Did Covid-19 come from nature or from a lab?
Source: Did Covid-19 come from nature or from a lab?
Archived: July 18, 2026
Starting Point Card
Starting point
Starting Point
Starting point
Zoonosis
Starting point
Lab Leak
What is the starting point?
The starting point in Bayesian analysis is the “priors” associated with an event, representing the initial probabilities or likelihoods of different hypotheses before any specific evidence is considered. These priors are crucial as they form the starting point from which analysis begins and beliefs are updated upon reviewing new, relevant data.
Starting Point
91%
Lab Leak
Min - Max
45% - 91%
9%
Zoonosis
Min - Max
9% - 55%
To evaluate the starting point for an analysis, we usually begin by selecting a subset of evidence that is easy to analyze and gather statistics for. In this case, estimating priors is challenging due to the rarity of major pandemics and of lab leaks.
Additionally, rapid advancements in genetic engineering complicate the assessment of the current risk of a major pandemic caused by
Gain of Function
research, relative to the lack of any known cases in the past.
Therefore, we calculate an estimated annual emergence rate for each hypothesis, specifically, the probability per year of a bat coronavirus pandemic starting in Wuhan.
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2 Starting points
NOW THAT WE KNOW WHERE TO START, LETS EXPLORE THE EVIDENCE
Summary of evidence
Summary of evidence
Location (HSM)
Evidence
There are 7 live animal shops in HSM and a total of 17 in the four Wuhan markets.
Evidence
HSM is the largest seafood market in central China
Evidence
28% of early cases (December 2019) were exposed to HSM
Best explanation
Either an animal or a human brought the virus to HSM
Best explanation
HSM is a conducive environment to forming an early SARS-CoV-2 cluster
What is a Summary of Evidence?
The Summary of Evidence is a factual description of an Evidence group. It can itself be broken down into multiple Evidence or Claim cards. Evidence can be grouped together - forming an Evidence group - if they have the same Best Explanation.
Location (HSM)
4%
Zoonosis
Min - Max
4% - 17%
2%
Lab Leak
Min - Max
0.7% - 2%
Many early cases were associated with the Huanan Seafood Market (HSM), the largest seafood market in central China and one of a handful of markets selling live animals in Wuhan.
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3 Evidence
2 Best explanations
Summary of evidence
Summary of evidence
Presence of an FCS
Best explanation
A new virus starting a pandemic is expected to have a novel feature
Best explanation
WIV is expected to add FCSs
What is a Summary of Evidence?
The Summary of Evidence is a factual description of an Evidence group. It can itself be broken down into multiple Evidence or Claim cards. Evidence can be grouped together - forming an Evidence group - if they have the same Best Explanation.
Presence of an FCS
x1
Zoonosis
Min - Max
x1 - x1
x1
Lab Leak
Min - Max
x1 - x1
SARS-CoV-2 has a
Furin Cleavage Site
(
FCS
), an amino acid sequence that causes the protease
furin
to cut the virus in a way that facilitates its entry into cells.
This evidence is noteworthy because the Wuhan Institute of Virology (
WIV
) showed interest in incorporating FCSs into viruses.
This evidence group only addresses the presence of an
FCS
, not its characteristics, which will be analyzed in the following evidence groups.
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2 Best explanations
Summary of evidence
Summary of evidence
12 nucleotides clean insertion
Best explanation
Unknown evolutionary advantage
Best explanation
Common engineering tool, possibly to explore the role of proline
What is a Summary of Evidence?
The Summary of Evidence is a factual description of an Evidence group. It can itself be broken down into multiple Evidence or Claim cards. Evidence can be grouped together - forming an Evidence group - if they have the same Best Explanation.
12 nucleotides clean insertion
What is a conditional probability
These numbers are conditional probabilities. They are a measure of how likely is each best explanation given its respective hypothesis.
10%
Lab Leak
Min - Max
10% - 10%
0.5%
Zoonosis
Min - Max
0.5% - 1%
The
FCS
emerged in SARS2’s genome as a clean 12 nucleotide insertion, implying three unexpected features :
-
It is an insertion, which are very rare. The
FCS
could have developed through standard single nucleotide variations (
SNV
), which are 10,000 times more common. In fact, several coronaviruses are a few mutations away from an
FCS
, and there is no known advantage to obtaining the
FCS
through an insertion rather than an
SNV
.
-
It is a long insertion instead of a more common short insertion (e.g. of 3 nucleotides only)
-
It is a clean insertion, appearing in a highly conserved area of the genome, with many synonymous
SNVs
.
This is in contrast to the far more likely alternative of acquiring an
FCS
through
SNVs
.
-
For example the RmYN02 virus is only one nucleotide mutation away from turning its PAAR sequence into RAAR, which is a suboptimal cleavage site that can later develop into a fuller RARR or RRAR cleavage site.
-
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2 Best explanations
Summary of evidence
Summary of evidence
Insertion is from a foreign source
Best explanation
The insertion is from genetic material in the cell
Best explanation
The insertion was chosen by the engineer
What is a Summary of Evidence?
