Researchers report a new variant of SARS-CoV-2 concern in Uganda

The etiological agent of coronavirus disease 2019 (COVID-19) – severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – was first identified in Wuhan, China, in December 2019. Since then, the virus has infected more than 107 million people around the world and caused more than 2.4 million deaths. Due to its high transmissibility, it was difficult to contain the virus in an epidemic region.

Towards the end of 2020, a new variant of SARS-CoV-2 (line B.1.1.7) appeared in England and another, (B.1.351), also known as 501Y.V2, in Africa South. It is observed that both have increased transmissibility, some early studies even suggesting an increase in virulence in these mutations.

In a new development, an interdisciplinary research team from Uganda and the United Kingdom reports the emergence and spread of a new SARS-CoV-2 variant of line A with multiple protein changes in the viral genome. Researchers recently published their findings in a preprint on medRxiv * Server.

The researchers report the appearance of sub-lines A, A.23 and A.23.1 of SARS-VOC-2.

The research team reports that sub-line A.23.1 is the most important virus line now observed in the Kampala region of Uganda. This sub-line is reported to encode several spike proteins, nsp6 (unstructural protein), ORF8 and ORF9 (open reading frames 8 and 9) protein modifications. Some of these replacements are functionally predicted to be similar to those observed in the line of concern (VOC) concerns.

The Kampala region has become an epicenter of viral transmission in the country; 60-80% of new cases in the country were identified daily there, from June 2020 to January 2021. The researchers generated SARS-CoV-2 genomic sequence data to monitor the movement of the virus and their changes.

The researchers also reported that in the entire epidemic of the region, 39% of the strains can be classified as major B line, while 61% are in line A. Interestingly, when the transport was characterized by land movements (mainly movements of truck drivers) and without flights, the stem of line B.1 predominated. However, during their study, the researchers unexpectedly discovered that, almost exclusively, the viruses of the A lineage are found in the Kampala region until the end of January 2021.

Because the researchers identify genealogical strain A as derived from a truck driver (strain UG053) as the basis for the new variant A.23, they recommend continuous monitoring of all truck drivers transiting in and out of Uganda. This will help to better understand the internal entry and exit and the circulation of strains in this region, where (large-scale) genomic surveillance is not yet exhaustive.

In particular, the genome sequences from 6 Ugandan fatalities belonged to two lines A.25 and B.1.393. While SARS-CoV-2 line A is less prevalent than line B in Europe, the United Kingdom and the United States, the presence of line A viruses in community fatalities throughout Uganda indicates that this line circulates in the country and is capable of infection. .

To monitor the epidemic in more detail, the researchers generated complete sequences of the SARS-CoV-2 genome from Uganda’s positive SARS-CoV-2 samples. From this analysis, the researchers present a phylogenetic tree with maximum probability, comparing all available Uganda sequences complete and with high coverage.

Several line variants were observed at low frequencies and only briefly and could be subject to apparent extinction, similar to models observed in the UK and Scotland, the researchers write.

The researchers also found that SARS-CoV-2 foci in and around prisons would be line A.23, with three amino acid changes (aa) encoded in the exposed S1 domain of the spike protein (F157L, V367F and Q613H). .

While the A.23.1 virus sequence encoded 4 or 5 amino acid changes in the spike protein plus additional protein changes in nsp3, nsp6, ORF8 and ORF9.

A plot of nucleotide changes over time for Ugandan A-line viruses showed a consistent evolutionary rate of approximately 2 nucleotide changes per month, which was observed for SARS-CoV-2 during the pandemic. ”

All organisms move. Viruses are found to have the highest mutation rates per base pair per generation. This study reports the emergence and spread of a new SARS-CoV-2 variant of line A (A.23.1) with multiple protein changes in the viral genome.

The spread of a new variant with increased transmissibility and / or virulence can put more pressure on the health system – and ultimately lead to a higher mortality rate. There is also a risk that the new variants will undermine current vaccines and therapies, aimed at preventing or mitigating COVID-19, based on previous strains.

From an examination of GISAID’s SARS-CoV-2 genomic data, the researchers observed that sub-lines A.23 and A.23.1 are now circulating in 12 countries outside Uganda (Africa, Asia, Europe, North America and Oceania); this indicates the global movement of the newly emerged variants.

This study also emphasizes the importance of rapid genomic surveillance of infectious pathogens and also the need to closely monitor virus movements. The significant changes observed in the spike protein – which can have an impact on transmission, infection and immune selection – are crucial to understanding the evolution of the virus and justify further studies on the functional consequences.

Although the clinical impact of variant A.23.1 is not yet clear, it is essential to continue close monitoring of this variant, as well as a rapid assessment of the consequences of changes in spike protein for vaccine efficacy. ”

*Important Note

medRxiv publishes preliminary scientific reports that are not evaluated by colleagues and therefore should not be considered conclusive, guide clinical practice / health-related behavior or be treated as established information.