Dr Peter Forster Tracing the origins of the coronavirus pandemic using phylogenetic network analysis

In the 1990s phylogenetic network analysis allowed the reconstruction of mankind's prehistoric colonisation of the planet from an African origin. In early 2020 we applied the technique to tracing the origins of the current coronavirus pandemic.

Three levels of origin need to be distinguished 1. Species jump from bat to human: on the basis of available genomic data, this could have happened up to 5 decades ago, but plausibly the transfer was recent and the responsible bat virus population has not been identified or is extinct. 2. Successful initial spread of the pathogenic virus in Asia: irrespective of whether the bat initially transferred an asymptomatic strain to humans which then mutated in humans to become symptomatic, or whether the virus was pathogenic from the outset, we genetically date the successful spread of the pathogenic virus to a time point between mid-September and early December 2019. The Achilles heel of our estimate is that we assume that the viral mutation rate in early 2020 is applicable to previous time periods. The area of origin is more likely to be outside Wuhan (Hubei province) and possibly in southern China, although the early sample size is too small for us to be certain. 3. Origin of current global strains: we noted in March 2020 the unusual shape of a portion of the network we labelled "B" and proposed viral adaptation as an explanation. Specifically, a type now known as B1, detected in February 2020 in Lombardy, Italy, has given rise to the global spread of major variants of concern. We investigate possibilities how this type arrived in Italy.

在 1990 年代，家譜網絡分析讓我們重建人类从非洲起源的史前殖民。

2020 年初，我們應用該技術來追踪當前冠狀病毒大流行的起源。

This lecture is an update of Phylogenetic network analysis of SARS-CoV-2 genomes. Peter Forster, Lucy Forster, Colin Renfrew, and Michael Forster. PNAS April 28, 2020 117 (17) 9241-9243.