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Shempela DM, Chambaro HM, Sikalima J, Cham F, Njuguna M, Morrison L, Mudenda S, Chanda D, Kasanga M, Daka V, Kwenda G, Musonda K, Munsaka S, Chilengi R, Sichinga K, Simulundu E. Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia: A Retrospective Genomic Surveillance Study. Int J Mol Sci 2024; 25:6338. [PMID: 38928045 PMCID: PMC11203853 DOI: 10.3390/ijms25126338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024] Open
Abstract
Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.
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Affiliation(s)
| | - Herman M. Chambaro
- Virology Unit, Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka 10101, Zambia;
| | - Jay Sikalima
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Fatim Cham
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Michael Njuguna
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Linden Morrison
- Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland; (F.C.); (M.N.); (L.M.)
| | - Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia;
| | - Duncan Chanda
- University Teaching Hospital, Ministry of Health, Lusaka 10101, Zambia;
| | - Maisa Kasanga
- Department of Epidemiology and Biostatistics, School of Public Health, Zhengzhou University, Zhengzhou 450001, China;
| | - Victor Daka
- Public Health Department, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola 21692, Zambia;
| | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Sody Munsaka
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (G.K.); (S.M.)
| | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia; (K.M.); (R.C.)
| | - Karen Sichinga
- Churches Health Association of Zambia, Lusaka 10101, Zambia; (J.S.); (K.S.)
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Macha Research Trust, Choma 20100, Zambia
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2
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Mudenda S, Daka V, Mufwambi W, Matafwali SK, Chabalenge B, Skosana P, Mfune RL, Kasanga M, Okonji OC, Mayoka G, Kampamba M, Hikaambo CN, Mukosha M, Kanaan MHG, Zikalala-Mabope LA, Sinkamba G, Okoro RN, Chulu M, Godman B, Fadare J. Student's perspectives, satisfaction and experiences with online and classroom learning during the COVID-19 pandemic: Findings and implications on blended learning. SAGE Open Med 2023; 11:20503121231218904. [PMID: 38146495 PMCID: PMC10749517 DOI: 10.1177/20503121231218904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 11/10/2023] [Indexed: 12/27/2023] Open
Abstract
Objectives The coronavirus disease 2019 (COVID-19) pandemic disrupted classroom-based learning, necessitating the adoption of online learning in most universities. However, there has been a lack of information on university students' perspectives regarding online learning during the COVID-19 pandemic. This study assessed the perspectives, satisfaction and experiences with online and classroom learning among human health students at the University of Zambia. Methods This cross-sectional study was conducted among 737 students at the University of Zambia from October 2022 to April 2023. Data were analysed using Stata version 16.1. Results Of the 737 participants, 51.6% were female and 56.5% agreed that blended learning should continue even after the COVID-19 pandemic. However, 78.4% of the students believed that group discussions were more suitable in the classroom than online learning. Most students (67.1%) disagreed that they preferred online learning to classroom learning. Furthermore, 77.6% of the students disagreed that online learning gave more satisfaction than classroom learning. Conclusions This study found that most students recommended the continuation of blended learning after the pandemic. However, they believed that follow-up tutorials and assessments were better undertaken in physical classrooms than online learning. These findings are important in sensitising stakeholders in the education sector and governments to consider blended learning as a teaching strategy in the future. There is a need to develop and implement curricula that offer blended learning to students as well as ensure the students have the necessary facilities and equipment to support such learning.
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Affiliation(s)
- Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Victor Daka
- Department of Public Health, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola, Zambia
| | - Webrod Mufwambi
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Scott Kaba Matafwali
- Faculty of Infectious and Tropical Diseases, Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Billy Chabalenge
- Department of Medicines Control, Zambia Medicines Regulatory Authority, Lusaka, Zambia
| | - Phumzile Skosana
- Department of Clinical Pharmacy, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Ruth Lindizyani Mfune
- Department of Public Health, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola, Zambia
| | - Maisa Kasanga
- College of Public Health, Zhengzhou University, Zhengzhou, China
| | | | - Godfrey Mayoka
- Department of Pharmacology and Pharmacognosy, School of Pharmacy, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Martin Kampamba
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | | | - Moses Mukosha
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | | | | | - George Sinkamba
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Roland Nnaemeka Okoro
- Faculty of Pharmacy, Department of Clinical Pharmacy and Pharmacy Administration, University of Maiduguri, Nigeria
| | - Martha Chulu
- Department of Pharmacy, School of Health Sciences, Levy Mwanawasa Medical University, Lusaka, Zambia
| | - Brian Godman
- Department of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria, South Africa
- Department of Pharmacoepidemiology, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK
| | - Joseph Fadare
- Department of Pharmacology and Therapeutics, Ekiti State University College of Medicine, Ado-Ekiti, Nigeria
- Department of Medicine, Ekiti State University Teaching Hospital, Ado-Ekiti, Nigeria
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3
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Mudenda S, Meyer JC, Fadare JO, Ogunleye OO, Saleem Z, Matafwali SK, Daka V, Chabalenge B, Chama J, Mukosha M, Skosana P, Witika BA, Kalungia AC, Hamachila A, Mufwambi W, Godman B. COVID-19 vaccine uptake and associated factors among adolescents and youths: Findings and implications for future vaccination programmes. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002385. [PMID: 37729153 PMCID: PMC10511127 DOI: 10.1371/journal.pgph.0002385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/22/2023] [Indexed: 09/22/2023]
Abstract
Adolescents and youths are a key part of the population that needs to be protected against the coronavirus disease 2019 (COVID-19). This is because they are more likely to spread the virus to vulnerable individuals. In view of these concerns, this study investigated the uptake of COVID-19 vaccines and associated factors among adolescents and youths attending secondary schools in Zambia. This cross-sectional study was conducted among 1500 school-going adolescents in Lusaka from September 2022 to November 2022. Overall, 1409 participants took part giving a response rate of 94%. Only 29.2% (n = 411) of the participants were vaccinated against COVID-19 at the time of the study. Compared to their unvaccinated counterparts, vaccinated adolescents and youths scored higher for knowledge (66.2% vs 57.8%) and attitudes (76.7% vs 39.4%) regarding COVID-19 vaccines. Healthcare workers, family/friends and social media were key sources of information regarding the vaccine. Factors associated with increased vaccine uptake were positive attitudes (AOR = 33.62, 95% CI: 19.92-56.73), indicating it was stressful to follow COVID-19 preventive measures (AOR = 1.47, 95% CI: 1.09-1.99), participants in Grade 12 (AOR = 3.39, 95% CI: 1.94-5.91), Grade 11 (AOR = 2.59, 95% CI: 1.94-5.91), Grade 10 (AOR = 3.48, 95% CI: 1.98-6.11) and Grade 9 (AOR = 3.04, 95% CI: 1.74-5.32) compared to Grade 8. This study found a relatively low uptake of COVID-19 vaccines among adolescents and youths in Zambia. There is a need to provide adequate strategies to address knowledge and attitude gaps regarding COVID-19 vaccines to improve uptake and reduce future morbidity and mortality.
