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Background Sex differences in human immunodeficiency virus (HIV) reservoir dynamics remain underexplored. Methods Longitudinal samples from virally suppressed midlife women (n = 59, median age 45 years) and age-matched men (n = 31) were analyzed retrospectively. At each time point, we measured sex hormones (by means of enzyme-linked immunosorbent assay) and cellular HIV DNA and RNA (by means of digital droplet polymerase chain reaction). Number of inducible HIV RNA+ cells, which provides an upper estimate of the replication-competent reservoir, was quantified longitudinally in a different subset of 14 women, across well-defined reproductive stages. Mixed-effects models included normalized reservoir outcomes and sex, time since antiretroviral therapy (ART) initiation, and the sex-by-time interaction as predictors. Results At ART initiation, women and men had median (interquartile range [IQR]) CD4+ T-cell counts of 204/μL (83–306/μL) versus 238/μL (120–284/μL), respectively; median ages of 45 (42–48) versus 47 (43–51) years; and median follow-up times of 79.2/μL (60.5–121.1/μL) versus 66.2/μL (43.2–80.6/μL) months. We observed a significant decline of total HIV DNA over time in both men and women (P Conclusions In contrast to men, in whom the HIV reservoir steadily declines with aging, the HIV reservoir in women is more dynamic. Total HIV DNA (including intact and defective genomes) declines more slowly in women than in men, while the inducible HIV RNA+ reservoir, which is highly enriched in replication-competent virus, increases in women after menopause.

Introduction The sudden arrival of the COVID-19 pandemic placed significant stresses on supply chains including viral transport medium (VTM). The VTM that was urgently required needed to support viral replication, as well as other routine diagnostic approaches. We describe the preparation and validation testing of VTM for rapidly expanding diagnostic testing, where the capacity of the VTM to preserve viral integrity, for culture, isolation and full sequence analysis, was maintained. Methods VTM was prepared using different methods of sterilization then ‘spiked’ with virus. The VTM was investigated using viral culture in Vero cells, and for nucleic acid detection by quantitative PCR. Results The best results were obtained by filter and autoclave-based sterilization. The VTM proved robust for culture-based analyses provided the inoculated VTM was stored at 4 °C, and tested within 48 h. The filtered VTM also supported PCR-based diagnosis for at least 5 days when the mock inoculated VTM was held at room temperature. Discussion The manual handling of VTM production, including filling and sterilization, was optimized. SARS-CoV-2 was spiked into VTM to assess different sterilization methods and measure the effects of storage time and temperature upon VTM performance. While most diagnostic protocols will not require replication competent virus, the use of high quality VTM will allow for the next phase of laboratory analysis in the COVID-19 pandemic, including drug and antibody susceptibility analysis of re-isolated SARS-CoV-2, and for the testing of vaccine escape mutants.

This is the accepted manuscript version of the work published in its final form as Ismail, S. D., Riou, C., Joseph, S. B., Archin, N. M., Margolis, D. M., Perelson, A. S., Cassidy, T., Abrahams, M., Moeser, M., Council, O. D., McKinnon, L. R., Osman, F., Karim, Q. A., Karim, S. S. A., Swanstrom, R., Williamson, C., Garrett, N. J., & Wendy A Burgers. (2021). Immunological Correlates of the HIV-1 Replication-Competent Reservoir Size.Clinical Infectious Diseases,73(8), 1528-1531. https://doi.org/10.1093/cid/ciab587 Deposited byshareyourpaper.organdopenaccessbutton.org. We've taken reasonable steps to ensure this content doesn't violate copyright. However, if you think it does you can request a takedown by emailinghelp@openaccessbutton.org.

Env-pseudotyped viruses are valuable reagents for studies of HIV-1 neutralizing antibodies. It is often assumed that all pseudovirus particles are capable of only a single round of infection, making them a safe alternative to work with live HIV-1. In this study, we show that some Env-pseudotyped virus preparations give rise to low levels of replication-competent virus. These levels did not compromise results in the TZM-bl neutralization assay; however, their presence highlights a need to adhere to the same level of biosafety when working with Env-pseudotyped viruses that are required for work with replication competent HIV-1.

Lentiviral vectors are being used in a growing number of clinical applications, including T cell immunotherapy for cancer. As this new technology moves forward, a safety concern is the inadvertent recombination and subsequent development of a replication-competent lentivirus (RCL) during the manufacture of the vector material. To assess this risk, regulators have required screening of T cell products infused into patients for RCL. Since vector particles have many of the proteins and nucleotide sequences found in RCL, a biologic assay has proven the most sensitive method for RCL detection. As regulators have required screening of up to 108 cells per T cell product, this method described a procedure for assessing RCL contamination of large-volume T cell products.

