COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome

Abstract

Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.

Keywords: COVID-19; Central African Republic; Delta variant; SARS-CoV-2; screening; severe acute respiratory syndrome coronavirus 2.

Figure 1

Geographic and demographic distribution of the samples. (A). Geographic distribution of the four different sampling checkpoints in Bangui, Central African Republic (CAR). (B). Sample distribution at the checkpoints (left); diverse percentage of subjects positive to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) depending on the test performed (middle) and depending on the collection point (right). (C). Demographic characteristics of the positive subjects compared to the totality of the participants: general gender distribution (left) and gender (middle) and age range (right) distribution according to the tests performed.

Figure 2

Phylogenetic tree of SARS-CoV-2 genomes circulating in the CAR. Neighbour Joining (NJ) phylogenetic tree of whole genome sequences of SARS-CoV-2 detected in the CAR, spanning from November 2020 to January 2022. Tree was built with MEGA X software. Bootstrap values ≥ 70 are shown on the branches. Pangolin clades and lineages are indicated with colours referred on the right side of the tree, with the Variants of Concern (VoCs) highlighted in bold. Reference sequences representing SARS-CoV-2 VoCs and CAR sequences from this study are labelled with an empty and a filled dot coloured according to the phylogenetic cluster they belong to, respectively. For VoCs, the date and country of the first report according to the World Health Organisation (WHO) are indicated between round brackets.

Figure 3

Non-structural proteins 3 (NSP3) schematic and tridimensional structure with reported mutations. (A). NSP3 structure scheme showing domain boundaries and non-synonymous mutations (coloured triangles). (B). NSP3 3D structure with the solved domains connected by dashed lines representing unsolved regions of the protein where most of the mutations found are indicated.

Figure 4

NSP5 schematic and tridimensional structure with reported mutations. (A) NSP5 structure scheme showing domain boundaries and the only one non-synonymous mutation found (in red). (B) NSP5 3D structure in the biological assembly as a dimer shown from different perspectives with the coloured mutation on each monomer.

Figure 5

NSP12-7-8 schematic and tridimensional structure with reported mutations. (A) NSP12 and its cofactors NSP7 and NSP8 structure schemes showing domain boundaries and non-synonymous mutations as coloured triangles. (B) RNA dependent RNA polymerase (RdRp) complex (NSP12-NSP7-NSP8-NSP8) 3D structure in different orientations to show the mutations found.

Figure 6

Nucleocapsid (N) schematic and tridimensional structure with reported mutations. (A) N structure scheme showing domain boundaries and non-synonymous mutations found as coloured triangles. (B) N 3D structure in the biological assembly as a dimer showing N-terminal Domain (NTD) and C-terminal Domain (CTD) solved portions with the coloured mutations on each monomer.

Figure 7

Spike protein (S) schematic and tridimensional structure with reported mutations. (A) S structure scheme showing domain boundaries and non-synonymous mutations as coloured triangles. (B) S 3D structure in its biological assembly as a trimer shown from two different perspectives with the coloured mutations on each monomer.