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Establishment of a PPR Global Research and Expertise Network (PPR-GREN)

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michael baron <[log in to unmask]>
Wed, 5 Feb 2014 15:03:46 +0000
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Dear all,

just to put a molecular biologist's input in on this matter...

When the reference labs put together PCR primer sets for detecting PPRV, they based their data on viruses from all the lineages, and made sure they worked on all the lineages. This is a reasonable way of making sure your target sequences are well conserved. For reasons best known to themselves, some labs do not want to use these primers (the sequences of which are freely available), but design new primer sets. However, they cannot test these against a wide range of viruses, because very few labs are allowed to keep isolates from around the world. There is always the possibility, therefore, that the new primer sets are not against totally conserved targets.
The confusion in the virus described (looking at the paper) is that they first used a set of primers based on a limited number of Indian sequences (which failed, presumably because the primers were not targeted at totally conserved sequences), and then a pair of universal N gene primers (which worked, as they were presumably against a better conserved region). I should note that the paper does not say where these N gene primer sequences were taken from. However, the Nkp1 virus was clearly a standard Lineage IV isolate, having N gene sequence essentially identical to a recent Gujarat isolate (the accession number cited). We can therefore say that this is an Indian PPRV within the normal range of such viruses, but with sequence that is slightly divergent from Sungri/96, which is only to be expected given how very large India is.

I would urge people to start with the primer pairs that CIRAD and ourselves have tested against a lot of viruses. They usually work, and have worked for a lot of people in different countries. If both of those pairs fail, I would suspect the virus is not PPRV.

So in this case we have a PPR isolate that has diverged in sequence from Sungri/96 (it can take as little as one base change to stop a primer pair working!). However, this PPRV will still be stopped by Sungri vaccination, as the huge spread of immune responses elicited by live PPRV will protect against all PPRV, as shown by Nigeria/75 vaccine being effective in China, and my own recent study in which Sungri/96 blocked an old Ivory Coast isolate. The failure of a hyperimmune serum against Sungri (presumably a rabbit serum) to react well with this isolate does not mean that the full immune response to Sungri vaccine will not be effective in sheep/goats. If nothing else, we should all remember that live vaccine elicits both humoral and T cell mediated responses, either of which may be protective. If rinderpest vaccine protects against PPRV, we should just accept that all PPRV vaccines will work at least as well as rinderpest, and get on with the more important business of sorting out the disease in the field.

best regards,
Michael



Michael D Baron PhD
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