SARS-CoV-2 Sequencing in the US: The Need for Collaboration


A team of cross-country investigators discuss their coordinated tracking of a new variant in the US earlier this year.

The Panel

Vaughn S. Cooper, PhD
Professor, Microbiology and Molecular Genetics
University of Pittsburgh

Jeremy Kamil, PhD
Associate Professor, Microbiology and Immunology
LSU Health Shreveport

Daryl Domman, PhD
Assistant Professor, Center for Global Health
University of New Mexico

Earlier this month, data from a team of nationwide investigators found a SARS-CoV-2 a variant first observed on October 23, 2020, had come to represent more than 27% and 11% of all sequenced pandemic virus genomes in Louisiana and New Mexico by mid-January.

The lineage B.1.2 variant carries a Q677P substitution in the Spike protein (S) and had been linked to 499 viral sequences as of February 3.

The uncovered variant has led to the makeshift team of microbiology investigators continuing assessment into the increasing prominent strain’s proteolytic processing, cell tropism, and cell transmissibility.

Their efforts also highlight the benefit of cross-country genomic surveillance during COVID-19—a practice which the US, in relation to other major countries, has lacked in since the beginning of the pandemic.

In fact, as the investigators explain in the video above, the variant’s mutation was first observed in New Mexico. Domman observed through a shared data and communication platform that Kamil’s team was reporting the same variant in Louisiana.

They began to collaborate on their research around the time that Cooper’s team in Pittsburgh began to observe a similar S substitution in variants, almost to the day.

“Within 2 days, we knew for sure there was more to the study than 1 lineage that Jeremy and Daryl had discovered,” Cooper explained.

While interpretation of the mutations’ function and influence on the virus’ transmission is still not fully formed, the discovery speaks to the value of bolstered surveillance and data-sharing—at regional, national, and global levels.

“One of the things we’d like to highlight is that open source and sharing data in real time has been absolutely fundamental to this entire effort globally, in terms of linking up scientists to understand how the virus is changing and transmitting through the globe and even locally,” Domman said.

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