A Deep Dive Look Into Global Monkeypox Transmissions — from January to July 2022.

Just as things were seeming to return to normal from the COVID-19 pandemic, reports of monkeypox started being shared around the globe. Many people were vaccinated against smallpox (the variola virus) in the 1950s-70s. So, how does monkeypox differ and why might we care about these new infections?

“A monkey holding a virus in the style of Dali” — Created with OpenAI’s Dall-E

Cowpox, monkeypox, smallpox, and other “pox” viruses are all in the same genus: Orthopoxvirus. They’re all quite related and similar, differing mainly by the organism they often infect (hence the animalistic naming scheme).

“Monkeypox” was coined in 1958 when a group of monkeys (held for research purposes) became ill with the familiar pox rash. From the 1970s on, there have been human cases of monkeypox, but these cases are almost always from individuals who traveled to certain central and western African countries.

Around May 2022, though, the number of monkeypox cases from people who had not traveled to particular African countries began to rise. This is the reason for the proposed alarm.

A couple of stats from the CDC and WHO:

  • The fatality rate of monkeypox is around 3–6%, usually due to severe infections that last 2+ weeks.
  • Monkeypox is less contagious than smallpox and causes less severe illness.
  • At the time of writing, there are over 16k cases worldwide and nearly 3k cases in the US.
  • In the US, there are two FDA-approved vaccines: JYNNEOS and ACAM2000. Both are smallpox-based, but are approved for monkeypox as well.

Not a “Gay Disease”

Monkeypox is spread through skin contact with anyone who is infected, the risk of which is amplified if the person has a rash/pustules. Can you get this from having sex with someone? Yes. Can you get this from shaking hands with someone at church? Yes. Can you get this from touching the ketchup dispenser at McDonald’s and then eating a 20 chicken McNuggets all by yourself without washing your hands first? Yes.

Let’s stop with the homophobia. That’s so 1980.

Building Transmission Networks

I retrieved a multiple sequence alignment of 560 monkeypox isolates from GISAID on 7/23/22. Then, using RAxML, I created a maximum likelihood-based phylogenetic tree of the taxa.

Using my R package called StrainHub, I created two transmission networks to visualize the flow of the virus between places geospatially (by continent and country). Using the isolate metadata from GISAID, I removed taxa that were collected before 2022 and added in some location metadata.

By Continent

If we look at the data by continent, it appears that there is a significant transmission from Europe to North America, though there’s quite a bit of circular transmission occurring all over.

StrainHub network of monkeypox transmissions by continent (from 2022). Nodes are shown as source-hub ratio. Edges are shown as count of state transitions.

By Country

If we drill in a bit to the country level, it appears that a bulk of the European transmissions are cycling through Germany and Portugal, but many of these transmissions involve the US and Canada.

Note how the transmissions from African countries (in blue) to other countries is relatively low in comparison.

StrainHub network of monkeypox transmissions by country (from 2022). Nodes are shown as source-hub ratio and colored by continent. Edges are shown as count of state transitions.

As this situation continues to emerge, I plan to continue looking into the transmission patterns globally. This will be important as we attempt to understand where the disease is coming from, ascertain the risks of traveling, etc.

Some Final Thoughts

  • As you can see in the transmission networks above, there is a considerable amount of transmission coming from Europe over to the North America. This is different that what we have seen occur in the past due to sporadic travel to/from Africa.
  • The StrainHub networks shown above are showing source-hub ratios, which is defined as:
  • Monkeypox is a DNA virus, so we shouldn’t see the rapid mutation/variant onslaught as we saw in SARS-CoV-2 (a RNA virus).
  • The monkeypox we see today isn’t all that different from isolates 30 years ago. This is good news for vaccines and keeping this under control.
  • In the US, we need to be doing a better job of sequencing a cataloging monkeypox infections. As of the time of writing, there were only a few US-based isolates with state information (Utah, Florida, New York, and California), though we know most states have seen cases of the virus this year.

All of these results and code are available at: https://github.com/colbyford/monkeypox_comparisons

Stay Curious



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Colby T. Ford, PhD

Colby T. Ford, PhD

Cloud genomics and AI guy and aspiring polymath. I am a recovering academic from machine learning and bioinformatics and I sometimes write things here.