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Affiliation(s)
- Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Johanna C. Meyer
- Department of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria, South Africa
- South African Vaccination and Immunisation Centre, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Joseph O. Fadare
- Department of Pharmacology and Therapeutics, Ekiti State University, Ado Ekiti, Nigeria
- Department of Medicine, Ekiti State University Teaching Hospital, Ado Ekiti, Nigeria
| | - Olayinka O. Ogunleye
- Department of Pharmacology, Therapeutics and Toxicology, Lagos State University College of Medicine, Ikeja, Lagos, Nigeria
- Department of Medicine, Lagos State University Teaching Hospital, Ikeja, Lagos, Nigeria
| | - Zikria Saleem
- Department of Pharmacy Practice, Faculty of Pharmacy, Bahauddin Zakariya University, Multan, Pakistan
| | - Scott K. Matafwali
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene &Tropical Medicine, London, United Kingdom
| | - Victor Daka
- Department of Public Health, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola, Zambia
| | - Billy Chabalenge
- Department of Medicines Control, Zambia Medicines Regulatory Authority, Lusaka, Zambia
| | - Jacob Chama
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Moses Mukosha
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
- HIV and Women’s Health Research Group, University Teaching Hospital, Lusaka, Zambia
| | - Phumzile Skosana
- Department of Clinical Pharmacy, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Bwalya A. Witika
- Department of Pharmaceutical Sciences, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria, South Africa
| | - Aubrey C. Kalungia
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Audrey Hamachila
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Webrod Mufwambi
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | - Brian Godman
- Department of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria, South Africa
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
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Chanda SL, Tembo E, Sinyange N, Kayeyi N, Musonda K, Chewe O, Kasonde M, Kapona O, Ngomah A, Hamukale A, Zulu PM, Kapina M. Characteristics of cases and deaths arising from SARS-CoV-2 infection in Zambia: March 2020 to April 2021. Pan Afr Med J 2023; 45:155. [PMID: 37869234 PMCID: PMC10589408 DOI: 10.11604/pamj.2023.45.155.32018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/09/2023] [Indexed: 10/24/2023] Open
Abstract
Introduction since March 2020, Zambia has been experiencing a SARS-CoV-2 epidemic. Little data has been reported on cases and deaths arising from COVID-19 in Africa. We described the demographic characteristics of these cases and deaths in Zambia. Methods we analyzed data on all persons testing positive for SARS-CoV-2 from 18th March 2020 to 25th April 2021 in Zambia. COVID-19 cases were identified through port-of-entry surveillance, contact-tracing, health-care-worker testing, health-facility-based and community-based screening and community-death screening. All diagnoses were confirmed using real-time-polymerase-chain-reaction and rapid-antigen-test-kits of nasopharyngeal specimens. We analyzed age, sex, and date-of-reporting according to whether the cases or deaths occurred during the first wave (1st July to 15th September 2020) or the second wave (15th December 2020 to 10th April 2021). We computed Mann-Whitney-U-test to compare medians of continuous variables and chi-square tests to compare differences between proportions using R. Results a total 1,246 (1.36%) deaths were recorded among 91,378 confirmed cases during March 2020-April 2021 in Zambia. Persons who died were older than those who did not (median age 50 years versus 32.0 years, p< 0.001). Although only 4.7% of cases were among persons aged >60 years, most deaths (31.6%) occurred in this age group (p<0.001). More deaths (83.5%) occurred in the community than in health facilities (p<0.001). Conclusion during the SARS-CoV-2 epidemic in Zambia, most deaths occurred in the community, indicating potential gaps in public health messaging about COVID-19. Improving health-seeking behaviors for COVID-19 through public messaging campaigns and engaging key community stakeholders in Zambia might reduce avoidable mortality. As the group most impacted by COVID-19 mortality, older persons might need enhanced outreach and linkage to care.
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Affiliation(s)
- Stephen Longa Chanda
- Field Epidemiology Training Program (FETP), Zambia National Public Health Institute, Lusaka, Zambia
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Emmanuel Tembo
- Field Epidemiology Training Program (FETP), Zambia National Public Health Institute, Lusaka, Zambia
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Nyambe Sinyange
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Nkomba Kayeyi
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Kunda Musonda
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Orbie Chewe
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Mpanga Kasonde
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Otridah Kapona
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Albertina Ngomah
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Amos Hamukale
- Field Epidemiology Training Program (FETP), Zambia National Public Health Institute, Lusaka, Zambia
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Paul Msanzya Zulu
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
| | - Muzala Kapina
- Zambia National Public Health Program, Surveillance and Disease Intelligence Cluster, Lusaka, Zambia
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5
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Sheppard RJ, Watson OJ, Pieciak R, Lungu J, Kwenda G, Moyo C, Chanda SL, Barnsley G, Brazeau NF, Gerard-Ursin ICG, Olivera Mesa D, Whittaker C, Gregson S, Okell LC, Ghani AC, MacLeod WB, Del Fava E, Melegaro A, Hines JZ, Mulenga LB, Walker PGT, Mwananyanda L, Gill CJ. Using mortuary and burial data to place COVID-19 in Lusaka, Zambia within a global context. Nat Commun 2023; 14:3840. [PMID: 37380650 PMCID: PMC10307769 DOI: 10.1038/s41467-023-39288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 06/06/2023] [Indexed: 06/30/2023] Open
Abstract
Reported COVID-19 cases and associated mortality remain low in many sub-Saharan countries relative to global averages, but true impact is difficult to estimate given limitations around surveillance and mortality registration. In Lusaka, Zambia, burial registration and SARS-CoV-2 prevalence data during 2020 allow estimation of excess mortality and transmission. Relative to pre-pandemic patterns, we estimate age-dependent mortality increases, totalling 3212 excess deaths (95% CrI: 2104-4591), representing an 18.5% (95% CrI: 13.0-25.2%) increase relative to pre-pandemic levels. Using a dynamical model-based inferential framework, we find that these mortality patterns and SARS-CoV-2 prevalence data are in agreement with established COVID-19 severity estimates. Our results support hypotheses that COVID-19 impact in Lusaka during 2020 was consistent with COVID-19 epidemics elsewhere, without requiring exceptional explanations for low reported figures. For more equitable decision-making during future pandemics, barriers to ascertaining attributable mortality in low-income settings must be addressed and factored into discourse around reported impact differences.
