Hello,
I am just do co-infection between swine influenza virus and porcine reproductive and respiratory syndrome virus (PRRSV). I will test differents conditions and I need to detect genetic variability on whole genome of each virus by RNA-sequencing, to observe the effect of the first virus on the second virus so my questions .
1- Have you idea about the best MOI for coinfection and the time between dual-infection
2- For sequencing I need to take just supernatant of cells or I cells !!!!!!
Have you any experience in this topic please some suggestions
Thank you so much
Hi Zeineb,
I'm reaaly very happy to have youe news. But, for your questions, you know that it is not my specialty. So, I can not help you. if you have any questions about animal nutrition, or physiology or meta-analysis method, I can help you.
1) This sounds like a scenario where you should do a checkerboard titration. That is, if you have the capacity to do this in multiple plates or multi-well microplates, you should titrate each virus from low to high in a crossed layout.
eg. on a 12-well plate, titrate influenza from column 1 to column 4 on the x axis and PRRSV from row A to row C on the Y axis.
Then you could also test the order of infection before/simultaneous/after using the same checkboard titration layout. Attached is an illustration of a possible design.
2) Sorry I don't know about swine influenza or PRRSV. But it's very possible you may get different copy numbers in the supernatant (free virus) versus in the cells. You should also test this.
You have at least 3 input factor variables, with multiple levels of each possible: Influenza MOI, PRRSV MOI, Influenza time of infection, time of infection relative to other virus. You may need to look up some resources for Design of Experiments (DoE) for multiple variables. This is a concept much used in industry we unfortunately don't get taught in academia much but it's really helpful.
here's an example http://www.prismtc.co.uk/quality-beer-design/
and a simple tutorial http://asq.org/learn-about-quality/data-collection-analysis-tools/overview/design-of-experiments-tutorial.html
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