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The CIDRZ Research Repository serves as an open-access archive for peer-reviewed publications, conference papers, and other scholarly outputs from CIDRZ researchers. Our goal is to promote the dissemination of knowledge and support evidence-based public health initiatives.
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Item Global trends in norovirus genotype distribution among medically attended children with acute gastroenteritis, 2020-2025.(2026-Jun) Cannon JL; Bonifacio J; Fumian TM; Pabbaraju K; Pietsch C; Gonzalez MD; Hossain ME; Selvarangan R; Buesa J; Pan CY; Sakon N; Chang JH; Hewitt J; Croucher D; White PA; Mercer LK; Chuchaona W; Martinez FJD; Moya ML; Trang NV; Hatyoka LM; Mans J; Niendorf S; Jacobsen S; Mendoza L; Alvarez CD; Gomes KA; Degiuseppe JI; Ingunza A; Varghese T; Lay MK; Santiago FG; Bartlett E; Relja B; Barclay L; Simuyandi M; Lanata CF; Rahman M; Poovorawan Y; Wu FT; Pang XL; Vinjé JBACKGROUND: Norovirus is a leading cause of acute gastroenteritis, with a broad diversity of genotypes infecting children. NoroSurv is an established global network for norovirus strain surveillance among medically attended children < 5 years of age. METHODS: Participating laboratories uploaded norovirus sequences from stool specimens collected from 2020 to 2025 to a web portal, which assigned norovirus genotypes and strain data. Norovirus seasons were defined as September 1 to August 31. RESULTS: Participants in 22 countries across 6 continental regions uploaded 4113 norovirus sequences, including 26 genotypes and 53 strains. GII.4 accounted for 53% (2167/4113), followed by GII.3 (12%), GII.17 (11%), GII.6 (7%), and GII.2 (5%). GII.4 Sydney was the most common variant (47%; 1912/4113), but new GII.4 variants/clusters emerged regionally, with GII.4 San Francisco, GII.4 Wichita and GII.4 Allegany more frequently detected than GII.4 Sydney in 2021-2022 in Africa, 2022-2023 in Central and South America and 2023-2024 in Central America. In 2023-2024, a dramatic rise in GII.17 detection was observed in most regions (32% of all 2024-2025 sequences). In North, Central and South America, Europe and Asia Pacific, GII.17 detection increased as GII.4 detection declined in 2024-2025. Other genotypes (GI.3, GII.1, GII.2, GII.3 and GII.6) had regional peaks, accounting for up to 37% of sequences during a specific season. CONCLUSIONS: Our data may help guide norovirus vaccine development and provide a baseline of global norovirus strain distribution for evaluating the effectiveness of future vaccines in children. We continue to monitor the shifting distribution of norovirus genotypes through NoroSurv surveillance.Item Global trends in norovirus genotype distribution among medically attended children with acute gastroenteritis, 2020-2025.(2026-May-07) Cannon JL; Bonifacio J; Fumian TM; Pabbaraju K; Pietsch C; Gonzalez MD; Hossain ME; Selvarangan R; Buesa J; Pan CY; Sakon N; Chang JH; Hewitt J; Croucher D; White PA; Mercer LK; Chuchaona W; Martinez FJD; Moya ML; Trang NV; Hatyoka LM; Mans J; Niendorf S; Jacobsen S; Mendoza L; Alvarez CD; Gomes KA; Degiuseppe JI; Ingunza A; Varghese T; Lay MK; Santiago FG; Bartlett E; Relja B; Barclay L; Simuyandi M; Lanata CF; Rahman M; Poovorawan Y; Wu FT; Pang XL; Vinjé JBACKGROUND: Norovirus is a leading cause of acute gastroenteritis, with a broad diversity of genotypes infecting children. NoroSurv is an established global network for norovirus strain surveillance among medically attended children < 5 years of age. METHODS: Participating laboratories uploaded norovirus sequences from stool specimens collected from 2020 to 2025 to a web portal, which assigned norovirus genotypes and strain data. Norovirus seasons were defined as September 1 to August 31. RESULTS: Participants in 22 countries across 6 continental regions uploaded 4113 norovirus sequences, including 26 genotypes and 53 strains. GII.4 accounted for 53% (2167/4113), followed by GII.3 (12%), GII.17 (11%), GII.6 (7%), and GII.2 (5%). GII.4 Sydney was the most common variant (47%; 1912/4113), but new GII.4 variants/clusters emerged