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Affiliation(s)
- Richard J Sheppard
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Rachel Pieciak
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | | | - Geoffrey Kwenda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka, Zambia
| | | | | | - Gregory Barnsley
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Nicholas F Brazeau
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Ines C G Gerard-Ursin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Daniela Olivera Mesa
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Charles Whittaker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Simon Gregson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
- Manicaland Centre for Public Health Research, Biomedical Research and Training Institute, Harare, Zimbabwe
| | - Lucy C Okell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK
| | - William B MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
| | - Emanuele Del Fava
- Carlo F. Dondena Centre for Research on Social Dynamics and Public Policy, Bocconi University, Milan, Italy
- Max Planck Institute for Demographic Research, Rostock, Germany
| | - Alessia Melegaro
- Carlo F. Dondena Centre for Research on Social Dynamics and Public Policy, Bocconi University, Milan, Italy
- Department of Social and Political Science, Bocconi University, Milano, Italy
| | - Jonas Z Hines
- Centers for Disease Control and Prevention, Lusaka, Zambia
| | | | - Patrick G T Walker
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College, London, UK.
| | - Lawrence Mwananyanda
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
- Avencion Limited, Lusaka, Zambia
| | - Christopher J Gill
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
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6
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Kafwanka P, Nalule FM, Michelo C. Poor adherence to antiretroviral therapy among adult people living with HIV initiated during the COVID-19 epidemic waves – observations at the University Teaching Hospital in Lusaka, Zambia. Front Public Health 2023; 11:1094214. [PMID: 36992897 PMCID: PMC10040650 DOI: 10.3389/fpubh.2023.1094214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/22/2023] [Indexed: 03/14/2023] Open
Abstract
BackgroundCoronavirus disease 2019 (COVID-19)-related disruptions in healthcare services and clinical outcomes have been predicted and documented. However, little is known about how antiretroviral therapy (ART) adherence disruptions caused by the COVID-19 pandemic have manifested amidst the ‘Undetectable = Untransmittable' campaign initiative. Using a patient's viral load as a proxy for medication adherence, our study aimed to determine the adherence to ART on first-line medications among adult people living with human immunodeficiency virus (PLWHIV) at the University Teaching Hospital in Lusaka, Zambia during the pandemic.MethodsThis was a hospital-based cross-sectional study. Secondary data of PLWHIV registered to receive ART from the Adult Infectious Disease Centre was extracted from the SmartCare® electronic health record system to constitute a resultant data set that this study used. The data extraction form was used to extract values of dependent (ART adherence measured by viral load detectability) and independent variables and imported them into the statistical analysis tool, STATA version 16.1 MP. Descriptive statistics of individual characteristics, testing for associations using Pearson's chi-square test, and stratified and combined multivariable logistic regression were performed.ResultsOf the 7,281 adult PLWHIV included in this study, 9.0% (95% CI 8.3–9.6%) were virally detectable. Estimates of the odds ratios of detectable viral load remained significantly higher among adult PLWHIV who were initiated on ART after the U=U campaign was launched in Zambia and were on a monthly 2.51 (1.31–9.03) or 6-monthly 4.75 (3.52–6.41) dispensing of a dolutegravir-based regimen and those on 6-monthly dispensing of an efavirenz-based regimen 4.67 (2.16–10.08) compared to their counterparts. Overall estimates showed us the same picture 4.14 (3.22–5.31), having adjusted for all other predictor variables.ConclusionWe found that a high proportion of people with detectable viral load in the study population, irrespective of medication refill interval and type of regimen, was concentrated among adult PLWHIV who started treatment during the COVID-19 epidemic waves, as compared to those who started treatment before the pandemic. This observed disparity suggests the inherent impact of the pandemic on the adherence to ART among adult PLWHIV in Lusaka, Zambia. This further illustrates how exposed program responses are to external shocks, especially in already weakened health systems, and the need to create program response buffers and resilient program-specific strategies to minimize the effect of external disruptions.
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Affiliation(s)
- Powell Kafwanka
- Department of Epidemiology and Biostatistics, School of Public Health, University of Zambia, Lusaka, Zambia
- Department of Internal Medicine, School of Medicine, University of Zambia, Lusaka, Zambia
- *Correspondence: Powell Kafwanka
| | | | - Charles Michelo
- Department of Epidemiology and Biostatistics, School of Public Health, University of Zambia, Lusaka, Zambia
- Strategic Centre for Health Systems Metrics (SCHEME), Lusaka, Zambia
- Global Health Institute, Nkwazi Research University, Lusaka, Zambia
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7
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Chibwana MG, Thole HW, Anscombe C, Ashton PM, Green E, Barnes KG, Cornick J, Turner A, Witte D, Nthala S, Thom C, Kanyandula F, Ainani A, Mtike N, Tambala H, N’goma V, Mwafulirwa D, Asima E, Morton B, Gmeiner M, Gundah Z, Kawalazira G, French N, Feasey N, Heyderman RS, Swarthout TD, Jambo KC. Different clinical features in Malawian outpatients presenting with COVID-19 prior to and during Omicron variant dominance: A prospective observational study. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0001575. [PMID: 36963090 PMCID: PMC10022204 DOI: 10.1371/journal.pgph.0001575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 02/03/2023] [Indexed: 03/11/2023]
Abstract
The SARS-CoV-2 Omicron variant has resulted in a high number of cases, but a relatively low incidence of severe disease and deaths, compared to the pre-Omicron variants. Therefore, we assessed the differences in symptom prevalence between Omicron and pre-Omicron infections in a sub-Saharan African population. We collected data from outpatients presenting at two primary healthcare facilities in Blantyre, Malawi, from November 2020 to March 2022. Eligible participants were aged >1month old, with signs suggestive of COVID-19, and those not suspected of COVID-19, from whom we collected nasopharyngeal swabs for SARS-CoV-2 PCR testing, and sequenced positive samples to identify infecting-variants. In addition, we calculated the risk of presenting with a given symptom in individuals testing SARS-CoV-2 PCR positive before and during the Omicron variant-dominated period. Among 5176 participants, 6.4% were under 5, and 77% were aged 18 to 50 years. SARS-CoV-2 infection prevalence peaked in January 2021 (Beta), July 2021 (Delta), and December 2021 (Omicron). We found that cough (risk ratio (RR), 1.50; 95% confidence interval (CI), 1.00 to 2.30), fatigue (RR 2.27; 95% CI, 1.29 to 3.86) and headache (RR 1.64; 95% CI, 1.15 to 2.34) were associated with a high risk of SARS-CoV-2 infection during the pre-Omicron period. In comparison, only headache (RR 1.41; 95% CI, 1.07 to 1.86) did associate with a high risk of SARS-CoV-2 infection during the Omicron-dominated period. In conclusion, clinical symptoms associated with Omicron infection differed from prior variants and were harder to identify clinically with current symptom guidelines. Our findings encourage regular review of case definitions and testing policies to ensure case ascertainment.
