The Omicron variant: More Genome Screening for Covid-19 Is Needed


Health officials announced on December 1 that the Omicron variant of Coronavirus has spread to more than 20 countries already. Scientists call the variant B.1.1.529 after a traveller who returned from South Africa infected the state.

During a White House press conference on Wednesday, Anthony Fauci, head of the National Institute of Allergy and Infectious Disease, said the individual was fully vaccinated and was experiencing mild symptoms, which are improving. This is the first confirmed case of Covid-19 in the United States caused by the Omicron variant.

Omicron might be more transmissible than other versions of the virus, and its arrival makes genome sequencing more urgent. Scientists can distinguish the various strains of SARS-CoV-2, the coronavirus that causes Covid-19, by examining their genes. Some of the traits that set it apart can be traced back to its origin. In some cases, they can predict how readily it will spread or how easily it will evade our immune system.

Kristian Andersen, a professor of immunology and microbiology at Scripps Research Institute in California, says the US has gotten way better at this kind of detective work. The country is still using ad hoc labs, so it’s hard for scientists to sequence genomes quickly and publish results. Even our own operation here in San Diego is still hacked together, Andersen said.

It is still rare for SARS-CoV-2 genes to be sequenced in some parts of the world. Those blank spaces may contain variants of the virus that are more dangerous. Because of this, scientists say the search for the next variant should not be limited to countries with the most resources and labs, such as the US. Wealthier countries are being urged not only to distribute Covid-19 vaccines and treatments, but also to increase viral sequencing around the globe.

Genome surveillance is why we know about the omicron variant at all

Omicron’s origins are still unknown, and we don’t know how it spread across the world. But it demonstrated the speed at which viruses can spread undetected.

The newly detected variant was detected in late November in South Africa and Botswana. Based on the number of cases detected, it may have been circulating in those countries for weeks. Belgium, Germany, and the Netherlands later reported that the omicron variant may have already been in Europe before South Africa and Botswana raised the alarm.

The fact that South Africa discovered it is no accident. The variant is more prevalent in South Africa than Europe – the higher the prevalence, the more likely it is to be detected, Andersen said. Nevertheless, South Africa’s surveillance is excellent, better than most other countries.”

According to California Gov. Gavin Newsom, genetic surveillance might explain why omicron was found in California first. California announcing the first case is not surprising in many ways, Newsom said at a press conference on Wednesday. He said the University of California San Francisco is one of the world’s leading genomic sequencing institutions.

Detecting new variants as they start to spread is a massive scientific and logistical challenge. Scientists and health officials often have to sequence the entire set of genes — the genome — that codes for the Coronavirus in a sample, a process that’s far more expensive and complicated than simply testing whether people are infected. SARS-CoV-2’s genome is about 30,000 base pairs long and codes for 29 proteins.

Researchers then look for telltale mutations that reveal the presence of a variant. (Some conventional Covid-19 PCR tests can also be tweaked to sort between different variants, but that requires a more sophisticated screening system.)

Companies say their current vaccine formulations still appear to be effective despite genetic data helping them tailor their immunizations to omicron. Travel restrictions from African countries followed the announcement of the variants, which scientists worry may discourage countries from reporting future variants. Information sharing globally is the most effective way to stay ahead of new mutations.

Genetic surveillance has been difficult for many countries to keep up with. Resources and money are often the problem. Additionally, the US has been criticized for not doing enough genome sequencing to stay ahead of new strains that emerged earlier this year. In January, Diane Griffin, a microbiologist at Johns Hopkins, told Vox that it was embarrassing.

The US has since stepped up its genetic surveillance of SARS-CoV-2, bolstered by an influx of more than $1 billion to the Centers for Disease Control and Prevention, city health departments, and state governments to identify the specific variants of the virus in circulation. Officials also invested in creating reporting systems for SARS-CoV-2 genomes. US government labs this year have more than doubled their rate of genome sequencing. Private labs and academic institutions have also chipped in.

US labs are now sequencing and reporting 29 genomes for every 1,000 Covid-19 cases detected, about 20,000 per week, which puts the US among the top 20 countries in the world. “We have very few blind spots in the US as a result of this,” Anderson told Vox.

Still, it takes the US a median time of 28 days to sequence these genomes and upload the results to international databases. Contrast that with the United Kingdom, which sequences 112 genomes per 1,000 cases, taking a median of 10 days to deposit their results. A delay of only a few days in detection can give variants time to silently spread within communities and across borders.

Massive gaps in Covid-19 genetic sequencing leave the world vulnerable to variants

The US and other wealthy countries are far ahead of the US and other large parts of the world in genome sequencing. Alina Chan, a molecular biologist at the Broad Institute, said in an email, “This means there is a delay in detecting and reporting novel variants in regions with low levels of sequencing and data sharing.”

Map of SARS-CoV-2 sequencing rates around the world.





Countries like the US are sequencing many more genomes of the SARS-CoV-2 virus than much of the rest of the world. That leaves openings for new Covid-19 variants to emerge undetected.


Other mutations in the SARS-CoV-2 virus may remain undetected due to shortfalls in genome sequencing in South America, Africa, and Asia. Whole-genome sequencing requires time and resources, it must also be balanced with other public health needs. The amount of money and lab capacity is limited in a pandemic, so health officials have to weigh testing, treatment, and vaccination against genetic surveillance.

“We can’t sequence every single person who tests positive,” says Emma Hodcroft, a molecular epidemiologist at the University of Bern. We’ll miss things like low-level circulating viruses.

Hodcroft and Andersen said the ideal benchmark would be to sequence 5 percent to 10 percent of the genomes in positive Covid-19 cases around the world. Yet, they admitted that this would be tough for countries with fewer resources. “Even getting a sequencing machine to a lot of these countries is a nightmare,” Hodcroft said. “We haven’t done a whole lot in this pandemic to support more global sequencing surveillance.”

Developing countries should also set up more genetic surveillance and reporting laboratories around the world in addition to sharing vaccines and tests for Covid-19 with developed countries. If not, another variant could emerge and undo some of the hard-fought progress against the virus.