ArticleInternational journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases2022
Whole-genome sequencing of SARS-CoV-2 reveals diverse mutations in circulating Alpha and Delta variants during the first, second, and third waves of COVID-19 in South Kivu, east of the Democratic Republic of the Congo.
Article in International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 27 citations in OpenAlex.
- Imported SARS-CoV-2 Infections at N'djili International Airport in Kinshasa, Democratic Republic of Congo: An Epidemiological and Genomic Analysis.Influenza and other respiratory viruses · 2026Article
- A tiled amplicon protocol for culture-free whole-genome sequencing ofJournal of clinical microbiology · 2026Article
- Article
- Suppnonsense-mediated decay-linked mutations in SARS-CoV-2 and their association with COVID-19 disease severity.BMC infectious diseases · 2025Article
- Factors predictive of epidemic waves of COVID-19 in Africa during the first 2 years of the pandemic.IJID regions · 2025Article
- SARS-CoV-2 excretion and genetic evolution in nasopharyngeal and stool samples from primary immunodeficiency and immunocompetent pediatric patients.Virology journal · 2025Article
- Rate, risk factors, and clinical outcomes of SARS-CoV-2 reinfection vs. primary infection in readmitted COVID-19 patients in Iran: a retrospective cohort study.Frontiers in public health · 2024Article
- Molecular epidemiology of SARS-CoV-2 in Mongolia, first experience with nanopore sequencing in lower- and middle-income countries setting.Immunity, inflammation and disease · 2023Article
- COVID-19 in 16 West African Countries: An Assessment of the Epidemiology and Genetic Diversity of SARS-CoV-2 after Four Epidemic Waves.The American journal of tropical medicine and hygiene · 2023Review
- Nanopore sequencing technology and its applications.MedComm · 2023Review
- Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective.ACS omega · 2023Review
- Clinical and Virological Features of SARS-CoV-2 Variants during the Four Waves of the Pandemic in the Mexican Southeast.Tropical medicine and infectious disease · 2023Article
- Safety and immunogenicity of the third (booster) dose of inactivated and recombinant protein SARS-CoV-2 vaccine for patients with endocrine-related cancer.Frontiers in public health · 2023Observational
- Five successive waves of SARS-CoV-2 infection in the Central African Republic: a prospective observational study from 2020-2022.The Pan African medical journal · 2023Observational
- Seroprevalence of SARS-CoV-2 antibodies and retrospective mortality in two African settings: Lubumbashi, Democratic Republic of the Congo and Abidjan, Côte d'Ivoire.PLOS global public health · 2023Article
- Safety and immunogenicity of inactivated SARS-CoV-2 vaccines in people with gastrointestinal cancer.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2022Observational
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
objectivesWe used whole-genome sequencing of SARS-CoV-2 to identify variants circulating in the Democratic Republic of the Congo and obtain molecular information useful for diagnosis, improving treatment, and general pandemic control strategies.
methodsA total of 74 SARS-CoV-2 isolates were sequenced using Oxford Nanopore platforms. Generated reads were processed to obtain consensus genome sequences. Sequences with more than 80% genome coverage were used for variant calling, phylogenetic analysis, and classification using Pangolin lineage annotation nomenclature.
resultsPhylogenetic analysis based on Pangolin classification clustered South Kivu sequences into seven lineages (A.23.1, B.1.1.6, B.1.214, B.1.617.2, B.1.351, C.16, and P.1). The Delta (B.1.617.2) variant was the most dominant and responsible for outbreaks during the third wave. Based on the Wuhan reference genome, 289 distinct mutations were detected, including 141 missenses, 123 synonymous, and 25 insertions/deletions when our isolates were mapped to the Wuhan reference strain. Most of these point mutations were located within the coding sequences of the SARS-CoV-2 genome that includes spike, ORF1ab, ORF3, and nucleocapsid protein genes. The most common mutation was D614G (1841A>G) observed in 61 sequences, followed by L4715L (14143 C>T) found in 60 sequences.
conclusionOur findings highlight multiple introductions of SARS-CoV-2 into South Kivu through different sources and subsequent circulation of variants in the province. These results emphasize the importance of timely monitoring of genetic variation and its effect on disease severity. This work set a foundation for the use of genomic surveillance as a tool for future global pandemic management and control.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.