Do you remember the strange "second peak" papers?

Finally got around to publishing them:

researchgate.net/publication/35…

Part 2 (Overview and Analysis) and the underlying data are also published under "Linked Data" if you scroll down.
Papers List 1 to 14 and 15 to 25
26 to 36 are not listed but are in the published PDF

26. Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans | mBio

journals.asm.org/doi/10.1128/mB…
27. Origin, Evolution, and Genotyping of Emergent Porcine Epidemic Diarrhea Virus Strains in the United States | mBio

journals.asm.org/doi/10.1128/mB…
28. Middle East Respiratory Syndrome Coronavirus: Another Zoonotic Betacoronavirus Causing SARS-Like Disease | Clinical Microbiology Reviews

journals.asm.org/doi/10.1128/CM…
29. Human Coronavirus EMC Does Not Require the SARS-Coronavirus Receptor and Maintains Broad Replicative Capability in Mammalian Cell Lines | mBio

journals.asm.org/doi/10.1128/mB…
30. A Case for the Ancient Origin of Coronaviruses | Journal of Virology

journals.asm.org/doi/10.1128/JV…
31. Severe Acute Respiratory Syndrome Coronavirus Phylogeny: toward Consensus | Journal of Virology

journals.asm.org/doi/10.1128/JV…
32. Genomic Characterization of a Newly Discovered Coronavirus Associated with Acute Respiratory Distress Syndrome in Humans | mBio

journals.asm.org/doi/10.1128/mB…
35. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats | PNAS

pnas.org/content/102/39…
36. Evolutionary Insights into the Ecology of Coronaviruses | Journal of Virology

journals.asm.org/doi/10.1128/jv…
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More from @BillyBostickson

19h
22. Biased Sampling distorts Geography!

They use a dataset skewed toward Yunnan & Laos (p. 16), leading to phylogeographic models that place SARS-CoV ancestors far from Wuhan & Guangdong (p. 12).

This sampling bias undermines the reliability of their geographic inferences.
23. Neglecting Alternative Hypotheses

No SARS-CoV-like viruses near emergence sites?

They completely overlook non-bat reservoirs, like civets or pangolins, which could explain local circulation (p. 15).

This omission weakens their claim of distant ancestor origins (p. 12).
24. Inconsistent Molecular Clock Rates

The paper misuses variable NRR-specific clock rates, which give inconsistent SARS-CoV ancestor dates (e.g., 1944–2014 for SARS-CoV-2, p. 9).

Without any validation of bat-specific rates, this approach has no rational grounding (p. 14).
Read 8 tweets
22h
5. Why did they resort to using the POW model?

To show that :

"our inferences of the time of the ancestors of human SARS-CoVs and their closest bat sarbecoviruses are UNBIASED"
6. Captain Obvious Strikes Again (1)

"we show that the ancestors of SARS-CoV-1 & SARS-CoV-2 likely circulated in horseshoe bat populations 100s to 1000s km away from the sites of the emergence of these viruses in humans & as recently as one to six years prior to this emergence"
7. Captain Obvious Strikes Again (2)

"Our findings indicate that there would not have been sufficient time for the direct bat virus ancestor to reach the locations of emergence of the human SARS-CoVs via normal dispersal through bat populations alone"
Read 12 tweets
22h
1. Last sick joke of the Zoonati?

Fragments of human SARS-CoVs share recent common ancestors with bat viruses

SARS-CoV-like viruses have circulated in Asia for millennia

Ancestors of human SARS-CoVs likely circulated in China & Laos

Ancestors traveled unexpectedly fast
2. No Pangolins allowed!

There is insufficient temporal signal when calibrating a molecular clock using tip dating with sarbecoviruses sampled from bats & pangolins, likely as a consequence of limited sampling across space & time.

Therefore, we used SARS-CoV-1 genomes!
3. Definitely no pangolins!

As sampling locations of SARS-CoV-1, 2 & pangolin sarbecoviruses likely do not represent where their direct bat virus ancestors circulated, we EXCLUDED their locations from phylogeographic analyses to avoid the IMPACT of dispersal of non-bat hosts!
Read 24 tweets
May 4
1⃣ Virological 🦠 Whistleblower 😮‍💨?

"I worked with researchers in this space - virology + combatting future pandemics - in the decade before the pandemic".
2⃣ One Fact

"The one fact that the last 5 years never readily disclosed is that the core ideology of this community of researchers was fundamentally divided"
3⃣ Lab based creation of super-viruses

"About half of the researchers, including many leading virologists whose names appeared in the news, believed and argued passionately for the lab-based creation of super-viruses and super-bacteria"
Read 12 tweets
Apr 23
1. The Second Lab Leak

Turning and turning in the petri dish,
The scientists cannot hear the warnings;
Genes recombine; the barriers cannot hold,
Evil virology is loosed upon the world,
The blood-dimmed tide is loosed, and everywhere
The ceremony of innocence is drowned;
2. The Second Lab Leak

The best lack critical thinking, while the professors
Are full of furious bias.
Surely some revelation is at hand;
Surely the cover up is now banned?
Lab Leak! Hardly are those words out
When a vast image out of Human Folly
Troubles my sight:
3. Somewhere in Wuhan

somewhere in the cell lines of a Chinese laboratory
A shape with pangolin body and the head of a bat,
A gaze blank and pitiless as the sun,
Is moving its long tongue, while all about it
Reel shadows of the indignant molested bats.
Read 6 tweets
Apr 22
🧵As promised, here is my counter critique & rebuttal of some points made by @gadboit about the Pangolin Papers Hypothesis.

His theory seems to be that SARS-COV-2 emerged like Aphrodite, from BANAL BAT viruses, possibly with some FCS tweaking & no Pangolins coronaviruses needed.
🧵1. Introduction

@gadboit claims BANAL-52’s 96.8% similarity and natural recombination outweigh my lab + PangolinCoV hypothesis for SARS-CoV-2’s origin.

However, my evidence shows PangolinCoV signatures, WIV lab work & recombination are stronger.

researchgate.net/publication/39…
@gadboit 🧵2. @gadboit claims BANAL-52’s 96.8% similarity & ACE2 binding make it closer to SARS-CoV-2 than PCoVs (~91%) & that PCoV features could come from bat CoVs.

But GD PCoV’s RBD (97% identity) needs no mutations for hACE2, unlike BANALs.

See Wrobel et al:

nature.com/articles/s4159…
Read 28 tweets

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