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Nakigozi H, Ategyeka PM, Nabadda S, Ndejjo R. Positivity rates, trends and experiences of health workers on human papillomavirus screened using genexpert in Uganda: a three-year retrospective cohort study. BMC Cancer 2024; 24:375. [PMID: 38528459 DOI: 10.1186/s12885-024-12141-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 03/18/2024] [Indexed: 03/27/2024] Open
Abstract
INTRODUCTION Cervical cancer is a major public health issue in Uganda, with high incidence due to limited screening especially in rural areas. In 2019, HPV DNA testing using GeneXpert was rolled out to improve screening access. Assessing progress and challenges since its introduction is important. AIM To determine genotype distribution and explore health worker experiences with HPV screening using GeneXpert in Uganda. METHODS We conducted a retrospective cohort study where HPV screening data from 66 GeneXpert labs from March 2021-May 2023 country wide was analyzed. We used descriptive statistics to provide percentages and proportions from the data. Seven focus group discussions and five interviews were done with health workers to understand experiences. RESULTS We extracted 24,497 HPV tests that were done, and 39.1% were HPV positive. Other high-risk HPV genotypes were the most common at 65%, followed by HPV 16 (17%) and HPV 18/45 (18%). 15% of the HPV positive cases had more than one genotype. Qualitative findings showed inconsistent health worker knowledge, high workload, and complex care seeking behaviors as main challenges. It also revealed low community awareness, care seeking from traditional healers, CONCLUSION: HPV DNA testing has been expanding since its rollout, but the yield of HPV cases is lower than expected, signaling need to address supply-side challenges. Limited information on HPV among health workers especially community health workers, demand-side barriers like myths, medical pluralism and social norms must also be tackled through trainings of health workers and awareness campaigns engaging communities. Although access to GeneXpert services has increased, health system weaknesses pose bottlenecks to screening HPV. Targeted interventions are required to strengthen HPV diagnosis, prevent cervical cancer and save lives.
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Affiliation(s)
- Harriet Nakigozi
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda.
| | - Paul Mukama Ategyeka
- School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Susan Nabadda
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Rawlance Ndejjo
- School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
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Nakigozi H, Ndejjo R, Bazeyo W, Nabaggala A, Achola C, Iga M, Kalyesubula S, Kanamwangi B, Mutungi G, Batte C, Mukunya D, Sserwanga L, Gemageine G, Oyoo CA, Nabadda S. Prevalence of genital high-risk human papillomavirus infections and associated factors among women living with human immunodeficiency virus in Uganda. BMC Cancer 2024; 24:243. [PMID: 38383366 PMCID: PMC10882885 DOI: 10.1186/s12885-024-11928-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/27/2024] [Indexed: 02/23/2024] Open
Abstract
BACKGROUND Women living with HIV are at risk for cervical dysplasia and cancer worldwide. In 2015, the World Health Organization (WHO) recommended that testing for high-risk HPV (hrHPV) infection be incorporated into cervical cancer screening programs using molecular nucleic acid tests (NATs) but this has not previously been done in Uganda. The country's coverage for Human Papilloma Virus (HPV) screening remains low at less than 10% for women aged 25-49 years. This study determined the genital prevalence of hrHPV infection and the associated factors among women living with HIV in Uganda. METHODS A descriptive cross-sectional study was conducted in 15 selected health facilities among participants who were on Antiretroviral therapy (ART). Participants who consented to participate were instructed on how to collect their own high vaginal swabs using a cervical brush for HPV molecular testing (HPV DNA or HPV RNA) and their demographics data was collected using a standard questionnaire. Laboratory diagnosis for HPV molecular testing was done using Gene xpert machines and Hologic Aptima Machine. Modified Poisson regression analysis was conducted to determine the associated factors. RESULTS This study involved 5856 HIV positive participants on ART. A total of 2006 out of 5856 (34.3%) participants had high risk HPV infections. HPV infections by genotypes were: HPV16 317(15.8%), HPV 18/45 308 (15.4%) and other high-risk HPV 1381 (68.8%). The independent factors associated with all hrHPV were parity, education level, having more than one partner, and engaging in early sex. Smoking was associated with HPV 16, HPV 18/45 and other hrHPV. Age was associated with all hrHPV, marital status with HPV 16, and occupation with HPV 16. CONCLUSIONS The prevalence of genital high-risk HPV infections among HIV positive women attending ART clinics in public facilities in Uganda was high. Other hrHPV genotype was the commonest compared to 18/45 and HPV 16. The integration of cervical cancer screening in ART programmes remains paramount to support the early detection of cervical cancer and Non-invasive self-collected urine and vaginal sampling for cervical cancer screening present an opportunity.
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Affiliation(s)
- Harriet Nakigozi
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda.
| | - Rawlance Ndejjo
- Department of Disease Control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - William Bazeyo
- Department of Disease Control and Environmental Health, School of Public Health, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Annet Nabaggala
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Caroline Achola
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Moses Iga
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Simeon Kalyesubula
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Ben Kanamwangi
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Gerald Mutungi
- Department of Non-communicable Diseases, Ministry of Health, Kampala, Uganda
| | - Charles Batte
- Department of Medicine, Lung Institute, School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | - David Mukunya
- Faculty of Health Sciences, Department of Community and Public Health, Busitema University, Mbale, Uganda
| | - Lawrence Sserwanga
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Godfrey Gemageine
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Charles Akiya Oyoo
- Department of Non-communicable Diseases, Ministry of Health, Kampala, Uganda
| | - Susan Nabadda
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
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Nanyeenya N, Nakanjako D, Makumbi F, Nakigozi G, Nalugoda F, Kigozi G, Nasuuna E, Kibira SPS, Nabadda S, Kiyaga C, Huzaifah M, Kiwanuka N. Effectiveness of intensive adherence counselling in achieving an undetectable viral load among people on antiretroviral therapy with low-level viraemia in Uganda. HIV Med 2024; 25:245-253. [PMID: 37853605 DOI: 10.1111/hiv.13568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023]
Abstract
INTRODUCTION Uganda was using a threshold of 1000 copies/mL to determine viral non-suppression for antiretroviral therapy monitoring among people living with HIV, prior to this study. It was not clear whether people living with HIV with low-level viraemia (LLV, ≥50 to <1000 copies/mL) would benefit from intensive adherence counselling (IAC). The purpose of this study was to determine the effectiveness of IAC among people living with HIV, receiving antiretroviral therapy, and with LLV in Uganda, to guide key policy decisions in HIV care, including the review of the viral load (VL) testing algorithm. METHODS This cluster-randomized clinical trial comprised adults from eight HIV clinics who were living with HIV, receiving ART, and had recent VL results indicating LLV (tested from July 2022 to October 2022). Participants in the intervention arm clinics received three once-monthly sessions of IAC, and those in the comparison non-intervention arm clinics received the standard of care. At the end of the study, all participants were re-tested for VL to determine the proportions of those who then had an undetectable VL (<50 copies/mL). We assessed the statistical association between cross-tabulated variables using Fisher's exact test and then modified Poisson regression. RESULTS A total of 136 participants were enrolled into the study at eight HIV clinics. All 68 participants in the intervention arm completed all IAC sessions. Only one participant in the non-intervention arm was lost to follow-up. The average follow-up time was 3.7 months (standard deviation [SD] 0.2) and 3.5 months (SD 0.1) in the intervention and non-intervention arms, respectively. In total, 59 (43.7%) of 135 people living with HIV achieved an undetectable VL during the study follow-up period. The effect of IAC on attaining an undetectable VL among people with LLV was nearly twice as high in the intervention arm (57.4%) than in the non-intervention arm (29.9%): adjusted risk ratio 1.9 (95% confidence interval 1.0-3.5), p = 0.037. CONCLUSION IAC doubled the likelihood of an undetectable VL among people living with HIV with LLV. Therefore, IAC has been instituted as an intervention to manage people living with HIV with LLV in Uganda, and this should also be adopted in other Sub-Saharan African countries with similar settings. CLINICALTRIALS GOV IDENTIFIER NCT05514418.
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Affiliation(s)
- Nicholus Nanyeenya
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
- Ministry of Health Central Public Health Laboratories, Kampala, Uganda
| | - Damalie Nakanjako
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fredrick Makumbi
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | | | | | | | - Esther Nasuuna
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Simon P S Kibira
- Department of Community Health and Behavioral Sciences, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Susan Nabadda
- Ministry of Health Central Public Health Laboratories, Kampala, Uganda
| | - Charles Kiyaga
- Ministry of Health Central Public Health Laboratories, Kampala, Uganda
| | - Mutyaba Huzaifah
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Noah Kiwanuka
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
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Agaba BB, Smith D, Travis J, Pasay C, Nabatanzi M, Arinaitwe E, Ssewanyana I, Nabadda S, Cunningham J, Kamya MR, Cheng Q. Limited threat of Plasmodium falciparum pfhrp2 and pfhrp3 gene deletion to the utility of HRP2-based malaria RDTs in Northern Uganda. Malar J 2024; 23:3. [PMID: 38167003 PMCID: PMC10759665 DOI: 10.1186/s12936-023-04830-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Rapid diagnostic tests (RDTs) that detect Plasmodium falciparum histidine-rich protein-2 (PfHRP2) are exclusively deployed in Uganda, but deletion of the pfhrp2/3 target gene threatens their usefulness as malaria diagnosis and surveillance tools. METHODS A cross-sectional survey was conducted at 40 sites across four regions of Uganda in Acholi, Lango, W. Nile and Karamoja from March 2021 to June 2023. Symptomatic malaria suspected patients were recruited and screened with both HRP2 and pan lactate dehydrogenase (pLDH) detecting RDTs. Dried blood spots (DBS) were collected from all patients and a random subset were used for genomic analysis to confirm parasite species and pfhrp2 and pfhrp3 gene status. Plasmodium species was determined using a conventional multiplex PCR while pfhrp2 and pfhrp3 gene deletions were determined using a real-time multiplex qPCR. Expression of the HRP2 protein antigen in a subset of samples was further assessed using a ELISA. RESULTS Out of 2435 symptomatic patients tested for malaria, 1504 (61.8%) were positive on pLDH RDT. Overall, qPCR confirmed single pfhrp2 gene deletion in 1 out of 416 (0.2%) randomly selected samples that were confirmed of P. falciparum mono-infections. CONCLUSION These findings show limited threat of pfhrp2/3 gene deletions in the survey areas suggesting that HRP2 RDTs are still useful diagnostic tools for surveillance and diagnosis of P. falciparum malaria infections in symptomatic patients in this setting. Periodic genomic surveillance is warranted to monitor the frequency and trend of gene deletions and its effect on RDTs.
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Affiliation(s)
- Bosco B Agaba
- Faculty of Medicine, Department of Medical Laboratory Sciences, Mbarara University of Science and Technology, Mbarara, Uganda.
- National Malaria Control Division, Kampala, Uganda.
- London School of Hygiene and Tropical Medicine, London, UK.
- Infectious Diseases Research Collaboration, Kampala, Uganda.
| | - David Smith
- QIMR Berghofer Medical Research Institute, Kelvin Grove, QLD, Australia
- Australian Defence Force Malaria and Infectious Disease Institute, Kelvin Grove, Australia
| | - Jye Travis
- QIMR Berghofer Medical Research Institute, Kelvin Grove, QLD, Australia
- Australian Defence Force Malaria and Infectious Disease Institute, Kelvin Grove, Australia
| | - Cielo Pasay
- QIMR Berghofer Medical Research Institute, Kelvin Grove, QLD, Australia
| | | | | | - Isaac Ssewanyana
- Infectious Diseases Research Collaboration, Kampala, Uganda
- National Health Laboratory Services/Central Public Health Laboratories, Kelvin Grove, Uganda
| | - Susan Nabadda
- National Health Laboratory Services/Central Public Health Laboratories, Kelvin Grove, Uganda
| | - Jane Cunningham
- Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Moses R Kamya
- Faculty of Medicine, Department of Medical Laboratory Sciences, Mbarara University of Science and Technology, Mbarara, Uganda
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Qin Cheng
- QIMR Berghofer Medical Research Institute, Kelvin Grove, QLD, Australia
- Australian Defence Force Malaria and Infectious Disease Institute, Kelvin Grove, Australia
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Balinandi S, Whitmer S, Mulei S, Nassuna C, Pimundu G, Muyigi T, Kainulainen M, Shedroff E, Krapiunaya I, Scholte F, Nyakarahuka L, Tumusiime A, Kyondo J, Baluku J, Kiconco J, Harris JR, Ario AR, Kagirita A, Bosa HK, Ssewanyana I, Nabadda S, Mwebesa HG, Aceng JR, Atwine D, Lutwama JJ, Shoemaker TR, Montgomery JM, Kaleebu P, Klena JD. Molecular characterization of the 2022 Sudan virus disease outbreak in Uganda. J Virol 2023; 97:e0059023. [PMID: 37750724 PMCID: PMC10617429 DOI: 10.1128/jvi.00590-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/08/2023] [Indexed: 09/27/2023] Open
Abstract
IMPORTANCE Ebola disease (EBOD) is a public health threat with a high case fatality rate. Most EBOD outbreaks have occurred in remote locations, but the 2013-2016 Western Africa outbreak demonstrated how devastating EBOD can be when it reaches an urban population. Here, the 2022 Sudan virus disease (SVD) outbreak in Mubende District, Uganda, is summarized, and the genetic relatedness of the new variant is evaluated. The Mubende variant exhibited 96% amino acid similarity with historic SUDV sequences from the 1970s and a high degree of conservation throughout the outbreak, which was important for ongoing diagnostics and highly promising for future therapy development. Genetic differences between viruses identified during the Mubende SVD outbreak were linked with epidemiological data to better interpret viral spread and contact tracing chains. This methodology should be used to better integrate discrete epidemiological and sequence data for future viral outbreaks.