regionally, with GII.4 San Francisco, GII.4 Wichita and GII.4 Allegany more frequently detected than GII.4 Sydney in 2021-2022 in Africa, 2022-2023 in Central and South America and 2023-2024 in Central America. In 2023-2024, a dramatic rise in GII.17 detection was observed in most regions (32% of all 2024-2025 sequences). In North, Central and South America, Europe and Asia Pacific, GII.17 detection increased as GII.4 detection declined in 2024-2025. Other genotypes (GI.3, GII.1, GII.2, GII.3 and GII.6) had regional peaks, accounting for up to 37% of sequences during a specific season. CONCLUSIONS: Our data may help guide norovirus vaccine development and provide a baseline of global norovirus strain distribution for evaluating the effectiveness of future vaccines in children. We continue to monitor the shifting distribution of norovirus genotypes through NoroSurv surveillance.Item Effect of HIV status and retinol on immunogenicity to oral cholera vaccine in adult population living in an endemic area of Lukanga Swamps, Zambia.(2021) Luchen CC; Mwaba J; Ng'ombe H; Alabi PIO; Simuyandi M; Chilyabanyama ON; Hatyoka LM; Mubanga C; Bosomprah S; Chilengi R; Chisenga CCBACKGROUND: We set out to assess the impact of human immunodeficiency virus (HIV) and micronutrient deficiency as indicated by serum retinol levels on the immune responses to Oral Cholera Vaccine (Shanchol™) in a cohort of participants in Lukanga Swamps, Zambia. Cholera remains endemic in Zambia with vaccines being the only effective preventive measures. However, the effect of these vaccines on populations living with HIV has not been widely documented. METHODS: HIV testing and confirmation was done using the Alere Determine™ HIV-1/2 and Uni-Gold™ kits while vibriocidal antibody assay was applied for vaccine immunogenicity. Serum retinol analysis was assessed by Shimadzu Prominence HCT-2010 High Performance Liquid Chromatography (HPLC). The primary outcome was log transformed geometric mean titre. RESULTS: From 47 participants screened for HIV, 51% (24) tested positive. There was a statistically significant reduction in Ogawa geometric mean ratio (GMR) by 67% (GMR = 0.33; 95% CI: -0.15, 0.76; p-value = 0.009) attributable to HIV positivity with a non-significant reduction in Inaba GMR by about 50% due to HIV positivity. When doubling of retinol levels modelled, GMR reduction against Ogawa were non-significant but that against Inaba resulted in a significant reduction in geometric mean titer (GMT) (GMT-0.33, C.I 0.16-0.66, p-value 0.002). At 1000copies/ml viral load cut off and 350 cells/μl CD4 counts, Ogawa GMT was two times higher 11.16 (95%CI: 8.20-15.19) versus 6.06 (95%CI: 4.04-9.10) in low viremia participants, and three times higher in above threshold CD4 count participants; 24.81 (95%CI: 18.94-32.50) versus 7.07 (95%CI: 5.22-9.58). CONCLUSION: Our results show that while Shanchol™ is immunogenic in both HIV+/- individuals, HIV + participants responded poorly. Viral load and CD4 count affected vaccine immunogenicity. More research is required for detailed understanding of this in order to appropriately inform policy and practice. DOI: 10.1371/journal.pone.0260552Item Immunogenicity and waning immunity from the oral cholera vaccine (Shanchol™) in adults residing in Lukanga Swamps of Zambia.(2022) Ng Ombe H; Simuyandi M; Mwaba J; Luchen CC; Alabi P; Chilyabanyama ON; Mubanga C; Hatyoka LM; Muchimba M; Bosomprah S; Chilengi R; Kwenda G; Chisenga CCINTRODUCTION: In cholera endemic areas, the periodicity of cholera outbreaks remains unpredictable, making it difficult to organize preventive efforts. Lack of data on duration of protection conferred by oral cholera vaccines further makes it difficult to determine when to deploy preemptive vaccination. We report on the immunogenicity and waning of immunity to Shanchol™ in Lukanga Swamps. METHODS: We enrolled a cohort of 223 participants aged between 18 and 65 years old from whom serum samples were collected at baseline, day 28 before administration of the second dose, and consecutively at 6, 12, 24, 30, 36, and 48 months. Vibriocidal antibody titres were measured and expressed as