Screening and Whole Genome Sequencing of SARS-CoV-2 Circulating During the First Three Waves of the COVID-19 Pandemic in Libreville and the Haut-Ogooué Province in Gabon

Abstract

Since the onset of the COVID-19 pandemic, the SARS-CoV-2 viral dynamics in Africa have been less documented than on other continents. In Gabon, a Central African country, a total number of 37,511 cases of COVID-19 and 281 deaths have been reported as of December 8, 2021. After the first COVID-19 case was reported on March 12, 2020, in the capital Libreville, the country experienced two successive waves. The first one, occurred in March 2020 to August 2020, and the second one in January 2021 to May 2021. The third wave began in September 2021 and ended in November 2021. In order to reduce the data gap regarding the dynamics of SARS-CoV-2 in Central Africa, we performed a retrospective genotyping study using 1,006 samples collected from COVID-19 patients in Gabon from 2020 to 2021. Using SARS-CoV-2 variant screening by Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) and whole genome sequencing (WGS), we genotyped 809 SARS-CoV-2 samples through qRT-PCR and identified to generated 291 new genomes. It allowed us to describe specific mutations and changes in the SARS-CoV-2 variants in Gabon. The qRT-PCR screening of 809 positive samples from March 2020 to September 2021 showed that 119 SARS-CoV-2 samples (14.7%) were classified as VOC Alpha (Pangolin lineage B.1.1.7), one (0.1%) was a VOC Beta (B.1.351), and 198 (24.5 %) were VOC Delta (B.1.617.2), while 491 samples (60.7%) remained negative for the variants sought. The B1.1 variant was predominant during the first wave while the VOC Alpha dominated the second wave. The B1.617.2 Delta variant is currently the dominant variant of the third wave. Similarly, the analysis of the 291 genome sequences indicated that the dominant variant during the first wave was lineage B.1.1, while the dominant variants of the second wave were lineages B.1.1.7 (50.6%) and B.1.1.318 (36.4%). The third wave started with the circulation of the Delta variant (B.1.617). Finally, we compared these results to the SARS-CoV-2 sequences reported in other African, European, American and Asian countries. Sequences of Gabonese SARS-CoV-2 strains presented the highest similarities with those of France, Belgium and neighboring countries of Central Africa, as well as West Africa.

Epidemiology of first cases of SARS-CoV-2 infection, from March to April 2020, in Gabon

“…The whole genome of 64 Gabonese strains of the beginning of the pandemic provided information on the predominant lineage B.1.1 (51/64) of this period. 23 In conclusion, this study reported the first data on the COVID-19 pandemic in Gabon. The data showed that most of the infected people were asymptomatic.…”

“… 22 We performed the whole genome of three of the samples from the first cases as part of a study on the genotyping of strains of SARS-CoV-2 circulating in Gabon. 23 These samples 34 (Accesion number GenBank MW512911, GISAID EPI_ISL_8886131), 56 (Accesion number GenBank MW512912, GISAID EPI_ISL_8886132) and 62 (Accesion number GenBank MW512913, GISAID EPI_ISL_8886133) belonged to lineage B.1, A, B.1.356 respectively. The introduction of lineage B was characteristic of the D614G mutation.…”

“…The whole genome of 64 Gabonese strains of the beginning of the pandemic provided information on the predominant lineage B.1.1 (51/64) of this period. 23 …”

Unravelling Antigenic Cross-Reactions toward the World of Coronaviruses: Extent of the Stability of Shared Epitopes and SARS-CoV-2 Anti-Spike Cross-Neutralizing Antibodies

“…We proposed several hypotheses that could possibly account for a late emergence and lower spread of COVID-19 in African countries, including the lack of detection and reporting of COVID-19 cases, social distancing, reduced international air traffic flows, climate, the relatively young (asymptomatic cases) and rural population, the genetic polymorphism of ACE2 or other genes involved in the control of viral replication, the use of anti-malarial drugs, and, ultimately, cross-immunity conferred by other viruses circulating in Africa [ 163 ]. Subsequently, our whole genome sequencing analyzes and those of other teams showed that African populations are sensitive to the same lineages as people from other continents [ 164 , 165 , 166 ]. Several studies have shown immune reactivity to SARS-CoV-2 proteins in samples from individuals that were collected before the COVID-19 pandemic, providing definitive evidence that SARS-CoV-2 cross-reactive immune responses may be derived from pre-existing immunity against previous non-SARS-CoV-2 infections.…”

COVID Seq as Laboratory Developed Test (LDT) for diagnosis of SARS-CoV-2 Variants of Concern (VOC)

“…Diagnosis of COVID-19 relies on detecting SARS-CoV-2 viral RNA from a nasopharyngeal or oropharyngeal specimen [1]. However, the rapid emergence of several variants with higher virulence and infectivity has provoked repeat waves of the deadly pandemic in many countries and raised anxieties about vaccine efficacy and diagnostic accuracy [2]. Rapid classification and tracking of emerging variants are critical for understanding the transmission dynamics of this disease and developing strategies for severing the transmission chain.…”