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Affiliation(s)
| | - Shannon Whitmer
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Sophia Mulei
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Godfrey Pimundu
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Tonny Muyigi
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Markus Kainulainen
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Elizabeth Shedroff
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Inna Krapiunaya
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Florine Scholte
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Luke Nyakarahuka
- Uganda Virus Research Institute, Entebbe, Uganda
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Jimmy Baluku
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | - Alex R. Ario
- Uganda Public Health Fellowship Program, Kampala, Uganda
| | | | - Henry K. Bosa
- Ministry of Health, Kampala, Uganda
- Kellogg College, University of Oxford, Oxford, United Kingdom
| | - Isaac Ssewanyana
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Susan Nabadda
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | | | | | | | | | - Trevor R. Shoemaker
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joel M. Montgomery
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Pontiano Kaleebu
- Uganda Virus Research Institute, Entebbe, Uganda
- MRC/UVRI & LSHTM Uganda Research Unit, Entebbe, Uganda
| | - John D. Klena
- Viral Special Pathogens Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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Nsawotebba A, Ibanda I, Mujuni D, Nabadda S, Nadunga D, Kabugo J, Adam I, Wekiya E, Nyombi A, Nsubuga R, Ademun P, Musisi K, Kangave F, Joloba M. Impact of randomized blinded rechecking program on the performance of the AFB Microscopy Laboratory Network in Uganda: a decadal retrospective study. BMC Infect Dis 2023; 23:494. [PMID: 37495964 PMCID: PMC10373387 DOI: 10.1186/s12879-023-08406-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
BACKGROUND Smear microscopy has remained the initial diagnostic test for presumptive tuberculosis (TB) patients in health facilities without the World Health Organization (WHO) recommended rapid diagnostic tools. In the Uganda TB laboratory network, the technique remains the only tool to monitor response to treatment among drug susceptible TB patients, with the country currently having over 1,600 microscopy TB testing units. It has been evidenced that acid-fast bacilli (AFB) microscopy's yield highly depends on the staining technique and reading ability of the laboratory personnel. For the quality of TB testing in the country, the TB control program set up a Randomized Blinded Rechecking (RBRC) program in 2008 to monitor the testing performance of laboratories to continuously improve the reliability and efficiency of results. This is the first study to determine the effectiveness and impact of the RBRC program on the performance of the participating laboratories in Uganda. METHODS This was a retrospective cross-sectional study based on a record review of the RBRC's annual results compilations between January 2008 and December 2017. RESULTS Between January 2008 and December 2017, a total of 265,523 smears were re-checked during the RBRC program. The number of enrolled laboratories in the RBRC program rose from 660 to 2008 to 1,406 in 2017. The RBRC program resulted in a statistically significant reduction in microscopy errors, with false positives decreasing from 12.8% to 2008 to 7.6% in 2017, false positive errors decreasing from 10 to 6.3%, false negative errors decreasing from 2.9 to 0.7%, quantification errors decreasing from 6.0 to 1.8%, and the overall sensitivity of smear microscopy compared to the controllers increased with statistical significance from 93 to 97%. CONCLUSION The study reveals an overall significant error reduction and an improved sensitivity of smear microscopy upon continuous implementation of the RBRC program in an AFB microscopy TB laboratory network. Implementation of a RBRC program is crucial and essential to maintaining a reliable TB laboratory service that can facilitate accurate diagnosis and offset the disadvantages of using smear microscopy.
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Affiliation(s)
- Andrew Nsawotebba
- Department of National Health Laboratory and Diagnostic Services, National Health Laboratory Services, Kampala, Uganda.
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda.
| | - Ivan Ibanda
- Department of National Health Laboratory and Diagnostic Services, National Health Laboratory Services, Kampala, Uganda
- Department of Pharmacology and Pharmacotherapeutics, School of Medicine and Surgery, King Ceasor University, Kampala, Uganda
| | - Dennis Mujuni
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Susan Nabadda
- Department of National Health Laboratory and Diagnostic Services, National Health Laboratory Services, Kampala, Uganda
| | - Diana Nadunga
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Joel Kabugo
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Isa Adam
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Enock Wekiya
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Abdunoor Nyombi
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Richard Nsubuga
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Patrick Ademun
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Kenneth Musisi
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Fredrick Kangave
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
| | - Moses Joloba
- World Health Organisation Supranational Reference Laboratory - Uganda National TB Reference Laboratory, Kampala, Uganda
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University, Kampala, Uganda
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Sendagire H, Kiwuwa S, Dhamani A, Akugizibwe R, Lwasa Y, Bukenya A, Mukasa HK, Kakeeto P, Nankinga Z, Bbosa G, Babirye J, Nankabirwa H, Nabadda S. Staging of COVID-19 disease; using selected laboratory profiles for prediction, prevention and management of severe SARS-CoV-2 infection in Africa-review. Afr Health Sci 2023; 23:1-15. [PMID: 37545952 PMCID: PMC10398495 DOI: 10.4314/ahs.v23i1.2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023] Open
Abstract
There are many uncertainties on the future management of the coronavirus disease 19 (COVID-19) in Africa. By July 2021, Africa had lagged behind the rest of the world in Covid-19 vaccines uptake, accounting for just 1.6% of doses administered globally. During that time COVID 19 was causing an average death rate of 2.6% in Africa, surpassing the then global average of 2.2%. There were no clear therapeutic guidelines, yet inappropriate and unnecessary treatments may have led to unwanted adverse events such as worsening of hyperglycemia and precipitating of ketoacidosis in administration of steroid therapy. in order to provide evidence-based policy guidelines, we examined peer-reviewed published articles in PubMed on COVID 19, or up-to date data, we focused our search on publications from 1st May 2020 to 15th July, 2021. For each of the studies, we extracted data on pathophysiology, selected clinical chemistry and immunological tests, clinical staging and treatment. Our review reports a gross unmet need for vaccination, inadequate laboratory capacity for immunological tests and the assessment of individual immune status, clinical staging and prediction of disease severity. We recommend selected laboratory tools in the assessment of individual immune status, prediction of disease severity and determination of the exact timing for suitable therapy, especially in individuals with co-morbidities.
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Affiliation(s)
- Hakim Sendagire
- College of Health Sciences, Makerere University, Kampala, Uganda
- Faculty of Health Sciences, Islamic University in Uganda
- National Health Laboratory and Diagnostics Services, Ministry of Health, Uganda
| | - Steven Kiwuwa
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Ali Dhamani
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Yasin Lwasa
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Andrew Bukenya
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | | | | | - Godfrey Bbosa
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - Juliet Babirye
- College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Susan Nabadda
- National Health Laboratory and Diagnostics Services, Ministry of Health, Uganda
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Nanyeenya N, Chang LW, Kiwanuka N, Nasuuna E, Nakanjako D, Nakigozi G, Kibira SPS, Nabadda S, Kiyaga C, Makumbi F. The association between low-level viraemia and subsequent viral non-suppression among people living with HIV/AIDS on antiretroviral therapy in Uganda. PLoS One 2023; 18:e0279479. [PMID: 36638086 PMCID: PMC9838846 DOI: 10.1371/journal.pone.0279479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/08/2022] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Uganda's efforts to end the HIV epidemic by 2030 are threatened by the increasing number of PLHIV with low-level viraemia (LLV). We conducted a study to determine the prevalence of LLV and the association between LLV and subsequent viral non-suppression from 2016 to 2020 among PLHIV on ART in Uganda. METHOD This was a retrospective cohort study, using the national viral load (VL) program data from 2016 to 2020. LLV was defined as a VL result of at least 50 copies/ml, but less than 1,000 copies/ml. Multivariable logistic regression was used to determine the factors associated with LLV, and cox proportional hazards regression model was used to determine the association between LLV and viral non-suppression. RESULTS A cohort of 17,783 PLHIV, of which 1,466 PLHIV (8.2%) had LLV and 16,317 (91.8%) had a non-detectable VL was retrospectively followed from 2016 to 2020. There were increasing numbers of PLHIV with LLV from 2.0% in 2016 to 8.6% in 2020; and LLV was associated with male sex, second line ART regimen and being of lower age. 32.5% of the PLHIV with LLV (476 out of 1,466 PLHIV) became non-suppressed, as compared to 7.7% of the PLHIV (1,254 out of 16,317 PLHIV) with a non-detectable viral load who became non-suppressed during the follow-up period. PLHIV with LLV had 4.1 times the hazard rate of developing viral non-suppression, as compared to PLHIV with a non-detectable VL (adjusted hazard ratio was 4.1, 95% CI: 3.7 to 4.7, p < 0.001). CONCLUSION Our study indicated that PLHIV with LLV increased from 2.0% in 2016 to 8.6% in 2020, and PLHIV with LLV had 4.1 times the hazard rate of developing viral non-suppression, as compared to PLHIV with a non-detectable VL. Hence the need to review the VL testing algorithm and also manage LLV in Uganda.
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Affiliation(s)
- Nicholus Nanyeenya
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
- Department of National Health Laboratory Services, Ministry of Health, Kampala Uganda
| | - Larry William Chang
- Department of Epidemiology, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Noah Kiwanuka
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Esther Nasuuna
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Damalie Nakanjako
- Department of Medicine, School of Medicine Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Simon P. S. Kibira
- Department of Community Health and Behavioral Sciences, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Susan Nabadda
- Department of National Health Laboratory Services, Ministry of Health, Kampala Uganda
| | - Charles Kiyaga
- Department of National Health Laboratory Services, Ministry of Health, Kampala Uganda
| | - Fredrick Makumbi
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
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9
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Joseph J, Demke O, Ameyan L, Bitilinyu-Bango J, Bourgoin B, Diop M, Guèye B, Kama J, Lubega M, Madzima B, Maparo T, Mhizha T, Musoke A, Nabadda S, Phiri T, Tchereni T, Wiwa O, Hariharan K, Peter T, Khan S. Human papillomavirus testing using existing nucleic acid testing platforms to screen women for cervical cancer: implementation studies from five sub-Saharan African countries. BMJ Open 2023; 13:e065074. [PMID: 36609331 PMCID: PMC9827237 DOI: 10.1136/bmjopen-2022-065074] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/02/2022] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVES To demonstrate acceptability and operational feasibility of introducing human papillomavirus (HPV) testing as a principal cervical cancer screening method in public health programmes in sub-Saharan Africa. SETTING 45 primary and secondary health clinics in Malawi, Nigeria, Senegal, Uganda and Zimbabwe. PARTICIPANTS 15 766 women aged 25-54 years presenting at outpatient departments (Senegal only, general population) or at antiretroviral therapy clinics (all other countries, HIV-positive women only). Eligibility criteria followed national guidelines for cervical cancer screening. INTERVENTIONS HPV testing was offered to eligible women as a primary screening for cervical cancer, and HPV-positive women were referred for visual inspection with acetic acid (VIA), and if lesions identified, received treatment or referral. PRIMARY AND SECONDARY OUTCOME MEASURES The primary outcomes were the proportion of HPV-positive women who received results and linked to VIA and the proportion of HPV-positive and VIA-positive women who received treatment. RESULTS A total of 15 766 women were screened and tested for HPV, among whom 14 564 (92%) had valid results and 4710/14 564 (32%) were HPV positive. 13 837 (95%) of valid results were returned to the clinic and 3376 (72%) of HPV-positive women received results. Of women receiving VIA (n=2735), 715 (26%) were VIA-positive and 622 (87%) received treatment, 75% on the same day as VIA. CONCLUSIONS HPV testing was found to be feasible across the five study countries in a public health setting, although attrition was seen at several key points in the cascade of care, namely results return to women and linkage to VIA. Once women received VIA, if eligible, the availability of on-site cryotherapy and thermal ablation allowed for same-day treatment. With sufficient resources and supportive infrastructure to ensure linkage to treatment, use of HPV testing for cervical cancer screening as recommended by WHO is a promising model in low-income and middle-income countries.
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Affiliation(s)
- Jessica Joseph
- Global Health Sciences, Clinton Health Access Initiative, Boston, Massachusetts, USA
| | - Owen Demke
- Global Diagnostics Team, Clinton Health Access Initiative, Boston, Massachusetts, USA
| | - Lola Ameyan
- Cervical Cancer, Clinton Health Access Initiative, Abuja, Nigeria
| | | | | | - Mamadou Diop
- Cancer Institute of Cheikh Anta Diop University, Aristide Le Dantec Hospital, Dakar, Senegal
| | - Babacar Guèye
- Disease Control, Ministère de la Santé et de l'Action Sociale, Dakar, Senegal
| | - Jibrin Kama
- Laboratory Access Program, Clinton Health Access Initiative, Abuja, Nigeria
| | - Marvin Lubega
- Laboratory Access Program, Clinton Health Access Initiative, Kampala, Uganda
| | - Bernard Madzima
- Family Health, Ministry of Health and Child Care, Harare, Zimbabwe
| | - Tatenda Maparo
- Laboratory Access Program, Clinton Health Access Initiative, Harare, Zimbabwe
| | - Tasimba Mhizha
- Laboratory Access Program, Clinton Health Access Initiative, Harare, Zimbabwe
| | | | - Susan Nabadda
- National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | | | - Timothy Tchereni
- Sexual, Reproductive, Maternal and Newborn Health, Clinton Health Access Initiative, Lilongwe, Malawi
| | - Owens Wiwa
- Clinton Health Access Initiative, Abuja, Nigeria
| | - Karen Hariharan
- Global Cervical Cancer and Nutrition, Clinton Health Access Initiative, Boston, Massachusetts, USA
| | - Trevor Peter
- Global Diagnostics Team, Clinton Health Access Initiative, Boston, Massachusetts, USA
| | - Shaukat Khan
- Global Diagnostics Team, Clinton Health Access Initiative, Boston, Massachusetts, USA
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10
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Nanyeenya N, Siu G, Kiwanuka N, Makumbi F, Nasuuna E, Nakanjako D, Nakigozi G, Nabadda S, Kiyaga C, Kibira SPS. Hopes, joys and fears: Meaning and perceptions of viral load testing and low-level viraemia among people on antiretroviral therapy in Uganda: A qualitative study. PLOS Glob Public Health 2023; 3:e0001797. [PMID: 37163527 PMCID: PMC10171654 DOI: 10.1371/journal.pgph.0001797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/12/2023] [Indexed: 05/12/2023]
Abstract
Uganda applies the World Health Organization threshold of 1,000 copies/ml to determine HIV viral non-suppression. While there is an emerging concern of low-level viraemia (≥50 to <1,000 copies/ml), there is limited understanding of how people on antiretroviral therapy perceive viral load testing and low-level viremia in resource-limited settings. This qualitative study used the health belief model to explore the meaning that people living with HIV attach to viral load testing and low-level viraemia in Uganda. We used stratified purposive sampling to select people on antiretroviral therapy from eight high volume health facilities from the Central, Eastern, Northern and Western regions of Uganda. We used an interview guide, based on the health belief model, to conduct 32 in-depth interviews, which were audio-recorded and transcribed verbatim. Thematic analysis technique was used to analyze the data with the help of ATLAS.ti 6. The descriptions of viral load testing used by the participants nearly matched the medical meaning, and many people living with HIV understood what viral load testing was. Perceived benefits for viral load testing were the ability to show; the amount of HIV in the body, how the people living with HIV take their drugs, whether the drugs are working, and also guide the next treatments steps for the patients. Participants reported HIV stigma, lack of transport, lack of awareness for viral load testing, delayed and missing viral load results and few health workers as the main barriers to viral load testing. On the contrary, most participants did not know what low-level viraemia meant, while several perceived it as having a reduced viral load that is suppressed. Many people living with HIV are unaware about low-level viraemia, and hence do not understand its associated risks. Likewise, some people living with HIV are still not aware about viral load testing. Lack of transport, HIV stigma and delayed viral load results are major barriers to viral load testing. Hence, there is an imminent need to institute more strategies to create awareness about both low-level viraemia and viral load testing, manage HIV related stigma, and improve turnaround time for viral load results.
