Publications – Team A. Claessens
See Antoine Claessens’ ORCID for complete publication list
| Main peer-reviewed publications | Comment |
| Bhardwaj I, Nyarko P, … Radulescu O, Claessens A (2024). Diverse var gene expression sustained by rapid switching facilitates malaria infection. Preprint, under revision in Plos Genetics. Corresponding senior author. | Using P.f. isolates from The Gambia, we measured the var gene switching rate in vivo and in vitro, and found it much higher than previously estimated. |
| Fogang B,… , Claessens A (2024). Detection of novel Plasmodium falciparum haplotypes under treatment pressure in pediatric severe malaria. PrePrint on MedRxiv, currently under review in Microbial Genomics. Corresponding senior author. | We found that Amplicon Sequencing is more sensitive than WGS in detecting multiple P. falciparum genomes in severe malaria cases. During parasite clearance we identified new parasite genotypes appearing in circulation after treatment, highlighting the complexity of infections. |
| Guery MA,… , Claessens A (2024). Household clustering and seasonal genetic variation of Plasmodium falciparum at the community-level in The Gambia. eLife. doi: 10.7554/eLife.103047.1 Corresponding senior author. | We collected ~ 400 P. falciparum genetic barcodes and ~200 genomes over 2 years in The Gambia. We found that parasite populations frequently recombine, with higher genetic relatedness observed within households, and that asymptomatic carriers play a critical role in sustaining malaria transmission. |
| Stewart LB, Lantero-Escolar E, Philpott J, Claessens A, Alfred Amambua-Ngwa, Conway D (2024). Higher multiplication rates of Plasmodium falciparum in isolates from hospital cases compared with community infections. Scientific Reports (in press). | Using P.f. isolates from The Gambia, we found that the in vitro parasite multiplication rate correlates with parasitaemia in vivo. Our hypothesis is that intrinsic natural variation in parasite multiplication rate may affect levels of parasitaemia achieved during infection. |
| Diffendall G, Claës A, …, Loew D, Claessens A, Scherf A (2024). RNA polymerase III is involved in regulating P falciparum virulence. eLife. doi: 10.7554/eLife.95879.2 | Together with Artur Scherf’s lab, we showed RNA polymerase III transcription in P falciparum is downregulated in field isolates during the dry season, this in turn controls RUF6 and var gene transcription. |
| Miotto O, MalariaGEN partners, (2024). A complex Plasmodium falciparum cryptotype circulating at low frequency across the African continent. Lancet Microbes. Doi: 10.1016/j.lanmic.2024.07.004 | In my humble opinion, the most exciting result in genomic epidemiology of the last few years: the discovery of a new, rare, “sub-species-like” of P. falciparum. We are planning on following up this work with isolates from the Centre National de Référence du Paludisme. |
| Fogang B, Lellouche L, …, Bousema T, Claessens A* (2024). Asymptomatic Plasmodium falciparum Carriage at the End of the Dry Season is Associated with Subsequent Infection and Clinical Malaria in Eastern Gambia. Malaria Journal. doi: 10.1186/s12936-024-04836-y. Corresponding senior author. | While I was based at the MRC-Gambia, we recruited ~2000 individuals over 2.5 years. It was thought that being asymptomatically infected with P. falciparum during the dry season would ‘boost’ the immune system and protect you from symptomatic malaria. However our data showed it is the other way around, being asymptomatic is a risk factor for subsequent symptomatic infections. |
| Claessens A*, Stewart L,…, David Conway (2023). Genomic variation during culture adaptation of genetically complex Plasmodium falciparum clinical isolates. Microbial Genomics. DOI 10.1099/mgen.0.001009. Corresponding author. | Most comprehensive characterisation of P. falciparum genomes during the process of culture adaptation, including from polyclonal infections. With WGS of the largest dataset of isolates under culture adaptation, we identified loss-of-function mutations and dynamic interactions between multiple P.f. genotypes. |
| MalariaGEN consortium (2023). Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide sample. Wellcome Open Research. | MalariaGEN is a consortium of ~40 laboratories working on Malaria Genetic Epidemiology. Together we have contributed to the largest database of P.f. genomes |
| Collins K, Ceesay S, …, Bousema T & Claessens A* (2022). A cohort study on the duration of Plasmodium falciparum infections during the dry season in The Gambia. Journal of Infectious Diseases. https://doi.org/10.1093/infdis/jiac116. Corresponding senior author. | From the cohort I had recruited in The Gambia, we characterised human hosts and parasites of chronic P.f. infections. Single-cell sequencing of these samples coming very soon… |