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Affiliation(s)
| | | | - Cat Anscombe
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Philip M. Ashton
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Edward Green
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kayla G. Barnes
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Harvard School of Public Health, Boston, MA, United States of America
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
- University of Glasgow MRC Centre for Virus Research, Glasgow, United Kingdom
| | - Jen Cornick
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Ann Turner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Desiree Witte
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Sharon Nthala
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
| | - Chikondi Thom
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
| | | | - Anna Ainani
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
| | - Natasha Mtike
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
| | - Hope Tambala
- Blantyre District Health Office, Ministry of Health, Blantyre, Malawi
| | | | | | - Erick Asima
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
| | - Ben Morton
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Markus Gmeiner
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
| | - Zaziwe Gundah
- Blantyre District Health Office, Ministry of Health, Blantyre, Malawi
| | - Gift Kawalazira
- Blantyre District Health Office, Ministry of Health, Blantyre, Malawi
| | - Neil French
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Robert S. Heyderman
- NIHR Global Health Research Unit on Mucosal Pathogens, University College London, London, United Kingdom
| | - Todd D. Swarthout
- NIHR Global Health Research Unit on Mucosal Pathogens, University College London, London, United Kingdom
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, Netherlands
| | - Kondwani C. Jambo
- Malawi-Liverpool-Wellcome Programme (MLW), Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Kamuzu University of Health Sciences, Blantyre, Malawi
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8
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Ncheka JM, Menon JA, Davies EB, Paul R, Mwaba SOC, Mudenda J, Wharrad H, Toutounchi P, Glazebrook C. Factors influencing COVID-19 health protective behaviours in Zambian university students with symptoms of low mood. BMC Public Health 2023; 23:336. [PMID: 36793103 PMCID: PMC9930037 DOI: 10.1186/s12889-023-15073-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 01/17/2023] [Indexed: 02/17/2023] Open
Abstract
BACKGROUND Health protective behaviours are crucial in the prevention of the spread of COVID-19, particularly in university students who typically live and study in large groups. Depression and anxiety are common in students and can impact young people's motivations to follow health advice. The study aims to assess the relationship between mental health and COVID-19 health-protective behaviours in Zambian university students with symptoms of low mood. METHODS The study was a cross-sectional, online survey of Zambian university students. Participants were also invited to take part in a semi-structured interview to explore views about COVID-19 vaccination. Invitation emails were sent explaining the study aims and directed students who self-identified as having low mood in the past two weeks to an online survey. Measures included COVID-19 preventive behaviours, COVID-19-related self-efficacy, and Hospital and Anxiety Depression scale. RESULTS A total of 620 students (n=308 female, n=306 male) participated in the study, with a mean participant age of 22.47±3.29 years (range 18-51). Students reported a mean protective behaviour score of 74.09/105 and 74% scored above the threshold for possible anxiety disorder. Three-way ANOVA showed lower COVID-19 protective behaviours in students with possible anxiety disorder (p=.024) and those with low self-efficacy (p<0.001). Only 168 (27%) said they would accept vaccination against COVID-19, with male students being twice as likely to be willing to accept COVID-19 vaccination (p<0.001). Of 50 students interviewed. 30 (60%) expressed fears about the vaccination and 16 (32%) were concerned about a lack of information. Only 8 (16%) participants expressed doubts about effectiveness. CONCLUSION Students who self-identify as having symptoms of depression have high levels of anxiety. The results suggest that interventions to reduce anxiety and promote self-efficacy might enhance students' COVID-19 protective behaviours. Qualitative data provided insight into the high rates of vaccine hesitancy in this population.
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Affiliation(s)
- Joyce M. Ncheka
- grid.12984.360000 0000 8914 5257Department of Psychiatry, School of Medicine, University of Zambia, Lusaka, Zambia
| | - J. Anitha Menon
- grid.12984.360000 0000 8914 5257Department of Psychology, School of Humanities and Social Sciences, University of Zambia, Lusaka, Zambia ,grid.411365.40000 0001 2218 0143Department of International Studies, American University of Sharjah, Sharjah, UAE
| | - E Bethan Davies
- grid.4563.40000 0004 1936 8868Institute of Mental Health, NIHR MindTech MedTech Co-Operative, The University of Nottingham, Nottingham, UK ,grid.4563.40000 0004 1936 8868Clinical Neurosciences and Mental Health, School of Medicine, The University of Nottingham, Nottingham, UK
| | - Ravi Paul
- grid.12984.360000 0000 8914 5257Department of Psychiatry, School of Medicine, University of Zambia, Lusaka, Zambia
| | - Sydney O. C. Mwaba
- grid.12984.360000 0000 8914 5257Department of Psychology, School of Humanities and Social Sciences, University of Zambia, Lusaka, Zambia
| | - John Mudenda
- grid.508092.60000 0004 5947 8201Lusaka Apex Medical University, Lusaka, Zambia
| | - Heather Wharrad
- grid.4563.40000 0004 1936 8868School of Health Sciences, University of Nottingham, Nottingham, UK
| | - Parisa Toutounchi
- grid.4563.40000 0004 1936 8868Clinical Neurosciences and Mental Health, School of Medicine, The University of Nottingham, Nottingham, UK
| | - Cris Glazebrook
- Institute of Mental Health, NIHR MindTech MedTech Co-Operative, The University of Nottingham, Nottingham, UK. .,Clinical Neurosciences and Mental Health, School of Medicine, The University of Nottingham, Nottingham, UK.
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9
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Anscombe C, Lissauer S, Thole H, Rylance J, Dula D, Menyere M, Kutambe B, van der Veer C, Phiri T, Banda NP, Mndolo KS, Mponda K, Phiri C, Mallewa J, Nyirenda M, Katha G, Mwandumba H, Gordon SB, Jambo KC, Cornick J, Feasey N, Barnes KG, Morton B, Ashton PM. A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study. BMC Infect Dis 2023; 23:79. [PMID: 36750921 PMCID: PMC9902830 DOI: 10.1186/s12879-022-07941-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/12/2022] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Compared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome. METHODS We enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinION™ in Blantyre. RESULTS We enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p < 0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p < 0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p = 0.05) compared to the first wave of infection. CONCLUSIONS Our data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave.
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Affiliation(s)
- Catherine Anscombe
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Samantha Lissauer
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
| | - Herbert Thole
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Jamie Rylance
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Dingase Dula
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Mavis Menyere
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Belson Kutambe
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Charlotte van der Veer
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - Tamara Phiri
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Ndaziona P Banda
- Kamuzu University of Health Sciences (Formerly University of Malawi-College of Medicine), Blantyre, Malawi
| | - Kwazizira S Mndolo
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Kelvin Mponda
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Chimota Phiri
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Jane Mallewa
- Kamuzu University of Health Sciences (Formerly University of Malawi-College of Medicine), Blantyre, Malawi
| | - Mulinda Nyirenda
- Kamuzu University of Health Sciences (Formerly University of Malawi-College of Medicine), Blantyre, Malawi
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Grace Katha
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Henry Mwandumba
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Kamuzu University of Health Sciences (Formerly University of Malawi-College of Medicine), Blantyre, Malawi
| | - Stephen B Gordon
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Kondwani C Jambo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Kamuzu University of Health Sciences (Formerly University of Malawi-College of Medicine), Blantyre, Malawi
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Kayla G Barnes
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Harvard School of Public Health, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- University of Glasgow MRC Centre for Virus Research, Glasgow, UK
| | - Ben Morton
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Liverpool University Hospitals Foundation Trust, Liverpool, UK
| | - Philip M Ashton
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi.
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK.
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10
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Sutcliffe CG, Sinywimaanzi P, Morales J, Sianyanda M, Muleka M, Fenstermacher KZJ, Monze M, Rothman RE, Pekosz A, Thuma PE, Simulundu E. Uptake of public health measures and vaccine acceptance during the COVID-19 pandemic in rural Zambia. Hum Vaccin Immunother 2022; 18:2153538. [PMID: 36482701 PMCID: PMC9762779 DOI: 10.1080/21645515.2022.2153538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Vaccines are effective tools to prevent COVID-19-related morbidity. However, coverage is low throughout sub-Saharan Africa. Uptake of public health measures, perceptions of COVID-19 illness and vaccines, and intention to vaccinate were evaluated in 2021-2022 in rural Zambia. Adherence to public health measures, perceptions of COVID-19 risk and severity, and vaccine acceptance increased significantly over time, particularly in December 2021, coinciding with the fourth pandemic wave and relaunch of the national vaccine campaign. Vaccine acceptance was associated with perceptions of vaccine safety and effectiveness, but not disease severity. These findings highlight the importance of strong pandemic response and public communication for increased uptake of mitigatory measures, including vaccine acceptance.
