Study: COVID-19 Variant Has Been Spreading in South, Southwest US Since October

Preprint data show a US-based variant has come to represent more than 27% and 11% of all sequenced genomes in Louisiana and New Mexico, respectively, through mid-January.

Assessments from multiple institutions suggest a SARS-CoV-2 variant initially detected in the US in late October 2020 has spread rapidly in the south and southwest regions of the country through mid-January.

New preprint, not yet peer-reviewed data from investigators at the University of New Mexico and Louisiana State University report that a variant first observed on October 23, 2020, has come to represent more than 27% and 11% of all sequenced SARS-CoV-2 genomes in Louisiana and New Mexico, respectively.

The lineage B.1.2 variant, which carries a Q677P substitution in the Spike protein (S), has been linked to 499 viral sequences as of February 3 of this year. The variant is believed to have borne at least 6 distinct lineages, per phylogenetic analyses—each containing approximately 100 or fewer sequenced cases thus far, predominately in the south and southwest.

The investigators are now evaluating the observed variant for its effects on proteolytic processing, cell tropism, and transmissibility. Initial perspective indicates this SARS-CoV-2 variant may be more difficult to contain than the currently dominant sequence.

“Although sampling bias and founder effects may have contributed to the rise of S:677 polymorphic variants, the proximity of this position to the polybasic cleavage site at the S1/S2 boundary are consistent with its potential functional relevance during cell entry, suggesting parallel evolution of a trait that may confer an advantage in spread or transmission,” investigators wrote in the preprint.

The abstract does not include reference to interpreting currently available coronavirus 2019 (COVID-19) vaccine efficacy against the new strain, but improved understanding of transmissibility, relative to vaccine trial’s in vivo assessments, would imply any effect it would have on current national immunization strategies.

At the height of new COVID-19 cases this January—during which time the observed variant increased in prevalence—Louisiana and New Mexico reported peak seven-day averages of 3722 and 1368 new cases, respectively, per the US Centers for Disease Control and Prevention (CDC).