Read on Twitter
1/15 COMPARATIVE "GENOMIC EFFICIENCY" OF COUNTRIES
Here are some quick and dirty graphs based on counts of genomes from GISAID, and population and GDP from Wikipedia. Here are the tables (sorry in advance for how messy it is): https://docs.google.com/spreadsheets/d/1Me5TUc_Wb5DrqXdvJsypFBUuHnwjQFAFFT2sBqtj24k/edit?usp=sharing
Here are some quick and dirty graphs based on counts of genomes from GISAID, and population and GDP from Wikipedia. Here are the tables (sorry in advance for how messy it is): https://docs.google.com/spreadsheets/d/1Me5TUc_Wb5DrqXdvJsypFBUuHnwjQFAFFT2sBqtj24k/edit?usp=sharing
2/ Out of all the graphs, the most interesting to me is the ranking of countries based on genomes/GDP. Let's take a look at the top 10.
3/ The UK tops all charts: in terms of absolute number of genomes (almost half in this list), genomes/population and genomes/GDP. Which means that they are leaders not only because of the size of their economy.
4/ This is what the genomic pathogen surveillance of all countries could look like given enough sequenced genomes (below I share why I think this is now possible) https://twitter.com/CovidGenomicsUK/status/1261305060702728197
5/ What is the reason for UK's leadership in genomics? The best source I could find is this 2015 report for @UK_Life_Science https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/464088/BIS-15-543-genomics-in-the-UK.pdf
A nice summary of the history of genomics. Note the establishment of @wellcometrust @sangerinstitute @emblebi @GenomicsEngland
A nice summary of the history of genomics. Note the establishment of @wellcometrust @sangerinstitute @emblebi @GenomicsEngland
6/ Congo has 133 SARS-CoV-2 genomes in GISAID. But this is extraordinarily high considering their GDP (rank#85). Perhaps the Ebola outbreaks in the past has prepared Congo with the personnel, training and sequencing machines to produce these genomes. https://twitter.com/cobbo3/status/1251943323704705035
7/ Another African country in the top 10 is Kenya. Their GDP is about double that of DRC and they have 112 SARS-CoV-2 genomes in GISAID. But this is still quite extraordinary. I wonder what they did right. https://twitter.com/george_l/status/1267895040782761987
8/ The only Asian in this list is SG. I visited last year and talked to a number of scientists in the genomics space. In their case, it appears that the prime mover is the government and its heavy investment in genomics, particularly for cancer research. https://twitter.com/NiranjanTW/status/1065495501196292096
9/ Portugal, Denmark, the Netherlands, Belgium, Australia and New Zealand are developed countries and have the means to conduct large scale sequencing. I still wonder what made them perform better than other developed countries.
10/ I'm even more interested in the bottom of this list. These are the countries that have less than 10 SARS-CoV-2 genomes in GISAID. These countries have a total of 1B people and they have less than 20 SARS-CoV-2 genomes in GISAID.
11/ Here is "How (developed) countries are using genomics to help avoid a second coronavirus wave" https://www.nature.com/articles/d41586-020-01573-5
How could we democratize access to genetic sequencing, especially given the high likelihood that future epidemics will originate from developing countries?
How could we democratize access to genetic sequencing, especially given the high likelihood that future epidemics will originate from developing countries?
12/ Consistent with the genomics leadership of the UK, the innovation that could bring genomic pathogen surveillance to the developing world is @nanopore
I'd like to suggest an alternative tagline for ONT: The People's Sequencer
I'd like to suggest an alternative tagline for ONT: The People's Sequencer
13/ Multiple scientists have shown its feasibility in developing countries. For RABV, @kirstynbrunker et al showed that cost per sequence could be as low as ~£35 to £45. Here's my list of lab-in-suitcase papers: https://scrapbox.io/kahlil/lab-in-suitcase_papers
14/ There are still a number of challenges. The cost and the logistical difficulty of bringing in reagents is perhaps the biggest one. Training in library preparation and bioinformatics will also be a challenge (though I'm hopeful solutions like @BugSeq could ease this).
15/ These problems appear quite solvable to me. Am I naive to think that these could be overcome with project execution, 3rd world street smarts and grit?
This is why we are hopeful with our @JustOneGiantLab project: https://app.jogl.io/project/285
DM me if you want to join the team!
This is why we are hopeful with our @JustOneGiantLab project: https://app.jogl.io/project/285
DM me if you want to join the team!
P.S. If you want to learn more about this project, you might want to join the project management training I'm giving on the 15th of June. The first part will be an explanation of the JOGL project https://twitter.com/kcorazo/status/1270887828323368960
P.P.S. Iceland turns out to be the most genomically (did I just invent a word?) efficient in terms of genomes/GDP! Could I have missed other smaller superstars? h/t @kristjanmoore https://twitter.com/kcorazo/status/1271069772206075904
P.P.P.S. deCODE in Iceland is a pretty interesting case study h/t @kevinpurcell https://twitter.com/kcorazo/status/1271348461053644801
