Gene therapy vector contamination assay
Certain viral gene therapy vectors are by design unable to replicate in a patient. Nonetheless, during manufacture of viral gene therapy vector, undesirable replication-competent virus (“RCV”) may form due to random mutation or other events. Viral gene therapy vector manufacturers thus assay for the presence of contaminating RCV. Regulatory agencies require this to be done by assaying for serial infection, i.e., transducing target cells with the viral vector, and then lysing the transduced cells, and then mixing the lysate with live assay cells, and then microscopically observing the assay cells to visually determine whether they have been infected with virus. We have tested various alternative approaches, and surprisingly found that digital PCR is not only faster than the prior art approach, but is also over an order of magnitude more sensitive, able to detect, for example, in 3×10 10 assay cells, as few as seven (7) replication competent adenoviruses (“RCA”).
1. A method for identifying presence of replication-competent virus in a sample of replication-deficient virus, the method comprising:
a. incubating live target cells with the sample to produce transduced cells;
b. lysing the transduced cells to produce a transduced cell lysate;
c. infecting assay cells with the transduced cell lysate;
d. lysing the assay cells to produce an assay cell lysate;
e. removing cellular debris from the assay cell lysate to produce an assay supernatant; and
f. adding a mixture comprising a probe directly to the assay supernatant, wherein the probe binds to a region of the viral genome of the replication-competent virus essential for viral replication and is detected using a method that comprises digital PCR, wherein,
if replication-competent virus is present in the sample, detecting binding of the probe to the region of the viral genome indicates presence of replication-competent virus in the sample; and
if replication-competent virus is not present in the sample, not detecting binding of the probe to the region of the viral genome indicates absence of replication-competent virus in the sample.
2. The method of claim 1 , wherein the replication-deficient virus is adenovirus and wherein the mixture comprises SEQ ID NO. 1, SEQ ID NO. 2 and SEQ ID NO. 3.
3. The method of claim 1 , wherein the method detects 25 or fewer of a replication-competent viral particle per 3×10 10 of a replication-deficient viral particle.
4. The method of claim 1 , wherein the replication-competent virus and replication-deficient virus comprise a transgene that encodes a polypeptide selected from the group consisting of: interferon and p53.
5. The method of claim 3 , wherein the method detects 7 or fewer of the replication-competent viral particle per 3×10 10 of the replication-deficient viral particle.
6. The method of claim 1 , wherein the replication-deficient virus comprises a mutation or deletion within the region of the viral genome of the replication-competent virus essential for viral replication.
7. The method of claim 6 , wherein the replication-competent virus comprises a reversion of the mutation or deletion to the wild-type viral genome.
8. The method of claim 1 , further comprising determining the approximate quantity of the replication-competent viral particle in the sample.
9. The method of claim 1 , wherein binding of the probe to the region of the viral genome is detected using a method that comprises droplet digital PCR (ddPCR).
10. The method of claim 1 , further comprising pretreating the assay supernatant with a proteinase K to release a viral DNA encapsulated inside the replication-competent viral particle.