TWiV 125 – TWiV infects FiB

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Hosts: Vincent Racaniello, Dickson DespommierAlan DoveRich Condit, and Marc Pelletier

This Week in Virology and Futures in Biotech join together in a science mashup to talk about a virophage at the origin of DNA transposons, and unintended spread of a recombinant retrovirus.

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Click the arrow above to play, or right-click to download TWiV #125 (59 MB .mp3, 81 minutes).

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Links for this episode:

Weekly Science Picks

Marc – JotNot
Dickson – New bunyavirus in China (NEJM)
Rich – Listening to the Deep Ocean Environment (LIDO) recording of the Hatsushima earthquake (ScienceDaily article) – thanks Bridget!
Alan –Walter and Ina: A Story of Love, War, and Science
Vincent – Icosahedral light fixture (thanks, Eric!)

Send your virology questions and comments (email or mp3 file) to, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at and tag them with twiv.

4 thoughts on “TWiV 125 – TWiV infects FiB”

  1. I’m no lab scientist (my background is clinical research) but the reverse of lab contamination being so ubiquitous via cell lines, reagents, etc. (and accounting for the “positive” XMRV studies) is why there were so many “negative” XMRV studies that were entirely negative, e.g. nothing found in the healthy controls OR the cases. If contamination is so common, those studies could have found some, if low, level of positivity in both cases and controls.

    Of course, this might get down to the level exactly of what cell lines, reagents, PCR amplifiers, prior experiments done in those labs, etc. are used but these questions need to be explored.

  2. “Not 100% at detecting contaminants” – this would also apply to replicating exogenous human retroviruses.

    “We suspect” is not an absolute for these agents being an actual problem now is it. Neither is the idea that “they might help”. If you say they night help, then you must also entertain the possibility that they might not help – yes “who knows”

    The comment on safety checks for vaccines is also not safe. It is only an assumption that we have all the correct testing in place, and that records are being properly kept. If this were the case Government researchers would have stopped looking at the dangers vaccines potentially pose. Furthermore, it is well know that places like the CDC ignore certain epidemic as being a disease, don’t recommend the tests that show abnormalities and get doctors to ignore the abnormal results when they are undertaken. Where is the evidence that they are “non-clinically relevant”? Thats a leap and each agent would have to be looked at separately. The possible ease of undetected contamination, and the rumour mill, could potentially make most studies become unsafe. That is, if you always assume without proof that there is contamination.

    It looks like it is the researchers that are fearful about this.

  3. Gerwyn, can you explain why you’ve put this excerpt from a Celia Farber article in your sig line on the ME/CFS forum?

    “John Coffin asserts, “I think a causal role for HIV is not really on the table anymore in a serious way.”

    You do know that he meant that HIV’s causative role was satisfactorily proven by that point and therefore no longer on the table for discussion, right? I’d hate to think you were trying to deliberately misrepresent what he meant as a means to try and discredit what he is saying about XMRV.

  4. With regards to safety checks for vaccines, this document does not inspire much confidence, at least as far as retroviral contamination is concerned:


    3.2.1 Tests for Retroviruses
    For the MCB and for cells cultured up to or beyond the limit of in vitro cell age used for production, tests for retroviruses, including infectivity assays in sensitive cell cultures and
    electron microscopy (EM) studies, should be carried out. If infectivity is not detected and no retrovirus or retrovirus-like particles have been observed by EM, reverse transcriptase (RT) or other appropriate assays should be performed to detect retroviruses which may be noninfectious. Induction studies have not been found to be useful.


    Case B: Where only a rodent retrovirus (or a retrovirus-like particle which is believed to be non-pathogenic, such as rodent A- and R-type particles) is present, process evaluation using a`specific “model” virus, such as a murine leukemia virus, should be performed. Purified bulk`should be tested using suitable methods having high specificity and sensitivity for the`detection of the virus in question. For marketing authorisation, data from at least 3 lots of`purified bulk at pilot-plant scale or commercial scale should be provided. Cell lines such as`CHO, C127, BHK and murine hybridoma cell lines have frequently been used as substrates`for drug production with no reported safety problems related to viral contamination of the`products. For these cell lines in which the endogenous particles have been extensively`characterised and clearance has been demonstrated (note limitations below), it is not usually necessary to assay for the`presence of the non-infectious particles in purified bulk. Studies with non-specific “model”`viruses, as in Case A, are appropriate.
    … Cell lines derived from rodents usually contain endogenous retrovirus particles or retrovirus-like particles, which may be infectious (C-type particles) or non-infectious (cytoplasmic A- and R-type particles). The capacity of the manufacturing process to remove and/or inactivate rodent retroviruses from products obtained from such cells should be determined. This may be accomplished by using a murine leukemia virus, a specific “model” virus in the case of cells of murine origin.

    6.4 Limitations of Viral Clearance Studies
    Viral clearance studies are useful for contributing to the assurance that an acceptable level of safety in the final product is achieved but do not by themselves establish safety.Number of factors in the design and execution of viral clearance studies MAY LEAD TO AN INCORRECT ESTIMATE OF THE PROCESS TO REMOVE VIRUS INFECTIVITY. These factors include the following:

    1. Virus preparations used in clearance studies for a production process are likely to be
    produced in tissue culture. The behaviour of a tissue culture virus in a production step
    may be different from that of the native virus; for example, if native and cultured
    viruses differ in purity or degree of aggregation.
    2. Inactivation of virus infectivity frequently follows a biphasic curve in which a rapid
    initial phase is followed by a slower phase. It is possible that VIRUS ESCAPING A FIRST INACTIVATION STEP MAY BE MORE RESISTANT TO SUBSEQUENT STEPS. For example, if the
    resistant fraction takes the form of virus aggregates, infectivity may be resistant to a
    range of different chemical treatments and to heating.
    3. The ability of the overall process to remove infectivity is expressed as the sum of the logarithm of the reductions at each step. The summation of the reduction factors of multiple steps, particularly of steps with little reduction (e.g., below 1 log10), MAY OVERESTIMATE THE TRUE POTENTIAL FOR VIRUS ELIMINATION. Furthermore, reduction values achieved by repetition of identical or near identical procedures should not be included unless justified.
    4. The expression of reduction factors as logarithmic reductions in titer implies that, while residual virus infectivity may be greatly reduced, IT WILL BE NEVER REDUCED TO ZERO.
    For example, a reduction in the infectivity of a preparation containing 8 log10 infectious units per ml by a factor of 8 log10 leaves zero log10 per ml or one infectious unit per ml, taking into consideration the limit of detection of the assay.
    5. Pilot-plant scale processing may differ from commercial-scale processing despite care taken to design the scaled-down process.
    6. Addition of individual virus reduction factors resulting from similar inactivation mechanisms along the manufacturing process may MAY OVERESTIMATE OVERALL VIRAL CLEARANCE.

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