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.
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.
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.
“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.
Internal CDC document cites "unpublished data from outbreak investigations and outside studies showing that vaccinated individuals infected with delta may be able to transmit the virus as easily as those who are unvaccinated." washingtonpost.com/health/2021/07…
"Even people who are vaccinated should wear masks indoors in communities with substantial viral spread or when in the presence of people who are particularly vulnerable to infection and illness, the CDC said."
"public trust in vaccines may be undermined when people experience or hear about breakthrough cases, especially after public health officials have described them as rare."
Leaders have to come up with a new protocol for emerging diseases: how scientists communicate vital info to the WHO and the public (important!), how peer reviewed confidentiality should be waived in these crises, and how to keep these systems accountable. dailymail.co.uk/news/article-9…
What I’m worried about is that this pandemic will drive leaders and scientists in the opposite direction towards less transparency.
What if more scientists start using Protonmail, Signal, and burner phones for future communications regarding emergencies?
The recent FOIAs revealing highly confidential conversations (or redactions) are likely to cause more people to shift to secure, non-FOI’able channels.
If so, this may be the one of the last pandemics/outbreaks we can shed much light on via FOIA.