Coronavirus Variants Through Recombination

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Day 319: Stay Safe Minnesota

According to some recent studies, coronavirus variants occurring through genetic recombination rather than more common single mutations.

In the New York Times, Roxanne Khamsi writes that the coronavirus is the master of mixing its genome thus contributing to the rise of dangerous variants. For example, the Coronavirus variants from South Africa, commonly known as B.1.351, are changes in a single ‘letter’ (or nucleotide) of the virus’s long genetic sequence, or RNA because during the virus replication such viruses have a robust system for proofreading its RNA code. That is the reason why scientists don’t observe so many variants everyday.

Recombination

Genetic recombination is described as “the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent”. “It joins variants that arise independently within the same molecule, creating new opportunities for viruses to overcome selective pressures and to adapt to new environments and hosts,” write Marcos Pérez-Losada and others in the journal Infection, Genetic and Evolution.

Kmsi writes in the Times that “The novel coronavirus has a propensity to mix large chunks of its genome when it makes copies of itself. Unlike small mutations, which are like typos in the sequence, a phenomenon called recombination resembles a major copy-and-paste error in which the second half of a sentence is completely overwritten with a slightly different version.”

Nels Elde, an evolutionary geneticist at the University of Utah told the Times:

“There’s no question that recombination is happening. And in fact, it’s probably a bit underappreciated and could be at play even in the emergence of some of the new variants of concern.”

Describing the recombination process in COVID variants, Dr Else told Times that recombination may have merged mutations from different variants that arose spontaneously within the same person over time or that co-infected someone simultaneously. “It’s really hard to see these invisible scars from a recombination event. And although getting infected with two variants at once is possible, it’s thought to be rare.”

Vincent Munster, a viral ecologist with the National Institute of Allergy and Infectious Diseases who has studied coronaviruses for years, told Times that there is not sufficient knowledge to fully explain ‘whether recombination could give rise to new pandemic coronaviruses’.

Recombination as Tool to Find Cure

Evolution biologists study virus recombination process not only to fend off the next pandemic, but to understand help fight the pandemic. In a recent study that is mentioned in the Times article, Dr. Denison of Vanderbilt University studied the recombination of three coronaviruses and found that blocking an enzyme known as nsp14-ExoN in a mouse coronavirus caused recombination events to plummet suggesting that the ‘enzyme is vital to coronaviruses’ ability to mix-and-match their RNA as they replicate’. This knowledge could provide insight whether the enzyme could be used as treatment option for COVID infection.

“Certain antiviral drugs such as remdesivir fight infections by serving as RNA decoys that gum up the viral replication process. But these medications don’t work as well as some had hoped for coronaviruses. One theory is that the nsp14-ExoN enzyme chucks out the errors caused by these drugs, thereby rescuing the virus,” explains Khamsi in Times.

The potential of nsp14-ExoN enzyme to prevent coronaviruses to repair any of its replication mistakes is being explored by researchers, according to the Times. “I think it’s a good idea, because you would push the virus into what’s known as ‘error catastrophe’ — basically that it would mutate so much that it’s lethal for the virus,” an evolutionary virologist Dr Stephen Goldstein told the Times.

B.1.1.7 Variant Becoming Dominant in US

In the CNN Health, Jamie Gumbrecht writes that cases of a more contagious coronavirus variant from UK ( known as B.1.1.7) is doubling every week and a half, similar to what was observed in other countries. According the preprint server MedRxiv, the B.1.1.7 variant is 35-45% more transmissible than strains that appeared earlier in the United States, and it’s doubling about every 10 days in the country.

“Our study shows that the U.S. is on a similar trajectory as other countries where B.1.1.7 rapidly became the dominant SARS-CoV-2 variant, requiring immediate and decisive action to minimize COVID-19 morbidity and mortality,” the researchers wrote in the study’s preprint.

According to the CDC reports, more than 610 cases of the B.1.1.7 variant have been found in 33 states in US, writes the CNN Health.

COVID-19 Vaccination Watch

According to the US Centers for Disease Control and Prevention (CDC) COVID vaccination tracker page (as of Feb 10, 9 a.m.) 65,972,575 doses have been distributed and 44,769,970 doses administered. According MDH COVID-19 Response vaccine data (as of Feb 08) a total of 753,019 doses of Covid-19 (Pfizer & Moderna) vaccines have been administered in Minnesota. According to the MDH latest tally (as of Feb 10, 11 a.m.) the confirmed COVID-19 cases in Minnesota are 469,905 (out of 6,828,887 tested) with 6,319 deaths.