The role of genomic sequencing in the COVID-19 pandemic

Monitoring of the COVID-19 pandemic has relied heavily on genomic sequencing, but experts warn more needs to be done to control the virus. 

Advances in genomics have allowed analysis of the pandemic on a previously unimaginable scale. As well as identifying new virus variants, SARS-CoV-2 genome sequencing has revealed the origin of new strains and even identified transmission chains from person to person.  

'Genomic epidemiology has come of age during this pandemic,' Professor Oliver Pybus, from the University of Oxford, told Nature. Professor Pybus himself recently published a study in the journal Science, where sequencing showed that the virus was imported over 1000 times prior to the first UK lockdown in March 2020 (see BioNews 1079).  

However, concerns are growing over significant gaps in SARS-CoV-2 genomic surveillance across the world. Last week the World Health Organization (WHO) convened to urge countries to ramp up the volume of SARS-CoV-2 genome sequencing, to help quickly identify and trace new – and potentially more dangerous – virus variants. 

While virus genome sequencing itself is relatively simple, establishing cohesive and consistent surveillance networks has proved more challenging for some countries than others. 

'It's very easy to sequence this viral genome: it's only 30,000 nucleotides, it's nothing,' said Dr Kári Stefánsson, CEO of deCODE Genetics in Reykjavik, Iceland. 

Iceland has to date sequenced all of its positive COVID-19 cases. Countries such as the UK and Denmark have also sequenced high proportions of samples, with the UK accounting for 45 percent of the over 360,000 publicly shared SARS-CoV-2 genome sequences. This has largely been thanks to pre-existing sequencing infrastructure, and the rapid establishment of the COVID-19 UK Genomics Consortium.

South Africa has developed a different approach. Despite limited resources, random sampling of only 50 to 100 virus genomes per week revealed the concerning 'N501Y' SARS-CoV-2 mutation. Speaking to Nature, Professor Tulio de Oliveira from the University of KwaZulu-Natal in Durban, South Africa, explained:

'What we did was not large numbers. It was a small number, but consistent and methodical.'

In contrast, in the US only 0.3 percent of COVID-19 cases have been sequenced – despite comprising over a quarter of total global infections. 

Joe Biden, then President-elect, admitted: 'We [the US] simply do not have the kind of robust surveillance capabilities that we need to track outbreaks and mutations,' and announced a boost in funding for SARS-CoV-2 genome sequencing. 

Without strong genomic surveillance networks, emerging SARS-CoV-2 strains could go undetected in some regions. At the WHO forum, epidemiologist and COVID-19 technical lead Dr Maria Van Kerkhove said: 

'We really need to expand this [genomic surveillance] so we have better eyes on the changes in this virus that are happening, especially in areas where transmission is most intense.'