This is my first post on the forum. I just want to say first that I'm extremely impressed with the work done by Dr. Niman and others here showing evidence for homologous recombination in Influenza. It is ridiculous that this work has apparently not been acknowledged by the Influenza field. The alignments speak for themselves.
I have one question that perhaps Dr. Niman or someone else on the board could clarify. When thinking of possible alternative explanations to the results presented here, the only thing I could come up with is that some contamination may be occurring in Influenza labs, i.e. the cultures from which the viruses to be sequenced are extracted might be infected by more than one strain. Then one could imagine that during the reverse transcription step prior to PCR, the reverse transcriptase jumps between the two different strains, creating a complementary DNA sequence that looks like a homologous recombinant. It's sort of analogous to the presumed mechanism for recombination itself, except the enzyme doing the jumping is the RT that is used to make the cDNA, rather than RNA polymerase.
I'm not sure if the procedures used in virology labs are foolproof against this type of contamination. From my limited experience I'd say virologists can be pretty sloppy...
I would be interested in anyone's thoughts on this.
Mark Hansen
I have one question that perhaps Dr. Niman or someone else on the board could clarify. When thinking of possible alternative explanations to the results presented here, the only thing I could come up with is that some contamination may be occurring in Influenza labs, i.e. the cultures from which the viruses to be sequenced are extracted might be infected by more than one strain. Then one could imagine that during the reverse transcription step prior to PCR, the reverse transcriptase jumps between the two different strains, creating a complementary DNA sequence that looks like a homologous recombinant. It's sort of analogous to the presumed mechanism for recombination itself, except the enzyme doing the jumping is the RT that is used to make the cDNA, rather than RNA polymerase.
I'm not sure if the procedures used in virology labs are foolproof against this type of contamination. From my limited experience I'd say virologists can be pretty sloppy...
I would be interested in anyone's thoughts on this.
Mark Hansen
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