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Namuwulya P, Ashraf S, Niebel M, Ssekagiri A, Tushabe P, Kakooza P, Tong L, Bukenya H, Jerome H, Davis C, Birungi M, Turyahabwe I, Mugaga A, Eliku JP, Francis A, Nakabazzi L, Nsubuga F, Katushabe E, Kisakye A, Ampeire I, Nanteza A, Kaleebu P, Bakamutumaho B, Nsamba P, Kazibwe A, da Silva Filipe A, Tweyongyere R, Bwogi J, Thomson EC. Viruses associated with measles-like illnesses in Uganda. J Infect 2024; 88:106148. [PMID: 38588959 PMCID: PMC11060986 DOI: 10.1016/j.jinf.2024.106148] [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: 08/26/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/10/2024]
Abstract
OBJECTIVES In this study, we investigated the causes of measles-like illnesses (MLI) in the Uganda national surveillance program in order to inform diagnostic assay selection and vaccination strategies. METHODS We used metagenomic next-generation sequencing (M-NGS) on the Illumina platform to identify viruses associated with MLI (defined as fever and rash in the presence of either cough, coryza or conjunctivitis) in patient samples that had tested IgM negative for measles between 2010 and 2019. RESULTS Viral genomes were identified in 87/271 (32%) of samples, of which 44/271 (16%) contained 12 known viral pathogens. Expected viruses included rubella, human parvovirus B19, Epstein Barr virus, human herpesvirus 6B, human cytomegalovirus, varicella zoster virus and measles virus (detected within the seronegative window-period of infection) and the blood-borne hepatitis B virus. We also detected Saffold virus, human parvovirus type 4, the human adenovirus C2 and vaccine-associated poliovirus type 1. CONCLUSIONS The study highlights the presence of undiagnosed viruses causing MLI in Uganda, including vaccine-preventable illnesses. NGS can be used to monitor common viral infections at a population level, especially in regions where such infections are prevalent, including low and middle income countries to guide vaccination policy and optimize diagnostic assays.
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Affiliation(s)
| | - Shirin Ashraf
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Marc Niebel
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | | | | | | | - Lily Tong
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Henry Bukenya
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | - Hanna Jerome
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Chris Davis
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK
| | - Molly Birungi
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Arnold Mugaga
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | - Aine Francis
- Uganda Virus Research Institute (UVRI), Entebbe, Uganda
| | | | | | | | | | | | - Ann Nanteza
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | | | - Peninah Nsamba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Anne Kazibwe
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | | | - Emma C Thomson
- MRC - University of Glasgow Centre for Virus Research (CVR), Glasgow, UK; London School of Hygiene and Tropical Medicine (LSHTM), London, UK.
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Tushabe P, Bakamutumaho B, Eliku JP, Birungi M, Aine F, Namuwulya P, Bukenya H, Ampeire I, Kisakye A, Byabamazima CR, Bwogi J. Rubella virus genotype 2B endemicity and related utility of serum-based molecular characterization in Uganda. BMC Res Notes 2023; 16:218. [PMID: 37710238 PMCID: PMC10503080 DOI: 10.1186/s13104-023-06499-5] [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: 09/01/2022] [Accepted: 09/04/2023] [Indexed: 09/16/2023] Open
Abstract
There are 13 globally recognized rubella virus genotypes of which only 2 (1E and 2B) have been detected recently. The largest percentage of all reported rubella virus sequences come from China and Japan with Africa reporting limited data. In a bid to address the lack of rubella genotype data in Uganda and the World Health Organization Africa region, we sought to characterize rubella viruses retrospectively using sera collected from suspected measles patients that turned out rubella IgM positive.Seven sequences belonging to genotype 2B sub-lineage 2B-L2c were obtained. These sequences clustered with other genotype 2B sequences previously reported from Uganda. None of the other genotypes (1E and 1G) reported from Uganda in the earlier years were detected. In addition, none of the sequences were obtained after the introduction of the measles-rubella containing vaccine. The above highlight the need for continuous rubella virological surveillance to confirm interruption of endemic rubella genotype circulation.
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Affiliation(s)
- Phionah Tushabe
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda.
