Covid has revealed the need for genomic sequencing around the world
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The writer, a Nobel laureate in physiology or medicine, chairs the WHO Science Council
The rapid spread of the Delta variant of Sars-Cov-2 has dashed hopes that the pandemic might soon be over. It has also raised the prospect that yet more dangerous variants, including those impervious to vaccines or prior infections, might arise.
While we lack complete knowledge of how the most dangerous variants of Sars-Cov-2 are generated, we do know that these emerge through mutations to the genome that occur when the virus replicates. Such mutations are more likely to arise in immune-compromised individuals in whom the virus can replicate repeatedly for extended periods. Variants of special concern are those that infect cells more efficiently or evade immune responses.
As long as the virus is spreading as widely as it is now — particularly in unvaccinated populations found both in wealthy countries with abundant vaccine and in low- and middle-income countries where vaccines are very limited — a substantial fraction of infected individuals needs to be monitored for viral variants. This cannot be done with the two widely available tests — through the polymerase chain reaction or an antibody test — since these tests are not designed to detect mutations. Instead, genome sequencing, performed by machines that can quickly read the order of the four chemical elements that compose viral genomes, must be used to identify mutations, followed by studies to determine whether any are responsible for changes in the behaviour of the virus.
The consequences of mutations may be dire, but they are difficult to predict from the genomic sequence alone and must be inferred. For example, if a variant is found more and more often among individuals in one area, it implies higher infectivity, while more severe disease implies greater pathogenicity. Infection of vaccinated and unvaccinated people at similar rates means that it can evade immune responses — an especially worrying development.
To uncover such critical information, it is essential to sequence viral genomes from infected individuals anywhere the virus is spreading; to correlate genome sequences with vaccination status, clinical findings and health outcomes; and to share the information efficiently, openly, and fairly.
Earlier this year, a new Science Council was convened by the World Health Organization in order to advise on technologies that should be used to improve global health. The council, which I chair, settled on the broad field of medical genomics as our first long-term target. The sequencing of human and microbial genomes has recently improved the diagnosis, treatment and prevention of disease in wealthier countries, but has been slowly adopted, if at all, in low- and middle-income countries.
Ensuring the responsible practice of genomics in all parts of the world — including countries with little technology or trained personnel, and dysfunctional governance — will not be easy and will require international assistance from multiple sources. The WHO cannot afford to do the technical work on its own. Relatively rich countries and well-endowed foundations must act, whether from generosity or self-interest, to expand genomics and information exchange. There are strong precedents for such actions, for example, the President’s Emergency Plan for Aids Relief allowed the US to reverse the devastating course of HIV/Aids in many poor countries, especially in Africa.
The benefits of such investments would not be limited to Sars-Cov-2. Establishing a technological “beachhead” could be a prelude to sustained growth of genomic capacities that improve medical care and public health more generally. It could foster research in many fields, such as in agricultural productivity, and endow other enterprises, such as biotechnology, with economic and cultural value. In this way, the pandemic could become more than a crisis: it is an opportunity to advance global health.