Browsing by Author "Simusika P"

Now showing 1 - 4 of 4

Challenges that may impact achieving and maintaining accreditation in clinical laboratories in Zambia during the COVID-19 pandemic.
(2021) Daka V; Mubanga M; Mukanga B; Mfune RL; Chileshe M; Machiko A; Mudenda S; Chikwanda E; Mudenda T; Simusika P; Mwale S; Musalula S; Ndola Teaching Hospital, Ndola, Zambia.; Mary Begg Health Services, Ndola, Zambia.; University of Zambia, School of Veterinary Medicine, Lusaka, Zambia.; Public Health Department, School of Medicine, Copperbelt University, Ndola, Zambia.; University of Zambia, School of Health Sciences, Lusaka, Zambia.; Tropical Diseases Research Centre, Ndola, Zambia.; Centre for Infectious Disease Research in Zambia, Lusaka, Zambia.; CIDRZ; Centre for Infectious Disease Research in Zambia (CIDRZ)
Characterization of human respiratory syncytial virus in children with severe acute respiratory infection before and during the COVID-19 pandemic.
(2024-Jun) Simusika P; Okamoto M; Dapat C; Muleya W; Malisheni M; Azam S; Imamura T; Saito M; Mwape I; Mpabalwani E; Monze M; Oshitani H; Tohoku University Graduate School of Medicine, Department of Virology, Sendai, Japan.; Center for Infectious Disease Research in Zambia, Lusaka, Zambia.; University Teaching Hospitals, Pathology and Microbiology Department, Virology Laboratory, Lusaka, Zambia.; University of Zambia, School of Veterinary Medicine, Department of Biomedical Sciences, Lusaka, Zambia.; University of Zambia, School of Medicine, Department of Pediatrics and Child Health, Lusaka, Zambia.; Levy Mwanawasa Medical University, Institute of Basic and Biomedical Sciences ,Lusaka, Zambia.; CIDRZ; Centre for Infectious Disease Research in Zambia (CIDRZ)
OBJECTIVES: Annual outbreaks of human respiratory syncytial virus (HRSV) are caused by newly introduced and locally persistent strains. During the COVID-19 pandemic, global and local circulation of HRSV significantly decreased. This study was conducted to characterize HRSV in 2018-2022 and to analyze the impact of COVID-19 on the evolution of HRSV. DESIGN/METHODS: Combined oropharyngeal and nasopharyngeal swabs were collected from children hospitalized with severe acute respiratory infection at two hospitals in Zambia. The second hypervariable region of the attachment gene G was targeted for phylogenetic analysis. RESULTS: Of 3113 specimens, 504 (16.2%) were positive for HRSV, of which 131 (26.0%) and 66 (13.1%) were identified as HRSVA and HRSVB, respectively. In early 2021, an increase in HRSV was detected, caused by multiple distinct clades of HRSVA and HRSVB. Some were newly introduced, whereas others resulted from local persistence. CONCLUSIONS: This study provides insights into the evolution of HRSV, driven by global and local circulation. The COVID-19 pandemic had a temporal impact on the evolution pattern of HRSV. Understanding the evolution of HRSV is vital for developing strategies for its control.
Characterization of Rotavirus Strains Responsible for Breakthrough Diarrheal Diseases among Zambian Children Using Whole Genome Sequencing.