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Affiliation(s)
- Nicholus Nanyeenya
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
- Ministry of Health Central Public Health Laboratories, Kampala Uganda
| | - Godfrey Siu
- Child Health and Development Centre, School of Medicine Makerere University College of Health Sciences, Kampala, Uganda
| | - Noah Kiwanuka
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fredrick Makumbi
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Esther Nasuuna
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Damalie Nakanjako
- Department of Medicine, School of Medicine Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Susan Nabadda
- Ministry of Health Central Public Health Laboratories, Kampala Uganda
| | - Charles Kiyaga
- Ministry of Health Central Public Health Laboratories, Kampala Uganda
| | - Simon P S Kibira
- Department of Community Health and Behavioral Sciences, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
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11
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Fonjungo PN, Lecher S, Zeh C, Rottinghaus E, Chun H, Adje-Toure C, Lloyd S, Mwangi JW, Mwasekaga M, Eshete YM, Pati R, Mots’oane T, Mitruka K, Beukes A, Mwangi C, Bowen N, Hamunime N, Beard RS, Kabuje A, Nabadda S, Auld AF, Balachandra S, Zungu I, Kandulu J, Alemnji G, Ehui E, Alexander H, Ellenberger D. Progress in scale up of HIV viral load testing in select sub-Saharan African countries 2016-2018. PLoS One 2023; 18:e0282652. [PMID: 36920918 PMCID: PMC10016655 DOI: 10.1371/journal.pone.0282652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 02/19/2023] [Indexed: 03/16/2023] Open
Abstract
INTRODUCTION We assessed progress in HIV viral load (VL) scale up across seven sub-Saharan African (SSA) countries and discussed challenges and strategies for improving VL coverage among patients on anti-retroviral therapy (ART). METHODS A retrospective review of VL testing was conducted in Côte d'Ivoire, Kenya, Lesotho, Malawi, Namibia, Tanzania, and Uganda from January 2016 through June 2018. Data were collected and included the cumulative number of ART patients, number of patients with ≥ 1 VL test result (within the preceding 12 months), the percent of VL test results indicating viral suppression, and the mean turnaround time for VL testing. RESULTS Between 2016 and 2018, the proportion of PLHIV on ART in all 7 countries increased (range 5.7%-50.2%). During the same time period, the cumulative number of patients with one or more VL test increased from 22,996 to 917,980. Overall, viral suppression rates exceeded 85% for all countries except for Côte d'Ivoire at 78% by June 2018. Reported turnaround times for VL testing results improved in 5 out of 7 countries by between 5.4 days and 27.5 days. CONCLUSIONS These data demonstrate that remarkable progress has been made in the scale-up of HIV VL testing in the seven SSA countries.
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Affiliation(s)
- Peter N. Fonjungo
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
- * E-mail:
| | - Shirley Lecher
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
| | - Clement Zeh
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
| | - Erin Rottinghaus
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
| | - Helen Chun
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
| | - Christiane Adje-Toure
- Division of Global HIV and TB, Center for Global Health, CDC, Abidjan, Côte d’Ivoire
| | - Spencer Lloyd
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
| | - Jane W. Mwangi
- Division of Global HIV and TB, Center for Global Health, CDC, Nairobi, Kenya
| | - Michael Mwasekaga
- Division of Global HIV and TB, Center for Global Health, CDC, Dar es Salaam, Tanzania
| | | | - Rituparna Pati
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
| | | | - Kiren Mitruka
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
| | - Anita Beukes
- Namibia Institute of Pathology, Windhoek, Namibia
| | - Christina Mwangi
- Division of Global HIV and TB, Center for Global Health, CDC, Kampala, Uganda
| | | | | | - Rachel S. Beard
- Division of Global HIV and TB, Center for Global Health, CDC, Windhoek, Namibia
| | | | | | - Andrew F. Auld
- Division of Global HIV and TB, Center for Global Health, CDC, Lilongwe, Malawi
| | - Shirish Balachandra
- Division of Global HIV and TB, Center for Global Health, CDC, Abidjan, Côte d’Ivoire
| | - Innocent Zungu
- Division of Global HIV and TB, Center for Global Health, CDC, Lilongwe, Malawi
| | | | - George Alemnji
- Office of the Global AIDS Coordinator and Health Diplomacy, U.S. Department of State, Washington, DC, United States of America
| | - Eboi Ehui
- Ministry of Health, Abidjan, Côte D’Ivoire
| | - Heather Alexander
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
| | - Dennis Ellenberger
- Division of Global HIV and TB, Center for Global Health, CDC, Atlanta, Georgia, United States of America
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12
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Agaba BB, Rugera SP, Mpirirwe R, Atekat M, Okubal S, Masereka K, Erionu M, Adranya B, Nabirwa G, Odong PB, Mukiibi Y, Ssewanyana I, Nabadda S, Muwanguzi E. Asymptomatic malaria infection, associated factors and accuracy of diagnostic tests in a historically high transmission setting in Northern Uganda. Malar J 2022; 21:392. [PMID: 36550492 PMCID: PMC9783970 DOI: 10.1186/s12936-022-04421-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/17/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Asymptomatic malaria infections are important parasite reservoirs and could sustain transmission in the population, but they are often unreported. A community-based survey was conducted to investigate the prevalence and factors associated with asymptomatic malaria infections in a historically high transmission setting in northern Uganda. METHODS Using a cross-sectional design, 288 children aged 2-15 years were enrolled and tested for the presence of malaria parasites using rapid diagnostic tests (RDTs) and blood smear microscopy between January to May 2022. Statistical analysis was performed using the exact binomial and Fisher's exact test with p ≤ 0.05 indicating significance. The logistic regression was used to explore factors associated with asymptomatic malaria infections. RESULTS Overall, the prevalence of asymptomatic infection was 34.7% (95% CI 29.2-40.5) with the highest observed in children 5-10 years 45.9% (95% CI 35.0-57.0). Gweri village accounted for 39.1% (95% CI 27.6-51.6) of malaria infections. Median parasite density was 1500 parasites/µl of blood. Plasmodium falciparum was the dominant species (86%) followed by Plasmodium malariae (5%). Factors associated with asymptomatic malaria infection were sleeping under mosquito net (Adjusted Odds Ratio (aOR) 0.27; 95% CI 0.13-0.56), p = 0.001 and presence of village health teams (VHTs) (aOR 0.02; 95% CI 0.01-0.45), p = 0.001. Sensitivity and specificity were higher for the P. falciparum/pLDH RDTs compared to HRP2-only RDTs, 90% (95% CI 86.5-93.5) and 95.2% (95% CI 92.8-97.7), p = 0.001, respectively. CONCLUSION Asymptomatic malaria infections were present in the study population and this varied with place and person in the different age groups. Plasmodium falciparum was the dominant parasite species however the presence of P. malariae and Plasmodium ovale was observed, which may have implication for the choice and deployment of diagnostic tools. Individuals who slept under mosquito net or had presence of functional VHTs were less likely to have asymptomatic malaria infection. P.f/pLDH RDTs performed better than the routinely used HRP2 RDTs. In view of these findings, investigation and reporting of asymptomatic malaria reservoirs through community surveys is recommended for accurate disease burden estimate and better targeting of control.
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Affiliation(s)
- Bosco B. Agaba
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda ,grid.415705.2National Malaria Control Division, Ministry of Health, Kampala, Uganda ,National Malaria Reference Laboratory, Central Public Health Laboratory Services, Kampala, Uganda ,grid.463352.50000 0004 8340 3103Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Simon P. Rugera
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Ruth Mpirirwe
- grid.11194.3c0000 0004 0620 0548Department of Statistics, Makerere University, Kampala, Uganda
| | - Martha Atekat
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Samuel Okubal
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Khalid Masereka
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Miseal Erionu
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Bosco Adranya
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Gertrude Nabirwa
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Patrick B. Odong
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Yasin Mukiibi
- Uganda Institute of Allied and Management Sciences, Kampala, Uganda
| | - Isaac Ssewanyana
- National Malaria Reference Laboratory, Central Public Health Laboratory Services, Kampala, Uganda ,grid.463352.50000 0004 8340 3103Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Susan Nabadda
- National Malaria Reference Laboratory, Central Public Health Laboratory Services, Kampala, Uganda
| | - Enoch Muwanguzi
- grid.33440.300000 0001 0232 6272Department of Medical Laboratory Science, Mbarara University of Science and Technology, Mbarara, Uganda ,Uganda Institute of Allied and Management Sciences, Kampala, Uganda
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13
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Romano ER, Sleeman K, Hall-Eidson P, Zeh C, Bhairavabhotla R, Zhang G, Adhikari A, Alemnji G, Cardo YR, Pinheiro A, Pocongo B, Eno LT, Shang JD, Ndongmo CB, Rosario H, Moreno O, De León LADLC, Fonjungo P, Kabwe C, Ahuke-Mundeke S, Gama D, Dlamini S, Maphalala G, Abreha T, Purfield A, Gebrehiwot YT, Desalegn DM, Basiye F, Mwangi J, Bowen N, Mengistu Y, Lecher S, Kampira E, Kaba M, Bitilinyu-Bangoh J, Masamha G, Viegas SO, Beard RS, van Rooyen G, Shiningavamwe AN, I J M, Iriemenam NC, Mba N, Okoi C, Katoro J, Kenyi DL, Bior BK, Mwangi C, Nabadda S, Kaleebu P, Yingst SL, Chikwanda P, Veri L, Simbi R, Alexander H. Contribution of PEPFAR-Supported HIV and TB Molecular Diagnostic Networks to COVID-19 Testing Preparedness in 16 Countries. Emerg Infect Dis 2022; 28:S59-S68. [PMID: 36502414 PMCID: PMC9745242 DOI: 10.3201/eid2813.220789] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The US President's Emergency Plan for AIDS Relief (PEPFAR) supports molecular HIV and tuberculosis diagnostic networks and information management systems in low- and middle-income countries. We describe how national programs leveraged these PEPFAR-supported laboratory resources for SARS-CoV-2 testing during the COVID-19 pandemic. We sent a spreadsheet template consisting of 46 indicators for assessing the use of PEPFAR-supported diagnostic networks for COVID-19 pandemic response activities during April 1, 2020, to March 31, 2021, to 27 PEPFAR-supported countries or regions. A total of 109 PEPFAR-supported centralized HIV viral load and early infant diagnosis laboratories and 138 decentralized HIV and TB sites reported performing SARS-CoV-2 testing in 16 countries. Together, these sites contributed to >3.4 million SARS-CoV-2 tests during the 1-year period. Our findings illustrate that PEPFAR-supported diagnostic networks provided a wide range of resources to respond to emergency COVID-19 diagnostic testing in 16 low- and middle-income countries.
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Gehre F, Lagu H, Achol E, Omari N, Ochido G, Duraffour S, Hinzmann J, Kezakarayagwa E, Kabatesi F, Nkeshimana A, Nyandwi J, Samson DD, Nykwec GA, Lokore ML, Deng LL, Kelly ME, Mkama PBM, Magesa A, Beyanga M, Roba A, Ndia M, Lokamar P, Kiiru J, Kabanda A, Mukagatare I, Kabalisa E, Rutayisire R, Sewanyana I, Nambozo EJ, Muyigi T, Pimundu G, May J, Katende M, Nabadda S, Nzeyimana E, Affara M. The East African Community’s mobile laboratory network’s rapid response during the first 2 weeks of the Ebola Sudan virus disease (SVD) outbreak in Uganda and pandemic preparedness activities in South Sudan, Rwanda, Tanzania, Burundi, Kenya. BMJ Glob Health 2022; 7:bmjgh-2022-011073. [DOI: 10.1136/bmjgh-2022-011073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/19/2022] [Indexed: 12/15/2022] Open
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15
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Kiggundu T, Ario AR, Kadobera D, Kwesiga B, Migisha R, Makumbi I, Eurien D, Kabami Z, Kayiwa J, Lubwama B, Okethwangu D, Nabadda S, Bwire G, Mulei S, Harris JR, Dirlikov E, Fitzmaurice AG, Nabatanzi S, Tegegn Y, Muruta AN, Kyabayinze D, Boore AL, Kagirita A, Kyobe-Bosa H, Mwebesa HG, Atwine D, Aceng Ocero JR. Notes from the Field: Outbreak of Ebola Virus Disease Caused by Sudan ebolavirus - Uganda, August-October 2022. MMWR Morb Mortal Wkly Rep 2022; 71:1457-1459. [PMID: 36355610 PMCID: PMC9707349 DOI: 10.15585/mmwr.mm7145a5] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2023]
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16
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Nanyeenya N, Kiwanuka N, Nakanjako D, Nakigozi G, Kibira SP, Nabadda S, Kiyaga C, Sewanyana I, Nasuuna E, Makumbi F. Low-level viraemia: An emerging concern among people living with HIV in Uganda and across sub-Saharan Africa. Afr J Lab Med 2022; 11:1899. [PMID: 36353193 PMCID: PMC9639359 DOI: 10.4102/ajlm.v11i1.1899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/29/2022] [Indexed: 11/04/2023] Open
Abstract
Attaining viral load (VL) suppression for over 95% of the people living with HIV on antiretroviral therapy is a fundamental step in enabling Uganda and other sub-Saharan African countries to achieve global Sustainable Development Goal targets to end the HIV/AIDS epidemic by 2030. In line with the 2013 World Health Organization recommendations, several sub-Saharan African countries, including Uganda, use a threshold of 1000 HIV viral RNA copies/mL to determine HIV viral non-suppression. The United States Centers for Disease Control and Prevention and the International Association of Providers of AIDS Care deem this threshold very high, and hence recommend using 200 copies/mL to determine viral non-suppression. Using 1000 copies/mL as a threshold ignores people living with HIV who have low-level viraemia (LLV; HIV VL of at least 50 copies/mL but less than 1000 copies/mL). Despite the 2021 World Health Organization recommendations of using intensive adherence counselling for people living with HIV with LLV, several sub-Saharan African countries have no interventions to address LLV. However, recent studies have associated LLV with increased risks of HIV drug resistance, virologic failure and transmission. The purpose of this narrative review is to provide insights on the emerging concern of LLV among people living with HIV receiving antiretroviral therapy in sub-Saharan Africa. The review also provides guidance for Uganda and other sub-Saharan African countries to implement immediate appropriate interventions like intensive adherence counselling, reducing VL thresholds for non-suppression and conducting more research to manage LLV which threatens progress towards ending HIV by 2030.
