Genomic Epidemiology of SARS-CoV-2 in Urban Settings in Senegal

Abstract

We used whole genome sequencing to identify and analyze mutations in SARS-CoV-2 in urban settings during the deadliest wave of the COVID-19 epidemic-from March to April 2021-in Senegal. Nasopharyngeal samples testing positive for SARS-CoV-2 were sequenced on the Illumina NovaSeq 6000 sequencing system using the COVIDSeq protocol. A total of 291 genotypable consensus genome sequences were obtained. Phylogenetic analyses grouped the genomes into 16 distinct PANGOLIN lineages. The major lineage was B.1.1.420, despite circulation of the Alpha variant of concern (VOC). A total of 1125 different SNPs, identified relative to the Wuhan reference genome, were detected. These included 13 SNPs in non-coding regions. An average density of 37.2 SNPs per 1000 nucleotides was found, with the highest density occurring in ORF10. This analysis allowed, for the first time, the detection of a Senegalese SARS-CoV-2 strain belonging to the P.1.14 (GR/20J, Gamma V3) sublineage of the Brazilian P.1 lineage (or Gamma VOC). Overall, our results highlight substantial SARS-CoV-2 diversification in Senegal during the study period.

Keywords: COVIDSeq; SARS-CoV-2; SNPs; Senegal; epidemiology; genomic.

Figure 1

Distribution of the different clades and lineages of SARS-CoV-2 in the Dakar and Thiès regions of Senegal. (A) Distribution of 291 genotypable individuals into 16 lineages according to the PANGOLIN (Phylogenetic Assignment of Named Global Outbreak Lineages) classification. Lineage B.1.1.420 was the major lineage (131/291, 45%,), followed by lineage B.1.1.7 (100/291, 34%), B.1.525 (21/291, 7%) and B.1.416 (16/291, 6%). The remaining lineages (A.27, B.1, B.1.160, B.1.617, B.1.629, B.1.1, B.1.1.318, P.2, R.1 and P.1.14) represented 8% of the sequences. (B) Distribution of the 291 genotypable sequences into six Nextstain clades using the Nextclade web tool. Clade 20B was predominant (136/291), followed by clade 20I, Alpha V1 (100/291) and clade 20A (30/291). Clades 21D, 19B and 20J Gamma V3 contained 21, 3 and 1 of the genotypable sequences, respectively.

Figure 2

Maximum likelihood phylogenetic tree of the 291 whole genome sequences of Senegalese SARS-CoV-2 strains. The tree shows the clades circulating in Senegal during the second wave of the epidemic. The 291 sequences are grouped into six clades based on the Nextstrain nomenclature. Clade 19B includes strains of the PANGOLIN A.27 lineage; Clade 20A includes strains from PANGOLIN lineages B.1, B.1.160, B.1.214.2, B.1.416, B.1.617 and B.1.629; strains of PANGOLIN lineages B.1.1, B.1.1.318, B.1.1.420, B.1.1.442, P.2 and R.1 are grouped in clade 20B; clade 20I contains strains of PANGOLIN lineage B.1.1.7; clade 20J contains the single isolate of PANGOLIN lineage P.1.14; strains of PANGOLIN lineage B.1.525 are grouped in clade 21D.

Figure 3

Representation of the mutational analysis of 291 whole genome sequences of Senegalese SARS-CoV-2. (A) Representation of the 10 most frequently detected SNPs (Single Nucleotide Polymorphisms): A23403G, C3037T, C14408T, C241T, G28883C, G28881A, G28882A, C28310T, C5548T and C5178T. (B) Representation of the 10 most frequent nucleotide substitutions. Among the 1125 SNPs, the following 10 nucleotide substitutions were the most common: C>U transversion, G>U transversion, A>G transition, U>C transversion, G>A transversion, A>U transversion, G>C transversion, U>A transversion, C>A transversion, U>G transversion, A>C transversion and C>G transversion. (C) Distribution of SNPs in different regions of the Senegalese SARS-CoV-2 genomes. The greatest number of SNPs was counted in ORF1a, followed by ORF1b and the S gene. A total of 140 SNPs were counted in the other ORFs (Open Reading Frames). A total of 87, 32 and 10 SNPs were counted in the genes coding for the N, M and E proteins, respectively. A total of 31 SNPs were identified in the 5′ and 3′ UTRs (UnTranslated Regions) of the Senegalese SARS-CoV-2 genomes. (D) Distribution of non-synonymous mutations across different regions of the genomes. Non-synonymous mutations were found in all coding regions of the Senegalese SARS-CoV-2 genomes. The largest number of non-synonymous mutations was found in ORF1a while the smallest number was found in ORF6.

Figure 4

Representation of the Senegalese isolate of the Gamma sublineage (P.1.14). (A) Phylogenetic analysis of the Senegalese isolate P.1.14. The isolate was linked to 59 genomes classified as gamma variants of concern in the Global Initiative on Sharing Avian Influenza Data (GISAID) database. These gamma variants originated from the United States, Canada, Mexico, Argentina and Brazil. The Audacity Instant application in GISAID was used to generate a phylogenetic tree. Branch lengths are based on the genetic distance (the number of estimated mutations). Sequences in the tree are designated by their GISAID accession numbers or the number of genomes in the group. The Senegalese isolate P.1.14 is represented on the tree by a red dot. (B) 3D structural visualization of the spike glycoprotein of the Senegalese isolate P.1.14. The 10 amino acid changes identified in the Senegalese isolate in comparison with the Wuhan reference sequence are visualized by colored balls according to the following legend: non-synonymous mutations with a possible phenotypic effect are colored in yellow: L18F, K417T, D614G; non-synonymous mutations with an unknown effect are colored in pink and blue: T20N, P26S, D138Y, T1027I, P1162S, V1176F, H655Y.