(2023-Nov-26) Mwape I; Laban NM; Chibesa K; Moono A; Silwamba S; Malisheni MM; Chisenga C; Chauwa A; Simusika P; Phiri M; Simuyandi M; Chilengi R; De Beer C; Ojok D; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK.; Institute of Basic and Biomedical Sciences, Levy Mwanawasa Medical University, Lusaka 10101, Zambia.; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, P.O. Box 241, Cape Town 8000, South Africa.; Influenza Research Institute, University of Wisconsin-Madison, Madison, WI 53706-13380, USA.; University Teaching Hospitals, Lusaka 10101, Zambia.; Enteric Disease and Vaccine Research Unit, Centre for Infectious Disease Research in Zambia, Lusaka P.O. Box 34681, Zambia.; Division of Medical Virology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein P.O. Box 339, South Africa.; CIDRZ; Centre for Infectious Disease Research in Zambia (CIDRZ)
The occurrence of rotavirus (RV) infection among vaccinated children in high-burden settings poses a threat to further disease burden reduction. Genetically altered viruses have the potential to evade both natural infection and vaccine-induced immune responses, leading to diarrheal diseases among vaccinated children. Studies characterizing RV strains responsible for breakthrough infections in resource-limited countries where RV-associated diarrheal diseases are endemic are limited. We aimed to characterize RV strains detected in fully vaccinated children residing in Zambia using next-generation sequencing. We conducted whole genome sequencing on Illumina MiSeq. Whole genome assembly was performed using Geneious Prime 2023.1.2. A total of 76 diarrheal stool specimens were screened for RV, and 4/76 (5.2%) were RV-positive. Whole genome analysis revealed RVA/Human-wt/ZMB/CIDRZ-RV2088/2020/
Identification of viral and bacterial pathogens from hospitalized children with severe acute respiratory illness in Lusaka, Zambia, 2011-2012: a cross-sectional study.
(2015-Feb-12) Simusika P; Bateman AC; Theo A; Kwenda G; Mfula C; Chentulo E; Monze M; Centre for Infectious Disease Research in Zambia, 34681, Lusaka, Zambia. bateman.allen@gmail.com.; Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia. psimusika@yahoo.co.uk.; Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia. mmonze@uthlabs.org.zm.; Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia. masoziuk@gmail.com.; Virology Laboratory, University Teaching Hospital, RW1X, Lusaka, Zambia. edwardchents@yahoo.com.; Department of Biomedical Sciences, School of Medicine, University of Zambia, P.O. Box 50110, Lusaka, Zambia. jaffekwenda@gmail.com.; Department of Biomedical Sciences, School of Medicine, University of Zambia, P.O. Box 50110, Lusaka, Zambia. christine.mfula@gmail.com.; CIDRZ; Centre for Infectious Disease Research in Zambia (CIDRZ)
BACKGROUND: Morbidity and mortality from respiratory infections are higher in resource-limited countries than developed countries, but limited studies have been conducted in resource-limited settings to examine pathogens from patients with acute respiratory infections. Influenza surveillance has been conducted in Zambia since 2008; however, only 4.3% of patients enrolled in 2011-2012 were positive for influenza. Therefore, we examined non-influenza respiratory pathogens in children with severe acute respiratory illness (SARI) in Zambia, to estimate the scope of disease burden and determine commonly-identified respiratory pathogens. METHODS: Two reverse transcriptase polymerase chain reaction (rRT-PCR) methods (single and multiplex) were used to analyze nasopharyngeal and throat swabs collected from SARI cases under five years of age from January 2011 through December 2012. All specimens were negative for influenza by rRT-PCR. The panel of singleplex reactions targeted seven viruses, while the multiplex assay targeted thirty-three bacteria, fungi, and viruses. RESULTS: A set of 297 specimens were tested by singleplex rRT-PCR, and a different set of 199 were tested by multiplex rRT-PCR. Using the singleplex assay, 184/297 (61.9%) specimens were positive for one or more viruses. The most prevalent viruses were human rhinovirus (57/297; 19.2%), human adenovirus (50/297; 16.8%), and respiratory syncytial virus (RSV) (45/297; 15.2%). Using multiplex PCR, at least one virus was detected from 167/199 (83.9%) specimens, and at least one bacteria was detected from 197/199 (99.0%) specimens. Cytomegalovirus (415/199; 208.5%) and RSV (67/199; 33.7%) were the most commonly detected viruses, while Streptococcus pneumonie (109/199; 54.8%) and Moraxella catarrhalis (92/199; 46.2%) were the most commonly detected bacteria. CONCLUSIONS: Single infections and co-infections of many viruses and bacteria were identified in children with SARI. These results provide an estimate of the prevalence of infection and show which respiratory pathogens are commonly identified in patients. Further studies should investigate causal associations between individual pathogens and SARI.