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Affiliation(s)
- Nicholus Nanyeenya
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
- Ministry of Health Central Public Health Laboratories, Kampala, Uganda
| | - Noah Kiwanuka
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Damalie Nakanjako
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Simon P.S. Kibira
- Department of Community Health and Behavioral Sciences, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
| | - Susan Nabadda
- Ministry of Health Central Public Health Laboratories, Kampala, Uganda
| | - Charles Kiyaga
- Ministry of Health Central Public Health Laboratories, Kampala, Uganda
| | - Isaac Sewanyana
- Ministry of Health Central Public Health Laboratories, Kampala, Uganda
| | - Esther Nasuuna
- Infectious Diseases Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Fredrick Makumbi
- Department of Epidemiology and Biostatistics, School of Public Health, Makerere University College of Health Sciences, Kampala, Uganda
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Tegally H, San JE, Cotten M, Moir M, Tegomoh B, Mboowa G, Martin DP, Baxter C, Lambisia AW, Diallo A, Amoako DG, Diagne MM, Sisay A, Zekri ARN, Gueye AS, Sangare AK, Ouedraogo AS, Sow A, Musa AO, Sesay AK, Abias AG, Elzagheid AI, Lagare A, Kemi AS, Abar AE, Johnson AA, Fowotade A, Oluwapelumi AO, Amuri AA, Juru A, Kandeil A, Mostafa A, Rebai A, Sayed A, Kazeem A, Balde A, Christoffels A, Trotter AJ, Campbell A, Keita AK, Kone A, Bouzid A, Souissi A, Agweyu A, Naguib A, Gutierrez AV, Nkeshimana A, Page AJ, Yadouleton A, Vinze A, Happi AN, Chouikha A, Iranzadeh A, Maharaj A, Batchi-Bouyou AL, Ismail A, Sylverken AA, Goba A, Femi A, Sijuwola AE, Marycelin B, Salako BL, Oderinde BS, Bolajoko B, Diarra B, Herring BL, Tsofa B, Lekana-Douki B, Mvula B, Njanpop-Lafourcade BM, Marondera BT, Khaireh BA, Kouriba B, Adu B, Pool B, McInnis B, Brook C, Williamson C, Nduwimana C, Anscombe C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Mapanguy CM, Loucoubar C, Onwuamah CK, Ihekweazu C, Malaka CN, Peyrefitte C, Grace C, Omoruyi CE, Rafaï CD, Morang’a CM, Erameh C, Lule DB, Bridges DJ, Mukadi-Bamuleka D, Park D, Rasmussen DA, Baker D, Nokes DJ, Ssemwanga D, Tshiabuila D, Amuzu DSY, Goedhals D, Grant DS, Omuoyo DO, Maruapula D, Wanjohi DW, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Abworo EO, Otieno E, Shumba E, Barasa E, Ahmed EB, Ahmed EA, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Manuel E, Leendertz F, Taweh FM, Wasfi F, Abdelmoula F, Takawira FT, Derrar F, Ajogbasile FV, Treurnicht F, Onikepe F, Ntoumi F, Muyembe FM, Ragomzingba FEZ, Dratibi FA, Iyanu FA, Mbunsu GK, Thilliez G, Kay GL, Akpede GO, van Zyl GU, Awandare GA, Kpeli GS, Schubert G, Maphalala GP, Ranaivoson HC, Omunakwe HE, Onywera H, Abe H, Karray H, Nansumba H, Triki H, Kadjo HAA, Elgahzaly H, Gumbo H, Mathieu H, Kavunga-Membo H, Smeti I, Olawoye IB, Adetifa IMO, Odia I, Ben Boubaker IB, Mohammad IA, Ssewanyana I, Wurie I, Konstantinus IS, Halatoko JWA, Ayei J, Sonoo J, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Musyoki J, Nkurunziza J, Uwanibe JN, Bhiman JN, Yasuda J, Morais J, Kiconco J, Sandi JD, Huddleston J, Odoom JK, Morobe JM, Gyapong JO, Kayiwa JT, Okolie JC, Xavier JS, Gyamfi J, Wamala JF, Bonney JHK, Nyandwi J, Everatt J, Nakaseegu J, Ngoi JM, Namulondo J, Oguzie JU, Andeko JC, Lutwama JJ, Mogga JJH, O’Grady J, Siddle KJ, Victoir K, Adeyemi KT, Tumedi KA, Carvalho KS, Mohammed KS, Dellagi K, Musonda KG, Duedu KO, Fki-Berrajah L, Singh L, Kepler LM, Biscornet L, de Oliveira Martins L, Chabuka L, Olubayo L, Ojok LD, Deng LL, Ochola-Oyier LI, Tyers L, Mine M, Ramuth M, Mastouri M, ElHefnawi M, Mbanne M, Matsheka MI, Kebabonye M, Diop M, Momoh M, Lima Mendonça MDL, Venter M, Paye MF, Faye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina MG, Owusu M, Wiley MR, Tatfeng MY, Ayekaba MO, Abouelhoda M, Beloufa MA, Seadawy MG, Khalifa MK, Matobo MM, Kane M, Salou M, Mbulawa MB, Mwenda M, Allam M, Phan MVT, Abid N, Rujeni N, Abuzaid N, Ismael N, Elguindy N, Top NM, Dia N, Mabunda N, Hsiao NY, Silochi NB, Francisco NM, Saasa N, Bbosa N, Murunga N, Gumede N, Wolter N, Sitharam N, Ndodo N, Ajayi NA, Tordo N, Mbhele N, Razanajatovo NH, Iguosadolo N, Mba N, Kingsley OC, Sylvanus O, Femi O, Adewumi OM, Testimony O, Ogunsanya OA, Fakayode O, Ogah OE, Oludayo OE, Faye O, Smith-Lawrence P, Ondoa P, Combe P, Nabisubi P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Okokhere PO, Bejon P, Dussart P, Bester PA, Mbala PK, Kaleebu P, Abechi P, El-Shesheny R, Joseph R, Aziz RK, Essomba RG, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Neto Rodrigues RMDESA, Audu RA, Carr RAA, Gargouri S, Masmoudi S, Bootsma S, Sankhe S, Mohamed SI, Femi S, Mhalla S, Hosch S, Kassim SK, Metha S, Trabelsi S, Agwa SH, Mwangi SW, Doumbia S, Makiala-Mandanda S, Aryeetey S, Ahmed SS, Ahmed SM, Elhamoumi S, Moyo S, Lutucuta S, Gaseitsiwe S, Jalloh S, Andriamandimby SF, Oguntope S, Grayo S, Lekana-Douki S, Prosolek S, Ouangraoua S, van Wyk S, Schaffner SF, Kanyerezi S, Ahuka-Mundeke S, Rudder S, Pillay S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Mohale T, Le-Viet T, Velavan TP, Schindler T, Maponga TG, Bedford T, Anyaneji UJ, Chinedu U, Ramphal U, George UE, Enouf V, Nene V, Gorova V, Roshdy WH, Karim WA, Ampofo WK, Preiser W, Choga WT, Ahmed YA, Ramphal Y, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Ouma AEO, von Gottberg A, Githinji G, Moeti M, Tomori O, Sabeti PC, Sall AA, Oyola SO, Tebeje YK, Tessema SK, de Oliveira T, Happi C, Lessells R, Nkengasong J, Wilkinson E. The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance. Science 2022; 378:eabq5358. [PMID: 36108049 PMCID: PMC9529057 DOI: 10.1126/science.abq5358] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 09/12/2022] [Indexed: 11/25/2022]
Abstract
Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.
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Affiliation(s)
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Bryan Tegomoh
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
| | - Gerald Mboowa
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | | | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
| | | | - Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Abdou Salam Gueye
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abdualmoniem O. Musa
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
| | | | - Abe G. Abias
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Adamou Lagare
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
| | | | - Aden Elmi Abar
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
| | - Adeniji A. Johnson
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeola Fowotade
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Adeyemi O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Agnes Juru
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ahmed Sayed
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Aladje Balde
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
| | - Alan Christoffels
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | | | - Allan Campbell
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | - Amadou Kone
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Amel Naguib
- Central Public Health Laboratories (CPHL), Cairo, Egypt
| | | | | | | | - Anges Yadouleton
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
| | - Anika Vinze
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Anise N. Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Anissa Chouikha
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arisha Maharaj
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Armel L. Batchi-Bouyou
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Augustina A. Sylverken
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustine Goba
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Ayotunde E. Sijuwola
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
| | - Babatunde L. Salako
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Bassirou Diarra
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Belinda L. Herring
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | | | - Bernard Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
| | - Bernard Mvula
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
| | | | | | - Bouh Abdi Khaireh
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
| | - Bourema Kouriba
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Brigitte Pool
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Catherine Anscombe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | - Chastel M. Mapanguy
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
| | | | - Chika K. Onwuamah
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Chikwe Ihekweazu
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Christian N. Malaka
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
| | | | - Chukwa Grace
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Chukwuma E. Omoruyi
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Clotaire D. Rafaï
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Cyril Erameh
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Daniel B. Lule
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Daniel Mukadi-Bamuleka
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Danny Park
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | | | - David J. Nokes
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
| | - Donald S. Grant
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | - Dorcas W. Wanjohi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
| | | | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Edward O. Abworo
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Edward Otieno
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Edwine Barasa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - El Bara Ahmed
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
| | - Elhadi A. Ahmed
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Eusebio Manuel
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
| | | | - Fahn M. Taweh
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
| | - Fares Wasfi
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | - Fawzi Derrar
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
| | - Fehintola V. Ajogbasile
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Florette Treurnicht
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Francine Ntoumi
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Fred A. Dratibi
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Fred-Akintunwa Iyanu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | | | - George O. Akpede
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Gert U. van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Grace S. Kpeli
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | | | - Gugu P. Maphalala
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hannah E. Omunakwe
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
| | - Harris Onywera
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Henda Triki
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
| | | | - Hesham Elgahzaly
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Hota Mathieu
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
| | - Hugo Kavunga-Membo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Idowu B. Olawoye
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ifedayo M. O. Adetifa
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ikponmwosa Odia
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
| | - Iluoreh Ahmed Mohammad
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Isatta Wurie
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
| | | | | | - James Ayei
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Janaki Sonoo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Jessica N. Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Morais
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
| | | | - John D. Sandi
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - John K. Odoom
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Joicymara S. Xavier
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - Joseph H. K. Bonney
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Joseph Nyandwi
- National Institute of Public Health, Bujumbura, Burundi
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
| | - Josie Everatt
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | | | - Judith U. Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Katherine J. Siddle
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | | | | | | | | | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Lenora M. Kepler
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Leon Biscornet
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
| | | | | | - Luicer Olubayo
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
| | - Lul Deng Ojok
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | - Lul Lojok Deng
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahmoud ElHefnawi
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
| | - Maimouna Mbanne
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Mambu Momoh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
| | | | - Marietjie Venter
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Marietou F. Paye
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Martin Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | | | - Maximillian G. Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael R. Wiley
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- PraesensBio, Lincoln, NE, USA
| | - Mirabeau Y. Tatfeng
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | | | - Mohamed G. Seadawy
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
| | | | | | - Mouhamed Kane
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | | | | | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Nadir Abuzaid
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
| | - Nalia Ismael
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | | | | | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nédio Mabunda
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngiambudulu M. Francisco
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
| | - Nicholas Bbosa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | | | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Nicole Wolter
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Nikita Sitharam
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Nnaemeka Ndodo
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Noël Tordo
- Institut Pasteur de Guinée, Conarky, Guinea
| | - Nokuzola Mbhele
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Nwando Mba
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Okogbenin Sylvanus
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
| | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olubusuyi M. Adewumi
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Olusola A. Ogunsanya
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oluwatosin Fakayode
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ope-Ewe Oludayo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | - Patricia Nabisubi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
| | - Peter Kojo Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Peter O. Okokhere
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Pontiano Kaleebu
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Priscilla Abechi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
| | - Rageema Joseph
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Ramy Karam Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
| | - René G. Essomba
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
| | - Reuben Ayivor-Djanie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosa Maria D. E. S. A. Neto Rodrigues
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
| | - Rosemary A. Audu
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | | | - Saibu Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Salma Mhalla
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Samar Kamal Kassim
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Samar Metha
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Sara Hassan Agwa
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sarah Wambui Mwangi
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Seydou Doumbia
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
| | - Sheila Makiala-Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | | | - Siham Elhamoumi
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Silvia Lutucuta
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simbirie Jalloh
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
| | | | - Sobajo Oguntope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Stephen F. Schaffner
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Stephen Kanyerezi
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Steve Ahuka-Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
| | | | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Tapfumanei Mashe
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- World Health Organization, Harare, Zimbabwe
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Thirumalaisamy P. Velavan
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
| | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- University of Basel, Basel, Switzerland
| | - Tongai G. Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwem E. George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
| | - Vishvanath Nene
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - Wasim Abdul Karim
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - William K. Ampofo
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yahaya Ali Ahmed
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Yajna Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Yemaachi Biotech, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Africa Pathogen Genomics Initiative (Africa PGI)
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- The Biotechnology Centre of the University of Yaoundé I, Yaoundé, Cameroon
- CDC Foundation, Atlanta, Georgia, Nebraska Department of Health and Human Services, Lincoln, NE, USA
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Health Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, KwaZulu-Natal, South Africa
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo, Egypt
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
- West African Health Organisation, Bobo-Dioulasso, Burkina Faso
- Faculty of Medicine and Health Sciences, Kassala University, Kassala City, Sudan
- Department of Microbiology, Faculty of Medical Laboratory Sciences, University of Gezira, Gezira, Sudan
- General Administration of Laboratories and Blood Banks, Ministry of Health, Kassala State, Sudan
