Researchers have reconstructed the early "evolutionary paths" of COVID-19 in humans using phylogenetic network analysis. By analyzing the first 160 complete virus genomes to be sequenced from human patients, the scientists have mapped some of the original spread of the new coronavirus through its mutations, which creates different viral lineages.

"There are too many rapid mutations to neatly trace a COVID-19 family tree. We used a mathematical network algorithm to visualise all the plausible trees simultaneously," said geneticist Dr Peter Forster, lead author of a paper published yesterday in PNAS.

The team used data from virus genomes sampled from across the world between December 24, 2019 and March 4, 2020. The research revealed three distinct "variants" of COVID-19, consisting of clusters of closely related lineages, which they label 'A', 'B' and 'C'. Forster and colleagues found that the closest type of COVID-19 to the one discovered in bats—type 'A', the "original human virus genome"—was present in Wuhan, but surprisingly was not the city's predominant virus type.

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Mutated versions of 'A' were seen in Americans reported to have lived in Wuhan, and a large number of A-type viruses were found in patients from the U.S. and Australia. Wuhan's major virus type, 'B', was prevalent in patients from across East Asia. However, the variant didn't travel much beyond the region without further mutations—implying a "founder event" in Wuhan, or "resistance" against this type of COVID-19 outside East Asia, say researchers.

The 'C' variant is the major European type, found in early patients from France, Italy, Sweden, and England. It is absent from the study's Chinese mainland sample, but seen in Singapore, Hong Kong, and South Korea.

The new analysis also suggests that one of the earliest introductions of the virus into Italy came via the first documented German infection on January 27, and that another early Italian infection route was related to a "Singapore cluster".

The software used in the study, as well as classifications for over 1,000 coronavirus genomes and counting, is available free at http://www.fluxus-technology.com.