Browsing by Author "Lambarey, Humaira"

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    An investigation of Fusarium verticillioides infection in maize using physiological and molecular approaches
    (2017) Lambarey, Humaira; Rafudeen, Suhail; Murray, Shane
    Abstract Maize (Zea mays L.) is an important staple food crop in sub-Saharan Africa providing food security to millions of people. Fusarium verticillioides is an important fungal pathogen that infects maize and causes 'Fusarium Ear Rot' which decreases maize kernel yield and quality. In addition, the fungus produces mycotoxins which contaminate the kernel and upon ingestion have negative health consequences for both people and livestock. To this date, there is still no African maize line completely resistant to infection by F. verticillioides. In this study, an African maize line, Zea mays CML144, was infected with F. verticillioides using a soak-seed inoculation method and grown for two weeks under controlled conditions. Analysis of the morphological characteristics showed that compared to the control (mock-infected) maize, infected maize seedlings displayed signs of stunting with leaves shorter & thinner while roots were shorter and displayed visible signs of rotting. Control and infected maize plants were also characterised physiologically and biochemically. Electrolyte leakage experiments were conducted on the meristem regions of the plants after week one and two of infection and showed that leakage increased over time in both control and infected samples with no significant difference observed between the two groups. Biochemical characterisation by analysing superoxide dismutase (SOD), catalase (CAT) and glutathione reductase (GR) antioxidant enzymes showed an increase after the two weeks of infection, indicating a defense response by the plants in response to infection by the fungal pathogen. RNA-sequencing, the main aim of this study was conducted on control and infected plants after two weeks of infection to identify differentially expressed genes (DEGs) involved in F. verticillioides infection. The Illumina NextSeq 500 platform was used to sequence the transcriptome and quantify changes in gene expression. Analysis of the RNA-seq data using the Tuxedo suite of protocols revealed significant DEGs that were both up- and down-regulated in the infected samples compared to the control. Data analysis was conducted using the DNA subway online bioinformatics tool and these results were compared to those obtained using a separate analysis which also incorporated the Tuxedo suite of protocols. Bioinformatic analysis on the RNA-seq DEGs were performed using the agriGO analysis tool which revealed three significant Gene Ontology (GO) terms for both the up- and down-regulated genes, respectively, with the 'response to stimulus' GO-term (within the down-regulated genes) being of specific interest. Other GO-terms included response to chemical stimulus, carbohydrate metabolic process and ion bonding, which also played a role in the defense response when plants were infected by the fungal pathogen. Quantitative Real-Time PCR was performed on five DEGs that were either up- or down-regulated in response to F. verticillioides infection to validate RNA-seq data as well as the GO-analysis results. Quantitative Real-Time PCR was also used as a pre-validation (before RNA-seq) on shrunken-1, a down-regulated gene found in a previously conducted study. We observed that in response to infection by F. verticillioides, expression of shrunken-1 was down-regulated, however, this was not shown to be significant (p>0.05). The results in the current study and the identification of the genes in Zea mays CML144 responding to fungal infection will aid in the goal to develop a maize line completely resistant to F. verticillioides in Africa and in particular South Africa. This would provide improved food security and minimise health risks to the population in the long term. To our knowledge, this is the first study investigating F. verticillioides infection in the African maize line Zea mays CML144 using the soak-seed inoculation method.
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    SARS-CoV-2 Infection Is Associated with Uncontrolled HIV Viral Load in Non-Hospitalized HIV-Infected Patients from Gugulethu, South Africa
    (2022-06-03) Lambarey, Humaira; Blumenthal, Melissa J; Chetram, Abeen; Joyimbana, Wendy; Jennings, Lauren; Tincho, Marius B; Burgers, Wendy A; Orrell, Catherine; Schäfer, Georgia
    In South Africa, high exposure to SARS-CoV-2 occurs primarily in densely populated, low-income communities, which are additionally burdened by highly prevalent Human Immunodeficiency Virus (HIV). With the aim to assess SARS-CoV-2 seroprevalence and its association with HIV-related clinical parameters in non-hospitalized patients likely to be highly exposed to SARS-CoV-2, this observational cross-sectional study was conducted at the Gugulethu Community Health Centre Antiretroviral clinic between October 2020 and June 2021, after the first COVID-19 wave in South Africa and during the second and beginning of the third wave. A total of 150 adult (median age 39 years [range 20–65 years]) HIV-infected patients (69% female; 31% male) were recruited. 95.3% of the cohort was on antiretroviral therapy (ART), had a median CD4 count of 220 cells/µL (range 17–604 cells/µL) and a median HIV viral load (VL) of 49 copies/mL (range 1–1,050,867 copies/mL). Furthermore, 106 patients (70.7%) were SARS-CoV-2 seropositive, and 0% were vaccinated. When stratified for HIV VL, patients with uncontrolled HIV viremia (HIV VL > 1000 copies/mL) had significantly higher odds of SARS-CoV-2 seropositivity than patients with HIV VL < 1000 copies/mL, after adjusting for age, sex and ART status (p = 0.035, adjusted OR 2.961 [95% CI: 1.078–8.133]). Although the cause–effect relationship could not be determined due to the cross-sectional study design, these results point towards a higher risk of SARS-CoV-2 susceptibility among viremic HIV patients, or impaired HIV viral control due to previous co-infection with SARS-CoV-2.