- MRC Unit The Gambia at LSHTM, Fajara, Gambia
- National Public Health Laboratory, Ministry of Health, Juba, Republic of South Sudan
- Libyan Biotechnology Research Center, Tripoli, Libya
- Center for Medical and Sanitary Research (CERMES), Niamey, Niger
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Laboratoire de la Caisse Nationale de Sécurité Sociale, Djibouti, Republic of Djibouti
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Infectious Disease Institute, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Biorepository Clinical Virology Laboratory, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
- The Pirbright Institute, Woking, UK
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, the Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, the Democratic Republic of the Congo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo, Egypt
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Genomics and Epigenomics Program, Research Department CCHE57357, Cairo, Egypt
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
- Laboratório de Biologia Molecular Jean Piaget, Bissau, Guinea-Bissau
- University Jean Piaget in Guinea-Bissau, Bissau, Guinea-Bissau
- SAMRC Bioinformatics Unit, SA Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
- Quadram Institute Bioscience, Norwich, UK
- Central Public Health Reference Laboratories, Freetown, Sierra Leone
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Institut de Recherche pour le Développement, Institut National de la Santé et de la Recherche Médicale (INSERM), Montpellier University, 34090, Montpellier, France
- University Clinical Research Center (UCRC), University of Sciences, Techniques and Technology of Bamako, Bamako, Mali
- Sharjah Institute for Medical Research, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
- Central Public Health Laboratories (CPHL), Cairo, Egypt
- National Institute of Public Health, Bujumbura, Burundi
- Laboratoire des Fièvres Hémorragiques Virales du Benin, Cotonou, Benin
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Laboratory of Clinical Virology, WHO Reference Laboratory for Poliomyelitis and Measles in the Eastern Mediterranean Region, Pasteur Institute of Tunis, University Tunis El Manar (UTM), Tunis 1002, Tunisia
- Research Laboratory “Virus, Vectors and Hosts: One Health Apporach and Technological Innovation for a Better Health”, LR20IPT02, Pasteur Institute, Tunis 1002, Tunisia
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of the Congo
- Marien Ngouabi, Brazzaville, Republic of the Congo
- Kwame Nkrumah University of Science and Technology, Department of Theoretical and Applied Biology, Kumasi, Ghana
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Viral Haemorrhagic Fever Laboratory, Kenema Government Hospital, Kenema, Sierra Leone
- Ministry of Health and Sanitation, Freetown, Sierra Leone
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, P.M.B. 1069, Maiduguri, Borno State, Nigeria
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
- Département de Parasitologie-Mycologie Université des Sciences de la Santé (USS), Libreville, Gabon
- National HIV Reference Laboratory, Community Health Sciences Unit, Ministry of Health, Lilongwe, Malawi
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
- National Medical and Molecular Biology Laboratory, Ministry of Health, Djibouti, Republic of Djibouti
- Africa CDC, Rapid Responder, Team Djibouti, Djibouti, Djibouti
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Seychelles Public Health Laboratory, Public Health Authority, Ministry of Health Seychelles, Victoria, Seychelles
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
- National Health Laboratory Service (NHLS), Cape Town, South Africa
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
- University of Nebraska Medical Center (UNMC), Omaha, NE, USA
- SAMRC Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
- UFR Sciences Médicales, Universite Alassane Ouattara, Bouaké, Côte d’Ivoire
- School of Public Health, Pwani University, Kilifi, Kenya
- Faculty of Science and Techniques, University Marien Ngouabi, Brazzaville, Republic of the Congo
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Nigeria Centre for Disease Control and Prevention, Abuja, Nigeria
- Laboratoire des Arbovirus, Fièvres Hémorragiques virales, Virus Emergents et Zoonoses, Institut Pasteur de Bangui, Bangui, Central African Republic
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Institute of Lassa Fever Research and Control, Irrua Specialist Teaching Hospital, Irrua, Nigeria
- PATH, Lusaka, Zambia
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
- Uganda Virus Research Institute, Entebbe, Uganda
- PathCare Vermaak, Pretoria, South Africa and Division of Virology, University of the Free State, Bloemfontein, South Africa
- College of Medicine and Allied Health Sciences, University of Sierra Leone, Freetown, Sierra Leone
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Macha Research Trust, Choma, Zambia
- International Livestock Research Institute (ILRI), Nairobi, Kenya
- INRSP, Nouakchott, Mauritania
- Faculté de Médecine de Nouakchott, Nouakchott, Mauritani
- Rwanda National Reference Laboratory, Kigali, Rwanda
- Robert Koch-Institute, Berlin, Germany
- G5 Evolutionary Genomics of RNA Viruses, Institut Pasteur, Paris, France
- Direcção Nacional da Saúde Pública, Ministério da Saúde, Luanda, Angola
- National Public Health Reference Laboratory–National Public Health Institute of Liberia, Monrovia, Liberia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
- National Influenza Centre, Institut Pasteur d’Algérie, Algiers, Algeria
- Department of Virology, National Health Laboratory Service (NHLS), Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Tübingen, Germany
- Ministère de Santé Publique et de la Solidarité Nationale, Ndjamena, Chad
- WHO Int Comoros, Moroni, Union of Comoros
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
- Department of Biomedical Sciences, University of Health and Allied Sciences, PMB 31, Ho, Ghana
- Ministry of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
- Satellite Molecular Laboratory, Rivers State University Teaching Hospital, Port Harcourt, Nigeria
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
- Central Public Health Laboratories (CPHL), Kampala, Uganda
- Institut Pasteur de Côte d’Ivoire, Departement des Virus Epidemiques, Abidjan, Côte d’Ivoire
- Faculty of Medicine Ain Shams Research Institute (MASRI), Ain Shams University, Cairo, Egypt
- Doctoral School of Technical and Environmental Sciences, Department of Biology and Human Health, N’Djamena, Chad
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, Tunis, Tunisia
- University of Tunis El Manar, Faculty of Medicine of Tunis, Research Laboratory LR99ES09, Tunis, Tunisia
- College of Medicine and Allied Health Science, University of Sierra Leone, Freetown, Sierra Leone
- Namibia Institute of Pathology, Windhoek, Namibia
- National Institute of Hygiene, Lomé, Togo
- Virology/Molecular Biology Department, Central Health Laboratory, Victoria Hospital, Ministry of Health and Wellness, Port Louis, Mauritius
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
- WHO Burundi, Gitega, Burundi
- Grupo de Investigação Microbiana e Imunológica, Instituto Nacional de Investigação em Saúde (National Institute for Health Research), Luanda, Angola
- Departamento de Bioquímica, Faculdade de Medicina, Universidade Agostinho Neto, Luanda, Angola
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Institute of Agricultural Sciences, Universidade Federal dos Vales do Jequitinhonha e Mucuri, Unaí, Brazil
- WHO South Sudan, Juba, South Sudan
- Faculty of Medicine, University of Burundi, Bujumbura, Burundi
- Pasteur Network, Institut Pasteur, Paris, France
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
- Instituto Nacional de Saúde Pública, Praia, Cape Verde
- Zambia National Public Health Institute, Lusaka, Zambia
- Public Health Institute of Malawi, Lilongwe, Malawi
- National Health Laboratory, Gaborone, Botswana
- Laboratory of Transmissible Diseases and Biologically Active Substances (LR99ES27), Faculty of Pharmacy, University of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
- Biomedical Informatics and Chemoinformatics Group, Informatics and Systems Department, National Research Centre, Cairo, Egypt
- Ministry of Health and Wellness, Gaborone, Botswana
- Eastern Technical University of Sierra Leone, Kenema, Sierra Leone
- Zoonotic Arbo and Respiratory Virus Program, Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- National Reference Laboratory Lesotho, Maseru, Lesotho
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Insitute, Ifakara, Tanzania
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- PraesensBio, Lincoln, NE, USA
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
- Biological Prevention Department, Ministry of Defence, Cairo, Egypt
- Faculty of Science, Fayoum University, Fayoum, Egypt
- Molecular Pathology Lab, Children’s Cancer Hospital, Cairo, Egypt
- Laboratoire Biolim FSS/Université de Lomé, Lomé, Togo
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
- High Institute of Biotechnology of Monastir, University of Monastir, Rue Taher Haddad 5000, Monastir, Tunisia
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Department of Microbiology, Faculty of Medical Laboratory Sciences, Omdurman Islamic University, Sudan
- Instituto Nacional de Saúde (INS), Marracuene, Mozambique
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Institut Pasteur de Guinée, Conarky, Guinea
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences. College of Health Sciences. University of Ilorin, Ilorin, Kwara State, Nigeria
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
- Mayotte Hospital Center, Mayotte, France
- The African Center of Excellence in Bioinformatics and Data-Intensive Sciences, The Infectious Diseases Institute, Kampala, Uganda
- Immunology and Molecular Biology, Makerere University, Kampala, Uganda
- Department of Medicine, Faculty of Clinical Sciences, College of Medicine, Ambrose Alli University, Ekpoma, Edo State, Nigeria
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
- Infectious Hazards Preparedness, World Health Organization, Eastern Mediterranean Regional Office, Cairo, Egypt
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Cairo, Egypt
- Microbiology and Immunology Research Program, Children’s Cancer Hospital Egypt, Cairo, Egypt
- National Public Health Laboratory, Ministry of Public Health of Cameroon, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé, Yaoundé, Cameroon
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
- Coordenadora da rede do Diagnóstico Tuberculose/HIV/COVID-19 na Instituição - Laboratório Nacional de Referência da Tuberculose em São Tomé e Príncipe, São Tomé, São Tomé and Principe
- Ponto focal para Melhoria da qualidade dos Laboratórios (SLIPTA) ao nível de São Tomé e Príncipe, São Tomé, São Tomé and Principe
- National Public Health Reference Laboratory (NPHRL), Mogadishu, Somalia
- Faculty of Medicine of Monastir, University of Monastir, Monastir, Tunisia
- University of Basel, Basel, Switzerland
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, Université Paris Cité, Institut Pasteur, Paris, France
- World Health Organization, Harare, Zimbabwe
- Vietnamese-German Center for Medical Research, Hanoi, Vietnam
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
- Department of Virology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
- Yemaachi Biotech, Accra, Ghana
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Matshidiso Moeti
- World Health Organization, Africa Region, Brazzaville, Republic of the Congo
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pardis C. Sabeti
- Infectious Disease and Microbiome Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Samuel O. Oyola
- International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer’s University, Ede, Osun State, Nigeria
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
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Bwogi J, Lutalo T, Tushabe P, Bukenya H, Eliku JP, Ssewanyana I, Nabadda S, Nsereko C, Cotten M, Downing R, Lutwama J, Kaleebu P. Field evaluation of the performance of seven Antigen Rapid diagnostic tests for the diagnosis of SARs-CoV-2 virus infection in Uganda. PLoS One 2022; 17:e0265334. [PMID: 35536792 PMCID: PMC9089886 DOI: 10.1371/journal.pone.0265334] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 02/28/2022] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE The objective of this study was to evaluate the performance of seven antigen rapid diagnostic tests (Ag RDTs) in a clinical setting to identify those that could be recommended for use in the diagnosis of SARS-CoV-2 infection in Uganda. METHODS This was a cross-sectional prospective study. Nasopharyngeal swabs were collected consecutively from COVID-19 PCR positive and COVID-19 PCR negative participants at isolation centers and points of entry, and tested with the SARS-CoV-2 Ag RDTs. Test sensitivity and specificity were generated by comparing results against qRT-PCR results (Berlin Protocol) at a cycle threshold (Ct) cut-off of ≤39. Sensitivity was also calculated at Ct cut-offs ≤29 and ≤33. RESULTS None of the Ag RDTs had a sensitivity of ≥80% at Ct cut-off values ≤33 and ≤39. Two kits, Panbio™ COVID-19 Ag and VivaDiag™ SARS-CoV-2 Ag had a sensitivity of ≥80% at a Ct cut-off value of ≤29. Four kits: BIOCREDIT COVID -19 Ag, COVID-19 Ag Respi-Strip, MEDsan® SARS-CoV-2 Antigen Rapid Test and Panbio™ COVID-19 Ag Rapid Test had a specificity of ≥97%. CONCLUSIONS This evaluation identified one Ag RDT, Panbio™ COVID-19 Ag with a performance at high viral load (Ct value ≤29) reaching that recommended by WHO. This kit was recommended for screening of patients with COVID -19-like symptoms presenting at health facilities.
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Affiliation(s)
| | - Tom Lutalo
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | | | | | | | | | - Matthew Cotten
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
| | | | | | - Pontiano Kaleebu
- Uganda Virus Research Institute, Entebbe, Uganda
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, Entebbe, Uganda
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Bbosa N, Ssemwanga D, Namagembe H, Kiiza R, Kiconco J, Kayiwa J, Lutalo T, Lutwama J, Ssekagiri A, Ssewanyana I, Nabadda S, Kyobe-Bbosa H, Giandhari J, Pillay S, Ramphal U, Ramphal Y, Naidoo Y, Tshiabuila D, Tegally H, San EJ, Wilkinson E, de Oliveira T, Kaleebu P. Rapid Replacement of SARS-CoV-2 Variants by Delta and Subsequent Arrival of Omicron, Uganda, 2021. Emerg Infect Dis 2022; 28:1021-1025. [PMID: 35320700 PMCID: PMC9045417 DOI: 10.3201/eid2805.220121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Genomic surveillance in Uganda showed rapid replacement of severe acute respiratory syndrome coronavirus 2 over time by variants, dominated by Delta. However, detection of the more transmissible Omicron variant among travelers and increasing community transmission highlight the need for near-real-time genomic surveillance and adherence to infection control measures to prevent future pandemic waves.
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Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, Martin DP, Rasmussen DA, Zekri ARN, Sangare AK, Ouedraogo AS, Sesay AK, Priscilla A, Kemi AS, Olubusuyi AM, Oluwapelumi AOO, Hammami A, Amuri AA, Sayed A, Ouma AEO, Elargoubi A, Ajayi NA, Victoria AF, Kazeem A, George A, Trotter AJ, Yahaya AA, Keita AK, Diallo A, Kone A, Souissi A, Chtourou A, Gutierrez AV, Page AJ, Vinze A, Iranzadeh A, Lambisia A, Ismail A, Rosemary A, Sylverken A, Femi A, Ibrahimi A, Marycelin B, Oderinde BS, Bolajoko B, Dhaala B, Herring BL, Njanpop-Lafourcade BM, Kleinhans B, McInnis B, Tegomoh B, Brook C, Pratt CB, Scheepers C, Akoua-Koffi CG, Agoti CN, Peyrefitte C, Daubenberger C, Morang’a CM, Nokes DJ, Amoako DG, Bugembe DL, Park D, Baker D, Doolabh D, Ssemwanga D, Tshiabuila D, Bassirou D, Amuzu DSY, Goedhals D, Omuoyo DO, Maruapula D, Foster-Nyarko E, Lusamaki EK, Simulundu E, Ong’era EM, Ngabana EN, Shumba E, El Fahime E, Lokilo E, Mukantwari E, Philomena E, Belarbi E, Simon-Loriere E, Anoh EA, Leendertz F, Ajili F, Enoch FO, Wasfi F, Abdelmoula F, Mosha FS, Takawira FT, Derrar F, Bouzid F, Onikepe F, Adeola F, Muyembe FM, Tanser F, Dratibi FA, Mbunsu GK, Thilliez G, Kay GL, Githinji G, van Zyl G, Awandare GA, Schubert G, Maphalala GP, Ranaivoson HC, Lemriss H, Anise H, Abe H, Karray HH, Nansumba H, Elgahzaly HA, Gumbo H, Smeti I, Ayed IB, Odia I, Ben Boubaker IB, Gaaloul I, Gazy I, Mudau I, Ssewanyana I, Konstantinus I, Lekana-Douk JB, Makangara JCC, Tamfum JJM, Heraud JM, Shaffer JG, Giandhari J, Li J, Yasuda J, Mends JQ, Kiconco J, Morobe JM, Gyapong JO, Okolie JC, Kayiwa JT, Edwards JA, Gyamfi J, Farah J, Nakaseegu J, Ngoi JM, Namulondo J, Andeko JC, Lutwama JJ, O’Grady J, Siddle K, Adeyemi KT, Tumedi KA, Said KM, Hae-Young K, Duedu KO, Belyamani L, Fki-Berrajah L, Singh L, Martins LDO, Tyers L, Ramuth M, Mastouri M, Aouni M, el Hefnawi M, Matsheka MI, Kebabonye M, Diop M, Turki M, Paye M, Nyaga MM, Mareka M, Damaris MM, Mburu MW, Mpina M, Nwando M, Owusu M, Wiley MR, Youtchou MT, Ayekaba MO, Abouelhoda M, Seadawy MG, Khalifa MK, Sekhele M, Ouadghiri M, Diagne MM, Mwenda M, Allam M, Phan MVT, Abid N, Touil N, Rujeni N, Kharrat N, Ismael N, Dia N, Mabunda N, Hsiao NY, Silochi NB, Nsenga N, Gumede N, Mulder N, Ndodo N, Razanajatovo NH, Iguosadolo N, Judith O, Kingsley OC, Sylvanus O, Peter O, Femi O, Idowu O, Testimony O, Chukwuma OE, Ogah OE, Onwuamah CK, Cyril O, Faye O, Tomori O, Ondoa P, Combe P, Semanda P, Oluniyi PE, Arnaldo P, Quashie PK, Dussart P, Bester PA, Mbala PK, Ayivor-Djanie R, Njouom R, Phillips RO, Gorman R, Kingsley RA, Carr RAA, El Kabbaj S, Gargouri S, Masmoudi S, Sankhe S, Lawal SB, Kassim S, Trabelsi S, Metha S, Kammoun S, Lemriss S, Agwa SHA, Calvignac-Spencer S, Schaffner SF, Doumbia S, Mandanda SM, Aryeetey S, Ahmed SS, Elhamoumi S, Andriamandimby S, Tope S, Lekana-Douki S, Prosolek S, Ouangraoua S, Mundeke SA, Rudder S, Panji S, Pillay S, Engelbrecht S, Nabadda S, Behillil S, Budiaki SL, van der Werf S, Mashe T, Aanniz T, Mohale T, Le-Viet T, Schindler T, Anyaneji UJ, Chinedu U, Ramphal U, Jessica U, George U, Fonseca V, Enouf V, Gorova V, Roshdy WH, Ampofo WK, Preiser W, Choga WT, Bediako Y, Naidoo Y, Butera Y, de Laurent ZR, Sall AA, Rebai A, von Gottberg A, Kouriba B, Williamson C, Bridges DJ, Chikwe I, Bhiman JN, Mine M, Cotten M, Moyo S, Gaseitsiwe S, Saasa N, Sabeti PC, Kaleebu P, Tebeje YK, Tessema SK, Happi C, Nkengasong J, de Oliveira T. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science 2021; 374:423-431. [PMID: 34672751 PMCID: PMC7613315 DOI: 10.1126/science.abj4336] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023]
Abstract
The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants.
