Validation of a next generation sequencing method for adventitious virus detection: Demonstration of sensitivity in multiple cell lines.

In the past few years NGS has become the technology of choice to replace animal-based virus safety methods and this has been strengthened by the recent revision to the ICHQ5A virus safety chapter. Here we describe the validation of an NGS method using an agnostic analysis to detect and identify RNA virus and actively replicating DNA virus contaminants in cell banks. We report the results of the validation of each step in the sequencing process that established quality criteria to ensure consistent sequencing data. Furthermore, the validation of the analysis algorithm designed to identify virus specific sequences is described along with steps undertaken to ensure the integrity of the sequencing data from generation to analysis. Lastly, the validated sequencing and analysis systems were used to establish a limit of detection (LOD) for model viruses in cells that are commonly used in biomanufacturing. The LOD from these studies ranged from 1E+03 to 1E+04 genome copies and were dependent on the virus type with little variability between the different cell types. Thus, the validation of the NGS method for adventitious agent testing and the establishment of a general LOD for cell-based samples provides a suitable alternative to traditional virus detection methods.

Historical evaluation of the in vivo adventitious virus test and its potential for replacement with next generation sequencing (NGS).

The Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) collected historical data from 20 biopharmaceutical industry members on their experience with the in vivo adventitious virus test, the in vitro virus test, and the use of next generation sequencing (NGS) for viral safety. Over the past 20 years, only three positive in vivo adventitious virus test results were reported, and all were also detected in another concurrent assay. In more than three cases, data collected as a part of this study also found that the in vivo adventitious virus test had given a negative result for a sample that was later found to contain virus. Additionally, the in vivo adventitious virus test had experienced at least 21 false positives and had to be repeated an additional 21 times all while using more than 84,000 animals. These data support the consideration and need for alternative broad spectrum viral detection tests that are faster, more sensitive, more accurate, more specific, and more humane. NGS is one technology that may meet this need. Eighty one percent of survey respondents are either already actively using or exploring the use of NGS for viral safety. The risks and challenges of replacing in vivo adventitious virus testing with NGS are discussed. It is proposed to update the overall virus safety program for new biopharmaceutical products by replacing in vivo adventitious virus testing approaches with modern methodologies, such as NGS, that maintain or even improve the final safety of the product.

TSG101 exposure on the surface of HIV-1 infected cells: implications for monoclonal antibody therapy for HIV/AIDS.

HIV infection remains a major global public health problem, in part because of the ability of the virus to elude antiretroviral therapies. Most conventional drugs were designed to directly target virus-encoded mechanisms. However, there is increasing appreciation that certain host-encoded molecules are comparably important for the viral life cycle and could therefore represent potential antiviral targets. Prominent among these is TSG101, a cytoplasmic molecule that is "hijacked" by HIV and used to facilitate viral budding and release. In our present report, we demonstrate thatTSG101 is uniquely exposed on the surface of HIV-infected cells and is available to antibody-based therapies. We also characterize the development of a monoclonal antibody, CB8-2, which reduces virus production from infected cells. These studies demonstrate the potential of TSG101-directed antibodies to combat HIV/AIDS.

VCAM-1 expression on CD8+ cells correlates with enhanced anti-HIV suppressing activity.

CD8(+) cells from HIV-infected individuals showing the CD8(+) cell noncytotoxic antiviral response unexpectedly revealed mRNA for VCAM-1, a cell surface molecule found on endothelial cells. Uninfected subjects had undetectable levels of VCAM-1 mRNA in their CD8(+) cells. Flow cytometry analysis showed that up to 12% of the CD8(+) cells from HIV-positive individuals expressed VCAM-1 compared with 0.8% of the CD8(+) cells of HIV-negative individuals. Enrichment of the CD8(+)VCAM-1(+) cell population and subsequent coculture with CD4(+) cells acutely infected with HIV-1 showed that the VCAM-1(+)CD8(+) cells were able to suppress viral replication with 50% less input cells than the unseparated CD8(+) cell population. This study demonstrates, for the first time, the expression of VCAM-1 on CD8(+) cells. Moreover, the CD8(+)VCAM-1(+) cells show enhanced CD8(+) cell noncytotoxic antiviral response activity that could have clinical importance in HIV infection.

alpha-Defensins can have anti-HIV activity but are not CD8 cell anti-HIV factors.

BACKGROUND: CD8 T cells from healthy HIV-infected individuals inhibit HIV replication in infected CD4 T cells by a non-cytotoxic mechanism mediated by a soluble CD8 cell antiviral factor, CAF. Recently, the antimicrobial peptides, alpha-defensins, were reported to constitute CAF. OBJECTIVE: To examine the antiviral activity of alpha-defensins and address their potential role in CD8 cell non-cytotoxic antiviral responses. DESIGN AND METHODS: A purified mixture of human neutrophil proteins (HNP) 1-3 (alpha-defensins) was used to examine the effect of alpha-defensins on HIV virions and on HIV replication in CD4 cells treated prior to or post infection. alpha-Defensin expression was analyzed at the RNA and protein level in CD8 cells as well as in various other cell types. Antibodies to the defensins were tested for their ability to inhibit CAF activity in CD8 cell culture fluids. RESULTS: The alpha-defensins exhibited anti-HIV activity on at least two levels: directly inactivating virus particles; and affecting the ability of target CD4 cells to replicate the virus. However, while we could demonstrate alpha-defensins in neutrophils and monocytes, we found no evidence for the production of these peptides by CD8 T cells. No messenger RNA encoding these proteins was detected in purified CD8 T cells, nor did these cells produce intracellular or extracellular alpha-defensin peptides. Moreover, antibodies specific for human alpha-defensins 1, 2, and 3 did not block the antiviral activity of CAF-active CD8 cell culture fluids. CONCLUSIONS: The alpha-defensins are not produced by CD8 cells but unexpectedly were found to be expressed in monocytes. alpha-Defensins can have anti-HIV activity but are not CD8 cell antiviral factors.

Differential gene expression in CD8+ cells exhibiting noncytotoxic anti-HIV activity.

Suppressive subtractive hybridization with polymerase chain reaction was used to identify the gene(s) associated with the CD8+ cell noncytotoxic anti-HIV response. The differences in gene expression profiles of CD8+ cells from a pair of discordant HIV-positive identical twins were studied. Forty-nine genes were identified as expressed at higher levels in the CD8+ cells from the infected twin that inhibited viral replication. The differential expression of these genes was then evaluated using Q-PCR to determine if this gene expression pattern is evident in CD8+ cells from other HIV-positive subjects showing this antiviral activity. Three genes, including one unknown, were found to have significantly increased expression in antiviral CD8+ cells.