On Singapore’s recent delta variant covid cluster: “The cluster’s index case, Case 62873, is an 88-year-old cleaner who worked at Changi Airport Terminal 3. He tested positive on May 5 despite being fully vaccinated.” channelnewsasia.com/news/singapore…
Another delta cluster in Singapore at a hospital: “A fully vaccinated 46-year-old female nurse at TTSH, or case 62541, became the first case linked to the cluster after she tested positive on Apr 27.”
“In the Delta variant clusters, Prof Leo has seen vaccinated cases with family members who have tested positive. This means it could still be possible for vaccinated people to spread the virus.”
“The experts stressed that new variant strains arise when viruses evolve to adapt and evade human defences”
“Disorganised, half-hearted attempts are exactly the prescription for viral mutants.”
Singapore’s tracking of covid cases is incredible. It’s only when you can clearly follow the chains of transmission that you can understand whether a new variant can infect and be spread by vaccinated individuals (only Pfizer and Moderna in Singapore btw).
The good thing is that full vaccination still confers protection against new variants, even if efficacy is slightly reduced. So it’s very important for people in high risk groups to get vaccinated, especially in places where there are low vax rates and new variants circulating.
For example, did any of the fully vaccinated airport workers who still got infected with the Delta end up transmitting it to other people?
@romeo_ph20 Looking at the Bukit Merah market cluster, you can see (if the data is indeed correct) that some vaccinated people are transmitting covid / SARS2 to other people.
Green = fully vaccinated (pfizer/moderna)
Yellow = 1 dose
The selected (blue) vaccinated person is 23 years old.
@romeo_ph20 The selected vaccinated person in this cluster is 39 years old. A chef working at Changi prison.
36 year old dealer at Marina Bays Sands Casino
18 year old national service man at the Civil Defence Academy
The site also tells you who was asymptomatic or symptomatic when they tested positive for covid-19.
For example, in this mini-cluster of 3 fully vaccinated people, the connector person was asymptomatic.
The purpose of getting vaccinated is preventing severe disease/death. And when your community has high vaccination rates, the likelihood of clusters is diminished. This protects the elderly/vulnerable who may not be fully protected even after vaccination.
This Covid-tracking app in Singapore is super useful for understanding how transmissible the virus is among vaccinated individuals.
Green = 2 doses
Yellow = 1 dose
The central person is 35 years old. This looks like a workplace cluster. 3 fully vaxed people transmitted to others.
I'm not too worried about vax'ed people being infected because ideally the vaccine would've protective effect. But I'm worried about the people who distrust the healthcare system and refuse to get vax'ed. The virus can spread via vax'ed people. covid.viz.sg
Wanted to give a shoutout to our own site @CovidCgcovidcg.org you can track the lineages and variants in each country over time.
In the USA you can see the % of sequenced SARS-CoV-2 that are the delta / B.1.617.2 / Indian (light blue) have also been growing, displacing the alpha / B.1.1.7 / UK (dark blue) over time. Gamma / P.1 / Brazilian is in green.
Not as striking as the UK. Delta has completely overtaken Alpha.
Plotting similar data for other countries, but measured in counts (like for Singapore above) as opposed to % (US and UK above).
Australia, Japan, S Korea, S Africa.
Another way to use covidcg.org is to plot the new % of sequences that are delta variant per month in each country of interest.
For example, in Singapore, 94% of the June sequences were the delta variant. UK 92%, Australia 60%, Japan 46%, USA 23% etc.
Switching the plot to show the new % of sequences that are the alpha variant per month.
The beta variant.
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Regarding the possibility that Covid may have spread at the Oct 2019 Wuhan military games, my main question is why noone across multiple countries had the presence of mind to collect & store samples from patients till tests were available.
There should be changes going forward.
According to Under Secretary of Defense for Personnel and Readiness: "Service members were not tested... as testing was not available at this early stage of the pandemic." freebeacon.com/wp-content/upl…
"athletes noticed that something was amiss in the city of Wuhan.. described it as a “ghost town.”"
"athletes from several countries.. claimed publicly they had contracted what they believed to be covid.. based on their symptoms and how their illnesses spread to their loved ones" washingtonpost.com/opinions/2021/…
I encourage experts who have insisted on a natural origin of Covid-19 to gracefully change their public stance instead of doubling down on the threadbare evidence for the wet market hypothesis.
You could acknowledge that you initially trusted your colleagues in China/US to tell the truth. But time and time again over the past 5 years, it has been shown that they withheld critical evidence from you and the public:
1⃣The 2018 Defuse proposal
2⃣Low biosafety standards for experiments where live viruses are produced and used in human cell infection studies
3⃣Risky pathogen experiments and surprising gain of function
4⃣Missing pathogen sample database, viruses discovered after 2015 largely not shared with US collaborators
5⃣Closest virus relative that we know of was collected from a mine where people died from suspected SARS-like virus infection
The studies published last month where Wuhan scientists experimented with potentially dangerous pathogens at low biosafety opened your eyes to the level of reckless ambition in their research.