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Affiliation(s)
- Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Marta Giovanetti
- Laboratorio de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - James E. San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diego Cuadros
- Department of Geography and GIS, University of Cincinnati, Cincinnati, OH, USA
| | - Darren P. Martin
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - David A. Rasmussen
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC, USA
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC, USA
| | - Abdel-Rahman N. Zekri
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Abdoul K. Sangare
- Centre d’Infectiologie Charles Mérieux-Mali (CICM-Mali), Bamako, Mali
| | - Abdoul-Salam Ouedraogo
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | | | - Abechi Priscilla
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Adedotun-Sulaiman Kemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | - Adeyemi O. O. Oluwapelumi
- Department of Medical Microbiology and Parasitology, Faculty of Basic Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Adnène Hammami
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Adrienne A. Amuri
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Ahmad Sayed
- Genomics Research Program, Children’s Cancer Hospital, Cairo, Egypt
| | - Ahmed E. O. Ouma
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Aida Elargoubi
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Nnennaya A. Ajayi
- Internal Medicine Department, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Ajogbasile F. Victoria
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Akano Kazeem
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Ali A. Yahaya
- World Health Organization, Africa Region, Brazzaville Congo
| | - Alpha K. Keita
- Centre de Recherche et de Formation en Infectiologie de Guinée (CERFIG), Université de Conakry, Conakry, Guinea
- TransVIHMI, Montpellier University/IRD/INSERM, Montpellier, France
| | - Amadou Diallo
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Kone
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Amal Souissi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amel Chtourou
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | | | - Anika Vinze
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Arash Iranzadeh
- Institute of Infectious Diseases and Molecular Medicine, Department of Integrative Biomedical Sciences, Computational Biology Division, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Arnold Lambisia
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Arshad Ismail
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - Audu Rosemary
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ayoade Femi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Azeddine Ibrahimi
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Baba Marycelin
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bamidele S. Oderinde
- Department of Immunology, University of Maiduguri Teaching Hospital, P.M.B. 1414, Maiduguri, Nigeria
| | - Bankole Bolajoko
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | | | - Bronwyn Kleinhans
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
| | - Bronwyn McInnis
- Cancer Biology Department, Virology and Immunology Unit, National Cancer Institute, Cairo University, Cairo 11796, Egypt
| | - Bryan Tegomoh
- The Biotechnology Center of the University of Yaoundé I, Cameroon and CDC Foundation, Yaounde, Cameroon
| | - Cara Brook
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | | | - Cathrine Scheepers
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- Antibody Immunity Research Unit, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Chantal G. Akoua-Koffi
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | - Charles N. Agoti
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Public Health, Pwani University, Kilifi, Kenya
| | | | | | - Collins M. Morang’a
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - D. James Nokes
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Daniel G. Amoako
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Danny Park
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | | | - Deelan Doolabh
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Deogratius Ssemwanga
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Derek Tshiabuila
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Diarra Bassirou
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Dominic S. Y. Amuzu
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Dominique Goedhals
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | | | - Dorcas Maruapula
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
| | | | - Eddy K. Lusamaki
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edgar Simulundu
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | - Edith N. Ngabana
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Edwin Shumba
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | - Elmostafa El Fahime
- Functional Genomic Platform/National Centre for Scientific and Technical Research (CNRST), Rabat, Morocco
| | - Emmanuel Lokilo
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
| | | | - Eromon Philomena
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | | | | | - Etilé A. Anoh
- CHU de Bouaké, Laboratoire/Unité de Diagnostic des Virus des Fièvres Hémorragiques et Virus Émergents, Bouaké, Côte d’Ivoire
| | | | - Faida Ajili
- Research Unit of Autoimmune Diseases UR17DN02, Military Hospital of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Fakayode O. Enoch
- Department of Public Health, Ministry of Health, Ilorin, Kwara State, Nigeria
| | - Fares Wasfi
- Laboratory of Clinical Virology, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Fatma Abdelmoula
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
- Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | | | | | - Fawzi Derrar
- National Influenza Centre, Viral Respiratory Laboratory, Algiers, Algeria
| | - Feriel Bouzid
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Folarin Onikepe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Fowotade Adeola
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Francisca M. Muyembe
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Frank Tanser
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | | | - Gabriel K. Mbunsu
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | - George Githinji
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Gordon A. Awandare
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Gugu P. Maphalala
- Institution and Department, Ministry Of Health, COVID-19 Testing Laboratory, Mbabane, Kingdom of Eswatini
| | | | - Hajar Lemriss
- Laboratory of Health Sciences and Technologies, High Institute of Health Sciences, Hassan 1st University, Settat, Morocco
| | - Happi Anise
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Haruka Abe
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Hela H. Karray
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | | | - Hesham A. Elgahzaly
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Hlanai Gumbo
- National Microbiology Reference Laboratory, Harare, Zimbabwe
| | - Ibtihel Smeti
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Ikhlas B. Ayed
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | | | - Ilhem Boutiba Ben Boubaker
- Charles Nicolle Hospital, Laboratory of Microbiology, National Influenza Center, 1006 Tunis, Tunisia
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Imed Gaaloul
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Inbal Gazy
- Department of Biochemistry and Molecular Biology, The Institute for Medical Research Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Innocent Mudau
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | | | - Jean B. Lekana-Douk
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | - Jean-Claude C. Makangara
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Jacques M. Tamfum
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Jean-Michel Heraud
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Jeffrey G. Shaffer
- Department of Biostatistics and Data Science, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Jingjing Li
- Urban Health Collaborative, Dornsife School of Public Health, Drexel University, Philadelphia, PA, USA
| | - Jiro Yasuda
- Department of Emerging Infectious Diseases, Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | - Joana Q. Mends
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | - John M. Morobe
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - John O. Gyapong
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Johnson C. Okolie
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John T. Kayiwa
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Johnathan A. Edwards
- Lincoln International Institute for Rural Health, University of Lincoln, Lincoln, UK
- Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Jones Gyamfi
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | | | | | - Joyce M. Ngoi
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | | | - Julia C. Andeko
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | | | | | - Kayode T. Adeyemi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Kefentse A. Tumedi
- Botswana Institute for Technology Research and Innovation, Gaborone, Botswana
| | - Khadija M. Said
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Kim Hae-Young
- New York University Grossman School of Medicine, New York City, NY, USA
| | - Kwabena O. Duedu
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Lahcen Belyamani
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Lamia Fki-Berrajah
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | | | - Lynn Tyers
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Magalutcheemee Ramuth
- Virology/Molecular Biology Department, Central Health Laboratory, Ministry of Health and Wellness, Mauritius
| | - Maha Mastouri
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
- Laboratory of Microbiology, University Hospital of Monastir, Monastir, Tunisia
| | - Mahjoub Aouni
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, Monastir, Tunisia
| | - Mahmoud el Hefnawi
- Center of Scientific Excellence for Influenza Viruses, National Research Centre (NRC), Cairo Egypt
| | | | | | - Mamadou Diop
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Manel Turki
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Marietou Paye
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Martin M. Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa
| | | | - Matoke-Muhia Damaris
- Centre for Biotechnology Research and Development, Kenya Medical Research Institute, Nairobi, Kenya
| | - Maureen W. Mburu
- KEMRI-Wellcome Trust Research Programme/KEMRI-CGMR-C, Kilifi, Kenya
| | - Maximillian Mpina
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
- Ifakara Health Institute, Dar-es-Salaam, Tanzania
| | - Mba Nwando
- Nigeria Centre for Disease Control, Abuja, Nigeria
| | - Michael Owusu
- Department of Medical Diagnostics, Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Mirabeau T. Youtchou
- Department of Medical Laboratory Science, Niger Delta University, Bayelsa State, Nigeria
| | | | - Mohamed Abouelhoda
- Systems and Biomedical Engineering Department, Faculty of Engineering, Cairo University, Cairo 12613, Egypt
- King Faisal Specialist Hospital and Research Center, Riyadh, Kingdom of Saudi Arabia
| | - Mohamed G. Seadawy
- Biological Prevention Department, Main Chemical Laboratories, Egypt Army, Cairo, Egypt
| | | | - Mooko Sekhele
- National Reference Laboratory Lesotho, Maseru, Lesotho
| | - Mouna Ouadghiri
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | | | | | - Mushal Allam
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | - My V. T. Phan
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
| | - Nabil Abid
- Laboratory of Transmissible Diseases and Biological Active Substances (LR99ES27), Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
- Department of Biotechnology, High Institute of Biotechnology of Sidi Thabet, University of Manouba, BP-66, 2020 Ariana-Tunis, Tunisia
| | - Nadia Touil
- Genomic Center for Human Pathologies (GENOPATH), Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
| | - Najla Kharrat
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Nalia Ismael
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Ndongo Dia
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Nedio Mabunda
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Nei-yuan Hsiao
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | - Ngoy Nsenga
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicksy Gumede
- World Health Organization, Africa Region, Brazzaville Congo
| | - Nicola Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | | | | | - Nosamiefan Iguosadolo
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Oguzie Judith
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Ojide C. Kingsley
- Virology Laboratory, Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | | | | | - Oladiji Femi
- Department of Epidemiology and Community Health, Faculty of Clinical Sciences, College of Health Sciences, University of Ilorin, Ilorin, Kwara State, Nigeria
| | - Olawoye Idowu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Olumade Testimony
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Omoruyi E. Chukwuma
- Medical Microbiology and Parasitology Department, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onwe E. Ogah
- Alex Ekwueme Federal University Teaching Hospital, Abakaliki, Nigeria
| | - Chika K. Onwuamah
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
- Centre for Human Virology and Genomics, Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | | | - Ousmane Faye
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Pascale Ondoa
- African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | | | - Paul E. Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Paulo Arnaldo
- Instituto Nacional de Saude (INS), Maputo, Mozambique
| | - Peter K. Quashie
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Philippe Dussart
- Virology Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Phillip A. Bester
- Division of Virology, National Health Laboratory Service and University of the Free State, Bloemfontein, South Africa
| | - Placide K. Mbala
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | - Reuben Ayivor-Djanie
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Richard Njouom
- Virology Service, Centre Pasteur of Cameroun, Yaounde, Cameroon
| | - Richard O. Phillips
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | | | - Rosina A. A. Carr
- UHAS COVID-19 Testing and Research Centre, University of Health and Allied Sciences, Ho, Ghana
| | - Saâd El Kabbaj
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Saba Gargouri
- CHU Habib Bourguiba, Laboratory of Microbiology, Faculty of Medicine of sFax, University of sFax, sFax, Tunisia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Safietou Sankhe
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Salako B. Lawal
- The Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria
| | - Samar Kassim
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | - Sameh Trabelsi
- Clinical and Experimental Pharmacology Lab, LR16SP02, National Center of Pharmacovigilance, University of Tunis El Manar, Tunis, Tunisia
| | - Samar Metha
- Broad Insitute of Harvard and MIT, Cambridge, MA, USA
| | - Sami Kammoun
- CHU Hedi Chaker Sfax, Service de Pneumologie, Tunis, Tunisia
| | - Sanaâ Lemriss
- Laboratoire de Recherche et d’Analyses Médicales de la Gendarmerie Royale, Rabat, Morocco
| | - Sara H. A. Agwa
- Faculty of Medicine Ain Shams Research institute (MASRI), Ain Shams University, Cairo, Egypt
| | | | | | - Seydou Doumbia
- Mali-University Clinical Research Center (UCRC), Bamako, Mali
| | - Sheila M. Mandanda
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | | | | | | | - Sobajo Tope
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Sonia Lekana-Douki
- Centre Interdisciplinaires de Recherches Medicales de Franceville (CIRMF), Franceville, Gabon
| | | | - Soumeya Ouangraoua
- Centre MURAZ, Ouagadougou, Burkina Faso
- National Institute of Public Health of Burkina Faso (INSP/BF), Ouagadougou, Burkina Faso
| | - Steve A. Mundeke
- Pathogen Sequencing Lab, Institut National de Recherche Biomédicale (INRB), Kinshasa, Democratic Republic of the Congo
- Université de Kinshasa (UNIKIN), Kinshasa, Democratic Republic of the Congo
| | | | - Sumir Panji
- Computational Biology Division, Department of Integrative Biomedical Sciences, IDM, CIDRI Africa Wellcome Trust Centre, University of Cape Town, Cape Town, South Africa
| | - Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Susan Engelbrecht
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Susan Nabadda
- Central Public Health Laboratories (CPHL), Kampala, Uganda
| | - Sylvie Behillil
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Sylvie van der Werf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | | | - Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical and Pharmacy School, Mohammed V University, Rabat, Morocco
| | - Thabo Mohale
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
| | | | - Tobias Schindler
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Laboratorio de Investigaciones de Baney, Baney, Equatorial Guinea
| | - Ugochukwu J. Anyaneji
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Ugwu Chinedu
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Sub-Saharan African Network For TB/HIV Research Excellence (SANTHE), Durban, South Africa
| | - Uwanibe Jessica
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - Vagner Fonseca
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | - Vincent Enouf
- National Reference Center for Respiratory Viruses, Molecular Genetics of RNA Viruses, UMR 3569 CNRS, University of Paris, Institut Pasteur, Paris, France
| | - Vivianne Gorova
- World Health Organization, WHO Lesotho, Maseru, Lesotho
- Med24 Medical Centre, Ruwa, Zimbabwe
| | | | - William K. Ampofo
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, Cape Town, South Africa
- National Health Laboratory Service (NHLS), Tygerberg, Cape Town, South Africa
| | - Wonderful T. Choga
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Division of Human Genetics, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yaw Bediako
- West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Yeshnee Naidoo
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Yvan Butera
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Amadou A. Sall
- Virology Department, Institut Pasteur de Dakar, Dakar, Senegal
| | - Ahmed Rebai
- Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Anne von Gottberg
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Bourema Kouriba
- Bacteriology and Virology Department Souro Sanou University Hospital, Bobo-Dioulasso, Burkina Faso
| | - Carolyn Williamson
- Division of Medical Virology, Wellcome Centre for Infectious Diseases in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- National Health Laboratory Service (NHLS), Cape Town, South Africa
| | | | | | - Jinal N. Bhiman
- National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service (NHLS), Johannesburg, South Africa
- School of Pathology, Faculty of Health Science, University of the Witwatersrand, Johannesburg, South Africa
| | - Madisa Mine
- National Health Laboratory, Gaborone, Botswana
| | - Matthew Cotten
- MRC/UVRI and LSHTM Uganda Research Unit, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership and Botswana Harvard HIV Reference Laboratory, Gaborone, Botswana
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Ngonda Saasa
- University of Zambia, School of Veterinary Medicine, Department of Disease Control, Lusaka, Zambia
| | | | | | - Yenew K. Tebeje
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Sofonias K. Tessema
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer’s University, Ede, Osun State, Nigeria
| | - John Nkengasong
- Institute of Pathogen Genomics, Africa Centres for Disease Control and Prevention (Africa CDC), Addis Ababa, Ethiopia
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
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21
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Nabadda S, Kakooza F, Kiggundu R, Walwema R, Bazira J, Mayito J, Mugerwa I, Sekamatte M, Kambugu A, Lamorde M, Kajumbula H, Mwebasa H. Implementation of the World Health Organization Global Antimicrobial Resistance Surveillance System in Uganda, 2015-2020: Mixed-Methods Study Using National Surveillance Data. JMIR Public Health Surveill 2021; 7:e29954. [PMID: 34673531 PMCID: PMC8569544 DOI: 10.2196/29954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/04/2021] [Accepted: 08/04/2021] [Indexed: 12/17/2022] Open
Abstract
Background Antimicrobial resistance (AMR) is an emerging public health crisis in Uganda. The World Health Organization (WHO) Global Action Plan recommends that countries should develop and implement National Action Plans for AMR. We describe the establishment of the national AMR program in Uganda and present the early microbial sensitivity results from the program. Objective The aim of this study is to describe a national surveillance program that was developed to perform the systematic and continuous collection, analysis, and interpretation of AMR data. Methods A systematic qualitative description of the process and progress made in the establishment of the national AMR program is provided, detailing the progress made from 2015 to 2020. This is followed by a report of the findings of the isolates that were collected from AMR surveillance sites. Identification and antimicrobial susceptibility testing (AST) of the bacterial isolates were performed using standard methods at both the surveillance sites and the reference laboratory. Results Remarkable progress has been achieved in the establishment of the national AMR program, which is guided by the WHO Global Laboratory AMR Surveillance System (GLASS) in Uganda. A functional national coordinating center for AMR has been established with a supporting designated reference laboratory. WHONET software for AMR data management has been installed in the surveillance sites and laboratory staff trained on data quality assurance. Uganda has progressively submitted data to the WHO GLASS reporting system. Of the 19,216 isolates from WHO GLASS priority specimens collected from October 2015 to June 2020, 22.95% (n=4411) had community-acquired infections, 9.46% (n=1818) had hospital-acquired infections, and 68.57% (n=12,987) had infections of unknown origin. The highest proportion of the specimens was blood (12,398/19,216, 64.52%), followed by urine (5278/19,216, 27.47%) and stool (1266/19,216, 6.59%), whereas the lowest proportion was urogenital swabs (274/19,216, 1.4%). The mean age was 19.1 (SD 19.8 years), whereas the median age was 13 years (IQR 28). Approximately 49.13% (9440/19,216) of the participants were female and 50.51% (9706/19,216) were male. Participants with community-acquired infections were older (mean age 28, SD 18.6 years; median age 26, IQR 20.5 years) than those with hospital-acquired infections (mean age 17.3, SD 20.9 years; median age 8, IQR 26 years). All gram-negative (Escherichia coli, Klebsiella pneumoniae, and Neisseria gonorrhoeae) and gram-positive (Staphylococcus aureus and Enterococcus sp) bacteria with AST showed resistance to each of the tested antibiotics. Conclusions Uganda is the first African country to implement a structured national AMR surveillance program in alignment with the WHO GLASS. The reported AST data indicate very high resistance to the recommended and prescribed antibiotics for treatment of infections. More effort is required regarding quality assurance of laboratory testing methodologies to ensure optimal adherence to WHO GLASS–recommended pathogen-antimicrobial combinations. The current AMR data will inform the development of treatment algorithms and clinical guidelines.
