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Thu Aug 5, 2021, 01:25 PM

Phylogeographic Mapping of Newly Discovered Coronaviruses

Phylogeographic Mapping of Newly Discovered Coronaviruses Pinpoints the Direct Progenitor of SARS-CoV-2 as Originating from Mojiang, China

https://www.independentsciencenews.org/commentaries/phylogeographic-mapping-of-newly-discovered-coronaviruses-pinpoints-direct-progenitor-of-sars-cov-2-as-originating-from-mojiang/

In this article we reveal that the new coronavirus genomes from Asia contain sufficient information to narrow down the geographical source of the direct bat progenitor of SARS-CoV-2 to a quite small region, the south-central part of the Chinese province of Yunnan. In other words, this analysis identifies with good confidence and quite precisely the location where a bat virus that ultimately became SARS-CoV-2 left its bat reservoir host, initiating the chain of events that led to the COVID-19 pandemic.

The analysis does not specify the precise nature of this initiation event. The jump out of bats may have been into an intermediate host (that later went on to infect a human), or it may have been a jump directly into a human; or even the virus may have been procured as part of a research project.

Nevertheless, such a very substantial narrowing of the location of the jump from bats represents a major step forward. Its implications for understanding the origin of SARS-CoV-2 are profound because the requirement for a Yunnan connection markedly constrains origin theories. For example, advocates of the imported frozen food theory favoured in China now have to explain how imported food came to Wuhan carrying a virus from Yunnan (Zhou and Shi, 2021). Likewise, ideas that have circulated about possible European origins of the virus must now explain how a European patient zero could have acquired that virus from Yunnan. Also importantly, the bioweapon theory of Dr Li-Meng Yan is ruled out by the newly discovered viruses discussed here.

But perhaps the greatest significance of this finding will turn out to be that the region of Yunnan indicated as the likely geographic origin is centred on a place called the Mojiang mine. This mine is already well-known to COVID-19 origins investigators.

Much more at link. I tend to agree with their currently favored hypothesis: that the 2012 incident involving miners who contracted a respiratory disease from a bat guano-filled mineshaft represents the most parsimonious proximal origin story for Covid.

We favour this theory because it explains numerous otherwise puzzling features of SARS-CoV-2. These features are (1) the high improbability of a zoonotic appearance of a SARS-related coronavirus in Wuhan; (2) the apparently pre-adapted nature of the virus to humans (Piplani et al., 2021; van Dorp et al., 2020; Zhan et al, 2020); (3) a minerís passage predicts a single zoonotic jump to humans [which fits the data on early human sequences (Bloom, 2021)] and which is inconsistent with most viral zoonoses, which typically feature multiple jumps into humans; (4) a miner-derived virus also explains the proclivity of SARS-CoV-2 for human lungs, which is a characteristic that many coronaviruses lack; (5) the theory can also explain the extensive attempts to deny or obscure research occurring at the WIV (see also the Zhou P. et al., 2020a addendum). The Mojiang miners hypothesis even has an evolutionary explanation for the infamous furin cleavage site. However, none of this precludes the possibility that the miner-derived virus was also lab-altered.

Since the theory specifically postulates that patient zero was a Mojiang miner who acquired one or more SARS-CoV-2-related viruses directly from the bats in the mine, the miners passaging theory matches perfectly the phylogeography of SARS-CoV-2 lineage revealed above. Indeed, it is an explicit prediction of the Mojiang miner passage theory that SARS-CoV-2 is composed of viruses originating there. Consequently, a miner passage origin is also consistent with SARS-CoV-2 being a mosaic of RmYN02, RpYN06, PrC31 and RaTG13 since, as the phylogeography shows, these viruses, or their close relatives, could have been present in the mine when the miners fell ill.

A miner passage is therefore not just compatible with but greatly strengthened by all the new evidence from wild viruses that has emerged since the pandemic began.

It's a long read, but worthwhile, IMHO. There are many more issues raised in the article that merit discussion.

Shall we discuss?

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Reply Phylogeographic Mapping of Newly Discovered Coronaviruses (Original post)
intrepidity Aug 2021 OP
Random Boomer Aug 2021 #1
NH Ethylene Aug 2021 #2
NH Ethylene Aug 2021 #3

Response to intrepidity (Original post)

Thu Aug 5, 2021, 03:58 PM

1. Yes, definitely worth a read for anyone curious about the origins of SARS-CoV-2

It's too technical for me to debate any of the points, but I found this particularly interesting:

In other words, the Mojiang area of Yunnan was the site of the key zoonotic leap where SARS-CoV-2ís ancestor exited its bat reservoir. This leap may have been directly into a human. Alternatively, the leap may have been into an intermediate host. The third possibility is that the leap was assisted by scientists collecting or researching bat viruses.

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Response to Random Boomer (Reply #1)

Thu Aug 5, 2021, 05:43 PM

2. That's helpful, actually, I think.

It puts the research above accusations of political bias. I can't imagine how bad it would feel to invest so much work, then have your results dismissed by people who could barely pass Biology in high school.

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Response to intrepidity (Original post)

Thu Aug 5, 2021, 06:13 PM

3. The miner passage theory seems well supported,

Although the article was long and dense, so a bit challenging for me. But the bottom line seems to be that the virus's closest relative came from bats in a cave in SW China, and how or in what intermediary it mutated to its starting pandemic form is not known.

With one exception, "every virus in the SARS-CoV-2 clade falls on an almost perfect straight line. Beginning from the discovery location of RaTG13 (closest genome match to Covid 19), the further away from the mine (in Yunnan) a virus was found, the less closely related to SARS-CoV-2 it is."

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