Biology subjects

Rajahram, G. S.

Publications and source records attributed to Rajahram, G. S..

5 recordsLinked to original sources

bioRxiv2026

Pfcrt copy number amplification detected in a Plasmodium falciparum outbreak

Antimalarial resistance is one of the greatest threats to malaria elimination. Following an outbreak of Plasmodium falciparum infection in Sabah Malaysia in 2019, 98 samples were sequenced to search for adaptations driving the outbreak. The genomic data revealed evidence of clonal expansion of a strain carrying multiple copies of the chloroquine resistance transporter gene (pfcrt) in 86 cases. A TaqMan qPCR assay was developed to quantify pfcrt copy number, confirming the in silico evidence of duplication. Whilst point mutations in pfcrt have been associated with resistance to chloroquine and other drugs, copy number amplification has not been widely explored as a resistance mechanism. We investigated the genetic architecture of the duplication, revealing a wildtype haplotype (3D7 reference-type with 76K variant) and a novel mutant (with 76T mutation). Application of the TaqMan assay in 43 P. falciparum cases from neighbouring Palawan Island, the Philippines, identified a further two cases with pfcrt duplication. Assessment of the global genomic data in the MalariaGEN Pf8 repository identified a further 86 cases, including 73 (85%) from West Africa with evidence of pfcrt duplication. Amongst 47 monoclonal MalariaGEN cases, majority (95%) comprised wild type and mutant variants at codon 76. Our study reveals a potential previously unconsidered antimalarial resistance mechanism for P. falciparum and provides an assay for surveillance in other populations.

genomics↗

bioRxiv2026

Integrative genomics of Plasmodium knowlesi reveals parasite-intrinsic regulators of severe human malaria

To dissect parasite determinants of clinical disease severity in Plasmodium knowlesi, we performed the first integrative genome-wide association (GWAS), transcriptomic, and expression quantitative trait locus (eQTL) analysis from clinical malaria isolates. We identify distinct parasite programs associated with WHO-defined severe disease, characterized by transcriptional activation of stress-response and host-interaction pathways. In contrast, invasion-linked programs were more strongly associated with parasite burden, while immune-evasion pathways showed overlapping but distinct associations with both burden and severity. GWAS and eQTL analyses revealed genetic regulation of transcriptional states, including immune-evasion variant antigen families (SICAvar and kir) and chromatin-associated regulators. Mature gametocyte transcripts were detectable across infections, including those with low parasitaemia, indicating that transmission-stage expression occurs independently of both clinical severity and parasite density. Together, these findings show that severe P. knowlesi malaria is associated with genetically regulated parasite transcriptional programs that are not fully explained by parasite burden.

genomics↗

bioRxiv2024

A virus associated with the zoonotic pathogen Plasmodium knowlesi causing human malaria is a member of a diverse and unclassified viral taxon

Apicomplexa are single-celled eukaryotes that can infect humans and include the mosquito-borne parasite Plasmodium, the cause of malaria. Increasing rates of drug resistance in human-only Plasmodium species are reducing the efficacy of control efforts and antimalarial treatments. There are also rising cases of P. knowlesi, the only zoonotic Plasmodium species that causes severe disease and death in humans. Thus, there is a need to develop additional innovative strategies to combat malaria. Viruses that infect non-Plasmodium spp. disease-causing protozoa have been shown to affect pathogen life cycle and disease outcomes. However, only one virus (Matryoshka RNA virus 1) has been identified in Plasmodium, and none have been identified in zoonotic Plasmodium species. The rapid expansion of the known RNA virosphere using structure- and artificial intelligence-based methods suggests that this dearth is due to the divergent nature of RNA viruses that infect protozoa. We leveraged these newly uncovered data sets to explore the virome of human-infecting Plasmodium species collected in Sabah, east (Borneo) Malaysia. We identified a highly divergent RNA virus in two human-infecting P. knowlesi isolates that is related to the unclassified group ormycoviruses. By characterising fifteen additional ormycoviruses identified in the transcriptomes of arthropods we show that this group of viruses exhibits a complex ecology at the arthropod-mammal interface. Through the application of artificial intelligence methods, we then demonstrate that the ormycoviruses are part of a diverse and unclassified viral taxon. This is the first observation of an RNA virus in a zoonotic Plasmodium species. By linking small-scale experimental data to large-scale virus discovery advances, we characterise the diversity and genomic architecture of an unclassified viral taxon. This approach should be used to further explore the virome of disease-causing Apicomplexa and better understand how protozoa-infecting viruses may affect parasite fitness, pathobiology, and treatment outcomes.

evolutionary biology↗

bioRxiv2024

Genomic epidemiology of Plasmodium knowlesi reveals putative genetic drivers of adaptation in Malaysia.

