As the discovery of the new omicron variant illustrates, new COVID-19 variants will continue to emerge on a regular basis. In an effort to make sense of these new variants, scientists at the Los Alamos National Laboratory have developed methods to quantify how more or less transmissible they are, which could have far-reaching implications for public health by terms of COVID-19 risk and vaccination levels required to achieve herd immunity.
“In general, newer variants of COVID-19 are simply discussed in terms of being more dangerous or spreading faster than previous strains,” said Ethan Romero-Severson, computer epidemiologist in the Theoretical Division of Los Alamos and main author of the article published in Nature Communication. “We have shown that it is possible to calculate the transmission benefit of new strains while taking into account alternative explanations such as migration and random genetic drift. Our collection of methods allows us to examine both the global situation in general and specific countries in more detail using publicly available genetic sequence data. “
Los Alamos’ research is “a method of integrating molecular epidemiological surveillance into surveillance systems using publicly available data streams,” Romero-Severson noted.
The team used two distinct but complementary approaches. The first is derived from classical methods of population genetics that relate the increased transmissibility of a variant of COVID-19 to the expected frequency of that variant in the population over time.
“We modified this model to include migration as a possible alternative explanation for increased transmissibility and implemented it in a hierarchical modeling framework that allowed us to estimate the unique selection effect for each variant. in every country in which it has appeared, ”he said.
The second, more detailed method used a stochastic epidemiological model (allowing for uncertainty) to predict both changes in the frequencies of COVID-19 variants and deaths over time, taking into account natural and random variations in the virus both between and within countries over time.
Together, these approaches have shown that the pattern of emerging and increasing variants of COVID-19 around the world is due to sharp increases in the transmissibility of the virus over time. The methods also clearly established that early detection of variants of concern is possible even when the overall frequency of new variants is as low as 5 percent.
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