Thread by @NathanGrubaugh

🚨 We used travel surveillance and genomic epidemiology to detect an unreported #Zika outbreak at an unexpected time.

Felt more like writing a detective novel 🕵️‍♂️🔎 than a scientific article...

“Zika files: case of the missing outbreak”

👇thread

cell.com/cell/fulltext/…

Tl;dr ▶️ watch the video abstract 👀

Our story started in 2016 by following local and travel case reports wanting to know when the Zika epidemic would be over.

We found this interesting spike in travel-related Zika cases from the Caribbean in 2017, when local cases were waning 🧐

🔎👩‍💻Looking more closely, we found that most of these 2017 Zika infected travelers were coming from Cuba… but Cuba didn’t report any local cases (at least not to the international community)

A missing outbreak?!

Now it was time to investigate 🕵️‍♂️👩‍💻👨‍🔬.

We found that the epi curves from local incidence rates matched travel incidence rates (travel cases/total travelers) from other locations, giving us confidence that the travel cases from Cuba were indeed from a missing local Zika outbreak

We then constructed a model 📈 to estimate that 1,000-20,000 Zika cases should have been reported in Cuba from 2016-2017 (187 Zika cases were reported in 2016 & none were reported in 2017).

Our estimates would put this on par with reported Zika outbreaks in the Caribbean 🏝️

@TAlexPerkins @RJOidtman So we detected an unreported Zika outbreak in Cuba, but the second part of this mystery is why did it occur in 2017 instead of 2016, when Zika outbreaks were peaking throughout the Americas 🌎?

And should we have expected this delay? 🤔

@TAlexPerkins @RJOidtman Based on our ✈️ travel surveillance, the #chikungunya outbreak in Cuba (which also was not reported) coincided with the rest of the Caribbean.

So no, outbreaks in Cuba are not somehow just universally disconnected from the rest of the Caribbean/Americas 🌎.

@TAlexPerkins @RJOidtman Next we ask, was the Zika outbreak delayed due to low transmission in Cuba, or because ZIKV was established later?

Here’s where we turned to the sequencing data 🦠🧬, which shows ZIKV was established in Cuba one year after other locations.

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele Now the question is what caused the delayed establishment of ZIKV in Cuba?

Was it due to less ✈️ travel from places 🌎 with Zika outbreaks? No🚫
Was it due to unsuitable mosquito 🦟 conditions for outbreaks? No🚫
Was it due to mosquito 🦟☠️ control? Maybe❓

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele Cuba reported a large mosquito 🦟 control campaign starting in early 2016.

Its timing⌚️ corresponded with a drop 📉 in dengue cases and low ZIKV transmission, despite suitable predicted mosquito transmission potential 🌡️🦟.

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele Thus it looks like Cuba did an excellent job initially at control...

but perhaps the program waned and there were still too many opportunities for ZIKV to become established - and 💥 outbreak. (last part speculation)

👇 🦟Spray truck in Havana (@NBCNews)

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews Who cares if there was an unreported outbreak that happened at an unexpected time? 🤷‍♂️

Well, because the world is so connected ✈️🌏, this could lead to silent 🤫 transmission to other locations. #yourproblemsaremyproblems

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews @MOUGK We believe that our framework of travel surveillance and genomics can help to solve other mysteries too 🔎.

And importantly, help to identify gaps in our disease surveillance and reporting systems.

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews @MOUGK Oh behalf of our Sharada Saraf (badass undergrad!),
@gkay92, @profpathogen, Scott Michael & @K_G_Andersen

We’d like to say how awesome it was to work (again) with such a great team. Our collaboration with the Florida DOH -led by Andrea Morrison’s - has been especially great 👏

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews @MOUGK @profpathogen @K_G_Andersen Also SO to Kamran Khan's team that provided the travel volume data and @TAlexPerkins, @RJOidtman, @TexasDownUnder, @GuyBaele, @VogelsChantal, @jtladner, & many many others for providing data, analysis, and helping to design the study.

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews @MOUGK @profpathogen @K_G_Andersen @TexasDownUnder @VogelsChantal @jtladner And special SO to @profpathogen who did all of the artwork 👩‍🎨, including the cover of Cell ‼️

See her work 👉 steampunkphage.com

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews @MOUGK @profpathogen @K_G_Andersen @TexasDownUnder @VogelsChantal @jtladner of course, all of our data can be found here:
github.com/andersen-lab/p…

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews @MOUGK @profpathogen @K_G_Andersen @TexasDownUnder @VogelsChantal @jtladner Will link some of the press to the end of this thread.

https://twitter.com/LabPulse1/status/1164553310747017216

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews @MOUGK @profpathogen @K_G_Andersen @TexasDownUnder @VogelsChantal @jtladner this work was possible because @HealthyFla makes their data openly available!

floridahealth.gov/diseases-and-c…

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews @MOUGK @profpathogen @K_G_Andersen @TexasDownUnder @VogelsChantal @jtladner Nice article by @sciencecohen in @sciencemagazine, including quotes from @jennifergardy & @MichaelWorobey

sciencemag.org/news/2019/08/i…

@TAlexPerkins @RJOidtman @gkay92 @GuyBaele @NBCNews @MOUGK @profpathogen @K_G_Andersen @TexasDownUnder @VogelsChantal @jtladner @sciencecohen @sciencemagazine @jennifergardy @MichaelWorobey article by @carlzimmer in the @nytimes points out that the 'missing' outbreak may be a data mixup between Cuba and PAHO... 🤔 needs some more digging.

If Cuba is reporting ~1300 cases from 2017, then it validates our work.

https://twitter.com/carlzimmer/status/1164601598624112641