GREAT LIFE Scientific Publications
The following scientific publications were supported by the GREAT-LIFE project.
Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations
Otani et al. 2025
In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution. Sequencing 546 African hominid metagenomes, including those from indigenous Hadza and wild chimpanzees, identified similar bacterial richness and diversity surpassing those of westernized populations. While hominids share core bacterial communities, they also harbor distinct, population-specific bacterial taxa tailored to specific diets, ecology and lifestyles, differentiating non-indigenous and indigenous humans and chimpanzees.
DOI: https://doi.org/10.1080/19490976.2025.2484385 31 March 2025
Draft genomic sequences of Vibrio cholerae strains linked to the cholera outbreak in Kamituga, South Kivu, DRC
Leekitcharoenphon et al. 2025
Vibrio cholerae is responsible for outbreaks in Africa, but the cause of the outbreaks remains poorly understood. Here, we report the draft genomes of four Vibrio cholerae strains isolated from individuals affected by an outbreak in Kamituga, South Kivu, the Democratic Republic of the Congo, between January and May 2024.
DOI: https://doi.org/10.1128/mra.01044-24 20 March 2025
Epidemiological and genomic evolution of the ongoing outbreak of clade Ib mpox virus in the eastern Democratic Republic of the Congo
Leandre Murhula Masirika et al. 2025
In September 2023, an ongoing mpox outbreak emerged in South Kivu (Democratic Republic of the Congo) that spread to other regions and countries. Here we describe the epidemiological and genomic evolution of the outbreak between September 2023 and June 2024. Samples were collected from hospitalized patients, along with data on residence and possible exposures.
DOI: https://doi.org/10.1038/s41591-025-03582-1 11 February 2025
Prevalence, Etiology, and Treatment of Diarrheal Diseases in Kenya: A Scoping Review
Ogumbo et al. 2024
Annually, diarrhea causes approximately 1.6 million deaths worldwide, predominantly in Sub-Saharan Africa. In Kenya, diarrheal diseases are among the leading causes of morbidity and mortality, particularly affecting children under five. Despite various studies and interventions on diarrhea, the overall prevalence, distribution, pathogens and risk factors for diarrhea in Kenya remain inadequately investigated especially for atypical pathogens and adults. This scoping review aimed to synthesize available evidence on the prevalence, etiology, treatment, and risk factors associated with diarrheal diseases in Kenya across all age groups.
DOI: 10.12691/ajeid-12-4-1 22 December 2024
Rift Valley Fever outbreaks in the East African Community: insights from ProMed data (2010–2024)
Ndishimye et al. 2024
Rift Valley Fever (RVF) is a mosquito-borne zoonotic disease that poses a serious threat to both humans and livestock across various regions, particularly in Africa, the Arabian Peninsula, and parts of the Indian Ocean Islands. This study seeks to analyze the spatial and temporal distribution and trends of RVF outbreaks within the East African Community (EAC) countries, offering insights into the patterns and progression of these outbreaks in the region.
DOI: https://doi.org/10.3389/fpubh.2024.1298594 11 December 2024
Preliminary analysis of 98 genomic sequences of MPXV clade Ib cases from Burundi, July to September 2024
Nehemie Nzoyikorera and Bas Oude Munnink
A large mpox clade Ib virus outbreak started in the province of South Kivu in the Democratic Republic of the Congo (DRC) and is rapidly geographically expanding to other areas within the DRC as well as to other countries surrounding the DRC. Especially Burundi is severely affected with close to 1531 confirmed cases of mpox Clade Ib virus infections since the first detection at the end of July 2024. In addition, travel related cases linked to east African countries have been identified in Germany, Kenya, India, Sweden and Thailand.
https://virological.org/t/preliminary-analysis-of-98-genomic-sequences-of-mpxv-clade-ib-cases-from-burundi-july-to-september-2024/987/1 19 November 2024
Monkeypox Clade Ib virus introduction into Burundi: first findings, July to mid-August 2024
Nzoyikorera et al. 2024
From May 2023, a sharp increase of mpox cases due to MPXV Clade I was observed across the Democratic Republic of Congo (DRC), with cases occurring in areas where MPXV had not prior been detected. Investigations indicated ongoing virus evolution and the co-circulation of several different Clade I MPXV sub-lineages in DRC. Subsequent epidemiological, sequencing, and phylogenetic analyses revealed that MPXV of Clade Ib was spreading geographically within the DRC and cases were detected in other countries like Burundi, India, Kenya, Rwanda, Sweden, Tanzania, Thailand and Uganda.
