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Hurdles to Genomic Surveillance

Systemic issues make viral genomic sequencing in the US challenging, Nature News reports.

The identification of SARS-CoV-2 variants by the UK and South Africa, and now elsewhere, underscored the need for viral genomic surveillance, as the Globe and Mail reported in late December. But the US has had no national SARS-CoV-2 genome sequencing program, though both the Centers for Disease Control and Prevention and the Biden Administration have sought to boost sequencing efforts, including with funding as part of the pandemic relief bill.

Nature News reports that even with that increase in funding, viral genomic surveillance in the US will be tricky due in part due to its patchwork of healthcare systems. It adds that some labs are running below capacity as many diagnostic labs discard samples following testing, rather than store them for additional sequencing analysis. Other labs that do receive samples receive them with limited patient data, making it harder to tell if any variants spotted are more contagious or can evade natural- or vaccine-induced immunity, it adds.

Duncan MacCannell from the CDC's Office of Advanced Molecular Detection tells Nature News that he is "convinced that we can do this, and that we can be nimble." He adds, though, that "it is challenging in a pandemic.