Plotting the lineage percentages of new sequences each day over the past 6 months. Visualized using covidcg.org@CovidCg
Red = Alpha variant
Dark blue (outlined) = Delta variant
@CovidCg Under the blue wave of Delta which was first detected in the USA in Feb 2021, there is a green sliver indicating the newer AY.3 sublineage of Delta.
This means that almost all of the most recent USA sequences on the GISAID database are Delta.
New lineage percentages by day over the past 6 months.
Red = Alpha
Dark blue = Delta
Light blue = lineage R.1 (no greek letter)
@CovidCg Similar plots for India, same data from the past 6 months visualized two ways.
Left: new lineage % per day
Right: new lineage counts per day
Red = Alpha (B.1.1.7)
Pink = Kappa (B.1.617.1)
Dark blue = Delta (B.1.617.2) covidcg.org@CovidCg
@CovidCg Plots for Singapore.
Red = Alpha; Blue = Delta
Importantly, these numbers do not reflect actual case counts in each country.
The data plotted show the sequences from each country collected and shared with the GISAID database.
@CovidCg On the covidcg.org homepage you can track SARS-CoV-2 sequencing and sharing efforts by country.
Some of the countries sequencing many of their cases relative to case count are selected and shown here (dark blue bubbles).
@CovidCg The covidcg.org homepage also shows the rise and fall of lineages (variants) in each continent.
Right now the Delta is rising everywhere, but in South America, the Gamma (P.1) is still more prevalent.
@CovidCg For Canada, due to sampling pattern, it's better imo to split it into its provinces.
Let's start with Alberta. Covidcg.org allows users to select lineages of interest. For example, Gamma is shown in blue in one plot, and Alpha is shown in red in the next plot.
@CovidCg Not sure what happened to British Columbia, Canada but the last sequences shared with GISAID were collected on May 12, 2021.
Blue = Gamma (P.1)
Red = B.1.438.1
Pink (bottom, outlined) = B.1.2
Sliver of pink in the middle = Kappa (B.1.617.1)
@CovidCg Ontario has a strange sampling pattern where, if this is accurate, all sample sequences shared were collected from patients on the last day of each month. The sheer number of sequences shared by Ontario each month makes it better imo to analyze each Canadian province separately.
@CovidCg Another way to compare the Canadian provinces is using the Compare Locations feature in covidcg.org
Here the new Delta % per week is plotted for each province. In other words, each point shows what % of the virus sequences are Delta that week for each province.
@CovidCg The same plot for the seven US states with the most sequences shared on GISAID.
The % of SARS-CoV-2 sequences that are Delta each week is steadily rising across the board.
@CovidCg A similar plot for the same 7 states but this time showing the % of sequences that are Alpha over the past 6 months.
@CovidCg Another plot of the % of sequences that are from the B.1.2 lineage over the past 6 months.
B.1.2 used to be quite prevalent in some US states but was overtaken by Alpha, which has now been overtaken by Delta.
Going to stop with the rainbow plots for today.
The amazing thing is that covidcg.org@covidcg was built by and is actively maintained by only 2.5 (2 full-time, 1 part-time) brilliant & diligent individuals, leveraging data shared with GISAID. covidcg.org/?tab=acknowled…
@CovidCg The website's first year anniversary is coming up on Aug 26, 2021 and we'll have some super new features released by then.
I respect Dr Fauci's decades of service in gov. Being in charge during a pandemic is no small challenge & no one can lead for so long without making mistakes. However, it needs to be said that Dr Fauci has not surrounded himself with wise & honest people regarding #OriginOfCovid
These are the virologists & experts he trusted on #OriginOfCovid
In their private messages in early 2020, they mocked other virologists for not being able to predict their own lab leaks & misled a @nytimes journalist asking about a potential lab origin.
Dr Bob Garry admitted we don't know what viruses were studied in Wuhan labs. The papers he cited in support of natural #OriginOfCovid have been thoroughly refuted (see below).
A research-related #OriginOfCovid is plausible and even considered more likely by some experts and US intelligence agencies. goodjudgment.com/wp-content/upl…
Available data on early cases & market samples do not distinguish between a superspreader event versus spillover.
Even Dr Ralph Baric who collaborated with Wuhan scientists said the “market was a conduit for expansion of the disease. Is that where it started? I don’t think so.”
@COVIDSelect Baric said he forgot about the Defuse proposal & did not mention it at the Feb 1 call.
I believe Baric sharing Defuse would've prevented the publication of Proximal Origin and the use of it to dismiss a lab #OriginOfCovid in US gov and to the public.
@COVIDSelect Baric also could've told them at the Feb 1 meeting that novel SARS-like viruses were being used in infection experiments at BSL2 at the Wuhan Institute of Virology aka the Wild West according to Jeremy Farrar.
Peter Daszak, EcoHealth Alliance testified he didn't know Wuhan Institute of Virology bred 🦇, studied pangolin samples, engineered viruses without leaving a trace, and continued to collect viruses after 2015.
So how does he know they didn't cause Covid?
Daszak said he didn't know if WIV had started experiments described in the Defuse proposal and 🚨had not even asked them🚨.
He only had virus sequences from samples collected up to 2015. He believed that the WIV would've shared more sequences from 2016-2019 if they had them.
Reminder: EcoHealth Alliance still has not shared the sequences for the WIV's 220 SARS-CoV-1-like viruses (2022 interview) or 180 unique SARS-like viruses in their prior work not yet characterized for spillover potential (2018 proposal).
Those dismissing a lab #OriginOfCovid have had to make numerous concessions over the past 4 years.
We now know Wuhan scientists conducted risky experiments with novel SARS-like viruses at low biosafety & planned in 2018 to create viruses with the traits of the Covid-19 virus.
We also know the data on early cases & Huanan market shared by Chinese scientists do not shed light on #OriginOfCovid
Proponents of natural origin continue to argue that it is the totality of evidence that supports their hypothesis but this could be said for lab origin as well.
The latest defense for a natural #OriginOfCovid is that, if a lab leak had occurred, the Wuhan scientists would have acted all suspicious and essentially given the game away, thereby putting themselves, their colleagues & their families in immediate and deadly peril.
Freedom of speech is important in academia & science but difficult to navigate when it comes to politicized topics.
With #OriginOfCovid, some scientists, journals & reporters have competing interests & may be blamed if research they conducted, funded or glorified caused Covid.
On Tuesday’s hearing, chief editor of Science said the scientific community contributed to politicization of Covid & it was wrong to paint 'lab leak' as a conspiracy theory.
There was widespread consensus, Democrat or Republican, that #OriginOfCovid remains unresolved.
Several representatives asked for forward-facing solutions but none were presented. Today, the media continues to hang onto mistakes & politics of the past.
When confronted, many scientists or journalists who misled their peers & the public on #OriginOfCovid make no apologies.