COVID-19: Why a “U.S. variant” will likely be identified in early 2021

Last month the more transmissible “UK variant (B.1.1.7)” and “South African variant (B.1.351)” were reported to be spreading quickly in their respective countries, and were found in multiple other countries in the past 10 days. Additional variants with similar increased contagiousness should be expected in 2021, especially in nations such as the United States with many more infected patients than the United Kingdom or South Africa.

The origin and natural evolution of these two genetically different variants is uncertain. Reports of individual patients and discussions last month in the New England Journal of Medicine, Science,  and from the United Kingdom hypothesize a role for some mutations to occur during prolonged infections in immunocompromised patients and/or persons who have received convalescent plasma from survivors of COVID-19.

Thus, there are at least two reasons why a “U.S. variant” is likely to appear in early 2021, or is already here but not yet recognized. First, the U.S. has more than 20 million laboratory-confirmed infections, compared with just over 1 million in South Africa and 2.5 million in the UK. Second, the U.S. has a sizable population of both immunocompromised persons and patients who have received convalescent plasma.

Identification of patients with any “U.S. variant” has not yet occurred. The U.S. Centers for Disease Control and Prevention announced on Dec. 30 an expanded and integrated genomic surveillance program across the U.S. that involves many partners. Thus, the ability to identify any such “U.S. variants” is being rapidly enhanced.

Recognition of any such genomic variants must be compared with clinical and epidemiological observations as part of a template to evaluate variants e.g., 10 considerations:

1. Unusually severe or atypical clinical disease;
2. Reinfections;
3. Increased transmissibility;
4. Decreased effectiveness of monoclonal antibodies;
5. Decreased effectiveness of vaccines;
6. Changes in performance of diagnostic test accuracy;
7. Possibly a relative change in effectiveness of high-titer convalescent plasma from survivors infected with these variants (given to patients with and without this same variant);
8. Possibly a change in the incidence of the MIS-C inflammatory syndrome in children infected with any such variant;
9. The ability of variants to recombine either with other variants or with non-variants;
10. Actionable policies to stop national and international spread of any “U.S. variant.”

This post is the 6^th here since Dec. 20 that focuses on known and anticipated SARS-CoV-2 variants. (When unusually severe COVID is seen, rapid identification and virus sequencing are needed worldwide; "Nigeria variant:" NO cause for alarm from initial data; Why did the UK implement strong measures after finding only two patients with the South African variant?; South African Variant may be worse than UK variant; UK virus may be more contagious, triggers European travel bans.)