Omicron strain BA.2.86 emergence defies natural explanation

The omicron BA.2.86 lineage of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is known to have emerged suddenly with approximately 30 genetic mutations in the spike protein, similar to the earlier omicron BA.1 variant. However, BA.2.86 was not sufficiently infectious to become a dominant strain, and it was only after further mutating into the JN.1 variant that a significant surge in infections began to occur.

In this study, a researcher investigated the origin of the BA.2.86 lineage and found that sporadic cases were identified in multiple, geographically distant locations around the world during its initial appearance in the summer of 2023. Moreover, analysis of its mutation profile revealed significant differences from the patterns typically seen in human community transmission and in immunocompromised patients with immune escape.

A mutation spectrum that diverges from human patterns could emerge if the virus first infected humans, then evolved through repeated mutations in animals, and later re-entered the human population. However, the likelihood of identical mutations occurring naturally and independently in various locations worldwide is extremely low.

Explaining this phenomenon is particularly difficult; one plausible explanation is that virus samples cultured in non-human animals or in animal-derived cells—in laboratories may have been transported to research facilities in different countries under insufficient containment.

The work is published in the JMA Journal.

The omicron BA.2.86 lineage of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, is known to have emerged suddenly with approximately 30 genetic mutations in the spike protein, similar to the earlier omicron BA.1 variant. However, BA.2.86 was not sufficiently infectious to become a dominant strain, and it was only after further mutating into the JN.1 variant that a significant surge in infections began to occur.

In this study, a researcher investigated the origin of the BA.2.86 lineage and found that sporadic cases were identified in multiple, geographically distant locations around the world during its initial appearance in the summer of 2023. Moreover, analysis of its mutation profile revealed significant differences from the patterns typically seen in human community transmission and in immunocompromised patients with immune escape.

A mutation spectrum that diverges from human patterns could emerge if the virus first infected humans, then evolved through repeated mutations in animals, and later re-entered the human population. However, the likelihood of identical mutations occurring naturally and independently in various locations worldwide is extremely low.

Explaining this phenomenon is particularly difficult; one plausible explanation is that virus samples cultured in non-human animals or in animal-derived cells—in laboratories may have been transported to research facilities in different countries under insufficient containment.

The work is published in the JMA Journal.