Why The U.S. Needs To Step Up Covid-19 Genome Sequencing


SAN FRANCISCO, CA – JAN. 5: UCSF-Abbott Viral Diagnostics and Discovery Center lab director Dr. Charles Chiu demonstrates how to use the Illumina NextSeq550 sequencer used to read sequences of the COVID-19 virus in his lab in San Francisco, Calif.


The United Kingdom and South Africa discovered new SARS-CoV-2 variants in their domestic Covid-19 cases. The variants were found using genome sequencing techniques that analyze the structure of the virus and discern mutations. These genome sequencing techniques were regularly used worldwide at the start of the pandemic when we knew less about the virus, but they have since fallen by the wayside. The US and other countries should follow the UK and South Africa’s footsteps in terms of revamped genome sequencing regimes, as the next variant may be hiding in our backyard.

Genome sequencing is essentially determining the order of chemical “bases” of a DNA molecule. Scientists use these sequences to identify genes, regulatory instructions, or in the case of Covid-19, mutations to a virus. Sequencing efforts early on in the pandemic helped scientists determine the structure of the virus, as well as early mutations that helped the virus be transmissible enough to cause a massive pandemic.

More recently, genome sequencing was the key to identifying the more transmissible variant discovered in the UK. The Covid-19 Genomics Consortium has been tracking Covid-19’s genetic history for nearly a year, logging over 150,000 viral samples. Whereas most variants of the virus have one or two minor mutations from each other, the UK variant had 23 separate mutations. This discovery caused concern and further inspection by the Consortium, which determined the mutations led to an accelerated transmission process. The UK variant is thought to have fueled the massive influx of cases in the UK in recent weeks.

South Africa’s new SARS-CoV-2 variant was discovered under the same technique. The new strain was found in late November and was announced a month later after further research and analysis. Like the one found in the UK, this new strain was determined to be highly transmissible in comparison to the strains we have been working with for the majority of the pandemic. South Africa, which has weathered the Covid-19 storm relatively well, is now amid a surge in cases as the UK is.

In the United States, our sequencing efforts have waned over time. At the start of the pandemic, the global community was trying to figure out what this virus was, and at that time, many samples were genome sequenced in that effort. Today, only .3% of samples have been sequenced in the United States, which ranks 43rd according to the GISAID Initiative, a global genome sequencing database project.

Sequencing can aid in the fight against Covid-19 and the newly emerging variants. The UK and South Africa variants have already been detected in dozens of cases in the US. The transmissibility leads me to believe that cases involving these variants are already widespread, but our lack of genome sequencing allowed the variants to evade surveillance. In response to these new variants, the CDC announced a doubling of our sequencing effort.

A robust sequencing regime may find more than just additional cases of the UK and South Africa variants. The virus can mutate every time it transmits to a new host, and with tens of millions of recorded cases worldwide, there are likely variants hidden waiting to be discovered. In the United States alone, some estimates suggest that 15-20% of Americans have had Covid-19, which would make a new variant stemming from a case in the US quite possible. If a homegrown variant is out there, that may have aided in the recent surge in Covid-19 cases observed over the holiday season.

The prospect of a more contagious strain working its way through the US is scary enough, but there’s a chance that with enough mutations, a strain may be able to evade current vaccines. That is why efforts to find these strains must be bolstered. If a section of the population has a vaccine-resistant strain of Covid-19, national public health agencies must identify them and continue vaccine research from there. The hope is that these mutations haven’t occurred, but we don’t know for sure.

The vaccine may cover the new strains in the UK and South Africa, vaccine distribution will continue as planned in the coming months, and life will return to normal in the latter half of 2021. The opposite is also possible. Genome sequencing in the US and worldwide must be bolstered, and then new strains must be identified and isolated. Otherwise, we may be looking at a very long year.


Read the article on Forbes, (published January 8, 2021). 

© William A. Haseltine, PhD. All Rights Reserved.