Chikungunya Virus, 250 years old?

General
1

Hi, there:

I downloaded the high-depth sequence data for 4,590 Chikungunya Virus from GISAID, and run a nextstrain analysis. Please see the screenshot below. I am so surprised to see that the inferred root of the phylogenetic tree is somewhere in year 1777, which is around 250 years ago.

image
image1114×294 13.6 KB

That does not seem correct to me. I now put the fasta file, the metadata file, the Snakefile and configure file at this Github link 001/analysis at master · jielab/001 · GitHub . Can you please take a peek at your convenience and let me know if I somehow mis-used nextstrain?

Thank you very much!

Best regards,

Jie

2

Hi Jie,

time scaled phylogenetic analysis can be very sensitive to the quality of the temporal signal in the data. If a molecular rate and the location of the root can not be reliably inferred, time scaled trees can be quite far from the true timing. I’d advise to investigate the temporal signal and if necessary specify root and rate explicitly,

richard