Integrated Seroprevalence and Genome-Based Study of SARS-CoV-2 Viral Strains in N'Djamena: Insights Into Chad's COVID-19 Epicenter

Abstract

The COVID-19 epidemic has shown regional variations in transmission and outcomes. As a primary hotspot in Chad, N'Djamena is crucial for comprehensive epidemiological investigation. Our study employed two methodologies: seroprevalence data collection and whole-genome sequencing of SARS-CoV-2 strains. This dual approach assessed population exposure and virus genetic diversity. Seroprevalence data indicated broader exposure than confirmed cases suggested, and genome sequencing identified multiple strains, including globally recognized variants of concern. Integrating these data provided insights into transmission dynamics, potential herd immunity thresholds, and the impact of specific variants on disease progression. Our findings underscore the importance of integrated, multidisciplinary research in infectious disease epidemiology and inform targeted public health strategies, including social measures and vaccination, to combat infectious diseases in N'Djamena.

Keywords: Chad; SARS‐CoV‐2; genomic surveillance; seroprevalence.

Figure 1

Genetic diversity and sequencing statistics of SARS‐CoV‐2. The chart illustrates the percentage of the SARS‐CoV‐2 genome sequenced in relation to the RT‐qPCR Ct value for each of the 42 samples. Each circle represents a sequence recovered from an infected individual in Chad, with colors indicating lineage assignment.

Figure 2

Temporal distribution of SARS‐CoV‐2 variants in N'Djamena, Chad from November 2021 to January 2022.

Figure 3

Phylogenetic analysis of SARS‐CoV‐2 viral strains circulating in N'Djamena, Chad, between November 2021 and January 2022. A time‐resolved maximum‐likelihood tree of SARS‐CoV‐2, including novel isolates (n = 42) and representative worldwide subsample genomes (n = 3000) collected up to November 2022. The genomes are colored according to the lineages (VOC and ancestral lineages) as shown in the legend on the top left. The genomes generated in this study have been highlighted in the tree with circles: black circles represent genomes from patients with mild cases, while red circles represent genomes from patients with severe cases.