geometric mean titres. Box plots and 95% CI were computed at each visit for both Inaba and Ogawa. Seroconversion was defined as a four fold or greater increase in antibody titres compared to baseline titres. RESULTS: Overall, seroconversion against V. cholerae Inaba and Ogawa after 1st dose was 35/134 (26%) and 34/134 (25%) respectively. We observed a statistical difference in seroconversion between the two subgroups of baseline titres (low <80 and high ≥80) for both Inaba (p = 0.02) and Ogawa (p<0.0001). From a baseline of 13.58, anti-Ogawa GMT increased to 21.95 after the first dose, but rapidly waned to 14.52, 13.13, and 12.78 at months 6, 12 and 24 respectively, and then increased to 13.21, 18.67 and 23.65 at months 30, 36 and 48 respectively. A similar trend was observed for anti-Inaba GMT across the same time points. CONCLUSION: We found that Shanchol™ was immunogenic in our study population and that vibriocidal antibodies may not be a good marker for long-term immunity. The observed rise in titres after 36 months suggests natural exposure, and this may be a critical time window opening for natural transmission in an endemic areas. We recommend re-vaccination at this time point in high risk areas.Item T-Cell Responses after Rotavirus Infection or Vaccination in Children: A Systematic Review.(2022-Feb-23) Laban NM; Goodier MR; Bosomprah S; Simuyandi M; Chisenga C; Chilyabanyama ON; Chilengi RCellular immunity against rotavirus in children is incompletely understood. This review describes the current understanding of T-cell immunity to rotavirus in children. A systematic literature search was conducted in Embase, MEDLINE, Web of Science, and Global Health databases using a combination of "t-cell", "rotavirus" and "child" keywords to extract data from relevant articles published from January 1973 to March 2020. Only seventeen articles were identified. Rotavirus-specific T-cell immunity in children develops and broadens reactivity with increasing age. Whilst occurring in close association with antibody responses, T-cell responses are more transient but can occur in absence of detectable antibody responses. Rotavirus-induced T-cell immunity is largely of the gut homing phenotype and predominantly involves Th1 and cytotoxic subsets that may be influenced by IL-10 Tregs. However, rotavirus-specific T-cell responses in children are generally of low frequencies in peripheral blood and are limited in comparison to other infecting pathogens and in adults. The available research reviewed here characterizes the T-cell immune response in children. There is a need for further research investigating the protective associations of rotavirus-specific T-cell responses against infection or vaccination and the standardization of rotavirus-specific T-cells assays in children.Item Performance of Machine Learning Classifiers in Classifying Stunting among Under-Five Children in Zambia.(2022-Jul-20) Chilyabanyama ON; Chilengi R; Simuyandi M; Chisenga CC; Chirwa M; Hamusonde K; Saroj RK; Iqbal NT; Ngaruye I; Bosomprah SStunting is a global public health issue. We sought to train and evaluate machine learning (ML) classification algorithms on the Zambia Demographic Health Survey (ZDHS) dataset to predict stunting among children under the age of five in Zambia. We applied Logistic regression (LR), Random Forest (RF), SV classification (SVC), XG Boost (XgB) and Naïve Bayes (NB) algorithms to predict the probability of stunting among children under five years of age, on the 2018 ZDHS dataset. We calibrated predicted probabilities and plotted the calibration curves to compare model performance. We computed accuracy, recall, precision and F1 for each machine learning algorithm. About 2327 (34.2%) children were stunted. Thirteen of fifty-eight features were selected for inclusion in the model using random forest. Calibrating the predicted probabilities improved the performance of machine learning algorithms when evaluated using calibration curves. RF was the most accurate algorithm, with an accuracy score of 79% in the testing and 61.6% in the training data while Naïve Bayesian was the worst performing algorithm for predicting stunting among children under five in Zambia using the 2018 ZDHS dataset. ML models aids quick diagnosis of stunting and the timely development of interventions aimed at preventing stunting.Item Field evaluation of a novel, rapid diagnostic assay, and molecular epidemiology of enterotoxigenic E. coli among Zambian children presenting with diarrhea.