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Affiliation(s)
- Catherine G. Sutcliffe
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA,CONTACT Catherine G. Sutcliffe Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, 615 N. Wolfe Street, Room E6535, Baltimore, MD21205, USA
| | | | - Juliet Morales
- Department of International Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | | | | | | | - Mwaka Monze
- Virology Laboratory, University Teaching Hospital, Lusaka, Zambia
| | - Richard E. Rothman
- Department of Emergency Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Andrew Pekosz
- Department of Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
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11
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Mudenda S, Mukosha M, Godman B, Fadare JO, Ogunleye OO, Meyer JC, Skosana P, Chama J, Daka V, Matafwali SK, Chabalenge B, Witika BA. Knowledge, Attitudes, and Acceptance of COVID-19 Vaccines among Secondary School Pupils in Zambia: Implications for Future Educational and Sensitisation Programmes. Vaccines (Basel) 2022; 10:2141. [PMID: 36560551 PMCID: PMC9784903 DOI: 10.3390/vaccines10122141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/15/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic resulted in the closure of schools to slow the spread of the virus across populations, and the administration of vaccines to protect people from severe disease, including school children and adolescents. In Zambia, there is currently little information on the acceptance of COVID-19 vaccines among school-going children and adolescents despite their inclusion in the vaccination programme. This study assessed the knowledge, attitudes, and acceptance of COVID-19 vaccines among secondary school pupils in Lusaka, Zambia. A cross-sectional study was conducted from August 2022 to October 2022. Of the 998 participants, 646 (64.7%) were female, and 127 (12.7%) would accept to be vaccinated. Those who were willing to be vaccinated had better knowledge (68.5% vs. 56.3%) and a positive attitude (79.1% vs. 33.7%) compared to those who were hesitant. Overall, the odds of vaccine acceptance were higher among pupils who had higher knowledge scores (AOR = 11.75, 95% CI: 6.51-21.2), positive attitude scores (AOR = 9.85, 95% CI: 4.35-22.2), and those who knew a friend or relative who had died from COVID-19 (AOR = 3.27, 95% CI: 2.14-5.09). The low vaccine acceptance among pupils is of public health concern, emphasising the need for heightened sensitisation programmes that promote vaccine acceptance among pupils in Zambia.
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Affiliation(s)
- Steward Mudenda
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka P.O. Box 50110, Zambia
| | - Moses Mukosha
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka P.O. Box 50110, Zambia
| | - Brian Godman
- Department of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman 346, United Arab Emirates
- Department of Pharmacoepidemiology, Strathclyde Institute of Pharmacy and Biomedical Science (SIPBS), University of Strathclyde, Glasgow G4 0RE, UK
| | - Joseph O. Fadare
- Department of Pharmacology and Therapeutics, Ekiti State University College of Medicine, Ado-Ekiti 362103, Nigeria
- Department of Medicine, Ekiti State University Teaching Hospital, Ado-Ekiti 362103, Nigeria
| | - Olayinka O. Ogunleye
- Department of Pharmacology, Therapeutics and Toxicology, Lagos State University College of Medicine, Lagos 100271, Nigeria
- Department of Medicine, Lagos State University Teaching Hospital, Lagos 100271, Nigeria
| | - Johanna C. Meyer
- Department of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
- South African Vaccination and Immunisation and Centre, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
| | - Phumzile Skosana
- Department of Clinical Pharmacy, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
| | - Jacob Chama
- Department of Pharmacy, School of Health Sciences, University of Zambia, Lusaka P.O. Box 50110, Zambia
| | - Victor Daka
- Department of Public Health, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola P.O. Box 71191, Zambia
| | - Scott K. Matafwali
- Clinical Research Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Billy Chabalenge
- Department of Medicines Control, Zambia Medicines Regulatory Authority, Lusaka P.O. Box 31890, Zambia
| | - Bwalya A. Witika
- Department of Pharmaceutical Sciences, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria 0208, South Africa
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12
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Gill CJ, Mwananyanda L, MacLeod WB, Kwenda G, Pieciak RC, Etter L, Bridges D, Chikoti C, Chirwa S, Chimoga C, Forman L, Katowa B, Lapidot R, Lungu J, Matoba J, Mwinga G, Mubemba B, Mupila Z, Muleya W, Mwenda M, Ngoma B, Nakazwe R, Nzara D, Pawlak N, Pemba L, Saasa N, Simulundu E, Yankonde B, Thea DM. What is the prevalence of COVID-19 detection by PCR among deceased individuals in Lusaka, Zambia? A postmortem surveillance study. BMJ Open 2022; 12:e066763. [PMID: 36600354 PMCID: PMC9729848 DOI: 10.1136/bmjopen-2022-066763] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To determine the prevalence of COVID-19 postmortem setting in Lusaka, Zambia. DESIGN A systematic, postmortem prevalence study. SETTING A busy, inner-city morgue in Lusaka. PARTICIPANTS We sampled a random subset of all decedents who transited the University Teaching Hospital morgue. We sampled the posterior nasopharynx of decedents using quantitative PCR. Prevalence was weighted to account for age-specific enrolment strategies. INTERVENTIONS Not applicable-this was an observational study. PRIMARY OUTCOMES Prevalence of COVID-19 detections by PCR. Results were stratified by setting (facility vs community deaths), age, demographics and geography and time. SECONDARY OUTCOMES Shifts in viral variants; causal inferences based on cycle threshold values and other features; antemortem testing rates. RESULTS From 1118 decedents enrolled between January and June 2021, COVID-19 was detected among 32.0% (358/1116). Roughly four COVID-19+ community deaths occurred for every facility death. Antemortem testing occurred for 52.6% (302/574) of facility deaths but only 1.8% (10/544) of community deaths and overall, only ~10% of COVID-19+ deaths were identified in life. During peak transmission periods, COVID-19 was detected in ~90% of all deaths. We observed three waves of transmission that peaked in July 2020, January 2021 and ~June 2021: the AE.1 lineage and the Beta and Delta variants, respectively. PCR signals were strongest among those whose deaths were deemed 'probably due to COVID-19', and weakest among children, with an age-dependent increase in PCR signal intensity. CONCLUSIONS COVID-19 was common among deceased individuals in Lusaka. Antemortem testing was rarely done, and almost never for community deaths. Suspicion that COVID-19 was the cause of deaths was highest for those with a respiratory syndrome and lowest for individuals <19 years.
