I and others have been talking to @sheri_fink from the NYT over the last couple of days trying to trace the beginnings of Ebola in Sierra Leone. Sheri and her team has done a tremendous amount of investigations in West Africa over the last couple of months and their phenomenal article was just published:
This puts some of our earlier findings into perspective. E.g. we report in our Gire et al. paper that the outbreak started in Sierra Leone around mid-May (funeral of traditional healer), but the NYT article clearly shows that Ebola had been lingering undetected for quite some time. This is very disconcerting and the article describes in great details how this could have happened. For the purpose of this post, I’m interested in discussing some of the scientific/transmission implications.
One of the main findings we saw in the first dataset was the presence of two viral lineages in Sierra Leone in mid/late May. We speculated how this could be linked to the presence of two lineages in the traditional healer, or the presence of other infected individuals at the funeral. Given NYT’s story, it’s clear to me that these events are independent - the funeral was in April and much too early to have been directly responsible for the late-May cases. These cases must have been a result of a couple of already existing transmission chains, which also explains the presence of viral lineages (clades) 1 and 2.
I don’t think this influences our dating estimates (the individuals we initially sequenced were presenting around the 25th, which we use), but calculating in incubation time, can we use all this information to estimate when clades 1 and 2 split? A back-of-the-envelope calculation gives me something around early-mid April, which seems to fit very well with the article. The presence of lineage 2 in Liberia also fits very well with our findings.
Given new and previous data can we get better estimates of these events so we can understand the transmission events in more detail?