Compositions for use in identification of adventitious viruses

Abstract

The present invention provides compositions, kits and methods for rapid identification and quantification of adventitious contaminant viruses by molecular mass and base composition analysis.

Description

RELATED APPLICATIONS [0001] The present application 1) claims the benefit of priority to U.S. Provisional Application Ser. No. 60 / 658,248, filed Mar. 3, 2005; 2) claims the benefit of priority to U.S. Provisional Application Ser. No. 60 / 705,631, filed Aug. 3, 2005; 3) claims the benefit of priority to U.S. Provisional Application Ser. No. 60 / 732,539, filed Nov. 1, 2005 and 4) claims the benefit of priority to U.S. Provisional Application Ser. No. 60 / 740,617, filed Nov. 28, 2005. Each of the above listed U.S. Provisional Applications is incorporated herein by reference in entirety. Methods disclosed in U.S. application Ser. Nos. 10 / 156,608, 09 / 891,793, 10 / 418,514, 10 / 660,997, 10 / 660,122, 10,660,996, 10 / 660,998, 10 / 728,486, 10 / 405,756, 11 / 060,135, and 11 / 073,362, are commonly owned and incorporated herein by reference in their entirety for any purpose.STATEMENT OF GOVERNMENT SUPPORT [0002] This invention was made with United States Government support under NIH contract N01 AI40100. Th...

AI Technical Summary

Benefits of technology

[0041] In some embodiments, the present invention provides methods for detecting or quantifying adventitious contaminant virus by combining a nucleic acid amplification process with a mass determination process. In some embodiments, such methods identify or otherwise analyze the adventitious contaminant virus by comparing mass information from an amplification product with a calibration or control product. Such methods can be carried out in a highly multiplexed and / or parallel manner allowing for the analysis of as many as 300 samples per 24 hours on a single mass measurement platform. The accuracy of the mass determination methods in some embodiments of the present invention permits allows for the ability to discriminate between different adventitious viruses such as members of the following families: p\

Problems solved by technology

Adventitious viruses represent a major risk associated with the use of cell-substrate derived biologicals, including vaccines and antibodies, for human use.

This is a major obstacle to the use of neoplastic-immortalized cells for which the mechanism of transformation is unknown is that these could have a higher risk of containing oncogenic viruses.

However, the above techniques are not specific and do not provide any information regarding the source of the RT activity.

Further, while some studies demonstrate that a low level of RT activity is not generally associated with a replicating agent; major concerns remain regarding the consequences of the presence of such non-productive, non-replicating defective infections in the vaccine, as there is the potential for integration into the host genome.

First, there are large numbers of known viral agents that are potential contaminants, each with a large number of potential strain variants.

Second, history has shown that not all adventitious agents fall into anticipated families of viruses, so unanticipated virus families must also be considered.

DNA sequencing has significant disadvantages as an analysis method for routine use a clinical laboratory setting.

It is still relatively expensive and labor intensive, and thus is used only for very important analyses.

Drug resistance in HIV has now emerged as a significant problem in both untreated and drug-treated patient populations.

A drawback of sequencing is that DNA sequencing technology for identification of drug-resistant viruses is that it is not easily able to identify the components present in a mixed sample, particularly in a scenario where a fraction of the virus population has mutated.

However, the HIV populations that infect humans are not homogeneous, and RNA viruses such as HIV are known to rapidly mutate, creating a population of mixed sequences in each infected individual.

In the presence of drug selection, mutations that mediate drug resistance that occur at low frequency grow with a selective advantage and eventually can dominate the population, causing treatment failure.

DNA sequencing methods can identify mixed populations, but do so poorly.

However, 40% of a typical viral load (1,800 to 10,500 HIV copies / ml) means a blood burden (assuming 5 liters of blood) of up to 21 million drug-resistant viral copies.

Other analytical methods are capable of identifying mutations with more sensitivity than sequencing, but these methods are time consuming, laborious and not amenable to high throughput processes.

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