Yellow fever virus in Angola

Until last week, we (Nuno Faria and myself) thought there were no genetic sequences for the current outbreak of Yellow fever virus in Angola. However over lunch at the Sanger Institute, George Gao (China CDC) mentioned that a recent traveller who had returned from Angola to China had been diagnosed with YFV and that the sequence had been placed on GenBank. We think this is accession number KX010994. The GenBank entry says it was an imported case but does not mention Angola, so we can’t be 100% sure yet of its source. Thank you China CDC for publicly sharing data so quickly.

Here’s a provisional tree from Nuno that shows the Chinese import sequence (red). It groups strongly with the only other known Angola sequence (blue) from 1971, within the “East Africa” genotype. One interpretation of this is that YFV has been circulating undetected in Angola for 30-40 years!

Need to exclude contamination with the 1971 strain (likely to be a lab grown strain).

Doing a Blast shows 99% identity (10738/10823 nucleotides) with the 1971 strain. 85 nucleotide differences in 45 years as a rate (assuming no ancestral diversity) is 1.7x10^-4 subst/site/year so not implausible. But 1971 strain might be passaged.

Good point. A TempEst regression would be useful too. Might take a few days as Nuno is still on the bus…

Not sure TempEst is going to work that well on this - look at the relative positions of the 1920s and 1940s strains.

It turns out there are more China-import sequences on GenBank. Will post an updated tree (ML) soon.

Here’s a ML tree that now includes all 4 China import sequences. Three are similar to each other, whilst one is more similar to the Angola 1971 strain. It’d be interesting to guess the TMRCA of the triplet. As Andy suggested, the TempEst plot isn’t very informative. The plot below is only for the bottom clade of 8 sequences and isn’t well sampled enough to draw any conclusions.
[Many thanks to Julien Theze for running the analyses.]

YFV.complete_cds_bootstrap_100.txt (4.2 KB)

Just noticed this little snippet on the WHO website: “In March this year, Uganda gave official notification of an outbreak of yellow fever. The outbreak is not linked to the Angola outbreak. Results of sequencing indicate strong similarities to the virus which caused a yellow fever outbreak in Uganda in 2010.” So presumably there will be more sequences from Uganda-2016 dropping in soon.