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Affiliation(s)
- Christopher J Gill
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Lawrence Mwananyanda
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - William B MacLeod
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Geoffrey Kwenda
- Biomedical Sciences, University of Zambia, Ridgeway Campus, Lusaka, Lusaka, Zambia
| | - Rachel C Pieciak
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Lauren Etter
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Daniel Bridges
- Program for Applied Technology in Health (PATH), Lusaka, Zambia
| | | | | | | | - Leah Forman
- Biostatistics and Epidemiology Data Analytics Center, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Ben Katowa
- Macha Research Trust, Choma, Southern Province, Zambia
| | - Rotem Lapidot
- Pediatric Infectious Diseases, Boston Medical Center, Brookline, Massachusetts, USA
| | | | - Japhet Matoba
- Macha Research Trust, Choma, Southern Province, Zambia
| | | | - Benjamin Mubemba
- Wildlife Sciences, The Copperbelt University, Kitwe, Copperbelt, Zambia
| | | | - Walter Muleya
- Biomedical Sciences, University of Zambia School of Veterinary Medicine, Lusaka, Lusaka, Zambia
| | - Mulenga Mwenda
- Program for Applied Technology in Health, Lusaka, Zambia
| | | | - Ruth Nakazwe
- Biomedical Sciences, University of Zambia University Teaching Hospital, Lusaka, Lusaka, Zambia
| | | | - Natalie Pawlak
- Tufts University School of Medicine, Boston, Massachusetts, USA
| | | | - Ngonda Saasa
- University of Zambia School of Veterinary Medicine, Lusaka, Zambia
| | | | | | - Donald M Thea
- Department of Global Health, Boston University School of Public Health, Boston, Massachusetts, USA
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13
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HIV care experiences and health priorities during the first wave of COVID-19: clients' perspectives - a qualitative study in Lusaka, Zambia. BMC Public Health 2022; 22:2238. [PMID: 36451158 PMCID: PMC9713144 DOI: 10.1186/s12889-022-14493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 10/31/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The novel COVID-19 pandemic threatened to disrupt access to human immunodeficiency (HIV) treatment for persons living with HIV (PLHIV), two-thirds of whom live in sub-Saharan Africa. To inform a health system response supportive of continuity of care, we sought to understand clients' HIV care experiences and health priorities during the first wave of COVID-19 outbreak in Lusaka, Zambia. METHODS Leveraging a study cohort of those who completed periodic SMS surveys on HIV care, we purposefully sampled 25 PLHIV after first confirmed COVID-19 case was reported in Zambia on 18th March 2020. We phone-interviewed participants, iteratively refining interview guide to capture emergent themes on COVID-19 awareness, health facility interactions, and social circumstances, which we analyzed using matrix analysis. RESULTS All participants were aware of COVID-19, and HIV care experiences and health priorities of clients were affected by associated changes at health system, household, and individual level. The health system instituted early clinic visits to provide 6-months of antiretroviral therapy (ART) for stable patients and 3-months for unstable patients to reduce clinic visits and wait times. Most patients welcomed this long-desired extended appointment spacing. Some reported feeling respected and engaged when health care workers telephoned requesting their early clinic visit. However, others felt discouraged by an absence of physical distancing during their clinic visit due to 'severe acute respiratory syndrome coronavirus 2' (SARS-CoV-2) infection concerns. Several expressed a lack of clarity regarding next viral load monitoring date and means for receiving results. Patients suggested regular patient-facility communication by telephone and SMS. Patients emphasized that COVID-19 restrictions led to loss of employment and household income, exacerbating poverty and difficulties in taking ART. At individual level, most participants felt motivated to stay healthy during COVID-19 by ART adherence and regular laboratory monitoring. CONCLUSIONS Clients' HIV care and health priorities during the first wave of COVID-19 in Lusaka province were varied with a combination of positive and negative experiences that occurred especially at health system and individual levels, while at household level, the experiences were all negative. More research is needed to understand how patients practice resiliency in the widespread context of socio-economic instability. Governments and patients must work together to find local, health systems solutions to support ART adherence and monitoring. Additionally, the health system should consider how to build on changes for long-term HIV management and service delivery.
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Katowa B, Kalonda A, Mubemba B, Matoba J, Shempela DM, Sikalima J, Kabungo B, Changula K, Chitanga S, Kasonde M, Kapona O, Kapata N, Musonda K, Monze M, Tembo J, Bates M, Zumla A, Sutcliffe CG, Kajihara M, Yamagishi J, Takada A, Sawa H, Chilengi R, Mukonka V, Muleya W, Simulundu E. Genomic Surveillance of SARS-CoV-2 in the Southern Province of Zambia: Detection and Characterization of Alpha, Beta, Delta, and Omicron Variants of Concern. Viruses 2022; 14:v14091865. [PMID: 36146671 PMCID: PMC9504048 DOI: 10.3390/v14091865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/15/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) have significantly impacted the global epidemiology of the pandemic. From December 2020 to April 2022, we conducted genomic surveillance of SARS-CoV-2 in the Southern Province of Zambia, a region that shares international borders with Botswana, Namibia, and Zimbabwe and is a major tourist destination. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116), and multiple Omicron subvariants with the BA.1 subvariant being predominant. Whereas Beta, Delta, and Omicron variants were associated with the second, third, and fourth pandemic waves, respectively, the Alpha variant was not associated with any wave in the country. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. Across the 40 genomes analysed, a total of 292 mutations were observed, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. This study stresses the need for the continued monitoring of SARS-CoV-2 circulation in Zambia, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs.
