If anyone needs a good 😂 this is the figure from the China-WHO report showing the home address of covid-19 cases from Dec 11, 2019 or earlier.

A team of scientists, unable to access early case data, had no choice but to extract information from this fig using Adobe Illustrator.
Problematically, despite being already of such low resolution, the map still has 'unintended errors' as revealed by @washingtonpost
washingtonpost.com/world/asia_pac…
These errors are shown here in a diagram made by @InWuchang
I think it's important for @WHO to either put a huge warning label on their #OriginsOfCovid Report and Annex, or to take these down until corrections are made - before more scientists are misled by these unintended errors.
who.int/docs/default-s…
At the bare minimum, the authors of this Lancet study should be consulted to match their 41 lab-confirmed covid cases (Dec 2019-Jan 2, 2020) to this map - can it be done?
ncbi.nlm.nih.gov/pmc/articles/P…
Who is this person and which district did they live in? “The symptom onset date of the first patient identified was Dec 1, 2019. None of his family members developed fever or any respiratory symptoms. No epidemiological link was found between the first patient and later cases.”
We can see from the Lancet study that these 41 cases were most likely the tip of the iceberg even in Dec 2019. Large portion of the patients were in ICU even if young, not many cases below 25 years of age.

Earliest cases no link to the Huanan seafood market.
I think it’s useful to consult other maps of covid-19 cases even if these cover more Jan 2020 cases… why do these show greater case density in the district where the Huanan market wasn’t located but the WIV campus was?
That being said, I think over-reliance on a map of early cases by home address (especially one that cannot be independently reproduced due to lack of access to data) can mislead the search for the origin of Covid-19. ayjchan.medium.com/a-response-to-…
The early covid-19 case map from WHO (left) looks strikingly similar to the distribution of general population & elderly in Wuhan (right).

My bet is they were only seeing the worst Dec 2019 cases - making sense these map to most crowded parts of the city with the most elderly.
We also know from the China-WHO report that the criteria by which early cases had been identified suffered from ascertainment biases (Annex E3).

Exposure to the Huanan market was one of the key factors in determining whether a patient was a suspected case of Covid-19.
To be a suspected case you had to have at least two clinical manifestations, i.e., fever, (pulmonary) imaging characteristic of pneumonia, reduction in WBC/lymphocyte, or no improvement in response to three days of antibiotics.

I’d say this skews towards elderly cases.
Previous examples of natural spillovers and lab-acquired infections illustrate the importance of tracking down the earliest patients and identifying their exposures to various possible sources of the pathogen.

In a city, home address almost has no bearing on tracking origin.
For example, a Beijing researcher who was accidentally infected with SARS-CoV in 2004 was not actually the first case in the cluster to be diagnosed; a nurse that had treated the researcher was the first diagnosed…

Would the nurse’s home address be useful?
Furthermore, the researcher had traveled long distances via train across China while symptomatic. Another three researchers at the same institute were later found to have been separately infected with SARS-CoV.

Would all of their home addresses in Beijing be useful?
What matters is interviewing the early cases, getting their occupations and history of activities/exposures running up to when symptoms appeared. If the patients are not available, the doctors who tracked their cases (and blew the whistle) should be consulted.

Has this happened?

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More from @Ayjchan

9 Aug
On the question of whether covid-19 might’ve come from Europe.

TLDR it didn’t.
Also this is really how peer review should work. Open, honest and fair criticism of preprinted/published work. Now everyone can see what problems each study suffers from and decide for themselves whether they think the conclusions are well supported. Expertise is being shared.
On studies pointing to covid appearing in Europe earlier than Dec 2019, many somehow detect later variants (D614G) rather than the earliest form of SARS2.

This requires a virus endemic to South China/SE Asia to not only be able to time travel but also teleport across continents.
Read 9 tweets
8 Aug
Question for epidemiologists: in your field, is it acceptable to reverse engineer data out of a figure (left) using Illustrator to generate a nicer version (right) for your paper?

Sources:
who.int/docs/default-s…

zenodo.org/record/5075888… ImageImage
The original data cannot be accessed, legend is blurred out, the map itself is highly pixelated.

But would it be better to copy the original figure into one's new paper (with attribution) alongside the reverse-engineered figure so that readers are aware of the 'data' quality?
The authors do clarify in their supplementary (but not main text) that data loss occurred during reverse engineering:

"Map data was manually extracted from Fig 17.. using Adobe Illustrator. Because of multiple overlapping points there will be errors in the extraction process."
Read 4 tweets
7 Aug
I'm seeing a lot of confusion about this recent @CNN story about "reams of genetic data from Wuhan lab".

Nothing in the article specifies that this is the WIV pathogen database. It could just as likely be raw data deposited into public databases.

cnn.com/2021/08/05/pol…
(1) "genetic blueprints drawn from virus samples studied at the lab in Wuhan"

No time range specified. Could've even been post-covid.

No lab specified either. Could be just Wuhan labs in general.
(2) "the machines involved in creating and processing this kind of genetic data from viruses are typically connected to external cloud-based servers"

With the WIV pathogen database, it is unclear how many samples were sent for NGS, but my guess would be not a large %.
Read 7 tweets
6 Aug
I really like the idea of re-routing viral traffic, put forth by virologist Stephen Morse.

Natural routes of viral traffic continue to exist and be amplified. But new routes of viral traffic, related to research activity, have emerged in the modern era...
noemamag.com/the-routes-of-…
One early example of a novel pathogen emerging due to research activity is Marburg virus, "first recognized in 1967, when outbreaks of hemorrhagic fever occurred simultaneously in laboratories in Marburg and Frankfurt, Germany and in Belgrade, Yugoslavia"
cdc.gov/vhf/marburg/in…
And that was generations ago.

Today, we can go from a virus sample to a genome sequence in a few days, and from a genome sequence to a completely synthetic perfect (seamless) copy of that genome in a matter of weeks.
Read 5 tweets
31 Jul
Would be good to track the 2000+ individuals (all adults vaccinated) from this cruise who are disembarking in the Bahamas tomorrow and see how many test positive for Covid-19 over the next 2 weeks. usatoday.com/story/travel/c…
There are many things we don’t know *yet* about the delta variants and vaccines:

How much do our vaccines protect against infection, asymptomatic or symptomatic, by delta?

How much do infected vaxed individuals spread the virus compared to infected non-vaxed individuals?
We do know that several top vaccines continue to protect against severe covid-19. So it’s not particularly worrying when vaxed people get delta (although there are exceptions and some breakthrough cases suffer greatly). What’s worrying is the spread of delta to the unvaxed.
Read 7 tweets
30 Jul
NIH explained to Senator Grassley how NIH-funded SARS/MERS-like chimeric CoV work at WIV had not been determined to meet USG criteria for GOFROC covered by federal funding pause or P3CO Framework.

But more interesting than the ⚔️ on GOF definitions is…
grassley.senate.gov/imo/media/doc/…
“during the course of the grant, the grantee proposed to place a small portion of the newly identified bat coronaviruses into a larger portion of MERS-CoV to understand the potential origins of MERS-CoV in bats.. conducted at WIV”

Can this proposal pls be shared with the public?
Another question: Did NIH-funded WIV work turn out to be “instrumental to the unprecedented rapid development of vaccines, therapeutics, and diagnostics to address the COVID-19 pandemic”?

Important for this to be substantiated with data since similar work continues to be funded.
Read 7 tweets

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