Simian immunodeficiency virus SIVsab infection is completely controlled in rhesus macaques (RMs) through functional immune responses. We report that in SIVsab-infected RMs, (i) viral replication is controlled to + cell depletion is replication competent and genetically similar to the original virus stock, suggesting early reservoir seeding. This model permits assessment of strategies aimed at depleting the reservoir without multidrug antiretroviral therapy.

SIV DNA can be detected in lymphoid tissue–resident macrophages of chronically SIV-infected Asian macaques. These macrophages also contain evidence of recently phagocytosed SIV-infected CD4+ T cells. Here, we examine whether these macrophages contain replication-competent virus, whether viral DNA can be detected in tissue-resident macrophages from antiretroviral (ARV) therapy–treated animals and humans, and how the viral sequences amplified from macrophages and contemporaneous CD4+ T cells compare. In ARV-naive animals, we find that lymphoid tissue–resident macrophages contain replication-competent virus if they also contain viral DNA in ARV-naive Asian macaques. The genetic sequence of the virus within these macrophages is similar to those within CD4+ T cells from the same anatomic sites. In ARV-treated animals, we find that viral DNA can be amplified from lymphoid tissue–resident macrophages of SIV-infected Asian macaques that were treated with ARVs for at least 5 months, but we could not detect replication-competent virus from macrophages of animals treated with ARVs. Finally, we could not detect viral DNA in alveolar macrophages from HIV-infected individuals who received ARVs for 3 years and had undetectable viral loads. These data demonstrate that macrophages can contain replication-competent virus, but may not represent a significant reservoir for HIV in vivo.

Reverse-genetics systems are powerful tools enabling researchers to study the replication cycle of RNA viruses, including filoviruses and other hemorrhagic fever viruses, as well as to discover new antivirals. They include full-length clone systems as well as a number of life cycle modeling systems. Full-length clone systems allow for the generation of infectious, recombinant viruses, and thus are an important tool for studying the virus replication cycle in its entirety. In contrast, life cycle modeling systems such as minigenome and transcription and replication competent virus-like particle systems can be used to simulate and dissect parts of the virus life cycle outside of containment facilities. Minigenome systems are used to model viral genome replication and transcription, whereas transcription and replication competent virus-like particle systems also model morphogenesis and budding as well as infection of target cells. As such, these modeling systems have tremendous potential to further the discovery and screening of new antivirals targeting hemorrhagic fever viruses. This review provides an overview of currently established reverse genetics systems for hemorrhagic fever-causing negative-sense RNA viruses, with a particular emphasis on filoviruses, and the potential application of these systems for antiviral research.

Lentiviral vectors are a common tool used to introduce new and corrected genes into cell therapy products for treatment of human diseases. Although lentiviral vectors are ideal for delivery and stable integration of genes of interest into the host cell genome, they potentially pose risks to human health, such as integration-mediated transformation and generation of a replication competent lentivirus (RCL) capable of infecting non-target cells. In consideration of the latter risk, all cell-based products modified by lentiviral vectors and intended for patient use must be tested for RCL prior to treatment of the patient. Current Food and Drug Administration (FDA) guidelines recommend use of cell-based assays to this end, which can take up to 6 weeks for results. However, qPCR-based assays are a quick alternative for rapid assessment of RCL in products intended for fresh infusion. We describe here the development and qualification of a qPCR assay based on detection of envelope gene sequences (vesicular stomatitis virus G glycoprotein [VSV-G]) for RCL in accordance with Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines. Our results demonstrate the sensitivity, linearity, specificity, and reproducibility of detection of VSV-G sequences, with a low false-positive rate. These procedures are currently being used in our phase 1 clinical investigations.

Combination antiretroviral therapy (cART) can reduce HIV-1 viremia to clinically undetectable levels. However, replication competent virus persists in a long-lived latent reservoir in resting, memory CD4(+) T cells. The latent reservoir in resting CD4(+) T cells is the major barrier to curing HIV-1 infection. The recent case of the Berlin patient has suggested that it may be possible to cure HIV-1 infection in certain situations. As efforts to cure HIV-1 infection progress, it will become critical to measure the latent reservoir in patients participating in clinical trials of eradication strategies. Our laboratory has developed a limiting dilution virus outgrowth assay that can be used to demonstrate the presence and persistence of latent HIV-1 in patients. Here we describe both the original and a simplified version of the quantitative virus outgrowth assay (QVOA) to measure the frequency of latently infected resting CD4(+) T cells with replication competent provirus in patients on suppressive cART.

We consider a procedure for cancer therapy which consists of injecting replication-competent viruses into the tumor. The viruses infect tumor cells, replicate inside them, and eventually cause their death. As infected cells die, the viruses inside them are released and then proceed to infect adjacent tumor cells. This process is modelled as a free boundary problem for a nonlinear system of hyperbolic-parabolic differential equations, where the free boundary is the surface of the tumor. The unknowns are the densities of uninfected cells, infected cells, necrotic cells and free virus particles, and the velocity of cells within the tumor as well as the free boundary r = R( t). The purpose of this paper is to establish a rigorous mathematical analysis of the model, and to explore the reduction of the tumor size that can be achieved by this therapy.

