Comparative SARS-CoV-2 Sequencing Performance of 72 Countries (Part III)

By Kahlil Corazo

Highlights

GISAID.org just reached 2 Million SARS-CoV-2 genomes. More than a year after the pandemic started, the USA has overtaken the UK in terms of the number of SARS-CoV-2 genomes shared. The US and the UK combined still represent more than 50% of the shared genomes. However, eight countries still have less than 100 genomes in GISAID. Three have 0.

Denmark still leads in terms of genomes per capita, followed by Iceland, then the UK. For Denmark and Iceland, it appears that it only took one lab to make a difference.

Some countries have made huge strides. In June 2020, there were 38 countries with less than 100 genomes shared. Now, there are only eight. My country, the Philippines, went from 17 SARS-CoV-2 genomes to 4,307 🎉.

Figure 1.

Figure 2.

Background

This is the third time I've reported SARS-CoV-2 upload numbers in GISAID. The first two were Twitter threads:

• 1/15 COMPARATIVE "GENOMIC EFFICIENCY" OF COUNTRIES (June 11th, 2020)
• 1/ You've heard of the mutation. But how about this? (December 23rd, 2020)

Here are my assumptions:

• The ability to sequence pathogens is indicative of a country's resources to fight a pandemic.
• The willingness to share those sequences is indicative of a country's openness to the global science community.
• The number of SARS-CoV-2 genomes shared in GISAID, especially genomes per capita, is a good indicator of both.

The report gave us an idea on which countries we should focus on for Project Accessible Genomics.

Here's the spreadsheet I used. I manually reported the numbers (using country search). I don't have the chops, the bandwidth and the computing power to create reports straight from the database. I only included the 50 countries with the highest population plus the 50 countries with the highest GDP. Some of the graphs below are from a report created by Keith Robison of OmicsOmicsBlog, which has numbers up to March 2021. Here's the spreadsheet I used for that. If you are viewing those spreadsheets, apologies in advance for how messy they are.

For a background on the importance of sequencing and sharing data to fight this pandemic and future outbreaks, here's a nice article by Time.com: ​What We Learned About Genetic Sequencing During COVID-19 Could Revolutionize Public Health.

Okay, let's make some graphs!

Absolute counts

Figure 3. SARS-CoV-2 genomes per country in GISAID as of June, 2020.

Figure 4. SARS-CoV-2 genomes per country in GISAID as of December, 2020

Figure 5. SARS-CoV-2 genomes per country in GISAID as of June, 2021

Figure 6. SARS-CoV-2 genomes shared per month (>10k, log scale)

Most improved countries

Figure 7. Countries with less than 100 in June 2020 and more than 1000 by June 2021

26 countries with less than 1,000 genomes shared

Figure 8. Countries with less than 1,000 SARS-CoV-2 genomes in GISAID as of June 25, 2021

Genomes per capita

Team accessible genomics got to do a Q&A with Albertsen Lab, which is the reason why Denmark has the highest genomes per capita. Here's the recording: www.youtube.com/watch?v=HTV9BIxmFtk

In Iceland's case, it is probably also because of one lab (I have not confirmed this). While Albertesen Lab is an academic lab, Iceland's deCODE, a commercial genomics company (a subsidiary of Amgen).

The UK's leadership is probably due to its heavy investment in genomics in the 2000s' see twitter.com/kcorazo/status/1271010623544004608

Figure 9. Top 10 in terms of genomes/population as of June, 2021.

Figure 11. countries ranked by genomes/population

Figure 12. Bubble chart of genomes/population (size), genomes shared, and population.