Genomic surveillance of SARS-CoV-2 in the Republic of Congo

Ntoumi, Francine; Mapanguy, Claujens Chastel Mfoutou; Tomazatos, Alexandru; Pallerla, Srinivas Reddy; Linh, Le Thi Kieu; Casadei, Nicolas; Angelov, Angel; Sonnabend, Michael; Peter, Silke; Kremsner, Peter G.; Velavan, Thirumalaisamy P.

doi:10.1016/j.ijid.2021.03.036

Cited by 22 publications

(23 citation statements)

References 13 publications

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“…B.1.214.2 is linked with the parent lineage B.1.214, which spread in the early phases of the pandemics in the Democratic Republic of Congo (Ntoumi et al, 2021) and possibly in other neighboring countries where limited genomic surveillance was carried out in 2020. As a result of exportations, four distinct sister clades later spread, with different success, in Europe between December 2020 and the first months of 2021: B.1.214.1, the most basal of these and the only one to lack the T617I spike mutation, B.1.214.2, B.1.214.3 and B.1.214.4.…”

Section: Resultsmentioning

confidence: 99%

Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

Gerdol

2021

Preprint

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Tracking the evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) through genomic surveillance programs is undoubtedly one of the key priorities in the current pandemic situation. Although the genome of SARS-CoV-2 acquires mutations at a slower rate compared with other RNA viruses, evolutionary pressures derived from the widespread circulation of SARS-CoV-2 in the human population have progressively favored the global emergence though natural selection of several variants of concern that carry multiple non-synonymous mutations in the spike glycoprotein. Such mutations are often placed in key sites within major antibody epitopes and may therefore confer resistance to neutralizing antibodies, leading to partial immune escape, or otherwise compensate minor infectivity deficits associated with other mutations. As previously shown by other authors, several emerging variants carry recurrent deletion regions (RDRs) that display a partial overlap with antibody epitopes located in the spike N-terminal domain. Comparatively, very little attention has been directed towards spike insertion mutations, which often go unnoticed due to the use of insertion-unaware bioinformatics analysis pipelines. This manuscript describe a single recurrent insertion region (RIR1) in the N-terminal domain of SARS-CoV-2 spike protein, characterized by the independent acquisition of 3-4 additional codons between Arg214 and Asp215 in different viral lineages. Even though RIR1 is unlikely to confer antibody escape, its progressive increase in frequency and its association with two distinct emerging lineages (A.2.5 and B.1.214.2) warrant further investigation concerning its effects on spike structure and viral infectivity.

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Section: Resultsmentioning

confidence: 99%

Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

Gerdol

2021

Preprint

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“…SARS-CoV-2 mutants have been genetically characterized using NGS-based lineages [ 13 , 29 ]. To confirm the detection accuracy of the 5-SSG primer assay developed in this study for the SARS-CoV-2 mutants, NGS analysis results were used for a comparison.…”

Section: Resultsmentioning

confidence: 99%

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations

Lim

Park²,

Jung³

et al. 2021

PLoS ONE

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Novel strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring nucleotide changes (mutations) in the spike gene have emerged and are spreading rapidly. These mutations are associated with SARS-CoV-2 transmissibility, virulence, or resistance to some neutralizing antibodies. Thus, the accurate detection of spike mutants is crucial for controlling SARS-CoV-2 transmission and identifying neutralizing antibody-resistance caused by amino acid changes in the receptor-binding domain. Here, we developed five SARS-CoV-2 spike gene primer pairs (5-SSG primer assay; 69S, 144S, 417S, 484S, and 570S) and verified their ability to detect nine key spike mutations (ΔH69/V70, T95I, G142D, ΔY144, K417T/N, L452R, E484K/Q, N501Y, and H655Y) using a Sanger sequencing-based assay. The 5-SSG primer assay showed 100% specificity and a conservative limit of detection with a median tissue culture infective dose (TCID50) values of 1.4 × 102 TCID50/mL. The accuracy of the 5-SSG primer assay was confirmed by next generation sequencing. The results of these two approaches showed 100% consistency. Taken together, the ability of the 5-SSG primer assay to accurately detect key SARS-CoV-2 spike mutants is reliable. Thus, it is a useful tool for detecting SARS-CoV-2 spike gene mutants in a clinical setting, thereby helping to improve the management of patients with COVID-19.

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“…This suggests a common entry point or circulation of the B.1.128 lineage during this month ( Figure 6 ). In the Republic of Congo, the genomic surveillance of SARS-CoV-2 revealed that 9/11 sequences belonged to clade 20A while two sequences were part of clade 20C ( 33 ). Population movements and trade with the Republic of the Congo border could be another entry point of this strain.…”

Section: Discussionmentioning

confidence: 99%

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

et al. 2022

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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.

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Genomic surveillance of SARS-CoV-2 in the Republic of Congo

Cited by 22 publications

References 13 publications

Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

Emergence of a recurrent insertion in the N-terminal domain of the SARS-CoV-2 spike glycoprotein

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations

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

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