Khadija Said Mohammed
A5090004393- SARS-CoV-2 and COVID-19 Research
- SARS-CoV-2 detection and testing
- COVID-19 diagnosis using AI
- Hepatitis B Virus Studies
- Hepatitis C virus research
- Malaria Research and Control
- Liver Disease Diagnosis and Treatment
- Animal Virus Infections Studies
- Viral Infections and Outbreaks Research
- Genomics and Phylogenetic Studies
- COVID-19 epidemiological studies
- Bacteriophages and microbial interactions
- Virology and Viral Diseases
- Child Nutrition and Water Access
- Mosquito-borne diseases and control
- Cancer Genomics and Diagnostics
- Complement system in diseases
- Parasites and Host Interactions
- Respiratory viral infections research
- Viral gastroenteritis research and epidemiology
- Global Maternal and Child Health
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- Biosensors and Analytical Detection
- Education, Law, and Society
The Francis Crick Institute
2023-2025
University College London
2023-2024
Kenya Medical Research Institute
2018-2023
ORCID
2022
Wellcome Trust
2020-2022
World Health Organization - Pakistan
2021
University of Cambridge
2021
Addenbrooke's Hospital
2021
University of the West of Scotland
2018-2020
University Medical Center Utrecht
2018
The ARTIC Network's primer set and amplicon-based protocol is one of the most widely used SARS-CoV-2 sequencing protocol. An update to V3 was released on 18th June 2021 address amplicon drop-off observed among Delta variant concern. Here, we report an in-house optimization a modified version Network V4 that improves genome recovery in instances where original pooling strategy characterized by drop-offs.
Natural killer (NK) cells are potent immune effectors that can be activated via antibody-mediated Fc receptor engagement. Using multiparameter flow cytometry, we found NK degranulate and release IFN-γ upon stimulation with antibody-opsonized
Genomic surveillance of SARS-CoV-2 is important for understanding both the evolution and patterns local global transmission. Here, we generated 311 genomes from samples collected in coastal Kenya between 17
Abstract Ring-infected erythrocytes are the predominant asexual stage in peripheral circulation but rarely investigated context of acquired immunity against Plasmodium falciparum malaria. Here we compare antibody-dependent phagocytosis ring-infected parasite cultures samples from a controlled human malaria infection (CHMI) study (NCT02739763). Protected volunteers did not develop clinical symptoms, maintained parasitaemia below predefined threshold 500 parasites/μl and were treated until end...
Abstract Background Individuals living in endemic areas acquire immunity to malaria following repeated parasite exposure. We sought assess the controlled human infection (CHMI) model as a means of studying naturally acquired Kenyan adults with varying Methods analysed data from 142 three locations representing distinct endemicity (Ahero, Kilifi North and South) enrolled CHMI study Plasmodium falciparum sporozoites NF54 strain (Sanaria® PfSPZ Challenge). To identify vivo outcomes that most...
Abstract Hepatitis B virus (HBV) whole genome sequencing (WGS) is currently limited as the DNA viral loads (VL) of many clinical samples are below threshold required to generate full genomes using current methods. We developed two pan-genotypic enrichment methods, probe-based capture and tiled amplicon PCR (HEP-TILE) for HBV WGS. demonstrate mock that both methods (genotypes A-J). Using samples, we HEP-TILE amplification successfully amplifies at lowest VL tested (30 IU/ml), products can be...
<ns4:p><ns4:bold>Background.</ns4:bold> International recommendations for the control of coronavirus disease 2019 (COVID-19) pandemic emphasize central role laboratory testing severe acute respiratory syndrome 2 (SARS-CoV-2), etiological agent, at scale. The availability reagents, equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled (i.e. combining multiple samples in same reaction) has been suggested increase capacities period.</ns4:p><ns4:p>...
Detailed understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) regional transmission networks within sub-Saharan Africa is key for guiding local public health interventions against the pandemic. Here, we analysed 1139 SARS-CoV-2 genomes from positive samples collected between March 2020 and February 2021 across six counties Coastal Kenya (Mombasa, Kilifi, Taita Taveta, Kwale, Tana River, Lamu) to infer virus introductions patterns during first two waves infections....