The Summary of Evidence is a factual description of an Evidence group. It can itself be broken down into multiple Evidence or Claim cards. Evidence can be grouped together - forming an Evidence group - if they have the same Best Explanation.
Insertion is from a foreign source
What is a conditional probability
These numbers are conditional probabilities. They are a measure of how likely is each best explanation given its respective hypothesis.
80%
Lab Leak
Min - Max
70% - 80%
15%
Zoonosis
Min - Max
15% - 15%
The 12 nucleotides sequence does not appear anywhere else in the SARS2 genome, meaning it was not copied internally as insertions often happen, but instead the sequence came from some foreign source.
The two arginines are coded by the rarest codons for arginines (CGG) and the sequence CGGCGG doesn’t appear in the SARS2 genome
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2 Best explanations
Summary of evidence
Summary of evidence
Suboptimal features for an FCS to work
Best explanation
Evolution is expected to include random features
Best explanation
Unidentified factors
What is a Summary of Evidence?
The Summary of Evidence is a factual description of an Evidence group. It can itself be broken down into multiple Evidence or Claim cards. Evidence can be grouped together - forming an Evidence group - if they have the same Best Explanation.
Suboptimal features for an FCS to work
40%
Zoonosis
Min - Max
40% - 60%
10%
Lab Leak
Min - Max
3% - 10%
Three features are suboptimal for an
FCS
to work :
-
Leading proline : the amino acid sequence of the insert is PRRA, while theoretically RRA would suffice for engineering purposes.
-
Non-canonical
FCS
: the insertion creates the
FCS
RRAR instead of the more canonical cleavage sites RARR or RKRR.
-
“Out of frame” : the 12 nucleotides insertion could be interpreted to be out of frame (one nucleotide earlier than being in frame) or to be in frame with one
SNV
right before the insert.
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2 Best explanations
Summary of evidence
Summary of evidence
No intermediate host found & No additional spillover
Evidence
The final origin report from the WHO indicated that no intermediate host was found despite extensive testing
Evidence
Many animals were found to carry SARS2, indicating constant monitoring that should be able to identify infections related to ancestral SARS2 strains
Best explanation
Small group of isolated infected animals
Best explanation
No intermediate host or additional spillover is expected
What is a Summary of Evidence?
The Summary of Evidence is a factual description of an Evidence group. It can itself be broken down into multiple Evidence or Claim cards. Evidence can be grouped together - forming an Evidence group - if they have the same Best Explanation.
No intermediate host found & No additional spillover
What is a conditional probability
These numbers are conditional probabilities. They are a measure of how likely is each best explanation given its respective hypothesis.
100%
Lab Leak
Min - Max
100% - 100%
25%
Zoonosis
Min - Max
25% - 25%
No animal was found to be infected with a virus related to an ancestral strain of SARS2, i.e. which is genetically closer to bat coronavirus than the early SARS2 strains.
No SARS2 outbreak in the world is believed to be a new introduction to humans, except for the first one in Wuhan in late 2019.
- This observation contrasts with previous viral outbreaks such as SARS-CoV-1, HIV, and MERS, where multiple spillover events were documented. Furthermore, when SARS-CoV-2 was transmitted to minks, multiple spillover events occurred from humans to minks, resulting in numerous mutations. Subsequently, the virus was transmitted back from minks to humans.
None of the millions of SARS2 sequences are phylogenetically distant from the Wuhan strains, suggesting that they are not a separate introduction event.
- There is a claim that lineages A and B were introduced separately, but this is contested. Additionally, both lineages were present in Wuhan simultaneously.
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2 Evidence
2 Best explanations
Summary of evidence
Summary of evidence
Behavior
Evidence
WIV confirmed RaTG13 as BtCoV/4991; important details omitted
Evidence
Disruption of the bat and rodent viruses database
Evidence
WIV scientists acted normally at the beginning of the pandemic
Evidence
The official Chinese response was not transparent
Evidence
No published contact tracing efforts
Evidence
Not sharing genomes
Evidence
No whistleblower
Evidence
No strong leaks / intelligence
Evidence
No known WIV infections
Best explanation
General mistrust and academic competition
Best explanation
Small group of people in the know covered it up
What is a Summary of Evidence?
The Summary of Evidence is a factual description of an Evidence group. It can itself be broken down into multiple Evidence or Claim cards. Evidence can be grouped together - forming an Evidence group - if they have the same Best Explanation.
Behavior
x1
Zoonosis
Min - Max
x1 - x1
x1
Lab Leak
Min - Max
x1 - x1
There is contrasting behavioral evidence: on the one hand, there is behavioral evidence pointing to zoonosis, such as:
-
The regular behavior of
WIV
workers at the beginning of the pandemic
-
Some missing expected evidence : the absence of leaks, the lack of strong intelligence, the lack of reliable information on infections among
WIV
laboratory workers
On the other hand, there is behavioral evidence suggesting lab leak:
-
WIV
suspicious behavior: not sharing databases during a pandemic and their strange behavior around
RaTG13
.
-
The behavior of the Chinese government, which was not transparent, severely restricted the WHO team, and did not publish contact tracing efforts.
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9 Evidence
2 Best explanations
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