Updated phylogeography


Thanks Oliver. So the lab got 3 more Zika isolates from Thailand from 2011, 2013 and 2016 and in light of the rejection, now they may be asking me to hold off and instead of resubmitting elsewhere they’ll want me to reanalyze everything with the new isolates included and then submit. I have to discuss with them still. When we look to submit - I’ll definitely discuss virus evolution with them and get in touch with you.


But you are collecting and pooling the mosquitos from this very tight urban area because there are a cluster of human cases there. So the humans are still acting as sentinels.If you are trying to do surveillance in a broad geographical area, then I doubt mosquitos are going to be a good target. Still more straight forward to target sick humans I would think (unless there are political or ethical restrictions on these).


Yes, that’s very true - my statement of ‘not very rare’ is almost certainly only true in areas where you have active human transmission.

I think the key is probably to do both - human sampling and mossie sampling. Different selective pressures and population sizes, so would be key to get both if one is trying to look at transmission dynamics. For phylogeography and most other things, targeting patients is probably going to be easier.


I agree with Kristian’s above statement.

For reference, we quantified 10-10,000x more ZIKV copies in mosquitoes (total virus in the pool) than from 1ml of human urine (which we found to have the most ZIKV RNA). This is consistent with my previous work with DENV and WNV (though some birds can have very high titers as well). Mosquitoes are virus replicating machines.



Wow, that’s impressive!


Suggests that none of the mosquitos in the Zibra pools were actually infected. Perhaps this could be used to estimate prevalence in mosquito populations using pools (if you know how many mosquitos are in the pool).


Having done West Nile virus surveillance for a couple of years (and working with lab infected ZIKV + DENV mossies), actual positive mosquito pools are VERY obvious (ct 23-30). If you are uncertain, the mosquito is likely not infected.



Yeah, that’s a low Ct range. OK well more mosquito pools are getting analysed with new qRT-PCR probes this week so let’s see if any are positive. Hopefully test for YF, DENV and CHIKV too.


The GenBank entries for the French Polynesia genomes (KX447509 - KX447521) are curently listed in GenBank as unpublished. But I just found a paper describing them here:

Pettersson JH, Eldholm V, Seligman SJ, Lundkvist Å, Falconar AK, Gaunt MW,
Musso D, Nougairède A, Charrel R, Gould EA, de Lamballerie X.
How Did Zika Virus Emerge in the Pacific Islands and Latin America?
MBio. 2016 Oct 11;7(5). pii: e01239-16. doi: 10.1128/mBio.01239-16.
PubMed PMID: 27729507; PubMed Central PMCID: PMC5061869.

The analyses in this paper are pretty nice, and they agree with Oliver’s assessment of the data.