What proportion of CoV-SARS-2 infected people are asymptomatic?

This is my third attempt to examine this question.  The previous two versions died in draft because the results from various studies were in significant disagreement, so that I could come to no firm conclusion.  Fortunately I have now come across a meta-analysis that should give a clearer answer.  That meta-analysis is by Wenquing He, Grace Yi and Yayuan Zhu, all of the University of Western Otario.  Their paper is "Estimation of the basic reproduction number, averageincubation time, asymptomatic infection rate, and casefatality rate for COVID-19: Meta-analysis andsensitivity analysis" published by medRxiv.

When did the virus responsible for COVID-19 jump species?

With the Australian government following the US government in trying to impute culpability to Chinese handling of the outbreak of COVID-19; and with the Chinese trying to exonerate themselves, and implausibly shift the blame to the Americans, the exact timing of the jump of the virus responsible for COVID-19 (SARS-CoV-2) from animals to humans has become politically fraught.  Fortunately, some information about that event can be gleaned from phylogenetic data from the virus itself.  The determination of the event cannot be exact for a number of reasons; but it has the advantage of being free from politics, and of possible suppression of data.

So far as I have been able to determine from an extensive search of Google Scholar, there has been just one peer reviewed paper tackling that subject - "Evolutionary history, potential intermediate animal host, and cross‐species analyses of SARS‐CoV‐2" by Li et al.  They state in the abstract, "Based on Bayesian time‐scaled phylogenetic analysis using the tip‐dating method, we estimated the time to the most recent common ancestor and evolutionary rate of SARS‐CoV‐2, which ranged from 22 to 24 November 2019...", and more precisely, in the text, "Our results also suggest that the virus originated on 24 November 2019...".  The purpose of this post is to discuss in more detail those results, and what they actually mean.  I will also discuss the results of Andrew Rambaut of the University of Edinburgh, which were directly published to the web (and hence only subject to informal peer review).

Updated:14/5/2020

Did the Chinese report only 1 in 100 COVID-19 cases?

Did the Chinese report only 1 in 100 COVID-19 cases?  It seems like an extraordinary question, but that is the implication of an article (Tsang et al) published by a group of scientists from Hong Kong.  They write: 

"Among the 127 000 cases that we estimated in Wuhan by Feb 20, we estimated that there could have been approximately 11 000 infections (95% CrI 7000–21 000) that met version 5 of the case definition with illness onset by Jan 1, 2020. In the observed data, there were 114 confirmed COVID-19 cases with illness onset by Jan 1, 2020, corresponding to around 1% of our estimated total. Before Jan 23, we estimated that 92% (95% CrI 88–95) of cases were undetected." (My emphasis.)

The article was published in the Lancet, so it needs to be taken seriously.  Never-the-less, I think they are clearly wrong.  In the first instance, I think they are wrong because their model predicts approximately approximately 90 cases with disease onset on December 2nd, six days prior to the onset of symptoms in the first known case.  If that had been the case, the disease must have jumped to humans in early November at the latest; and cases would have started to find their way into intensive care units by late November - something clearly contradicted by the testimony of Chinese whistle-blowers.   

I have other, more direct criticisms which will be the subject of my post.  The most crucial of these criticisms is that when we confine the analysis to Wuhan patients, the logic of the definitions together with known clinical data show Tsang et al to massively over-estimate the effect of changes in the 'case definition' on the number of patients diagnosed with COVID-19.  

Before going further, however, I must clarify that the authors of the article do not suggest that any under counting was deliberate, or fraudulent; and nor do I suggest that there was no under counting.  Of necessity, in a new disease which can manifest in a mild form, there will be initial under counting of the disease.  That is because people with mild symptoms will likely not go to a doctor, and if they do, may dismissed as having an aberrant form of some other disease.  Therefore, in the case of COVID-19 there must have been under counting due to ignorance; and the authors do not suggest any other reason for the extent of the under counting.  Where we disagree is that I think they radically over estimate the level of under counting; and that they do so in part due to logical flaws in their paper.