Diagnosing and treating chronic hepatitis B virus (HBV) infection are key interventions to support progress towards elimination of viral by 2030. Although nucleos/tide analogue (NA) therapy is typically highly effective, challenges remain for load (VL) suppression, including medication access, incomplete adherence drug resistance. We present a case long-term HBV HIV coinfected adult prescribed with sequential NA regimens, episodes breakthrough viraemia. Multiple factors contribute...
Background. International recommendations for the control of coronavirus disease 2019 (COVID-19) pandemic emphasize central role laboratory testing severe acute respiratory syndrome 2 (SARS-CoV-2), etiological agent, at scale. The availability reagents, equipment and qualified staff are important bottlenecks to achieving this. Elsewhere, pooled (i.e. combining multiple samples in same reaction) has been suggested increase capacities period. Methods. We discuss our experience with SARS-CoV-2...
Abstract Background Human infection studies (HIS) that involve deliberately infecting healthy volunteers with a pathogen raise important ethical issues, including the need to ensure benefits and burdens are understood appropriately accounted for. Building on earlier work, we embedded social science research within an ongoing malaria human study in coastal Kenya understand experienced by stakeholders this low-resource setting assess wider implications for future planning policy. Methods Data...
<ns4:p><ns4:bold>Background: </ns4:bold>High-throughput whole genome sequencing facilitates investigation of minority sub-populations from virus positive samples. Minority variants are useful in understanding within and between host diversity, population dynamics can potentially help to elucidate person-person transmission chains. Several variant callers have been developed describe the sequence data. However, they differ on bioinformatics statistical approaches used discriminate errors...
<ns4:p><ns4:bold>Background:</ns4:bold> The global COVID-19 outbreak relies on a quantitative real-time polymerase chain reaction (qRT-PCR) for the detection of severe acute respiratory syndrome coronavirus (SARS-CoV-2), to facilitate roll-out patient care and infection control measures. There are several qRT-PCR assays with little evidence their comparability. We report alterations developers’ recommendations sustain testing capability in our setting, where supply reagents is...
<ns4:p><ns4:bold>Background: </ns4:bold>High-throughput whole genome sequencing facilitates investigation of minority virus sub-populations from positive samples. Minority variants are useful in understanding within and between host diversity, population dynamics can potentially assist elucidating person-person transmission pathways. Several variant callers have been developed to describe low frequency sequence data. These differ based on bioinformatics statistical methods used discriminate...
Studies of long-term malaria cohorts have provided essential insights into how
ABSTRACT Background The transmission networks of SARS-CoV-2 in sub-Saharan Africa remain poorly understood. Methods We undertook phylogenetic analysis 747 positive samples collected across six counties coastal Kenya during the first two waves (March 2020 - February 2021). Viral imports and exports from region were inferred using ancestral state reconstruction (ASR) approach. Results genomes classified into 35 Pango lineages, which accounted for 79% sequenced infections: B.1 (49%), B.1.535...
Hepatitis B virus (HBV) whole genome sequencing (WGS) is currently limited as the DNA viral loads (VL) of many clinical samples are below threshold required to generate full genomes using current methods. We developed two pan-genotypic enrichment methods, probe-based capture and tiled amplicon PCR (HEP-TILE) for HBV WGS. demonstrate mock that both methods (genotypes A-J). Using samples, we HEP-TILE amplification successfully amplifies at lowest VL tested (30 IU/ml), products can be sequenced...
<ns3:p><ns3:bold>Background:</ns3:bold> Studies of long-term malaria cohorts have provided essential insights into how <ns3:italic>Plasmodium falciparum </ns3:italic>interacts with humans, and influences the development antimalarial immunity. Immunity to is acquired gradually after multiple infections, some which present clinical symptoms. However, there considerable variation in number episodes experienced by children same age within cohort. Understanding this symptoms it relates naturally...