There are no pan-viral pcr primers. A large amount of genetic diversity exists within and between virus families. Many family specific primers (such as pan-picornaviridae, pan-coronaviridae, etc.) have been developed and published but even these primers can be limited for detecting novel viruses. There are viral microarray systems that can be used to screen samples for a wide range of known viruses. 

There are no pan-viral pcr primers. A large amount of genetic diversity exists within and between virus families. Many family specific primers (such as pan-picornaviridae, pan-coronaviridae, etc.) have been developed and published but even these primers can be limited for detecting novel viruses. There are viral microarray systems that can be used to screen samples for a wide range of known viruses. 

thanks a lot shamus for your response. 

Unfortunately there is no such thing as a universal viral gene you can target. I would suggest looking into literature about metagenomics or "viral discovery". Next generation sequencing allow very deep sequencing of a sample, followed by bioinformatic identification of viral sequences.

There are no universal viral genes as in eukaryotes and prokaryotes. However, there are "universal" primers for some viral families, such as polymerase-directed primers for nucleocytoplasmic large dna viruses.

I agree with the other folks that deep-sequencing/metagenomic approaches are very powerful techniques for identifying unknown viruses but I'm not sure it should be used very early in clinical diagnostics. I think you are better off focusing on eliminating potential agents through concurrent specific diagnostic tests. Since you would have to send the samples to someone else, the metagenomic analysis may take a little while and you could have completed many specific RT-PCR assays in the mean time.

All that being said, I think it might be a good idea to send your samples to someone else that can perform more thorough diagnostics. Especially considering other cases are being identified. 

Have you considered that possibility of MERS-CoV? There are multiple pan-coronavirus RT-PCR assays published in the literature that could be used. Also, I'm sure international health agencies could provide guidance and assistance for MERS diagnostics.  

Crimean-Congo haemorrhagic fever (CCHF) does occur in Iran.  It is spread by tick bite, with human-tom-human transmission only occurring with direct contact with infected fluids. 

Searching ProMED, there have been reports of SARS cononavirus, fatal influenza (but you have ruled that out, it seems) and not much else that I can see:

http://www.promedmail.org/mena

see: http://www.who.int/mediacentre/factsheets/fs208/en/

The Crimean-Congo haemorrhagic fever (CCHF) virus causes severe viral haemorrhagic fever outbreaks.

CCHF outbreaks have a case fatality rate of up to 40%.

The virus is primarily transmitted to people from ticks and livestock animals. Human-to-human transmission can occur resulting from close contact with the blood, secretions, organs or other bodily fluids of infected persons.

CCHF is endemic in Africa, the Balkans, the Middle East and Asia, in countries south of the 50th parallel north.

There is no vaccine available for either people or animals.

These authors describe a qPCR test: http://www.ncbi.nlm.nih.gov/pubmed/22651389

An end-point PCR is described in this paper: http://journal.isv.org.ir/files/site1/user_files_bc468b/admin-A-10-1-74-63c0d26.pdf

Hope it helps.

You might also contact CDC Special Pathogens Branch [email protected]

and perhaps Ian Lipkin [email protected]

Thanks Brian and Leandro for your replies.

No it is not possible because there are no such common region/protein sequences among the viruses. 

Is there any update on this?  More patients infected?  Pathogen identified yet?

The same is true in plant virology: there are a number of genus and family specific primers but nothing works for everything. One technique that is widely used in plant virology is dsRNA analysis (for RNA viruses only). It is fairly reliable as a generic technique for detecting RNA viruses and gives you some clues as to the size and number of RNAs in the virus' genome. This in turn allows you to narrow down the virus' family