Researchers report new SARS-CoV-2 source of 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 December 2019 in Wuhan, China. Since then, the virus has infected more than 107 people. million people worldwide and caused more than 2.4 million deaths. Due to the high transmissibility, it was difficult to contain the virus in an epidemic region.

By the latter part of 2020, a new variant of SARS-CoV-2 (lineage B.1.1.7) had emerged in England and another, (B.1.351), also known as 501Y.V2, in South -Africa. Both have observed that it has increased transmissibility, and some early studies even indicate an increase in virulence in these mutations.

In a related 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 the A lineage with multiple protein changes throughout the viral genome. The researchers recently presented their findings in a press release on the medRxiv * server.

The researchers report the emerging A sublines, A.23 and A.23.1 of the SARS-COV-2.

The research team reports that the A.23.1 sub-series is the most important virus line currently observed in the Kampala region of Uganda. Reportedly, this sub-line encodes multiple peak proteins, nsp6 (non-structural protein), ORF8 and ORF9 (open reading frame 8 and 9) protein changes. Some of these replacements are predicted to functionally correspond to those observed in line B variants of concern (VOCs).

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

The researchers also report that 39% of the tribes in the entire region’s epidemic can be classified as the most important B descent, while 61% are within the A tribe. Interestingly, when transportation was characterized by land travel (mainly truck drivers ’movements) and no flights, the B.1 tribes dominated. In the course of their study, however, the researchers unexpectedly found that almost exclusively the A-lineage viruses are found in the Kampala region until the end of January 2021.

Because the researchers identify the lineage A strain as the origin of a truck driver (strain UG053) as the basis for the emerging A.23 variant, they recommend that all truck drivers move back and forth through Uganda. This will help to better understand the rural entry and exit and distribution of the tribes in this region, where (large-scale) genomic surveys are not yet complete.

The genome series from 6 deadly Ugandan cases belonged mainly to two genera 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 USA, the presence of lineage A viruses from fatal community cases throughout Uganda indicates that this lineage is circulating in the country and severe infection.

To monitor the epidemic in more detail, the researchers generated the complete genome SARS-CoV-2 series from SARS-CoV-2-positive samples in Uganda. From this analysis, the researchers provide a phylogenetic tree with a maximum probability, comparing all available full and large coverages in Uganda.

Several descendants have been observed at low frequencies and only briefly and can apparently be erased, similar to patterns observed in the UK and Scotland, the researchers write.

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

While the A.23.1 virus’s sequence coded for 4 or 5 amino acid changes in the vein protein, plus additional protein changes in nsp3, nsp6, ORF8 and the ORF9.

A graph of nucleotide changes over time for Ugandan-derived A viruses showed a constant evolutionary rate of about 2 nucleotide changes per month observed during the SARS-CoV-2 pandemic. ‘

All organisms mutate. Viruses are found to have the highest per base pair per generation mutation rate. This study reports the emergence and distribution of a new SARS-CoV-2 variant of the A lineage (A.23.1) with multiple protein changes throughout the viral genome.

The proliferation of a new variant with increased transmission and / or virulence may put more pressure on the healthcare system – and ultimately result in a higher mortality rate. There is also the risk that new variants may undermine current vaccines and therapies aimed at preventing or ameliorating COVID-19 based on earlier strains.

From a display of the SARS-CoV-2 genomic data from GISAID, the researchers noted that sublines A.23 and A.23.1 are now present in 12 countries outside Uganda (from Africa, Asia, Europe, North America and Oceania) ; it indicates the worldwide movement of the emerging variants.

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

Although the clinical impact of the A.23.1 variant is not yet clear, it is essential to continue close monitoring of this variant as well as a rapid evaluation of the effects of the changes in the protein on vaccine efficacy. ‘

* Important notice

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