Phylogeography of 27,000 SARS-CoV-2 Genomes: Europe as the Major Source of the COVID-19 Pandemic

Abstract

The novel coronavirus SARS-CoV-2 emerged from a zoonotic transmission in China towards the end of 2019, rapidly leading to a global pandemic on a scale not seen for a century. In order to cast fresh light on the spread of the virus and on the effectiveness of the containment measures adopted globally, we used 26,869 SARS-CoV-2 genomes to build a phylogeny with 20,247 mutation events and adopted a phylogeographic approach. We confirmed that the phylogeny pinpoints China as the origin of the pandemic with major founders worldwide, mainly during January 2020. However, a single specific East Asian founder underwent massive radiation in Europe and became the main actor of the subsequent spread worldwide during March 2020. This lineage accounts for the great majority of cases detected globally and even spread back to the source in East Asia. Despite an East Asian source, therefore, the global pandemic was mainly fueled by its expansion across and out of Europe. It seems likely that travel bans established throughout the world in the second half of March helped to decrease the number of intercontinental exchanges, particularly from mainland China, but were less effective between Europe and North America where exchanges in both directions are visible up to April, long after bans were imposed.

Keywords: SARS-COV-2 lineages; intercontinental founders; molecular epidemiology; phylogenomics; phylogeography; travel bans.

Figure 1

Reduced-median network of the most common haplotypes in the SARS-CoV-2 genomic database. Networks are colored according to geography (A) and the time of collection (B). Size of the circles corresponds to the number of samples with the same haplotype and a scale is provided. Two haplotypes have more samples than the limit of the software and the number of samples is provided. Links correspond to inferred mutations between haplotypes. Given the complexity of the network, the length of the links is not fully additive (i.e., exactly scaled to the number of mutations). A defined nomenclature for the nodes of this network is presented in Figure S2, Figure S1 displays the mutations between haplotypes, and branch lengths are scaled to the number of mutations in the networks in the individual networks (Figures S7–S57).

Figure 2

Accumulative distribution of the number of founders in each continent/region from different sources for: (A). Africa, (B). East Asia, (C). Europe, (D). North America, (E). Oceania, (F). South America, (G). South Asia, and (H). Southwestern Asia.