Sequencing new strains: the United States is making efforts to catch up

The emergence of new SARS-CoV-2 variants of concern in recent months has highlighted the shortcomings of the United States in terms of monitoring these variants: more than 30 countries sequence more strains than the Americans. The more strains are sequenced, the more it is possible to follow, to understand and to anticipate the emergence of variants. In order to reinforce their surveillance, the Biden administration has increased investment in sequencing, in analysis and in improving institutions to enable them to provide more coherent and effective answers. But how exactly can these objectives be attained?

• Firstly, there is already an existing network of 130 laboratories in the country that support current genomic surveillance. These laboratories carry out high throughput sequencing, notably to monitor seasonal flu. However, these laboratories have recently been hit by severe cuts in budget and personnel. Supplementary funds are therefore necessary for investment in new technologies and infrastructure, but also to train professionals to work with these innovatory technologies.
• Funding is also indispensable for analysing the collected data and in particular for constructing and maintaining a data base of viral sequences and associated clinical data that will be nationally accessible. Currently, the data submitted by the sequencing laboratories is generally on restricted or even non-shared databases.
• Finally, the different systems of monitoring infectious diseases in the United States are relatively independent and separate. It would therefore be useful to put a new, more flexible surveillance structure into operation for monitoring pathogens, with improvements in co-operation between public health agencies and academic medicine.

The emergence of variants of concern has revealed shortcomings in genomic surveillance systems in the United States, as in other countries. The new anticipated investment will be an opportunity to redesign the system to make it more coherent and efficient, even though this challenge will not be easily met by the American authorities.