SARS-CoV-2 Sequence Reporting: Changing Mindsets


How observed changes in SARS-CoV-2 lineage have warranted heightened priority, and why sequencing deserves better resourcing beyond the pandemic.

Video highlights

0:08 Makeshift COVID-19 data-sharing networks
1:02 Interpreting SARS-CoV-2 sequence changes
3:27 Parallel vs convergent evolution
5:40 The D614G (Doug) mutation
8:00 Surviving SARS-CoV-2 remnants

The communication networks connecting major US laboratories conducting SARS-CoV-2 sequencing may not be any greater than a Slack channel established by the US Centers for Disease Control and Prevention (CDC).

But it’s proven to be more than enough for teams including Cooper, Kamil, and Domman, a trio of microbiology investigators who collaborated on recent research into a lineage B.1.2 variant with a Spike protein Q677P substitute in a growing proportion of cases in the South and Southwest regions earlier this year.

In the second segment of an interview with Contagion®, the team discussed the intricacies of SARS-CoV-2 sequencing and reporting—a matter which, given the urgent nature of the COVID-19 pandemic, conflicted against the scientific instincts of raised patience and scrutiny. Kamil and colleagues faced such conflict when observing the prevalent lineage.

“It’s so easy to get stuck in the hyper-cautious, ‘Wait, we need more proof’,” Kamil said. “It’s such a balance in science where you don’t want to want to be irresponsible but you also don’t want to sit on a story that’s real.”

For reference, Kamil discussed the caution placed around D614G mutation, nicknamed ‘Doug,’ by the scientific community in the late spring of 2020.

“We were all kind of too cautious about Doug,” Kamil explained. “It now is 98% of all the viruses in the world. It became a signal in June, and it probably popped up in maybe April or March—and it probably occurred first maybe February, January, or December (2019). It came from almost nothing to overtake all the population.”

But the opportunity to observe and share virus evolution first-hand is almost unprecedented in the modern history of sequencing, regardless of the means by which it’s being collected.

“I think it’s really valuable for everyone to know how quickly we were able to put this data together because of data-sharing, and because of scientific networks that we basically put together ad hoc,” Cooper said

It does speak to the benefit of improved resourcing for such monitoring—for COVID-19 and beyond.

“Sequencing is cheaper than it has ever been,” Kamil said. “Why are we not sequencing more? We have not updated our public health surveillance on any respiratory pathogens.”

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