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 worldwide and caused more than 2.4 million deaths. Due to its high transmissibility, it has been difficult to contain the virus in an epidemic region.

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

In a new development, an interdisciplinary research team from Uganda and the UK reports the emergence and spread of a new SARS-CoV-2 variant of lineage A with multiple protein changes throughout the viral genome. Recently, researchers published their findings in a prepress in the medRxiv * server.

Researchers report SARS-COV-2 emerging A sub-lineages, A.23 and A.23.1.

The research team reports that sub-lineage A.23.1 is the main virus lineage now observed in the Kampala region of Uganda. This sub-lineage has been reported to encode several spike proteins, nsp6 (nonstructural protein), ORF8, and ORF9 (open reading frames 8 and 9). Some of these substitutions are expected to be functionally similar to those observed in the worrisome variants of the B lineage (VOC).

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

Researchers also report that in the entire epidemic in the region, 39% of strains can be classified as the main B lineage, while 61% are within the A lineage. Interestingly, when transportation was characterized by travel by land (mainly truck driver movements) and without flights, strains of the B.1 lineage predominated. However, throughout their study, researchers unexpectedly found that almost exclusively A-line viruses are found in the Kampala region until the end of January 2021.

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

It should be noted that the genome sequences of 6 Ugandan lethal cases belonged to two lineages A.25 and B.1.393. Although SARS-CoV-2 lineage A is less common than lineage B in Europe, the United Kingdom, and the United States, the presence of lineage A viruses from lethal community cases throughout Uganda indicates that this lineage is circulating. in the country and is capable of infection.

To control the epidemic in more detail, the researchers generated the complete SARS-CoV-2 genome sequences from positive SARS-CoV-2 samples in Uganda. From this analysis, the researchers present a most likely phylogenetic tree that compares all available Uganda sequences, complete and high coverage.

Several variant lineages were observed at low frequencies and only briefly and may have suffered an apparent extinction, similar to the patterns observed in the United Kingdom and Scotland, the researchers write.

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

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

A plot of nucleotide changes over time for the Ugandan A lineage virus showed a consistent evolutionary rate of about 2 nucleotide changes per month that has been observed for SARS-CoV-2 throughout the pandemic. .

All organisms mutate. It is detected that viruses 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 lineage A (A.23.1) with multiple protein changes throughout the viral genome.

The spread of a new variant with increased transmissibility and / or virulence may put more pressure on the healthcare system and ultimately lead to a higher mortality rate. There is also a risk that new variants may undermine current vaccines and therapies, intended to prevent or mitigate COVID-19, based on previous strains.

From a screening of GISAID’s SARS-CoV-2 genomic data, the researchers observed that sub-lineages A.23 and A.23.1 are now circulating in 12 countries outside Uganda (from Africa, Asia, Europe, North America and Oceania); this indicates the overall movement of the emerging variants.

This study also highlights the importance of rapid genomic surveillance of infectious pathogens and also the need to closely monitor virus movements. Significant changes observed in spike protein (which can affect transmission, infection, and immune selection) are crucial to understanding the evolution of the virus and justify further studies on functional consequences.

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

* Important news

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