This is a very general question. There are various tick-borne pathogens. I suggest you screen through literatures and find the primers that have successfully been used by different authors. This will definitely takes a lot of time, but the result would be great.
Thanks a lot for your information Dr. Saied Reza Naddaf
I know it will take time, i will search on protozoa and Virus, especially Schmallenberg virus, because recently this virus appear in the area, after ISSI war, a large number of animal are enter the country.
Shameeran, I agree with Said Reza, the search in the data set will be the best way to find what are you neddd. For more clear you should decide what are microorganisms will you study and I can provide help in such way, where I am working now on the same your topic
Fine, the work with babesia and theileria are very interesting. Therefore, when you finish searching process, I would love review and summarize your search results if you like especially in epidemiological, molecular and nucleotide sequencing analyses.
I do microscopy of patients blood for tickborne infections.. Primarily focus on detection of spirochetes http://lymerick.net/MK-videomicroscopy.html Alan MacDonald has now 4 molecular DNA beacons for different types of Borrelia, including B miyamotoi and the brand new Borrelia mayonii!
I now share new scientific info on http://facebook.com/daninfekt
There is a new FB group "MY MICROSCOPI" where people doing microscopy or want to learn, share our experiences, give advice and learn new thing.. Some have worked with microscopy for tickborne microbes for many years, most are newcomers.. It is open for all interested people!
Our group of research has published some articles on tick morphology and tick-borne pathogens in the last 10 years. Just visit Bechara GH at medline website.
A brief survey at GenBank (http://www.ncbi.nlm.nih.gov/nuccore) with the terms "Schmallenberg Virus" retrieves over a hundred partial sequences, including segments L and M. It is possible to perform a multiple alignment of selected overlapping sequences with simple programs such as ClustalOmega
(http://www.ebi.ac.uk/Tools/msa/clustalo)
or T-Coffee
(http://www.ebi.ac.uk/Tools/msa/tcoffee).
Simply copy and paste your sequences in the respective program's submission box in the FASTA format (https://en.wikipedia.org/wiki/FASTA_format)
and wait to see the results.
With the results in hand it is possible to find conserved DNA sequences suitable to custom PCR primer design and in vitro synthesis of a small DNA segment with your isolates (and probably any other isolate depending on the conservation percentage).