Thank you. I agree that without all the facts, the best that can be done is to leverage the methods you have outlined to increase confidence in particular hypotheses as much as possible.

The details of treatment of the plague cases have actually been published in http://weekly.chinacdc.cn/en/article/id/d7876f39-9679-467b-a896-50e6451dcd73. Given that the CDC collected all the specimens, it really does cry out for a simple post-analysis of testing for Covid19. The most suspicious elements of the treatment descriptions is how resistant the clinical symptoms appeared to be to antibiotics, and the fact that the plague bacteria itself was not directly observed. If only antibodies and antigens to the plague were observed, doesn’t that present the possibility that the patient (Index Patient A) had been previously exposed to plague but was not currently actively infected? Thus, the possibility that symptoms were driven by a separate current pathogen not affected by antibiotics, such as of viral origin like Covid19, arises. At the very least, the CDC should be asked if they have tested the captured specimens for Covid19. With all tracked contacts being released by Nov 21st, and asymptomatic spread a significant threat, these cases need to be finally confirmed or refuted.

Thanks for the link.
I understand you questions and interrogations. This is one of the reasons why phylogenetics analysis is so interesting, it allows us overcoming the types of interrogations exemplified in the article: note that thanks to the phylogeny, the birth of the SARS-Cov-2 is timed as taking place between between 6 October 2019 and 11 December 2019, thus dates which are compatible with the “misdiagnosed plague” hypothesis.
And probably new analyses of the patients with plague would allow confirming or falsifying the hypothesis, but, if we do not have the answer, then phylogenetics nonetheless gives us a relatively certain framework to work with.
In science, and especially in international relations, we very rarely have access to all evidence, and most of the time, there is also no such thing as a truth that is out there and that one can discover. Sometimes there is, but we cannot access it, sometimes it is just not the way to proceed. So, we need to learn to live with hypotheses and uncertainty and to find ways to handle them at best (hence the scenario methodology). In the specific case of the birth of the COVID-19, it seems to me that the phylogeny is a good way to get the answers one need (at least for the questions I asked).
In the Chinese case, so many possible variables, beyond biological ones, come into play, such as provincial officials being afraid to be punished, or just systems not ready at the time to record and keep data, etc. and knowledge possibly being lost for ever. Using the “intention and capabilities” model could there also be interesting when evaluating dynamics of events.

Thank you for your answer. More recently I came upon an article that describes the focus of my questions in more detail: https://www.telegraphindia.com/india/coronavirus-pandemic-questions-over-wuhan-origin-december-date/cid/1774077

Still, it seems like journalists or government agencies should be pressing China for concrete evidence from these cases. If suspicions are valid, it alters the current assumptions of Covid19 “patient zero”.

Dear Nicola, you are most welcome!
Just to make sure, I would like to stress again I am an International Relations (political science) PhD and not a M.D. :). So my research implies building upon a vast array of multidisciplinary scientific research to get a good enough understanding of the epidemiological situation to be able then to understand if policy measures involve more or less risks for further spread of the pandemic and consequences in political terms. Thus, what I do does not involve at all medical advice. Considering your questions, it seems to me a virologist would be the qualified person with whom to talk? Sorry I cannot help you more.

Dear “Anonymous”,

Thanks for your comment and questions. Sorry but I do not have the answer to your questions. Maybe someone is doing this research or has already done it, but as it was not directly linked to my research question (the phylogeny analysis was enough for my purpose), I did not look in detail for the literature on this specific issue. I’ll keep it in mind though and if I find anything, I’ll let you know.

I have been surprised that there has been no retrospective examination of highly unusual plague cases in China in November 2019 since their collocation in time with the emergence of Covid19 is abnormal. Surely the blood samples of the patients could be quickly reanalyzed to see if they contained the antibodies for Covid19. My questions are really: could these cases have been misdiagnosed? Could these cases have contained both plague and Covid19? Did contact tracing of these cases reveal any paths that led to Wuhan?

Thank you Nicola. I relied on various biological, epidemiological and medical articles for my purpose, which is politics (in the largest sense of the term) and security. If I understand well your question, you don’t ask me to explain what is a serological test? If you are, then I saw the Telegraph published recently an article on the topic (https://www.telegraph.co.uk/news/2020/05/26/coronavirus-test-antibody-uk-covid-19-superdrug-buy/).
Actually, I assume your questions related to the articles I used. Those are grounded in phylogenetics (it is a bit like doing the genealogy of the virus). The scientists use genome sequences, which are obtained from patients when they are tested in hospital I assume, and which are kept in a global database called GISAID. You can have a look at their website that will certainly answer better your questions than me. And their application on the transmission of the virus in the world, and how it transforms in terms of genomes is absolutely fascinating. This is a whole scientific field, unfortunately not mine. Thus I trust the scientists working in this field, and I use their conclusions for my purpose. As far as the finding of dates are concerned, they use a specific system/software – according to what I read in one annex – that convert their genomic trees into something dated.
Your question on the way medical professionals should test their clients is truly very interesting… is there a way for medical professional to use more directly or practically the findings obtained through genomic epidemiology? That is really a good question… could that help in the future with handling better patients – and also with creating better, more adapted measures to contain the pandemic? To answer this, I think we need to create real multidisciplinary across fields and sciences… one of my dreams! Who knows, maybe a constructive outcome of the COID-19 tragedy could be to make such teams possible?
Regarding your question on someone in the UK, I don’t know her personally, but the contact scientist for one of the articles I used is Lucy van Dorp from the
UCL Genetics Institute, University College London, London WC1E 6BT, UK … thus you may try to contact her?
Thanks for your comment and very interesting questions!