Submitted by tanteidaiko t3_zdpa6g in askscience
feliciates t1_iz3cs0y wrote
Serotyping is a subtyping test based on differences in microbial (e.g., viral or bacterial) surfaces. Like salmonella is serotyped based on which type of O-Antigen and H-Antigen they have
Phenotype refers to the expressed features of an organism (that is, the way the genes are expressed). A genotype is the entire collection of an organism's genetic information. The genotype includes all the genetic information, regardless of whether it's being used and expressed or not.
Alwayssunnyinarizona t1_iz3dmgy wrote
Great answer. The serotypes, in a way, are a phenotype - one that is "seen" by the host's antibody response. Like a negative image, perhaps. The genotype codes for that "phenotype" in a way that we haven't quite figured out yet (ie, there aren't commonly PCR tests, or MALDI data for serotypes, but there are groups working on them almost tirelessly).
dave-the-scientist t1_iz50sxy wrote
We actually can do serotyping by sequence for a bunch of bacterial pathogens. Neisseria meningitidis, for one. Pasteurella multocida for another. Those are two I've done in the past couple months.
Bitchwar t1_iz3wh34 wrote
But a phenotype can be slightly different than the genotype, right? I mean depending on epigenetic factors and environmental factors.. Or am mistaken here?
MotsPassant t1_iz44ff9 wrote
You can't compare phenotype and genotype in this manner. Just like you can't play an instrument you don't have, you can't express genes that aren't in your genotype. Epigenetics will basically modify what genes are expressed. It will get you from phenotype A to phenotype B if you will, but saying it is "different from your genotype" doesn't make sense. All your possible phenotypes are contained in your genotype.
tanteidaiko OP t1_iz3zh1u wrote
I think this the interesting and crucial point. Are serotypes mainly influenced by genotypes or are there epigenetic factors at play also.
I have done many Dengue E1 Sequencing and I frequently BLAST the sequences. We do see that these sequences can be catergorised into the serotypes themselves. So does mean that the sequences, and therefore genotype, confers the serotypes?
Bitchwar t1_iz42itz wrote
Not familiar with the lingo. Blast, is that a method in itself?
Maybe I can ask a couple of questions if you have the time: Are you sequencing serotype, transcriptomics and DNA of white blood cells that are infected? And can you predict serotype from DNA? Or only from transcriptomics?
tanteidaiko OP t1_iz42y1y wrote
BLAST is an online sequence alignment tool by NCBI.
I am sequencing the genome of the Dengue virus itself that we extract from an infected person. And we are able to determine the serotype affecting a person via real time PCR itself. So we draw the patient's blood, spin it down into serums, then we do nucleic acid extraction to obtain the RNA. Then we do real time RT-PCR to detect the presence of any sereotype of the virus.
feliciates t1_iz4hxej wrote
That's a very good question. Back when I was in the lab, serotypes couldn't be distinguished by sequencing but we seem to have moved towards being able to do that and the serotypes of strep have evidence for having a genetic basis:
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