Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda

Abstract

Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs 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.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable.

Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity

“…Towards the end of 2020, we observed a selective sweep, with lineage A.23.1 taking over. This sub-lineage, first observed in Uganda in late 2020 was reported to contain at least four amino acid changes in the spike protein and amino acid changes in the proteins nsp3, nsp6, ORF8, and ORF9 9 . In particular, these authors suggest that the Q613H mutation in spike may be functionally equivalent to the D614G mutation that arose early in 2020 and is associated with increased viral transmissibility 10 .…”

“…Bugembe et al ref. 9 . describe a selective sweep across Uganda of this lineage, which is now the dominant lineage circulating in Uganda as well.…”

“…Our travel history-aware inference methodology further enables us to consider such unsampled countries to determine the intensity of exchanges between countries and potentially even infer one of the unsampled countries as the origin of the lineage. In our analysis of subtree B.1, which includes Rwandan lineage B.1.380, we inferred a minimum number of nine (HPD 95%: [8][9][10][11][12]) introduction events into Rwanda, with three of these events originating from Kenya (Fig. 7 and Supplementary Table S3).…”

Transmission networks of SARS-CoV-2 in coastal Kenya during the first two waves: a retrospective genomic study

“…Our study contributes to the limited but growing literature illuminating SARS-CoV-2 transmission patterns in Africa (11,13,(17)(18)(19). The patterns revealed have potential to inform pandemic mitigation strategies.…”

Evolutionary insights into the furin cleavage sites of SARS-CoV-2 variants from humans and animals

“…Data on the spread of mutants containing amino acid (aa) changes at positions 680-689 in the FCS of SARS-CoV-2 were collected as described previously [ 21 ]. All human and animal SARS-CoV-2 sequences that were deposited at the GISAID Initiative ( https://www.gisaid.org/help/search/ ) during the period of January 10, 2020 to April 18, 2021 were analyzed.…”