(2022-Aug) Silwamba S; Chilyabanyama ON; Liswaniso F; Chisenga CC; Chilengi R; Dougan G; Kwenda G; Chakraborty S; Simuyandi MBACKGROUND: Enterotoxigenic Escherichia coli (ETEC) is one of the top aetiologic agents of diarrhea in children under the age of 5 in low-middle income countries (LMICs). The lack of point of care diagnostic tools for routine ETEC diagnosis results in limited data regarding the actual burden and epidemiology in the endemic areas. We evaluated performance of the novel Rapid LAMP based Diagnostic Test (RLDT) for detection of ETEC in stool as a point of care diagnostic assay in a resource-limited setting. METHODS: We conducted a cross-sectional study of 324 randomly selected stool samples from children under 5 presenting with moderate to severe diarrhea (MSD). The samples were collected between November 2012 to September 2013 at selected health facilities in Zambia. The RLDT was evaluated by targeting three ETEC toxin genes [heat labile toxin (LT) and heat stable toxins (STh and STp)]. Quantitative PCR was used as the "gold standard" to evaluate the diagnostic sensitivity and specificity of RLDT for detection of ETEC. We additionally described the prevalence and seasonality of ETEC. RESULTS: The study included 324 participants, 50.6% of which were female. The overall prevalence of ETEC was 19.8% by qPCR and 19.4% by RLDT. The children between 12 to 59 months had the highest prevalence of 22%. The study determined ETEC toxin distribution was LT 28/321(9%), ST 18/321(6%) and LT/ST 16/321(5%). The sensitivity and specificity of the RLDT compared to qPCR using a Ct 35 as the cut-off, were 90.7% and 97.5% for LT, 85.2% and 99.3% for STh and 100% and 99.7% for STp, respectively. CONCLUSION: The results of this study suggest that RLDT is sufficiently sensitive and specific and easy to implement in the endemic countries. Being rapid and simple, the RLDT also presents as an attractive tool for point-of-care testing at the health facilities and laboratories in the resource-limited settings.Item Development of a diarrhoea severity scoring scale in a passive health facility-based surveillance system.(2022) St Jean DT; Chilyabanyama ON; Bosomprah S; Asombang M; Velu RM; Chibuye M; Mureithi F; Sukwa N; Chirwa M; Mokha P; Chilengi R; Simuyandi MBACKGROUND: Diarrhoeal disease remains a leading cause of death among children mostly in low and middle-income countries. Factors contributing to disease severity are complex and there is currently no consensus on a scoring tool for use in community-based studies. METHODS: Data were collected during a passive surveillance system in an outpatient health facility in Lusaka, Zambia from March 2019 to July 2019. Diarrhea episodes were assessed for severity using an in-house severity scoring tool (CIDRZ) and previously published scores (Vesikari, Clark, CODA, and DHAKA). The CIDRZ score was constructed using fieldworker-reported clinical signs and exploratory factor analysis. We used precision-recall curves measuring severe diarrhoea (i.e., requiring intravenous rehydration or referred for hospital admission) to determine the best performing scores. Then, we used Cronbach's alpha to assess the scale's internal consistency. Finally, we used Cohen's kappa to assess agreement between the scores. RESULTS: Of 110 diarrhea episodes, 3 (3%) required intravenous rehydration or were referred for hospital admission. The precision-recall area under the curve of each score as a predictor of severe diarrhoea requiring intravenous rehydration or hospital admission was 0.26 for Vesikari, 0.18 for CODA, 0.24 for Clark, 0.59 for DHAKA, and 0.59 for CIDRZ. The CIDRZ scale had substantial reliability and performed similarly to the DHAKA score. CONCLUSIONS: Diarrhoea severity scores focused on characteristics specific to dehydration status may better predict severe diarrhea among children in Lusaka. Aetiology-specific scoring tools may not be appropriate for use in community healthcare settings. Validation studies for the CIDRZ score in diverse settings and with larger sample sizes are warranted.Item Microbiologic and virulence characteristics of Moraxella catarrhalis isolates from Zambian children presenting with acute pneumonia.