Sabah, Malaysia, has amongst the highest burden of human Plasmodium knowlesi infection in the country, associated with increasing encroachment on the parasites macaque host habitat. However, the genomic make-up of P. knowlesi in Sabah was previously poorly understood. To inform on local patterns of transmission and putative adaptive drivers, we conduct population-level genetic analyses of P. knowlesi human infections using 52 new whole genomes from Sabah, Malaysia, in combination with publicly available data. We identify the emergence of distinct geographical subpopulations within the macaque-associated clusters using IBD-based connectivity analysis. Secondly, we report on introgression events between the clusters, which may be linked to differentiation of the subpopulations, and that overlap genes critical for survival in human and mosquito hosts. Using village-level locations from P. knowlesi infections, we also identify associations between several introgressed regions and both intact forest perimeter-area ratio and mosquito vector habitat suitability. Our findings provide further evidence of the complex role of changing ecosystems and sympatric macaque hosts in Malaysia driving distinct genetic changes seen in P. knowlesi populations. Future expanded analyses of evolving P. knowlesi genetics and environmental drivers of transmission will be important to guide public health surveillance and control strategies. Author SummaryThe zoonotic P. knowlesi parasite is an emerging, yet understudied, cause of malaria in Southeast Asia. Sabah, Malaysia, has amongst the highest burden of human P. knowlesi infection in the country, however, the region is currently understudied. Thus, we produced a collection of high-quality P. knowlesi genomes from Sabah, and in combination with publicly available data, performed an extensive population genetics analysis. Our work contributes novel insights for Plasmodium knowlesi population genetics and genetic epidemiology.

genomics↗

bioRxiv2019

Spatial and epidemiologic features of dengue in Sabah, Malaysia

In South East Asia, dengue epidemics have increased in size and geographical distribution in recent years. Most studies investigating dengue transmission and control have had an urban focus, while less consideration is currently given to rural settings, or where urban and rural areas overlap. We examined the spatiotemporal distribution and epidemiological characteristics of reported dengue cases in the predominantly rural state of Sabah, in Malaysian Borneo - an area where sylvatic and urban circulation of pathogens are known to intersect. We found that annual dengue incidence rates were spatially variable over the 7-year study period from 2010-2016 (state-wide mean annual incidence of 21 cases/100,000 people; range 5-42/100,000), but were highest in rural localities in the western districts of the state (Kuala Penyu, Nabawan, Tenom and Kota Marudu). The eastern districts exhibited lower overall dengue rates; however, we noted a concentration of severe (haemorrhagic) dengue cases (44%) in Sandakan and Tawau districts. Dengue incidence was slightly higher for males than females, and was significantly higher for both genders aged between 10 and 29 years (24/100,000; p=0.029). The largest ever recorded outbreaks occurred during 2015-2016, with the vector Aedes albopictus found to be most prevalent in both urban and rural households (House Index of 64%), compared with Ae. Aegypti (15%). These findings suggest that dengue outbreaks in Sabah are driven by the sporadic expansion of dengue virus in both urban and rural settings. This may require tailoring of preventative strategies to suit different transmission ecologies across Sabah. Further studies to better understand the drivers of dengue in Sabah may aid dengue control efforts in Malaysia, and more broadly in South East Asia.\n\nAuthor summaryIn order to combat the rising regional incidence of dengue in South East Asia, the drivers of transmission must be better characterised across different environmental settings. We conducted the first retrospective analysis of dengue epidemiology in the predominantly rural state of Sabah, Malaysia, where both urban and sylvatic transmission cycles exist. Human notification data over a 7-year period were reviewed and spatiotemporal and demographic risk factors identified. We found: O_LIUrban habitats and population density are not the only determinants mediating the spread of epidemic dengue in Sabah. Case from both urban and rural localities contributed equally to dengue outbreaks.\nC_LIO_LIHuman demographic risk factors included being aged between 10 and 29 years, and being male.\nC_LIO_LIHigh incidence areas for dengue do not predict the occurrence of severe dengue. Severe dengue was largely localised to lower incidence districts in the east of the state.\nC_LIO_LIThe sole presence of Aedes albopictus in and around the majority of urban and rural case households suggests that this vector may play a major role in facilitating outbreaks.\nC_LI\n\nA complex interplay of risk factors likely mediates dengue transmission in Sabah, influenced by both regional climate trends and localised human and ecological influences. This study emphasises that the increasing spread of dengue in urban South East Asia is also mirrored in more rural areas, and suggests a need for control strategies that address both urban and rural dengue risk.

epidemiology↗