Although CD4+ T cells represent the major reservoir of persistent HIV and SIV infection, accumulating evidence suggests that macrophages also contribute. However, investigations of the role of macrophages are often underrepresented at HIV pathogenesis and cure meetings. This was the impetus for a scientific workshop dedicated to this area of study, held in Cambridge, MA in January 2017. The workshop brought together experts in the fields of HIV/SIV immunology and virology, macrophage biology and immunology, and animal models of HIV/SIV infection to discuss the role of macrophages as a physiologically relevant viral reservoir, and the implications of macrophage infection for HIV pathogenesis and strategies for cure. While still controversial, there is an emerging theory that infected macrophages likely persist in the setting of combination antiretroviral therapy. These macrophages could then drive persistent inflammation and contribute to the viral reservoir, which indicates the importance of addressing macrophages as well as CD4+ T cells with future therapeutic strategies.

Hepatitis B virus (HBV) infection affects a large part of the world population. Within the different virological HBV categories that have been identified, patients with occult HBV infection represent a peculiar group. These individuals harbor a replication competent virus, inhibited in its replicative function. Accordingly, cases of reactivations have been observed in immunosuppressed individuals who lose immunological control over the infection. Patients with hematological malignancies (HM) are treated with intense myelo- and immunosuppressive chemotherapy regimens which favor HBV reactivation. This event can have severe consequences, such as hepatitis flare, hepatic failure and even death. In addition, it can lead to delays or interruptions of curative treatments, resulting in a decreased disease free and overall survival. In this review, we will examine the event of HBV reactivation in patients with signs of resolved HBV infection undergoing treatment for HM and propose possible management strategies.

Gene therapy vectors based on murine retroviruses have now been in clinical trials for over 20 years. During that time, a variety of novel vector pseudotypes were developed in an effort to improve gene transfer. Lentiviral vectors are now in clinical trials and a similar evolution of vector technology is anticipated. These modifications present challenges for those producing large-scale clinical materials. This chapter discusses approaches to process development for novel lentiviral vectors, highlight considerations, and methods to be incorporated into the development schema.

Amplification of retroviral vector sequences occurs in cocultures of ecotropic and amphotropic packaging cell lines. Mixed packaging line cocultures were used to determine both the host range and time of appearance of replication-competent virus after introduction of a retroviral vector. Replication-competent virus was generated at a characteristic time for a given ecotropic and amphotropic packaging line combination. The time required to generate replication-competent virus in a packaging line varied with the number of recombination events necessary to generate replication-competent virus from the retroviral sequences present in the line. The ψ2 packaging line generated replication-competent virus within 10 days after transfection of the N2 vector into a mixture of ψ2 (ecotropic) and PA317 (amphotropic) packaging cells. Under the same conditions, it took only 3 days to develop replication-competent virus in ψ2/PA12 cocultures. The host range of replication-competent virus was used to identify the packaging line that initially generates virus. Each packaging line combination generated replication-competent virus at a characteristic time and this time period can be used as a measure of the “safety” of the packaging line and vector combination.

Highly active antiretroviral therapy can decrease plasma HIV-1 levels to below the limit of detection. However, HIV-1 persists in latently infected resting-memory CD4+ T-cells carrying an integrated copy of the viral genome. The pool of latently infected cells is extremely stable and represents a major barrier to HIV-1 eradication. Identification and characterization of this reservoir required the development of methods for purifying resting CD4+ T-cells from HIV-1-infected individuals, activating the cells to induce virus production, and detecting and quantitating cells capable of releasing infectious virus. The development of an enhanced viral culture assay to quantitate the number of latently infected cells carrying replication competent virus is described here.

Replication-competent viruses have the potential to overcome the delivery barrier in tumors that has plagued traditional gene-therapy approaches to cancer treatment. However, recent clinical data suggests that a cytokine-based immune response against the virus-infected tumor cells may severely limit the efficacy of the replication-competent approach. This paper generalizes our earlier spatial model to incorporate an immune response against the infected tumor cells. An approximate but accurate condition is derived for the virus—if uniformly injected throughout the tumor—to eradicate the tumor in the presence of the immune response. To validate the model using clinical data describing the temporal interaction of tumor necrosis factor and free virus in the plasma, we needed the immune response to be time-delayed and experience either saturated stimulation or second-order clearance. The resulting estimates of some unknown parameters provide some implications for the delivery of treatment.

The lymphoproliferative disease virus of turkeys was molecularly cloned, structurally mapped, and shown to represent a distinct class of retroviruses evolutionarily related to the avian leukemia-sarcoma virus group. The cloned provirus did not contain any known oncogene or other cellularly derived sequences and was established as a replication-competent oncogenic entity capable of inducing the disease in the absence of any associated transforming counterpart.