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Affiliation(s)
- Ben Katowa
- Macha Research Trust, Choma 20100, Zambia
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Annie Kalonda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Benjamin Mubemba
- Department of Wildlife Sciences, School of Natural Resources, Copperbelt University, Kitwe 50100, Zambia
- Department of Biomedical Sciences, School of Medicine, Copperbelt University, Ndola 50100, Zambia
| | | | | | - Jay Sikalima
- Churches Health Association of Zambia, Lusaka 10101, Zambia
| | - Boniface Kabungo
- Southern Provincial Health Office, Ministry of Health, Choma 20100, Zambia
| | - Katendi Changula
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Simbarashe Chitanga
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia
- Department of Preclinical Studies, School of Veterinary Medicine, University of Namibia, Windhoek Private Bag 13301, Namibia
- School of Life Sciences, College of Agriculture, Engineering and Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South Africa
| | - Mpanga Kasonde
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Otridah Kapona
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Nathan Kapata
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Kunda Musonda
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Mwaka Monze
- Virology Laboratory, University Teaching Hospital, Lusaka 10101, Zambia
| | - John Tembo
- HerpeZ Infection Research and Training, University Teaching Hospital, Lusaka 10101, Zambia
| | - Matthew Bates
- HerpeZ Infection Research and Training, University Teaching Hospital, Lusaka 10101, Zambia
- School of Life and Environmental Sciences, University of Lincoln, Lincoln, Lincolnshire LN6 7TS, UK
| | - Alimuddin Zumla
- Division of Infection and Immunity, Centre for Clinical Microbiology, University College London, NIHR Biomedical Research Centre, University College London Hospitals NHS Foundation Trust, London NW3 2PF, UK
| | - Catherine G. Sutcliffe
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Junya Yamagishi
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- One Health Research Center, Hokkaido University, N18 W9, Kita-ku, Sapporo 001-0020, Japan
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Africa Centre of Excellence for Infectious Diseases of Humans and Animals, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Division of Collaboration and Education, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- One Health Research Center, Hokkaido University, N18 W9, Kita-ku, Sapporo 001-0020, Japan
- Division of Molecular Pathobiology, International Institute for Zoonosis Control, Hokkaido University, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Division of International Research Promotion, Hokkaido University International Institute for Zoonosis Control, N20 W10, Kita-ku, Sapporo 001-0020, Japan
- Global Virus Network, 725 W Lombard Street, Baltimore, MD 21201, USA
| | - Roma Chilengi
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
- Republic of Zambia State House, Lusaka 10101, Zambia
| | - Victor Mukonka
- Zambia National Public Health Institute, Ministry of Health, Lusaka 10101, Zambia
| | - Walter Muleya
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
| | - Edgar Simulundu
- Macha Research Trust, Choma 20100, Zambia
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
- Correspondence:
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15
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Anscombe C, Lissauer S, Thole H, Rylance J, Dula D, Menyere M, Kutambe B, van der Veer C, Phiri T, Banda NP, Mndolo KS, Mponda K, Phiri C, Mallewa J, Nyirenda M, Katha G, Mwandumba H, Gordon SB, Jambo KC, Cornick J, Feasey N, Barnes KG, Morton B, Ashton PM. A comparison of four epidemic waves of COVID-19 in Malawi; an observational cohort study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.02.17.22269742. [PMID: 35860218 PMCID: PMC9298135 DOI: 10.1101/2022.02.17.22269742] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Background Compared to the abundance of clinical and genomic information available on patients hospitalised with COVID-19 disease from high-income countries, there is a paucity of data from low-income countries. Our aim was to explore the relationship between viral lineage and patient outcome. Methods We enrolled a prospective observational cohort of adult patients hospitalised with PCR-confirmed COVID-19 disease between July 2020 and March 2022 from Blantyre, Malawi, covering four waves of SARS-CoV-2 infections. Clinical and diagnostic data were collected using an adapted ISARIC clinical characterization protocol for COVID-19. SARS-CoV-2 isolates were sequenced using the MinIONâ"¢ in Blantyre. Results We enrolled 314 patients, good quality sequencing data was available for 55 patients. The sequencing data showed that 8 of 11 participants recruited in wave one had B.1 infections, 6/6 in wave two had Beta, 25/26 in wave three had Delta and 11/12 in wave four had Omicron. Patients infected during the Delta and Omicron waves reported fewer underlying chronic conditions and a shorter time to presentation. Significantly fewer patients required oxygen (22.7% [17/75] vs. 58.6% [140/239], p<0.001) and steroids (38.7% [29/75] vs. 70.3% [167/239], p<0.001) in the Omicron wave compared with the other waves. Multivariable logistic-regression demonstrated a trend toward increased mortality in the Delta wave (OR 4.99 [95% CI 1.0-25.0 p=0.05) compared to the first wave of infection. Conclusions Our data show that each wave of patients hospitalised with SARS-CoV-2 was infected with a distinct viral variant. The clinical data suggests that patients with severe COVID-19 disease were more likely to die during the Delta wave. Summary We used genome sequencing to identify the variants of SARS-CoV-2 causing disease in Malawi, and found that each of the four waves was caused by a distinct variant. Clinical investigation suggested that the Delta wave had the highest mortality.
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Affiliation(s)
- Catherine Anscombe
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Samantha Lissauer
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Herbert Thole
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Jamie Rylance
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Dingase Dula
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Mavis Menyere
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Belson Kutambe
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Charlotte van der Veer
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Tamara Phiri
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Ndaziona P. Banda
- Kamuzu University of Health Sciences (formerly University of Malawi-College of Medicine) Blantyre, Malawi
| | | | - Kelvin Mponda
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Chimota Phiri
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Jane Mallewa
- Kamuzu University of Health Sciences (formerly University of Malawi-College of Medicine) Blantyre, Malawi
| | - Mulinda Nyirenda
- Kamuzu University of Health Sciences (formerly University of Malawi-College of Medicine) Blantyre, Malawi
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Grace Katha
- Department of Medicine, Queen Elizabeth Central Hospital, Blantyre, Malawi
| | - Henry Mwandumba
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Kamuzu University of Health Sciences (formerly University of Malawi-College of Medicine) Blantyre, Malawi
| | - Stephen B. Gordon
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kondwani C. Jambo
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Kamuzu University of Health Sciences (formerly University of Malawi-College of Medicine) Blantyre, Malawi
| | - Jennifer Cornick
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Nicholas Feasey
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Kayla G. Barnes
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
- Harvard School of Public Health, Boston, USA
- Broad Institute of MIT and Harvard, Cambridge, USA
- University of Glasgow MRC Centre for Virus Research, Glasgow, UK
| | - Ben Morton
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Liverpool University Hospitals Foundation Trust, Liverpool, UK
| | - Philip M. Ashton
- Malawi-Liverpool-Wellcome Clinical Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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Dutta D, Naiyer S, Mansuri S, Soni N, Singh V, Bhat KH, Singh N, Arora G, Mansuri MS. COVID-19 Diagnosis: A Comprehensive Review of the RT-qPCR Method for Detection of SARS-CoV-2. Diagnostics (Basel) 2022; 12:diagnostics12061503. [PMID: 35741313 PMCID: PMC9221722 DOI: 10.3390/diagnostics12061503] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 06/15/2022] [Accepted: 06/17/2022] [Indexed: 12/15/2022] Open
Abstract
The world is grappling with the coronavirus disease 2019 (COVID-19) pandemic, the causative agent of which is severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 symptoms are similar to the common cold, including fever, sore throat, cough, muscle and chest pain, brain fog, dyspnoea, anosmia, ageusia, and headache. The manifestation of the disease can vary from being asymptomatic to severe life-threatening conditions warranting hospitalization and ventilation support. Furthermore, the emergence of mutecated variants of concern (VOCs) is paramount to the devastating effect of the pandemic. This highly contagious virus and its emergent variants challenge the available advanced viral diagnostic methods for high-accuracy testing with faster result yields. This review is to shed light on the natural history, pathology, molecular biology, and efficient diagnostic methods of COVID-19, detecting SARS-CoV-2 in collected samples. We reviewed the gold standard RT-qPCR method for COVID-19 diagnosis to confer a better understanding and application to combat the COVID-19 pandemic. This comprehensive review may further develop awareness about the management of the COVID-19 pandemic.
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Affiliation(s)
- Debashis Dutta
- Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Correspondence: (D.D.); (M.S.M.)
| | - Sarah Naiyer
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, IL 60616, USA;
| | | | - Neeraj Soni
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Vandana Singh
- Department of Pathology and Microbiology, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, USA;
| | - Khalid Hussain Bhat
- SKUAST Kashmir, Division of Basic Science and Humanities, Faculty of Agriculture, Wadura Sopore 193201, JK, India;
| | - Nishant Singh
- Cell and Gene Therapy Absorption System, Exton, PA 19335, USA;
| | - Gunjan Arora
- Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA;
| | - M. Shahid Mansuri
- Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Correspondence: (D.D.); (M.S.M.)