(2022-Dec) Nawa M; Mwansa J; Mwaba J; Kaonga P; Mukubesa AN; Simuyandi M; Chisenga CC; Alabi P; Mwananyanda L; Thea DM; Chilengi R; Kwenda GBACKGROUND: Moraxella catarrhalis is one of the bacterial pathogens associated with childhood pneumonia, but its clinical importance is not clearly defined. OBJECTIVE: This study aimed to investigate the microbiologic and virulence characteristics of M. catarrhalis isolates obtained from children with pneumonia in Lusaka, Zambia. METHODS: This retrospective, cross-sectional study analyzed 91 M. catarrhalis isolates from induced sputum samples of children less than 5 years of age with pneumonia enrolled in the Pneumonia Etiology Research for Child Health study in Lusaka, Zambia between 2011 and 2014. Bacteria identification and virulence genes detection were performed by PCR and DNA sequencing, while antimicrobial susceptibility testing was determined by the Kirby-Bauer method. RESULTS: All the M. catarrhalis isolates were obtained from good-quality sputum samples and were the predominant bacteria. These isolates harbored virulence genes copB (100%), ompE (69.2%), ompCD (71.4%), uspA1 (92.3%), and uspA2 (69.2%) and were all β-lactamase producers. They showed resistance to ampicillin (100%), amoxicillin (100%), trimethoprim-sulfamethoxazole (92.3%), ciprofloxacin (46.2%), chloramphenicol (45.1%), erythromycin (36.3%), tetracycline (25.3%), cefuroxime (11.0%), and amoxicillin-clavulanate (2.2%), with 71.4% displaying multi-drug resistant phenotype but all susceptible to imipenem (100%). CONCLUSION: This study showed that M. catarrhalis isolates were the predominant or only bacterial isolates from the sputum samples analyzed. The findings provide supportive evidence for the pathogenic potential role of this bacterium in pediatric pneumonia. High multidrug resistance was also observed amongst the isolates, which can result in affected patients not responding to standard treatment, leading to prolonged illness, increased healthcare costs, and risk of death.Item Epstein-Barr Virus Detection in the Central Nervous System of HIV-Infected Patients.(2022-Sep-22) Musukuma-Chifulo K; Siddiqi OK; Chilyabanyama ON; Bates M; Chisenga CC; Simuyandi M; Sinkala E; Dang X; Koralnik IJ; Chilengi R; Munsaka SSimply detecting Epstein-Barr virus deoxyribonucleic acid (EBV-DNA) is insufficient to diagnose EBV-associated diseases. The current literature around EBV-DNA detection from cerebrospinal fluid (CSF) in human immunodeficiency virus (HIV)-positive non-lymphoma patients was systematically reviewed and a meta-analysis reporting the estimated pooled prevalence in this population when PCR methods are employed, targeting different sequence segments within the EBV genome, was conducted. Using a combination of three key concepts-Epstein-Barr virus detection, central nervous system disease, and human cerebrospinal fluid-and their MeSH terms, the PubMed database was searched. A total of 273 papers reporting the detection of EBV in CNS were screened, of which 13 met the inclusion criteria. The meta-analysis revealed a pooled prevalence of EBV-DNA in CSF of 20% (CI: 12-31%). The highest pooled prevalence was from studies conducted on the African population at 39% (CI: 27-51%). The investigation of the presence of EBV-DNA in the CSF was also very varied, with several gene targets used. While most patients from the articles included in this review and meta-analysis were symptomatic of CNS disorders, the pathogenicity of EBV in non-lymphoma HIV patients when detected in CSF has still not been determined. The presence of EBV-DNA in the CNS remains a concern, and further research is warranted to understand its significance in causing CNS disorders.