| | | | - James Peter Eliku
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Molly Birungi
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Francis Aine
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Prossy Namuwulya
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Henry Bukenya
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
| | - Immaculate Ampeire
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
- Ministry of Health Uganda, P.O. Box 7272, Kampala, Uganda
| | - Annet Kisakye
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
- World Health Organization, Uganda Country Office, P.O. Box 24578, Kampala, Uganda
| | - Charles R Byabamazima
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
- WHO Inter-Country Support Team Office for Eastern and Southern Africa (IST/ESA), Harare, Zimbabwe
| | - Josephine Bwogi
- EPI-Laboratory, Uganda Virus Research Institute, P.O. Box 49, Entebbe, Uganda
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Nanteza MB, Bakamutumaho B, Tushabe P, Namuwulya P, Birungi M, Dhatemwa R, Eliku JP, Tibanagwa M, Kakooza P, Bukenya H, Bwogi J, Byabamazima CR. Sabin polio virus protein 1 (VP1) evolution in patients with acute flaccid paralysis from 2010 to 2016 in Uganda. Virol J 2023; 20:172. [PMID: 37533043 PMCID: PMC10399017 DOI: 10.1186/s12985-023-02143-7] [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: 10/12/2022] [Accepted: 07/26/2023] [Indexed: 08/04/2023] Open
Abstract
Acute flaccid paralysis (AFP) is a rare side effect of the oral polio vaccine but can be associated with outbreaks and permanent disability in patients harboring circulating vaccine-derived polioviruses (cVDPVs). With the advancement of polio abolition in a glimpse, cVDPVs are causing outbreaks and slowing the polio eradication process. The polio virus protein 1 (VP1) contains the binding site that is key for virus transmission. Understanding the evolution of VP1 among AFP patients could yield more insight into the early events of cVDPVs. Polioviruses were identified from stool specimens of AFP patients using cell culture; and confirmed by the real time RT PCR intra-typic differentiation and vaccine-derived poliovirus assays. Seventy-nine (79) Sabin-like poliovirus 1 (SL1) and 86 Sabin-like poliovirus 3 (SL3) were sequenced. The VP1 amino acid substitutions T106A in Sabin poliovirus 1 and A54V in Sabin poliovirus 3 were common among the AFP patients as has been found in previous studies. Other substitutions that were associated with AFP were: T290A and A54T in SL1 and SL3 respectively. Nucleotide mutations that were common among the AFP patients included T402C, C670A, and T816C in SL1, and G22A, C375Y, A472R, and A694T in SL3 polioviruses. Characterizing mutations that are associated with AFP could contribute to efforts pursued to mitigate the risk of vaccine-derived polioviruses and promote development of safer vaccines.
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Affiliation(s)
- Mary Bridget Nanteza
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda.
| | - Barnabas Bakamutumaho
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Phionah Tushabe
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Prossy Namuwulya
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Molly Birungi
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Rajab Dhatemwa
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - James Peter Eliku
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Mayi Tibanagwa
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | | | - Henry Bukenya
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Josephine Bwogi
- Uganda Virus Research Institute, Plot 51-59 Nakiwogo Road, P. O. Box 49, Entebbe, Uganda
| | - Charles Rutebarika Byabamazima
- World Health Organization AFRO, East and Southern Africa (ESA), 82-86 Enterprise Road, Highlands, Belvedere, P. O. Box BE 773, Harare, Zimbabwe
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Tushabe P, Bwogi J, Eliku JP, Aine F, Birungi M, Gaizi J, Nakabazzi L, Kabaliisa T, Turyahabwe I, Namuwulya P, Nanteza MB, Bukenya H, Kanyesigye C, Katushabe E, Ampeire I, Kisakye A, Bakamutumaho B, Byabamazima CR. Environmental surveillance detects circulating vaccine-derived poliovirus type 2 that was undetected by acute flaccid paralysis surveillance in 2021 in Uganda. Arch Virol 2023; 168:140. [PMID: 37059887 PMCID: PMC10104764 DOI: 10.1007/s00705-023-05759-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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/14/2023] [Indexed: 04/16/2023]
Abstract
The success of the global polio eradication initiative is threatened by the genetic instability of the oral polio vaccine, which can result in the emergence of pathogenic vaccine-derived polioviruses following prolonged replication in the guts of individuals with primary immune deficiencies or in communities with low vaccination coverage. Through environmental surveillance, circulating vaccine-derived poliovirus type 2 was detected in Uganda in the absence of detection by acute flaccid paralysis (AFP) surveillance. This underscores the sensitivity of environmental surveillance and emphasizes its usefulness in supplementing AFP surveillance for poliovirus infections in the race towards global polio eradication.
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Affiliation(s)
- Phionah Tushabe
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda.
| | - Josephine Bwogi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - James Peter Eliku
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Francis Aine
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Molly Birungi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Joseph Gaizi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Lucy Nakabazzi
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Theopista Kabaliisa
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Irene Turyahabwe
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Prossy Namuwulya
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Mary Bridget Nanteza
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Henry Bukenya
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | | | - Edson Katushabe
- World Health Organization, Uganda Country Office, Kampala, Uganda
| | | | - Annet Kisakye
- World Health Organization, Uganda Country Office, Kampala, Uganda
| | - Barnabas Bakamutumaho
- Expanded Programme on Immunization Laboratory, Uganda Virus Research Institute, Entebbe, Uganda
| | - Charles R Byabamazima
- WHO Inter-Country Support Team Office for Eastern and Southern Africa (IST/ESA), Harare, Zimbabwe
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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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