key: cord-1002887-av95i3uy
authors: Lule Bugembe, D.; Phan, M. V. T.; Ssewanyana, I.; Semanda, P.; Nansumba, H.; Dhaala, B.; Nabadda, S.; O'Toole, A.; Rambaut, A.; Kaleebu, P.; Cotten, M.
title: A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic
date: 2021-02-11
journal: nan
DOI: 10.1101/2021.02.08.21251393
sha: c551597043213d2dd25342fbeebdbd576579e0d2
doc_id: 1002887
cord_uid: av95i3uy

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) was first detected in March 2020 in Uganda. Recently the epidemic showed a shift of SARS-CoV-2 variant distribution and we report here newly emerging A sub-lineages, A.23 and A.23.1, encoding replacements in the spike protein, nsp6, ORF8 and ORF9, with A.23.1 the major virus lineage now observed in Kampala. Although the clinical impact of the A.23.1 variant is not yet clear 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.

country, however the Kampala area is a major centre of virus infection where 60-80% of the 54 daily new cases have been identified during the months of June 2020 to January 2021 55 (Uganda COVID-19 Daily Situation Report). We have continued our efforts to generate 56 SARS-CoV-2 genomic sequence data to monitor virus movement and changes (8).

The genomes were classified into Pango lineages(4) using the Pangolin module 60 pangoLEARN https://github.com/cov-lineages/pangolin) and into NextStrain clades using 61 NextClade (9) (https://clades.nextstrain.org/). Across the entire epidemic, 80 (39%) strains 62 belonged to the major lineage B whereas 123 (61%) strains were classified as lineage A

(Supplementary Table 1 ). This distribution of lineages changed dramatically over the course is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 B.1.393 ( Figure 2 is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 Of note, the SARS-CoV-2 lineage A is far less prevalent than lineage B in Europe, frequencies and only briefly and may have undergone apparent extinction, similar to patterns 111 observed in the UK (12) and Scotland (13).

A genome identified from a truck driver is often observed basal to each cluster 113 ( Figure 2) is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101/2021.02.08.21251393 doi: medRxiv preprint predominantly in Europe and USA; in particular, D614G was reported to increase infectivity, 159 spike trimer stability and furin cleavage (19), (20) 

Of concern, the recent Kampala and global A.23.1 virus sequences from December is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101/2021.02.08.21251393 doi: medRxiv preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101/2021.02.08.21251393 doi: medRxiv preprint scores) of each pHMMs across a query genome provides a measure of protein changes (in 226 44 amino acid steps) across the viral genome ( Figure 5A ). Applying this method to the most 227 recent lineage A.23.1 genome sequences the changes in spike (discussed above) as well as 228 changes in the transmembrane protein nsp6 and the interferon modulators ORF8 and 9 229 ( Figure 5A ). Modest changes were also observed in nsp13. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101/2021.02.08.21251393 doi: medRxiv preprint Panel D. All P.1 full genomes lacking Ns present in GISAID on Jan 26 2021.

We asked if a similar pattern of evolution was appearing in VOCs as SARS-CoV-2 246 adapted to human infection. We applied the same pHMM analysis to compare set of VOC or is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 We report the emergence and spread of a new SARS-CoV-2 variant of the A lineage is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101/2021.02.08.21251393 doi: medRxiv preprint converted to cDNA and amplified using SARS-CoV specific 1500bp-amplicon spanning the entire genome as previously described(11).The resulting DNA amplicons were used to

The genome assembies were performed as previously described (8). Briefly, reads 300 from fast5 files were basecalled and demultiplexed using Guppy 3.6 running on the UMIC 301 HPC. Adapters and primers sequences were removed using Porechop 302 (https://github.com/rrwick/Porechop) and the resulting reads were mapped to the reference 303 genome Wuhan-1 (GenBank NC_045512.2) using minimap2(34) and consensus genomes 304 were generated in Geneious (Biomatters Ltd). Genome polishing was performed in Medaka,

and SNPs and mismatches were checked and resolved by consulting raw reads. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101 https://doi.org/10. /2021 is also part of the EDCTP2 programme supported by the European Union. The UMIC high performance computer was supported by MRC (grant number MC_EX_MR/L016273/1) to . CC-BY 4.0 International license It is made available under a perpetuity.

is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) preprint

The copyright holder for this this version posted February 11, 2021. ; https://doi.org/10.1101/2021.02.08.21251393 doi: medRxiv preprint

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