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Affiliation(s)
- Susan Nabadda
- Laboratory and Diagnostics Services Department, Ministry of Health, Kampala, Uganda
| | - Francis Kakooza
- Global Health Security Department, Infectious Diseases Institute, Kampala, Uganda.,Department of Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Reuben Kiggundu
- Global Health Security Department, Infectious Diseases Institute, Kampala, Uganda.,United States Agency for International Development Medicines, Technologies, and Pharmaceutical Services Program, Management Sciences for Health, Kampala, Uganda
| | - Richard Walwema
- Global Health Security Department, Infectious Diseases Institute, Kampala, Uganda
| | - Joel Bazira
- Department of Medical Microbiology, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Jonathan Mayito
- Global Health Security Department, Infectious Diseases Institute, Kampala, Uganda
| | - Ibrahimm Mugerwa
- Laboratory and Diagnostics Services Department, Ministry of Health, Kampala, Uganda.,Antimicrobial Resistance Sub-Committee, National One Health Platform, Kampala, Uganda
| | - Musa Sekamatte
- Antimicrobial Resistance Sub-Committee, National One Health Platform, Kampala, Uganda
| | - Andrew Kambugu
- Global Health Security Department, Infectious Diseases Institute, Kampala, Uganda
| | - Mohammed Lamorde
- Global Health Security Department, Infectious Diseases Institute, Kampala, Uganda
| | - Henry Kajumbula
- Antimicrobial Resistance Sub-Committee, National One Health Platform, Kampala, Uganda.,Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Henry Mwebasa
- Laboratory and Diagnostics Services Department, Ministry of Health, Kampala, Uganda.,Antimicrobial Resistance Sub-Committee, National One Health Platform, Kampala, Uganda
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22
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Bugembe DL, Phan MVT, Ssewanyana I, Semanda P, Nansumba H, Dhaala B, Nabadda S, O'Toole ÁN, Rambaut A, Kaleebu P, Cotten M. Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda. Nat Microbiol 2021; 6:1094-1101. [PMID: 34163035 PMCID: PMC8318884 DOI: 10.1038/s41564-021-00933-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/02/2021] [Indexed: 12/15/2022]
Abstract
Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable.
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Affiliation(s)
- Daniel Lule Bugembe
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - My V T Phan
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Isaac Ssewanyana
- Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda
| | - Patrick Semanda
- Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda
| | - Hellen Nansumba
- Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda
| | - Beatrice Dhaala
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Susan Nabadda
- Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda
| | - Áine Niamh O'Toole
- Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Matthew Cotten
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda.
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK.
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23
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Bugembe DL, Phan MVT, Ssewanyana I, Semanda P, Nansumba H, Dhaala B, Nabadda S, O'Toole ÁN, Rambaut A, Kaleebu P, Cotten M. Emergence and spread of a SARS-CoV-2 lineage A variant (A.23.1) with altered spike protein in Uganda. Nat Microbiol 2021; 6:1094-1101. [PMID: 34163035 DOI: 10.1101/2021.02.08.21251393] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/02/2021] [Indexed: 05/26/2023]
Abstract
Here, we report SARS-CoV-2 genomic surveillance from March 2020 until January 2021 in Uganda, a landlocked East African country with a population of approximately 40 million people. We report 322 full SARS-CoV-2 genomes from 39,424 reported SARS-CoV-2 infections, thus representing 0.8% of the reported cases. Phylogenetic analyses of these sequences revealed the emergence of lineage A.23.1 from lineage A.23. Lineage A.23.1 represented 88% of the genomes observed in December 2020, then 100% of the genomes observed in January 2021. The A.23.1 lineage was also reported in 26 other countries. Although the precise changes in A.23.1 differ from those reported in the first three SARS-CoV-2 variants of concern (VOCs), the A.23.1 spike-protein-coding region has changes similar to VOCs including a change at position 613, a change in the furin cleavage site that extends the basic amino acid motif and multiple changes in the immunogenic N-terminal domain. In addition, the A.23.1 lineage has changes in non-spike proteins including nsp6, ORF8 and ORF9 that are also altered in other VOCs. The clinical impact of the A.23.1 variant is not yet clear and it has not been designated as a VOC. However, our findings of emergence and spread of this variant indicate that careful monitoring of this variant, together with assessment of the consequences of the spike protein changes for COVID-19 vaccine performance, are advisable.
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Affiliation(s)
- Daniel Lule Bugembe
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - My V T Phan
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Isaac Ssewanyana
- Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda
| | - Patrick Semanda
- Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda
| | - Hellen Nansumba
- Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda
| | - Beatrice Dhaala
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
| | - Susan Nabadda
- Central Public Health Laboratories of the Republic of Uganda, Kampala, Uganda
| | - Áine Niamh O'Toole
- Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Andrew Rambaut
- Institute for Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Pontiano Kaleebu
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda
- Uganda Virus Research Institute, Entebbe, Uganda
| | - Matthew Cotten
- Medical Research Council/Uganda Virus Research Institute, London School of Hygiene & Tropical Medicine Uganda Research Unit, Entebbe, Uganda.
- Medical Research Council-University of Glasgow Centre for Virus Research, Glasgow, UK.
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24
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Nsawotebba A, Ibanda I, Ssewanyana I, Ogwok P, Ocen F, Okiira C, Kagirita A, Mujuni D, Tugumisirize D, Kabugo J, Nyombi A, Majwala RK, Bagaya BS, Kalyesubula-Kibuuka S, Ssengooba W, Nabadda S. Effectiveness of thermal screening in detection of COVID-19 among truck drivers at Mutukula Land Point of Entry, Uganda. PLoS One 2021; 16:e0251150. [PMID: 33983997 PMCID: PMC8118319 DOI: 10.1371/journal.pone.0251150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 04/21/2021] [Indexed: 01/08/2023] Open
Abstract
Introduction Despite the limited evidence for its effectiveness, thermal screening at points of entry has increasingly become a standard protocol in numerous parts of the globe in response to the COVID-19 pandemic. We sought to determine the effectiveness of thermal screening as a key step in diagnosing COVID-19 in a resource-limited setting. Materials and methods This was a retrospective cross-sectional study based on a review of body temperature and Xpert Xpress SARS CoV-2 test results records for truck drivers entering Uganda through Mutukula between 15th May and 30th July 2020. All records missing information for body temperature, age, gender, and Xpert Xpress SARS CoV-2 status were excluded from the data set. A data set of 7,181 entries was used to compare thermal screening and Xpert Xpress SARS CoV-2 assay test results using the diagnostic statistical test in STATAv15 software. The prevalence of COVID-19 amongst the truck drivers based on Xpert Xpress SARS CoV-2 assay results was determined. The sensitivity, specificity, positive predictive value, negative predictive value, positive and negative Likelihood ratios were obtained using Xpert Xpress SARS CoV-2 assay as the gold standard. Results Based on our gold standard test, the proportion of persons that tested positive for COVID-19 was 6.7% (95% CI: 6.1–7.3). Of the 7,181 persons that were thermally screened, 6,844 (95.3%) were male. The sample median age was 38 years (interquartile range, IQR: 31–45 years). The median body temperature was 36.5°C (IQR: 36.3–36.7) and only n (1.2%) had a body temperature above 37.5°C. The sensitivity and specificity of thermal screening were 9.9% (95% CI: 7.4–13.0) and 99.5% (95% CI: 99.3–99.6) respectively. The positive and negative predictive values were 57.8 (95% CI: 46.5–68.6) and 93.9 (95% CI: 93.3–94.4) respectively. The positive and negative Likelihood Ratios (LRs) were 19 (95% CI: 12.4–29.1) and 0.9 (95% CI: 0.88–0.93) respectively. Conclusion In this study population, the use of Thermal screening alone is ineffective in the detection of potential COVID-19 cases at point of entry. We recommend a combination of screening tests or additional testing using highly sensitive molecular diagnostics such as Polymerase Chain Reaction.
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Affiliation(s)
- Andrew Nsawotebba
- Department of National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
- * E-mail:
| | - Ivan Ibanda
- Department of National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Isaac Ssewanyana
- Department of National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Patrick Ogwok
- Department of National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
| | - Francis Ocen
- Africa Centres for Disease Control and Prevention/African Society for Laboratory Medicine, Addis Ababa, Ethiopia
| | | | | | - Dennis Mujuni
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
- Marascientific, Kampala, Uganda
| | - Didas Tugumisirize
- Tuberculosis and Leprosy Control Division, Ministry of Health, Kampala, Uganda
| | - Joel Kabugo
- Uganda National Tuberculosis Reference Laboratory /Supranational Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Abdunoor Nyombi
- Uganda National Tuberculosis Reference Laboratory /Supranational Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Robert Kaos Majwala
- Tuberculosis and Leprosy Control Division, Ministry of Health, Kampala, Uganda
| | - Bernard Ssentalo Bagaya
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
| | | | - Willy Ssengooba
- Department of Medical Microbiology, School of Biomedical Sciences, Makerere University College of Health Sciences, Kampala, Uganda
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Susan Nabadda
- Department of National Health Laboratory and Diagnostic Services, Ministry of Health, Kampala, Uganda
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Nalumansi A, Lutalo T, Kayiwa J, Watera C, Balinandi S, Kiconco J, Nakaseegu J, Olara D, Odwilo E, Serwanga J, Kikaire B, Ssemwanga D, Nabadda S, Ssewanyana I, Atwine D, Mwebesa H, Bosa HK, Nsereko C, Cotten M, Downing R, Lutwama J, Kaleebu P. Field evaluation of the performance of a SARS-CoV-2 antigen rapid diagnostic test in Uganda using nasopharyngeal samples. Int J Infect Dis 2021; 104:282-286. [PMID: 33130198 PMCID: PMC7836828 DOI: 10.1016/j.ijid.2020.10.073] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES There is a high demand for SARS-CoV-2 testing to identify COVID-19 cases. Real-time quantitative PCR (qRT-PCR) is the recommended diagnostic test but a number of constraints prevent its widespread implementation, including cost. The aim of this study was to evaluate a low cost and easy to use rapid antigen test for diagnosing COVID-19 at the point of care. METHODS Nasopharyngeal swabs from suspected COVID-19 cases and low-risk volunteers were tested with the STANDARD Q COVID-19 Ag Test and the results were compared with the qRT-PCR results. RESULTS In total, 262 samples were collected, including 90 qRT-PCR positives. The majority of samples were from males (89%) with a mean age of 34 years and only 13 (14%) of the positives were mildly symptomatic. The sensitivity and specificity of the antigen test were 70.0% (95% confidence interval (CI): 60-79) and 92% (95% CI: 87-96), respectively, and the diagnostic accuracy was 84% (95% CI: 79-88). The antigen test was more likely to be positive for samples with qRT-PCR Ct values ≤29, with a sensitivity of 92%. CONCLUSIONS The STANDARD Q COVID-19 Ag Test performed less than optimally in this evaluation. However, the test may still have an important role to play early in infection when timely access to molecular testing is not available but the results should be confirmed by qRT-PCR.
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Affiliation(s)
- Aminah Nalumansi
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Tom Lutalo
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - John Kayiwa
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Christine Watera
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Stephen Balinandi
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Jocelyn Kiconco
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Joweria Nakaseegu
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Denis Olara
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Emmanuel Odwilo
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Jennifer Serwanga
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda; Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Bernard Kikaire
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Deogratius Ssemwanga
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda; Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Susan Nabadda
- Central Public Health Laboratories, P.O. Box 7272, Plot 1062-106, Old Butabika Road, Kampala, Uganda
| | - Isaac Ssewanyana
- Central Public Health Laboratories, P.O. Box 7272, Plot 1062-106, Old Butabika Road, Kampala, Uganda
| | - Diane Atwine
- Ministry of Health, P.O. Box 7272, Plot 6, Lourdel Road, Kampala, Uganda
| | - Henry Mwebesa
- Ministry of Health, P.O. Box 7272, Plot 6, Lourdel Road, Kampala, Uganda
| | - Henry Kyobe Bosa
- Public Health Emergency Operations Centre, P.O. Box 7272, Lourdel Towers, Plot 1 Lourdel Road, Kampala, Uganda
| | - Christopher Nsereko
- Entebbe Regional Referral Hospital, P.O. Box 29, Kampala Road, Entebbe, Uganda
| | - Matthew Cotten
- Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Robert Downing
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Julius Lutwama
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda
| | - Pontiano Kaleebu
- Uganda Virus Research Institute, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda; Medical Research Council/Uganda Virus Research Institute & London School of Hygiene and Tropical Medicine, Uganda Research Unit, P.O. Box 49, Plot 51-59, Nakiwogo Road, Entebbe, Uganda.