Given these betrayals, it is fully within reason to retract your trust and re-evaluate all the available evidence. Those of you who have access to intelligence could say that the non-public evidence has cast a new light on the public evidence and strengthens the case for a lab origin of Covid-19.
This is better than continuing to argue that you somehow know all the viruses in the Wuhan lab's collection and somehow know they didn't follow through on their 2018 plans to put furin cleavage sites into SARS-like viruses and study these at low biosafety exactly like they said they would.
For those experts who haven't even looked at the Defuse proposal and its drafts, the Wuhan-US scientists clearly said they were interested in furin cleavage sites at the spike S1/S2 junction, and would insert these into novel SARS-like viruses in the lab (not closely related to the 2003 SARS virus as that would be dangerous). They would test the ability of these SARS-like viruses with inserted cleavage sites to infect human cells and cause pathogenesis in vivo.
The Wuhan lab was regularly synthesizing novel coronavirus genomes without leaving any sign of lab manipulation. They used a protocol with trypsin-supplemented media to retain cleavage sites in the viruses. They did much of the work, including infection experiments in human cells, at BSL-2. Their US collaborator Ralph Baric has repeatedly criticized them for doing the work at low biosafety.
h/t @emilyakopp for FOIA'ing the Defuse proposal drafts.
Some virologists may argue that the furin cleavage site in SARS-CoV-2 doesn't look canonical. You should read the citation in the Defuse draft for the computational model used to predict furin cleavage sites. The paper says it doesn't rely on the canonical motif and instead looks at a 20-residue sequence to make its predictions. The PRRAR motif exists in a feline coronavirus, MERS has a PRXXR S1/S2 furin cleavage site, and the RRXR motif is a functional furin cleavage site in numerous other proteins.
According to Zeit Online, German Chancellery consulted with US Director of National Intelligence in 2023, who said there was nothing to the lab leak hypothesis.
They doubted "Eierköpfe" (egghead) scientists in intelligence knew better than leading virologists around the world.
In the US, something similar was happening where scientists in intelligence agencies also assessed a likely lab origin of Covid but were sidelined.
"The dominant view within the intelligence community was clear when... the director of national intelligence, and a couple of her senior analysts, briefed Biden... concluded with “low confidence” that Covid-19 had emerged when the virus leapt from an animal to a human." wsj.com/politics/natio…
In both cases, government leaders favored the opinions of leading virologists over the scientists working in intelligence. Even though some of the leading virologists were public advocates and funders of "gain-of-function" research of concern with pathogens.
I am not 100% convinced Covid came from a lab. I still think there is a small chance the virus emerged in Wuhan without the help of research activities. However, this would mean:
1⃣ The Wuhan-US scientists' entire framework about the spillover risks of SARS-like viruses, building on research and data collected over more than a decade, was incorrect.
2⃣ A highly transmissible, super stealthy virus well adapted for causing uncontrollable outbreaks in multiple animal species left zero trace of its origin in the wildlife or fur farms of China/SE Asia after emerging in only Wuhan out of 1000s of other populous cities.
3⃣ Out of all possible viruses to cause a pandemic and all times for a pandemic to occur, it was an unprecedented SARS-like virus with a novel furin cleavage site, matching the description of a 2018 US-Wuhan research proposal, emerging in Wuhan where scientists worked with such viruses at low biosafety, less than 2 years after said proposal was drafted.
It's not impossible that leading experts were completely mistaken about the exceedingly low odds of such viruses emerging in Wuhan.
It's not impossible that, in 2019, nature churned out a virus matching the scientists' 2018 research plans and that virus emerged in only Wuhan of all places.
But you'd have to be very motivated to believe Covid-19 emerged naturally.
We are unlikely to reach 100% certainty unless a whistleblower appears or the Chinese authorities one day assess that it is in their interest to share the truth.
I am still hopeful that this will happen one day. I believe in human courage.
Before that day, there are several routes of investigation that remain to be explored by the US gov.
Conducting a rigorous, credible investigation of Covid origins can unearth more key evidence while also informing the implementation of new measures to prevent lab pandemics.
Top journals have the power to set global biosafety standards.
It's a problem that they do not see this as their moral responsibility. By publishing & celebrating risky research done at questionable biosafety, they incentivize the 'work fast break things' model of research.
I've given up on journals taking the initiative to be responsible members of the scientific community.
It is up to the U.S. government to tell them to behave responsibly or do business elsewhere.
I would love to be corrected if any top journal can show us that fostering a culture of accountability, scientific integrity, and 'do no harm' is one of their measurable goals as an organization & a strict criteria for decision-making regarding what research/groups to publish.