COVID-19 Variants that Arise During Single Infection Tracked

Researchers at Technion-Israel Institute of Technology have tracked how mutations in the SARS-CoV-2 virus creates new variants within the course of an individual infection. The insights could shed light on how the virus adapts to hosts and reveal exploitable weaknesses in the virus’s structure.  

Using technology initially developed for HIV research, the team was able to map the genome of individual virus cells and detect very low levels of virus found in tissue cells. They compared different variants that developed in a patient's respiratory system over the course of an infection, and found mutations not included in existing databases and even a new, previously unknown variant.

Happily, the mutations developed over the course of a single infection appear to produce variants with a relatively low adhesion capacity that are unlikely to be transmitted from person to person. This hypothesis still requires further research, the researchers emphasize, but these findings hold true for the 10 variants examined to date in the study.

The researchers also examined the efficacy of existing vaccines against these variants and found that the efficacy varies depending on the different types of mutations in the spike protein. One specific mutation in spike protein s2 did impair the effectiveness of antibodies battling the virus. "This identification is an important factor in understanding the adaptation of the virus to its host's body," says assistant professor Yotam Bar-On of the Rappaport Faculty of Medicine. “We appreciate that our findings may lead to the detection of weaknesses of the virus—mechanisms that weaken its ability to infect—and to develop new measures to curb infection."

Most studies of COVID-19 have focused on the development of new variants—the result of random mutations and natural selection—throughout populations. The majority of such mutations do not significantly alter the virus's ability to survive and infect, but some give it a significant advantage to thrive and spread in the community. 

The team at Technion-Israel Institute of Technology focused on mutations related to the Alpha variant, but estimate that a similar analysis of the Delta variant—currently the most dangerous strain—may increase the toolbox available to science and medicine in the fight against the pandemic.

The findings also show that analysis of the evolution of the virus at an individual level contributes to a better understanding of its development and of possible ways to combat it using vaccines and drugs.

The work  was published in a recent PLOS Pathogens.