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17
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Mudenda V, Mumba C, Pieciak RC, Mwananyanda L, Chimoga C, Ngoma B, Mupila Z, Kwenda G, Forman L, Lapidot R, MacLeod WB, Thea DM, Gill CJ. Histopathological Evaluation of Deceased Persons in Lusaka, Zambia With or Without Coronavirus Disease 2019 (COVID-19) Infection: Results Obtained From Minimally Invasive Tissue Sampling. Clin Infect Dis 2021; 73:S465-S471. [PMID: 34910177 PMCID: PMC8672753 DOI: 10.1093/cid/ciab858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Although much has been learned about the pathophysiology of coronavirus disease 2019 (COVID-19) infections, pathology data from patients who have died of COVID-19 in low- and middle-income country settings remain sparse. We integrated minimally invasive tissue sampling (MITS) into an ongoing postmortem surveillance study of COVID-19 in deceased individuals of all ages in Lusaka, Zambia. Methods We enrolled deceased subjects from the University Teaching Hospital Morgue in Lusaka, Zambia within 48 hours of death. We collected clinical and demographic information, a nasopharyngeal swab, and core tissue biopsies from the lung, liver, and kidneys for pathologic analysis. Individuals were considered eligible for MITS if they had a respiratory syndrome prior to death or a COVID-19+ polymerase chain reaction (PCR) nasopharyngeal swab specimen. Samples were retested using quantitative reverse transcriptase PCR. Results From June to September 2020 we performed MITS on 29 deceased individuals. PCR results were available for 28/29 (96.5%) cases. Three had a COVID-19+ diagnosis antemortem, and 5 more were identified postmortem using the recommended cycle threshold cut-point <40. When expanding the PCR threshold to 40 ≤ cycle threshold (Ct) ≤ 45, we identified 1 additional case. Most cases were male and occurred in the community The median age at death was 47 years (range 40–64). Human immunodeficiency virus (HIV)/AIDS, tuberculosis, and diabetes were more common among the COVID-19+ cases. Diffuse alveolar damage and interstitial pneumonitis were common among COVID-19+ cases; nonspecific findings of hepatic steatosis and acute kidney injury were also prevalent in the COVID-19+ group. Vascular thrombi were rarely detected. Conclusions Lung abnormalities typical of viral pneumonias were common among deceased COVID-19+ individuals, as were nonspecific findings in the liver and kidneys. Pulmonary vascular thrombi were rarely detected, which could be a limitation of the MITS technique. Nonetheless, MITS offers a valuable alternative to open autopsy for understanding pathological changes due to COVID-19.
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Affiliation(s)
- Victor Mudenda
- University Teaching Hospital, Department of Pathology, Lusaka, Zambia
| | - Chibamba Mumba
- University Teaching Hospital, Department of Pathology, Lusaka, Zambia
| | - Rachel C Pieciak
- Boston University School of Public Health, Department of Global Health, Boston, Massachusetts, USA
| | - Lawrence Mwananyanda
- Boston University School of Public Health, Department of Global Health, Boston, Massachusetts, USA.,Right to Care Zambia, Lusaka, Zambia
| | | | | | | | - Geoffrey Kwenda
- University of Zambia, School of Health Sciences, Department of Biomedical Sciences, Lusaka, Zambia
| | - Leah Forman
- Boston University School of Public Health, Biostatistics and Epidemiology Data Analytics Center (BEDAC), Boston, Massachusetts, USA
| | - Rotem Lapidot
- Boston University School of Medicine, Boston, Massachusetts, USA
| | - William B MacLeod
- Boston University School of Public Health, Department of Global Health, Boston, Massachusetts, USA
| | - Donald M Thea
- Boston University School of Public Health, Department of Global Health, Boston, Massachusetts, USA
| | - Christopher J Gill
- Boston University School of Public Health, Department of Global Health, Boston, Massachusetts, USA
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18
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Ntoumi F, Mfoutou Mapanguy CC, Tomazatos A, Pallerla SR, Linh LTK, Casadei N, Angelov A, Sonnabend M, Peter S, Kremsner PG, Velavan TP. Genomic surveillance of SARS-CoV-2 in the Republic of Congo. Int J Infect Dis 2021; 105:735-738. [PMID: 33737129 PMCID: PMC7959680 DOI: 10.1016/j.ijid.2021.03.036] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 11/26/2022] Open
Abstract
Objective The aim of this study was to carry out whole-genome sequencing (WGS) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), using samples collected from Congolese individuals between April and July 2020. Methods Ninety-six samples were screened for SARS-CoV-2 using RT-PCR, and 19 samples with Ct values <30 were sequenced using Illumina Next-Generation Sequencing (NGS). The genomes were annotated and screened for mutations using the web tool ‘coronapp’. Subsequently, different SARS-CoV-2 lineages were assigned using PANGOLIN and Nextclade. Results Eleven SARS-CoV-2 genomes were successfully sequenced and submitted to the GSAID database. All genomes carried the spike mutation D614G and were classified as part of the GH clade. The Congolese SARS-CoV-2 sequences were shown to belong to lineage B1 and Nextclade 20A and 20C, which split them into distinct clusters, indicating two separate introductions of the virus into the Republic of Congo. Conclusion This first study provides valuable information on SARS CoV-2 transmission in the central African region, contributing to SARS CoV-2 surveillance on a temporal and spatial scale.
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Affiliation(s)
- Francine Ntoumi
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany; Fondation Congolaise pour la Recherche Médicale (FCRM), Brazzaville, Republic of Congo; Faculty of Sciences and Technology, University Marien Ngouabi, Brazzaville, Republic of Congo
| | - Claujens Chastel Mfoutou Mapanguy
- Fondation Congolaise pour la Recherche Médicale (FCRM), Brazzaville, Republic of Congo; Faculty of Sciences and Technology, University Marien Ngouabi, Brazzaville, Republic of Congo
| | - Alexandru Tomazatos
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | | | - Le Thi Kieu Linh
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany; Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam
| | - Nicolas Casadei
- NGS Competence Center Tübingen (NCCT), Tübingen, Germany; Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Angel Angelov
- NGS Competence Center Tübingen (NCCT), Tübingen, Germany; Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Michael Sonnabend
- NGS Competence Center Tübingen (NCCT), Tübingen, Germany; Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Silke Peter
- NGS Competence Center Tübingen (NCCT), Tübingen, Germany; Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Peter G Kremsner
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany; Centre de Recherches Médicales de Lambaréné (CERMEL), Gabon
| | - Thirumalaisamy P Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany; Vietnamese-German Center for Medical Research, VG-CARE, Hanoi, Vietnam.
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19
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Mwenda M, Saasa N, Sinyange N, Busby G, Chipimo PJ, Hendry J, Kapona O, Yingst S, Hines JZ, Minchella P, Simulundu E, Changula K, Nalubamba KS, Sawa H, Kajihara M, Yamagishi J, Kapin'a M, Kapata N, Fwoloshi S, Zulu P, Mulenga LB, Agolory S, Mukonka V, Bridges DJ. Detection of B.1.351 SARS-CoV-2 Variant Strain - Zambia, December 2020. MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT 2021; 70:280-282. [PMID: 33630820 PMCID: PMC8344984 DOI: 10.15585/mmwr.mm7008e2] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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