| Sarah-Matio EM, Guillochon E, Nsango S, …, Claessens A, Lefèvre T, Berry A, Morlais I (2022). Genetic Diversity of Plasmodium falciparum and Distribution of Antimalarial Drug Resistance Mutations in Symptomatic and Asymptomatic Infections. Antimicrob Agents Chemother. doi: 10.1128/aac.00188-22 | My role was to analyse the Amplicon Sequencing data. |
| Guéry MA & Claessens A (2021). Order within chaos: Harnessing Plasmodium falciparum var gene extreme polymorphism for malaria epidemiology. Perspective (Commentary) on Tonkin-Hill et al, PLOS Genetics. Doi: 10.1371/journal.pgen.1009344. Corresponding senior author | Commentary paper. |
| MalariaGEN consortium (2021). An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Research. | MalariaGEN is a consortium of ~40 laboratories working on Malaria Genetic Epidemiology |
| Nyarko P & Claessens A (2021). Understanding Host-Pathogen-Vector Interactions with Chronic Asymptomatic Malaria Infections. Opinion in Trends in Parasitology. doi: 10.1016/j.pt.2020.09.017. Corresponding senior author. | Opinion Review describing our current and future projects. Corresponding author. |
| Stewart L, Diaz-Ingelmo, Claessens A, …, Conway DJ (2020).Intrinsic multiplication rate variation and plasticity of human blood stage malaria parasites. Communications Biology. https://doi.org/10.1038/s42003-020-01349-7 | Genetic basis of culture adaptation, I wrote a ‘Behind the paper’ blog about it. |
| Open Lab Notebook Consortium (2019). Open laboratory notebooks: good for science, good for society, good for scientists. F1000Research. Doi: 10.12688/f1000research.17710.2 | An international consortium going beyond the FAIR principles, to make Science more reproducible with ‘Open Notebooks’. |
| Otto T, Bohme U, …, Claessens A,…, Newbold C, Berriman M (2018). Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Research. doi: 10.12688/wellcomeopenres.14571.1 | Long-read sequencing of 15 P. falciparum isolates for comparative analysis of the entire genome with particular emphasis on the subtelomeric regions and the internal var genes clusters. |
| Claessens A, Harris LM, Stanojcic S, Chappell L, et al. (2018) RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics. PLoS Genetics. doi: 10.1371/journal.pgen.1007490 | First characterization of a protein involved in genome stability in P. falciparum. Cited 23 times (Google Scholar). |
Recent publications
Claessens A, Stewart LB, Drury E, Ahouidi AD, Amambua-Ngwa A, Diakite M, Kwiatkowski DP, Awandare GA, Conway DJ (2023) Genomic variation during culture adaptation of genetically complex Plasmodium falciparum clinical isolates. Microb Genom 9:mgen001009. doi:10.1099/mgen.0.001009
Diffendall G, Claës A, Barcons-Simon A, Nyarko P, Dingli F, Loew D, Claessens A, Scherf A (2023) RNA polymerase III is involved in regulating Plasmodium falciparum virulence. BioRxiv 2023.07.18.549525. doi:10.1101/2023.07.18.549525
MalariaGEN; Abdel Hamid MM et al (2023) Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome Open Res 8:22. doi:10.12688/wellcomeopenres
Claessens A, Stewart LB, Drury E, Ahouidi AD, Amambua-Ngwa A, Diakite M, Kwiatkowski DP, Awandare GA, Conway DJ (2022) Genomic variation during culture-adaptation of genetically complex Plasmodium falciparum clinical isolates. BioRxiv 2022.09.14.507918. doi:10.1101/2022.09.14.507918
Sarah-Matio EM, Guillochon E, Nsango SE, Abate L, Ngou CM, Bouopda GA, Feufack-Donfack LB, Bayibéki AN, Tchioffo Tsapi M, Talman A, Marin-Menendez A, Ayong L, Claessens A, Lefèvre T, Berry A, Morlais I (2022) Genetic Diversity of Plasmodium falciparum and Distribution of Antimalarial Drug Resistance Mutations in Symptomatic and Asymptomatic Infections. Antimicrob Agents Chemother 66:e0018822. doi:10.1128/aac.00188-22
Collins KA, Ceesay S, Drammeh S, Jaiteh FK, Guery MA, Lanke K, Grignard L, Stone W, Conway DJ, D’Alessandro U, Bousema T, Claessens A (2022) A Cohort Study on the Duration of Plasmodium falciparum Infections During the Dry Season in The Gambia. J Infect Dis 226:128-137. doi:10.1093/infdis/jiac116
MalariaGEN; Ahouidi A et al (2021) An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 6:42. doi:10.12688/wellcomeopenres
Guery MA, Claessens A (2021) Order within chaos: Harnessing Plasmodium falciparum var gene extreme polymorphism for malaria epidemiology. PLoS Genet 17:e1009344. doi:10.1371/journal.pgen.1009344
Nyarko PB, Claessens A (2021) Understanding Host-Pathogen-Vector Interactions with Chronic Asymptomatic Malaria Infections. Trends Parasitol 37:195-204. doi:10.1016/j.pt.2020.09.017
Stewart LB, Diaz-Ingelmo O, Claessens A, Abugri J, Pearson RD, Goncalves S, Drury E, Kwiatkowski DP, Awandare GA, Conway DJ (2020) Intrinsic multiplication rate variation and plasticity of human blood stage malaria parasites. Commun Biol 3:624. doi:10.1038/s42003-020-01349-7
Claessens A, Harris LM, Stanojcic S, Chappell L, Stanton A, Kuk N, Veneziano-Broccia P, Sterkers Y, Rayner JC, Merrick CJ (2018) RecQ helicases in the malaria parasite Plasmodium falciparum affect genome stability, gene expression patterns and DNA replication dynamics. PLoS Genet 14:e1007490. doi:10.1371/journal.pgen.1007490