourth edition of the textbook Principles of Virology, the authors decided to use the word reproduction to designate the production of new infectious virus particles, and replication when referring to nucleic acid synthesis. Recently I learned from Bill Summers, speaking at ASV 2019, how the historical use of these two words reflects our evolving concept of virus.

[Read more…] about Viral reproduction and replication

Filed Under: Basic virology, Commentary Tagged With: concept of virus, Luria, replication, reproduction, Summers, viral, virology, virology history, virus, viruses

TWiV 393: Lovers and livers

12 June 2016 by Vincent Racaniello

Possible sexual transmission of Zika virus, and a cell protein that allows hepatitis C virus replication in cell culture by enhancing vitamin E mediated protection against lipid peroxidation, are the subjects discussed by the TWiVerati on this week’s episode of the science show This Week in Virology.

You can find TWiV #393 at microbe.tv/twiv, or listen below.

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Filed Under: This Week in Virology Tagged With: cell culture, flavivirus, hepatitis C virus, lipid peroxidation, replication, replicon, SEC14L2, semen, sexual transmission, viral, virology, virus, viruses, vitamin E, zika virus

TWiV 374: Discordance in B

31 January 2016 by Vincent Racaniello

TWiVOn episode #374 of the science show This Week in Virology, the TWiVniks consider the role of a cell enzyme that removes a protein linked to the 5′-end of the picornavirus genome, and the connection between malaria, Epstein-Barr virus, and endemic Burkitt’s lymphoma.

You can find TWiV #374 at microbe.tv/twiv.

Filed Under: This Week in Virology Tagged With: 5'-tyrosyl DNA phosphodiesterase, activation-induced cytidine deaminase, AID, Burkitt, Burkitt's lymphoma, c-myc, cancer, coxsackievirus, Epstein-Barr virus, hypermutation, malaria, oncogene, picornavirus, Plasmodium falciparum, poliovirus, replication, rhinovirus, TDP2, translation, translocation, unlinkase, viral, virology, virus, viruses, VPg

Virology for planet Earth

5 May 2015 by Vincent Racaniello

Virology 2015It is the first week in May, which means that the spring semester has just ended at Columbia University, and my annual virology course is over.

Each year I teach an introductory undergraduate virology course that is organized around basic principles, including how virus particles are built, how they replicate, how they cause disease, and how to prevent infections. Some feel that it’s best to teach virology by virus: a lecture on influenza, herpesvirus, HIV, and on and on. But this approach is all wrong: you can’t learn virology by listening to lectures on a dozen different viruses. In the end all you will have is a list of facts but you won’t understand virology.

I record every one of my 26 introductory lectures as a videocast, and these are available on the course website, or on YouTube. If you have listened to my lectures before, you might be wondering what is new. I change about 10% of each lecture every year, updating the information and adding new figures. This year I’ve also added two new lectures, on on Ebolavirus and one on viral gene therapy.

Once you have taken my introductory course, then you will be ready for an advanced course on Viruses. A course in which we go into great detail on the replication, pathogenesis, and control of individual viruses. I am working on such a course and when it’s ready I’ll share it with everyone.

I want to be Earth’s virology professor, and this is my introductory virology course for the planet.

Filed Under: Basic virology, Information Tagged With: columbia university, control, course, lecture, pathogenesis, replication, videocast, viral, virology, virus

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by Vincent Racaniello

Earth’s virology Professor
Questions? virology@virology.ws

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ME/CFS
Inside a BSL-4
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Interviews With Virologists

Earth’s Virology Course

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