First COVID-19 case in humans may have occurred in early October 2019, according to scientists who analyzed 7666 virus genomes

radial tree of genetic divergence from Balloux et al paper

A ScienceDirect article published May 5 reports that:

Phylogenetic estimates support that the COVID-2 pandemic started sometimes around 6 October 2019–11 December 2019, which corresponds to the time of the host-jump into humans.

The corresponding author, Francois Balloux of the Genetics Institute at the University College London, UK, describes in this paper how the team “curated” 7666 separate virus genomes to reach its conclusions.  The pattern of mutations showed that there were introductions from animal to human hosts (zoonotic transmission) in late 2019, somewhere between October 6 and December 11.

Since then, there have been repeated mutations– the team studied 198 different changes (homoplasies– mutations that have emerged independently multiple times) that resulted in changes to the proteins in the virus.  Nearly 80% of the mutations resulted in “non-synonymous” amino acid changes in proteins that the virus uses as part of its structure or enzymes used in virus replication or assembly.  The mutations at four sites studied on the virus genome result in what is called “convergent evolution”, in which independent changes create similar features in descendants of the original virus.

These mutation sites indicate that the virus has been undergoing further adaptation to its human host since the jump from animal to human.  These adaptations are of unknown significance at present, but some may have resulted in increased transmissibility (spread from one host to the next).  Another, disputed paper claims that a mutation causing increased spread has taken over.  Note that this virus type has the ability to proofread its new creations with an “exonuclease” enzyme, reducing its mutation rate (quote from the first-cited paper):

…Coronaviridae having the unusual capacity amongst viruses of proofreading during nucleotide replication, thanks to the non-structural protein nsp14 exonuclease, which excises erroneous nucleotides inserted by their main RNA polymerase nsp12…

The analysis explained in this paper leads to the conclusion that the virus appeared among humans no earlier than August 2019 (at the absolute earliest) and most likely around October 6, 2019.  This analysis shows that the virus has spread all over the Earth rapidly and completely, notwithstanding our surveillance only identifying roughly 3.8 million infections worldwide as of today.  The virus has spread quickly due to its high transmissibility and its low impact on human health– most cases are asymptomatic, and they do not hinder a person’s ability to travel or conduct normal business.  Only the least healthy among us have been severely affected: the old and the infirm.  Many of those who are struck down are people who harbor hidden vulnerabilities, like autoimmune disorders and genetic susceptibility to overwhelming hyperimmune reactions.

The more we learn about the novel coronavirus, the more we find that it is at the pinnacle of evolution: its viral “intelligence” presents the greatest challenge we have ever faced as a human species.  Only our most enlightened and humane efforts will overcome the threat the virus poses to humanity.  This is no time to disintegrate into squabbling nationalities and political parties; we must now unite and face the situation as one human race.