Global Response to COVID-19 Hurt by Inadequate Sequencing of SARS-CoV-2 Variants

Better international sequencing efforts are needed to track and respond to novel SARS-CoV-2 variants.

The lack of sequencing of SARS-CoV-2 variants by the US and other countries jeopardizes the global response to the COVID-19 pandemic, Dana Crawford of Case Western Reserve University argues in a new viewpoint published in the journal PLOS Genetics .

Surveillance is essential for a successful and rapid response to disease outbreaks, but public health surveillance has traditionally focused on monitoring the number of cases, hospitalizations and deaths. Advances in genome sequencing now allow us to track genetic variation in evolving viruses in unprecedented detail. Despite the availability of sequencing in several countries, the adoption of genomics as a strategy for monitoring the SARS-CoV-2 virus, which causes COVID-19, has been slow, difficult and inconsistent. Crawford points out that as of early April 2021, the US was ranked 33rd in the world in SARS-CoV-2 sequencing for variant surveillance. She says the Centers for Disease Control and Prevention (CDC) has historically not prioritized genomic research for public health, and this bias has created a gaping hole in our understanding of the real-time evolution of SARS-CoV-2 and the impact on disease transmission and its severity.

Crawford cites insufficient funding, the lack of an effective sample tracking system and strict regulations on sample and data sharing as the causes of the inadequate sequencing efforts. Yet other countries, such as China and the UK, have successfully overcome these challenges. The CDC recently pledged more than $200 million to improve sequencing, but Crawford points out that this late investment means the US does not have an organized database of patient information for COVID-19 studies. She cautions that investments in SARS-CoV-2 genomics should continue and expand as new variants are likely to emerge due to variability in vaccination rates and compliance with COVID-19 precautions worldwide.

Since SARS-CoV-2 is a new zoonotic disease with no previous human infections, Crawford argues that sequencing and analysis are vital to understand both the trajectory of the outbreak and its evolution. Facilities are also desperately needed to link genetic data to clinical and epidemiological data sources for public health research. Finally, she concludes that ongoing international sequencing efforts are still needed to understand and respond to this constantly evolving virus that knows no international borders.

“COVID-19 control requires near real-time host pathogen genomic and public health data to monitor how SARS-CoV-2 has evolved and how this evolution affects disease transmission and severity,” adds Crawford. “U.S. and global sequencing efforts have been too little and too disjointed, underscoring the need to engage with human genomics and integrate its technologies into emerging public health responses to infectious diseases.”

Reference: “Global Variation in Sequencing Impedes SARS-CoV-2 Surveillance” by Dana C. Crawford and Scott M. Williams, July 15, 2021, PLoS Genetics.
DOI: 10.1371/journal.pgen.1009620