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Genomic analysis of COVID-19 spread. Situation report 2020-04-10.
Author: Sidney M. Bell, Nicola Müller, Cassia Wagner, Emma Hodcroft, James Hadfield, Richard Neher, Trevor Bedford 1
1 Fred Hutch, Seattle, USA; Biozentrum, Basel, Switzerland; CZI, CA, USA
This report uses publicly shared genomic data to track the spread of COVID-19. These reports are updated weekly.
Created: 2020 April 10
License: CC-BY
Executive summary
This week, we take a step back to trace how the outbreak has unfolded, month by month. We focus on transmission dynamics between regions of the world. Here, we cover:
- Background and resources.
- A note on sampling.
- Early spread within Asia.
- Initial introductions from Asia to North America, Europe and Oceania.
- Growth of North American & European outbreaks.
- Subsequent spread across international borders within regions.
- Spread from Europe and North America to the global south.
- Coming full circle: reintroductions to Asia.
- What you can do.
- Scientific credits.
COVID-19 Resources
We've prepared some resources that will make interpreting the data we present in this narrative easier.
Nextstrain Resources
External Resources
A note on sampling
We currently have sequences from samples taken in 57 countries across 6 continents. This is an incredible achievement -- sequencing an unknown, large RNA virus in the midst of a pandemic is difficult, and is only possible through the incredible work and timely sharing of data by scientists and physicians around the world. While this data enables us to infer many useful characteristics of the outbreak and track its spread in real time, it's important to emphasize that our conclusions are limited by the available data. For example, the map shows very few sequences from the global south. This is NOT because COVID-19 isn't circulating in these areas, or that these cases are not as crucial to understand; rather, we just don't have much data available from these areas. The size of each circle on the map indicates how much data is currently available from that area, rather than the true size of the outbreak.
Early spread within Asia
Here, we highlight samples from mid-December 2019 through mid-January 2020, during the first month of the outbreak. Tips of the tree represent samples from infected individuals. Each internal node, or branch point, represents an unsampled case, which was the ancestor of all of the other cases within the descendant clade. Tips are colored according to where they were sampled from; nodes (branch points) are colored by the inferred (most likely) location of the ancestral case. Comparing where a sequence was isolated from geographically to where its ancestors were circulating can help us understand not only where infections are occurring, but also where they may have been acquired. The common ancestor of circulating viruses appears to have emerged in Wuhan, China, in late Nov or early Dec 2019. Accordingly, the majority of sampled and inferred ancestral cases were located in Asia during this early period. This is consistent with circulation largely within China and some exported cases to other countries in Asia for the first month of the outbreak.
Initial introductions to other regions
During the 2nd month of the outbreak, from mid-January to mid-February 2020, we start to see individual cases crop up in North America, Europe and Oceania. These early cases still group with samples from Asia, and generally lack the hallmarks of local transmission. This is consistent with initial sparks being thrown from the main outbreak in Asia to other parts of the world. Although most of these sparks did not result in localized outbreaks, at least three of these introductions took off. These led to the large European and North American outbreaks, as well as more restricted spread in Oceania.