DOI: https://doi.org/10.2807/1560-7917.ES.2024.29.42.2400666 17 October 2024
Improved ability to utilize lactose and grow in milk as a potential explanation for emergence of the novel bovine Staphylococcus aureus ST5477
Aarestrup et al. 2024
Staphyloccous aureus belonging to sequence type 5477 have recently been identified as a predominant clone causing bovine mastitis in Rwanda and Tanzania. We compared nine S. aureus ST5477 to 17 isolates belonging to other sequence types by their biochemical profile and ability to acidify milk and grow in minimum media containing lactose. We found that ST5477 isolates all were positive in ONPG (o-nitrophenyl-β-D-galactopyranoside) test and negative for mannitol fermentation potentially challenging the correct identification of this sequence type as S. aureus.
DOI: https://doi.org/10.1016/j.ijmm.2024.151637 11 October 2024
Real-time PCR assay to detect the novel Clade Ib monkeypox virus, September 2023 to May 2024
Schuele et al. 2024
In 2022, a global outbreak of Clade II monkeypox virus (MPXV) spread to more than 111 countries that had not previously reported cases, predominantly affecting the community of men who have sex with men in Europe and the Americas. In the following year, the number of MPXV Clade I virus cases surged in Africa, with reports of more than 20,000 cases and 1,000 deaths spanning 25 of the 26 provinces in the Democratic Republic of the Congo (DRC) by June 2024. We recently showed that part of this is due to a separate mpox outbreak, which started in September 2023 in the South Kivu province from mostly heterosexual transmission and caused by a highly divergent Clade I virus, now designated Clade Ib.
DOI: https://doi.org/10.2807/1560-7917.ES.2024.29.32.2400486 08 August 2024
NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads
Hallgren et al. 2024
Rapid advancements in sequencing technologies have led to significant progress in microbial genomics, yet challenges persist in accurately identifying microbial strain diversity in metagenomic samples, especially when working with noisy long-read data from platforms like Oxford Nanopore Technologies (ONT). In this article, we introduce NanoMGT, a tool designed to enhance marker gene typing in low-complexity mono-species samples, leveraging the unique properties of long reads.
DOI: https://doi.org/10.1093/biomethods/bpae057 06 August 2024
Preliminary analysis of full genome sequences of 58 MPXV clade Ib cases from Kamituga and Kamanyola, South-Kivu , DRC
Bas B. Oude Munnink et al. 2024
Recently, we showed that the MPXV outbreak in South Kivu is associated with a novel sub- lineage of clade I viruses (Murhula Masirika et al, 2024). The majority of these cases seem to be transmitted through heterosexual contact, with also person-to-person transmission within and outside the households. Here we provide an update of the ongoing sequencing effort.
Ongoing mpox outbreak in Kamituga, South Kivu province, associated with monkeypox virus of a novel Clade I sub-lineage, Democratic Republic of the Congo, 2024
Leandre Murhula Masirika et al. 2024
Since the beginning of 2023, the number of people with suspected monkeypox virus (MPXV) infection have sharply increased in the Democratic Republic of the Congo (DRC). We report near-to-complete MPXV genome sequences derived from six cases from the South Kivu province. Phylogenetic analyses reveal that the MPXV affecting the cases belongs to a novel Clade I sub-lineage. The outbreak strain genome lacks the target sequence of the probe and primers of a commonly used Clade I-specific real-time PCR.
DOI: https://doi.org/10.2807/1560-7917.ES.2024.29.11.2400106 14 March 2024