Hello everyone,

I am about to do my PhD candidacy exam, and one of the evaluators raised an important point of the genotyping malaria project. Basically, in the malaria field it is very common to genotype different strains by using length markers or just polymorphic markers of the same size. The number of different variations of size or SNPs will determine the number of different clones found in a human host infected with malaria. MOI is define as 'multiplicity of infection' and it basically tells you this number of clones found in an individual. When looking at publications, it is very common to see a MOI of 1, 2, 3, 4, 5, and even 6. However, one of my PhD examiners asked this question:

"How is it possible to have 1 to 6 genotypes of malaria, when its genome is 23'000,000 bases, and it can populate the human host to 1x10^12 cells?"

Since then I am struggling with it and I have narrowed down some evidence to answer this question... In the pathogenesis of malaria, it is common to see a few bottlenecks of transmission. When a mosquito inoculates a human host with the plasmodium parasite, between 10 to 200 circumsporozoites will make it to the liver. After an incubation period of 7 to 10 days, each circumsporozoite will release 30,000 daughter cells into the bloodstream. Each cell will replicate into 8-32 times inside a red blood cell (RBC). So in theory, all of these cells should be clones of the parent cells. However that is not the case given that the average mutation rate of malaria is 4x10e-10 base substitutions per mitosis. How can I answer this question?

In practice is common to see the use of polymorphic genes with a expected heterozygosity close to 1.0, that would yield as many genotype retrievals as possible, and those genes typically vary in size of 300 to 500 base pairs. Some people use a panel of microsatellites to determine these genotypes.

Am I missing a key concept here?

Thanks everyone!