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Well there alot of challenges faced by biologist researchers during the research of infectious disease, however major of those include the followings:
1- Defining and measuring the fitness for pathogens across the scales
2- Developing models to capture the impact of co-infection on the evolutionary process
3- Modeling how pathogen characteristics shape the evolution of hose immune diversity
4- Understanding the maintenance of pathogen diversity
5- Developing the better models for the impact of genetic systems on pathogen evolution .

Answer:

The main challenge faced by a microbiologist researching infectious disease is to prevent the spreading of infectious disease to itself and others.  

So to prevent the spreading of infectious disease microbiologist takes a lot of precautions like they work in an area which has negative pressure that do not allow the infectious particles to move out from that area.

They wear protective clothing that protects them from any spillage during the research work but even then it is a great challenge to scientists to prevent the spreading of these infectious diseases.

Some scientists and doctors working on ebola virus are killed by the disease ebola because they came in contact with this virus during their work.

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