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    The Impact of Co-Infections for Human Gammaherpesvirus Infection and Associated Pathologies
    (Multidisciplinary Digital Publishing Institute, 2023-08-22) Chinna, Prishanta; Bratl, Katrin; Lambarey, Humaira; Blumenthal, Melissa J.; Schäfer, Georgia
    The two oncogenic human gammaherpesviruses Epstein-Barr virus (EBV) and Kaposi’s sarcoma-associated herpesvirus (KSHV) cause significant disease burden, particularly in immunosuppressed individuals. Both viruses display latent and lytic phases of their life cycle with different outcomes for their associated pathologies. The high prevalence of infectious diseases in Sub-Saharan Africa (SSA), particularly HIV/AIDS, tuberculosis, malaria, and more recently, COVID-19, as well as their associated inflammatory responses, could potentially impact either virus’ infectious course. However, acute or lytically active EBV and/or KSHV infections often present with symptoms mimicking these predominant diseases leading to misdiagnosis or underdiagnosis of oncogenic herpesvirus-associated pathologies. EBV and/or KSHV infections are generally acquired early in life and remain latent until lytic reactivation is triggered by various stimuli. This review summarizes known associations between infectious agents prevalent in SSA and underlying EBV and/or KSHV infection. While presenting an overview of both viruses’ biphasic life cycles, this review aims to highlight the importance of co-infections in the correct identification of risk factors for and diagnoses of EBV- and/or KSHV-associated pathologies, particularly in SSA, where both oncogenic herpesviruses as well as other infectious agents are highly pervasive and can lead to substantial morbidity and mortality.
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    The reactivation of Kaposi's Sarcoma-associated Herpesvirus (KSHV) by SARS-CoV-2 in non-hospitalised HIV-infected patients
    (2025) Lambarey, Humaira; Schafer, Georgia; Blumenthal, Melissa
    High exposure to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the COVID-19 pandemic, occurred primarily in densely populated, low-income communities which are additionally burdened by a high prevalence of Human Immunodeficiency Virus (HIV) and Kaposi's Sarcoma Associated Herpes Virus (KSHV). SARS-CoV-2 co-infection with herpesviruses has been suggested to have an impact on acute and/or long-term disease progression by triggering their reactivation from latency. We have previously reported that lytic KSHV infection (assessed by blood viral load (VL)) was associated with morbidity and mortality in critically ill COVID-19 patients. However, the impact of SARS-CoV-2 exposure on HIV/KSHV co-infected non-hospitalised individuals is currently unknown. We therefore performed a longitudinal observational cross-sectional study (n = 407) on non-hospitalised HIV-infected adult patients attending antiretroviral therapy (ART) services in Gugulethu, South Africa, from October 2020 to April 2023. The start of recruitment for this study coincided with the decline of SARS-CoV-2 infections from the first COVID-19 wave and before nation-wide COVID-19 vaccine roll-out, continuing throughout subsequent waves and vaccine introduction. Exposure to SARS-CoV-2 was very high and increased from an initial quarterly 76.2 % seropositivity (before COVID-19 vaccine roll-out) to 94.9 % by the end of the recruitment; 32.2 % of this cohort was self-reportedly vaccinated against COVID-19. The overall KSHV seroprevalence was 53.5 %, with the quarterly percentage of patients with detectable KSHV VL in the peripheral blood increasing from 3.3 % to 69.2 %. When assessing SARS-CoV-2 seroprevalence and its potential association with KSHV reactivation, we found that KSHV VL presence was significantly associated with SARS-CoV-2 RBD IgG antibody titres in unvaccinated patients, and logistic regression revealed significantly higher odds of KSHV lytic reactivation in unvaccinated patients who were previously exposed to SARS-CoV-2 (adjusted OR 1.28 [95 % CI: 1.05 – 1.55], p = 0.015), compared to vaccinated patients (adjusted OR 0.83 [95 % CI: 0.67 – 1.02], p = 0.080). In addition, we