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I'm reading this paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC392475/ and I can't work out why a certain immune serum didn't work on the same viral protein but from different strains.

The serum was extracted from tumour-carrying animals infected with the 'SR' strain of Rous sarcoma virus and was later used to immunoprecipitate out the viral protein p60-src from virusinfected cells. The cells in question had been infected either with SR or other closely-related strains, all strains express the same protein. But the antiserum only extracted the SR strain's p60-src and not the same protein from other strains. I thought it could be because the serum had by chance targeted an epitope specific to the SR strain, so you get a lot of proliferation of B cells complimentary to this epitope, therefore overshadowing the detection of other epitopes. But 1. I think the serum was taken from multiple rabbits and surely they wouldn't all have happened to do this. and 2. a later paper I read said that p60-src is 98% the same across SR, Pr, Br strain etc so it seems unlikely to have latched onto an SR-specific bit. And yet, the authors state that due to similarities between SRC genes, "... similar gene products are probably present in cells transformed by other strains of ASV, but they are not detected because of a lack of crossreaction with the currently available antisera."

So my question is, what is causing this lack of crossreaction? Apologies if the answer is very obvious, I am new to the subject and have very little knowledge of experimental methods currently. Thank you in advance for any insights, or corrections on the conclusions I've drawn so far as they might be inaccurate too.

Note: thanks mods for letting me edit the question to improve privacy.

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    – AliceD ♦
    Commented Aug 29, 2021 at 11:46
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    – Chris ♦
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As you note, the viral strains are not identical; it's unclear from your question the actual amount and position of amino-acid differences among them, but it's not surprising that even a portion of the protein would have an immunodominant epitope and thus drive reproducible strain-specificity of any immune serum produced.

Remember that the rabbits or other animals used to produce antibodies are typically at least somewhat inbred strains raised for lab use and so are likely to have less genetic diversity among individuals than you might otherwise expect.

Another paper from this time period reports that different immune sera generated from related virus strains and produced in different animals ranged from immunoprecipitating the src viral protein in zero of the viral strains tested up to immunoprecipitating the protein in all viral strains tested: "Detection of the Viral Sarcoma Gene Product in Cells Infected with Various Strains of Avian Sarcoma Virus ..." Brugge et al (1979) Journal of Virology Vol 29 No 3 p 1196-1203

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  • $\begingroup$ They may be; they also might not be. I would think that in general you would expect to see less variability in the immune response (not necessarily in the range of targets) among lab animals. However naturally-generated immune sera are quite complex and need to be individually characterized once they are generated. Also remember that the paper you are reading is from 40+ years ago, before PCR, before easy DNA sequencing, before most bio-informatics, before most understanding of oncogenes, etc. $\endgroup$
    – Armand
    Commented Aug 21, 2021 at 20:47

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