Researchers report on SARS-CoV-2 variant evolution in Uganda

In 2021, researchers reported that a new variant of SARS-CoV-2, the virus that causes Covid-19, emerged in Uganda and spread to 26 other countries. They named the variant “A.23.1”, and said it has many of the same changes in proteins that researchers have observed in other variants of concern globally around this time. 

Scientists track how coronavirus variants change so that they can better understand how well vaccines might work against new variants.

Covid-19 has killed many people around the world. In a process known as genomic surveillance, scientists monitor how the genetics and proteins of the virus changes as it spreads.

They use this information to manage the disease and guide vaccine development. For example, by understanding the structure of the virus’s spike proteins, researchers can design vaccines that better target those proteins to help prevent the virus from entering human cells.

In this study, researchers looked specifically at how SARS-CoV-2 was evolving in Uganda.

Researchers determined the genetic sequences of the virus in COVID-19 positive samples collected throughout Uganda. They used computer software to trace the lineage (or family history) of the new variant they identified in this way (called A.23.1), and were able to see where the variant fit into the SARS-CoV-2 family tree.

Their results showed that the A.23.1 variant recently evolved from another variant called A.23, and was detected in 90% of all positive samples. In other words, it had dominated Ugandan samples since October 2020. They also found that the A.23.1 variant had several changes in the spike protein similar to changes seen in other variants of concern. The changes likely makes the variant more transmissible (it spreads faster), and more resistant to vaccines and treatments.

This study adds to ongoing efforts to sequence SARS-CoV-2 variants globally. The results add to growing evidence that SARS-CoV-2 rapidly evolves as it spreads to infect more people and evade vaccines.

However, more research is needed to understand what exactly the effects or functions of spike protein changes in the A.23.1 variant would be.

The researchers recommend more genomic surveillance to help us understand how virus variants respond to vaccines available in Uganda and other countries. They also say monitoring international travel is important so that researchers can better understand how the virus circulates locally.

Abstract

SARS-CoV-2 genomic surveillance in Uganda provides an opportunity to provide a focused description of the virus evolution in a small landlocked East African country. Here we show a recent shift in the local epidemic with a newly emerging lineage A.23 evolving into A.23.1 which is now dominating the Uganda cases and has spread to 26 other countries. Although the precise changes in A.23.1 as it has adapted are different from the changes in the variants of concern (VOC), the evolution shows convergence on a similar set of proteins. The A.23.1 spike protein coding region has accumulated changes that resemble many of the changes seen in VOC including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif, and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1lineage encodes changes in non-spike proteins that other VOC show (nsp6, ORF8 and ORF9). The clinical impact of the A.23.1 variant is not yet clear, however it is essential to continue careful monitoring of this variant, as well as rapid assessment of the consequences of the spike protein changes for vaccine efficacy.

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