invited KSHV seropositive patients with or without previous SARS-CoV-2 infection for follow-up (FU) (n = 46) every 6 months over a 12-month period to determine the effect of SARS-CoV-2 infection on lytic reactivation of KSHV. Supporting our observations of the cross-sectional study design, the number of unvaccinated individuals with detectable KSHV VL increased, particularly from the 6- (13.3 %) to 12-month (22.2 %) visit but decreased steadily in the vaccinated patients from initial recruitment (15.8 %) to 12-month FU (0 %). Further analysis using a cox regression model confirmed a higher probability of KSHV detection (as a measure of KSHV reactivation) over time in unvaccinated compared to vaccinated patients in response to SARS-CoV-2 exposure. Moreover, we identified one patient with an unusually high KSHV VL early in the recruitment phase who self-reportedly remained unvaccinated against COVID-19 throughout the study period. This patient was invited for FU visits every 6 months for a total of 2 years and exhibited persistent KSHV viremia, together with increased SARS-CoV-2 and KSHV serology. While non-adherence to TB/HIV treatment, his living circumstances and/or malnutrition may be the cause of his uncontrolled KSHV viremia, other underlying infections and specifically (repeated) SARS-CoV-2 infection may have played contributing roles. Cumulatively, the results of this study indicate a positive association between high SARS-CoV-2 exposure and the risk of KSHV reactivation in unvaccinated HIV-infected patients suggesting that, conversely, COVID-19 vaccination plays a protective role against the downstream effects of SARS-CoV-2 infection that we postulate causes lytic reactivation. As lytic reactivation of KSHV may have long-term consequences, particularly in the context of patients with impaired immune functions, identifying and monitoring patients at risk for KSHV reactivation, prevention of KSHV-associated pathologies and appropriate treatment strategies are therefore important in the post-pandemic era.
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    Transcriptomic Analysis of a Susceptible African Maize Line to Fusarium verticillioides Infection
    (2020-08-28) Lambarey, Humaira; Moola, Naadirah; Veenstra, Amy; Murray, Shane; Suhail Rafudeen, Mohamed
    Maize (Zea mays L.) is a staple crop providing food security to millions of people in sub Saharan Africa. Fusarium verticillioides, an important fungal pathogen, infects maize causing ‘Fusarium Ear Rot’ disease, which decreases maize kernel yield and the quality of the crop harvested. Currently, no African maize line is completely resistant to infection by F. verticillioides. This study investigated an African maize line, Zea mays CML144, infected with F. verticillioides. Analysis of morphological characteristics showed significant differences between mock-infected and infected plants. RNA-sequencing (RNA-seq) was conducted on plants 14 days post-inoculation to identify differentially expressed genes (DEGs) involved in F. verticillioides infection. Analysis of RNA-seq data revealed DEGs that were both significantly up- and down-regulated in the infected samples compared to the mock-infected control. The maize TPS1 and cytochrome P450 genes were up-regulated, suggesting that kauralexins were involved in the CML144 defense response. This was substantiated by kauralexin analyses, which showed that kauralexins, belonging to class A and B, accumulated in infected maize tissue. Gene ontology terms relating to response to stimulus, chemical stimulus and carbohydrate metabolic processes were enriched, and the genes belonging to these GO-terms were down-regulated. Quantitative real-time PCR was performed on selected DEGs and measurement of phytoalexin accumulation validated the RNA-seq data and GO-analysis results. A comparison of DEGs from this study to DEGs found in F. verticillioides (ITEM 1744) infected susceptible (CO354) and resistant (CO441) maize genotypes in a previous study, matched 18 DEGs with 17 up-regulated and one down-regulated, respectively. This is the first transcriptomic study on the African maize line, CML144, in response to F. verticillioides infection.