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Lubega J, Nabadda S, Wasswa P, Mbabazi O, Cubbage M, Munube D, Gaikwad A, Elghetany T, Adesina A, Allen C, Lutwama F, Scheurer M, Gastier-Foster J. Strategies to Improve Pediatric Cancer Pathology and Tissue Handling for Clinical Care and Research in Low-Resource Settings. JCO Glob Oncol 2020. [DOI: 10.1200/go.20.57000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Evidence-based pediatric cancer control is dependent on accurate, timely cancer diagnosis, as well as maintenance of tissue integrity and annotation for clinical diagnosis and clinical/translational research. Scarcity of cancer pathology infrastructure and the delinkage of clinical pathology and research workflows in low- and middle-income countries thwarts real-time, high-resolution diagnosis, risk stratification, and maintenance of tissue integrity for future research. This renders the application of evidence-based treatments and conduct of translational research and clinical trials, particularly across multiple centers in low- and middle-income countries, impractical. We present the innovative approach and impact of a Texas Children’s Global HOPE model designed to overcome these systemic obstacles in a sub-Saharan Africa setting. METHODS We designed a pathology algorithm at Mulago Hospital Complex in Uganda with the following goals: integrate clinical and research workflows, ensure safe and optimal tissue biopsies, and maintain tissue integrity for clinical and research assays. We introduced new assays built on locally available technology platforms for anatomic pathology and immunophenotyping. RESULTS The novel workflow and assays enabled consistent real-time hematoxylin and eosin microscopy, immunohistochemistry, and multiparametric flow cytometry. The proportion of cancer diagnoses based on tissue pathology increased from 67.5% to 100%. Streamlined pathology processes improved the timeliness of commencement of treatment from 4 to 6 weeks to 24 hours in the case of acute leukemias. The refined diagnosis process has enabled implementation of risk-adapted treatment regimens. Overall, these strategies contributed to improved overall survival from 30% to 85% at 1 month, and have revealed hitherto unrecognized clinical patterns of pediatric cancers in sub-Saharan Africa. CONCLUSION Accurate real-time pathology for pediatric cancers improves survival. Improvements should aim at enhancing the capabilities of existing in-country platforms and skilled personnel. Future efforts will focus on scaling up these practices to other sites and integrating molecular diagnostics that reduce overall cost and improve diagnostic accuracy or risk stratification.
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Affiliation(s)
- Joseph Lubega
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
| | - Susan Nabadda
- Central Public Health Laboratories, Ministry of Health, Kampala, Uganda
| | - Peter Wasswa
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
| | - Olive Mbabazi
- Infectious Disease Institute, Makerere University, Kampala, Uganda
| | - Mike Cubbage
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
| | | | - Amos Gaikwad
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
| | - Tarek Elghetany
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
| | - Adekunle Adesina
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
| | - Carl Allen
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
| | - Fredrick Lutwama
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
| | - Michael Scheurer
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
| | - Julie Gastier-Foster
- Baylor College of Medicine, Texas Children's Hospital Global HOPE Program, Houston, TX
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27
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Aceng JR, Ario AR, Muruta AN, Makumbi I, Nanyunja M, Komakech I, Bakainaga AN, Talisuna AO, Mwesigye C, Mpairwe AM, Tusiime JB, Lali WZ, Katushabe E, Ocom F, Kaggwa M, Bongomin B, Kasule H, Mwoga JN, Sensasi B, Mwebembezi E, Katureebe C, Sentumbwe O, Nalwadda R, Mbaka P, Fatunmbi BS, Nakiire L, Lamorde M, Walwema R, Kambugu A, Nanyondo J, Okware S, Ahabwe PB, Nabukenya I, Kayiwa J, Wetaka MM, Kyazze S, Kwesiga B, Kadobera D, Bulage L, Nanziri C, Monje F, Aliddeki DM, Ntono V, Gonahasa D, Nabatanzi S, Nsereko G, Nakinsige A, Mabumba E, Lubwama B, Sekamatte M, Kibuule M, Muwanguzi D, Amone J, Upenytho GD, Driwale A, Seru M, Sebisubi F, Akello H, Kabanda R, Mutengeki DK, Bakyaita T, Serwanjja VN, Okwi R, Okiria J, Ainebyoona E, Opar BT, Mimbe D, Kyabaggu D, Ayebazibwe C, Sentumbwe J, Mwanja M, Ndumu DB, Bwogi J, Balinandi S, Nyakarahuka L, Tumusiime A, Kyondo J, Mulei S, Lutwama J, Kaleebu P, Kagirita A, Nabadda S, Oumo P, Lukwago R, Kasozi J, Masylukov O, Kyobe HB, Berdaga V, Lwanga M, Opio JC, Matseketse D, Eyul J, Oteba MO, Bukirwa H, Bulya N, Masiira B, Kihembo C, Ohuabunwo C, Antara SN, Owembabazi W, Okot PB, Okwera J, Amoros I, Kajja V, Mukunda BS, Sorela I, Adams G, Shoemaker T, Klena JD, Taboy CH, Ward SE, Merrill RD, Carter RJ, Harris JR, Banage F, Nsibambi T, Ojwang J, Kasule JN, Stowell DF, Brown VR, Zhu BP, Homsy J, Nelson LJ, Tusiime PK, Olaro C, Mwebesa HG, Woldemariam YT. Uganda's experience in Ebola virus disease outbreak preparedness, 2018-2019. Global Health 2020; 16:24. [PMID: 32192540 PMCID: PMC7081536 DOI: 10.1186/s12992-020-00548-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 02/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the declaration of the 10th Ebola Virus Disease (EVD) outbreak in DRC on 1st Aug 2018, several neighboring countries have been developing and implementing preparedness efforts to prevent EVD cross-border transmission to enable timely detection, investigation, and response in the event of a confirmed EVD outbreak in the country. We describe Uganda's experience in EVD preparedness. RESULTS On 4 August 2018, the Uganda Ministry of Health (MoH) activated the Public Health Emergency Operations Centre (PHEOC) and the National Task Force (NTF) for public health emergencies to plan, guide, and coordinate EVD preparedness in the country. The NTF selected an Incident Management Team (IMT), constituting a National Rapid Response Team (NRRT) that supported activation of the District Task Forces (DTFs) and District Rapid Response Teams (DRRTs) that jointly assessed levels of preparedness in 30 designated high-risk districts representing category 1 (20 districts) and category 2 (10 districts). The MoH, with technical guidance from the World Health Organisation (WHO), led EVD preparedness activities and worked together with other ministries and partner organisations to enhance community-based surveillance systems, develop and disseminate risk communication messages, engage communities, reinforce EVD screening and infection prevention measures at Points of Entry (PoEs) and in high-risk health facilities, construct and equip EVD isolation and treatment units, and establish coordination and procurement mechanisms. CONCLUSION As of 31 May 2019, there was no confirmed case of EVD as Uganda has continued to make significant and verifiable progress in EVD preparedness. There is a need to sustain these efforts, not only in EVD preparedness but also across the entire spectrum of a multi-hazard framework. These efforts strengthen country capacity and compel the country to avail resources for preparedness and management of incidents at the source while effectively cutting costs of using a "fire-fighting" approach during public health emergencies.
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Affiliation(s)
| | - Alex R Ario
- Ministry of Health, Kampala, Uganda.
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda.
| | | | - Issa Makumbi
- Ministry of Health, Kampala, Uganda
- Public Health Emergency Operations Centre, Ministry of Health, Kampala, Uganda
| | | | | | | | | | | | | | | | - William Z Lali
- World Health Organisation, Country Office, Kampala, Uganda
| | | | - Felix Ocom
- World Health Organisation, Country Office, Kampala, Uganda
| | - Mugagga Kaggwa
- World Health Organisation, Country Office, Kampala, Uganda
| | - Bodo Bongomin
- World Health Organisation, Country Office, Kampala, Uganda
| | - Hafisa Kasule
- World Health Organisation, Country Office, Kampala, Uganda
| | - Joseph N Mwoga
- World Health Organisation, Country Office, Kampala, Uganda
| | | | | | | | | | - Rita Nalwadda
- World Health Organisation, Country Office, Kampala, Uganda
| | - Paul Mbaka
- World Health Organisation, Country Office, Kampala, Uganda
| | | | | | | | | | | | | | - Solome Okware
- Ministry of Health, Kampala, Uganda
- Infectious Disease Institute, Kampala, Uganda
| | | | - Immaculate Nabukenya
- Ministry of Health, Kampala, Uganda
- Infectious Disease Institute, Kampala, Uganda
| | - Joshua Kayiwa
- Public Health Emergency Operations Centre, Ministry of Health, Kampala, Uganda
| | - Milton M Wetaka
- Public Health Emergency Operations Centre, Ministry of Health, Kampala, Uganda
| | - Simon Kyazze
- Public Health Emergency Operations Centre, Ministry of Health, Kampala, Uganda
| | - Benon Kwesiga
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Daniel Kadobera
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Lilian Bulage
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
- African Field Epidemiology Network, Kampala, Uganda
| | - Carol Nanziri
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Fred Monje
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Dativa M Aliddeki
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Vivian Ntono
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Doreen Gonahasa
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Sandra Nabatanzi
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | - Godfrey Nsereko
- Uganda Public Health Fellowship Program, Ministry of Health, Kampala, Uganda
| | | | | | | | | | | | | | | | | | | | | | | | - Harriet Akello
- Ministry of Health, Kampala, Uganda
- Management Sciences for Health, Kampala, Uganda
| | | | | | | | | | | | | | | | | | - Derrick Mimbe
- Makerere University Walter Reed Project, Kampala, Uganda
| | - Denis Kyabaggu
- East African Public Health Laboratory Network, Kampala, Uganda
| | | | - Juliet Sentumbwe
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Moses Mwanja
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | - Deo B Ndumu
- Ministry of Agriculture, Animal Industry and Fisheries, Entebbe, Uganda
| | | | | | | | | | | | - Sophia Mulei
- Uganda Virus Research Institute, Entebbe, Uganda
| | | | | | - Atek Kagirita
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Susan Nabadda
- Uganda National Health Laboratory Services, Ministry of Health, Kampala, Uganda
| | - Peter Oumo
- Ministry of Internal Affairs, Uganda Police Force, Kampala, Uganda
| | - Robinah Lukwago
- Department for International Development, UKAID, Kampala, Uganda
| | - Julius Kasozi
- United Nations High Commissioner for Refugees, Kampala, Uganda
| | | | | | | | | | - Joe C Opio
- United Nations Children's Fund, Kampala, Uganda
| | | | - James Eyul
- Civil Aviation Authority, Entebbe, Uganda
| | | | | | - Nulu Bulya
- African Field Epidemiology Network, Kampala, Uganda
| | - Ben Masiira
- African Field Epidemiology Network, Kampala, Uganda
| | | | | | | | | | | | | | | | - Victoria Kajja
- Intenational Organisation for Migration, Kampala, Uganda
| | | | - Isabel Sorela
- Intenational Organisation for Migration, Kampala, Uganda
| | - Gregory Adams
- United States Agency for International Development, Kampala, Uganda
| | - Trevor Shoemaker
- National Center for Emerging and Zoonotic Infectious Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John D Klena
- National Center for Emerging and Zoonotic Infectious Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Celine H Taboy
- National Center for Emerging and Zoonotic Infectious Diseases, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Sarah E Ward
- Division of Global Migration and Quarantine, Global Border Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rebecca D Merrill
- Division of Global Migration and Quarantine, Global Border Health, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Rosalind J Carter
- Global Immunization Division, US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Julie R Harris
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Flora Banage
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Thomas Nsibambi
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Joseph Ojwang
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Juliet N Kasule
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Dan F Stowell
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Vance R Brown
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Bao-Ping Zhu
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Jaco Homsy
- US Centers for Disease Control and Prevention, Kampala, Uganda
| | - Lisa J Nelson
- US Centers for Disease Control and Prevention, Kampala, Uganda
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Butler EK, Hume H, Birungi I, Ainomugisha B, Namazzi R, Ddungu H, Kajja I, Nabadda S, McCullough J. Blood utilization at a national referral hospital in sub-Saharan Africa. Transfusion 2015; 55:1058-66. [PMID: 25646993 DOI: 10.1111/trf.13010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 10/02/2014] [Accepted: 10/02/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND A safe and adequate supply of blood is critical to improving health care systems in sub-Saharan Africa, where little is known about the current use of blood. The aim of this study was to comprehensively describe the use of blood at a tertiary care hospital to inform future efforts to strengthen blood programs in resource-limited settings. STUDY DESIGN AND METHODS Data were collected from blood bank documentation for all units issued at Mulago Hospital Complex in Kampala, Uganda, from mid-January to mid-April 2014. RESULTS A total of 6330 units (69% whole blood, 32% red blood cells, 6% platelets, 2% plasma) were issued over the 3-month study period to 3662 unique patients. Transfusion recipients were 58% female and median age was 27 years (interquartile range [IQR], 14-41). Median pretransfusion hemoglobin was 5.6 g/dL (IQR, 4.0-7.2 g/dL, n = 1090). Strikingly, cancer was the top indication for transfusion (33.5%), followed by pregnancy-related complications (12.4%) and sickle cell disease (6.9%). CONCLUSION This study provides a comprehensive picture of blood use at a national referral hospital in sub-Saharan Africa. Noncommunicable diseases, particularly oncologic conditions, represent a large proportion of demand for transfusion services.
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Affiliation(s)
- Elissa K Butler
- University of Minnesota Medical School, Minneapolis, Minnesota
| | - Heather Hume
- School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda.,Centre Hospitalier Universitaire Sainte-Justine, University of Montreal, Montreal, Quebec, Canada
| | | | - Brenda Ainomugisha
- School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Ruth Namazzi
- School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Henry Ddungu
- School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda.,Uganda Cancer Institute, Kampala, Uganda
| | - Isaac Kajja
- School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
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Nabadda S, Odida M, Wabinga H. Myelodysplasia in Ugandan patients with HIV/AIDS: an autopsy study. East Afr Med J 2011; 88:24-27. [PMID: 24968599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
BACKGROUND Myelodysplasia has been reported to occur quite frequently in the spectrum of HIV/AIDS disease and is thought to be partly responsible for bone marrow failure in these patients. However, the frequency and type of myelodysplasia appear to differ at different stages of the disease in different populations with mechanisms of its development not well understood. OBJECTIVE To document the pattern of myelodysplasia in Ugandan patients with terminal HIV/AIDS disease. DESIGN Prospective descriptive study. SETTING Department of Pathology, Faculty of Medicine, Makerere University College of Health Sciences SUBJECTS Bone marrow necropsies from patients who died with AIDS disease at Mulago teaching hospital in Kampala, Uganda during a one-year period. RESULTS Eighty-four (84%) of the 50 cases studied had myelodysplasia with 39 cases having megakaryocytic myelodysplasia. Myelodysplasia involving erythroid cell series occurred in 23 and in 20 of these cases was in combination with megakaryocytic dysplasia. Granulocyte myelodysplastic features were observed in only two cases and these two cases did not have other cell lines involved. CONCLUSION Myelodysplastic features are common in HIV patients with megakaryocytic and eythroid cell lines being the most affected. This could be due to the direct HIV effect, or the combined effect of opportunistic infections, neoplasms, drugs and HIV itself affecting the haemopoietic stem cell and or its microenvironment.
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