COVID-19: Geneticists criticize poor sequencing efforts in US

“Know your enemy” has been the mantra of generals at least since the 5th century BC when the Chinese military strategist Sun Tzu coined the phrase in The Art of War. The principle is just as important when your enemy is a rapidly evolving virus that has claimed the lives of more than 4 million people worldwide.Traditionally, surveillance of infectious diseases by public bodies, such as the World Health Organization (WHO) and the Centers for Disease Control and Prevention (CDC), has focused on data such as case numbers, hospitalizations, and deaths.More recently, however, rapid genome sequencing has allowed public health experts to survey variation between pathogens down to the level of their DNA or RNA bases, which are the chemical letters of the genetic code.However, according to population geneticists at Case Western Reserve University in Cleveland, OH, some countries have neglected this vital line of information during the COVID-19 pandemic.“Despite the availability and ubiquity of sequencing in several countries, the adoption of genomics as a strategy for pathogen surveillance has been slow, difficult, and inconsistent,” write Dana Crawford, Ph.D. and Scott Williams, Ph.D., in the journal PLOS Genetics.The scientists, who work at the university’s Department of Population and Quantitative Health Sciences, single out the U.S. for particular criticism.“For a country that led the sequencing of the human genome more than 2 decades ago, the lack of accrual of sequencing data in the midst of this pandemic is unbelievable and problematic,” they write.They note that the country has the capacity and expertise to carry out the necessary sequencing work, but these resources have remained “relatively dormant” until recently.For example, there were fewer than 7,000 new sequences of the virus in the week of March 6, 2021, out of more than 415,000 new recorded cases in the same week. In contrast to the “relatively uncoordinated and antiquated approach” to SARS-CoV-2 genomic surveillance in the U.S., they write that successful public health sequencing surveillance programs elsewhere embraced the technology early in the pandemic.China published the first SARS-CoV-2 sequence in February 2020, which enabled sequence comparisons as the virus evolved and the unprecedentedly rapid development of vaccines.The U.K. formed the COVID-19 Genomics UK Consortium in April 2020 and has since recorded more than 650,000 sequences.The authors write that while funding impeded early efforts in the U.S., in February 2021, the CDC committed more than $200 million to sequencing.In April 2021, the White House announced a further $1 billion injection of funds to boost sequencing capacity.The major issue now is that the U.S. does not have an organized, ongoing population-based cohort of individuals that it can use for COVID-19 studies, say Profs.